Starting phenix.refine on Sat Dec 28 21:06:33 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_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.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_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.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 } 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 } } 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: 2.13, per 1000 atoms: 0.63 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: 0.97 Conformation dependent library (CDL) restraints added in 252.2 milliseconds Time building geometry restraints manager: 0.79 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 2.450 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.834 2.450 ... (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 } 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 } } 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 = 26.104038 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 0.1209 0.1462 0.0253 0.008 1.0 1.0 0.5 0.0 0 13.052 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.09 14.62 2.53 3.013 19.074 2036.653 0.017 12.46 15.43 2.97 3.326 19.632 2036.653 0.016 Individual atomic B min max mean iso aniso Overall: 8.67 118.98 21.16 2.88 0 1785 Protein: 8.67 118.98 18.01 2.88 0 1519 Water: 11.15 114.51 39.43 N/A 0 258 Other: 23.58 38.07 29.90 N/A 0 8 Chain A: 8.67 118.98 21.16 N/A 0 1785 Histogram: Values Number of atoms 8.67 - 19.70 1208 19.70 - 30.73 231 30.73 - 41.76 156 41.76 - 52.79 109 52.79 - 63.82 49 63.82 - 74.86 18 74.86 - 85.89 7 85.89 - 96.92 2 96.92 - 107.95 2 107.95 - 118.98 3 =========================== Idealize ADP of riding H ========================== r_work=0.1247 r_free=0.1543 r_work=0.1251 r_free=0.1548 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1251 r_free = 0.1548 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1250 r_free = 0.1550 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 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= 0.1250 r_free= 0.1550 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015450 | | target function (ls_wunit_k1) not normalized (work): 1286.955928 | | target function (ls_wunit_k1) not normalized (free): 114.198015 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1265 0.1250 0.1550 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1711 0.1710 0.1775 n_refl.: 87593 remove outliers: r(all,work,free)=0.1711 0.1710 0.1775 n_refl.: 87593 overall B=0.12 to atoms: r(all,work,free)=0.1731 0.1731 0.1790 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1262 0.1248 0.1542 n_refl.: 87593 remove outliers: r(all,work,free)=0.1261 0.1247 0.1542 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 0.3654 298.054 276.922 0.687 0.923 0.380 11.894-9.307 99.02 97 4 0.1603 477.467 465.404 0.982 0.924 0.365 9.237-7.194 100.00 213 7 0.1816 390.509 384.962 1.028 0.925 0.350 7.162-5.571 100.00 427 22 0.1728 293.055 287.455 0.998 0.925 0.290 5.546-4.326 100.00 867 58 0.0911 402.292 399.504 1.028 0.926 0.204 4.315-3.360 100.00 1859 96 0.0771 382.583 381.557 1.074 0.927 0.190 3.356-2.611 100.00 3867 181 0.1014 251.337 250.636 1.077 0.929 0.110 2.608-2.026 99.99 8198 413 0.0978 166.614 166.002 1.087 0.931 0.000 2.025-1.573 100.00 17313 902 0.1219 81.365 81.539 1.088 0.936 0.000 1.573-1.221 100.00 36679 1900 0.1665 36.081 35.540 1.065 