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_4596863.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4596863.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4596863.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== 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: 1.65, per 1000 atoms: 0.49 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: 0.53 Conformation dependent library (CDL) restraints added in 181.6 milliseconds Time building geometry restraints manager: 0.73 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: 435 0.89 - 1.14: 1155 1.14 - 1.39: 580 1.39 - 1.64: 897 1.64 - 1.89: 86 Bond restraints: 3153 Sorted by residual: bond pdb=" C SER A 3 " pdb=" N LYS A 4 " ideal model delta sigma weight residual 1.330 1.053 0.277 1.31e-02 5.83e+03 4.48e+02 bond pdb=" CA LEU A 7 " pdb=" C LEU A 7 " ideal model delta sigma weight residual 1.524 1.264 0.260 1.23e-02 6.61e+03 4.47e+02 bond pdb=" N VAL A 23 " pdb=" CA VAL A 23 " ideal model delta sigma weight residual 1.461 1.249 0.212 1.19e-02 7.06e+03 3.17e+02 bond pdb=" N VAL A 71 " pdb=" CA VAL A 71 " ideal model delta sigma weight residual 1.459 1.664 -0.205 1.20e-02 6.94e+03 2.93e+02 bond pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " ideal model delta sigma weight residual 1.326 1.139 0.187 1.10e-02 8.26e+03 2.88e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.23: 2914 4.23 - 8.45: 1849 8.45 - 12.67: 774 12.67 - 16.89: 199 16.89 - 21.11: 41 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O LEU A 7 " pdb=" C LEU A 7 " pdb=" N VAL A 8 " ideal model delta sigma weight residual 123.22 106.34 16.88 1.14e+00 7.69e-01 2.19e+02 angle pdb=" CA ASP A 68 " pdb=" CB ASP A 68 " pdb=" CG ASP A 68 " ideal model delta sigma weight residual 112.60 98.68 13.92 1.00e+00 1.00e+00 1.94e+02 angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.35 133.91 -12.56 9.20e-01 1.18e+00 1.86e+02 angle pdb=" CA THR A 140 " pdb=" C THR A 140 " pdb=" O THR A 140 " ideal model delta sigma weight residual 120.36 134.87 -14.51 1.08e+00 8.57e-01 1.81e+02 angle pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" O SER A 155 " ideal model delta sigma weight residual 121.36 107.47 13.89 1.06e+00 8.90e-01 1.72e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 953 17.94 - 35.87: 106 35.87 - 53.81: 38 53.81 - 71.74: 12 71.74 - 89.68: 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 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual 180.00 -160.09 -19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA LEU A 72 " pdb=" C LEU A 72 " pdb=" N PRO A 73 " pdb=" CA PRO A 73 " ideal model delta harmonic sigma weight residual 180.00 160.19 19.81 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.188: 93 0.188 - 0.376: 68 0.376 - 0.564: 37 0.564 - 0.752: 33 0.752 - 0.940: 12 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ARG A 98 " pdb=" N ARG A 98 " pdb=" C ARG A 98 " pdb=" CB ARG A 98 " both_signs ideal model delta sigma weight residual False 2.51 1.57 0.94 2.00e-01 2.50e+01 2.21e+01 chirality pdb=" CA ALYS A 132 " pdb=" N ALYS A 132 " pdb=" C ALYS A 132 " pdb=" CB ALYS A 132 " both_signs ideal model delta sigma weight residual False 2.51 3.41 -0.90 2.00e-01 2.50e+01 2.01e+01 chirality pdb=" CA ALEU A 153 " pdb=" N ALEU A 153 " pdb=" C ALEU A 153 " pdb=" CB ALEU A 153 " both_signs ideal model delta sigma weight residual False 2.51 3.36 -0.85 2.00e-01 2.50e+01 1.82e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.137 2.00e-02 2.50e+03 6.25e-02 1.17e+02 pdb=" CG PHE A 164 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.066 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.081 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.088 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.072 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.056 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " -0.007 2.00e-02 2.50e+03 6.44e-02 9.34e+01 pdb=" CG HIS A 126 " 0.081 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " -0.114 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " 0.060 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.052 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " -0.094 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " -0.024 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " 0.043 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.003 2.00e-02 2.50e+03 5.12e-02 7.85e+01 pdb=" CG BTYR A 67 " 0.061 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.050 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.002 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.092 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.003 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.085 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.031 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.067 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.040 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.027 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.041 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 720 2.27 - 2.85: 7773 2.85 - 3.43: 10651 3.43 - 4.02: 15412 4.02 - 4.60: 22048 Nonbonded interactions: 56604 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.687 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.736 1.850 x-y,-y,-z-4/3 nonbonded pdb=" O LEU A 185 " pdb=" H GLY A 159 " model vdw sym.op. 1.736 1.850 x-y,-y,-z-4/3 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.813 1.850 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.824 2.100 ... (remaining 56599 