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_2112196.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 { 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_2112196.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2112196.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.98, per 1000 atoms: 0.59 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: 0.28 Conformation dependent library (CDL) restraints added in 127.1 milliseconds Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.91: 514 0.91 - 1.16: 1113 1.16 - 1.41: 590 1.41 - 1.66: 883 1.66 - 1.90: 53 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ALA A 183 " pdb=" CB ALA A 183 " ideal model delta sigma weight residual 1.536 1.353 0.183 9.10e-03 1.21e+04 4.04e+02 bond pdb=" C PHE A 162 " pdb=" N GLU A 163 " ideal model delta sigma weight residual 1.334 1.111 0.223 1.27e-02 6.20e+03 3.10e+02 bond pdb=" C AASN A 76 " pdb=" N LEU A 77 " ideal model delta sigma weight residual 1.332 1.599 -0.267 1.53e-02 4.27e+03 3.04e+02 bond pdb=" N ACYS A 53 " pdb=" CA ACYS A 53 " ideal model delta sigma weight residual 1.454 1.661 -0.207 1.21e-02 6.83e+03 2.92e+02 bond pdb=" CA SER A 155 " pdb=" C SER A 155 " ideal model delta sigma weight residual 1.523 1.314 0.209 1.24e-02 6.50e+03 2.84e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.76: 3197 4.76 - 9.53: 1848 9.53 - 14.29: 619 14.29 - 19.05: 100 19.05 - 23.81: 13 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA AASN A 76 " pdb=" C AASN A 76 " pdb=" O AASN A 76 " ideal model delta sigma weight residual 120.90 138.71 -17.81 1.07e+00 8.73e-01 2.77e+02 angle pdb=" NE ARG A 48 " pdb=" CZ ARG A 48 " pdb=" NH2 ARG A 48 " ideal model delta sigma weight residual 119.20 133.32 -14.12 9.00e-01 1.23e+00 2.46e+02 angle pdb=" O GLY A 78 " pdb=" C GLY A 78 " pdb=" N ALA A 79 " ideal model delta sigma weight residual 122.19 107.40 14.79 9.60e-01 1.09e+00 2.37e+02 angle pdb=" N BPRO A 66 " pdb=" CA BPRO A 66 " pdb=" CB BPRO A 66 " ideal model delta sigma weight residual 102.60 117.09 -14.49 1.10e+00 8.26e-01 1.74e+02 angle pdb=" CA PHE A 162 " pdb=" C PHE A 162 " pdb=" O PHE A 162 " ideal model delta sigma weight residual 120.42 106.78 13.64 1.06e+00 8.90e-01 1.66e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 15.36: 918 15.36 - 30.72: 125 30.72 - 46.08: 42 46.08 - 61.44: 22 61.44 - 76.80: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: 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 -159.09 -20.91 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA LEU A 172 " pdb=" C LEU A 172 " pdb=" N ASN A 173 " pdb=" CA ASN A 173 " ideal model delta harmonic sigma weight residual -180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 162.62 17.38 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.277: 121 0.277 - 0.550: 77 0.550 - 0.822: 32 0.822 - 1.095: 11 1.095 - 1.368: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.22 -1.37 2.00e-01 2.50e+01 4.68e+01 chirality pdb=" CA ARG A 48 " pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CB ARG A 48 " both_signs ideal model delta sigma weight residual False 2.51 1.29 1.22 2.00e-01 2.50e+01 3.70e+01 chirality pdb=" CA THR A 110 " pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CB THR A 110 " both_signs ideal model delta sigma weight residual False 2.53 1.55 0.98 2.00e-01 2.50e+01 2.40e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.004 2.00e-02 2.50e+03 6.87e-02 1.42e+02 pdb=" CG ATYR A 67 " -0.103 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " -0.012 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.101 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.083 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " 0.077 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " 0.028 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.011 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.056 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.094 2.00e-02 2.50e+03 6.84e-02 1.40e+02 pdb=" CG PHE A 119 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.047 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.063 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.114 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.068 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.068 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.086 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 98 " 0.081 9.50e-02 1.11e+02 7.45e-02 1.09e+02 pdb=" NE ARG A 98 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 98 " -0.071 2.00e-02 2.50e+03 pdb=" NH1 ARG A 98 " -0.068 2.00e-02 2.50e+03 pdb=" NH2 ARG A 98 " -0.120 2.00e-02 2.50e+03 pdb="HH11 ARG A 98 " 0.090 2.00e-02 2.50e+03 pdb="HH12 ARG A 98 " 0.002 2.00e-02 2.50e+03 pdb="HH21 ARG A 98 " 0.072 2.00e-02 2.50e+03 pdb="HH22 ARG A 98 " 0.077 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 383 2.19 - 2.79: 7023 2.79 - 3.40: 10961 3.40 - 4.00: 15534 4.00 - 4.60: 22743 Nonbonded interactions: 56644 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.591 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.758 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.790 2.100 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.800 1.850 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.834 1.850 ... (remaining 56639 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_2112196_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= 0.2600 r_free= 0.1935 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787748 | | target function (ml) not normalized (work): 232236.096060 | | target function (ml) not normalized (free): 