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_4596863.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4596863.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4596863.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" 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 =============================================================================== 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: 2.23, per 1000 atoms: 0.66 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: 0.81 Conformation dependent library (CDL) restraints added in 322.5 milliseconds Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.89: 435 0.89 - 1.14: 1155 1.14 - 1.39: 580 1.39 - 1.64: 897 1.64 - 1.89: 86 Bond restraints: 3153 Sorted by residual: bond pdb=" C SER A 3 " pdb=" N LYS A 4 " ideal model delta sigma weight residual 1.330 1.053 0.277 1.31e-02 5.83e+03 4.48e+02 bond pdb=" CA LEU A 7 " pdb=" C LEU A 7 " ideal model delta sigma weight residual 1.524 1.264 0.260 1.23e-02 6.61e+03 4.47e+02 bond pdb=" N VAL A 23 " pdb=" CA VAL A 23 " ideal model delta sigma weight residual 1.461 1.249 0.212 1.19e-02 7.06e+03 3.17e+02 bond pdb=" N VAL A 71 " pdb=" CA VAL A 71 " ideal model delta sigma weight residual 1.459 1.664 -0.205 1.20e-02 6.94e+03 2.93e+02 bond pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " ideal model delta sigma weight residual 1.326 1.139 0.187 1.10e-02 8.26e+03 2.88e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.23: 2914 4.23 - 8.45: 1849 8.45 - 12.67: 774 12.67 - 16.89: 199 16.89 - 21.11: 41 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O LEU A 7 " pdb=" C LEU A 7 " pdb=" N VAL A 8 " ideal model delta sigma weight residual 123.22 106.34 16.88 1.14e+00 7.69e-01 2.19e+02 angle pdb=" CA ASP A 68 " pdb=" CB ASP A 68 " pdb=" CG ASP A 68 " ideal model delta sigma weight residual 112.60 98.68 13.92 1.00e+00 1.00e+00 1.94e+02 angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.35 133.91 -12.56 9.20e-01 1.18e+00 1.86e+02 angle pdb=" CA THR A 140 " pdb=" C THR A 140 " pdb=" O THR A 140 " ideal model delta sigma weight residual 120.36 134.87 -14.51 1.08e+00 8.57e-01 1.81e+02 angle pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" O SER A 155 " ideal model delta sigma weight residual 121.36 107.47 13.89 1.06e+00 8.90e-01 1.72e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 953 17.94 - 35.87: 106 35.87 - 53.81: 38 53.81 - 71.74: 12 71.74 - 89.68: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual 180.00 -160.09 -19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA LEU A 72 " pdb=" C LEU A 72 " pdb=" N PRO A 73 " pdb=" CA PRO A 73 " ideal model delta harmonic sigma weight residual 180.00 160.19 19.81 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.188: 93 0.188 - 0.376: 68 0.376 - 0.564: 37 0.564 - 0.752: 33 0.752 - 0.940: 12 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ARG A 98 " pdb=" N ARG A 98 " pdb=" C ARG A 98 " pdb=" CB ARG A 98 " both_signs ideal model delta sigma weight residual False 2.51 1.57 0.94 2.00e-01 2.50e+01 2.21e+01 chirality pdb=" CA ALYS A 132 " pdb=" N ALYS A 132 " pdb=" C ALYS A 132 " pdb=" CB ALYS A 132 " both_signs ideal model delta sigma weight residual False 2.51 3.41 -0.90 2.00e-01 2.50e+01 2.01e+01 chirality pdb=" CA ALEU A 153 " pdb=" N ALEU A 153 " pdb=" C ALEU A 153 " pdb=" CB ALEU A 153 " both_signs ideal model delta sigma weight residual False 2.51 3.36 -0.85 2.00e-01 2.50e+01 1.82e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.137 2.00e-02 2.50e+03 6.25e-02 1.17e+02 pdb=" CG PHE A 164 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.066 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.081 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.088 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.072 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.056 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " -0.007 2.00e-02 2.50e+03 6.44e-02 9.34e+01 pdb=" CG HIS A 126 " 0.081 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " -0.114 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " 0.060 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.052 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " -0.094 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " -0.024 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " 0.043 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.003 2.00e-02 2.50e+03 5.12e-02 7.85e+01 pdb=" CG BTYR A 67 " 0.061 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.050 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.002 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.092 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.003 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.085 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.031 