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_4596863_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2606 r_free= 0.1941 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787939 | | target function (ml) not normalized (work): 232252.063759 | | target function (ml) not normalized (free): 11807.553961 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3028 0.2071 6.9991 4.9407| | 2: 3.57 - 2.84 1.00 2876 122 0.2431 0.1887 4.3568 4.3467| | 3: 2.84 - 2.48 1.00 2833 165 0.2403 0.1590 4.1353 4.1461| | 4: 2.47 - 2.25 1.00 2825 136 0.2296 0.1463 3.8374 3.8388| | 5: 2.25 - 2.09 1.00 2756 127 0.2459 0.1646 3.8034 3.8193| | 6: 2.09 - 1.97 1.00 2846 113 0.2536 0.1744 3.4676 3.5585| | 7: 1.97 - 1.87 1.00 2787 165 0.2575 0.1838 3.1286 3.2306| | 8: 1.87 - 1.79 1.00 2789 144 0.2475 0.1765 3.0541 3.0745| | 9: 1.79 - 1.72 1.00 2745 138 0.2465 0.1891 2.8899 2.9378| | 10: 1.72 - 1.66 1.00 2789 158 0.2376 0.2115 2.7791 2.9131| | 11: 1.66 - 1.61 1.00 2740 147 0.2498 0.1907 2.7521 2.7968| | 12: 1.61 - 1.56 1.00 2787 146 0.2488 0.2009 2.6196 2.6532| | 13: 1.56 - 1.52 1.00 2745 130 0.2529 0.1926 2.5664 2.6171| | 14: 1.52 - 1.48 1.00 2803 134 0.2510 0.2002 2.4856 2.581| | 15: 1.48 - 1.45 1.00 2738 128 0.2558 0.1975 2.4268 2.4493| | 16: 1.45 - 1.42 1.00 2756 161 0.2623 0.2148 2.391 2.4153| | 17: 1.42 - 1.39 1.00 2785 139 0.2712 0.2315 2.3351 2.439| | 18: 1.39 - 1.36 1.00 2741 179 0.2685 0.1917 2.2819 2.2465| | 19: 1.36 - 1.34 1.00 2807 134 0.2631 0.2312 2.2359 2.2849| | 20: 1.34 - 1.32 1.00 2696 147 0.2673 0.2174 2.1872 2.2406| | 21: 1.32 - 1.30 1.00 2785 112 0.2697 0.2131 2.1748 2.1445| | 22: 1.29 - 1.27 1.00 2704 152 0.2776 0.2781 2.1432 2.2465| | 23: 1.27 - 1.26 1.00 2802 156 0.2798 0.2335 2.1161 2.1301| | 24: 1.26 - 1.24 1.00 2744 132 0.2738 0.2336 2.0682 2.0974| | 25: 1.24 - 1.22 1.00 2734 148 0.2825 0.2519 2.0386 2.0664| | 26: 1.22 - 1.21 1.00 2727 135 0.2895 0.2307 2.0239 2.0964| | 27: 1.21 - 1.19 1.00 2814 148 0.3029 0.2624 2.0115 2.0159| | 28: 1.19 - 1.18 1.00 2671 147 0.3001 0.2786 1.983 2.0074| | 29: 1.18 - 1.16 1.00 2800 134 0.2992 0.2724 1.9516 2.0228| | 30: 1.16 - 1.15 1.00 2740 148 0.3075 0.2829 1.9419 1.9582| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 1508.94| | 2: 3.57 - 2.84 2876 122 0.80 26.36 1.27 0.23 1508.94| | 3: 2.84 - 2.48 2833 165 0.74 32.36 1.25 0.23 1249.96| | 4: 2.47 - 2.25 2825 136 0.81 25.70 1.25 0.25 577.88| | 5: 2.25 - 2.09 2756 127 0.77 29.48 1.28 0.25 577.88| | 6: 2.09 - 1.97 2846 113 0.83 22.67 1.29 0.25 313.99| | 7: 1.97 - 1.87 2787 165 0.90 16.38 1.29 0.26 88.93| | 8: 1.87 - 1.79 2789 144 0.86 20.87 1.25 0.26 88.93| | 9: 1.79 - 1.72 2745 138 0.88 18.37 1.24 0.26 54.65| | 10: 1.72 - 1.66 2789 158 0.87 20.07 1.23 0.25 47.79| | 11: 1.66 - 1.61 2740 147 0.86 21.04 1.23 0.25 46.12| | 12: 1.61 - 1.56 2787 146 0.88 18.57 1.23 0.25 29.25| | 13: 1.56 - 1.52 2745 130 0.87 20.25 1.24 0.25 29.25| | 14: 1.52 - 1.48 2803 134 0.86 20.62 1.23 0.25 26.04| | 15: 1.48 - 1.45 2738 128 0.88 19.65 1.22 0.25 20.15| | 16: 1.45 - 1.42 2756 161 0.86 21.28 1.23 0.25 20.15| | 17: 1.42 - 1.39 2785 139 0.87 20.46 1.24 0.25 17.02| | 18: 1.39 - 1.36 2741 179 0.87 20.61 1.23 0.25 15.21| | 19: 1.36 - 1.34 2807 134 0.86 21.59 1.22 0.25 15.21| | 20: 1.34 - 1.32 2696 147 0.87 20.57 1.22 0.25 12.71| | 21: 1.32 - 1.30 2785 112 0.86 21.58 1.20 0.25 12.53| | 22: 1.29 - 1.27 2704 152 0.86 21.95 1.21 0.25 12.24| | 23: 1.27 - 1.26 2802 156 0.86 21.68 1.21 0.24 10.79| | 24: 1.26 - 1.24 2744 132 0.86 22.32 1.20 0.24 10.79| | 25: 1.24 - 1.22 2734 148 0.85 23.21 1.20 0.24 10.33| | 26: 1.22 - 1.21 2727 135 0.84 23.95 1.20 0.23 9.83| | 27: 1.21 - 1.19 2814 148 0.83 24.77 1.21 0.23 9.83| | 28: 1.19 - 1.18 2671 147 0.83 25.40 1.19 0.23 9.37| | 29: 1.18 - 1.16 2800 134 0.82 25.99 1.16 0.23 9.20| | 30: 1.16 - 1.15 2740 148 0.81 27.25 1.15 0.23 9.20| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 9.20 max = 1508.94 mean = 217.76| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 22.47| |phase err.(test): min = 0.00 max = 89.85 mean = 22.24| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.277 1557 Z= 5.572 Angle : 5.344 17.887 2118 Z= 3.807 Chirality : 0.386 0.940 243 Planarity : 0.032 0.082 284 Dihedral : 13.763 89.679 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.48 % Allowed : 3.11 % Favored : 94.41 % Cbeta Deviations : 29.73 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.48), residues: 224 helix: -2.55 (0.37), residues: 108 sheet: 0.00 (1.01), residues: 24 loop : 0.45 (0.56), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.074 0.020 ARG A 98 TYR 0.098 0.047 TYR A 141 PHE 0.101 0.044 PHE A 164 HIS 0.106 0.032 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2606 r_free= 0.1941 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787939 | | target function (ml) not normalized (work): 232252.063759 | | target function (ml) not normalized (free): 11807.553961 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2564 0.2606 0.1941 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2564 0.2606 0.1941 n_refl.: 87602 remove outliers: r(all,work,free)=0.1977 0.1982 0.1941 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2003 0.2008 0.1954 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1641 0.1634 0.1773 n_refl.: 87594 remove outliers: r(all,work,free)=0.1640 0.1633 0.1773 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 0.3823 386.254 358.787 0.665 1.001 0.401 11.894-9.307 99.02 97 4 0.1838 613.546 594.672 0.923 1.003 0.370 9.237-7.194 100.00 213 7 0.2155 501.805 490.595 0.956 1.003 0.360 7.162-5.571 100.00 427 22 0.2206 376.577 364.019 0.934 1.003 0.320 5.546-4.326 100.00 867 58 0.1271 516.947 510.838 0.961 