11805.126253 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3043 0.2104 7.0941 4.9478| | 2: 3.57 - 2.84 1.00 2876 122 0.2408 0.1747 4.3417 4.3368| | 3: 2.84 - 2.48 1.00 2833 165 0.2353 0.1657 4.1248 4.1746| | 4: 2.47 - 2.25 1.00 2825 136 0.2323 0.1493 3.8246 3.8236| | 5: 2.25 - 2.09 1.00 2756 127 0.2470 0.1523 3.7936 3.8196| | 6: 2.09 - 1.97 1.00 2846 113 0.2540 0.1741 3.4679 3.5693| | 7: 1.97 - 1.87 1.00 2787 165 0.2542 0.1683 3.1308 3.1482| | 8: 1.87 - 1.79 1.00 2789 144 0.2472 0.2184 3.051 3.2086| | 9: 1.79 - 1.72 1.00 2745 138 0.2431 0.1919 2.8984 2.9642| | 10: 1.72 - 1.66 1.00 2789 158 0.2414 0.1813 2.815 2.8339| | 11: 1.66 - 1.61 1.00 2740 147 0.2513 0.1817 2.7522 2.7462| | 12: 1.61 - 1.56 1.00 2787 146 0.2470 0.2118 2.6116 2.7275| | 13: 1.56 - 1.52 1.00 2745 130 0.2519 0.1871 2.57 2.6268| | 14: 1.52 - 1.48 1.00 2803 134 0.2562 0.2052 2.5017 2.5644| | 15: 1.48 - 1.45 1.00 2738 128 0.2642 0.2198 2.4402 2.5409| | 16: 1.45 - 1.42 1.00 2756 161 0.2614 0.2087 2.3699 2.4265| | 17: 1.42 - 1.39 1.00 2785 139 0.2715 0.2070 2.3493 2.3313| | 18: 1.39 - 1.36 1.00 2741 179 0.2719 0.2380 2.2831 2.433| | 19: 1.36 - 1.34 1.00 2807 134 0.2605 0.2368 2.2429 2.286| | 20: 1.34 - 1.32 1.00 2696 147 0.2655 0.1987 2.193 2.1342| | 21: 1.32 - 1.30 1.00 2785 112 0.2629 0.2520 2.1466 2.2419| | 22: 1.29 - 1.27 1.00 2704 152 0.2704 0.2655 2.1278 2.2339| | 23: 1.27 - 1.26 1.00 2802 156 0.2760 0.2344 2.0962 2.127| | 24: 1.26 - 1.24 1.00 2744 132 0.2702 0.2142 2.0482 2.0317| | 25: 1.24 - 1.22 1.00 2734 148 0.2838 0.2486 2.04 2.0662| | 26: 1.22 - 1.21 1.00 2727 135 0.2814 0.2243 2.0019 2.0278| | 27: 1.21 - 1.19 1.00 2814 148 0.2936 0.2528 1.989 2.0017| | 28: 1.19 - 1.18 1.00 2671 147 0.2989 0.2879 1.9829 2.0151| | 29: 1.18 - 1.16 1.00 2800 134 0.2955 0.2550 1.9551 1.9876| | 30: 1.16 - 1.15 1.00 2740 148 0.3036 0.2597 1.931 1.9114| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.80 0.76 0.23 1471.56| | 2: 3.57 - 2.84 2876 122 0.81 25.93 1.27 0.23 1471.56| | 3: 2.84 - 2.48 2833 165 0.74 31.88 1.25 0.24 1220.10| | 4: 2.47 - 2.25 2825 136 0.81 25.49 1.26 0.25 567.53| | 5: 2.25 - 2.09 2756 127 0.77 29.26 1.28 0.25 567.53| | 6: 2.09 - 1.97 2846 113 0.83 22.65 1.29 0.25 310.43| | 7: 1.97 - 1.87 2787 165 0.90 16.79 1.28 0.26 91.16| | 8: 1.87 - 1.79 2789 144 0.86 21.09 1.25 0.26 91.16| | 9: 1.79 - 1.72 2745 138 0.88 18.91 1.23 0.25 56.80| | 10: 1.72 - 1.66 2789 158 0.86 20.44 1.23 0.25 49.92| | 11: 1.66 - 1.61 2740 147 0.85 22.00 1.24 0.25 48.17| | 12: 1.61 - 1.56 2787 146 0.88 18.92 1.24 0.25 30.45| | 13: 1.56 - 1.52 2745 130 0.86 20.87 1.23 0.25 30.45| | 14: 1.52 - 1.48 2803 134 0.86 21.24 1.24 0.25 27.24| | 15: 1.48 - 1.45 2738 128 0.87 20.61 1.24 0.25 21.37| | 16: 1.45 - 1.42 2756 161 0.85 22.24 1.23 0.25 21.37| | 17: 1.42 - 1.39 2785 139 0.86 21.00 1.24 0.25 18.02| | 18: 1.39 - 1.36 2741 179 0.86 21.63 1.23 0.25 16.08| | 19: 1.36 - 1.34 2807 134 0.86 21.98 1.21 0.25 16.08| | 20: 1.34 - 1.32 2696 147 0.87 20.52 1.21 0.25 12.80| | 21: 1.32 - 1.30 2785 112 0.87 21.30 1.20 0.25 12.57| | 22: 1.29 - 1.27 2704 152 0.86 21.79 1.21 0.25 12.23| | 23: 1.27 - 1.26 2802 156 0.86 21.39 1.21 0.24 10.51| | 24: 1.26 - 1.24 2744 132 0.86 21.65 1.20 0.24 10.51| | 25: 1.24 - 1.22 2734 148 0.85 22.71 1.20 0.24 9.88| | 26: 1.22 - 1.21 2727 135 0.86 22.57 1.20 0.24 9.19| | 27: 1.21 - 1.19 2814 148 0.85 23.43 1.21 0.24 9.19| | 28: 1.19 - 1.18 2671 147 0.84 24.06 1.19 0.23 8.66| | 29: 1.18 - 1.16 2800 134 0.84 24.40 1.17 0.23 8.46| | 30: 1.16 - 1.15 2740 148 0.82 25.78 1.14 0.23 8.46| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.46 max = 1471.56 mean = 213.83| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 22.38| |phase err.(test): min = 0.00 max = 89.85 mean = 22.23| |-----------------------------------------------------------------------------| ----------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 : 0.080 0.267 1557 Z= 5.280 Angle : 5.370 19.386 2118 Z= 3.767 Chirality : 0.421 1.368 243 Planarity : 0.031 0.086 284 Dihedral : 13.675 76.798 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.86 % Allowed : 4.35 % Favored : 93.79 % Cbeta Deviations : 33.51 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.47), residues: 224 helix: -3.04 (0.35), residues: 108 sheet: -0.35 (0.92), residues: 28 loop : -0.94 (0.58), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.063 0.017 ARG A 145 TYR 0.088 0.033 TYR A 139 PHE 0.078 0.035 PHE A 162 HIS 0.055 0.021 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2600 r_free= 0.1935 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787748 | | target function (ml) not normalized (work): 232236.096060 | | target function (ml) not normalized (free): 11805.126253 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2558 0.2600 0.1935 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2558 0.2600 0.1935 n_refl.: 87602 remove outliers: r(all,work,free)=0.1969 0.1972 0.1935 n_refl.: 87594 overall B=0.22 to atoms: r(all,work,free)=0.1995 0.1999 0.1948 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1632 0.1626 0.1761 n_refl.: 87594 remove outliers: r(all,work,free)=0.1632 0.1625 0.1761 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3864 386.106 356.552 0.730 0.910 0.401 11.894-9.307 99.02 97 4 0.1901 613.311 594.469 1.019 0.911 0.380 9.237-7.194 100.00 213 7 0.2135 501.613 490.732 1.053 0.912 0.370 7.162-5.571 100.00 427 22 0.2169 376.432 365.810 1.017 0.913 0.330 5.546-4.326 100.00 867 58 0.1299 516.749 510.432 1.061 0.913 0.214 4.315-3.360 100.00 1859 96 0.1131 491.432 487.497 1.098 0.915 0.199 3.356-2.611 100.00 3867 181 0.1443 322.845 319.408 1.088 