Starting phenix.refine on Sat Dec 28 21:06:34 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6727304.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_6727304.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6727304.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: 2.38, 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: 0.72 Conformation dependent library (CDL) restraints added in 241.5 milliseconds Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.60 - 0.87: 330 0.87 - 1.15: 1271 1.15 - 1.42: 675 1.42 - 1.69: 851 1.69 - 1.96: 26 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 91 " pdb=" CB ILE A 91 " ideal model delta sigma weight residual 1.540 1.756 -0.217 1.11e-02 8.12e+03 3.80e+02 bond pdb=" C ALA A 61 " pdb=" O ALA A 61 " ideal model delta sigma weight residual 1.237 1.459 -0.223 1.19e-02 7.06e+03 3.51e+02 bond pdb=" CA VAL A 177 " pdb=" C VAL A 177 " ideal model delta sigma weight residual 1.523 1.744 -0.221 1.27e-02 6.20e+03 3.03e+02 bond pdb=" CA ILE A 117 " pdb=" CB ILE A 117 " ideal model delta sigma weight residual 1.537 1.336 0.202 1.17e-02 7.31e+03 2.97e+02 bond pdb=" N LYS A 130 " pdb=" CA LYS A 130 " ideal model delta sigma weight residual 1.459 1.261 0.198 1.16e-02 7.43e+03 2.91e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.00: 3270 5.00 - 9.99: 1905 9.99 - 14.98: 523 14.98 - 19.98: 74 19.98 - 24.97: 5 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 157 " pdb=" C GLY A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 121.77 106.55 15.22 1.00e+00 1.00e+00 2.32e+02 angle pdb=" CA PHE A 164 " pdb=" CB PHE A 164 " pdb=" CG PHE A 164 " ideal model delta sigma weight residual 113.80 127.87 -14.07 1.00e+00 1.00e+00 1.98e+02 angle pdb=" O ALA A 104 " pdb=" C ALA A 104 " pdb=" N ILE A 105 " ideal model delta sigma weight residual 123.31 108.07 15.24 1.17e+00 7.31e-01 1.70e+02 angle pdb=" O ILE A 168 " pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 121.80 107.45 14.35 1.13e+00 7.83e-01 1.61e+02 angle pdb=" CA LYS A 89 " pdb=" C LYS A 89 " pdb=" O LYS A 89 " ideal model delta sigma weight residual 120.20 106.35 13.85 1.12e+00 7.97e-01 1.53e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.96: 945 17.96 - 35.91: 117 35.91 - 53.86: 36 53.86 - 71.81: 10 71.81 - 89.76: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: 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 180.00 154.00 26.00 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA ARG A 48 " pdb=" C ARG A 48 " pdb=" N ASP A 49 " pdb=" CA ASP A 49 " ideal model delta harmonic sigma weight residual 180.00 156.53 23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA CYS A 46 " pdb=" C CYS A 46 " pdb=" N SER A 47 " pdb=" CA SER A 47 " ideal model delta harmonic sigma weight residual -180.00 -160.71 -19.29 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.214: 99 0.214 - 0.428: 81 0.428 - 0.641: 46 0.641 - 0.855: 13 0.855 - 1.068: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" C3 ADTT A 201 " pdb=" C2 ADTT A 201 " pdb=" C4 ADTT A 201 " pdb=" O3 ADTT A 201 " both_signs ideal model delta sigma weight residual False 2.56 3.62 -1.07 2.00e-01 2.50e+01 2.85e+01 chirality pdb=" CA LEU A 185 " pdb=" N LEU A 185 " pdb=" C LEU A 185 " pdb=" CB LEU A 185 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.34e+01 chirality pdb=" CA LEU A 112 " pdb=" N LEU A 112 " pdb=" C LEU A 112 " pdb=" CB LEU A 112 " both_signs ideal model delta sigma weight residual False 2.51 1.58 0.93 2.00e-01 2.50e+01 2.18e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.064 2.00e-02 2.50e+03 6.92e-02 1.44e+02 pdb=" CG PHE A 119 " -0.145 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.101 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.060 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.069 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.066 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.039 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.033 2.00e-02 2.50e+03 5.55e-02 9.25e+01 pdb=" CG TYR A 139 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.067 