1.003 0.224 4.315-3.360 100.00 1859 96 0.1136 491.620 487.925 1.004 1.003 0.199 3.356-2.611 100.00 3867 181 0.1439 322.969 319.838 0.998 1.002 0.052 2.608-2.026 99.99 8198 413 0.1359 214.099 212.120 1.005 1.001 0.000 2.025-1.573 100.00 17313 902 0.1634 104.555 103.929 1.015 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2054 46.364 45.015 1.003 0.995 0.000 1.221-1.150 99.97 13689 708 0.2608 29.212 26.908 0.978 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0488 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1633 r_free=0.1773 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1636 r_free=0.1777 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.188704 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2025.725125 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 0.1769 0.1888 0.0120 0.002 0.4 4.5 0.0 0.0 0 0.125 0.1597 0.1736 0.0139 0.001 0.4 4.5 0.0 0.0 0 0.250 0.1467 0.1635 0.0168 0.002 0.4 3.5 0.0 0.0 0 0.500 0.1401 0.1594 0.0193 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1351 0.1553 0.0202 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1372 0.1573 0.0201 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1293 0.1508 0.0215 0.002 0.6 2.9 0.5 0.0 0 2.000 0.1277 0.1501 0.0225 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1256 0.1483 0.0226 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1249 0.1479 0.0230 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1245 0.1478 0.0233 0.004 0.8 3.5 0.5 0.0 0 6.000 0.1240 0.1477 0.0236 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1237 0.1474 0.0237 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1233 0.1472 0.0239 0.006 0.8 3.5 0.5 0.0 0 9.000 0.1231 0.1469 0.0238 0.006 0.9 4.2 0.5 0.0 0 10.000 0.1230 0.1474 0.0245 0.007 0.9 4.2 0.5 0.6 0 11.000 0.1226 0.1471 0.0244 0.007 0.9 3.8 0.5 0.6 0 12.000 0.1225 0.1474 0.0250 0.007 1.0 4.2 0.5 0.6 0 13.094 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1231 0.1469 0.0238 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 12.31 14.69 2.38 3.013 19.072 2025.725 0.017 12.31 14.69 2.38 3.012 19.072 60.772 0.017 12.37 14.65 2.28 2.668 19.070 253.216 0.017 12.70 15.33 2.63 2.767 19.254 1012.863 0.017 12.55 15.47 2.92 3.255 19.596 2025.725 0.016 12.46 15.49 3.03 3.316 19.642 3038.588 0.016 12.35 15.42 3.08 3.363 19.654 4051.450 0.015 12.33 15.49 3.15 3.355 19.633 5064.313 0.015 12.21 15.36 3.14 3.280 19.598 6077.175 0.015 12.21 15.35 3.15 3.203 19.542 7090.038 0.015 12.20 15.39 3.19 3.296 19.580 8102.900 0.015 12.16 15.41 3.25 3.373 19.609 9115.763 0.015 12.19 15.43 3.24 3.411 19.621 10128.626 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: 253.216 Accepted refinement result: 12.37 14.65 2.28 2.668 19.070 253.216 0.017 Individual atomic B min max mean iso aniso Overall: 9.07 119.46 20.10 3.31 0 1785 Protein: 9.07 115.00 17.00 3.32 0 1519 Water: 11.48 119.46 38.24 N/A 0 258 Other: 19.75 26.62 22.07 N/A 0 8 Chain A: 9.07 119.46 20.10 N/A 0 1785 Histogram: Values Number of atoms 9.07 - 20.11 1272 20.11 - 31.15 227 31.15 - 42.19 125 42.19 - 53.23 94 53.23 - 64.26 42 64.26 - 75.30 11 75.30 - 86.34 7 86.34 - 97.38 4 97.38 - 108.42 1 108.42 - 119.46 2 =========================== Idealize ADP of riding H ========================== r_work=0.1237 r_free=0.1465 r_work=0.1239 r_free=0.1469 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1239 r_free = 0.1469 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 = 0.1459 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1232 r_free= 0.1459 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016971 | | target function (ls_wunit_k1) not normalized (work): 1413.593406 | | target function (ls_wunit_k1) not normalized (free): 108.409713 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1243 0.1232 0.1459 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1676 0.1677 0.1698 n_refl.: 87593 remove outliers: r(all,work,free)=0.1676 0.1677 0.1698 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1681 0.1682 0.1702 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1240 0.1229 0.1451 n_refl.: 87593 remove outliers: r(all,work,free)=0.1240 0.1229 0.1451 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 0.3552 301.178 281.771 0.652 1.002 0.378 11.894-9.307 99.02 97 4 0.1698 482.470 468.863 0.922 1.003 0.377 9.237-7.194 100.00 213 7 0.1904 394.601 388.534 0.963 1.003 0.350 7.162-5.571 100.00 427 22 0.1833 296.126 290.104 0.937 1.003 0.263 5.546-4.326 100.00 867 58 0.1001 406.508 403.568 0.963 1.003 0.204 4.315-3.360 100.00 1859 96 0.0873 386.592 385.454 1.008 1.002 0.180 3.356-2.611 100.00 3867 181 0.1177 253.971 252.873 1.010 1.002 0.048 2.608-2.026 99.99 8198 413 0.1024 168.360 167.643 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1114 82.218 82.401 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1450 36.459 35.965 1.020 0.997 0.000 1.221-1.150 99.97 13689 708 0.2252 22.972 21.455 0.982 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0450 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1229 r_free=0.1451 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=0.1229 r_free=0.1451 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1229 r_free=0.1451 | n_water=258 | time (s): 1.650 (total time: 1.650) Filter (dist) r_work=0.1239 r_free=0.1448 | n_water=251 | time (s): 23.360 (total time: 25.010) Filter (q & B) r_work=0.1241 r_free=0.1448 | n_water=248 | time (s): 2.590 (total time: 27.600) Compute maps r_work=0.1241 r_free=0.1448 | n_water=248 | time (s): 1.310 (total time: 28.910) Filter (map) r_work=0.1255 r_free=0.1446 | n_water=224 | time (s): 2.530 (total time: 31.440) Find peaks r_work=0.1255 r_free=0.1446 | n_water=224 | time (s): 0.500 (total time: 31.940) Add new water r_work=0.1399 r_free=0.1608 | n_water=433 | time (s): 2.730 (total time: 34.670) Refine new water occ: r_work=0.1305 r_free=0.1475 adp: r_work=0.1224 r_free=0.1422 occ: r_work=0.1237 r_free=0.1409 adp: r_work=0.1204 r_free=0.1396 occ: r_work=0.1208 r_free=0.1389 adp: r_work=0.1197 r_free=0.1385 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1385 r_work=0.1197 r_free=0.1385 | n_water=433 | time (s): 51.430 (total time: 86.100) Filter (q & B) r_work=0.1201 r_free=0.1388 | n_water=417 | time (s): 3.210 (total time: 89.310) Filter (dist only) r_work=0.1201 r_free=0.1388 | n_water=416 | time (s): 33.470 (total time: 122.