0.943 0.000 1.221-1.150 99.97 13689 708 0.2373 22.733 21.267 1.021 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0467 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1247 r_free=0.1542 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=0.1249 r_free=0.1543 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1249 r_free=0.1543 | n_water=258 | time (s): 2.390 (total time: 2.390) Filter (dist) r_work=0.1258 r_free=0.1543 | n_water=252 | time (s): 27.550 (total time: 29.940) Filter (q & B) r_work=0.1261 r_free=0.1542 | n_water=249 | time (s): 3.470 (total time: 33.410) Compute maps r_work=0.1261 r_free=0.1542 | n_water=249 | time (s): 1.860 (total time: 35.270) Filter (map) r_work=0.1273 r_free=0.1551 | n_water=237 | time (s): 3.710 (total time: 38.980) Find peaks r_work=0.1273 r_free=0.1551 | n_water=237 | time (s): 0.740 (total time: 39.720) Add new water r_work=0.1428 r_free=0.1691 | n_water=451 | time (s): 3.710 (total time: 43.430) Refine new water occ: r_work=0.1342 r_free=0.1567 adp: r_work=0.1262 r_free=0.1512 occ: r_work=0.1277 r_free=0.1509 adp: r_work=0.1240 r_free=0.1490 occ: r_work=0.1243 r_free=0.1484 adp: r_work=0.1234 r_free=0.1484 ADP+occupancy (water only), MIN, final r_work=0.1234 r_free=0.1484 r_work=0.1234 r_free=0.1484 | n_water=451 | time (s): 72.130 (total time: 115.560) Filter (q & B) r_work=0.1239 r_free=0.1492 | n_water=429 | time (s): 3.800 (total time: 119.360) Filter (dist only) r_work=0.1239 r_free=0.1492 | n_water=429 | time (s): 40.200 (total time: 159.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.154094 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1583.105539 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 0.1235 0.1518 0.0283 0.007 0.9 2.9 0.5 0.0 0 12.577 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.35 15.18 2.83 3.815 23.325 1583.106 0.015 11.96 14.79 2.83 4.275 23.119 1583.106 0.015 Individual atomic B min max mean iso aniso Overall: 8.67 114.10 23.29 2.62 192 1764 Protein: 8.67 114.10 17.73 2.63 0 1519 Water: 11.21 72.56 42.86 N/A 192 237 Other: 24.50 35.57 29.06 N/A 0 8 Chain A: 8.67 114.10 20.47 N/A 0 1764 Chain S: 13.65 72.56 49.20 N/A 192 0 Histogram: Values Number of atoms 8.67 - 19.21 1203 19.21 - 29.75 245 29.75 - 40.30 194 40.30 - 50.84 136 50.84 - 61.38 110 61.38 - 71.93 54 71.93 - 82.47 8 82.47 - 93.01 3 93.01 - 103.56 1 103.56 - 114.10 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1479 r_work=0.1196 r_free=0.1479 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1479 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1474 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 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= 0.1197 r_free= 0.1474 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.014004 | | target function (ls_wunit_k1) not normalized (work): 1166.480144 | | target function (ls_wunit_k1) not normalized (free): 101.892874 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1211 0.1197 0.1474 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1609 0.1608 0.1678 n_refl.: 87592 remove outliers: r(all,work,free)=0.1609 0.1608 0.1678 n_refl.: 87592 overall B=0.02 to atoms: r(all,work,free)=0.1613 0.1612 0.1680 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1195 0.1470 n_refl.: 87592 remove outliers: r(all,work,free)=0.1207 0.1194 0.1470 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3451 