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_2731660.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" 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2731660.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2731660.pdb" } 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 1 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: 2.37, per 1000 atoms: 0.70 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: 0.86 Conformation dependent library (CDL) restraints added in 328.9 milliseconds Time building geometry restraints manager: 0.83 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: 420 0.89 - 1.15: 1201 1.15 - 1.41: 598 1.41 - 1.66: 895 1.66 - 1.92: 39 Bond restraints: 3153 Sorted by residual: bond pdb=" N ATYR A 67 " pdb=" CA ATYR A 67 " ideal model delta sigma weight residual 1.455 1.217 0.238 1.21e-02 6.83e+03 3.86e+02 bond pdb=" CA GLU A 176 " pdb=" C GLU A 176 " ideal model delta sigma weight residual 1.524 1.762 -0.238 1.27e-02 6.20e+03 3.52e+02 bond pdb=" C ILE A 91 " pdb=" O ILE A 91 " ideal model delta sigma weight residual 1.237 1.032 0.205 1.14e-02 7.69e+03 3.24e+02 bond pdb=" C BGLU A 90 " pdb=" O BGLU A 90 " ideal model delta sigma weight residual 1.237 1.026 0.210 1.17e-02 7.31e+03 3.23e+02 bond pdb=" N LEU A 166 " pdb=" CA LEU A 166 " ideal model delta sigma weight residual 1.459 1.245 0.214 1.28e-02 6.10e+03 2.80e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.20: 2852 4.20 - 8.39: 1891 8.39 - 12.58: 799 12.58 - 16.78: 204 16.78 - 20.97: 31 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O HIS A 126 " pdb=" C HIS A 126 " pdb=" N PRO A 127 " ideal model delta sigma weight residual 121.30 106.14 15.16 1.03e+00 9.43e-01 2.17e+02 angle pdb=" CA ILE A 9 " pdb=" C ILE A 9 " pdb=" O ILE A 9 " ideal model delta sigma weight residual 120.53 135.60 -15.07 1.07e+00 8.73e-01 1.98e+02 angle pdb=" CA THR A 19 " pdb=" C THR A 19 " pdb=" O THR A 19 " ideal model delta sigma weight residual 120.56 137.52 -16.96 1.21e+00 6.83e-01 1.96e+02 angle pdb=" O GLU A 176 " pdb=" C GLU A 176 " pdb=" N VAL A 177 " ideal model delta sigma weight residual 122.07 136.33 -14.26 1.03e+00 9.43e-01 1.92e+02 angle pdb=" O SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " ideal model delta sigma weight residual 123.26 108.99 14.27 1.05e+00 9.07e-01 1.85e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 943 17.51 - 35.02: 119 35.02 - 52.53: 31 52.53 - 70.04: 16 70.04 - 87.55: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA MET A 133 " pdb=" C MET A 133 " pdb=" N MET A 134 " pdb=" CA MET A 134 " ideal model delta harmonic sigma weight residual -180.00 -157.77 -22.23 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CG PHE A 119 " pdb=" CD1 PHE A 119 " pdb=" CE1 PHE A 119 " pdb=" HE1 PHE A 119 " ideal model delta harmonic sigma weight residual -180.00 -159.94 -20.06 0 5.00e+00 4.00e-02 1.61e+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 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.217: 92 0.217 - 0.432: 85 0.432 - 0.647: 36 0.647 - 0.862: 23 0.862 - 1.077: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 33 " pdb=" CA VAL A 33 " pdb=" CG1 VAL A 33 " pdb=" CG2 VAL A 33 " both_signs ideal model delta sigma weight residual False -2.63 -1.55 -1.08 2.00e-01 2.50e+01 2.90e+01 chirality pdb=" CA LEU A 151 " pdb=" N LEU A 151 " pdb=" C LEU A 151 " pdb=" CB LEU A 151 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.14e+01 chirality pdb=" CB VAL A 169 " pdb=" CA VAL A 169 " pdb=" CG1 VAL A 169 " pdb=" CG2 VAL A 169 " both_signs ideal model delta sigma weight residual False -2.63 -1.71 -0.92 2.00e-01 2.50e+01 2.12e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.107 2.00e-02 2.50e+03 7.43e-02 1.66e+02 pdb=" CG TYR A 141 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.098 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.081 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.133 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.027 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.040 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.042 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " -0.016 9.50e-02 1.11e+02 7.27e-02 1.18e+02 pdb=" NE ARG A 5 " -0.075 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " 0.149 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " -0.104 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " 0.057 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " 0.033 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " 0.016 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " -0.014 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.032 2.00e-02 2.50e+03 5.88e-02 1.04e+02 pdb=" CG PHE A 162 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.088 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.052 