Starting phenix.refine on Sat Dec 28 21:06:32 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4735076.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_4735076.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4735076.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: 2.26, per 1000 atoms: 0.67 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: 0.91 Conformation dependent library (CDL) restraints added in 312.9 milliseconds Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 390 0.89 - 1.15: 1214 1.15 - 1.40: 614 1.40 - 1.66: 889 1.66 - 1.92: 46 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 36 " pdb=" CA ALA A 36 " ideal model delta sigma weight residual 1.456 1.690 -0.233 1.23e-02 6.61e+03 3.60e+02 bond pdb=" C GLN A 180 " pdb=" O GLN A 180 " ideal model delta sigma weight residual 1.236 0.997 0.239 1.29e-02 6.01e+03 3.42e+02 bond pdb=" C GLY A 78 " pdb=" O GLY A 78 " ideal model delta sigma weight residual 1.234 1.455 -0.222 1.21e-02 6.83e+03 3.36e+02 bond pdb=" C LYS A 12 " pdb=" O LYS A 12 " ideal model delta sigma weight residual 1.234 1.016 0.219 1.20e-02 6.94e+03 3.33e+02 bond pdb=" C GLY A 157 " pdb=" O GLY A 157 " ideal model delta sigma weight residual 1.235 1.479 -0.244 1.35e-02 5.49e+03 3.26e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.47: 3088 4.47 - 8.94: 1853 8.94 - 13.41: 670 13.41 - 17.88: 152 17.88 - 22.35: 14 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.83 109.48 11.35 5.90e-01 2.87e+00 3.70e+02 angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.42 130.43 -10.01 6.40e-01 2.44e+00 2.45e+02 angle pdb=" CA GLU A 116 " pdb=" C GLU A 116 " pdb=" O GLU A 116 " ideal model delta sigma weight residual 120.98 104.33 16.65 1.24e+00 6.50e-01 1.80e+02 angle pdb=" O ALEU A 153 " pdb=" C ALEU A 153 " pdb=" N THR A 154 " ideal model delta sigma weight residual 123.12 140.58 -17.46 1.32e+00 5.74e-01 1.75e+02 angle pdb=" CG HIS A 115 " pdb=" CD2 HIS A 115 " pdb=" NE2 HIS A 115 " ideal model delta sigma weight residual 107.20 94.55 12.65 1.00e+00 1.00e+00 1.60e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 942 16.87 - 33.74: 114 33.74 - 50.61: 35 50.61 - 67.47: 17 67.47 - 84.34: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " pdb=" CA SER A 57 " ideal model delta harmonic sigma weight residual 180.00 151.20 28.80 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual 180.00 -153.25 -26.75 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 157.22 22.78 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.198: 89 0.198 - 0.393: 77 0.393 - 0.588: 43 0.588 - 0.783: 25 0.783 - 0.978: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA LEU A 58 " pdb=" N LEU A 58 " pdb=" C LEU A 58 " pdb=" CB LEU A 58 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.39e+01 chirality pdb=" CA ALA A 183 " pdb=" N ALA A 183 " pdb=" C ALA A 183 " pdb=" CB ALA A 183 " both_signs ideal model delta sigma weight residual False 2.48 1.52 0.97 2.00e-01 2.50e+01 2.34e+01 chirality pdb=" CA BLYS A 99 " pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CB BLYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.29e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.018 2.00e-02 2.50e+03 6.78e-02 1.38e+02 pdb=" CG PHE A 119 " -0.170 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.038 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.102 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.066 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.083 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.035 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.007 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.013 2.00e-02 2.50e+03 6.68e-02 1.34e+02 pdb=" CG TYR A 139 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.083 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.084 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.080 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.071 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.065 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.015 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.099 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.020 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.108 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " 0.035 9.50e-02 1.11e+02 7.54e-02 1.25e+02 pdb=" NE ARG A 5 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " -0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " -0.063 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " -0.072 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " 0.096 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " 0.021 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " 0.154 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " -0.053 