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.083 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.034 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.082 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.013 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.120 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.010 2.00e-02 2.50e+03 5.50e-02 9.07e+01 pdb=" CG PHE A 164 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.069 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.069 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.081 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.030 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.025 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.039 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.065 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.061 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.071 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 990 2.31 - 2.88: 7948 2.88 - 3.45: 10630 3.45 - 4.03: 15219 4.03 - 4.60: 21827 Nonbonded interactions: 56614 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.737 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.796 2.450 nonbonded pdb=" H LYS A 122 " pdb=" OD2 ASP A 149 " model vdw 1.810 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.825 2.100 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.840 2.450 ... (remaining 56609 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_6727304_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2606 r_free= 0.1951 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789777 | | target function (ml) not normalized (work): 232405.150905 | | target function (ml) not normalized (free): 11828.986722 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3038 0.2083 6.993 4.9387| | 2: 3.57 - 2.84 1.00 2876 122 0.2450 0.1985 4.3599 4.3825| | 3: 2.84 - 2.48 1.00 2833 165 0.2319 0.1609 4.1377 4.1638| | 4: 2.47 - 2.25 1.00 2825 136 0.2361 0.1487 3.8498 3.8401| | 5: 2.25 - 2.09 1.00 2756 127 0.2430 0.1604 3.8071 3.8484| | 6: 2.09 - 1.97 1.00 2846 113 0.2574 0.1637 3.4659 3.5521| | 7: 1.97 - 1.87 1.00 2787 165 0.2588 0.1821 3.1459 3.193| | 8: 1.87 - 1.79 1.00 2789 144 0.2512 0.2063 3.062 3.1827| | 9: 1.79 - 1.72 1.00 2745 138 0.2392 0.1985 2.912 2.9608| | 10: 1.72 - 1.66 1.00 2789 158 0.2386 0.1983 2.8056 2.8609| | 11: 1.66 - 1.61 1.00 2740 147 0.2511 0.1684 2.7501 2.7025| | 12: 1.61 - 1.56 1.00 2787 146 0.2527 0.1999 2.6301 2.6688| | 13: 1.56 - 1.52 1.00 2745 130 0.2555 0.1790 2.561 2.5974| | 14: 1.52 - 1.48 1.00 2803 134 0.2582 0.1796 2.513 2.5138| | 15: 1.48 - 1.45 1.00 2738 128 0.2587 0.1860 2.4338 2.39| | 16: 1.45 - 1.42 1.00 2756 161 0.2612 0.2264 2.3761 2.481| | 17: 1.42 - 1.39 1.00 2785 139 0.2694 0.2237 2.3415 2.474| | 18: 1.39 - 1.36 1.00 2741 179 0.2678 0.2188 2.283 2.3077| | 19: 1.36 - 1.34 1.00 2807 134 0.2585 0.2321 2.2393 2.3083| | 20: 1.34 - 1.32 1.00 2696 147 0.2608 0.2292 2.1863 2.2284| | 21: 1.32 - 1.30 1.00 2785 112 0.2670 0.2106 2.1427 2.1581| | 22: 1.29 - 1.27 1.00 2704 152 0.2726 0.2471 2.1346 2.1477| | 23: 1.27 - 1.26 1.00 2802 156 0.2723 0.2593 2.0882 2.2308| | 24: 1.26 - 1.24 1.00 2744 132 0.2766 0.2426 2.0722 2.1208| | 25: 1.24 - 1.22 1.00 2734 148 0.2850 0.2531 2.0288 2.0588| | 26: 1.22 - 1.21 1.00 2727 135 0.2870 0.2381 2.0136 2.1311| | 27: 1.21 - 1.19 1.00 2814 148 0.2954 0.2372 2.0073 1.992| | 28: 1.19 - 1.18 1.00 2671 147 0.2984 0.2876 1.9899 2.0173| | 29: 1.18 - 1.16 1.00 2800 134 0.2920 0.2816 1.9659 2.0491| | 30: 1.16 - 1.15 1.00 2740 148 0.3096 0.2849 1.9443 1.9564| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.20 0.76 0.23 1525.90| | 2: 3.57 - 2.84 2876 122 0.80 26.50 1.28 0.23 1525.90| | 3: 2.84 - 2.48 2833 165 0.74 32.34 1.24 0.24 1265.17| | 4: 2.47 - 2.25 2825 136 0.81 25.90 1.26 0.25 588.52| | 5: 2.25 - 2.09 2756 127 0.77 29.64 1.28 0.25 588.52| | 6: 2.09 - 1.97 2846 113 0.83 23.11 1.30 0.25 321.30| | 7: 1.97 - 1.87 2787 165 0.90 16.92 1.29 0.26 93.40| | 8: 1.87 - 1.79 2789 144 0.85 21.61 1.26 0.26 93.40| | 9: 1.79 - 1.72 2745 138 0.88 18.81 1.23 0.26 56.38| | 10: 1.72 - 1.66 2789 158 