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.014 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.077 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.078 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.115 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.36: 1314 2.36 - 2.92: 8268 2.92 - 3.48: 10480 3.48 - 4.04: 15127 4.04 - 4.60: 21440 Nonbonded interactions: 56629 Sorted by model distance: nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.794 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.836 2.100 nonbonded pdb=" HG2 LYS A 12 " pdb=" HZ2 LYS A 12 " model vdw 1.838 2.270 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.842 2.100 nonbonded pdb=" H ALA A 104 " pdb=" O ALEU A 153 " model vdw 1.846 2.450 ... (remaining 56624 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_2731660_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= 0.2610 r_free= 0.1920 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788486 | | target function (ml) not normalized (work): 232297.590165 | | target function (ml) not normalized (free): 11803.691513 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3022 0.2050 7.1285 4.9389| | 2: 3.57 - 2.84 1.00 2876 122 0.2441 0.1764 4.3388 4.3345| | 3: 2.84 - 2.48 1.00 2833 165 0.2370 0.1675 4.1222 4.1577| | 4: 2.47 - 2.25 1.00 2825 136 0.2355 0.1469 3.8284 3.8534| | 5: 2.25 - 2.09 1.00 2756 127 0.2479 0.1508 3.7943 3.8169| | 6: 2.09 - 1.97 1.00 2846 113 0.2547 0.1702 3.4511 3.5287| | 7: 1.97 - 1.87 1.00 2787 165 0.2505 0.1887 3.1238 3.2213| | 8: 1.87 - 1.79 1.00 2789 144 0.2469 0.1784 3.064 3.1068| | 9: 1.79 - 1.72 1.00 2745 138 0.2442 0.1751 2.8863 2.9113| | 10: 1.72 - 1.66 1.00 2789 158 0.2430 0.2172 2.8045 2.9639| | 11: 1.66 - 1.61 1.00 2740 147 0.2490 0.1680 2.7498 2.7047| | 12: 1.61 - 1.56 1.00 2787 146 0.2529 0.2024 2.6222 2.6696| | 13: 1.56 - 1.52 1.00 2745 130 0.2535 0.1811 2.5635 2.5734| | 14: 1.52 - 1.48 1.00 2803 134 0.2569 0.1943 2.4984 2.5026| | 15: 1.48 - 1.45 1.00 2738 128 0.2624 0.2203 2.4279 2.5398| | 16: 1.45 - 1.42 1.00 2756 161 0.2688 0.2196 2.3747 2.4101| | 17: 1.42 - 1.39 1.00 2785 139 0.2697 0.2038 2.3196 2.3739| | 18: 1.39 - 1.36 1.00 2741 179 0.2697 0.2092 2.2665 2.3127| | 19: 1.36 - 1.34 1.00 2807 134 0.2648 0.2125 2.2193 2.2324| | 20: 1.34 - 1.32 1.00 2696 147 0.2711 0.2254 2.1853 2.2159| | 21: 1.32 - 1.30 1.00 2785 112 0.2723 0.2267 2.1731 2.2076| | 22: 1.29 - 1.27 1.00 2704 152 0.2684 0.2570 2.1291 2.2044| | 23: 1.27 - 1.26 1.00 2802 156 0.2770 0.2391 2.1097 2.1372| | 24: 1.26 - 1.24 1.00 2744 132 0.2749 0.2599 2.0698 2.184| | 25: 1.24 - 1.22 1.00 2734 148 0.2859 0.2485 2.0441 2.0775| | 26: 1.22 - 1.21 1.00 2727 135 0.2902 0.2296 2.0255 2.0497| | 27: 1.21 - 1.19 1.00 2814 148 0.2971 0.2632 2.0028 2.0375| | 28: 1.19 - 1.18 1.00 2671 147 0.2958 0.2683 1.975 1.9699| | 29: 1.18 - 1.16 1.00 2800 134 0.3005 0.2905 1.9614 2.0769| | 30: 1.16 - 1.15 1.00 2740 148 0.3084 0.2852 1.935 1.9665| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 18.64 0.76 0.23 1452.67| | 2: 3.57 - 2.84 2876 122 0.81 25.75 1.27 0.23 1452.67| | 3: 2.84 - 2.48 2833 165 0.74 31.68 1.24 0.24 1204.89| | 4: 2.47 - 2.25 2825 136 0.81 25.28 1.26 0.25 561.85| | 5: 2.25 - 2.09 2756 127 0.77 29.08 1.28 0.25 561.85| | 6: 2.09 - 1.97 2846 113 0.84 22.42 1.29 0.25 307.65| | 7: 1.97 - 1.87 2787 165 0.90 16.42 1.28 0.26 90.85| | 8: 1.87 - 1.79 2789 144 0.86 21.06 1.25 0.26 90.85| | 9: 1.79 - 1.72 2745 138 0.88 18.62 1.24 0.26 54.56| | 10: 1.72 - 1.66 2789 158 0.87 19.83 1.22 0.26 47.29| | 11: 1.66 - 1.61 2740 147 0.86 20.81 1.24 0.26 45.57| | 12: 1.61 - 1.56 2787 146 0.89 17.97 1.23 0.25 28.12| | 13: 1.56 - 1.52 2745 130 0.87 19.88 1.23 0.25 28.12| | 14: 1.52 - 1.48 2803 134 0.87 20.09 1.24 0.25 25.17| | 15: 1.48 - 1.45 2738 128 0.87 19.66 1.24 0.25 19.76| | 16: 1.45 - 1.42 2756 161 0.86 20.96 1.25 0.25 19.76| | 17: 1.42 - 1.39 2785 139 0.87 20.08 1.25 0.25 16.83| | 18: 1.39 - 1.36 2741 179 0.87 20.56 1.24 0.25 15.13| | 19: 1.36 - 1.34 2807 134 0.86 21.47 1.22 0.25 15.13| | 20: 1.34 - 1.32 2696 147 0.87 20.68 1.22 0.25 12.75| | 21: 1.32 - 1.30 2785 112 0.86 21.65 1.20 0.25 12.58| | 22: 1.29 - 1.27 2704 152 0.86 21.83 1.21 0.24 12.33| | 23: 1.27 - 1.26 2802 156 0.86 21.97 1.21 0.24 11.05| | 24: 1.26 - 1.24 2744 132 0.85 22.89 1.20 0.24 11.05| | 25: 1.24 - 1.22 2734 148 0.84 23.89 1.20 0.24 10.62| | 26: 1.22 - 1.21 2727 135 0.84 24.14 1.21 0.23 10.15| | 27: 1.21 - 1.19 2814 148 0.83 25.23 1.21 0.23 10.15| | 28: 1.19 - 1.18 2671 147 0.82 25.80 1.18 0.23 9.70| | 29: 1.18 - 1.16 2800 134 0.81 26.54 1.17 0.23 9.53| | 30: 1.16 - 1.15 2740 148 0.80 28.01 1.16 0.23 9.53| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 9.53 max = 1452.67 mean = 211.05| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 22.43| |phase err.