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.542134 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1479.247145 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 0.0115 0.001 0.4 7.7 0.0 0.0 0 0.125 0.1521 0.1654 0.0132 0.001 0.4 6.4 0.0 0.0 0 0.250 0.1419 0.1570 0.0150 0.001 0.4 5.4 0.0 0.0 0 0.500 0.1370 0.1534 0.0164 0.002 0.4 4.5 0.0 0.0 0 0.750 0.1332 0.1506 0.0173 0.002 0.5 4.2 0.0 0.0 0 1.000 0.1335 0.1509 0.0173 0.002 0.5 4.2 0.0 0.0 0 1.000 0.1262 0.1458 0.0196 0.002 0.5 4.2 0.5 0.0 0 2.000 0.1229 0.1436 0.0207 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1219 0.1431 0.0212 0.003 0.7 4.8 0.5 0.0 0 4.000 0.1213 0.1426 0.0213 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1207 0.1423 0.0216 0.004 0.7 5.1 0.5 0.0 0 6.000 0.1201 0.1420 0.0219 0.005 0.8 5.1 0.5 0.0 0 7.000 0.1200 0.1426 0.0226 0.005 0.8 5.1 0.5 0.0 0 8.000 0.1195 0.1417 0.0222 0.006 0.8 5.4 0.5 0.0 0 9.000 0.1194 0.1419 0.0225 0.006 0.9 4.5 0.5 0.0 0 10.000 0.1190 0.1410 0.0220 0.007 0.9 5.1 0.5 0.0 0 11.000 0.1188 0.1416 0.0228 0.007 0.9 5.4 0.5 0.0 0 12.000 0.1188 0.1410 0.0223 0.007 0.9 5.4 0.5 0.6 0 13.000 0.1186 0.1412 0.0226 0.008 0.9 5.1 0.5 0.6 0 14.271 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1410 0.0220 0.007 0.9 5.1 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 14.10 2.20 3.776 21.772 1479.247 0.016 11.90 14.10 2.20 3.776 21.772 44.377 0.016 11.90 14.10 2.20 3.776 21.772 184.906 0.016 12.11 14.47 2.36 3.638 21.772 739.624 0.016 12.07 14.84 2.77 3.452 22.004 1479.247 0.015 11.92 14.79 2.87 3.445 22.042 2218.871 0.015 11.84 14.73 2.90 3.497 21.947 2958.494 0.014 11.75 14.67 2.92 3.479 22.006 3698.118 0.014 11.69 14.60 2.92 3.493 22.005 4437.741 0.014 11.67 14.67 3.00 3.510 21.992 5177.365 0.014 11.69 14.72 3.03 3.524 22.109 5916.989 0.014 11.67 14.74 3.07 3.536 22.122 6656.612 0.014 11.69 14.82 3.13 3.562 22.080 7396.236 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: 44.377 Accepted refinement result: 11.90 14.10 2.20 3.776 21.772 44.377 0.016 Individual atomic B min max mean iso aniso Overall: 9.10 115.03 22.17 3.31 192 1751 Protein: 9.10 115.03 17.03 3.32 0 1519 Water: 11.51 76.70 40.91 N/A 192 224 Other: 19.78 26.65 22.10 N/A 0 8 Chain A: 9.10 115.03 19.42 N/A 0 1751 Chain S: 14.56 60.00 47.20 N/A 192 0 Histogram: Values Number of atoms 9.10 - 19.70 1259 19.70 - 30.29 245 30.29 - 40.88 166 40.88 - 51.47 128 51.47 - 62.07 123 62.07 - 72.66 11 72.66 - 83.25 5 83.25 - 93.85 4 93.85 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1410 r_work=0.1190 r_free=0.1410 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1410 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1407 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 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= 0.1189 r_free= 0.1407 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015138 | | target function (ls_wunit_k1) not normalized (work): 1260.900408 | | target function (ls_wunit_k1) not normalized (free): 101.953743 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1189 0.1407 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1590 0.1588 0.1659 n_refl.: 87592 remove outliers: r(all,work,free)=0.1590 0.1588 0.1659 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1591 0.1589 0.1659 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1187 0.1400 n_refl.: 87592 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 0.3370 299.727 273.662 0.594 1.002 0.350 11.894-9.307 99.02 97 4 0.1692 482.470 477.233 0.918 1.003 0.333 9.237-7.194 100.00 213 7 0.1646 394.601 395.193 0.988 1.003 0.280 7.162-5.571 100.00 427 22 0.1623 296.126 291.413 0.935 1.003 0.224 5.546-4.326 100.00 867 58 0.0895 406.508 403.707 0.960 1.003 0.200 4.315-3.360 100.00 1859 96 0.0773 386.592 385.513 1.005 1.002 0.190 3.356-2.611 100.00 3867 181 0.1090 253.971 252.989 1.009 1.002 0.110 2.608-2.026 99.99 8198 413 0.1018 168.360 167.785 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1096 82.218 82.436 1.030 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1443 36.459 35.996 1.025 0.997 0.000 1.221-1.150 99.97 13689 708 0.2250 22.972 21.486 0.988 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0082 ============================ 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... No N/Q/H corrections needed this macrocycle 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=416 | time (s): 2.070 (total time: 2.070) Filter (dist) r_work=0.1185 r_free=0.1399 | n_water=413 | time (s): 34.690 (total time: 36.760) Filter (q & B) r_work=0.1185 r_free=0.1399 | n_water=413 | time (s): 0.920 (total time: 37.680) Compute maps r_work=0.1185 r_free=0.1399 | n_water=413 | time (s): 1.740 (total time: 39.420) Filter (map) r_work=0.1224 r_free=0.1410 | n_water=287 | time (s): 3.040 (total time: 42.460) Find peaks r_work=0.1224 r_free=0.1410 | n_water=287 | time (s): 