0.86 20.24 1.22 0.26 48.96| | 11: 1.66 - 1.61 2740 147 0.85 21.52 1.25 0.26 47.12| | 12: 1.61 - 1.56 2787 146 0.89 17.98 1.23 0.25 28.49| | 13: 1.56 - 1.52 2745 130 0.87 19.83 1.24 0.25 28.49| | 14: 1.52 - 1.48 2803 134 0.87 19.99 1.24 0.25 25.48| | 15: 1.48 - 1.45 2738 128 0.88 19.56 1.23 0.25 19.96| | 16: 1.45 - 1.42 2756 161 0.86 21.02 1.23 0.25 19.96| | 17: 1.42 - 1.39 2785 139 0.87 20.35 1.23 0.25 17.20| | 18: 1.39 - 1.36 2741 179 0.87 20.89 1.22 0.25 15.60| | 19: 1.36 - 1.34 2807 134 0.86 21.59 1.21 0.25 15.60| | 20: 1.34 - 1.32 2696 147 0.87 20.70 1.20 0.25 12.97| | 21: 1.32 - 1.30 2785 112 0.86 21.86 1.20 0.25 12.78| | 22: 1.29 - 1.27 2704 152 0.85 22.31 1.21 0.25 12.51| | 23: 1.27 - 1.26 2802 156 0.86 21.89 1.21 0.24 11.14| | 24: 1.26 - 1.24 2744 132 0.85 22.75 1.20 0.24 11.14| | 25: 1.24 - 1.22 2734 148 0.84 23.80 1.22 0.24 10.63| | 26: 1.22 - 1.21 2727 135 0.84 24.40 1.20 0.23 10.06| | 27: 1.21 - 1.19 2814 148 0.83 24.66 1.20 0.23 10.06| | 28: 1.19 - 1.18 2671 147 0.82 25.87 1.18 0.23 9.63| | 29: 1.18 - 1.16 2800 134 0.82 26.11 1.15 0.22 9.47| | 30: 1.16 - 1.15 2740 148 0.80 28.09 1.14 0.22 9.47| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.47 max = 1525.90 mean = 220.91| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.96 mean = 22.65| |phase err.(test): min = 0.00 max = 89.47 mean = 22.43| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.275 1557 Z= 5.356 Angle : 5.237 16.778 2118 Z= 3.690 Chirality : 0.368 1.068 243 Planarity : 0.032 0.087 284 Dihedral : 14.189 89.760 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 30.27 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.43), residues: 224 helix: -3.42 (0.30), residues: 109 sheet: -2.32 (0.88), residues: 28 loop : -0.61 (0.53), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.057 0.019 ARG A 98 TYR 0.061 0.031 TYR A 141 PHE 0.123 0.036 PHE A 119 HIS 0.033 0.016 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2606 r_free= 0.1951 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789777 | | target function (ml) not normalized (work): 232405.150905 | | target function (ml) not normalized (free): 11828.986722 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2607 0.1952 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2607 0.1952 n_refl.: 87602 remove outliers: r(all,work,free)=0.1980 0.1984 0.1952 n_refl.: 87594 overall B=0.23 to atoms: r(all,work,free)=0.2009 0.2013 0.1969 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1647 0.1640 0.1774 n_refl.: 87594 remove outliers: r(all,work,free)=0.1646 0.1640 0.1774 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 0.3759 386.187 358.160 0.668 1.004 0.397 11.894-9.307 99.02 97 4 0.1800 613.439 592.167 0.923 1.004 0.380 9.237-7.194 100.00 213 7 0.2208 501.717 489.001 0.954 1.005 0.380 7.162-5.571 100.00 427 22 0.2191 376.511 364.315 0.928 1.004 0.329 5.546-4.326 100.00 867 58 0.1274 516.857 511.066 0.962 1.004 0.249 4.315-3.360 100.00 1859 96 0.1151 491.534 487.260 1.002 1.004 0.189 3.356-2.611 100.00 3867 181 0.1449 322.913 319.769 0.996 1.003 0.089 2.608-2.026 99.99 8198 413 0.1354 214.062 211.924 1.004 1.001 0.000 2.025-1.573 100.00 17313 902 0.1660 104.537 103.782 1.015 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2053 46.356 45.052 1.005 0.994 0.000 1.221-1.150 99.97 13689 708 0.2594 29.207 26.928 0.975 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0533 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1640 r_free=0.1774 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN Total number of N/Q/H flips: 2 r_work=0.1643 r_free=0.1772 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.063219 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1995.955070 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 0.1214 0.1469 0.0255 0.007 1.0 1.3 0.5 0.0 0 13.032 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.14 14.69 2.55 3.013 19.091 1995.955 0.017 12.41 15.41 3.00 3.074 19.488 1995.955 0.016 Individual atomic B min max mean iso aniso Overall: 8.55 118.40 20.87 2.88 0 1785 Protein: 8.55 118.40 17.78 2.88 0 1519 Water: 11.04 114.78 38.84 