294.004 270.876 0.585 1.002 0.360 11.894-9.307 99.02 97 4 0.1555 477.467 475.057 0.916 1.003 0.336 9.237-7.194 100.00 213 7 0.1713 390.509 390.108 0.982 1.003 0.280 7.162-5.571 100.00 427 22 0.1551 293.055 289.876 0.935 1.003 0.260 5.546-4.326 100.00 867 58 0.0833 402.292 399.849 0.958 1.003 0.220 4.315-3.360 100.00 1859 96 0.0710 382.583 381.593 1.000 1.003 0.203 3.356-2.611 100.00 3867 181 0.0957 251.337 250.754 1.010 1.002 0.062 2.608-2.026 99.99 8198 413 0.0948 166.614 166.200 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1172 81.365 81.554 1.029 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1609 36.081 35.577 1.021 0.998 0.000 1.221-1.150 99.97 13689 708 0.2339 22.733 21.272 0.982 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0341 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1470 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=0.1194 r_free=0.1470 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1470 | n_water=429 | time (s): 2.150 (total time: 2.150) Filter (dist) r_work=0.1193 r_free=0.1470 | n_water=427 | time (s): 38.530 (total time: 40.680) Filter (q & B) r_work=0.1193 r_free=0.1470 | n_water=427 | time (s): 1.230 (total time: 41.910) Compute maps r_work=0.1193 r_free=0.1470 | n_water=427 | time (s): 1.640 (total time: 43.550) Filter (map) r_work=0.1239 r_free=0.1474 | n_water=286 | time (s): 3.230 (total time: 46.780) Find peaks r_work=0.1239 r_free=0.1474 | n_water=286 | time (s): 0.480 (total time: 47.260) Add new water r_work=0.1365 r_free=0.1584 | n_water=482 | time (s): 3.410 (total time: 50.670) Refine new water occ: r_work=0.1262 r_free=0.1498 adp: r_work=0.1262 r_free=0.1500 occ: r_work=0.1240 r_free=0.1477 adp: r_work=0.1236 r_free=0.1477 occ: r_work=0.1224 r_free=0.1467 adp: r_work=0.1218 r_free=0.1462 ADP+occupancy (water only), MIN, final r_work=0.1218 r_free=0.1462 r_work=0.1218 r_free=0.1462 | n_water=482 | time (s): 147.860 (total time: 198.530) Filter (q & B) r_work=0.1221 r_free=0.1462 | n_water=447 | time (s): 3.480 (total time: 202.010) Filter (dist only) r_work=0.1221 r_free=0.1462 | n_water=447 | time (s): 35.930 (total time: 237.940) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.035115 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 36.819679 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 0.1227 0.1441 0.0214 0.006 0.9 1.6 0.5 0.0 0 1.018 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.27 14.41 2.14 3.639 22.133 36.820 3.720 12.22 13.99 1.77 3.999 21.991 36.820 3.659 Individual atomic B min max mean iso aniso Overall: 9.20 109.53 21.74 2.31 213 1761 Protein: 9.20 109.53 17.40 2.31 0 1519 Water: 11.57 71.56 36.38 N/A 213 234 Other: 20.60 31.78 26.78 N/A 0 8 Chain A: 9.20 109.53 20.11 N/A 0 1761 Chain S: 14.87 57.75 35.20 N/A 213 0 Histogram: Values Number of atoms 9.20 - 19.24 1224 19.24 - 29.27 278 29.27 - 39.30 231 39.30 - 49.33 136 49.33 - 59.37 74 59.37 - 69.40 17 69.40 - 79.43 8 79.43 - 89.46 3 89.46 - 99.49 1 99.49 - 109.53 2 =========================== Idealize ADP of riding H ========================== r_work=0.1222 r_free=0.1399 r_work=0.1223 r_free=0.1400 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1223 r_free = 0.1400 target_work(ml) = 3.659 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1219 r_free = 0.1404 target_work(ml) = 3.658 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1219 