0.700 (total time: 43.160) Add new water r_work=0.1339 r_free=0.1543 | n_water=469 | time (s): 2.990 (total time: 46.150) Refine new water occ: r_work=0.1243 r_free=0.1444 adp: r_work=0.1244 r_free=0.1445 occ: r_work=0.1223 r_free=0.1421 adp: r_work=0.1222 r_free=0.1421 occ: r_work=0.1209 r_free=0.1402 adp: r_work=0.1203 r_free=0.1400 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1400 r_work=0.1203 r_free=0.1400 | n_water=469 | time (s): 191.980 (total time: 238.130) Filter (q & B) r_work=0.1208 r_free=0.1398 | n_water=439 | time (s): 2.610 (total time: 240.740) Filter (dist only) r_work=0.1208 r_free=0.1399 | n_water=437 | time (s): 37.350 (total time: 278.090) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.784075 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.087481 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 0.1242 0.1369 0.0127 0.002 0.6 4.5 0.5 0.0 0 0.089 0.1194 0.1333 0.0140 0.003 0.7 3.5 0.5 0.0 0 0.268 0.1177 0.1320 0.0142 0.004 0.8 3.2 0.5 0.0 0 0.535 0.1167 0.1315 0.0148 0.005 0.9 4.2 0.5 0.0 0 0.803 0.1164 0.1310 0.0146 0.006 1.0 3.8 0.5 0.0 0 1.070 0.1161 0.1308 0.0147 0.007 1.0 4.5 0.5 0.0 0 1.338 0.1159 0.1307 0.0148 0.007 1.1 4.2 0.5 0.0 0 1.606 0.1157 0.1307 0.0150 0.008 1.1 4.5 0.5 0.0 0 1.873 0.1167 0.1312 0.0145 0.005 0.9 3.8 0.5 0.0 0 0.892 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1159 0.1307 0.0148 0.007 1.1 4.2 0.5 0.0 0 1.606 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.59 13.07 1.48 3.779 21.239 42.087 3.619 11.59 13.07 1.48 3.779 21.239 1.263 3.619 11.60 13.07 1.47 3.769 21.239 5.261 3.619 11.64 13.12 1.48 3.708 21.231 21.044 3.613 11.69 13.25 1.55 3.724 21.201 42.087 3.615 11.61 13.21 1.60 3.747 21.188 63.131 3.609 11.55 13.17 1.62 3.764 21.185 84.175 3.604 11.52 13.16 1.64 3.773 21.179 105.219 3.601 11.49 13.15 1.66 3.785 21.173 126.262 3.599 11.50 13.19 1.69 3.800 21.160 147.306 3.599 11.49 13.18 1.69 3.810 21.152 168.350 3.598 11.47 13.16 1.69 3.819 21.151 189.394 3.596 11.45 13.14 1.69 3.825 21.152 210.437 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: 5.261 Accepted refinement result: 11.60 13.07 1.47 3.769 21.239 5.261 3.619 Individual atomic B min max mean iso aniso Overall: 9.12 114.92 21.19 3.28 216 1748 Protein: 9.12 114.92 17.04 3.28 0 1519 Water: 11.52 76.70 35.59 N/A 216 221 Other: 19.74 26.61 22.10 N/A 0 8 Chain A: 9.12 114.92 19.38 N/A 0 1748 Chain S: 14.57 60.00 35.79 N/A 216 0 Histogram: Values Number of atoms 9.12 - 19.70 1260 19.70 - 30.28 294 30.28 - 40.86 209 40.86 - 51.44 123 51.44 - 62.02 56 62.02 - 72.60 10 72.60 - 83.18 6 83.18 - 93.76 4 93.76 - 104.34 0 104.34 - 114.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1160 r_free=0.1307 r_work=0.1160 r_free=0.1307 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1160 r_free = 0.1307 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1152 r_free = 0.1305 target_work(ml) = 3.612 | | occupancies: max = 1.00 min = 0.21 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= 0.1152 r_free= 0.1305 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.612301 | | target function (ml) not normalized (work): 300882.982656 | | target function (ml) not normalized (free): 15837.470659 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1160 0.1152 0.1305 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1503 0.1502 0.1539 n_refl.: 87590 remove outliers: r(all,work,free)=0.1503 0.1502 0.1539 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1501 0.1500 0.1538 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1156 0.1149 0.1301 n_refl.: 87590 remove outliers: r(all,work,free)=0.1154 0.1146 0.1301 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 92.71 84 5 0.3918 297.085 271.926 0.509 1.000 0.330 11.894-9.307 97.06 95 4 0.2069 482.694 462.152 0.877 1.002 0.289 9.237-7.194 98.18 209 7 0.2168 386.082 388.850 0.956 1.002 0.222 7.162-5.571 100.00 427 22 0.2054 296.126 285.958 0.914 1.002 0.197 5.546-4.326 100.00 867 58 0.1119 406.508 401.952 0.954 1.002 0.166 4.315-3.360 100.00 1859 96 0.0948 386.592 384.187 0.994 1.002 0.147 3.356-2.611 100.00 3867 181 0.1154 253.971 251.831 0.997 1.002 0.100 2.608-2.026 99.99 8198 413 0.0941 168.360 167.613 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0901 82.218 82.499 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1256 36.459 36.049 1.020 0.997 0.000 1.221-1.150 99.97 13689 708 0.2163 22.972 21.523 0.982 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0277 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1146 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=0.1146 r_free=0.1301 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1146 r_free=0.1301 | n_water=437 | time (s): 2.530 (total time: 2.530) Filter (dist) r_work=0.1146 r_free=0.1299 | n_water=436 | time (s): 45.210 (total time: 47.740) Filter (q & B) r_work=0.1146 r_free=0.1299 | n_water=436 | time (s): 1.380 (total time: 49.120) Compute maps r_work=0.1146 r_free=0.1299 | n_water=436 | time (s): 1.860 (total time: 50.980) Filter (map) r_work=0.1173 r_free=0.1322 | n_water=324 | time (s): 3.690 (total time: 54.670) Find peaks r_work=0.1173 r_free=0.1322 | n_water=324 | time (s): 0.720 (total time: 55.390) Add new water r_work=0.1244 r_free=0.1413 | n_water=476 | time (s): 3.520 (total time: 58.910) Refine new water occ: r_work=0.1173 r_free=0.1345 adp: r_work=0.1173 r_free=0.1347 occ: r_work=0.1158 r_free=0.1330 adp: r_work=0.1157 r_free=0.1331 occ: r_work=0.1145 r_free=0.1317 adp: r_work=0.1142 r_free=0.1317 ADP+occupancy (water only), MIN, final r_work=0.1142 r_free=0.1317 r_work=0.1142 r_free=0.1317 | n_water=476 | time (s): 295.810 (total time: 354.720) Filter (q & B) r_work=0.1146 r_free=0.1323 | n_water=445 | time (s): 4.110 (total time: 358.830) Filter (dist only) r_work=0.1147 r_free=0.1322 | n_water=444 | time (s): 47.340 (total time: 406.170) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.740562 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 39.701672 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 0.1219 0.1357 0.0139 0.002 0.6 5.1 0.5 0.0 0 0.087 0.1170 0.1328 0.0158 0.003 0.8 5.4 0.5 0.0 0 0.261 0.1160 0.1328 0.0168 0.004 0.9 4.5 0.5 0.0 0 0.522 0.1154 0.1326 0.0172 0.005 0.9 4.5 0.5 0.0 0 0.783 0.1150 0.1325 0.0176 0.006 1.0 4.5 0.5 0.0 0 1.044 0.1147 0.1326 0.0179 0.007 1.0 4.5 0.5 0.0 0 1.305 0.1145 0.1321 0.0176 0.008 1.1 5.1 0.5 0.0 0 1.567 0.1144 0.1321 0.0177 0.008 1.1 5.1 0.5 0.0 0 1.828 0.1153 0.1328 0.0175 0.006 1.0 4.2 0.5 0.0 0 0.870 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1145 0.1321 0.0176 0.008 1.1 5.1 0.5 0.0 0 1.567 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.45 13.21 1.76 3.765 21.135 39.702 3.611 11.45 13.21 1.76 3.765 21.135 1.191 3.611 11.45 13.21 1.76 3.765 21.135 4.963 3.611 11.49 13.25 1.75 3.698 21.129 19.851 3.607 11.50 13.32 1.82 3.720 21.112 39.702 3.606 11.51 13.38 1.87 3.739 21.090 59.553 3.605 11.44 13.33 1.89 3.755 21.086 79.403 3.599 11.42 13.30 1.89 3.765 21.083 99.254 3.597 11.38 13.27 1.89 3.772 21.084 119.105 3.594 11.37 13.29 1.92 3.788 21.075 138.956 3.593 11.37 13.30 1.92 3.804 21.064 158.807 3.593 11.37 13.30 1.94 3.814 21.061 178.658 3.592 11.35 13.28 1.93 3.817 21.063 198.508 3.591 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.191 Accepted refinement result: 11.45 13.21 1.76 3.765 21.135 1.191 3.611 Individual atomic B min max mean iso aniso Overall: 9.11 114.91 21.01 3.28 226 1745 Protein: 9.11 114.91 17.03 3.28 0 1519 Water: 11.50 76.69 34.60 N/A 226 218 Other: 19.73 26.60 22.09 N/A 0 8 Chain A: 9.11 114.91 19.32 N/A 0 1745 Chain S: 14.56 59.99 34.05 N/A 226 0 Histogram: Values Number of atoms 9.11 - 19.69 1263 19.69 - 30.27 303 30.27 - 40.85 221 40.85 - 51.43 118 51.43 - 62.01 45 62.01 - 72.59 10 72.59 - 83.17 5 83.17 - 93.75 4 93.75 - 104.33 0 104.33 - 114.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1145 r_free=0.1321 r_work=0.1145 r_free=0.1321 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1145 r_free = 0.1321 target_work(ml) = 3.611 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1140 r_free = 0.1316 target_work(ml) = 3.608 | | 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= 0.1316 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.607915 | | target function (ml) not normalized (work): 300492.453239 | | target function (ml) not normalized (free): 15833.904528 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1149 0.1140 0.1316 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1486 0.1485 0.1533 n_refl.: 87583 remove outliers: r(all,work,free)=0.1486 0.1485 0.1533 n_refl.: 87583 overall B=-0.01 to atoms: r(all,work,free)=0.1484 0.1483 0.1532 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1148 0.1139 0.1318 n_refl.: 87583 remove outliers: r(all,work,free)=0.1147 0.1138 0.1318 n_refl.: 87581 ======================== 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 0.4059 291.639 256.875 0.475 1.000 0.313 11.894-9.307 96.08 94 4 0.2336 475.840 467.217 0.873 1.002 0.249 9.237-7.194 98.18 209 7 0.2398 386.082 379.885 0.929 1.002 0.200 7.162-5.571 100.00 427 22 0.2193 296.126 284.065 0.913 1.003 0.180 5.546-4.326 100.00 867 58 0.1142 406.508 401.515 0.961 1.003 0.121 4.315-3.360 100.00 1859 96 0.0931 386.592 384.746 1.003 1.002 0.103 3.356-2.611 100.00 3867 181 0.1123 253.971 251.955 1.010 1.002 0.034 2.608-2.026 99.99 8198 413 0.0917 168.360 167.718 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0887 82.218 82.545 1.036 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1248 36.459 36.055 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 22.972 21.513 0.991 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0187 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1138 r_free=0.1318 After: r_work=0.1140 r_free=0.1317 ================================== NQH flips ================================== r_work=0.1140 r_free=0.1317 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=0.1317 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1140 r_free=0.1317 | n_water=444 | time (s): 2.490 (total time: 2.490) Filter (dist) r_work=0.1140 r_free=0.1317 | n_water=444 | time (s): 43.320 (total time: 45.810) Filter (q & B) r_work=0.1140 r_free=0.1319 | n_water=442 | time (s): 3.960 (total time: 49.770) Compute maps r_work=0.1140 r_free=0.1319 | n_water=442 | time (s): 1.900 (total time: 51.670) Filter (map) r_work=0.1168 r_free=0.1313 | n_water=346 | time (s): 3.940 (total time: 55.610) Find peaks r_work=0.1168 r_free=0.1313 | n_water=346 | time (s): 0.690 (total time: 56.300) Add new water r_work=0.1218 r_free=0.1365 | n_water=490 | time (s): 3.750 (total time: 60.050) Refine new water occ: r_work=0.1161 r_free=0.1312 adp: r_work=0.1162 r_free=0.1315 occ: r_work=0.1150 r_free=0.1299 adp: r_work=0.1149 r_free=0.1301 occ: r_work=0.1142 r_free=0.1291 adp: r_work=0.1139 r_free=0.1291 ADP+occupancy (water only), MIN, final r_work=0.1139 r_free=0.1291 r_work=0.1139 r_free=0.1291 | n_water=490 | time (s): 236.190 (total time: 296.240) Filter (q & B) r_work=0.1146 r_free=0.1298 | n_water=454 | time (s): 4.320 (total time: 300.560) Filter (dist only) r_work=0.1146 r_free=0.1299 | n_water=452 | time (s): 47.060 (total time: 