N/A 0 258 Other: 22.54 35.32 28.42 N/A 0 8 Chain A: 8.55 118.40 20.87 N/A 0 1785 Histogram: Values Number of atoms 8.55 - 19.54 1213 19.54 - 30.52 231 30.52 - 41.51 162 41.51 - 52.49 98 52.49 - 63.48 52 63.48 - 74.46 18 74.46 - 85.45 4 85.45 - 96.43 4 96.43 - 107.42 0 107.42 - 118.40 3 =========================== Idealize ADP of riding H ========================== r_work=0.1242 r_free=0.1541 r_work=0.1246 r_free=0.1546 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1246 r_free = 0.1546 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 = 0.1243 r_free = 0.1547 target_work(ls_wunit_k1) = 0.015 | | 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= 0.1243 r_free= 0.1547 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015385 | | target function (ls_wunit_k1) not normalized (work): 1281.545922 | | target function (ls_wunit_k1) not normalized (free): 113.745259 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1258 0.1243 0.1547 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1701 0.1700 0.1773 n_refl.: 87593 remove outliers: r(all,work,free)=0.1701 0.1700 0.1773 n_refl.: 87593 overall B=0.13 to atoms: r(all,work,free)=0.1723 0.1722 0.1788 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1254 0.1239 0.1536 n_refl.: 87593 remove outliers: r(all,work,free)=0.1253 0.1239 0.1536 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3598 298.591 278.025 0.692 0.924 0.380 11.894-9.307 99.02 97 4 0.1639 478.326 467.261 0.985 0.925 0.369 9.237-7.194 100.00 213 7 0.1817 391.212 386.235 1.026 0.925 0.340 7.162-5.571 100.00 427 22 0.1708 293.583 288.286 0.997 0.926 0.263 5.546-4.326 100.00 867 58 0.0922 403.017 400.236 1.028 0.926 0.209 4.315-3.360 100.00 1859 96 0.0772 383.272 382.368 1.075 0.927 0.190 3.356-2.611 100.00 3867 181 0.1017 251.790 251.079 1.077 0.929 0.110 2.608-2.026 99.99 8198 413 0.0974 166.914 166.334 1.083 0.932 0.000 2.025-1.573 100.00 17313 902 0.1200 81.512 81.706 1.086 0.937 0.000 1.573-1.221 100.00 36679 1900 0.1646 36.146 35.607 1.062 0.945 0.000 1.221-1.150 99.97 13689 708 0.2365 22.774 21.302 1.017 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0509 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1239 r_free=0.1536 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN Total number of N/Q/H flips: 1 r_work=0.1240 r_free=0.1537 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1240 r_free=0.1537 | n_water=258 | time (s): 2.580 (total time: 2.580) Filter (dist) r_work=0.1249 r_free=0.1534 | n_water=252 | time (s): 26.640 (total time: 29.220) Filter (q & B) r_work=0.1253 r_free=0.1533 | n_water=249 | time (s): 3.900 (total time: 33.120) Compute maps r_work=0.1253 r_free=0.1533 | n_water=249 | time (s): 1.910 (total time: 35.030) Filter (map) r_work=0.1265 r_free=0.1542 | n_water=237 | time (s): 4.020 (total time: 39.050) Find peaks r_work=0.1265 r_free=0.1542 | n_water=237 | time (s): 0.720 (total time: 39.770) Add new water r_work=0.1421 r_free=0.1690 | n_water=453 | time (s): 3.900 (total time: 43.670) Refine new water occ: r_work=0.1325 r_free=0.1555 adp: r_work=0.1247 r_free=0.1510 occ: r_work=0.1261 r_free=0.1502 adp: r_work=0.1225 r_free=0.1491 occ: r_work=0.1229 r_free=0.1478 adp: r_work=0.1219 r_free=0.1482 ADP+occupancy (water only), MIN, final r_work=0.1219 r_free=0.1482 r_work=0.1219 r_free=0.1482 | n_water=453 | time (s): 91.240 (total time: 134.910) Filter (q & B) r_work=0.1224 r_free=0.1487 | n_water=434 | time (s): 3.950 (total time: 138.860) Filter (dist only) r_work=0.1224 r_free=0.1487 | n_water=434 | time (s): 41.130 (total time: 179.990) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.137845 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1604.603444 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 0.1224 0.1518 0.0295 0.007 0.9 1.3 0.5 0.0 0 12.569 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.24 15.18 2.95 3.768 23.028 1604.603 0.015 11.92 14.92 3.00 4.075 22.874 1604.603 0.015 Individual atomic B min max mean iso aniso Overall: 8.80 114.55 23.07 2.61 197 1764 Protein: 8.80 114.55 17.62 2.61 0 1519 Water: 11.00 72.27 42.04 N/A 