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.28: 759 2.28 - 2.86: 7804 2.86 - 3.44: 10629 3.44 - 4.02: 15316 4.02 - 4.60: 22095 Nonbonded interactions: 56603 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.695 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.721 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.781 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.801 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.835 2.450 ... (remaining 56598 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_4735076_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= 0.2608 r_free= 0.1920 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.790287 | | target function (ml) not normalized (work): 232447.646542 | | target function (ml) not normalized (free): 11735.341920 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3042 0.2068 7.0128 4.9413| | 2: 3.57 - 2.84 1.00 2876 122 0.2423 0.1854 4.3531 4.341| | 3: 2.84 - 2.48 1.00 2833 165 0.2365 0.1630 4.1352 4.1709| | 4: 2.47 - 2.25 1.00 2825 136 0.2334 0.1412 3.8359 3.8346| | 5: 2.25 - 2.09 1.00 2756 127 0.2490 0.1650 3.8002 3.8362| | 6: 2.09 - 1.97 1.00 2846 113 0.2521 0.1749 3.4681 3.5208| | 7: 1.97 - 1.87 1.00 2787 165 0.2487 0.1767 3.1149 3.1669| | 8: 1.87 - 1.79 1.00 2789 144 0.2470 0.1826 3.052 3.0976| | 9: 1.79 - 1.72 1.00 2745 138 0.2427 0.1947 2.903 2.9901| | 10: 1.72 - 1.66 1.00 2789 158 0.2392 0.1895 2.794 2.8488| | 11: 1.66 - 1.61 1.00 2740 147 0.2479 0.1821 2.7357 2.7609| | 12: 1.61 - 1.56 1.00 2787 146 0.2611 0.1851 2.6384 2.6146| | 13: 1.56 - 1.52 1.00 2745 130 0.2626 0.1905 2.5588 2.5998| | 14: 1.52 - 1.48 1.00 2803 134 0.2574 0.1790 2.5179 2.4982| | 15: 1.48 - 1.45 1.00 2738 128 0.2578 0.2180 2.4305 2.5064| | 16: 1.45 - 1.42 1.00 2756 161 0.2675 0.2169 2.4179 2.438| | 17: 1.42 - 1.39 1.00 2785 139 0.2691 0.2143 2.3516 2.3693| | 18: 1.39 - 1.36 1.00 2741 179 0.2597 0.2291 2.2686 2.3646| | 19: 1.36 - 1.34 1.00 2807 134 0.2620 0.2234 2.2443 2.2483| | 20: 1.34 - 1.32 1.00 2696 147 0.2689 0.1959 2.1932 2.0844| | 21: 1.32 - 1.30 1.00 2785 112 0.2668 0.2273 2.1568 2.1266| | 22: 1.29 - 1.27 1.00 2704 152 0.2759 0.2191 2.141 2.0797| | 23: 1.27 - 1.26 1.00 2802 156 0.2811 0.2367 2.0987 2.1628| | 24: 1.26 - 1.24 1.00 2744 132 0.2832 0.2427 2.0825 2.1294| | 25: 1.24 - 1.22 1.00 2734 148 0.2869 0.2486 2.0489 2.0579| | 26: 1.22 - 1.21 1.00 2727 135 0.2852 0.2300 2.0208 2.0622| | 27: 1.21 - 1.19 1.00 2814 148 0.2965 0.2584 2.0073 1.9852| | 28: 1.19 - 1.18 1.00 2671 147 0.2952 0.2933 1.9805 2.006| | 29: 1.18 - 1.16 1.00 2800 134 0.3006 0.2677 1.9649 2.0113| | 30: 1.16 - 1.15 1.00 2740 148 0.3070 0.2803 1.9277 1.9378| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.02 0.76 0.23 1503.85| | 2: 3.57 - 2.84 2876 122 0.80 26.37 1.27 0.23 1503.85| | 3: 2.84 - 2.48 2833 165 0.74 32.12 1.24 0.23 1245.98| | 4: 2.47 - 2.25 2825 136 0.81 25.62 1.26 0.25 576.77| | 5: 2.25 - 2.09 2756 127 0.77 29.46 1.28 0.25 576.77| | 6: 2.09 - 1.97 2846 113 0.83 22.57 1.29 0.25 313.29| | 7: 1.97 - 1.87 2787 165 0.90 16.29 1.28 0.26 88.58| | 8: 1.87 - 1.79 2789 144 0.86 20.80 1.25 0.26 88.58| | 9: 1.79 - 1.72 2745 138 0.88 18.33 1.23 0.25 54.20| | 10: 1.72 - 1.66 2789 158 0.87 19.89 1.22 0.25 47.31| | 11: 1.66 - 1.61 2740 147 0.86 20.96 1.24 0.25 45.62| | 12: 1.61 - 1.56 2787 146 0.89 18.33 1.25 0.25 28.47| | 13: 1.56 - 1.52 2745 130 0.87 20.19 1.25 0.25 28.47| | 14: 1.52 - 1.48 2803 134 0.87 20.33 1.23 0.25 25.51| | 15: 1.48 - 1.45 2738 128 0.87 19.86 1.23 0.25 20.09| | 16: 1.45 - 1.42 2756 161 0.86 21.00 1.23 0.25 20.09| | 17: 1.42 - 1.39 2785 139 0.87 20.18 1.23 0.25 16.90| | 18: 1.39 - 1.36 2741 179 0.87 20.36 1.21 0.25 15.06| | 19: 1.36 - 1.34 2807 134 0.86 21.33 1.21 0.25 15.06| | 20: 1.34 - 1.32 2696 147 0.88 19.84 1.21 0.25 11.96| | 21: 1.32 - 1.30 2785 112 0.87 20.60 1.20 0.25 11.74| | 22: 1.29 - 1.27 2704 152 0.87 21.03 1.21 0.25 11.47| | 23: 1.27 - 1.26 2802 156 0.87 20.84 1.22 0.24 10.11| | 24: 1.26 - 1.24 2744 132 0.86 21.61 1.20 0.24 10.11| | 25: 1.24 - 1.22 2734 148 0.85 22.55 1.20 0.24 9.69| | 26: 1.22 - 1.21 2727 135 0.85 22.82 1.19 0.24 9.22| | 27: 1.21 - 1.19 2814 148 0.84 23.63 1.20 0.24 9.22| | 28: 1.19 - 1.18 2671 147 0.83 24.87 1.17 0.23 8.91| | 29: 1.18 - 1.16 2800 134 0.83 25.49 1.16 0.22 8.80| | 30: 1.16 - 1.15 2740 148 0.81 27.02 1.15 0.22 8.80| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 8.80 max = 1503.85 mean = 216.79| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 22.12| |phase err.