0.917 0.089 2.608-2.026 99.99 8198 413 0.1328 214.017 212.039 1.095 0.921 0.000 2.025-1.573 100.00 17313 902 0.1634 104.515 103.780 1.092 0.927 0.000 1.573-1.221 100.00 36679 1900 0.2050 46.346 45.051 1.067 0.936 0.000 1.221-1.150 99.97 13689 708 0.2568 29.201 27.039 1.028 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0493 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1625 r_free=0.1761 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1626 r_free=0.1761 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.947809 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2036.653218 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 0.1691 0.1824 0.0133 0.001 0.4 4.2 0.0 0.0 0 0.125 0.1558 0.1709 0.0151 0.001 0.5 4.2 0.0 0.0 0 0.250 0.1457 0.1627 0.0170 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1384 0.1570 0.0186 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1346 0.1549 0.0203 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1371 0.1569 0.0198 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1307 0.1529 0.0222 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1268 0.1494 0.0225 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1253 0.1485 0.0232 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1251 0.1485 0.0234 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1240 0.1481 0.0240 0.004 0.8 3.5 0.5 0.0 0 6.000 0.1236 0.1475 0.0238 0.005 0.8 3.5 0.5 0.0 0 7.000 0.1236 0.1476 0.0240 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1231 0.1474 0.0243 0.006 0.9 3.5 0.5 0.0 0 9.000 0.1229 0.1473 0.0245 0.006 0.9 3.8 0.5 0.0 0 10.000 0.1227 0.1471 0.0244 0.007 0.9 4.2 0.5 0.0 0 11.000 0.1225 0.1474 0.0249 0.007 0.9 4.2 0.5 0.6 0 12.000 0.1225 0.1477 0.0252 0.008 1.0 4.2 0.5 0.6 0 13.974 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1227 0.1471 0.0244 0.007 0.9 4.2 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.27 14.71 2.44 3.013 19.074 2036.653 0.017 12.28 14.71 2.43 2.989 19.074 61.100 0.017 12.34 14.69 2.35 2.669 19.072 254.582 0.017 12.70 15.36 2.66 2.823 19.295 1018.327 0.016 12.49 15.44 2.94 3.067 19.483 2036.653 0.016 12.39 15.40 3.02 3.158 19.551 3054.980 0.015 12.33 15.41 3.07 3.348 19.653 4073.306 0.015 12.30 15.45 3.15 3.332 19.632 5091.633 0.015 12.28 15.48 3.21 3.377 19.646 6109.960 0.015 12.22 15.45 3.24 3.339 19.619 7128.286 0.015 12.24 15.56 3.32 3.415 19.644 8146.613 0.015 12.20 15.56 3.36 3.523 19.702 9164.939 0.015 12.17 15.51 3.34 3.440 19.638 10183.266 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: 254.582 Accepted refinement result: 12.34 14.69 2.35 2.669 19.072 254.582 0.017 Individual atomic B min max mean iso aniso Overall: 9.09 119.46 20.10 3.31 0 1785 Protein: 9.09 115.02 17.01 3.32 0 1519 Water: 11.49 119.46 38.24 N/A 0 258 Other: 19.74 26.62 22.07 N/A 0 8 Chain A: 9.09 119.46 20.10 N/A 0 1785 Histogram: Values Number of atoms 9.09 - 20.12 1272 20.12 - 31.16 227 31.16 - 42.20 125 42.20 - 53.24 94 53.24 - 64.27 42 64.27 - 75.31 11 75.31 - 86.35 7 86.35 - 97.39 4 97.39 - 108.42 1 108.42 - 119.46 2 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1469 r_work=0.1236 r_free=0.1473 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1236 r_free = 0.1473 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 = 0.1229 r_free = 0.1467 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.17 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= 0.1229 r_free= 0.1467 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016806 | | target function (ls_wunit_k1) not normalized (work): 1399.898225 | | target function (ls_wunit_k1) not normalized (free): 110.480589 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1241 0.1229 0.1467 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1675 0.1676 0.1698 n_refl.: 87593 remove outliers: r(all,work,free)=0.1675 0.1676 0.1698 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1680 0.1681 0.1702 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1228 0.1457 n_refl.: 87593 remove outliers: r(all,work,free)=0.1239 0.1227 0.1457 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 0.3514 301.195 280.478 0.652 1.003 0.380 11.894-9.307 99.02 97 4 0.1634 482.498 470.685 0.924 1.003 0.370 9.237-7.194 100.00 213 7 0.1844 394.624 390.649 0.965 1.003 0.324 7.162-5.571 100.00 427 22 0.1830 296.143 290.350 0.936 1.003 0.263 5.546-4.326 100.00 867 58 0.1003 406.532 403.656 0.964 1.003 0.204 4.315-3.360 100.00 1859 96 0.0872 386.614 385.556 1.007 1.003 0.180 3.356-2.611 100.00 3867 181 0.1175 253.986 252.851 1.010 1.002 0.110 2.608-2.026 99.99 8198 413 0.1025 168.369 167.652 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1111 82.223 82.421 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1453 36.461 35.962 1.020 0.996 0.000 1.221-1.150 99.97 13689 708 0.2250 22.973 21.460 0.984 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0425 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1227 r_free=0.1457 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1229 r_free=0.1461 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1229 r_free=0.1461 | n_water=258 | time (s): 1.970 (total time: 1.970) Filter (dist) r_work=0.1238 r_free=0.1459 | n_water=251 | time (s): 22.480 (total time: 24.450) Filter (q & B) r_work=0.1240 r_free=0.1459 | n_water=248 | time (s): 3.160 (total time: 27.610) Compute maps r_work=0.1240 r_free=0.1459 | n_water=248 | time (s): 1.480 (total time: 29.090) Filter (map) r_work=0.1256 r_free=0.1459 | n_water=224 | time (s): 2.540 (total time: 31.630) Find peaks r_work=0.1256 r_free=0.1459 | n_water=224 | time (s): 0.570 (total time: 