r_free= 0.1404 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.658425 | | target function (ml) not normalized (work): 304721.208089 | | target function (ml) not normalized (free): 16077.960150 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1228 0.1219 0.1404 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1549 0.1549 0.1584 n_refl.: 87589 remove outliers: r(all,work,free)=0.1549 0.1549 0.1584 n_refl.: 87589 overall B=-0.02 to atoms: r(all,work,free)=0.1546 0.1546 0.1582 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1217 0.1209 0.1383 n_refl.: 87589 remove outliers: r(all,work,free)=0.1215 0.1206 0.1383 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 90.62 82 5 0.4045 291.168 260.240 0.471 0.999 0.324 11.894-9.307 98.04 96 4 0.2501 470.817 456.748 0.844 1.001 0.272 9.237-7.194 98.18 209 7 0.2365 382.078 382.111 0.940 1.002 0.195 7.162-5.571 100.00 427 22 0.2074 293.055 282.792 0.908 1.002 0.168 5.546-4.326 100.00 867 58 0.1088 402.292 398.200 0.953 1.002 0.157 4.315-3.360 100.00 1859 96 0.0919 382.583 379.910 0.994 1.002 0.147 3.356-2.611 100.00 3867 181 0.1147 251.337 249.478 1.000 1.002 0.057 2.608-2.026 99.99 8198 413 0.1041 166.614 165.589 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1039 81.365 81.491 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1315 36.081 35.631 1.022 0.998 0.000 1.221-1.150 99.97 13689 708 0.2143 22.733 21.329 0.982 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0473 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1206 r_free=0.1383 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=0.1206 r_free=0.1383 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1206 r_free=0.1383 | n_water=447 | time (s): 2.160 (total time: 2.160) Filter (dist) r_work=0.1206 r_free=0.1383 | n_water=447 | time (s): 36.600 (total time: 38.760) Filter (q & B) r_work=0.1206 r_free=0.1384 | n_water=445 | time (s): 2.560 (total time: 41.320) Compute maps r_work=0.1206 r_free=0.1384 | n_water=445 | time (s): 1.160 (total time: 42.480) Filter (map) r_work=0.1227 r_free=0.1387 | n_water=313 | time (s): 2.600 (total time: 45.080) Find peaks r_work=0.1227 r_free=0.1387 | n_water=313 | time (s): 0.440 (total time: 45.520) Add new water r_work=0.1292 r_free=0.1444 | n_water=472 | time (s): 2.420 (total time: 47.940) Refine new water occ: r_work=0.1217 r_free=0.1361 adp: r_work=0.1218 r_free=0.1364 occ: r_work=0.1204 r_free=0.1350 adp: r_work=0.1202 r_free=0.1351 occ: r_work=0.1194 r_free=0.1344 adp: r_work=0.1190 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1344 r_work=0.1190 r_free=0.1344 | n_water=472 | time (s): 149.110 (total time: 197.050) Filter (q & B) r_work=0.1197 r_free=0.1348 | n_water=438 | time (s): 3.200 (total time: 200.250) Filter (dist only) r_work=0.1197 r_free=0.1347 | n_water=436 | time (s): 38.320 (total time: 238.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.898937 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 36.562495 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 0.1203 0.1356 0.0152 0.006 0.9 1.6 0.5 0.0 0 0.949 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.56 1.52 3.456 21.666 36.562 3.644 11.90 13.50 1.60 3.900 21.521 36.562 3.629 Individual atomic B min max mean iso aniso Overall: 9.24 105.02 21.31 2.16 203 1760 Protein: 9.24 105.02 17.07 2.16 0 1519 Water: 11.58 70.48 36.02 N/A 203 233 Other: 18.76 28.63 24.07 N/A 0 8 Chain A: 9.24 105.02 19.73 N/A 0 1760 Chain S: 15.13 57.84 34.98 N/A 203 0 Histogram: Values Number of atoms 9.24 - 18.82 1225 18.82 - 28.39 277 28.39 - 37.97 211 37.97 - 47.55 138 47.55 - 57.13 71 57.13 - 66.71 26 66.71 - 76.29 10 76.29 - 85.86 2 85.86 - 95.44 1 95.44 - 105.