(test): min = 0.00 max = 88.87 mean = 22.11| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.244 1557 Z= 5.545 Angle : 5.417 18.814 2118 Z= 3.858 Chirality : 0.388 0.978 243 Planarity : 0.031 0.133 284 Dihedral : 14.032 84.343 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.86 % Allowed : 1.86 % Favored : 96.27 % Cbeta Deviations : 34.05 % 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: -1.98 (0.49), residues: 224 helix: -2.23 (0.41), residues: 109 sheet: 0.06 (0.95), residues: 28 loop : -0.17 (0.55), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.066 0.020 ARG A 48 TYR 0.077 0.042 TYR A 139 PHE 0.142 0.046 PHE A 119 HIS 0.057 0.028 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= 0.2608 r_free= 0.1920 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.790287 | | target function (ml) not normalized (work): 232447.646542 | | target function (ml) not normalized (free): 11735.341920 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2609 0.1921 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2609 0.1921 n_refl.: 87602 remove outliers: r(all,work,free)=0.1979 0.1984 0.1921 n_refl.: 87594 overall B=0.22 to atoms: r(all,work,free)=0.2005 0.2011 0.1938 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1643 0.1637 0.1754 n_refl.: 87594 remove outliers: r(all,work,free)=0.1643 0.1637 0.1754 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 0.3883 386.248 356.542 0.721 0.931 0.402 11.894-9.307 99.02 97 4 0.1829 613.536 594.060 0.994 0.932 0.390 9.237-7.194 100.00 213 7 0.2154 501.797 490.488 1.032 0.932 0.359 7.162-5.571 100.00 427 22 0.2190 376.571 365.241 1.012 0.932 0.340 5.546-4.326 100.00 867 58 0.1304 516.939 510.771 1.035 0.932 0.214 4.315-3.360 100.00 1859 96 0.1152 491.612 488.028 1.083 0.932 0.189 3.356-2.611 100.00 3867 181 0.1431 322.964 319.384 1.069 0.931 0.109 2.608-2.026 99.99 8198 413 0.1347 214.096 212.154 1.083 0.931 0.000 2.025-1.573 100.00 17313 902 0.1628 104.553 103.826 1.085 0.930 0.000 1.573-1.221 100.00 36679 1900 0.2084 46.363 45.049 1.077 0.928 0.000 1.221-1.150 99.97 13689 708 0.2596 29.212 26.972 1.046 0.927 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0501 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1637 r_free=0.1754 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1644 r_free=0.1766 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.967397 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2005.753629 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 0.1210 0.1466 0.0256 0.008 1.0 1.3 0.5 0.0 0 12.984 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 14.66 2.56 3.012 19.077 2005.754 0.017 12.46 15.41 2.95 3.271 19.595 2005.754 0.016 Individual atomic B min max mean iso aniso Overall: 8.61 118.94 21.08 2.88 0 1785 Protein: 8.61 118.94 17.94 2.88 0 1519 Water: 11.09 114.52 39.32 N/A 0 258 Other: 23.16 37.27 29.55 N/A 0 8 Chain A: 8.61 118.94 21.08 N/A 0 1785 Histogram: Values Number of atoms 8.61 - 19.64 1209 19.64 - 30.67 227 30.67 - 41.71 162 41.71 - 52.74 103 52.74 - 63.77 55 63.77 - 74.81 15 74.81 - 85.84 7 85.84 - 96.88 4 96.88 - 107.91 0 107.91 - 118.94 3 =========================== Idealize ADP of riding H ========================== r_work=0.1247 r_free=0.1541 r_work=0.1252 r_free=0.1545 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1252 r_free = 0.1545 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 = 0.1546 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.28 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= 0.1546 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015615 | | target function (ls_wunit_k1) not normalized (work): 1300.698475 | | target function (ls_wunit_k1) not normalized (free): 112.238996 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1265 0.1250 0.1546 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1710 0.1710 0.1770 n_refl.: 87593 remove outliers: r(all,work,free)=0.1710 0.1710 0.1770 n_refl.: 87593 overall B=0.13 to atoms: r(all,work,free)=0.1732 0.1732 0.1786 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1262 0.1249 0.1536 n_refl.: 87593 remove outliers: r(all,work,free)=0.1262 0.1248 0.1536 n_refl.: 87591 ======================== 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 94.79 86 5 0.3623 294.962 278.504 0.676 0.921 0.373 11.894-9.307 99.02 97 4 0.1645 477.968 466.130 0.983 0.922 0.368 9.237-7.194 100.00 213 7 0.1805 390.919 385.829 1.029 0.922 0.340 7.162-5.571 100.00 427 22 0.1747 293.363 287.210 1.002 0.923 0.258 5.546-4.326 100.00 867 58 0.0929 402.715 399.922 1.029 0.924 0.199 4.315-3.360 100.00 1859 96 0.0775 382.984 381.905 1.079 0.925 0.180 3.356-2.611 100.00 3867 181 0.1019 251.601 250.846 1.078 0.927 0.110 2.608-2.026 99.99 8198 413 0.0979 166.788 166.160 1.087 0.931 0.000 2.025-1.573 100.00 17313 902 0.1218 81.451 81.631 1.087 0.936 0.000 1.573-1.221 100.00 36679 1900 0.1659 36.119 35.578 1.061 0.946 0.000 1.221-1.150 99.97 13689 708 0.2365 22.757 21.282 1.015 0.953 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=0.0523 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1248 