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.067 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.040 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.027 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.041 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 720 2.27 - 2.85: 7773 2.85 - 3.43: 10651 3.43 - 4.02: 15412 4.02 - 4.60: 22048 Nonbonded interactions: 56604 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.687 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.736 2.450 x-y,-y,-z-4/3 nonbonded pdb=" O LEU A 185 " pdb=" H GLY A 159 " model vdw sym.op. 1.736 2.450 x-y,-y,-z-4/3 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.813 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.824 2.100 ... (remaining 56599 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 3 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False } 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_4596863_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2606 r_free= 0.1941 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787939 | | target function (ml) not normalized (work): 232252.063759 | | target function (ml) not normalized (free): 11807.553961 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.58 1.00 2941 171 0.3028 0.2071 6.9991 4.9407| | 2: 3.57 - 2.84 1.00 2876 122 0.2431 0.1887 4.3568 4.3467| | 3: 2.84 - 2.48 1.00 2833 165 0.2403 0.1590 4.1353 4.1461| | 4: 2.47 - 2.25 1.00 2825 136 0.2296 0.1463 3.8374 3.8388| | 5: 2.25 - 2.09 1.00 2756 127 0.2459 0.1646 3.8034 3.8193| | 6: 2.09 - 1.97 1.00 2846 113 0.2536 0.1744 3.4676 3.5585| | 7: 1.97 - 1.87 1.00 2787 165 0.2575 0.1838 3.1286 3.2306| | 8: 1.87 - 1.79 1.00 2789 144 0.2475 0.1765 3.0541 3.0745| | 9: 1.79 - 1.72 1.00 2745 138 0.2465 0.1891 2.8899 2.9378| | 10: 1.72 - 1.66 1.00 2789 158 0.2376 0.2115 2.7791 2.9131| | 11: 1.66 - 1.61 1.00 2740 147 0.2498 0.1907 2.7521 2.7968| | 12: 1.61 - 1.56 1.00 2787 146 0.2488 0.2009 2.6196 2.6532| | 13: 1.56 - 1.52 1.00 2745 130 0.2529 0.1926 2.5664 2.6171| | 14: 1.52 - 1.48 1.00 2803 134 0.2510 0.2002 2.4856 2.581| | 15: 1.48 - 1.45 1.00 2738 128 0.2558 0.1975 2.4268 2.4493| | 16: 1.45 - 1.42 1.00 2756 161 0.2623 0.2148 2.391 2.4153| | 17: 1.42 - 1.39 1.00 2785 139 0.2712 0.2315 2.3351 2.439| | 18: 1.39 - 1.36 1.00 2741 179 0.2685 0.1917 2.2819 2.2465| | 19: 1.36 - 1.34 1.00 2807 134 0.2631 0.2312 2.2359 2.2849| | 20: 1.34 - 1.32 1.00 2696 147 0.2673 0.2174 2.1872 2.2406| | 21: 1.32 - 1.30 1.00 2785 112 0.2697 0.2131 2.1748 2.1445| | 22: 1.29 - 1.27 1.00 2704 152 0.2776 0.2781 2.1432 2.2465| | 23: 1.27 - 1.26 1.00 2802 156 0.2798 0.2335 2.1161 2.1301| | 24: 1.26 - 1.24 1.00 2744 132 0.2738 0.2336 2.0682 2.0974| | 25: 1.24 - 1.22 1.00 2734 148 0.2825 0.2519 2.0386 2.0664| | 26: 1.22 - 1.21 1.00 2727 135 0.2895 0.2307 2.0239 2.0964| | 27: 1.21 - 1.19 1.00 2814 148 0.3029 0.2624 2.0115 2.0159| | 28: 1.19 - 1.18 1.00 2671 147 0.3001 0.2786 1.983 2.0074| | 29: 1.18 - 1.16 1.00 2800 134 0.2992 0.2724 1.9516 2.0228| | 30: 1.16 - 1.15 1.00 2740 148 0.3075 0.2829 1.9419 1.9582| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 19.01 0.76 0.23 1508.94| | 2: 3.57 - 2.84 2876 122 0.80 26.36 1.27 0.23 1508.94| | 3: 2.84 - 2.48 2833 165 0.74 32.36 1.25 0.23 1249.96| | 4: 2.47 - 2.25 2825 136 0.81 25.70 1.25 0.25 577.88| | 5: 2.25 - 2.09 2756 127 0.77 29.48 1.28 0.25 577.88| | 6: 2.09 - 1.97 2846 113 0.83 22.67 1.29 0.25 313.99| | 7: 1.97 - 1.87 2787 165 0.90 16.38 1.29 0.26 88.93| | 8: 1.87 - 1.79 2789 144 0.86 20.87 1.25 0.26 88.93| | 9: 1.79 - 1.72 2745 138 0.88 18.37 1.24 0.26 54.65| | 10: 1.72 - 1.66 2789 158 0.87 20.07 1.23 0.25 47.79| | 11: 1.66 - 1.61 2740 147 0.86 21.04 1.23 0.25 46.12| | 12: 1.61 - 1.56 2787 146 0.88 18.57 1.23 0.25 29.25| | 13: 1.56 - 1.52 2745 130 0.87 20.25 1.24 0.25 29.25| | 14: 1.52 - 1.48 2803 134 0.86 20.62 1.23 0.25 26.04| | 15: 1.48 - 1.45 2738 128 0.88 19.65 1.22 0.25 20.15| | 16: 1.45 - 1.42 2756 161 0.86 21.28 1.23 0.25 20.15| | 17: 1.42 - 1.39 2785 139 0.87 20.46 1.24 0.25 17.02| | 18: 1.39 - 1.36 2741 179 0.87 20.61 1.23 0.25 15.21| | 19: 1.36 - 1.34 2807 134 0.86 21.59 1.22 0.25 15.21| | 20: 1.34 - 1.32 2696 147 0.87 20.57 1.22 0.25 12.71| | 21: 1.32 - 1.30 2785 112 0.86 21.58 1.20 0.25 12.53| | 22: 1.29 - 1.27 2704 152 0.86 21.95 1.21 0.25 12.24| | 23: 1.27 - 1.26 2802 156 0.86 21.68 1.21 0.24 10.79| | 24: 1.26 - 1.24 2744 132 0.86 22.32 1.20 0.24 10.79| | 25: 1.24 - 1.22 2734 148 0.85 23.21 1.20 0.24 10.33| | 26: 1.22 - 1.21 2727 135 0.84 23.95 1.20 0.23 9.83| | 27: 1.21 - 1.19 2814 148 0.83 24.77 1.21 0.23 9.83| | 28: 1.19 - 1.18 2671 147 0.83 25.40 1.19 0.23 9.37| | 29: 1.18 - 1.16 2800 134 0.82 25.99 1.16 0.23 9.20| | 30: 1.16 - 1.15 2740 148 0.81 27.25 1.15 0.23 9.20| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 9.20 max = 1508.94 mean = 217.76| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 22.47| |phase err.