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1350 r_work=0.1191 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1350 target_work(ml) = 3.630 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1187 r_free = 0.1346 target_work(ml) = 3.628 | | occupancies: max = 1.00 min = 0.14 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= 0.1187 r_free= 0.1346 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.628097 | | target function (ml) not normalized (work): 302169.669359 | | target function (ml) not normalized (free): 15945.464456 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1187 0.1346 n_refl.: 87582 re-set all scales: r(all,work,free)=0.1525 0.1525 0.1557 n_refl.: 87582 remove outliers: r(all,work,free)=0.1525 0.1525 0.1557 n_refl.: 87582 overall B=-0.02 to atoms: r(all,work,free)=0.1522 0.1521 0.1554 n_refl.: 87582 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1187 0.1348 n_refl.: 87582 remove outliers: r(all,work,free)=0.1193 0.1185 0.1348 n_refl.: 87577 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3979 288.748 247.434 0.446 1.000 0.314 11.894-9.307 96.08 94 4 0.2242 476.551 455.674 0.836 1.002 0.260 9.237-7.194 97.73 208 7 0.2402 383.150 375.741 0.918 1.002 0.185 7.162-5.571 100.00 427 22 0.2075 293.055 283.825 0.911 1.002 0.160 5.546-4.326 100.00 867 58 0.1123 402.292 398.474 0.954 1.002 0.150 4.315-3.360 100.00 1859 96 0.0920 382.583 380.367 0.995 1.002 0.140 3.356-2.611 100.00 3867 181 0.1152 251.337 249.734 1.001 1.002 0.057 2.608-2.026 99.99 8198 413 0.1029 166.614 165.824 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0994 81.365 81.643 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1266 36.081 35.706 1.025 0.996 0.000 1.221-1.150 99.97 13689 708 0.2139 22.733 21.364 0.985 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0498 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1185 r_free=0.1348 After: r_work=0.1185 r_free=0.1348 ================================== NQH flips ================================== r_work=0.1185 r_free=0.1348 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 76 ASN B Total number of N/Q/H flips: 2 r_work=0.1186 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1186 r_free=0.1351 | n_water=436 | time (s): 1.830 (total time: 1.830) Filter (dist) r_work=0.1186 r_free=0.1351 | n_water=436 | time (s): 33.900 (total time: 35.730) Filter (q & B) r_work=0.1186 r_free=0.1351 | n_water=434 | time (s): 3.020 (total time: 38.750) Compute maps r_work=0.1186 r_free=0.1351 | n_water=434 | time (s): 1.300 (total time: 40.050) Filter (map) r_work=0.1207 r_free=0.1383 | n_water=331 | time (s): 3.110 (total time: 43.160) Find peaks r_work=0.1207 r_free=0.1383 | n_water=331 | time (s): 0.500 (total time: 43.660) Add new water r_work=0.1262 r_free=0.1435 | n_water=478 | time (s): 2.580 (total time: 46.240) Refine new water occ: r_work=0.1198 r_free=0.1369 adp: r_work=0.1198 r_free=0.1370 occ: r_work=0.1186 r_free=0.1361 adp: r_work=0.1185 r_free=0.1361 occ: r_work=0.1178 r_free=0.1354 adp: r_work=0.1175 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1175 r_free=0.1353 r_work=0.1175 r_free=0.1353 | n_water=478 | time (s): 159.800 (total time: 206.040) Filter (q & B) r_work=0.1183 r_free=0.1361 | n_water=441 | time (s): 3.360 (total time: 209.400) Filter (dist only) r_work=0.1184 r_free=0.1360 | n_water=440 | time (s): 38.830 (total time: 248.