(test): min = 0.00 max = 89.96 mean = 22.30| |-----------------------------------------------------------------------------| ----------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 : 0.082 0.238 1557 Z= 5.523 Angle : 5.295 17.793 2118 Z= 3.754 Chirality : 0.405 1.077 243 Planarity : 0.033 0.101 284 Dihedral : 13.758 87.555 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.86 % Allowed : 1.86 % Favored : 96.27 % Cbeta Deviations : 38.92 % 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: -2.42 (0.47), residues: 224 helix: -2.39 (0.38), residues: 109 sheet: -0.53 (0.97), residues: 28 loop : -0.54 (0.57), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.142 0.025 ARG A 5 TYR 0.109 0.052 TYR A 141 PHE 0.088 0.033 PHE A 119 HIS 0.058 0.025 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= 0.2610 r_free= 0.1920 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788486 | | target function (ml) not normalized (work): 232297.590165 | | target function (ml) not normalized (free): 11803.691513 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2567 0.2611 0.1921 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2567 0.2611 0.1921 n_refl.: 87602 remove outliers: r(all,work,free)=0.1976 0.1981 0.1921 n_refl.: 87594 overall B=0.14 to atoms: r(all,work,free)=0.1993 0.1998 0.1930 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1639 0.1633 0.1748 n_refl.: 87594 remove outliers: r(all,work,free)=0.1638 0.1632 0.1748 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 0.3850 386.571 356.797 0.667 1.002 0.401 11.894-9.307 99.02 97 4 0.1764 614.050 595.842 0.934 1.003 0.380 9.237-7.194 100.00 213 7 0.2139 502.217 492.264 0.969 1.003 0.352 7.162-5.571 100.00 427 22 0.2255 376.886 364.096 0.931 1.003 0.290 5.546-4.326 100.00 867 58 0.1271 517.371 511.482 0.967 1.003 0.229 4.315-3.360 100.00 1859 96 0.1130 492.024 487.748 1.008 1.003 0.209 3.356-2.611 100.00 3867 181 0.1442 323.234 319.929 1.002 1.003 0.100 2.608-2.026 99.99 8198 413 0.1359 214.275 211.917 1.010 1.002 0.000 2.025-1.573 100.00 17313 902 0.1641 104.641 103.928 1.012 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2051 46.402 45.145 1.005 0.997 0.000 1.221-1.150 99.97 13689 708 0.2571 29.236 27.053 0.978 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0531 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1632 r_free=0.1748 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1637 r_free=0.1755 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.276246 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2030.578479 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 0.1211 0.1460 0.0249 0.007 0.9 1.0 0.5 0.0 0 12.138 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 14.60 2.49 3.013 18.995 2030.578 0.017 12.40 15.32 2.93 3.238 19.515 2030.578 0.016 Individual atomic B min max mean iso aniso Overall: 8.45 118.56 21.01 2.88 0 1785 Protein: 8.45 118.56 17.87 2.88 0 1519 Water: 11.03 114.56 39.21 N/A 0 258 Other: 22.78 36.32 29.10 N/A 0 8 Chain A: 8.45 118.56 21.01 N/A 0 1785 Histogram: Values Number of atoms 8.45 - 19.46 1208 19.46 - 30.47 228 30.47 - 41.48 163 41.48 - 52.50 103 52.50 - 63.51 53 63.51 - 74.52 16 74.52 - 85.53 7 85.53 - 96.54 4 96.54 - 107.55 0 107.55 - 118.56 3 =========================== Idealize ADP of riding H ========================== r_work=0.1240 r_free=0.1532 r_work=0.1244 r_free=0.1536 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1244 r_free = 0.1536 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 = 0.1244 r_free = 0.1538 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.24 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= 0.1244 r_free= 0.1538 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015484 | | target function (ls_wunit_k1) not normalized (work): 1289.809944 | | target function (ls_wunit_k1) not normalized (free): 113.738837 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1259 0.1244 0.1538 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1697 0.1696 0.1768 n_refl.: 87593 remove outliers: r(all,work,free)=0.1697 0.1696 0.1768 n_refl.: 87593 overall B=0.14 to atoms: r(all,work,free)=0.1720 0.1719 0.1784 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1258 0.1243 0.1535 n_refl.: 87593 remove outliers: r(all,work,free)=0.1258 0.1243 0.1535 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 96.88 88 5 0.3633 302.732 281.182 0.648 1.002 0.393 11.894-9.307 99.02 97 4 0.1640 480.874 468.969 0.906 1.002 0.360 9.237-7.194 100.00 213 7 0.1838 393.296 387.559 0.949 1.003 0.340 7.162-5.571 100.00 427 22 0.1745 295.147 289.741 0.920 1.003 0.280 5.546-4.326 100.00 867 58 0.0926 405.164 402.411 0.949 1.003 0.204 4.315-3.360 100.00 1859 96 0.0783 385.313 384.243 0.994 1.002 0.190 3.356-2.611 100.00 3867 181 0.1024 253.131 252.493 1.000 1.002 0.052 2.608-2.026 99.99 8198 