347.620) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.727428 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 34.979772 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 0.1216 0.1345 0.0129 0.004 0.7 4.8 0.0 0.0 0 0.086 0.1177 0.1319 0.0142 0.004 0.8 4.2 0.0 0.0 0 0.259 0.1161 0.1308 0.0147 0.005 0.9 4.5 0.5 0.0 0 0.518 0.1152 0.1301 0.0149 0.006 1.0 4.2 0.5 0.0 0 0.777 0.1148 0.1299 0.0151 0.007 1.1 4.2 0.5 0.0 0 1.036 0.1146 0.1299 0.0153 0.008 1.1 4.2 0.5 0.0 0 1.296 0.1146 0.1299 0.0153 0.008 1.1 4.2 0.5 0.0 0 1.555 0.1146 0.1299 0.0153 0.008 1.1 4.2 0.5 0.0 0 1.814 0.1151 0.1300 0.0150 0.006 1.0 4.2 0.5 0.0 0 0.864 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1146 0.1299 0.0153 0.008 1.1 4.2 0.5 0.0 0 1.296 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.46 12.99 1.53 3.764 21.190 34.980 3.607 11.46 12.99 1.53 3.764 21.190 1.049 3.607 11.46 12.99 1.53 3.764 21.190 4.372 3.607 11.50 13.01 1.51 3.696 21.182 17.490 3.603 11.49 13.07 1.58 3.713 21.170 34.980 3.602 11.46 13.10 1.64 3.734 21.154 52.470 3.600 11.44 13.11 1.67 3.749 21.142 69.960 3.597 11.43 13.12 1.69 3.758 21.136 87.449 3.595 11.39 13.06 1.67 3.766 21.139 104.939 3.591 11.36 13.05 1.69 3.774 21.138 122.429 3.590 11.36 13.07 1.71 3.786 21.131 139.919 3.589 11.35 13.08 1.72 3.800 21.124 157.409 3.589 11.35 13.08 1.73 3.811 21.120 174.899 3.589 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 4.372 Accepted refinement result: 11.46 12.99 1.53 3.764 21.190 4.372 3.607 Individual atomic B min max mean iso aniso Overall: 9.10 114.90 21.11 3.28 235 1744 Protein: 9.10 114.90 17.02 3.28 0 1519 Water: 11.50 76.68 34.85 N/A 235 217 Other: 19.72 26.60 22.08 N/A 0 8 Chain A: 9.10 114.90 19.29 N/A 0 1744 Chain S: 14.55 60.00 34.62 N/A 235 0 Histogram: Values Number of atoms 9.10 - 19.68 1262 19.68 - 30.26 307 30.26 - 40.84 216 40.84 - 51.42 123 51.42 - 62.00 50 62.00 - 72.58 10 72.58 - 83.16 5 83.16 - 93.74 4 93.74 - 104.32 0 104.32 - 114.90 2 =========================== Idealize ADP of riding H ========================== r_work=0.1146 r_free=0.1299 r_work=0.1146 r_free=0.1299 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1146 r_free = 0.1299 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1142 r_free = 0.1293 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1142 r_free= 0.1293 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.604139 | | target function (ml) not normalized (work): 300170.747125 | | target function (ml) not normalized (free): 15796.461973 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2923 171 0.1364 0.1346 5.6786 5.5963| | 2: 3.57 - 2.84 1.00 2888 124 0.1079 0.1401 5.1621 5.2264| | 3: 2.83 - 2.48 1.00 2820 163 0.1108 0.1227 4.9394 4.9774| | 4: 2.47 - 2.25 1.00 2825 136 0.0903 0.1003 4.6252 4.6449| | 5: 2.25 - 2.09 1.00 2756 127 0.0864 0.0999 4.5704 4.6287| | 6: 2.09 - 1.97 1.00 2846 113 0.0866 0.1006 4.2704 4.3644| | 7: 1.97 - 1.87 1.00 2787 165 0.0892 0.1091 3.9861 4.0795| | 8: 1.87 - 1.79 1.00 2789 144 0.0920 0.1107 3.8931 3.9957| | 9: 1.79 - 1.72 1.00 2745 138 0.0875 0.1179 3.6487 3.8215| | 10: 1.72 - 1.66 1.00 2831 160 0.0930 0.1201 3.5668 3.7124| | 11: 1.66 - 1.61 1.00 2712 147 0.0867 0.1037 3.4951 3.5721| | 12: 1.61 - 1.56 1.00 2773 144 0.0902 0.1148 3.3286 3.4661| | 13: 1.56 - 1.52 1.00 2745 130 0.0954 0.1042 3.3104 3.4036| | 14: 1.52 - 1.48 1.00 2803 134 0.0984 0.1040 3.2389 3.3171| | 15: 1.48 - 1.45 1.00 2738 128 0.1002 0.1221 3.1515 3.2612| | 16: 1.45 - 1.42 1.00 2756 161 0.1050 0.1213 3.1312 3.2212| | 17: 1.42 - 1.39 1.00 2785 139 0.1130 0.1302 3.1127 3.2268| | 18: 1.39 - 1.36 1.00 2741 179 0.1188 0.1308 3.0993 3.227| | 19: 1.36 - 1.34 1.00 2807 134 0.1259 0.1555 3.1085 3.2588| | 20: 1.34 - 1.32 1.00 2696 147 0.1367 0.1470 3.1103 3.1497| | 21: 1.32 - 1.30 1.00 2785 112 0.1469 0.1516 3.1111 3.108| | 22: 1.29 - 1.27 1.00 2704 152 0.1561 0.1979 3.1218 3.2916| | 23: 1.27 - 1.26 1.00 2802 156 0.1647 0.1803 3.1315 3.1999| | 24: 1.26 - 1.24 1.00 2744 132 0.1708 0.1841 3.1262 3.2294| | 25: 1.24 - 1.22 1.00 2733 148 0.1885 0.2164 3.1418 3.2622| | 26: 1.22 - 1.21 1.00 2727 135 0.1910 0.1765 3.1484 3.2016| | 27: 1.21 - 1.19 1.00 2814 148 0.2075 0.2169 3.171 3.163| | 28: 1.19 - 1.18 1.00 2671 147 0.2200 0.2289 3.1652 3.1697| | 29: 1.18 - 1.16 1.00 2800 134 0.2269 0.2391 3.148 3.2288| | 30: 1.16 - 1.15 1.00 2739 148 0.2447 0.2447 3.1428 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 2923 171 0.95 8.29 1.00 0.97 5594.58| | 2: 3.57 - 2.84 2888 124 0.93 12.32 1.01 0.97 5594.58| | 3: 2.83 - 2.48 2820 163 0.90 16.29 0.99 0.97 4679.10| | 4: 2.47 - 2.25 2825 136 0.92 13.32 1.00 0.98 2318.37| | 5: 2.25 - 2.09 2756 127 0.90 15.45 1.01 0.98 2318.37| | 6: 2.09 - 1.97 2846 113 0.93 12.34 1.02 0.98 1348.13| | 7: 1.97 - 1.87 2787 165 0.95 9.47 1.02 0.97 520.63| | 8: 1.87 - 1.79 2789 144 0.92 12.83 1.00 0.97 520.63| | 9: 1.79 - 1.72 2745 138 0.94 10.18 0.98 0.97 292.79| | 10: 1.72 - 1.66 2831 160 0.94 11.23 0.98 0.97 247.16| | 11: 1.66 - 1.61 2712 147 0.93 11.82 0.98 0.97 236.66| | 12: 1.61 - 1.56 2773 144 0.95 8.88 0.99 0.97 137.58| | 13: 1.56 - 1.52 2745 130 0.95 10.43 1.03 0.97 137.58| | 14: 1.52 - 1.48 2803 134 0.94 10.77 1.02 0.98 123.11| | 15: 1.48 - 1.45 2738 128 0.95 9.84 1.02 0.98 96.62| | 16: 1.45 - 1.42 2756 161 0.94 11.02 1.02 0.98 96.62| | 17: 1.42 - 1.39 2785 139 0.95 10.82 1.01 0.98 87.98| | 18: 1.39 - 1.36 2741 179 0.94 11.44 1.01 0.98 82.98| | 19: 1.36 - 1.34 2807 134 0.94 11.79 0.99 0.98 82.98| | 20: 1.34 - 1.32 2696 147 0.94 12.06 0.98 0.96 79.34| | 21: 1.32 - 1.30 2785 112 0.94 13.04 0.98 0.96 79.08| | 22: 1.29 - 1.27 2704 152 0.93 13.58 0.98 0.96 79.55| | 23: 1.27 - 1.26 2802 156 0.92 14.82 0.97 0.94 81.91| | 24: 1.26 - 1.24 2744 132 0.93 14.83 0.96 0.94 81.91| | 25: 1.24 - 1.22 2733 148 0.91 16.36 0.96 0.94 83.97| | 26: 1.22 - 1.21 2727 135 0.90 18.12 1.02 0.93 86.25| | 27: 1.21 - 1.19 2814 148 0.89 18.75 1.02 0.93 86.25| | 28: 1.19 - 1.18 2671 147 0.88 20.39 1.01 0.92 89.90| | 29: 1.18 - 1.16 2800 134 0.88 20.52 0.99 0.92 91.27| | 30: 1.16 - 1.15 2739 148 0.86 22.03 0.98 0.92 91.27| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.08 max = 5594.58 mean = 869.62| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.97 mean = 13.42| |phase err.