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.986287 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 30.627648 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 0.1201 0.1371 0.0170 0.007 1.1 2.2 0.5 0.0 0 0.993 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.71 1.70 3.316 21.238 30.628 3.634 12.06 13.71 1.65 3.390 21.207 30.628 3.630 Individual atomic B min max mean iso aniso Overall: 9.32 102.64 21.14 2.05 209 1758 Protein: 9.32 102.64 16.98 2.05 0 1519 Water: 11.29 70.27 35.45 N/A 209 231 Other: 18.76 27.74 23.84 N/A 0 8 Chain A: 9.32 102.64 19.60 N/A 0 1758 Chain S: 15.40 57.81 34.09 N/A 209 0 Histogram: Values Number of atoms 9.32 - 18.65 1226 18.65 - 27.98 280 27.98 - 37.32 210 37.32 - 46.65 135 46.65 - 55.98 72 55.98 - 65.31 28 65.31 - 74.65 11 74.65 - 83.98 2 83.98 - 93.31 1 93.31 - 102.64 2 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1371 r_work=0.1206 r_free=0.1371 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1371 target_work(ml) = 3.630 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1370 target_work(ml) = 3.630 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1204 r_free= 0.1370 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.629899 | | target function (ml) not normalized (work): 302301.649093 | | target function (ml) not normalized (free): 15951.462227 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2919 171 0.1414 0.1387 5.6775 5.6106| | 2: 3.57 - 2.84 1.00 2888 124 0.1100 0.1473 5.1891 5.2695| | 3: 2.83 - 2.48 1.00 2820 163 0.1200 0.1287 4.9947 5.0046| | 4: 2.47 - 2.25 1.00 2825 136 0.1015 0.1132 4.6967 4.7476| | 5: 2.25 - 2.09 1.00 2756 127 0.1014 0.1073 4.6472 4.7079| | 6: 2.09 - 1.97 1.00 2846 113 0.0999 0.1206 4.3592 4.4877| | 7: 1.97 - 1.87 1.00 2787 165 0.1010 0.1216 4.082 4.1767| | 8: 1.87 - 1.79 1.00 2789 144 0.1045 0.1282 3.9984 4.0952| | 9: 1.79 - 1.72 1.00 2745 138 0.0989 0.1359 3.7383 3.9561| | 10: 1.72 - 1.66 1.00 2831 160 0.1035 0.1263 3.6582 3.7774| | 11: 1.66 - 1.61 1.00 2712 147 0.1000 0.1103 3.5915 3.6191| | 12: 1.61 - 1.56 1.00 2773 144 0.0949 0.1169 3.3714 3.4787| | 13: 1.56 - 1.52 1.00 2745 130 0.1006 0.1080 3.3563 3.4439| | 14: 1.52 - 1.48 1.00 2803 134 0.1023 0.1147 3.2789 3.3498| | 15: 1.48 - 1.45 1.00 2738 128 0.1043 0.1357 3.1877 3.3319| | 16: 1.45 - 1.42 1.00 2756 161 0.1102 0.1266 3.1724 3.2469| | 17: 1.42 - 1.39 1.00 2785 139 0.1146 0.1255 3.1296 3.2124| | 18: 1.39 - 1.36 1.00 2741 179 0.1182 0.1427 3.1021 3.279| | 19: 1.36 - 1.34 1.00 2807 134 0.1248 0.1635 3.108 3.2902| | 20: 1.34 - 1.32 1.00 2696 147 0.1332 0.1482 3.0971 3.1323| | 21: 1.32 - 1.30 1.00 2785 112 0.1436 0.1631 3.0953 3.168| | 22: 1.29 - 1.27 1.00 2704 152 0.1497 0.1969 3.0943 3.3034| | 23: 1.27 - 1.26 1.00 2802 156 0.1600 0.1861 3.1119 3.2118| | 24: 1.26 - 1.24 1.00 2744 132 0.1644 0.1774 3.1015 3.197| | 25: 1.24 - 1.22 1.00 2733 148 0.1800 0.2320 3.1118 3.2947| | 26: 1.22 - 1.21 1.00 2727 135 0.1871 0.1799 3.1271 3.2036| | 27: 1.21 - 1.19 1.00 2814 148 0.2023 0.2099 3.1423 3.1425| | 28: 1.19 - 1.18 1.00 2671 