r_free=0.1536 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 GLN Total number of N/Q/H flips: 3 r_work=0.1252 r_free=0.1537 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1252 r_free=0.1537 | n_water=258 | time (s): 2.490 (total time: 2.490) Filter (dist) r_work=0.1260 r_free=0.1533 | n_water=252 | time (s): 27.910 (total time: 30.400) Filter (q & B) r_work=0.1263 r_free=0.1533 | n_water=249 | time (s): 3.840 (total time: 34.240) Compute maps r_work=0.1263 r_free=0.1533 | n_water=249 | time (s): 1.920 (total time: 36.160) Filter (map) r_work=0.1275 r_free=0.1542 | n_water=237 | time (s): 3.820 (total time: 39.980) Find peaks r_work=0.1275 r_free=0.1542 | n_water=237 | time (s): 0.770 (total time: 40.750) Add new water r_work=0.1429 r_free=0.1702 | n_water=459 | time (s): 3.810 (total time: 44.560) Refine new water occ: r_work=0.1340 r_free=0.1553 adp: r_work=0.1259 r_free=0.1507 occ: r_work=0.1272 r_free=0.1485 adp: r_work=0.1238 r_free=0.1479 occ: r_work=0.1241 r_free=0.1463 adp: r_work=0.1232 r_free=0.1466 ADP+occupancy (water only), MIN, final r_work=0.1232 r_free=0.1466 r_work=0.1232 r_free=0.1466 | n_water=459 | time (s): 77.300 (total time: 121.860) Filter (q & B) r_work=0.1239 r_free=0.1470 | n_water=436 | time (s): 3.870 (total time: 125.730) Filter (dist only) r_work=0.1239 r_free=0.1470 | n_water=436 | time (s): 39.820 (total time: 165.550) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.571589 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1481.803365 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 0.1505 0.0271 0.007 0.9 2.6 0.5 0.0 0 12.786 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.34 15.05 2.71 3.802 23.270 1481.803 0.015 12.01 14.84 2.84 4.267 23.067 1481.803 0.015 Individual atomic B min max mean iso aniso Overall: 8.86 114.15 23.25 2.61 199 1764 Protein: 8.86 114.15 17.70 2.61 0 1519 Water: 11.01 74.23 42.54 N/A 199 237 Other: 20.64 33.33 26.10 N/A 0 8 Chain A: 8.86 114.15 20.40 N/A 0 1764 Chain S: 13.97 74.23 48.49 N/A 199 0 Histogram: Values Number of atoms 8.86 - 19.39 1209 19.39 - 29.92 253 29.92 - 40.44 183 40.44 - 50.97 144 50.97 - 61.50 109 61.50 - 72.03 52 72.03 - 82.56 7 82.56 - 93.09 3 93.09 - 103.62 1 103.62 - 114.15 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1484 r_work=0.1201 r_free=0.1484 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1484 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 = 0.1202 r_free = 0.1478 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.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1202 r_free= 0.1478 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013892 | | target function (ls_wunit_k1) not normalized (work): 1157.108518 | | target function (ls_wunit_k1) not normalized (free): 98.152170 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1202 0.1478 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1601 0.1599 0.1693 n_refl.: 87591 remove outliers: r(all,work,free)=0.1601 0.1599 0.1693 n_refl.: 87591 overall B=0.04 to atoms: r(all,work,free)=0.1608 0.1605 0.1697 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1200 0.1474 n_refl.: 87591 remove outliers: r(all,work,free)=0.1212 0.1199 0.1474 n_refl.: 87588 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3251 291.079 271.628 0.585 1.002 0.354 11.894-9.307 99.02 97 4 0.1537 477.968 474.159 0.915 1.002 0.344 9.237-7.194 100.00 213 7 0.1644 390.919 390.689 0.976 1.003 0.290 7.162-5.571 100.00 427 22 0.1458 293.363 289.454 0.939 1.003 0.229 5.546-4.326 100.00 867 58 0.0823 402.715 400.188 0.956 1.003 0.205 4.315-3.360 100.00 1859 96 0.0716 382.984 381.753 1.002 1.002 0.200 3.356-2.611 100.00 3867 181 0.0964 251.601 250.938 1.009 1.002 0.140 2.608-2.026 99.99 8198 413 0.0963 166.788 166.404 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1186 81.451 81.673 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1616 36.119 35.619 1.016 0.999 0.000 1.221-1.150 99.97 13689 708 0.2342 22.757 21.298 0.975 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0615 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1474 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1474 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1474 | n_water=436 | time (s): 2.210 (total time: 2.210) Filter (dist) r_work=0.1199 r_free=0.1473 | n_water=434 | time (s): 39.000 (total time: 41.210) Filter (q & B) r_work=0.1199 r_free=0.1473 | n_water=434 | time (s): 0.810 (total time: 42.020) Compute maps r_work=0.1199 r_free=0.1473 | n_water=434 | time (s): 1.600 (total time: 43.620) Filter (map) r_work=0.1241 r_free=0.1488 | n_water=292 | time (s): 3.640 (total time: 47.260) Find peaks r_work=0.1241 r_free=0.1488 | n_water=292 | time (s): 0.650 (total time: 47.910) Add new water r_work=0.1365 r_free=0.1617 | n_water=483 | time (s): 3.280 (total time: 51.190) Refine new water occ: r_work=0.1266 r_free=0.1533 adp: r_work=0.1267 r_free=0.1535 occ: r_work=0.1243 r_free=0.1510 adp: r_work=0.1241 r_free=0.1510 occ: r_work=0.1227 r_free=0.1493 adp: r_work=0.1220 r_free=0.1490 ADP+occupancy (water only), MIN, final r_work=0.1220 r_free=0.1490 r_work=0.1220 r_free=0.1490 | n_water=483 | time (s): 161.190 (total time: 212.380) Filter (q & B) r_work=0.1223 r_free=0.1492 | n_water=447 | time (s): 3.130 (total time: 215.510) Filter (dist only) r_work=0.1223 r_free=0.1490 | n_water=446 | time (s): 37.000 (total time: 252.510) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.966402 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.223555 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 0.1229 0.1453 0.0224 0.005 0.9 1.9 0.5 0.0 0 0.983 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.53 2.24 3.625 22.128 50.224 3.726 12.09 13.97 1.88 4.178 21.923 50.224 3.650 Individual atomic B min max mean iso aniso Overall: 9.23 109.19 21.67 2.33 210 1763 Protein: 9.23 109.19 17.20 2.33 0 1519 Water: 11.51 70.76 36.82 N/A 210 236 Other: 19.40 30.11 24.44 N/A 0 8 Chain A: 9.23 109.19 19.91 N/A 0 1763 Chain S: 15.01 68.17 36.46 N/A 210 0 Histogram: Values Number of atoms 9.23 - 19.23 1234 19.23 - 29.22 272 29.22 - 39.22 218 39.22 - 49.22 139 49.22 - 59.21 76 59.21 - 69.21 20 69.21 - 79.20 8 79.20 - 89.20 3 89.20 - 99.20 1 99.20 - 109.19 2 =========================== Idealize ADP of riding H ========================== r_work=0.1209 r_free=0.1397 r_work=0.1210 r_free=0.1398 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1210 r_free = 0.1398 target_work(ml) = 3.650 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1395 target_work(ml) = 3.647 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1202 r_free= 0.1395 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.646651 | | target function (ml) not normalized (work): 303736.813543 | | target function (ml) not normalized (free): 16037.051730 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1211 0.1202 0.1395 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1535 0.1534 0.1579 n_refl.: 87588 remove outliers: r(all,work,free)=0.1535 0.1534 0.1579 n_refl.: 87588 overall B=-0.01 to atoms: r(all,work,free)=0.1533 0.1533 0.1577 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1195 0.1371 n_refl.: 87588 remove outliers: r(all,work,free)=0.1200 0.1191 0.1371 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 88.54 80 5 0.3809 283.023 258.838 0.466 0.999 0.299 11.894-9.307 97.06 95 4 0.2380 481.922 462.717 0.849 1.001 0.283 9.237-7.194 98.64 210 7 0.2390 384.488 383.734 0.942 1.001 0.184 7.162-5.571 100.00 427 22 0.2002 293.363 283.545 0.916 1.002 0.173 5.546-4.326 100.00 867 58 0.1077 402.715 398.620 0.952 1.002 0.162 4.315-3.360 100.00 1859 96 0.0911 382.984 380.258 0.994 1.002 0.157 3.356-2.611 100.00 3867 181 0.1151 251.601 249.768 0.999 1.002 0.120 2.608-2.026 99.99 8198 413 0.1035 166.788 165.876 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1014 81.451 81.635 1.026 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1295 36.119 35.694 1.018 1.000 0.000 1.221-1.150 99.97 13689 708 0.2135 22.757 21.374 0.976 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0274 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1371 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1371 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1371 | n_water=446 | time (s): 1.990 (total time: 1.990) Filter (dist) r_work=0.1192 r_free=0.1371 | n_water=445 | time (s): 38.230 (total time: 40.220) Filter (q & B) r_work=0.1192 r_free=0.1372 | n_water=444 | time (s): 3.290 (total time: 43.510) Compute maps r_work=0.1192 r_free=0.1372 | n_water=444 | time (s): 1.550 (total time: 45.060) Filter (map) r_work=0.1220 r_free=0.1399 | n_water=311 | time (s): 2.690 (total time: 47.750) Find peaks r_work=0.1220 r_free=0.1399 | n_water=311 | time (s): 0.560 (total time: 48.310) Add new water r_work=0.1287 r_free=0.1469 | n_water=480 | time (s): 3.210 (total time: 51.520) Refine new water occ: r_work=0.1213 r_free=0.1385 adp: r_work=0.1213 r_free=0.1389 occ: r_work=0.1196 r_free=0.1363 adp: r_work=0.1195 r_free=0.1369 occ: r_work=0.1184 r_free=0.1346 adp: r_work=0.1180 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1180 r_free=0.1350 r_work=0.1180 r_free=0.1350 | n_water=480 | time (s): 211.540 (total time: 263.060) Filter (q & B) r_work=0.1186 r_free=0.1352 | n_water=449 | time (s): 3.390 (total time: 266.450) Filter (dist only) r_work=0.1186 r_free=0.1351 | n_water=448 | time (s): 35.760 (total time: 302.210) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.885959 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.120549 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 0.1191 0.1351 0.0160 0.006 0.9 1.9 0.5 0.0 0 0.943 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.51 1.60 3.421 21.448 50.121 3.634 11.78 13.44 1.66 3.769 21.340 50.121 3.618 Individual atomic B min max mean iso aniso Overall: 9.24 105.92 21.21 2.18 216 1759 Protein: 9.24 105.92 16.95 2.18 0 1519 Water: 11.54 69.24 35.63 N/A 216 232 Other: 19.08 27.01 22.79 N/A 0 8 Chain A: 9.24 105.92 19.53 N/A 0 1759 Chain S: 15.12 58.60 34.89 N/A 216 0 Histogram: Values Number of atoms 9.24 - 18.91 1232 18.91 - 28.57 286 28.57 - 38.24 213 38.24 - 47.91 131 47.91 - 57.58 77 57.58 - 67.25 22 67.25 - 76.91 9 76.91 - 86.58 2 86.58 - 96.25 1 96.25 - 105.