197 237 Other: 24.30 36.27 29.36 N/A 0 8 Chain A: 8.80 114.55 20.30 N/A 0 1764 Chain S: 14.58 70.24 47.89 N/A 197 0 Histogram: Values Number of atoms 8.80 - 19.37 1208 19.37 - 29.95 258 29.95 - 40.52 184 40.52 - 51.10 154 51.10 - 61.67 99 61.67 - 72.25 48 72.25 - 82.82 4 82.82 - 93.40 3 93.40 - 103.97 1 103.97 - 114.55 2 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1492 r_work=0.1192 r_free=0.1492 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1492 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 = 0.1196 r_free = 0.1484 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1196 r_free= 0.1484 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013956 | | target function (ls_wunit_k1) not normalized (work): 1162.465214 | | target function (ls_wunit_k1) not normalized (free): 103.043836 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1210 0.1196 0.1484 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1600 0.1594 0.1738 n_refl.: 87592 remove outliers: r(all,work,free)=0.1600 0.1594 0.1738 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1606 0.1600 0.1742 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1194 0.1485 n_refl.: 87592 remove outliers: r(all,work,free)=0.1207 0.1193 0.1485 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3322 294.534 271.037 0.594 1.002 0.360 11.894-9.307 99.02 97 4 0.1564 478.326 474.856 0.920 1.002 0.350 9.237-7.194 100.00 213 7 0.1693 391.212 391.365 0.973 1.002 0.290 7.162-5.571 100.00 427 22 0.1512 293.583 289.595 0.939 1.002 0.234 5.546-4.326 100.00 867 58 0.0849 403.017 400.879 0.958 1.002 0.215 4.315-3.360 100.00 1859 96 0.0705 383.272 382.422 1.002 1.002 0.210 3.356-2.611 100.00 3867 181 0.0962 251.790 250.969 1.010 1.002 0.140 2.608-2.026 99.99 8198 413 0.0954 166.914 166.491 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1173 81.512 81.719 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1601 36.146 35.647 1.017 0.997 0.000 1.221-1.150 99.97 13689 708 0.2327 22.774 21.309 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=0.0597 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1485 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1485 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1485 | n_water=434 | time (s): 2.340 (total time: 2.340) Filter (dist) r_work=0.1193 r_free=0.1485 | n_water=433 | time (s): 40.390 (total time: 42.730) Filter (q & B) r_work=0.1194 r_free=0.1486 | n_water=432 | time (s): 2.670 (total time: 45.400) Compute maps r_work=0.1194 r_free=0.1486 | n_water=432 | time (s): 1.500 (total time: 46.900) Filter (map) r_work=0.1234 r_free=0.1483 | n_water=295 | time (s): 2.630 (total time: 49.530) Find peaks r_work=0.1234 r_free=0.1483 | n_water=295 | time (s): 0.580 (total time: 50.110) Add new water r_work=0.1360 r_free=0.1604 | n_water=483 | time (s): 2.480 (total time: 52.590) Refine new water occ: r_work=0.1257 r_free=0.1512 adp: r_work=0.1258 r_free=0.1513 occ: r_work=0.1234 r_free=0.1493 adp: r_work=0.1232 r_free=0.1493 occ: r_work=0.1218 r_free=0.1482 adp: r_work=0.1212 r_free=0.1478 ADP+occupancy (water only), MIN, final r_work=0.1212 r_free=0.1478 r_work=0.1212 r_free=0.1478 | n_water=483 | time (s): 214.380 (total time: 266.970) Filter (q & B) r_work=0.1216 r_free=0.1479 | n_water=444 | time (s): 2.810 (total time: 269.780) Filter (dist only) r_work=0.1216 r_free=0.1479 | n_water=444 | time (s): 34.350 (total time: 304.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.034913 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 40.199590 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 0.1217 0.1439 0.0221 0.006 0.9 1.6 0.5 0.0 0 1.017 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.17 14.39 2.21 3.614 22.045 40.200 3.714 12.17 13.99 1.82 4.067 21.870 40.200 3.652 Individual atomic B min max mean iso aniso Overall: 9.18 110.07 21.60 2.30 210 1761 Protein: 9.18 110.07 17.21 2.30 0 1519 Water: 11.66 71.42 36.52 N/A 210 234 Other: 20.43 32.41 26.83 N/A 0 8 Chain A: 9.18 110.07 19.86 N/A 0 1761 Chain S: 15.85 64.78 36.24 N/A 210 0 Histogram: Values Number of atoms 9.18 - 19.27 1232 