413 0.0979 167.803 167.213 1.010 1.002 0.000 2.025-1.573 100.00 17313 902 0.1205 81.946 82.132 1.016 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1640 36.338 35.799 1.005 0.999 0.000 1.221-1.150 99.97 13689 708 0.2357 22.896 21.399 0.968 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0541 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1243 r_free=0.1535 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=0.1243 r_free=0.1535 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1243 r_free=0.1535 | n_water=258 | time (s): 2.540 (total time: 2.540) Filter (dist) r_work=0.1253 r_free=0.1535 | n_water=251 | time (s): 27.930 (total time: 30.470) Filter (q & B) r_work=0.1256 r_free=0.1534 | n_water=248 | time (s): 4.030 (total time: 34.500) Compute maps r_work=0.1256 r_free=0.1534 | n_water=248 | time (s): 1.960 (total time: 36.460) Filter (map) r_work=0.1269 r_free=0.1544 | n_water=236 | time (s): 3.980 (total time: 40.440) Find peaks r_work=0.1269 r_free=0.1544 | n_water=236 | time (s): 0.720 (total time: 41.160) Add new water r_work=0.1420 r_free=0.1678 | n_water=452 | time (s): 3.890 (total time: 45.050) Refine new water occ: r_work=0.1330 r_free=0.1550 adp: r_work=0.1251 r_free=0.1506 occ: r_work=0.1264 r_free=0.1497 adp: r_work=0.1230 r_free=0.1487 occ: r_work=0.1233 r_free=0.1474 adp: r_work=0.1223 r_free=0.1477 ADP+occupancy (water only), MIN, final r_work=0.1223 r_free=0.1477 r_work=0.1223 r_free=0.1477 | n_water=452 | time (s): 79.400 (total time: 124.450) Filter (q & B) r_work=0.1229 r_free=0.1486 | n_water=432 | time (s): 3.990 (total time: 128.440) Filter (dist only) r_work=0.1229 r_free=0.1486 | n_water=432 | time (s): 41.650 (total time: 170.090) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.411437 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1575.913962 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 0.1228 0.1520 0.0292 0.007 0.9 1.9 0.5 0.0 0 12.206 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.28 15.20 2.92 3.793 23.191 1575.914 0.015 12.00 14.92 2.93 4.199 23.010 1575.914 0.015 Individual atomic B min max mean iso aniso Overall: 8.72 113.72 23.20 2.61 196 1763 Protein: 8.72 113.72 17.67 2.62 0 1519 Water: 10.72 71.72 42.52 N/A 196 236 Other: 26.25 37.72 31.19 N/A 0 8 Chain A: 8.72 113.72 20.37 N/A 0 1763 Chain S: 16.72 70.64 48.67 N/A 196 0 Histogram: Values Number of atoms 8.72 - 19.22 1204 19.22 - 29.72 251 29.72 - 40.22 189 40.22 - 50.72 133 50.72 - 61.22 115 61.22 - 71.72 56 71.72 - 82.22 5 82.22 - 92.72 3 92.72 - 103.22 1 103.22 - 113.72 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1492 r_work=0.1200 r_free=0.1492 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1492 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1484 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1203 r_free= 0.1484 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014031 | | target function (ls_wunit_k1) not normalized (work): 1168.741706 | | target function (ls_wunit_k1) not normalized (free): 104.478464 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1216 0.1203 0.1484 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1611 0.1607 0.1725 n_refl.: 87593 remove outliers: r(all,work,free)=0.1611 0.1607 0.1725 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1617 0.1612 0.1729 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1199 0.1481 n_refl.: 87593 remove outliers: r(all,work,free)=0.1211 0.1197 0.1481 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 0.3372 298.736 274.006 0.602 1.001 0.370 11.894-9.307 99.02 97 4 0.1482 480.874 476.214 0.919 1.003 0.324 9.237-7.194 100.00 213 7 0.1667 393.296 393.494 0.980 1.003 0.269 7.162-5.571 100.00 427 22 0.1536 295.147 291.990 0.936 1.003 0.234 5.546-4.326 100.00 867 58 0.0851 405.164 402.533 0.958 1.003 0.220 4.315-3.360 100.00 1859 96 0.0718 385.313 384.177 1.001 1.003 0.200 3.356-2.611 100.00 3867 181 0.0955 253.131 252.437 1.009 1.002 0.072 2.608-2.026 99.99 8198 413 0.0958 167.803 167.370 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1178 81.946 82.137 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1610 36.338 35.834 1.017 0.998 0.000 1.221-1.150 99.97 13689 708 0.2340 22.896 21.418 0.978 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0555 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1481 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1481 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1481 | n_water=432 | time (s): 1.970 (total time: 1.970) Filter (dist) r_work=0.1198 r_free=0.1478 | n_water=429 | time (s): 38.690 (total time: 40.660) Filter (q & B) r_work=0.1198 r_free=0.1478 | n_water=429 | time (s): 1.250 (total time: 41.910) Compute maps r_work=0.1198 r_free=0.1478 | n_water=429 | time (s): 1.850 (total time: 43.760) Filter (map) r_work=0.1239 