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1178 r_free=0.1344 r_work=0.1179 r_free=0.1344 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1179 r_free = 0.1344 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1174 r_free = 0.1341 target_work(ml) = 3.616 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1174 r_free= 0.1341 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.616288 | | target function (ml) not normalized (work): 301178.916339 | | target function (ml) not normalized (free): 15916.821838 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1182 0.1174 0.1341 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1494 0.1492 0.1545 n_refl.: 87580 remove outliers: r(all,work,free)=0.1494 0.1492 0.1545 n_refl.: 87580 overall B=-0.01 to atoms: r(all,work,free)=0.1492 0.1490 0.1544 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1182 0.1173 0.1342 n_refl.: 87580 remove outliers: r(all,work,free)=0.1178 0.1170 0.1342 n_refl.: 87571 ======================== 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 0.4024 283.023 250.956 0.429 1.000 0.281 11.894-9.307 91.18 89 4 0.2317 464.479 449.579 0.843 1.001 0.260 9.237-7.194 97.27 207 7 0.2456 383.079 377.206 0.915 1.002 0.150 7.162-5.571 100.00 427 22 0.2162 293.363 282.878 0.906 1.002 0.132 5.546-4.326 100.00 867 58 0.1129 402.715 398.309 0.952 1.002 0.130 4.315-3.360 100.00 1859 96 0.0929 382.984 380.497 0.994 1.002 0.117 3.356-2.611 100.00 3867 181 0.1141 251.601 249.776 0.999 1.002 0.043 2.608-2.026 99.99 8198 413 0.1012 166.788 165.877 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.0960 81.451 81.712 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1239 36.119 35.738 1.020 0.998 0.000 1.221-1.150 99.97 13689 708 0.2123 22.757 21.380 0.977 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0302 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1170 r_free=0.1342 After: r_work=0.1170 r_free=0.1342 ================================== NQH flips ================================== r_work=0.1170 r_free=0.1342 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=0.1170 r_free=0.1342 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1170 r_free=0.1342 | n_water=448 | time (s): 1.490 (total time: 1.490) Filter (dist) r_work=0.1170 r_free=0.1342 | n_water=448 | time (s): 36.010 (total time: 37.500) Filter (q & B) r_work=0.1171 r_free=0.1342 | n_water=446 | time (s): 2.660 (total time: 40.160) Compute maps r_work=0.1171 r_free=0.1342 | n_water=446 | time (s): 1.300 (total time: 41.460) Filter (map) r_work=0.1197 r_free=0.1372 | n_water=336 | time (s): 2.450 (total time: 43.910) Find peaks r_work=0.1197 r_free=0.1372 | n_water=336 | time (s): 0.570 (total time: 44.480) Add new water r_work=0.1244 r_free=0.1420 | n_water=492 | time (s): 2.260 (total time: 46.740) Refine new water occ: r_work=0.1183 r_free=0.1357 adp: r_work=0.1183 r_free=0.1360 occ: r_work=0.1171 r_free=0.1340 adp: r_work=0.1170 r_free=0.1343 occ: r_work=0.1162 r_free=0.1326 adp: r_work=0.1159 r_free=0.1329 ADP+occupancy (water only), MIN, final r_work=0.1159 r_free=0.1329 r_work=0.1159 r_free=0.1329 | n_water=492 | time (s): 110.130 (total time: 156.870) Filter (q & B) r_work=0.1167 r_free=0.1336 | n_water=455 | time (s): 2.710 (total time: 159.580) Filter (dist only) r_work=0.1167 r_free=0.1333 | n_water=453 | time (s): 40.550 (total time: 200.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.996873 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 36.594367 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 0.1180 0.1342 0.0163 0.007 1.0 4.8 0.5 0.0 0 0.998 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.80 13.42 1.63 3.298 21.154 36.594 3.615 11.80 13.39 1.59 3.325 21.135 36.594 3.613 Individual atomic B min max mean iso aniso Overall: 9.26 105.00 21.14 2.12 223 1757 Protein: 9.26 105.00 16.89 2.12 0 1519 Water: 11.53 69.14 35.36 N/A 223 230 Other: 19.25 26.89 22.81 N/A 0 8 Chain A: 9.26 105.00 19.43 N/A 0 1757 Chain S: 15.25 58.93 34.62 N/A 223 0 Histogram: Values Number of atoms 9.26 - 18.83 1230 18.83 - 28.41 291 28.41 - 37.98 209 37.98 - 47.56 141 47.56 - 57.13 71 57.13 - 66.71 24 66.71 - 76.28 9 76.28 - 85.85 2 85.85 - 95.43 1 95.43 - 105.