32.200) Add new water r_work=0.1404 r_free=0.1622 | n_water=427 | time (s): 3.240 (total time: 35.440) Refine new water occ: r_work=0.1310 r_free=0.1499 adp: r_work=0.1228 r_free=0.1445 occ: r_work=0.1240 r_free=0.1426 adp: r_work=0.1207 r_free=0.1415 occ: r_work=0.1210 r_free=0.1404 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=427 | time (s): 61.140 (total time: 96.580) Filter (q & B) r_work=0.1202 r_free=0.1404 | n_water=414 | time (s): 2.600 (total time: 99.180) Filter (dist only) r_work=0.1203 r_free=0.1403 | n_water=413 | time (s): 35.090 (total time: 134.270) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.604525 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1478.366861 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 0.1608 0.1731 0.0124 0.001 0.4 7.7 0.0 0.0 0 0.125 0.1507 0.1647 0.0139 0.001 0.4 7.0 0.0 0.0 0 0.250 0.1389 0.1550 0.0161 0.001 0.5 6.4 0.0 0.0 0 0.500 0.1364 0.1538 0.0173 0.002 0.4 4.5 0.0 0.0 0 0.750 0.1317 0.1501 0.0184 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1326 0.1508 0.0182 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1250 0.1456 0.0207 0.002 0.6 4.5 0.5 0.0 0 2.000 0.1228 0.1448 0.0220 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1217 0.1441 0.0224 0.003 0.7 4.2 0.5 0.0 0 4.000 0.1208 0.1436 0.0228 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1203 0.1433 0.0230 0.004 0.7 4.2 0.5 0.0 0 6.000 0.1199 0.1433 0.0233 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1195 0.1425 0.0231 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1192 0.1426 0.0234 0.006 0.8 4.2 0.5 0.0 0 9.000 0.1191 0.1431 0.0241 0.006 0.9 3.8 0.5 0.0 0 10.000 0.1189 0.1425 0.0236 0.007 0.9 4.5 0.5 0.0 0 11.000 0.1187 0.1420 0.0233 0.007 0.9 4.8 0.5 0.6 0 12.000 0.1186 0.1422 0.0236 0.008 1.0 5.4 0.5 0.6 0 13.802 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1187 0.1420 0.0233 0.007 0.9 4.8 0.5 0.6 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.87 14.20 2.33 3.777 21.779 1478.367 0.016 11.87 14.20 2.33 3.777 21.779 44.351 0.016 11.87 14.20 2.33 3.777 21.779 184.796 0.016 12.02 14.57 2.55 3.631 21.782 739.183 0.015 12.04 14.90 2.86 3.446 22.023 1478.367 0.015 11.93 14.90 2.97 3.456 22.132 2217.550 0.014 11.85 14.90 3.05 3.485 21.972 2956.734 0.014 11.74 14.80 3.06 3.483 22.130 3695.917 0.014 11.71 14.78 3.07 3.508 22.090 4435.101 0.014 11.72 14.84 3.12 3.539 22.154 5174.284 0.014 11.68 14.83 3.14 3.547 22.141 5913.467 0.014 11.72 14.97 3.25 3.604 22.219 6652.651 0.014 11.65 14.88 3.23 3.603 22.228 7391.834 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: 44.351 Accepted refinement result: 11.87 14.20 2.33 3.777 21.779 44.351 0.016 Individual atomic B min max mean iso aniso Overall: 9.11 115.05 22.18 3.31 189 1751 Protein: 9.11 115.05 17.03 3.32 0 1519 Water: 11.52 76.70 41.10 N/A 189 224 Other: 19.77 26.65 22.10 N/A 0 8 Chain A: 9.11 115.05 19.43 N/A 0 1751 Chain S: 15.85 60.00 47.61 N/A 189 0 Histogram: Values Number of atoms 9.11 - 19.71 1260 19.71 - 30.30 241 30.30 - 40.89 164 40.89 - 51.49 129 51.49 - 62.08 123 62.08 - 72.67 12 72.67 - 83.27 5 83.27 - 93.86 4 93.86 - 104.45 0 104.45 - 115.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1187 r_free=0.1420 r_work=0.1187 r_free=0.1420 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1187 r_free = 0.1420 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1418 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.22 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= 0.1418 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014997 | | target function (ls_wunit_k1) not normalized (work): 1249.153637 | | target function (ls_wunit_k1) not normalized (free): 104.368487 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1189 0.1418 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1585 0.1583 0.1655 n_refl.: 87592 remove outliers: r(all,work,free)=0.1585 0.1583 0.1655 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1586 0.1584 0.1656 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1186 0.1411 n_refl.: 87592 remove outliers: r(all,work,free)=0.1196 0.1185 0.1411 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 0.3364 299.744 274.216 0.596 1.002 0.350 11.894-9.307 99.02 97 4 0.1650 482.498 475.194 0.917 1.003 0.327 9.237-7.194 100.00 213 7 0.1661 394.624 395.603 0.986 1.003 0.260 7.162-5.571 100.00 427 22 0.1586 296.143 291.996 0.939 1.003 0.250 5.546-4.326 100.00 867 58 0.0904 406.532 403.596 0.957 1.003 0.210 4.315-3.360 100.00 1859 96 0.0785 386.614 385.962 1.005 1.002 0.190 3.356-2.611 100.00 3867 181 0.1083 253.986 253.141 1.011 1.002 0.130 2.608-2.026 99.99 8198 413 0.1017 168.369 167.817 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1095 82.223 82.428 1.031 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1441 36.461 35.993 1.025 0.996 0.000 1.221-1.150 99.97 13689 708 0.2250 22.973 21.486 0.989 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0103 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1185 r_free=0.1411 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1185 r_free=0.1411 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1185 r_free=0.1411 | n_water=413 | time (s): 2.270 (total time: 2.270) Filter (dist) r_work=0.1185 r_free=0.1412 | n_water=411 | time (s): 35.340 (total time: 37.610) Filter (q & B) r_work=0.1185 r_free=0.1412 | n_water=411 | time (s): 0.770 (total time: 38.380) Compute maps r_work=0.1185 r_free=0.1412 | n_water=411 | time (s): 1.530 (total time: 39.910) Filter (map) r_work=0.1220 r_free=0.1409 | n_water=280 | time (s): 3.520 (total time: 43.430) Find peaks r_work=0.1220 r_free=0.1409 | n_water=280 | time (s): 0.680 (total time: 44.110) Add new water r_work=0.1341 r_free=0.1558 | n_water=469 | time (s): 3.280 (total time: 47.390) Refine new water occ: r_work=0.1252 r_free=0.1469 adp: r_work=0.1253 r_free=0.1470 occ: r_work=0.1230 r_free=0.1442 adp: r_work=0.1230 r_free=0.1443 occ: r_work=0.1212 r_free=0.1414 adp: r_work=0.1207 r_free=0.1413 ADP+occupancy (water only), MIN, final r_work=0.1207 r_free=0.1413 r_work=0.1207 r_free=0.1413 | n_water=469 | time (s): 145.200 (total time: 192.590) Filter (q & B) r_work=0.1212 r_free=0.1415 | n_water=434 | time (s): 2.700 (total time: 195.290) Filter (dist only) r_work=0.1212 r_free=0.1413 | n_water=433 | time (s): 35.840 (total time: 231.