r_free=0.1483 | n_water=290 | time (s): 3.410 (total time: 47.170) Find peaks r_work=0.1239 r_free=0.1483 | n_water=290 | time (s): 0.500 (total time: 47.670) Add new water r_work=0.1374 r_free=0.1628 | n_water=489 | time (s): 3.120 (total time: 50.790) Refine new water occ: r_work=0.1273 r_free=0.1534 adp: r_work=0.1274 r_free=0.1535 occ: r_work=0.1250 r_free=0.1509 adp: r_work=0.1249 r_free=0.1511 occ: r_work=0.1234 r_free=0.1488 adp: r_work=0.1227 r_free=0.1489 ADP+occupancy (water only), MIN, final r_work=0.1227 r_free=0.1489 r_work=0.1227 r_free=0.1489 | n_water=489 | time (s): 180.210 (total time: 231.000) Filter (q & B) r_work=0.1233 r_free=0.1497 | n_water=449 | time (s): 3.230 (total time: 234.230) Filter (dist only) r_work=0.1232 r_free=0.1497 | n_water=448 | time (s): 40.850 (total time: 275.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.027502 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.061394 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 0.1238 0.1466 0.0229 0.006 0.9 1.9 0.5 0.0 0 1.014 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.38 14.66 2.29 3.628 22.117 49.061 3.735 12.26 14.24 1.98 4.045 21.949 49.061 3.666 Individual atomic B min max mean iso aniso Overall: 9.17 109.71 21.70 2.35 215 1760 Protein: 9.17 109.71 17.28 2.35 0 1519 Water: 11.41 70.91 36.54 N/A 215 233 Other: 21.88 33.91 28.51 N/A 0 8 Chain A: 9.17 109.71 19.95 N/A 0 1760 Chain S: 15.19 64.76 36.02 N/A 215 0 Histogram: Values Number of atoms 9.17 - 19.22 1231 19.22 - 29.28 277 29.28 - 39.33 223 39.33 - 49.39 131 49.39 - 59.44 76 59.44 - 69.49 24 69.49 - 79.55 7 79.55 - 89.60 3 89.60 - 99.66 1 99.66 - 109.71 2 =========================== Idealize ADP of riding H ========================== r_work=0.1226 r_free=0.1424 r_work=0.1227 r_free=0.1425 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1227 r_free = 0.1425 target_work(ml) = 3.666 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1221 r_free = 0.1426 target_work(ml) = 3.663 | | occupancies: max = 1.00 min = 0.17 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= 0.1221 r_free= 0.1426 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.663382 | | target function (ml) not normalized (work): 305137.771152 | | target function (ml) not normalized (free): 16110.811223 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1221 0.1426 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1539 0.1538 0.1600 n_refl.: 87590 remove outliers: r(all,work,free)=0.1539 0.1538 0.1600 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1538 0.1536 0.1598 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1218 0.1209 0.1384 n_refl.: 87590 remove outliers: r(all,work,free)=0.1213 0.1205 0.1384 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 90.62 82 5 0.3903 292.840 263.356 0.464 1.000 0.295 11.894-9.307 96.08 94 4 0.2411 479.926 460.212 0.845 1.001 0.277 9.237-7.194 97.73 208 7 0.2424 385.884 385.422 0.940 1.002 0.170 7.162-5.571 100.00 427 22 0.2144 295.147 284.274 0.905 1.002 0.152 5.546-4.326 100.00 867 58 0.1105 405.164 400.706 0.953 1.002 0.150 4.315-3.360 100.00 1859 96 0.0940 385.313 382.671 0.993 1.002 0.150 3.356-2.611 100.00 3867 181 0.1153 253.131 251.241 1.000 1.002 0.067 2.608-2.026 99.99 8198 413 0.1055 167.803 166.836 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1020 81.946 82.092 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1292 36.338 35.904 1.019 0.998 0.000 1.221-1.150 99.97 13689 708 0.2130 22.896 21.493 0.978 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0229 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1205 r_free=0.1384 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1205 r_free=0.1387 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1205 r_free=0.1387 | n_water=448 | time (s): 2.240 (total time: 2.240) Filter (dist) r_work=0.1205 r_free=0.1388 | n_water=446 | time (s): 38.890 (total time: 41.130) Filter (q & B) r_work=0.1205 r_free=0.1388 | n_water=446 | time (s): 1.140 (total time: 42.270) Compute maps r_work=0.1205 r_free=0.1388 | n_water=446 | time (s): 1.600 (total time: 43.870) Filter (map) r_work=0.1232 r_free=0.1395 | n_water=308 | time (s): 3.470 (total time: 47.340) Find peaks r_work=0.1232 r_free=0.1395 | n_water=308 | time (s): 0.660 (total time: 48.000) Add new water r_work=0.1296 r_free=0.1468 | n_water=472 | time (s): 3.320 (total time: 51.320) Refine new water occ: r_work=0.1224 r_free=0.1395 adp: r_work=0.1224 r_free=0.1396 occ: r_work=0.1208 r_free=0.1382 adp: r_work=0.1207 r_free=0.1381 occ: r_work=0.1197 r_free=0.1374 adp: r_work=0.1193 r_free=0.1372 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1372 r_work=0.1193 r_free=0.1372 | n_water=472 | time (s): 228.720 (total time: 280.040) Filter (q & B) r_work=0.1200 r_free=0.1378 | n_water=437 | time (s): 2.790 (total time: 282.830) Filter (dist only) r_work=0.1200 r_free=0.1377 | n_water=436 | time (s): 36.650 (total time: 319.