(test): min = 0.00 max = 90.00 mean = 13.38| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1149 0.1142 0.1293 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1474 0.1474 0.1507 n_refl.: 87581 remove outliers: r(all,work,free)=0.1474 0.1474 0.1507 n_refl.: 87581 overall B=-0.01 to atoms: r(all,work,free)=0.1474 0.1473 0.1506 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1149 0.1141 0.1296 n_refl.: 87581 remove outliers: r(all,work,free)=0.1147 0.1140 0.1296 n_refl.: 87578 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.4040 290.845 251.684 0.445 1.000 0.304 11.894-9.307 96.08 94 4 0.2437 475.840 461.644 0.864 1.002 0.223 9.237-7.194 97.73 208 7 0.2380 387.165 379.884 0.924 1.002 0.150 7.162-5.571 100.00 427 22 0.2163 296.126 284.102 0.909 1.002 0.150 5.546-4.326 100.00 867 58 0.1135 406.508 401.658 0.961 1.002 0.125 4.315-3.360 100.00 1859 96 0.0940 386.592 384.878 1.005 1.002 0.120 3.356-2.611 100.00 3867 181 0.1122 253.971 252.174 1.011 1.002 0.029 2.608-2.026 99.99 8198 413 0.0914 168.360 167.802 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0893 82.218 82.585 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.459 36.070 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2170 22.972 21.520 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0144 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2606 0.1941 0.084 5.344 8.8 119.3 19.9 258 0.000 1_bss: 0.1633 0.1773 0.084 5.344 9.1 119.5 20.1 258 0.000 1_settarget: 0.1633 0.1773 0.084 5.344 9.1 119.5 20.1 258 0.000 1_nqh: 0.1636 0.1777 0.084 5.344 9.1 119.5 20.1 258 0.003 1_weight: 0.1636 0.1777 0.084 5.344 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1231 0.1469 0.006 0.879 9.1 119.5 20.1 258 0.140 1_adp: 0.1237 0.1465 0.006 0.879 9.1 119.5 20.1 258 0.140 1_regHadp: 0.1239 0.1469 0.006 0.879 9.1 119.5 20.1 258 0.140 1_occ: 0.1232 0.1459 0.006 0.879 9.1 119.5 20.1 258 0.140 2_bss: 0.1229 0.1451 0.006 0.879 9.1 119.5 20.1 258 0.140 2_settarget: 0.1229 0.1451 0.006 0.879 9.1 119.5 20.1 258 0.140 2_updatecdl: 0.1229 0.1451 0.006 0.887 9.1 119.5 20.1 258 0.140 2_nqh: 0.1229 0.1451 0.006 0.887 9.1 119.5 20.1 258 0.140 2_sol: 0.1201 0.1388 0.006 0.887 9.1 115.0 22.2 416 n/a 2_weight: 0.1201 0.1388 0.006 0.887 9.1 115.0 22.2 416 n/a 2_xyzrec: 0.1190 0.1410 0.007 0.884 9.1 115.0 22.2 416 n/a 2_adp: 0.1190 0.1410 0.007 0.884 9.1 115.0 22.2 416 n/a 2_regHadp: 0.1190 0.1410 0.007 0.884 9.1 115.0 22.2 416 n/a 2_occ: 0.1189 0.1407 0.007 0.884 9.1 115.0 22.2 416 n/a 3_bss: 0.1186 0.1400 0.007 0.884 9.1 115.0 22.2 416 n/a 3_settarget: 0.1186 0.1400 0.007 0.884 9.1 115.0 22.2 416 n/a 3_updatecdl: 0.1186 0.1400 0.007 0.885 9.1 115.0 22.2 416 n/a 3_nqh: 0.1186 0.1400 0.007 0.885 9.1 115.0 22.2 416 n/a 3_sol: 0.1208 0.1399 0.007 0.885 9.1 115.0 21.2 437 n/a 3_weight: 0.1208 0.1399 0.007 0.885 9.1 115.0 21.2 437 n/a 3_xyzrec: 0.1159 0.1307 0.007 1.057 9.1 115.0 21.2 437 n/a 3_adp: 0.1160 0.1307 0.007 1.057 9.1 114.9 21.2 437 n/a 3_regHadp: 0.1160 0.1307 0.007 1.057 9.1 114.9 21.2 437 n/a 3_occ: 0.1152 0.1305 0.007 1.057 9.1 114.9 21.2 437 n/a 4_bss: 0.1146 0.1301 0.007 1.057 9.1 114.9 21.2 437 n/a 4_settarget: 0.1146 0.1301 0.007 1.057 9.1 114.9 21.2 437 n/a 4_updatecdl: 0.1146 0.1301 0.007 1.060 9.1 114.9 21.2 437 n/a 4_nqh: 0.1146 0.1301 0.007 1.060 9.1 114.9 21.2 437 n/a 4_sol: 0.1147 0.1322 0.007 1.060 9.1 114.9 21.0 444 n/a 4_weight: 0.1147 0.1322 0.007 1.060 9.1 114.9 21.0 444 n/a 4_xyzrec: 0.1145 0.1321 0.008 1.090 9.1 114.9 21.0 444 n/a 4_adp: 0.1145 0.1321 0.008 1.090 9.1 114.9 21.0 444 n/a 4_regHadp: 0.1145 0.1321 0.008 1.090 9.1 114.9 21.0 444 n/a 4_occ: 0.1140 0.1316 0.008 1.090 9.1 114.9 21.0 444 n/a 5_bss: 0.1138 0.1318 0.008 1.090 9.1 114.9 21.0 444 n/a 5_settarget: 0.1138 0.1318 0.008 1.090 9.1 114.9 21.0 444 n/a 5_updatecdl: 0.1138 0.1318 0.008 1.088 9.1 114.9 21.0 444 n/a 5_setrh: 0.1140 0.1317 0.008 1.088 9.1 114.9 21.0 444 n/a 5_nqh: 0.1140 0.1317 0.008 1.088 9.1 114.9 21.0 444 n/a 5_sol: 0.1146 0.1299 0.008 1.088 9.1 114.9 21.1 452 n/a 5_weight: 0.1146 0.1299 0.008 1.088 9.1 114.9 21.1 452 n/a 5_xyzrec: 0.1146 0.1299 0.008 1.088 9.1 114.9 21.1 452 n/a 5_adp: 0.1146 0.1299 0.008 1.088 9.1 114.9 21.1 452 n/a 5_regHadp: 0.1146 0.1299 0.008 1.088 9.1 114.9 21.1 452 n/a 5_occ: 0.1142 0.1293 0.008 1.088 9.1 114.9 21.1 452 n/a end: 0.1140 0.1296 0.008 1.088 9.1 114.9 21.1 452 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_4596863_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_4596863_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.0700 Refinement macro-cycles (run) : 13606.4700 Write final files (write_after_run_outputs) : 89.6300 Total : 13699.1700 Total CPU time: 3.81 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:07:46 PST -0800 (1735366066.71 s) Start R-work = 0.1633, R-free = 0.1773 Final R-work = 0.1140, R-free = 0.1296 =============================================================================== Job complete usr+sys time: 13880.43 seconds wall clock time: 251 minutes 56.10 seconds (15116.10 seconds total)