19.27 - 29.36 280 29.36 - 39.45 215 39.45 - 49.54 137 49.54 - 59.63 74 59.63 - 69.72 21 69.72 - 79.80 6 79.80 - 89.89 3 89.89 - 99.98 1 99.98 - 110.07 2 =========================== Idealize ADP of riding H ========================== r_work=0.1217 r_free=0.1399 r_work=0.1218 r_free=0.1400 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1218 r_free = 0.1400 target_work(ml) = 3.652 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1210 r_free = 0.1398 target_work(ml) = 3.649 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1210 r_free= 0.1398 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.649007 | | target function (ml) not normalized (work): 303936.771461 | | target function (ml) not normalized (free): 16050.172614 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1220 0.1210 0.1398 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1542 0.1542 0.1579 n_refl.: 87589 remove outliers: r(all,work,free)=0.1542 0.1542 0.1579 n_refl.: 87589 overall B=-0.00 to atoms: r(all,work,free)=0.1542 0.1541 0.1578 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1211 0.1203 0.1374 n_refl.: 87589 remove outliers: r(all,work,free)=0.1208 0.1200 0.1374 n_refl.: 87582 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3954 291.692 261.997 0.505 1.000 0.354 11.894-9.307 98.04 96 4 0.2285 471.664 466.863 0.868 1.002 0.320 9.237-7.194 98.18 209 7 0.2252 382.766 383.891 0.953 1.002 0.220 7.162-5.571 100.00 427 22 0.1987 293.583 284.758 0.923 1.002 0.178 5.546-4.326 100.00 867 58 0.1076 403.017 398.059 0.962 1.002 0.168 4.315-3.360 100.00 1859 96 0.0923 383.272 380.569 1.003 1.002 0.167 3.356-2.611 100.00 3867 181 0.1158 251.790 249.713 1.008 1.002 0.150 2.608-2.026 99.99 8198 413 0.1065 166.914 165.833 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1025 81.512 81.639 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1295 36.146 35.696 1.028 0.998 0.000 1.221-1.150 99.97 13689 708 0.2132 22.774 21.365 0.985 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0134 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1374 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1374 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1374 | n_water=444 | time (s): 1.770 (total time: 1.770) Filter (dist) r_work=0.1203 r_free=0.1379 | n_water=443 | time (s): 37.910 (total time: 39.680) Filter (q & B) r_work=0.1203 r_free=0.1377 | n_water=441 | time (s): 3.280 (total time: 42.960) Compute maps r_work=0.1203 r_free=0.1377 | n_water=441 | time (s): 1.660 (total time: 44.620) Filter (map) r_work=0.1227 r_free=0.1392 | n_water=317 | time (s): 3.490 (total time: 48.110) Find peaks r_work=0.1227 r_free=0.1392 | n_water=317 | time (s): 0.520 (total time: 48.630) Add new water r_work=0.1309 r_free=0.1463 | n_water=487 | time (s): 3.290 (total time: 51.920) Refine new water occ: r_work=0.1227 r_free=0.1386 adp: r_work=0.1228 r_free=0.1388 occ: r_work=0.1210 r_free=0.1373 adp: r_work=0.1209 r_free=0.1373 occ: r_work=0.1197 r_free=0.1365 adp: r_work=0.1193 r_free=0.1362 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1362 r_work=0.1193 r_free=0.1362 | n_water=487 | time (s): 178.080 (total time: 230.000) Filter (q & B) r_work=0.1198 r_free=0.1363 | n_water=458 | time (s): 2.710 (total time: 232.710) Filter (dist only) r_work=0.1198 r_free=0.1362 | n_water=456 | time (s): 37.360 (total time: 270.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.023904 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.761288 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 0.1369 0.0159 0.006 1.0 1.6 0.5 0.0 0 1.012 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 13.69 1.59 3.418 21.535 45.761 3.640 11.89 13.61 1.72 3.868 21.403 45.761 3.624 Individual atomic B min max mean iso aniso Overall: 9.23 105.13 21.27 2.16 226 1757 Protein: 9.23 105.13 16.90 2.17 0 1519 Water: 11.45 70.07 35.77 N/A 226 230 Other: 20.45 29.37 24.87 N/A 0 8 Chain A: 9.23 105.13 19.44 N/A 0 1757 Chain S: 15.73 64.94 35.52 N/A 226 0 Histogram: Values Number of atoms 9.23 - 18.82 1227 18.82 - 28.41 291 28.41 - 38.00 221 38.00 - 47.59 131 47.59 - 57.18 