(test): min = 0.00 max = 89.85 mean = 22.24| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 0.277 1557 Z= 5.572 Angle : 5.344 17.887 2118 Z= 3.807 Chirality : 0.386 0.940 243 Planarity : 0.032 0.082 284 Dihedral : 13.763 89.679 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.48 % Allowed : 3.11 % Favored : 94.41 % Cbeta Deviations : 29.73 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.48), residues: 224 helix: -2.55 (0.37), residues: 108 sheet: 0.00 (1.01), residues: 24 loop : 0.45 (0.56), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.074 0.020 ARG A 98 TYR 0.098 0.047 TYR A 141 PHE 0.101 0.044 PHE A 164 HIS 0.106 0.032 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2606 r_free= 0.1941 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787939 | | target function (ml) not normalized (work): 232252.063759 | | target function (ml) not normalized (free): 11807.553961 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2564 0.2606 0.1941 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2564 0.2606 0.1941 n_refl.: 87602 remove outliers: r(all,work,free)=0.1977 0.1982 0.1941 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2003 0.2008 0.1954 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1641 0.1634 0.1773 n_refl.: 87594 remove outliers: r(all,work,free)=0.1640 0.1633 0.1773 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3823 386.254 358.787 0.665 1.001 0.401 11.894-9.307 99.02 97 4 0.1838 613.546 594.672 0.923 1.003 0.370 9.237-7.194 100.00 213 7 0.2155 501.805 490.595 0.956 1.003 0.360 7.162-5.571 100.00 427 22 0.2206 376.577 364.019 0.934 1.003 0.320 5.546-4.326 100.00 867 58 0.1271 516.947 510.838 0.961 1.003 0.224 4.315-3.360 100.00 1859 96 0.1136 491.620 487.925 1.004 1.003 0.199 3.356-2.611 100.00 3867 181 0.1439 322.969 319.838 0.998 1.002 0.052 2.608-2.026 99.99 8198 413 0.1359 214.099 212.120 1.005 1.001 0.000 2.025-1.573 100.00 17313 902 0.1634 104.555 103.929 1.015 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2054 46.364 45.015 1.003 0.995 0.000 1.221-1.150 99.97 13689 708 0.2608 29.212 26.908 0.978 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0488 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1633 r_free=0.1773 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1636 r_free=0.1777 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.320810 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2025.725125 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1213 0.1465 0.0252 0.007 0.9 1.0 0.5 0.0 0 12.160 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.13 14.65 2.52 3.013 19.072 2025.725 0.017 12.43 15.44 3.00 3.188 19.550 2025.725 0.016 Individual atomic B min max mean iso aniso Overall: 8.63 118.72 21.01 2.88 0 1785 Protein: 8.63 118.72 17.88 2.88 0 1519 Water: 11.14 114.71 39.14 N/A 0 258 Other: 23.09 36.19 29.01 N/A 0 8 Chain A: 8.63 118.72 21.01 N/A 0 1785 Histogram: Values Number of atoms 8.63 - 19.64 1211 19.64 - 30.65 228 30.65 - 41.66 165 41.66 - 52.66 100 52.66 - 63.67 52 63.67 - 74.68 17 74.68 - 85.69 5 85.69 - 96.70 4 96.70 - 107.71 0 107.71 - 118.72 3 =========================== Idealize ADP of riding H ========================== r_work=0.1244 r_free=0.1544 r_work=0.1248 r_free=0.1548 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1248 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 = 0.1248 r_free = 0.1553 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.19 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= 0.1248 r_free= 0.1553 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015485 | | target function (ls_wunit_k1) not normalized (work): 1289.876747 | | target function (ls_wunit_k1) not normalized (free): 113.860430 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1263 0.1248 0.1553 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1704 0.1703 0.1777 n_refl.: 87593 remove outliers: r(all,work,free)=0.1704 0.1703 0.1777 n_refl.: 87593 overall B=0.12 to atoms: r(all,work,free)=0.1725 0.1724 0.1792 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1260 0.1245 0.1544 n_refl.: 87593 remove outliers: r(all,work,free)=0.1259 0.1245 0.1544 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 0.3598 298.652 278.505 0.628 1.001 0.372 11.894-9.307 99.02 97 4 0.1629 478.425 466.867 0.905 1.002 0.367 9.237-7.194 100.00 213 7 0.1843 391.293 386.555 0.948 1.002 0.314 7.162-5.571 100.00 427 22 0.1712 293.643 288.270 0.925 1.003 0.258 5.546-4.326 100.00 867 58 0.0907 403.100 400.531 0.949 1.003 0.209 4.315-3.360 100.00 1859 96 0.0774 383.351 382.327 0.995 1.002 0.190 3.356-2.611 100.00 3867 181 0.1020 251.842 251.148 0.999 1.002 0.110 