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.985692 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.148424 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 0.1200 0.1389 0.0189 0.006 0.9 1.9 0.5 0.0 0 0.993 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.89 1.89 3.452 21.523 43.148 3.646 11.91 13.83 1.92 3.774 21.408 43.148 3.635 Individual atomic B min max mean iso aniso Overall: 9.21 105.72 21.20 2.18 206 1757 Protein: 9.21 105.72 17.04 2.18 0 1519 Water: 11.40 70.07 35.61 N/A 206 230 Other: 21.85 31.55 27.13 N/A 0 8 Chain A: 9.21 105.72 19.61 N/A 0 1757 Chain S: 15.98 65.13 34.76 N/A 206 0 Histogram: Values Number of atoms 9.21 - 18.86 1235 18.86 - 28.51 270 28.51 - 38.16 214 38.16 - 47.81 137 47.81 - 57.46 64 57.46 - 67.12 28 67.12 - 76.77 10 76.77 - 86.42 2 86.42 - 96.07 1 96.07 - 105.72 2 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1383 r_work=0.1192 r_free=0.1384 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1384 target_work(ml) = 3.636 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1381 target_work(ml) = 3.635 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1188 r_free= 0.1381 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.634515 | | target function (ml) not normalized (work): 302693.330516 | | target function (ml) not normalized (free): 15983.887779 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1188 0.1381 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1503 0.1501 0.1575 n_refl.: 87579 remove outliers: r(all,work,free)=0.1503 0.1501 0.1575 n_refl.: 87579 overall B=-0.01 to atoms: r(all,work,free)=0.1501 0.1498 0.1573 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1188 0.1380 n_refl.: 87579 remove outliers: r(all,work,free)=0.1195 0.1185 0.1380 n_refl.: 87573 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4155 290.809 249.576 0.436 1.001 0.304 11.894-9.307 92.16 90 4 0.2249 483.554 458.123 0.841 1.002 0.290 9.237-7.194 97.73 208 7 0.2482 385.884 379.213 0.913 1.002 0.144 7.162-5.571 100.00 427 22 0.2205 295.147 285.166 0.900 1.002 0.130 5.546-4.326 100.00 867 58 0.1151 405.164 400.611 0.954 1.002 0.130 4.315-3.360 100.00 1859 96 0.0960 385.313 382.885 0.994 1.002 0.130 3.356-2.611 100.00 3867 181 0.1146 253.131 251.321 1.002 1.002 0.090 2.608-2.026 99.99 8198 413 0.1018 167.803 166.945 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0980 81.946 82.228 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1251 36.338 35.965 1.021 0.998 0.000 1.221-1.150 99.97 13689 708 0.2125 22.896 21.521 0.980 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0380 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1185 r_free=0.1381 After: r_work=0.1185 r_free=0.1380 ================================== NQH flips ================================== r_work=0.1185 r_free=0.1380 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=0.1185 r_free=0.1380 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1185 r_free=0.1380 | n_water=436 | time (s): 1.820 (total time: 1.820) Filter (dist) r_work=0.1185 r_free=0.1380 | n_water=436 | time (s): 33.950 (total time: 35.770) Filter (q & B) r_work=0.1186 r_free=0.1381 | n_water=435 | time (s): 3.390 (total time: 39.160) Compute maps r_work=0.1186 r_free=0.1381 | n_water=435 | time (s): 1.430 (total time: 40.590) Filter (map) r_work=0.1210 r_free=0.1387 | n_water=332 | time (s): 3.730 (total time: 44.320) Find peaks r_work=0.1210 r_free=0.1387 | n_water=332 | time (s): 0.550 (total time: 44.870) Add new water r_work=0.1255 r_free=0.1434 | n_water=475 | time (s): 2.530 (total time: 47.400) Refine new water occ: r_work=0.1197 r_free=0.1376 adp: r_work=0.1198 r_free=0.1377 occ: r_work=0.1185 r_free=0.1364 adp: r_work=0.1184 r_free=0.1364 occ: r_work=0.1175 r_free=0.1355 adp: r_work=0.1173 r_free=0.1355 ADP+occupancy (water only), MIN, final r_work=0.1173 r_free=0.1355 r_work=0.1173 r_free=0.1355 | n_water=475 | time (s): 186.230 (total time: 233.630) Filter (q & B) r_work=0.1182 r_free=0.1365 | n_water=435 | time (s): 3.400 (total time: 237.030) Filter (dist only) r_work=0.1182 r_free=0.1364 | n_water=434 | time (s): 38.420 (total time: 275.450) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.279470 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 38.136135 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 0.1367 0.0171 0.007 1.1 4.2 0.5 0.0 0 1.140 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.67 1.71 3.328 21.159 38.136 3.634 12.06 13.70 1.64 3.618 21.057 38.136 3.631 Individual atomic B min max mean iso aniso Overall: 9.25 101.41 20.87 2.02 206 1755 Protein: 9.25 101.41 16.79 2.02 0 1519 Water: 11.53 69.22 35.01 N/A 206 228 Other: 21.72 30.45 