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.773887 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.277886 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 0.1387 0.0145 0.002 0.6 4.5 0.5 0.0 0 0.089 0.1200 0.1355 0.0154 0.003 0.7 3.5 0.5 0.0 0 0.266 0.1183 0.1342 0.0159 0.004 0.8 3.2 0.5 0.0 0 0.532 0.1175 0.1340 0.0166 0.005 0.9 3.2 0.5 0.0 0 0.798 0.1171 0.1337 0.0166 0.006 1.0 3.2 0.5 0.0 0 1.064 0.1167 0.1336 0.0169 0.007 1.0 3.2 0.5 0.0 0 1.330 0.1165 0.1335 0.0170 0.007 1.1 3.5 0.5 0.6 0 1.596 0.1163 0.1334 0.0171 0.008 1.1 3.5 0.5 0.6 0 1.863 0.1173 0.1337 0.0164 0.005 0.9 3.2 0.5 0.0 0 0.887 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1163 0.1334 0.0171 0.008 1.1 3.5 0.5 0.6 0 1.863 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.63 13.34 1.71 3.780 21.220 48.278 3.622 11.63 13.34 1.71 3.780 21.220 1.448 3.622 11.64 13.34 1.70 3.765 21.220 6.035 3.621 11.70 13.44 1.74 3.713 21.202 24.139 3.617 11.72 13.52 1.80 3.727 21.168 48.278 3.614 11.64 13.48 1.85 3.758 21.158 72.417 3.609 11.58 13.45 1.86 3.773 21.154 96.556 3.605 11.56 13.46 1.90 3.787 21.143 120.695 3.603 11.54 13.46 1.92 3.799 21.129 144.834 3.601 11.53 13.47 1.94 3.814 21.123 168.973 3.601 11.52 13.44 1.92 3.821 21.113 193.112 3.598 11.50 13.44 1.94 3.829 21.116 217.250 3.598 11.50 13.44 1.94 3.839 21.110 241.389 3.598 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.448 Accepted refinement result: 11.63 13.34 1.71 3.780 21.220 1.448 3.622 Individual atomic B min max mean iso aniso Overall: 9.12 115.05 21.15 3.31 213 1747 Protein: 9.12 115.05 17.04 3.32 0 1519 Water: 11.53 76.70 35.55 N/A 213 220 Other: 19.77 26.65 22.11 N/A 0 8 Chain A: 9.12 115.05 19.36 N/A 0 1747 Chain S: 15.86 60.01 35.84 N/A 213 0 Histogram: Values Number of atoms 9.12 - 19.71 1261 19.71 - 30.31 288 30.31 - 40.90 214 40.90 - 51.49 121 51.49 - 62.09 53 62.09 - 72.68 12 72.68 - 83.27 5 83.27 - 93.87 4 93.87 - 104.46 0 104.46 - 115.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1163 r_free=0.1334 r_work=0.1163 r_free=0.1334 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1163 r_free = 0.1334 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1151 r_free = 0.1320 target_work(ml) = 3.613 | | 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= 0.1151 r_free= 0.1320 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.613003 | | target function (ml) not normalized (work): 300941.448774 | | target function (ml) not normalized (free): 15841.971493 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1159 0.1151 0.1320 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1487 0.1486 0.1536 n_refl.: 87590 remove outliers: r(all,work,free)=0.1487 0.1486 0.1536 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1486 0.1485 0.1535 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1154 0.1146 0.1315 n_refl.: 87590 remove outliers: r(all,work,free)=0.1151 0.1142 0.1315 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 0.3897 299.312 266.874 0.473 1.000 0.292 11.894-9.307 97.06 95 4 0.2419 475.836 462.892 0.859 1.002 0.273 9.237-7.194 98.18 209 7 0.2289 386.104 385.723 0.947 1.002 0.198 7.162-5.571 100.00 427 22 0.2095 296.143 285.929 0.908 1.002 0.170 5.546-4.326 100.00 867 58 0.1135 406.532 401.469 0.953 1.002 0.150 4.315-3.360 100.00 1859 96 0.0935 386.614 384.162 0.995 1.002 0.150 3.356-2.611 100.00 3867 181 0.1136 253.986 251.712 0.999 1.002 0.038 2.608-2.026 99.99 8198 413 0.0925 168.369 167.537 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0894 82.223 82.487 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1254 36.461 36.038 1.018 0.998 0.000 1.221-1.150 99.97 13689 708 0.2164 22.973 21.513 0.980 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0207 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1142 r_free=0.1315 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=0.1142 r_free=0.1315 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1142 r_free=0.1315 | n_water=433 | time (s): 2.440 (total time: 2.440) Filter (dist) r_work=0.1142 r_free=0.1316 | n_water=431 | time (s): 45.270 (total time: 47.710) Filter (q & B) r_work=0.1142 r_free=0.1316 | n_water=430 | time (s): 3.810 (total time: 51.520) Compute maps r_work=0.1142 r_free=0.1316 | n_water=430 | time (s): 1.850 (total time: 53.370) Filter (map) r_work=0.1168 r_free=0.1318 | n_water=316 | time (s): 3.860 (total time: 57.230) Find peaks r_work=0.1168 r_free=0.1318 | n_water=316 | time (s): 0.700 (total time: 57.930) Add new water r_work=0.1234 r_free=0.1386 | n_water=476 | time (s): 3.720 (total time: 61.650) Refine new water occ: r_work=0.1165 r_free=0.1313 adp: r_work=0.1166 r_free=0.1316 occ: r_work=0.1150 r_free=0.1299 adp: r_work=0.1149 r_free=0.1301 occ: r_work=0.1138 r_free=0.1287 adp: r_work=0.1134 r_free=0.1286 ADP+occupancy (water only), MIN, final r_work=0.1134 r_free=0.1286 r_work=0.1134 