2.608-2.026 99.99 8198 413 0.0978 166.948 166.401 1.009 1.002 0.000 2.025-1.573 100.00 17313 902 0.1213 81.529 81.708 1.018 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1658 36.153 35.614 1.005 0.999 0.000 1.221-1.150 99.97 13689 708 0.2364 22.779 21.290 0.969 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0485 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1245 r_free=0.1544 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=0.1245 r_free=0.1544 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1245 r_free=0.1544 | n_water=258 | time (s): 2.440 (total time: 2.440) Filter (dist) r_work=0.1254 r_free=0.1541 | n_water=252 | time (s): 26.360 (total time: 28.800) Filter (q & B) r_work=0.1257 r_free=0.1540 | n_water=249 | time (s): 3.880 (total time: 32.680) Compute maps r_work=0.1257 r_free=0.1540 | n_water=249 | time (s): 1.770 (total time: 34.450) Filter (map) r_work=0.1279 r_free=0.1546 | n_water=233 | time (s): 3.940 (total time: 38.390) Find peaks r_work=0.1279 r_free=0.1546 | n_water=233 | time (s): 0.780 (total time: 39.170) Add new water r_work=0.1433 r_free=0.1710 | n_water=455 | time (s): 3.980 (total time: 43.150) Refine new water occ: r_work=0.1335 r_free=0.1576 adp: r_work=0.1255 r_free=0.1530 occ: r_work=0.1269 r_free=0.1524 adp: r_work=0.1235 r_free=0.1510 occ: r_work=0.1238 r_free=0.1500 adp: r_work=0.1228 r_free=0.1499 ADP+occupancy (water only), MIN, final r_work=0.1228 r_free=0.1499 r_work=0.1228 r_free=0.1499 | n_water=455 | time (s): 116.660 (total time: 159.810) Filter (q & B) r_work=0.1236 r_free=0.1506 | n_water=432 | time (s): 3.710 (total time: 163.520) Filter (dist only) r_work=0.1236 r_free=0.1506 | n_water=432 | time (s): 41.430 (total time: 204.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.006870 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1570.416312 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 0.1234 0.1532 0.0298 0.007 0.9 1.9 0.5 0.0 0 12.503 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.34 15.32 2.98 3.790 23.154 1570.416 0.015 12.03 14.99 2.96 4.161 22.955 1570.416 0.015 Individual atomic B min max mean iso aniso Overall: 8.77 114.67 23.11 2.62 199 1760 Protein: 8.77 114.67 17.66 2.62 0 1519 Water: 10.77 70.62 42.14 N/A 199 233 Other: 24.18 36.00 29.25 N/A 0 8 Chain A: 8.77 114.67 20.32 N/A 0 1760 Chain S: 15.87 67.92 47.74 N/A 199 0 Histogram: Values Number of atoms 8.77 - 19.36 1208 19.36 - 29.95 252 29.95 - 40.54 188 40.54 - 51.13 138 51.13 - 61.72 119 61.72 - 72.31 43 72.31 - 82.90 5 82.90 - 93.49 3 93.49 - 104.08 1 104.08 - 114.67 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1499 r_work=0.1203 r_free=0.1499 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1499 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1205 r_free = 0.1493 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1205 r_free= 0.1493 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014038 | | target function (ls_wunit_k1) not normalized (work): 1169.289481 | | target function (ls_wunit_k1) not normalized (free): 108.274425 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1205 0.1493 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1603 0.1596 0.1748 n_refl.: 87592 remove outliers: r(all,work,free)=0.1603 0.1596 0.1748 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1609 0.1603 0.1752 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1216 0.1202 0.1491 n_refl.: 87592 remove outliers: r(all,work,free)=0.1215 0.1201 0.1491 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 0.3465 297.214 273.043 0.628 0.938 0.372 11.894-9.307 99.02 97 4 0.1543 478.425 475.563 0.972 0.939 0.360 9.237-7.194 100.00 213 7 0.1703 391.293 392.429 1.040 0.939 0.280 7.162-5.571 100.00 427 22 0.1482 293.643 289.610 1.003 0.940 0.219 5.546-4.326 100.00 867 58 0.0831 403.100 400.060 1.020 0.940 0.210 4.315-3.360 100.00 1859 96 0.0723 383.351 382.114 1.068 0.941 0.210 3.356-2.611 100.00 3867 181 0.0952 251.842 251.116 1.074 0.941 0.150 2.608-2.026 99.99 8198 413 0.0970 166.948 166.536 1.080 0.943 0.000 2.025-1.573 100.00 17313 902 0.1185 81.529 81.722 1.086 0.945 0.000 1.573-1.221 100.00 36679 1900 0.1612 36.153 35.660 1.068 0.950 0.000 1.221-1.150 99.97 13689 708 0.2341 22.779 21.332 1.023 0.953 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0602 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1491 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=0.1201 r_free=0.1491 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1491 | n_water=432 | time (s): 1.760 (total time: 1.760) Filter (dist) r_work=0.1201 r_free=0.1490 | n_water=431 | time (s): 39.040 (total time: 40.800) Filter (q & B) r_work=0.1201 r_free=0.1490 | n_water=431 | time (s): 1.110 (total time: 41.910) Compute maps r_work=0.1201 r_free=0.1490 | n_water=431 | time (s): 1.390 (total time: 43.300) Filter (map) r_work=0.1242 r_free=0.1478 | n_water=286 | time (s): 2.670 (total time: 45.970) Find peaks r_work=0.1242 r_free=0.1478 | n_water=286 | time (s): 0.580 (total time: 46.550) Add new water r_work=0.1370 r_free=0.1603 | n_water=468 | time (s): 3.500 (total time: 50.050) Refine new water occ: r_work=0.1269 r_free=0.1505 adp: r_work=0.1270 r_free=0.1507 occ: r_work=0.1246 r_free=0.1480 adp: r_work=0.1244 r_free=0.1482 occ: r_work=0.1231 r_free=0.1461 adp: r_work=0.1224 r_free=0.1460 ADP+occupancy (water only), MIN, final r_work=0.1224 r_free=0.1460 r_work=0.1224 r_free=0.1460 | n_water=468 | time (s): 149.730 (total time: 199.780) Filter (q & B) r_work=0.1229 r_free=0.1467 | n_water=439 | time (s): 3.440 (total time: 203.220) Filter (dist only) r_work=0.1229 r_free=0.1467 | n_water=439 | time (s): 37.290 (total time: 240.510) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.020488 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.056498 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1230 0.1426 0.0196 0.006 0.9 2.2 0.5 0.0 0 1.010 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.30 14.26 1.96 3.630 22.077 45.056 3.721 12.18 13.83 1.64 4.084 21.904 45.056 3.651 Individual atomic B min max mean iso aniso Overall: 9.19 110.08 21.62 2.33 209 1757 Protein: 9.19 110.08 17.27 2.33 0 1519 Water: 11.50 69.92 36.56 N/A 209 230 Other: 19.96 32.18 26.37 N/A 0 8 Chain A: 9.19 110.08 19.88 N/A 0 1757 Chain S: 16.85 61.37 36.19 N/A 209 0 Histogram: Values Number of atoms 9.19 - 19.28 1227 19.28 - 29.37 284 29.37 - 39.46 217 39.46 - 49.55 132 49.55 - 59.64 73 59.64 - 69.73 20 69.73 - 79.81 7 79.81 - 89.90 3 89.90 - 99.99 1 99.99 - 110.08 2 =========================== Idealize ADP of riding H ========================== r_work=0.1218 r_free=0.1383 r_work=0.1219 r_free=0.1384 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1219 r_free = 0.1384 target_work(ml) = 3.651 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1213 r_free = 0.1377 target_work(ml) = 3.648 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1213 r_free= 0.1377 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.648004 | | target function (ml) not normalized (work): 303856.838061 | | target function (ml) not normalized (free): 16027.625163 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1221 0.1213 0.1377 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1546 0.1545 0.1589 n_refl.: 87590 remove outliers: r(all,work,free)=0.1546 0.1545 0.1589 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1544 0.1543 0.1588 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1211 0.1204 0.1354 n_refl.: 87590 remove outliers: r(all,work,free)=0.1207 0.1200 0.1354 n_refl.: 87580 ======================== 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 0.3742 293.961 262.186 0.483 1.000 0.320 11.894-9.307 98.04 96 4 0.2342 478.549 461.354 0.851 1.001 0.320 9.237-7.194 97.73 208 7 0.2292 383.918 385.546 0.945 1.002 0.190 7.162-5.571 100.00 427 22 0.2050 293.643 283.681 0.915 1.002 0.164 5.546-4.326 100.00 867 58 0.1102 403.100 398.472 0.950 1.002 0.155 4.315-3.360 100.00 1859 96 0.0939 383.351 380.700 0.995 1.002 0.150 3.356-2.611 100.00 3867 181 0.1160 251.842 250.015 1.000 1.002 0.057 2.608-2.026 99.99 8198 413 0.1046 166.948 166.015 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1018 81.529 81.676 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1295 36.153 35.733 1.020 0.999 0.000 1.221-1.150 99.97 13689 708 0.2129 22.779 21.392 0.979 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0334 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1354 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=0.1200 r_free=0.1354 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1354 | n_water=439 | time (s): 1.810 (total time: 1.810) Filter (dist) r_work=0.1200 r_free=0.1354 | n_water=439 | time (s): 38.260 (total time: 40.070) Filter (q & B) r_work=0.1200 r_free=0.1354 | n_water=437 | time (s): 3.790 (total time: 43.860) Compute maps r_work=0.1200 r_free=0.1354 | n_water=437 | time (s): 1.460 (total time: 45.320) Filter (map) r_work=0.1222 r_free=0.1369 | n_water=307 | time (s): 2.690 (total time: 48.010) Find peaks r_work=0.1222 r_free=0.1369 | n_water=307 | time (s): 0.460 (total time: 48.470) Add new water r_work=0.1286 r_free=0.1442 | n_water=473 | time (s): 2.810 (total time: 51.280) Refine new water occ: r_work=0.1213 r_free=0.1362 adp: r_work=0.1214 r_free=0.1365 occ: r_work=0.1199 r_free=0.1346 adp: r_work=0.1198 r_free=0.1349 occ: r_work=0.1187 r_free=0.1334 adp: r_work=0.1185 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1335 r_work=0.1185 r_free=0.1335 | n_water=473 | time (s): 178.180 (total time: 229.460) Filter (q & B) r_work=0.1192 r_free=0.1341 | n_water=439 | time (s): 3.890 (total time: 233.350) Filter (dist only) r_work=0.1192 r_free=0.1340 | n_water=437 | time (s): 37.980 (total time: 271.330) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.920308 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.579915 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 0.1197 0.1360 0.0163 0.006 0.9 2.2 0.5 0.0 0 0.960 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.60 1.63 3.442 21.464 50.580 3.638 11.82 13.51 1.69 3.845 21.337 50.580 3.623 Individual atomic B min max mean iso aniso Overall: 9.24 105.64 21.09 2.19 208 1756 Protein: 9.24 105.64 16.98 2.19 0 1519 Water: 11.51 69.08 35.34 N/A 208 229 Other: 19.41 28.94 24.22 N/A 0 8 Chain A: 9.24 105.64 19.53 N/A 0 1756 Chain S: 16.42 61.53 34.27 N/A 208 0 Histogram: Values Number of atoms 9.24 - 18.88 1224 18.88 - 28.52 292 28.52 - 38.16 216 38.16 - 47.80 127 47.80 - 57.44 67 57.44 - 67.08 25 67.08 - 76.72 8 76.72 - 86.36 2 86.36 - 96.00 1 96.00 - 105.64 2 =========================== Idealize ADP of riding H ========================== r_work=0.1182 r_free=0.1351 r_work=0.1182 r_free=0.1351 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1182 r_free = 0.1351 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1178 r_free = 0.1348 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1178 r_free= 0.1348 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.621320 | | target function (ml) not normalized (work): 301598.000012 | | target function (ml) not normalized (free): 15935.999398 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1187 0.1178 0.1348 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1509 0.1508 0.1551 n_refl.: 87580 remove outliers: r(all,work,free)=0.1509 0.1508 0.1551 n_refl.: 87580 overall B=-0.02 to atoms: r(all,work,free)=0.1506 0.1505 0.1549 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1185 0.1177 0.1343 n_refl.: 87580 remove outliers: r(all,work,free)=0.1185 0.1177 0.1343 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 88.54 80 5 0.3894 289.328 259.523 0.469 1.000 0.312 11.894-9.307 98.04 96 4 0.2526 478.549 463.899 0.848 1.001 0.292 9.237-7.194 97.73 208 7 0.2477 383.918 377.302 0.911 1.002 0.160 7.162-5.571 100.00 427 22 0.2192 293.643 282.692 0.907 1.002 0.134 5.546-4.326 100.00 867 58 0.1142 403.100 398.262 0.949 1.002 0.125 4.315-3.360 100.00 1859 96 0.0936 383.351 381.130 0.994 1.002 0.119 3.356-2.611 100.00 3867 181 0.1150 251.842 250.110 1.002 1.002 0.048 2.608-2.026 99.99 8198 413 0.1014 166.948 166.100 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.0962 81.529 81.785 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1241 36.153 35.782 1.022 0.998 0.000 1.221-1.150 99.97 13689 708 0.2121 22.779 21.416 0.980 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0427 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1177 r_free=0.1343 After: r_work=0.1177 r_free=0.1344 ================================== NQH flips ================================== r_work=0.1177 r_free=0.1344 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1177 r_free=0.1344 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1177 r_free=0.1344 | n_water=437 | time (s): 1.930 (total time: 1.930) Filter (dist) r_work=0.1177 r_free=0.1344 | n_water=437 | time (s): 37.860 (total time: 39.790) Filter (q & B) r_work=0.1178 r_free=0.1344 | n_water=435 | time (s): 2.970 (total time: 42.760) Compute maps r_work=0.1178 r_free=0.1344 | n_water=435 | time (s): 1.380 (total time: 44.140) Filter (map) r_work=0.1206 r_free=0.1381 | n_water=324 | time (s): 3.470 (total time: 47.610) Find peaks r_work=0.1206 r_free=0.1381 | n_water=324 | time (s): 0.630 (total time: 48.240) Add new water r_work=0.1256 r_free=0.1429 | n_water=490 | time (s): 2.450 (total time: 50.690) Refine new water occ: r_work=0.1189 r_free=0.1347 adp: r_work=0.1190 r_free=0.1350 occ: r_work=0.1178 r_free=0.1333 adp: r_work=0.1177 r_free=0.1336 occ: r_work=0.1171 r_free=0.1319 adp: r_work=0.1167 r_free=0.1322 ADP+occupancy (water only), MIN, final r_work=0.1167 r_free=0.1322 r_work=0.1167 r_free=0.1322 | n_water=490 | time (s): 167.990 (total time: 218.680) Filter (q & B) r_work=0.1176 r_free=0.1334 | n_water=447 | time (s): 2.790 (total time: 221.470) Filter (dist only) r_work=0.1176 r_free=0.1334 | n_water=446 | time (s): 36.560 (total time: 258.