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1180 r_free=0.1339 r_work=0.1180 r_free=0.1339 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1180 r_free = 0.1339 target_work(ml) = 3.613 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1179 r_free = 0.1338 target_work(ml) = 3.612 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87571 (all), 4.91 % free)------------| | | | r_work= 0.1179 r_free= 0.1338 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.612108 | | target function (ml) not normalized (work): 300798.274493 | | target function (ml) not normalized (free): 15885.658676 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2913 171 0.1358 0.1304 5.6435 5.5332| | 2: 3.57 - 2.84 1.00 2888 124 0.1082 0.1413 5.1514 5.247| | 3: 2.83 - 2.48 1.00 2820 163 0.1199 0.1316 4.9599 5.0095| | 4: 2.47 - 2.25 1.00 2825 136 0.1007 0.1090 4.6648 4.7132| | 5: 2.25 - 2.09 1.00 2756 127 0.0988 0.1064 4.6051 4.6702| | 6: 2.09 - 1.97 1.00 2846 113 0.0967 0.1232 4.3312 4.4452| | 7: 1.97 - 1.87 1.00 2787 165 0.0987 0.1173 4.0665 4.1494| | 8: 1.87 - 1.79 1.00 2789 144 0.1015 0.1282 3.9777 4.0946| | 9: 1.79 - 1.72 1.00 2745 138 0.0957 0.1307 3.7107 3.9203| | 10: 1.72 - 1.66 1.00 2831 160 0.1005 0.1233 3.6297 3.7461| | 11: 1.66 - 1.61 1.00 2712 147 0.0972 0.1071 3.5639 3.5952| | 12: 1.61 - 1.56 1.00 2773 144 0.0922 0.1128 3.3455 3.4586| | 13: 1.56 - 1.52 1.00 2745 130 0.0982 0.1031 3.3367 3.413| | 14: 1.52 - 1.48 1.00 2803 134 0.0992 0.1121 3.2588 3.3392| | 15: 1.48 - 1.45 1.00 2738 128 0.1011 0.1339 3.1655 3.3143| | 16: 1.45 - 1.42 1.00 2756 161 0.1069 0.1243 3.1499 3.2329| | 17: 1.42 - 1.39 1.00 2785 139 0.1123 0.1293 3.116 3.2322| | 18: 1.39 - 1.36 1.00 2741 179 0.1164 0.1407 3.0877 3.2804| | 19: 1.36 - 1.34 1.00 2807 134 0.1219 0.1558 3.0902 3.2659| | 20: 1.34 - 1.32 1.00 2696 147 0.1321 0.1478 3.086 3.131| | 21: 1.32 - 1.30 1.00 2785 112 0.1415 0.1640 3.0855 3.1693| | 22: 1.29 - 1.27 1.00 2704 152 0.1475 0.1917 3.0847 3.2813| | 23: 1.27 - 1.26 1.00 2802 156 0.1588 0.1844 3.1066 3.2094| | 24: 1.26 - 1.24 1.00 2744 132 0.1637 0.1778 3.0978 3.1912| | 25: 1.24 - 1.22 1.00 2733 148 0.1805 0.2333 3.1106 3.2978| | 26: 1.22 - 1.21 1.00 2727 135 0.1867 0.1789 3.1258 3.2001| | 27: 1.21 - 1.19 1.00 2814 148 0.2012 0.2079 3.1412 3.138| | 28: 1.19 - 1.18 1.00 2671 147 0.2150 0.2299 3.1393 3.151| | 29: 1.18 - 1.16 1.00 2800 134 0.2226 0.2345 3.1291 3.2215| | 30: 1.16 - 1.15 1.00 2739 148 0.2383 0.2516 3.1176 3.1719| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2913 171 0.95 8.34 1.00 0.97 5458.48| | 2: 3.57 - 2.84 2888 124 0.93 12.24 1.01 0.97 5458.48| | 3: 2.83 - 2.48 2820 163 0.90 16.36 0.99 0.97 4591.00| | 4: 2.47 - 2.25 2825 136 0.92 13.72 1.00 0.98 2354.03| | 5: 2.25 - 2.09 2756 127 0.90 15.89 1.01 0.98 2354.03| | 6: 2.09 - 1.97 2846 113 0.92 13.02 1.02 0.97 1410.47| | 7: 1.97 - 1.87 2787 165 0.94 10.62 1.02 0.97 605.75| | 8: 1.87 - 1.79 2789 144 0.91 14.18 0.99 0.97 605.75| | 9: 1.79 - 1.72 2745 138 0.94 11.28 0.98 0.97 332.67| | 10: 1.72 - 1.66 2831 160 0.93 12.19 0.98 0.97 277.98| | 11: 1.66 - 1.61 2712 147 0.93 12.80 0.98 0.97 265.26| | 12: 1.61 - 1.56 2773 144 0.95 9.39 0.99 0.97 145.31| | 13: 1.56 - 1.52 2745 130 0.94 11.01 1.02 0.97 145.31| | 14: 1.52 - 1.48 2803 134 0.94 11.19 1.02 0.97 129.92| | 15: 1.48 - 1.45 2738 128 0.95 10.35 1.01 0.98 101.73| | 16: 1.45 - 1.42 2756 161 0.94 11.51 1.01 0.98 101.73| | 17: 1.42 - 1.39 2785 139 0.95 11.33 1.01 0.98 92.20| | 18: 1.39 - 1.36 2741 179 0.94 11.74 1.01 0.98 86.68| | 19: 1.36 - 1.34 2807 134 0.94 12.24 1.00 0.98 86.68| | 20: 1.34 - 1.32 2696 147 0.94 12.39 0.99 0.96 81.86| | 21: 1.32 - 1.30 2785 112 0.94 13.36 0.98 0.96 81.52| | 22: 1.29 - 1.27 2704 152 0.93 13.86 0.98 0.96 81.71| | 23: 1.27 - 1.26 2802 156 0.92 14.83 0.97 0.95 82.66| | 24: 1.26 - 1.24 2744 132 0.92 14.93 0.97 0.95 82.66| | 25: 1.24 - 1.22 2733 148 0.91 16.36 0.96 0.94 84.15| | 26: 1.22 - 1.21 2727 135 0.90 18.08 1.02 0.93 85.80| | 27: 1.21 - 1.19 2814 148 0.89 18.69 1.02 0.93 85.80| | 28: 1.19 - 1.18 2671 147 0.88 20.17 1.01 0.93 89.01| | 29: 1.18 - 1.16 2800 134 0.88 20.50 0.99 0.93 90.22| | 30: 1.16 - 1.15 2739 148 0.86 21.94 0.98 0.93 90.22| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 81.52 max = 5458.48 mean = 871.73| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.94 mean = 13.80| |phase err.