r_free=0.1286 | n_water=476 | time (s): 228.970 (total time: 290.620) Filter (q & B) r_work=0.1142 r_free=0.1294 | n_water=441 | time (s): 4.070 (total time: 294.690) Filter (dist only) r_work=0.1142 r_free=0.1293 | n_water=440 | time (s): 46.780 (total time: 341.470) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.772528 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.813862 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 0.1205 0.1331 0.0126 0.002 0.6 4.2 0.5 0.0 0 0.089 0.1168 0.1306 0.0138 0.003 0.7 3.2 0.5 0.0 0 0.266 0.1154 0.1295 0.0142 0.005 0.9 3.8 0.5 0.0 0 0.532 0.1148 0.1293 0.0146 0.006 1.0 3.5 0.5 0.6 0 0.798 0.1144 0.1297 0.0154 0.006 1.0 3.2 0.5 0.0 0 1.064 0.1140 0.1296 0.0155 0.007 1.1 3.2 0.5 0.0 0 1.329 0.1139 0.1294 0.0156 0.008 1.1 3.2 0.5 0.0 0 1.595 0.1137 0.1292 0.0155 0.009 1.1 3.2 0.5 0.6 0 1.861 0.1146 0.1295 0.0149 0.006 1.0 3.5 0.5 0.0 0 0.886 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1137 0.1292 0.0155 0.009 1.1 3.2 0.5 0.6 0 1.861 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.37 12.92 1.55 3.781 21.148 41.814 3.603 11.37 12.92 1.55 3.781 21.148 1.254 3.603 11.37 12.92 1.55 3.781 21.148 5.227 3.603 11.41 12.97 1.56 3.714 21.139 20.907 3.599 11.50 13.11 1.61 3.732 21.106 41.814 3.603 11.41 13.07 1.66 3.759 21.096 62.721 3.596 11.33 13.02 1.69 3.769 21.097 83.628 3.591 11.32 13.00 1.69 3.780 21.091 104.535 3.588 11.31 13.03 1.72 3.793 21.083 125.442 3.587 11.32 13.09 1.77 3.812 21.068 146.349 3.587 11.30 13.07 1.77 3.821 21.068 167.255 3.586 11.29 13.08 1.78 3.833 21.063 188.162 3.585 11.28 13.06 1.78 3.838 21.060 209.069 3.584 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.227 Accepted refinement result: 11.37 12.92 1.55 3.781 21.148 5.227 3.603 Individual atomic B min max mean iso aniso Overall: 9.11 115.05 21.03 3.31 220 1747 Protein: 9.11 115.05 17.03 3.32 0 1519 Water: 11.52 76.70 34.79 N/A 220 220 Other: 19.77 26.64 22.10 N/A 0 8 Chain A: 9.11 115.05 19.35 N/A 0 1747 Chain S: 15.85 60.00 34.32 N/A 220 0 Histogram: Values Number of atoms 9.11 - 19.71 1262 19.71 - 30.30 297 30.30 - 40.89 220 40.89 - 51.49 121 51.49 - 62.08 44 62.08 - 72.67 12 72.67 - 83.27 5 83.27 - 93.86 4 93.86 - 104.45 0 104.45 - 115.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1137 r_free=0.1292 r_work=0.1137 r_free=0.1292 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1137 r_free = 0.1292 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1133 r_free = 0.1287 target_work(ml) = 3.601 | | 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= 0.1133 r_free= 0.1287 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.601245 | | target function (ml) not normalized (work): 299933.278587 | | target function (ml) not normalized (free): 15794.180498 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1140 0.1133 0.1287 n_refl.: 87582 re-set all scales: r(all,work,free)=0.1459 0.1460 0.1477 n_refl.: 87582 remove outliers: r(all,work,free)=0.1459 0.1460 0.1477 n_refl.: 87582 overall B=-0.01 to atoms: r(all,work,free)=0.1458 0.1459 0.1476 n_refl.: 87582 bulk-solvent and scaling: r(all,work,free)=0.1139 0.1132 0.1288 n_refl.: 87582 remove outliers: r(all,work,free)=0.1138 0.1131 0.1288 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.3996 296.463 257.441 0.468 1.000 0.320 11.894-9.307 96.08 94 4 0.2333 479.702 465.089 0.861 1.002 0.248 9.237-7.194 98.18 209 7 0.2346 386.104 379.459 0.931 1.003 0.180 7.162-5.571 100.00 427 22 0.2140 296.143 286.493 0.916 1.003 0.170 5.546-4.326 100.00 867 58 0.1138 406.532 401.964 0.961 1.003 0.119 4.315-3.360 100.00 1859 96 0.0918 386.614 384.455 1.003 1.003 0.100 3.356-2.611 100.00 3867 181 0.1116 253.986 251.924 1.010 1.002 0.050 2.608-2.026 99.99 8198 413 0.0908 168.369 167.735 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0879 82.223 82.571 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1246 36.461 36.070 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2165 22.973 21.528 0.991 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0178 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1131 r_free=0.1288 After: r_work=0.1132 r_free=0.1288 ================================== NQH flips ================================== r_work=0.1132 r_free=0.1288 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=0.1132 r_free=0.1288 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1132 r_free=0.1288 | n_water=440 | time (s): 2.400 (total time: 2.400) Filter (dist) r_work=0.1132 r_free=0.1288 | n_water=440 | time (s): 45.380 (total time: 47.780) Filter (q & B) r_work=0.1132 r_free=0.1288 | n_water=440 | time (s): 1.400 (total time: 49.180) Compute maps r_work=0.1132 r_free=0.1288 | n_water=440 | time (s): 1.880 (total time: 51.060) Filter (map) r_work=0.1159 r_free=0.1307 | n_water=342 | time (s): 3.930 (total time: 54.990) Find peaks r_work=0.1159 r_free=0.1307 | n_water=342 | time (s): 0.700 (total time: 55.690) Add new water r_work=0.1208 r_free=0.1353 | n_water=490 | time (s): 3.820 (total time: 59.510) Refine new water occ: r_work=0.1151 r_free=0.1295 adp: r_work=0.1151 r_free=0.1298 occ: r_work=0.1138 r_free=0.1283 adp: r_work=0.1137 r_free=0.1285 occ: r_work=0.1129 r_free=0.1275 adp: r_work=0.1126 r_free=0.1275 ADP+occupancy (water only), MIN, final r_work=0.1126 r_free=0.1275 r_work=0.1126 r_free=0.1275 | n_water=490 | time (s): 237.990 (total time: 297.500) Filter (q & B) r_work=0.1134 r_free=0.1286 | n_water=451 | time (s): 3.660 (total time: 301.160) Filter (dist only) r_work=0.1134 r_free=0.1287 | n_water=449 | time (s): 47.580 (total time: 348.740) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.680604 