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.950993 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.099295 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 0.1196 0.1349 0.0153 0.007 1.0 2.6 0.5 0.0 0 0.975 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.49 1.53 3.314 21.137 49.099 3.626 12.01 13.54 1.53 3.535 21.069 49.099 3.620 Individual atomic B min max mean iso aniso Overall: 9.28 101.58 20.97 2.06 219 1754 Protein: 9.28 101.58 16.79 2.06 0 1519 Water: 11.47 68.43 35.15 N/A 219 227 Other: 19.18 27.25 23.45 N/A 0 8 Chain A: 9.28 101.58 19.30 N/A 0 1754 Chain S: 15.30 59.32 34.33 N/A 219 0 Histogram: Values Number of atoms 9.28 - 18.51 1214 18.51 - 27.74 297 27.74 - 36.97 204 36.97 - 46.20 148 46.20 - 55.43 68 55.43 - 64.66 27 64.66 - 73.89 10 73.89 - 83.12 2 83.12 - 92.35 1 92.35 - 101.58 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1354 r_work=0.1201 r_free=0.1354 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1354 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1352 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1199 r_free= 0.1352 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.619533 | | target function (ml) not normalized (work): 301445.567732 | | target function (ml) not normalized (free): 15922.487543 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1421 0.1391 5.6961 5.6345| | 2: 3.57 - 2.84 1.00 2888 124 0.1118 0.1399 5.1945 5.2367| | 3: 2.83 - 2.48 1.00 2820 163 0.1245 0.1218 5.0033 5.0061| | 4: 2.47 - 2.25 1.00 2825 136 0.1030 0.1161 4.7016 4.7509| | 5: 2.25 - 2.09 1.00 2756 127 0.1000 0.1127 4.6424 4.7281| | 6: 2.09 - 1.97 1.00 2846 113 0.0973 0.1196 4.3441 4.4738| | 7: 1.97 - 1.87 1.00 2787 165 0.0986 0.1188 4.0683 4.1601| | 8: 1.87 - 1.79 1.00 2789 144 0.1031 0.1239 3.9862 4.0693| | 9: 1.79 - 1.72 1.00 2745 138 0.0956 0.1287 3.7126 3.8791| | 10: 1.72 - 1.66 1.00 2831 160 0.0996 0.1214 3.6265 3.7406| | 11: 1.66 - 1.61 1.00 2712 147 0.0949 0.1125 3.5576 3.6139| | 12: 1.61 - 1.56 1.00 2773 144 0.0919 0.1167 3.3463 3.4839| | 13: 1.56 - 1.52 1.00 2745 130 0.0981 0.1067 3.3364 3.4286| | 14: 1.52 - 1.48 1.00 2803 134 0.0985 0.1125 3.2581 3.3488| | 15: 1.48 - 1.45 1.00 2738 128 0.1014 0.1333 3.1696 3.3233| | 16: 1.45 - 1.42 1.00 2756 161 0.1070 0.1265 3.1519 3.2435| | 17: 1.42 - 1.39 1.00 2785 139 0.1122 0.1283 3.1151 3.2264| | 18: 1.39 - 1.36 1.00 2741 179 0.1148 0.1381 3.0849 3.2773| | 19: 1.36 - 1.34 1.00 2807 134 0.1214 0.1589 3.0909 3.2665| | 20: 1.34 - 1.32 1.00 2696 147 0.1314 0.1495 3.0877 3.149| | 21: 1.32 - 1.30 1.00 2785 112 0.1413 0.1601 3.0871 3.1539| | 22: 1.29 - 1.27 1.00 2704 152 0.1468 0.1908 3.0833 3.2859| | 23: 1.27 - 1.26 1.00 2802 156 0.1573 0.1863 3.1017 3.2093| | 24: 1.26 - 1.24 1.00 2744 132 0.1621 0.1761 3.0943 3.1925| | 25: 1.24 - 1.22 1.00 2733 148 0.1789 0.2315 3.1084 3.2924| | 26: 1.22 - 1.21 1.00 2727 135 0.1863 0.1781 3.1224 3.2001| | 27: 1.21 - 1.19 1.00 2814 148 0.2012 0.2067 3.1389 3.1437| | 28: 1.19 - 1.18 1.00 2671 147 0.2142 0.2294 3.1379 3.162| | 29: 1.18 - 1.16 1.00 2800 134 0.2216 0.2354 3.1265 3.2266| | 30: 1.16 - 1.15 1.00 2739 148 0.2376 0.2486 3.1152 3.163| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.89 1.00 0.97 6104.68| | 2: 3.57 - 2.84 2888 124 0.92 13.12 1.01 0.97 6104.68| | 3: 2.83 - 2.48 2820 163 0.89 17.21 0.98 0.97 5119.13| | 4: 2.47 - 2.25 2825 136 0.91 14.37 1.00 0.98 2577.74| | 5: 2.25 - 2.09 2756 127 0.90 16.64 1.01 0.98 2577.74| | 6: 2.09 - 1.97 2846 113 0.92 13.46 1.02 0.98 1518.46| | 7: 1.97 - 1.87 2787 165 0.94 10.64 1.02 0.97 615.04| | 8: 1.87 - 1.79 2789 144 0.91 14.27 1.00 0.97 615.04| | 9: 1.79 - 1.72 2745 138 0.93 11.27 0.98 0.97 333.18| | 10: 1.72 - 1.66 2831 160 0.93 12.09 0.98 0.97 276.73| | 11: 1.66 - 1.61 2712 147 0.93 12.75 0.98 0.97 264.36| | 12: 1.61 - 1.56 2773 144 0.95 9.57 0.99 0.97 147.66| | 13: 1.56 - 1.52 2745 130 0.94 11.10 1.02 0.97 147.66| | 14: 1.52 - 1.48 2803 134 0.94 11.28 1.02 0.97 132.07| | 15: 1.48 - 1.45 2738 128 0.95 10.44 1.01 0.98 103.51| | 16: 1.45 - 1.42 2756 161 0.94 11.60 1.02 0.98 103.51| | 17: 1.42 - 1.39 2785 139 0.94 11.49 1.01 0.98 93.55| | 18: 1.39 - 1.36 2741 179 0.94 11.82 1.01 0.98 87.78| | 19: 1.36 - 1.34 2807 134 0.94 12.37 1.00 0.98 87.78| | 20: 1.34 - 1.32 2696 147 0.94 12.44 0.99 0.97 82.57| | 21: 1.32 - 1.30 2785 112 0.94 13.36 0.98 0.96 82.20| | 22: 1.29 - 1.27 2704 152 0.93 13.90 0.98 0.96 82.32| | 23: 1.27 - 1.26 2802 156 0.92 14.79 0.98 0.95 82.93| | 24: 1.26 - 1.24 2744 132 0.92 14.95 0.97 0.95 82.93| | 25: 1.24 - 1.22 2733 148 0.91 16.32 0.96 0.94 84.45| | 26: 1.22 - 1.21 2727 135 0.90 18.05 1.02 0.93 86.15| | 27: 1.21 - 1.19 2814 148 0.89 18.72 1.02 0.93 86.15| | 28: 1.19 - 1.18 2671 147 0.88 20.22 1.01 0.93 89.48| | 29: 1.18 - 1.16 2800 134 0.88 20.56 0.99 0.93 90.73| | 30: 1.16 - 1.15 2739 148 0.86 21.94 0.98 0.93 90.73| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 82.20 max = 6104.68 mean = 955.00| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.98 mean = 13.97| |phase err.