71 57.18 - 66.77 29 66.77 - 76.36 8 76.36 - 85.95 2 85.95 - 95.54 1 95.54 - 105.13 2 =========================== Idealize ADP of riding H ========================== r_work=0.1189 r_free=0.1361 r_work=0.1189 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1189 r_free = 0.1361 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1182 r_free = 0.1357 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87582 (all), 4.91 % free)------------| | | | r_work= 0.1182 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.621688 | | target function (ml) not normalized (work): 301635.879655 | | target function (ml) not normalized (free): 15944.961706 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1182 0.1357 n_refl.: 87582 re-set all scales: r(all,work,free)=0.1513 0.1512 0.1564 n_refl.: 87582 remove outliers: r(all,work,free)=0.1513 0.1512 0.1564 n_refl.: 87582 overall B=-0.01 to atoms: r(all,work,free)=0.1512 0.1510 0.1563 n_refl.: 87582 bulk-solvent and scaling: r(all,work,free)=0.1188 0.1179 0.1357 n_refl.: 87582 remove outliers: r(all,work,free)=0.1185 0.1176 0.1357 n_refl.: 87575 ======================== 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 0.4027 289.268 244.812 0.435 1.001 0.314 11.894-9.307 93.14 91 4 0.2229 471.385 446.159 0.835 1.002 0.232 9.237-7.194 98.18 209 7 0.2437 382.766 377.353 0.912 1.002 0.160 7.162-5.571 100.00 427 22 0.2137 293.583 283.852 0.906 1.003 0.129 5.546-4.326 100.00 867 58 0.1146 403.017 398.252 0.951 1.002 0.124 4.315-3.360 100.00 1859 96 0.0954 383.272 380.883 0.993 1.002 0.117 3.356-2.611 100.00 3867 181 0.1141 251.790 250.264 1.001 1.002 0.110 2.608-2.026 99.99 8198 413 0.1023 166.914 166.113 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.0960 81.512 81.805 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1244 36.146 35.779 1.021 0.997 0.000 1.221-1.150 99.97 13689 708 0.2129 22.774 21.396 0.978 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0259 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1176 r_free=0.1357 After: r_work=0.1177 r_free=0.1357 ================================== NQH flips ================================== r_work=0.1177 r_free=0.1357 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=0.1177 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1177 r_free=0.1357 | n_water=456 | time (s): 1.600 (total time: 1.600) Filter (dist) r_work=0.1177 r_free=0.1357 | n_water=456 | time (s): 34.750 (total time: 36.350) Filter (q & B) r_work=0.1177 r_free=0.1358 | n_water=454 | time (s): 3.000 (total time: 39.350) Compute maps r_work=0.1177 r_free=0.1358 | n_water=454 | time (s): 1.310 (total time: 40.660) Filter (map) r_work=0.1209 r_free=0.1381 | n_water=335 | time (s): 3.190 (total time: 43.850) Find peaks r_work=0.1209 r_free=0.1381 | n_water=335 | time (s): 0.670 (total time: 44.520) Add new water r_work=0.1256 r_free=0.1424 | n_water=492 | time (s): 3.170 (total time: 47.690) Refine new water occ: r_work=0.1192 r_free=0.1367 adp: r_work=0.1192 r_free=0.1369 occ: r_work=0.1179 r_free=0.1354 adp: r_work=0.1178 r_free=0.1356 occ: r_work=0.1170 r_free=0.1345 adp: r_work=0.1168 r_free=0.1346 ADP+occupancy (water only), MIN, final r_work=0.1168 r_free=0.1346 r_work=0.1168 r_free=0.1346 | n_water=492 | time (s): 202.790 (total time: 250.480) Filter (q & B) r_work=0.1175 r_free=0.1349 | n_water=453 | time (s): 2.570 (total time: 253.050) Filter (dist only) r_work=0.1175 r_free=0.1348 | n_water=451 | time (s): 39.530 (total time: 292.580) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.931264 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.101060 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 0.1193 0.1366 0.0173 0.008 1.0 2.2 0.5 0.0 0 0.966 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.66 1.73 3.286 21.124 46.101 3.626 11.96 13.64 1.69 3.404 21.077 46.101 3.619 Individual atomic B min max mean iso aniso Overall: 9.21 102.25 21.07 2.06 224 1754 Protein: 9.21 102.25 16.78 2.06 0 1519 Water: 11.48 69.60 35.45 N/A 224 227 Other: 20.06 28.40 24.51 N/A 0 8 Chain A: 9.21 102.25 19.25 N/A 0 1754 Chain S: 15.28 65.07 35.26 