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.784182 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 0.1232 0.1353 0.0121 0.004 0.7 6.1 0.5 0.0 0 0.084 0.1176 0.1312 0.0136 0.004 0.8 4.5 0.0 0.0 0 0.252 0.1155 0.1298 0.0143 0.005 0.9 3.8 0.5 0.0 0 0.504 0.1146 0.1292 0.0147 0.005 1.0 4.2 0.5 0.0 0 0.756 0.1141 0.1290 0.0148 0.006 1.1 3.8 0.5 0.6 0 1.008 0.1138 0.1288 0.0150 0.007 1.1 3.8 0.5 0.6 0 1.260 0.1135 0.1287 0.0152 0.008 1.1 3.8 0.5 0.6 0 1.513 0.1134 0.1287 0.0153 0.008 1.1 3.8 0.5 0.6 0 1.765 0.1145 0.1292 0.0147 0.006 1.0 4.2 0.5 0.0 0 0.840 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1135 0.1287 0.0152 0.008 1.1 3.8 0.5 0.6 0 1.513 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.35 12.87 1.52 3.780 21.165 46.784 3.602 11.35 12.87 1.52 3.780 21.165 1.404 3.602 11.36 12.87 1.51 3.768 21.165 5.848 3.602 11.40 12.93 1.53 3.712 21.154 23.392 3.597 11.43 13.02 1.59 3.738 21.126 46.784 3.597 11.37 12.99 1.62 3.759 21.116 70.176 3.592 11.31 12.95 1.64 3.774 21.115 93.568 3.588 11.28 12.93 1.65 3.783 21.112 116.960 3.585 11.27 12.94 1.68 3.795 21.106 140.353 3.584 11.28 13.00 1.72 3.817 21.092 163.745 3.585 11.26 12.99 1.72 3.826 21.091 187.137 3.583 11.24 12.95 1.70 3.830 21.089 210.529 3.581 11.22 12.93 1.71 3.829 21.095 233.921 3.580 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.404 Accepted refinement result: 11.35 12.87 1.52 3.780 21.165 1.404 3.602 Individual atomic B min max mean iso aniso Overall: 9.11 115.04 21.06 3.31 229 1747 Protein: 9.11 115.04 17.03 3.32 0 1519 Water: 11.51 76.69 34.71 N/A 229 220 Other: 19.76 26.64 22.09 N/A 0 8 Chain A: 9.11 115.04 19.35 N/A 0 1747 Chain S: 15.84 59.99 34.18 N/A 229 0 Histogram: Values Number of atoms 9.11 - 19.70 1262 19.70 - 30.29 300 30.29 - 40.89 222 40.89 - 51.48 126 51.48 - 62.07 43 62.07 - 72.67 12 72.67 - 83.26 5 83.26 - 93.85 4 93.85 - 104.45 0 104.45 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1135 r_free=0.1287 r_work=0.1135 r_free=0.1287 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1135 r_free = 0.1287 target_work(ml) = 3.602 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1131 r_free = 0.1284 target_work(ml) = 3.601 | | 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= 0.1131 r_free= 0.1284 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.600835 | | target function (ml) not normalized (work): 299888.358990 | | target function (ml) not normalized (free): 15791.265922 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1349 0.1347 5.6429 5.6176| | 2: 3.57 - 2.84 1.00 2888 124 0.1072 0.1400 5.1664 5.2213| | 3: 2.83 - 2.48 1.00 2820 163 0.1098 0.1179 4.9468 4.9695| | 4: 2.47 - 2.25 1.00 2825 136 0.0885 0.1014 4.6282 4.6633| | 5: 2.25 - 2.09 1.00 2756 127 0.0853 0.0962 4.5763 4.6337| | 6: 2.09 - 1.97 1.00 2846 113 0.0839 0.1017 4.2591 4.3711| | 7: 1.97 - 1.87 1.00 2787 165 0.0874 0.1074 3.9694 4.0714| | 8: 1.87 - 1.79 1.00 2789 144 0.0897 0.1086 3.8773 3.9787| | 9: 1.79 - 1.72 1.00 2745 138 0.0866 0.1175 3.6376 3.813| | 10: 1.72 - 1.66 1.00 2831 160 0.0910 0.1213 3.5544 3.7125| | 11: 1.66 - 1.61 1.00 2712 147 0.0866 0.0995 3.4879 3.5459| | 12: 1.61 - 1.56 1.00 2773 144 0.0900 0.1152 3.3222 3.4652| | 13: 1.56 - 1.52 1.00 2745 130 0.0941 0.1013 3.2993 3.3738| | 14: 1.52 - 1.48 1.00 2803 134 0.0979 0.1029 3.2332 3.3127| | 15: 1.48 - 1.45 1.00 2738 128 0.1006 0.1197 3.1516 3.2531| | 16: 1.45 - 1.42 1.00 2756 161 0.1055 0.1230 3.132 3.2393| | 17: 1.42 - 1.39 1.00 2785 139 0.1140 0.1280 3.1165 3.22| | 18: 1.39 - 1.36 1.00 2741 179 0.1198 0.1320 3.1031 3.2346| | 19: 1.36 - 1.34 1.00 2807 134 0.1260 0.1570 3.1111 3.2742| | 20: 1.34 - 1.32 1.00 2696 147 0.1370 0.1452 3.1116 3.148| | 21: 1.32 - 1.30 1.00 2785 112 0.1472 0.1508 3.1134 3.1034| | 22: 1.29 - 1.27 1.00 2704 152 0.1565 0.1993 3.1238 3.2942| | 23: 1.27 - 1.26 1.00 2802 156 0.1648 0.1792 3.1326 3.1996| | 24: 1.26 - 1.24 1.00 2744 132 0.1710 0.1833 3.1273 3.2266| | 25: 1.24 - 1.22 1.00 2733 148 0.1879 0.2141 3.1414 3.254| | 26: 1.22 - 1.21 1.00 2727 135 0.1905 0.1761 3.147 3.2013| | 27: 1.21 - 1.19 1.00 2814 148 0.2074 0.2164 3.171 3.1625| | 28: 1.19 - 1.18 1.00 2671 147 0.2203 0.2307 3.1659 3.1747| | 29: 1.18 - 1.16 1.00 2800 134 0.2264 0.2384 3.1473 3.2286| | 30: 1.16 - 1.15 1.00 2739 148 0.2446 0.2443 3.1427 3.1654| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.45 1.00 0.97 5816.22| | 2: 3.57 - 2.84 2888 124 0.93 12.66 1.01 0.97 5816.22| | 3: 2.83 - 2.48 2820 163 0.89 16.61 0.99 0.97 4855.54| | 4: 2.47 - 2.25 2825 136 0.92 13.53 1.00 0.98 2378.28| | 5: 2.25 - 2.09 2756 127 0.90 15.72 1.01 0.98 2378.28| | 6: 2.09 - 1.97 2846 113 0.92 12.37 1.02 0.98 1367.05| | 7: 1.97 - 1.87 2787 165 0.95 9.23 1.02 0.97 504.61| | 8: 1.87 - 1.79 2789 144 0.93 12.57 1.00 0.97 504.61| | 9: 1.79 - 1.72 2745 138 0.95 9.91 0.98 0.97 284.21| | 10: 1.72 - 1.66 2831 160 0.94 10.98 0.98 0.97 240.08| | 11: 1.66 - 1.61 2712 147 0.94 11.60 0.98 0.97 229.97| | 12: 1.61 - 1.56 2773 144 0.96 8.76 0.99 0.97 134.64| | 13: 1.56 - 1.52 2745 130 0.95 10.25 1.02 0.97 134.64| | 14: 1.52 - 1.48 2803 134 0.94 10.62 1.02 0.98 120.93| | 15: 1.48 - 1.45 2738 128 0.95 9.73 1.02 0.98 95.81| | 16: 1.45 - 1.42 2756 161 0.94 10.92 1.02 0.98 95.81| | 17: 1.42 - 1.39 2785 139 0.95 10.79 1.01 0.98 87.70| | 18: 1.39 - 1.36 2741 179 0.94 11.47 1.01 0.98 83.00| | 19: 1.36 - 1.34 2807 134 0.94 11.77 0.99 0.98 83.00| | 20: 1.34 - 1.32 2696 147 0.94 12.09 0.98 0.96 79.50| | 21: 1.32 - 1.30 2785 112 0.94 13.05 0.98 0.96 79.25| | 22: 1.29 - 1.27 2704 152 0.93 13.62 0.98 0.96 79.69| | 23: 1.27 - 1.26 2802 156 0.92 14.80 0.97 0.94 81.94| | 24: 1.26 - 1.24 2744 132 0.92 14.84 0.96 0.94 81.94| | 25: 1.24 - 1.22 2733 148 0.91 16.31 0.96 0.94 83.93| | 26: 1.22 - 1.21 2727 135 0.90 18.09 1.02 0.93 86.14| | 27: 1.21 - 1.19 2814 148 0.89 18.75 1.02 0.93 86.14| | 28: 1.19 - 1.18 2671 147 0.88 20.39 1.01 0.93 89.89| | 29: 1.18 - 1.16 2800 134 0.88 20.49 0.98 0.92 91.30| | 30: 1.16 - 1.15 2739 148 0.86 22.03 0.98 0.92 91.30| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.25 max = 5816.22 mean = 893.47| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.95 mean = 13.40| |phase err.