(test): min = 0.00 max = 89.96 mean = 14.12| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1199 0.1352 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1520 0.1520 0.1551 n_refl.: 87579 remove outliers: r(all,work,free)=0.1520 0.1520 0.1551 n_refl.: 87579 overall B=-0.01 to atoms: r(all,work,free)=0.1517 0.1517 0.1549 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1199 0.1354 n_refl.: 87579 remove outliers: r(all,work,free)=0.1206 0.1198 0.1354 n_refl.: 87576 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3886 289.328 256.157 0.442 1.000 0.283 11.894-9.307 96.08 94 4 0.2482 471.850 460.384 0.852 1.002 0.263 9.237-7.194 97.27 207 7 0.2533 384.461 375.749 0.901 1.002 0.150 7.162-5.571 100.00 427 22 0.2255 293.643 283.281 0.901 1.002 0.150 5.546-4.326 100.00 867 58 0.1200 403.100 398.096 0.951 1.002 0.125 4.315-3.360 100.00 1859 96 0.0980 383.351 380.777 0.995 1.002 0.117 3.356-2.611 100.00 3867 181 0.1197 251.842 249.833 1.001 1.002 0.048 2.608-2.026 99.99 8198 413 0.1046 166.948 166.025 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0975 81.529 81.776 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1224 36.153 35.798 1.023 0.997 0.000 1.221-1.150 99.97 13689 708 0.2116 22.779 21.414 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0408 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2606 0.1941 0.084 5.344 8.8 119.3 19.9 258 0.000 1_bss: 0.1633 0.1773 0.084 5.344 9.1 119.5 20.1 258 0.000 1_settarget: 0.1633 0.1773 0.084 5.344 9.1 119.5 20.1 258 0.000 1_nqh: 0.1636 0.1777 0.084 5.344 9.1 119.5 20.1 258 0.003 1_weight: 0.1636 0.1777 0.084 5.344 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1213 0.1465 0.007 0.940 9.1 119.5 20.1 258 0.129 1_adp: 0.1244 0.1544 0.007 0.940 8.6 118.7 21.0 258 0.129 1_regHadp: 0.1248 0.1548 0.007 0.940 8.6 118.7 21.0 258 0.129 1_occ: 0.1248 0.1553 0.007 0.940 8.6 118.7 21.0 258 0.129 2_bss: 0.1245 0.1544 0.007 0.940 8.8 118.8 21.1 258 0.129 2_settarget: 0.1245 0.1544 0.007 0.940 8.8 118.8 21.1 258 0.129 2_updatecdl: 0.1245 0.1544 0.007 0.944 8.8 118.8 21.1 258 0.129 2_nqh: 0.1245 0.1544 0.007 0.944 8.8 118.8 21.1 258 0.129 2_sol: 0.1236 0.1506 0.007 0.944 8.8 118.8 23.5 432 n/a 2_weight: 0.1236 0.1506 0.007 0.944 8.8 118.8 23.5 432 n/a 2_xyzrec: 0.1234 0.1532 0.007 0.867 8.8 118.8 23.5 432 n/a 2_adp: 0.1203 0.1499 0.007 0.867 8.8 114.7 23.1 432 n/a 2_regHadp: 0.1203 0.1499 0.007 0.867 8.8 114.7 23.1 432 n/a 2_occ: 0.1205 0.1493 0.007 0.867 8.8 114.7 23.1 432 n/a 3_bss: 0.1201 0.1491 0.007 0.867 8.8 114.7 23.1 432 n/a 3_settarget: 0.1201 0.1491 0.007 0.867 8.8 114.7 23.1 432 n/a 3_updatecdl: 0.1201 0.1491 0.007 0.868 8.8 114.7 23.1 432 n/a 3_nqh: 0.1201 0.1491 0.007 0.868 8.8 114.7 23.1 432 n/a 3_sol: 0.1229 0.1467 0.007 0.868 8.8 114.7 21.9 439 n/a 3_weight: 0.1229 0.1467 0.007 0.868 8.8 114.7 21.9 439 n/a 3_xyzrec: 0.1230 0.1426 0.006 0.912 8.8 114.7 21.9 439 n/a 3_adp: 0.1218 0.1383 0.006 0.912 9.2 110.1 21.6 439 n/a 3_regHadp: 0.1219 0.1384 0.006 0.912 9.2 110.1 21.6 439 n/a 3_occ: 0.1213 0.1377 0.006 0.912 9.2 110.1 21.6 439 n/a 4_bss: 0.1200 0.1354 0.006 0.912 9.2 110.1 21.6 439 n/a 4_settarget: 0.1200 0.1354 0.006 0.912 9.2 110.1 21.6 439 n/a 4_updatecdl: 0.1200 0.1354 0.006 0.911 9.2 110.1 21.6 439 n/a 4_nqh: 0.1200 0.1354 0.006 0.911 9.2 110.1 21.6 439 n/a 4_sol: 0.1192 0.1340 0.006 0.911 9.2 110.1 21.3 437 n/a 4_weight: 0.1192 0.1340 0.006 0.911 9.2 110.1 21.3 437 n/a 4_xyzrec: 0.1197 0.1360 0.006 0.945 9.2 110.1 21.3 437 n/a 4_adp: 0.1182 0.1351 0.006 0.945 9.2 105.6 21.1 437 n/a 4_regHadp: 0.1182 0.1351 0.006 0.945 9.2 105.6 21.1 437 n/a 4_occ: 0.1178 0.1348 0.006 0.945 9.2 105.6 21.1 437 n/a 5_bss: 0.1177 0.1343 0.006 0.945 9.2 105.6 21.1 437 n/a 5_settarget: 0.1177 0.1343 0.006 0.945 9.2 105.6 21.1 437 n/a 5_updatecdl: 0.1177 0.1343 0.006 0.946 9.2 105.6 21.1 437 n/a 5_setrh: 0.1177 0.1344 0.006 0.946 9.2 105.6 21.1 437 n/a 5_nqh: 0.1177 0.1344 0.006 0.946 9.2 105.6 21.1 437 n/a 5_sol: 0.1176 0.1334 0.006 0.946 9.2 105.6 21.1 446 n/a 5_weight: 0.1176 0.1334 0.006 0.946 9.2 105.6 21.1 446 n/a 5_xyzrec: 0.1196 0.1349 0.007 1.038 9.2 105.6 21.1 446 n/a 5_adp: 0.1201 0.1354 0.007 1.038 9.3 101.6 21.0 446 n/a 5_regHadp: 0.1201 0.1354 0.007 1.038 9.3 101.6 21.0 446 n/a 5_occ: 0.1199 0.1352 0.007 1.038 9.3 101.6 21.0 446 n/a end: 0.1198 0.1354 0.007 1.038 9.3 101.6 21.0 446 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_4596863_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_4596863_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.9200 Refinement macro-cycles (run) : 3483.4000 Write final files (write_after_run_outputs) : 66.5800 Total : 3554.9000 Total CPU time: 59.87 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:15 PST -0800 (1735452675.77 s) Start R-work = 0.1633, R-free = 0.1773 Final R-work = 0.1198, R-free = 0.1354 =============================================================================== Job complete usr+sys time: 3694.67 seconds wall clock time: 66 minutes 30.37 seconds (3990.37 seconds total)