26.39 N/A 0 8 Chain A: 9.25 101.41 19.32 N/A 0 1755 Chain S: 15.05 60.31 33.99 N/A 206 0 Histogram: Values Number of atoms 9.25 - 18.46 1223 18.46 - 27.68 274 27.68 - 36.89 215 36.89 - 46.11 138 46.11 - 55.33 72 55.33 - 64.54 22 64.54 - 73.76 12 73.76 - 82.98 2 82.98 - 92.19 1 92.19 - 101.41 2 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1371 r_work=0.1207 r_free=0.1371 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1207 r_free = 0.1371 target_work(ml) = 3.631 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1367 target_work(ml) = 3.630 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87573 (all), 4.91 % free)------------| | | | r_work= 0.1203 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 3.629522 | | target function (ml) not normalized (work): 302255.738645 | | target function (ml) not normalized (free): 15967.806311 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2915 171 0.1417 0.1402 5.6906 5.6341| | 2: 3.57 - 2.84 1.00 2888 124 0.1130 0.1408 5.2135 5.2764| | 3: 2.83 - 2.48 1.00 2820 163 0.1246 0.1346 5.0179 5.0493| | 4: 2.47 - 2.25 1.00 2825 136 0.1035 0.1109 4.7179 4.7551| | 5: 2.25 - 2.09 1.00 2756 127 0.0994 0.1098 4.6564 4.7204| | 6: 2.09 - 1.97 1.00 2846 113 0.0974 0.1200 4.3613 4.4945| | 7: 1.97 - 1.87 1.00 2787 165 0.1001 0.1229 4.0872 4.198| | 8: 1.87 - 1.79 1.00 2789 144 0.1038 0.1263 4.0012 4.095| | 9: 1.79 - 1.72 1.00 2745 138 0.0962 0.1278 3.7224 3.896| | 10: 1.72 - 1.66 1.00 2831 160 0.1002 0.1202 3.6367 3.7609| | 11: 1.66 - 1.61 1.00 2712 147 0.0970 0.1108 3.576 3.6271| | 12: 1.61 - 1.56 1.00 2773 144 0.0922 0.1207 3.3599 3.5109| | 13: 1.56 - 1.52 1.00 2745 130 0.0981 0.1106 3.3488 3.4648| | 14: 1.52 - 1.48 1.00 2803 134 0.0990 0.1127 3.2688 3.3381| | 15: 1.48 - 1.45 1.00 2738 128 0.1014 0.1372 3.1755 3.3475| | 16: 1.45 - 1.42 1.00 2756 161 0.1078 0.1226 3.1619 3.234| | 17: 1.42 - 1.39 1.00 2785 139 0.1130 0.1293 3.124 3.228| | 18: 1.39 - 1.36 1.00 2741 179 0.1157 0.1361 3.0929 3.2585| | 19: 1.36 - 1.34 1.00 2807 134 0.1227 0.1623 3.1007 3.2756| | 20: 1.34 - 1.32 1.00 2696 147 0.1332 0.1495 3.0985 3.1428| | 21: 1.32 - 1.30 1.00 2785 112 0.1425 0.1633 3.0937 3.1676| | 22: 1.29 - 1.27 1.00 2704 152 0.1486 0.1896 3.091 3.2914| | 23: 1.27 - 1.26 1.00 2802 156 0.1575 0.1877 3.1079 3.2157| | 24: 1.26 - 1.24 1.00 2744 132 0.1637 0.1782 3.1017 3.1941| | 25: 1.24 - 1.22 1.00 2733 148 0.1801 0.2314 3.1154 3.2933| | 26: 1.22 - 1.21 1.00 2727 135 0.1854 0.1775 3.1291 3.2041| | 27: 1.21 - 1.19 1.00 2814 148 0.2007 0.2090 3.145 3.1517| | 28: 1.19 - 1.18 1.00 2671 147 0.2146 0.2325 3.146 3.169| | 29: 1.18 - 1.16 1.00 2800 134 0.2220 0.2372 3.1323 3.2278| | 30: 1.16 - 1.15 1.00 2739 148 0.2372 0.2493 3.1197 3.1732| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2915 171 0.94 9.29 1.00 0.97 6385.44| | 2: 3.57 - 2.84 2888 124 0.92 13.46 1.01 0.97 6385.44| | 3: 2.83 - 2.48 2820 163 0.88 17.70 0.98 0.97 5352.68| | 4: 2.47 - 2.25 2825 136 0.91 14.70 1.00 0.98 2689.53| | 5: 2.25 - 2.09 2756 127 0.89 16.93 1.01 0.98 2689.53| | 6: 2.09 - 1.97 2846 113 0.92 13.67 1.02 0.98 1581.19| | 7: 1.97 - 1.87 2787 165 0.94 10.86 1.02 0.98 635.93| | 8: 1.87 - 1.79 2789 144 0.91 14.48 0.99 0.98 635.93| | 9: 1.79 - 1.72 2745 138 0.93 11.46 0.98 0.97 343.69| | 10: 1.72 - 1.66 2831 160 0.93 12.30 0.98 0.97 285.16| | 11: 1.66 - 1.61 2712 147 0.93 12.95 0.98 0.97 272.36| | 12: 1.61 - 1.56 2773 144 0.95 9.63 0.99 0.97 151.62| | 13: 1.56 - 1.52 2745 130 0.94 11.22 1.02 0.97 151.62| | 14: 1.52 - 1.48 2803 134 0.94 11.39 1.02 0.98 135.07| | 15: 1.48 - 1.45 2738 128 0.95 10.51 1.01 0.98 104.76| | 16: 1.45 - 1.42 2756 161 0.94 11.67 1.01 0.98 104.76| | 17: 1.42 - 1.39 2785 139 0.94 11.50 1.01 0.99 94.21| | 18: 1.39 - 1.36 2741 179 0.94 11.74 1.01 0.99 88.11| | 19: 1.36 - 1.34 2807 134 0.94 12.31 1.00 0.99 88.11| | 20: 1.34 - 1.32 2696 147 0.94 12.40 0.99 0.97 82.99| | 21: 1.32 - 1.30 2785 112 0.93 13.41 0.98 0.97 82.63| | 22: 1.29 - 1.27 2704 152 0.93 13.94 0.98 0.96 82.82| | 23: 1.27 - 1.26 2802 156 0.92 14.80 0.97 0.95 83.77| | 24: 1.26 - 1.24 2744 132 0.92 14.98 0.97 0.95 83.77| | 25: 1.24 - 1.22 2733 148 0.91 16.40 0.96 0.94 85.38| | 26: 1.22 - 1.21 2727 135 0.90 18.12 1.02 0.94 87.16| | 27: 1.21 - 1.19 2814 148 0.89 18.77 1.02 0.94 87.16| | 28: 1.19 - 1.18 2671 147 0.88 20.28 1.01 0.93 90.35| | 29: 1.18 - 1.16 2800 134 0.88 20.56 0.99 0.93 91.55| | 30: 1.16 - 1.15 2739 148 0.86 22.00 0.98 0.93 91.55| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 82.63 max = 6385.44 mean = 994.80| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.90 mean = 14.10| |phase err.