147 0.2148 0.2332 3.1392 3.1609| | 29: 1.18 - 1.16 1.00 2800 134 0.2231 0.2328 3.1291 3.2119| | 30: 1.16 - 1.15 1.00 2739 148 0.2385 0.2506 3.1161 3.1705| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2919 171 0.95 8.98 1.00 0.97 6153.92| | 2: 3.57 - 2.84 2888 124 0.92 13.26 1.01 0.97 6153.92| | 3: 2.83 - 2.48 2820 163 0.89 17.42 0.99 0.97 5160.84| | 4: 2.47 - 2.25 2825 136 0.91 14.47 1.00 0.98 2600.00| | 5: 2.25 - 2.09 2756 127 0.90 16.71 1.01 0.98 2600.00| | 6: 2.09 - 1.97 2846 113 0.92 13.60 1.02 0.97 1532.98| | 7: 1.97 - 1.87 2787 165 0.94 10.84 1.02 0.97 622.95| | 8: 1.87 - 1.79 2789 144 0.91 14.38 1.00 0.97 622.95| | 9: 1.79 - 1.72 2745 138 0.93 11.60 0.98 0.97 346.23| | 10: 1.72 - 1.66 2831 160 0.93 12.53 0.98 0.97 290.81| | 11: 1.66 - 1.61 2712 147 0.92 13.19 0.98 0.97 277.45| | 12: 1.61 - 1.56 2773 144 0.95 9.72 0.99 0.97 151.43| | 13: 1.56 - 1.52 2745 130 0.94 11.34 1.02 0.97 151.43| | 14: 1.52 - 1.48 2803 134 0.94 11.53 1.02 0.97 135.23| | 15: 1.48 - 1.45 2738 128 0.95 10.62 1.01 0.98 105.58| | 16: 1.45 - 1.42 2756 161 0.94 11.80 1.02 0.98 105.58| | 17: 1.42 - 1.39 2785 139 0.94 11.61 1.01 0.98 94.95| | 18: 1.39 - 1.36 2741 179 0.94 11.95 1.01 0.98 88.80| | 19: 1.36 - 1.34 2807 134 0.94 12.47 1.00 0.98 88.80| | 20: 1.34 - 1.32 2696 147 0.94 12.60 0.99 0.96 83.57| | 21: 1.32 - 1.30 2785 112 0.93 13.60 0.99 0.96 83.21| | 22: 1.29 - 1.27 2704 152 0.93 14.07 0.98 0.96 83.29| | 23: 1.27 - 1.26 2802 156 0.92 14.97 0.98 0.95 83.73| | 24: 1.26 - 1.24 2744 132 0.92 15.10 0.97 0.95 83.73| | 25: 1.24 - 1.22 2733 148 0.91 16.51 0.96 0.94 84.97| | 26: 1.22 - 1.21 2727 135 0.90 18.18 1.02 0.93 86.33| | 27: 1.21 - 1.19 2814 148 0.89 18.81 1.02 0.93 86.33| | 28: 1.19 - 1.18 2671 147 0.88 20.23 1.01 0.93 88.91| | 29: 1.18 - 1.16 2800 134 0.88 20.51 0.99 0.92 89.88| | 30: 1.16 - 1.15 2739 148 0.86 21.93 0.98 0.92 89.88| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 83.21 max = 6153.92 mean = 964.29| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.95 mean = 14.14| |phase err.(test): min = 0.00 max = 86.72 mean = 14.25| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1212 0.1204 0.1370 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1526 0.1525 0.1575 n_refl.: 87577 remove outliers: r(all,work,free)=0.1526 0.1525 0.1575 n_refl.: 87577 overall B=-0.02 to atoms: r(all,work,free)=0.1523 0.1522 0.1573 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1205 0.1373 n_refl.: 87577 remove outliers: r(all,work,free)=0.1211 0.1203 0.1373 n_refl.: 87573 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4178 288.748 251.162 0.424 1.000 0.279 11.894-9.307 93.14 91 4 0.2432 473.043 450.398 0.834 1.002 0.257 9.237-7.194 97.27 207 7 0.2521 382.677 374.745 0.903 1.002 0.167 7.162-5.571 100.00 427 22 0.2256 293.055 281.623 0.901 1.002 0.133 5.546-4.326 100.00 867 58 0.1179 402.292 398.107 0.954 1.002 0.116 4.315-3.360 100.00 1859 96 0.0971 382.583 380.155 0.995 1.002 0.107 3.356-2.611 100.00 3867 181 0.1161 251.337 249.498 1.002 1.001 0.090 2.608-2.026 99.99 8198 413 0.1043 166.614 165.707 1.015 1.000 0.000 2.025-1.573 100.00 17313 902 0.1005 81.365 81.603 1.029 0.998 0.000 1.573-1.221 100.00 36679 1900 0.1254 36.081 35.708 1.025 0.996 0.000 1.221-1.150 99.97 13689 708 0.2128 22.733 21.357 0.984 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0441 ================= 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: 