(test): min = 0.00 max = 89.19 mean = 13.88| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1186 0.1179 0.1338 n_refl.: 87571 re-set all scales: r(all,work,free)=0.1493 0.1492 0.1539 n_refl.: 87571 remove outliers: r(all,work,free)=0.1493 0.1492 0.1539 n_refl.: 87571 overall B=-0.01 to atoms: r(all,work,free)=0.1491 0.1490 0.1538 n_refl.: 87571 bulk-solvent and scaling: r(all,work,free)=0.1187 0.1179 0.1341 n_refl.: 87571 remove outliers: r(all,work,free)=0.1187 0.1179 0.1341 n_refl.: 87570 ======================== 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 0.4095 283.023 249.003 0.418 1.000 0.287 11.894-9.307 90.20 88 4 0.2276 464.973 449.506 0.833 1.002 0.208 9.237-7.194 97.27 207 7 0.2427 383.079 377.268 0.912 1.002 0.151 7.162-5.571 100.00 427 22 0.2114 293.363 283.730 0.902 1.002 0.128 5.546-4.326 100.00 867 58 0.1158 402.715 398.646 0.955 1.002 0.123 4.315-3.360 100.00 1859 96 0.0950 382.984 380.393 0.996 1.002 0.120 3.356-2.611 100.00 3867 181 0.1150 251.601 249.798 0.999 1.002 0.110 2.608-2.026 99.99 8198 413 0.1027 166.788 165.877 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0975 81.451 81.716 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1232 36.119 35.747 1.021 0.997 0.000 1.221-1.150 99.97 13689 708 0.2123 22.757 21.380 0.979 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0261 ================= 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 : 0.2608 0.1920 0.083 5.417 8.8 119.3 19.9 258 0.000 1_bss: 0.1637 0.1754 0.083 5.417 9.1 119.5 20.1 258 0.000 1_settarget: 0.1637 0.1754 0.083 5.417 9.1 119.5 20.1 258 0.000 1_nqh: 0.1644 0.1766 0.083 5.417 9.1 119.5 20.1 258 0.003 1_weight: 0.1644 0.1766 0.083 5.417 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1210 0.1466 0.008 0.978 9.1 119.5 20.1 258 0.123 1_adp: 0.1247 0.1541 0.008 0.978 8.6 118.9 21.1 258 0.123 1_regHadp: 0.1252 0.1545 0.008 0.978 8.6 118.9 21.1 258 0.123 1_occ: 0.1250 0.1546 0.008 0.978 8.6 118.9 21.1 258 0.123 2_bss: 0.1248 0.1536 0.008 0.978 8.7 119.1 21.2 258 0.123 2_settarget: 0.1248 0.1536 0.008 0.978 8.7 119.1 21.2 258 0.123 2_updatecdl: 0.1248 0.1536 0.008 0.970 8.7 119.1 21.2 258 0.123 2_nqh: 0.1252 0.1537 0.008 0.970 8.7 119.1 21.2 258 0.126 2_sol: 0.1239 0.1470 0.008 0.970 8.7 119.1 23.6 436 n/a 2_weight: 0.1239 0.1470 0.008 0.970 8.7 119.1 23.6 436 n/a 2_xyzrec: 0.1234 0.1505 0.007 0.872 8.7 119.1 23.6 436 n/a 2_adp: 0.1201 0.1484 0.007 0.872 8.9 114.1 23.3 436 n/a 2_regHadp: 0.1201 0.1484 0.007 0.872 8.9 114.1 23.3 436 n/a 2_occ: 0.1202 0.1478 0.007 0.872 8.9 114.1 23.3 436 n/a 3_bss: 0.1199 0.1474 0.007 0.872 8.9 114.2 23.3 436 n/a 3_settarget: 0.1199 0.1474 0.007 0.872 8.9 114.2 23.3 436 n/a 3_updatecdl: 0.1199 0.1474 0.007 0.873 8.9 114.2 23.3 436 n/a 3_nqh: 0.1199 0.1474 0.007 0.873 8.9 114.2 23.3 436 n/a 3_sol: 0.1223 0.1490 0.007 0.873 8.9 114.2 22.0 446 n/a 3_weight: 0.1223 0.1490 0.007 0.873 8.9 114.2 22.0 446 n/a 3_xyzrec: 0.1229 0.1453 0.005 0.913 8.9 114.2 22.0 446 n/a 3_adp: 0.1209 0.1397 0.005 0.913 9.2 109.2 21.7 446 n/a 3_regHadp: 0.1210 0.1398 0.005 0.913 9.2 109.2 21.7 446 n/a 3_occ: 0.1202 0.1395 0.005 0.913 9.2 109.2 21.7 446 n/a 4_bss: 0.1191 0.1371 0.005 0.913 9.2 109.2 21.7 446 n/a 4_settarget: 0.1191 0.1371 0.005 0.913 9.2 109.2 21.7 446 n/a 4_updatecdl: 0.1191 0.1371 0.005 0.910 9.2 109.2 21.7 446 n/a 4_nqh: 0.1191 0.1371 0.005 0.910 9.2 109.2 21.7 446 n/a 4_sol: 0.1186 0.1351 0.005 0.910 9.2 109.2 21.4 448 n/a 4_weight: 0.1186 0.1351 0.005 0.910 9.2 109.2 21.4 448 n/a 4_xyzrec: 0.1191 0.1351 0.006 0.946 9.2 109.2 21.4 448 n/a 4_adp: 0.1178 0.1344 0.006 0.946 9.2 105.9 21.2 448 n/a 4_regHadp: 0.1179 0.1344 0.006 0.946 9.2 105.9 21.2 448 n/a 4_occ: 0.1174 0.1341 0.006 0.946 9.2 105.9 21.2 448 n/a 5_bss: 0.1170 0.1342 0.006 0.946 9.2 105.9 21.2 448 n/a 5_settarget: 0.1170 0.1342 0.006 0.946 9.2 105.9 21.2 448 n/a 5_updatecdl: 0.1170 0.1342 0.006 0.949 9.2 105.9 21.2 448 n/a 5_setrh: 0.1170 0.1342 0.006 0.949 9.2 105.9 21.2 448 n/a 5_nqh: 0.1170 0.1342 0.006 0.949 9.2 105.9 21.2 448 n/a 5_sol: 0.1167 0.1333 0.006 0.949 9.2 105.9 21.2 453 n/a 5_weight: 0.1167 0.1333 0.006 0.949 9.2 105.9 21.2 453 n/a 5_xyzrec: 0.1180 0.1342 0.007 1.048 9.2 105.9 21.2 453 n/a 5_adp: 0.1180 0.1339 0.007 1.048 9.3 105.0 21.1 453 n/a 5_regHadp: 0.1180 0.1339 0.007 1.048 9.3 105.0 21.1 453 n/a 5_occ: 0.1179 0.1338 0.007 1.048 9.3 105.0 21.1 453 n/a end: 0.1179 0.1341 0.007 1.048 9.2 105.0 21.1 453 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_4735076_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_4735076_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8800 Refinement macro-cycles (run) : 3285.7000 Write final files (write_after_run_outputs) : 70.6600 Total : 3361.2400 Total CPU time: 56.64 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:07:33 PST -0800 (1735452453.02 s) Start R-work = 0.1637, R-free = 0.1754 Final R-work = 0.1179, R-free = 0.1341 =============================================================================== Job complete usr+sys time: 3519.75 seconds wall clock time: 63 minutes 7.07 seconds (3787.07 seconds total)