(test): min = 0.00 max = 89.79 mean = 14.24| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1211 0.1203 0.1367 n_refl.: 87573 re-set all scales: r(all,work,free)=0.1513 0.1513 0.1542 n_refl.: 87573 remove outliers: r(all,work,free)=0.1513 0.1513 0.1542 n_refl.: 87573 overall B=-0.01 to atoms: r(all,work,free)=0.1511 0.1511 0.1540 n_refl.: 87573 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1203 0.1369 n_refl.: 87573 remove outliers: r(all,work,free)=0.1212 0.1203 0.1369 n_refl.: 87573 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4102 290.809 251.970 0.454 1.002 0.324 11.894-9.307 92.16 90 4 0.2282 483.554 467.393 0.871 1.003 0.253 9.237-7.194 97.73 208 7 0.2532 385.884 376.669 0.900 1.003 0.170 7.162-5.571 100.00 427 22 0.2292 295.147 284.124 0.896 1.003 0.138 5.546-4.326 100.00 867 58 0.1193 405.164 400.421 0.956 1.003 0.127 4.315-3.360 100.00 1859 96 0.0995 385.313 382.707 0.995 1.002 0.127 3.356-2.611 100.00 3867 181 0.1200 253.131 250.911 1.000 1.002 0.120 2.608-2.026 99.99 8198 413 0.1048 167.803 166.725 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0984 81.946 82.183 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1233 36.338 35.949 1.021 0.997 0.000 1.221-1.150 99.97 13689 708 0.2113 22.896 21.511 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=-0.0318 ================= 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 : 0.2610 0.1920 0.082 5.295 8.8 119.3 19.9 258 0.000 1_bss: 0.1632 0.1748 0.082 5.295 9.0 119.4 20.0 258 0.000 1_settarget: 0.1632 0.1748 0.082 5.295 9.0 119.4 20.0 258 0.000 1_nqh: 0.1637 0.1755 0.082 5.295 9.0 119.4 20.0 258 0.003 1_weight: 0.1637 0.1755 0.082 5.295 9.0 119.4 20.0 258 0.003 1_xyzrec: 0.1211 0.1460 0.007 0.938 9.0 119.4 20.0 258 0.130 1_adp: 0.1240 0.1532 0.007 0.938 8.5 118.6 21.0 258 0.130 1_regHadp: 0.1244 0.1536 0.007 0.938 8.5 118.6 21.0 258 0.130 1_occ: 0.1244 0.1538 0.007 0.938 8.5 118.6 21.0 258 0.130 2_bss: 0.1243 0.1535 0.007 0.938 8.6 118.7 21.1 258 0.130 2_settarget: 0.1243 0.1535 0.007 0.938 8.6 118.7 21.1 258 0.130 2_updatecdl: 0.1243 0.1535 0.007 0.946 8.6 118.7 21.1 258 0.130 2_nqh: 0.1243 0.1535 0.007 0.946 8.6 118.7 21.1 258 0.130 2_sol: 0.1229 0.1486 0.007 0.946 8.6 118.7 23.5 432 n/a 2_weight: 0.1229 0.1486 0.007 0.946 8.6 118.7 23.5 432 n/a 2_xyzrec: 0.1228 0.1520 0.007 0.866 8.6 118.7 23.5 432 n/a 2_adp: 0.1200 0.1492 0.007 0.866 8.7 113.7 23.2 432 n/a 2_regHadp: 0.1200 0.1492 0.007 0.866 8.7 113.7 23.2 432 n/a 2_occ: 0.1203 0.1484 0.007 0.866 8.7 113.7 23.2 432 n/a 3_bss: 0.1197 0.1481 0.007 0.866 8.8 113.8 23.2 432 n/a 3_settarget: 0.1197 0.1481 0.007 0.866 8.8 113.8 23.2 432 n/a 3_updatecdl: 0.1197 0.1481 0.007 0.866 8.8 113.8 23.2 432 n/a 3_nqh: 0.1197 0.1481 0.007 0.866 8.8 113.8 23.2 432 n/a 3_sol: 0.1232 0.1497 0.007 0.866 8.8 113.8 22.0 448 n/a 3_weight: 0.1232 0.1497 0.007 0.866 8.8 113.8 22.0 448 n/a 3_xyzrec: 0.1238 0.1466 0.006 0.929 8.8 113.8 22.0 448 n/a 3_adp: 0.1226 0.1424 0.006 0.929 9.2 109.7 21.7 448 n/a 3_regHadp: 0.1227 0.1425 0.006 0.929 9.2 109.7 21.7 448 n/a 3_occ: 0.1221 0.1426 0.006 0.929 9.2 109.7 21.7 448 n/a 4_bss: 0.1205 0.1384 0.006 0.929 9.2 109.7 21.7 448 n/a 4_settarget: 0.1205 0.1384 0.006 0.929 9.2 109.7 21.7 448 n/a 4_updatecdl: 0.1205 0.1384 0.006 0.927 9.2 109.7 21.7 448 n/a 4_nqh: 0.1205 0.1387 0.006 0.927 9.2 109.7 21.7 448 n/a 4_sol: 0.1200 0.1377 0.006 0.927 9.2 109.7 21.4 436 n/a 4_weight: 0.1200 0.1377 0.006 0.927 9.2 109.7 21.4 436 n/a 4_xyzrec: 0.1200 0.1389 0.006 0.945 9.2 109.7 21.4 436 n/a 4_adp: 0.1191 0.1383 0.006 0.945 9.2 105.7 21.2 436 n/a 4_regHadp: 0.1192 0.1384 0.006 0.945 9.2 105.7 21.2 436 n/a 4_occ: 0.1188 0.1381 0.006 0.945 9.2 105.7 21.2 436 n/a 5_bss: 0.1185 0.1381 0.006 0.945 9.2 105.7 21.2 436 n/a 5_settarget: 0.1185 0.1381 0.006 0.945 9.2 105.7 21.2 436 n/a 5_updatecdl: 0.1185 0.1381 0.006 0.948 9.2 105.7 21.2 436 n/a 5_setrh: 0.1185 0.1380 0.006 0.948 9.2 105.7 21.2 436 n/a 5_nqh: 0.1185 0.1380 0.006 0.948 9.2 105.7 21.2 436 n/a 5_sol: 0.1182 0.1364 0.006 0.948 9.2 105.7 21.1 434 n/a 5_weight: 0.1182 0.1364 0.006 0.948 9.2 105.7 21.1 434 n/a 5_xyzrec: 0.1197 0.1367 0.007 1.054 9.2 105.7 21.1 434 n/a 5_adp: 0.1206 0.1371 0.007 1.054 9.2 101.4 20.9 434 n/a 5_regHadp: 0.1207 0.1371 0.007 1.054 9.2 101.4 20.9 434 n/a 5_occ: 0.1203 0.1367 0.007 1.054 9.2 101.4 20.9 434 n/a end: 0.1203 0.1369 0.007 1.054 9.2 101.4 20.9 434 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_2731660_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_2731660_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.0600 Refinement macro-cycles (run) : 3549.3100 Write final files (write_after_run_outputs) : 72.9900 Total : 3627.3600 Total CPU time: 61.08 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:59 PST -0800 (1735452719.38 s) Start R-work = 0.1632, R-free = 0.1748 Final R-work = 0.1203, R-free = 0.1369 =============================================================================== Job complete usr+sys time: 3767.21 seconds wall clock time: 67 minutes 14.64 seconds (4034.64 seconds total)