0.1209 0.1462 0.008 0.968 9.1 119.5 20.1 258 0.124 1_adp: 0.1247 0.1543 0.008 0.968 8.7 119.0 21.2 258 0.124 1_regHadp: 0.1251 0.1548 0.008 0.968 8.7 119.0 21.2 258 0.124 1_occ: 0.1250 0.1550 0.008 0.968 8.7 119.0 21.2 258 0.124 2_bss: 0.1247 0.1542 0.008 0.968 8.8 119.1 21.3 258 0.124 2_settarget: 0.1247 0.1542 0.008 0.968 8.8 119.1 21.3 258 0.124 2_updatecdl: 0.1247 0.1542 0.008 0.975 8.8 119.1 21.3 258 0.124 2_nqh: 0.1249 0.1543 0.008 0.975 8.8 119.1 21.3 258 0.124 2_sol: 0.1239 0.1492 0.008 0.975 8.8 119.1 23.7 429 n/a 2_weight: 0.1239 0.1492 0.008 0.975 8.8 119.1 23.7 429 n/a 2_xyzrec: 0.1235 0.1518 0.007 0.868 8.8 119.1 23.7 429 n/a 2_adp: 0.1196 0.1479 0.007 0.868 8.7 114.1 23.3 429 n/a 2_regHadp: 0.1196 0.1479 0.007 0.868 8.7 114.1 23.3 429 n/a 2_occ: 0.1197 0.1474 0.007 0.868 8.7 114.1 23.3 429 n/a 3_bss: 0.1194 0.1470 0.007 0.868 8.7 114.1 23.3 429 n/a 3_settarget: 0.1194 0.1470 0.007 0.868 8.7 114.1 23.3 429 n/a 3_updatecdl: 0.1194 0.1470 0.007 0.870 8.7 114.1 23.3 429 n/a 3_nqh: 0.1194 0.1470 0.007 0.870 8.7 114.1 23.3 429 n/a 3_sol: 0.1221 0.1462 0.007 0.870 8.7 114.1 22.0 447 n/a 3_weight: 0.1221 0.1462 0.007 0.870 8.7 114.1 22.0 447 n/a 3_xyzrec: 0.1227 0.1441 0.006 0.921 8.7 114.1 22.0 447 n/a 3_adp: 0.1222 0.1399 0.006 0.921 9.2 109.5 21.7 447 n/a 3_regHadp: 0.1223 0.1400 0.006 0.921 9.2 109.5 21.7 447 n/a 3_occ: 0.1219 0.1404 0.006 0.921 9.2 109.5 21.7 447 n/a 4_bss: 0.1206 0.1383 0.006 0.921 9.2 109.5 21.7 447 n/a 4_settarget: 0.1206 0.1383 0.006 0.921 9.2 109.5 21.7 447 n/a 4_updatecdl: 0.1206 0.1383 0.006 0.920 9.2 109.5 21.7 447 n/a 4_nqh: 0.1206 0.1383 0.006 0.920 9.2 109.5 21.7 447 n/a 4_sol: 0.1197 0.1347 0.006 0.920 9.2 109.5 21.6 436 n/a 4_weight: 0.1197 0.1347 0.006 0.920 9.2 109.5 21.6 436 n/a 4_xyzrec: 0.1203 0.1356 0.006 0.945 9.2 109.5 21.6 436 n/a 4_adp: 0.1190 0.1350 0.006 0.945 9.2 105.0 21.3 436 n/a 4_regHadp: 0.1191 0.1350 0.006 0.945 9.2 105.0 21.3 436 n/a 4_occ: 0.1187 0.1346 0.006 0.945 9.2 105.0 21.3 436 n/a 5_bss: 0.1185 0.1348 0.006 0.945 9.2 105.0 21.3 436 n/a 5_settarget: 0.1185 0.1348 0.006 0.945 9.2 105.0 21.3 436 n/a 5_updatecdl: 0.1185 0.1348 0.006 0.948 9.2 105.0 21.3 436 n/a 5_setrh: 0.1185 0.1348 0.006 0.948 9.2 105.0 21.3 436 n/a 5_nqh: 0.1186 0.1351 0.006 0.948 9.2 105.0 21.3 436 n/a 5_sol: 0.1184 0.1360 0.006 0.948 9.2 105.0 21.2 440 n/a 5_weight: 0.1184 0.1360 0.006 0.948 9.2 105.0 21.2 440 n/a 5_xyzrec: 0.1201 0.1371 0.007 1.064 9.2 105.0 21.2 440 n/a 5_adp: 0.1206 0.1371 0.007 1.064 9.3 102.6 21.1 440 n/a 5_regHadp: 0.1206 0.1371 0.007 1.064 9.3 102.6 21.1 440 n/a 5_occ: 0.1204 0.1370 0.007 1.064 9.3 102.6 21.1 440 n/a end: 0.1203 0.1373 0.007 1.064 9.3 102.6 21.1 440 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_2112196_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_2112196_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.5800 Refinement macro-cycles (run) : 3279.9200 Write final files (write_after_run_outputs) : 71.1800 Total : 3355.6800 Total CPU time: 56.54 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:07:26 PST -0800 (1735452446.70 s) Start R-work = 0.1625, R-free = 0.1761 Final R-work = 0.1203, R-free = 0.1373 =============================================================================== Job complete usr+sys time: 3507.97 seconds wall clock time: 62 minutes 55.12 seconds (3775.12 seconds total)