(test): min = 0.00 max = 89.36 mean = 13.41| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1139 0.1131 0.1284 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1452 0.1453 0.1469 n_refl.: 87579 remove outliers: r(all,work,free)=0.1452 0.1453 0.1469 n_refl.: 87579 overall B=-0.00 to atoms: r(all,work,free)=0.1451 0.1452 0.1468 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1139 0.1132 0.1286 n_refl.: 87579 remove outliers: r(all,work,free)=0.1139 0.1132 0.1286 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 0.4051 296.463 260.568 0.451 1.000 0.283 11.894-9.307 95.10 93 4 0.2384 481.683 465.548 0.859 1.002 0.264 9.237-7.194 98.18 209 7 0.2453 386.104 377.576 0.923 1.002 0.170 7.162-5.571 100.00 427 22 0.2147 296.143 285.971 0.911 1.002 0.134 5.546-4.326 100.00 867 58 0.1140 406.532 401.820 0.961 1.003 0.108 4.315-3.360 100.00 1859 96 0.0933 386.614 384.447 1.003 1.002 0.090 3.356-2.611 100.00 3867 181 0.1110 253.986 252.073 1.011 1.002 0.019 2.608-2.026 99.99 8198 413 0.0896 168.369 167.772 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0878 82.223 82.574 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1251 36.461 36.071 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 22.973 21.525 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0125 ================= 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 : 0.2600 0.1935 0.080 5.370 8.8 119.3 19.9 258 0.000 1_bss: 0.1625 0.1761 0.080 5.370 9.1 119.5 20.1 258 0.000 1_settarget: 0.1625 0.1761 0.080 5.370 9.1 119.5 20.1 258 0.000 1_nqh: 0.1626 0.1761 0.080 5.370 9.1 119.5 20.1 258 0.003 1_weight: 0.1626 0.1761 0.080 5.370 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1227 0.1471 0.007 0.901 9.1 119.5 20.1 258 0.136 1_adp: 0.1234 0.1469 0.007 0.901 9.1 119.5 20.1 258 0.136 1_regHadp: 0.1236 0.1473 0.007 0.901 9.1 119.5 20.1 258 0.136 1_occ: 0.1229 0.1467 0.007 0.901 9.1 119.5 20.1 258 0.136 2_bss: 0.1227 0.1457 0.007 0.901 9.1 119.5 20.1 258 0.136 2_settarget: 0.1227 0.1457 0.007 0.901 9.1 119.5 20.1 258 0.136 2_updatecdl: 0.1227 0.1457 0.007 0.913 9.1 119.5 20.1 258 0.136 2_nqh: 0.1229 0.1461 0.007 0.913 9.1 119.5 20.1 258 0.136 2_sol: 0.1203 0.1403 0.007 0.913 9.1 115.0 22.2 413 n/a 2_weight: 0.1203 0.1403 0.007 0.913 9.1 115.0 22.2 413 n/a 2_xyzrec: 0.1187 0.1420 0.007 0.909 9.1 115.0 22.2 413 n/a 2_adp: 0.1187 0.1420 0.007 0.909 9.1 115.0 22.2 413 n/a 2_regHadp: 0.1187 0.1420 0.007 0.909 9.1 115.0 22.2 413 n/a 2_occ: 0.1189 0.1418 0.007 0.909 9.1 115.0 22.2 413 n/a 3_bss: 0.1185 0.1411 0.007 0.909 9.1 115.1 22.2 413 n/a 3_settarget: 0.1185 0.1411 0.007 0.909 9.1 115.1 22.2 413 n/a 3_updatecdl: 0.1185 0.1411 0.007 0.908 9.1 115.1 22.2 413 n/a 3_nqh: 0.1185 0.1411 0.007 0.908 9.1 115.1 22.2 413 n/a 3_sol: 0.1212 0.1413 0.007 0.908 9.1 115.1 21.2 433 n/a 3_weight: 0.1212 0.1413 0.007 0.908 9.1 115.1 21.2 433 n/a 3_xyzrec: 0.1163 0.1334 0.008 1.087 9.1 115.1 21.2 433 n/a 3_adp: 0.1163 0.1334 0.008 1.087 9.1 115.1 21.2 433 n/a 3_regHadp: 0.1163 0.1334 0.008 1.087 9.1 115.1 21.2 433 n/a 3_occ: 0.1151 0.1320 0.008 1.087 9.1 115.1 21.2 433 n/a 4_bss: 0.1142 0.1315 0.008 1.087 9.1 115.0 21.1 433 n/a 4_settarget: 0.1142 0.1315 0.008 1.087 9.1 115.0 21.1 433 n/a 4_updatecdl: 0.1142 0.1315 0.008 1.088 9.1 115.0 21.1 433 n/a 4_nqh: 0.1142 0.1315 0.008 1.088 9.1 115.0 21.1 433 n/a 4_sol: 0.1142 0.1293 0.008 1.088 9.1 115.0 21.0 440 n/a 4_weight: 0.1142 0.1293 0.008 1.088 9.1 115.0 21.0 440 n/a 4_xyzrec: 0.1137 0.1292 0.009 1.126 9.1 115.0 21.0 440 n/a 4_adp: 0.1137 0.1292 0.009 1.126 9.1 115.0 21.0 440 n/a 4_regHadp: 0.1137 0.1292 0.009 1.126 9.1 115.0 21.0 440 n/a 4_occ: 0.1133 0.1287 0.009 1.126 9.1 115.0 21.0 440 n/a 5_bss: 0.1131 0.1288 0.009 1.126 9.1 115.0 21.0 440 n/a 5_settarget: 0.1131 0.1288 0.009 1.126 9.1 115.0 21.0 440 n/a 5_updatecdl: 0.1131 0.1288 0.009 1.129 9.1 115.0 21.0 440 n/a 5_setrh: 0.1132 0.1288 0.009 1.129 9.1 115.0 21.0 440 n/a 5_nqh: 0.1132 0.1288 0.009 1.129 9.1 115.0 21.0 440 n/a 5_sol: 0.1134 0.1287 0.009 1.129 9.1 115.0 21.1 449 n/a 5_weight: 0.1134 0.1287 0.009 1.129 9.1 115.0 21.1 449 n/a 5_xyzrec: 0.1135 0.1287 0.008 1.125 9.1 115.0 21.1 449 n/a 5_adp: 0.1135 0.1287 0.008 1.125 9.1 115.0 21.1 449 n/a 5_regHadp: 0.1135 0.1287 0.008 1.125 9.1 115.0 21.1 449 n/a 5_occ: 0.1131 0.1284 0.008 1.125 9.1 115.0 21.1 449 n/a end: 0.1132 0.1286 0.008 1.125 9.1 115.0 21.1 449 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_2112196_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_2112196_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2000 Refinement macro-cycles (run) : 13630.7400 Write final files (write_after_run_outputs) : 103.7700 Total : 13737.7100 Total CPU time: 3.82 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:08:23 PST -0800 (1735366103.34 s) Start R-work = 0.1625, R-free = 0.1761 Final R-work = 0.1132, R-free = 0.1286 =============================================================================== Job complete usr+sys time: 13925.69 seconds wall clock time: 252 minutes 43.26 seconds (15163.26 seconds total)