N/A 224 0 Histogram: Values Number of atoms 9.21 - 18.51 1223 18.51 - 27.82 283 27.82 - 37.12 216 37.12 - 46.43 145 46.43 - 55.73 69 55.73 - 65.03 25 65.03 - 74.34 13 74.34 - 83.64 1 83.64 - 92.94 1 92.94 - 102.25 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1364 r_work=0.1196 r_free=0.1364 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1364 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1362 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1192 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.617899 | | target function (ml) not normalized (work): 301295.043457 | | target function (ml) not normalized (free): 15933.190283 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2917 171 0.1402 0.1383 5.6589 5.6204| | 2: 3.57 - 2.84 1.00 2888 124 0.1117 0.1441 5.191 5.2466| | 3: 2.83 - 2.48 1.00 2820 163 0.1228 0.1253 4.9935 4.998| | 4: 2.47 - 2.25 1.00 2825 136 0.1021 0.1113 4.6953 4.7304| | 5: 2.25 - 2.09 1.00 2756 127 0.1000 0.1116 4.6364 4.7204| | 6: 2.09 - 1.97 1.00 2846 113 0.0962 0.1219 4.3412 4.4796| | 7: 1.97 - 1.87 1.00 2787 165 0.0993 0.1205 4.0767 4.1765| | 8: 1.87 - 1.79 1.00 2789 144 0.1012 0.1288 3.9872 4.0928| | 9: 1.79 - 1.72 1.00 2745 138 0.0952 0.1315 3.7166 3.9087| | 10: 1.72 - 1.66 1.00 2831 160 0.1001 0.1227 3.6349 3.7633| | 11: 1.66 - 1.61 1.00 2712 147 0.0953 0.1115 3.5683 3.6113| | 12: 1.61 - 1.56 1.00 2773 144 0.0919 0.1229 3.3496 3.5022| | 13: 1.56 - 1.52 1.00 2745 130 0.0973 0.1100 3.3411 3.442| | 14: 1.52 - 1.48 1.00 2803 134 0.0987 0.1113 3.262 3.3396| | 15: 1.48 - 1.45 1.00 2738 128 0.1007 0.1348 3.1665 3.3213| | 16: 1.45 - 1.42 1.00 2756 161 0.1060 0.1274 3.1478 3.2497| | 17: 1.42 - 1.39 1.00 2785 139 0.1116 0.1301 3.1129 3.2258| | 18: 1.39 - 1.36 1.00 2741 179 0.1146 0.1387 3.0837 3.2675| | 19: 1.36 - 1.34 1.00 2807 134 0.1211 0.1588 3.0901 3.268| | 20: 1.34 - 1.32 1.00 2696 147 0.1319 0.1484 3.086 3.1448| | 21: 1.32 - 1.30 1.00 2785 112 0.1412 0.1617 3.084 3.1586| | 22: 1.29 - 1.27 1.00 2704 152 0.1467 0.1903 3.0819 3.2818| | 23: 1.27 - 1.26 1.00 2802 156 0.1570 0.1860 3.1 3.2106| | 24: 1.26 - 1.24 1.00 2744 132 0.1622 0.1792 3.091 3.1939| | 25: 1.24 - 1.22 1.00 2733 148 0.1797 0.2327 3.1075 3.2999| | 26: 1.22 - 1.21 1.00 2727 135 0.1859 0.1773 3.1238 3.1986| | 27: 1.21 - 1.19 1.00 2814 148 0.2007 0.2103 3.1398 3.1486| | 28: 1.19 - 1.18 1.00 2671 147 0.2136 0.2296 3.1375 3.1573| | 29: 1.18 - 1.16 1.00 2800 134 0.2216 0.2379 3.1251 3.2243| | 30: 1.16 - 1.15 1.00 2739 148 0.2379 0.2508 3.1156 3.1653| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2917 171 0.95 8.84 1.00 0.97 5991.50| | 2: 3.57 - 2.84 2888 124 0.92 12.98 1.01 0.97 5991.50| | 3: 2.83 - 2.48 2820 163 0.89 17.16 0.98 0.97 5029.76| | 4: 2.47 - 2.25 2825 136 0.91 14.30 1.00 0.98 2549.77| | 5: 2.25 - 2.09 2756 127 0.90 16.59 1.01 0.98 2549.77| | 6: 2.09 - 1.97 2846 113 0.92 13.50 1.02 0.97 1512.01| | 7: 1.97 - 1.87 2787 165 0.94 10.85 1.02 0.97 626.94| | 8: 1.87 - 1.79 2789 144 0.91 14.44 1.00 0.97 626.94| | 9: 1.79 - 1.72 2745 138 0.93 11.50 0.98 0.97 343.02| | 10: 1.72 - 1.66 2831 160 0.93 12.39 0.98 0.97 286.17| | 11: 1.66 - 1.61 2712 147 0.93 13.05 0.98 0.97 273.13| | 12: 1.61 - 1.56 2773 144 0.95 9.70 0.99 0.97 150.14| | 13: 1.56 - 1.52 2745 130 0.94 11.22 1.02 0.97 150.14| | 14: 1.52 - 1.48 2803 134 0.94 11.39 1.02 0.97 133.72| | 15: 1.48 - 1.45 2738 128 0.95 10.49 1.01 0.98 103.65| | 16: 1.45 - 1.42 2756 161 0.94 11.66 1.01 0.98 103.65| | 17: 1.42 - 1.39 2785 139 0.94 11.44 1.01 0.98 93.35| | 18: 1.39 - 1.36 2741 179 0.94 11.76 1.01 0.98 87.39| | 19: 1.36 - 1.34 2807 134 0.94 12.33 1.00 0.98 87.39| | 20: 1.34 - 1.32 2696 147 0.94 12.43 0.99 0.96 82.35| | 21: 1.32 - 1.30 2785 112 0.94 13.34 0.98 0.96 81.99| | 22: 1.29 - 1.27 2704 152 0.93 13.85 0.98 0.96 82.16| | 23: 1.27 - 1.26 2802 156 0.92 14.83 0.97 0.94 83.02| | 24: 1.26 - 1.24 2744 132 0.92 14.98 0.96 0.94 83.02| | 25: 1.24 - 1.22 2733 148 0.91 16.39 0.96 0.94 84.49| | 26: 1.22 - 1.21 2727 135 0.90 18.13 1.02 0.93 86.13| | 27: 1.21 - 1.19 2814 148 0.89 18.75 1.02 0.93 86.13| | 28: 1.19 - 1.18 2671 147 0.88 20.19 1.01 0.93 89.07| | 29: 1.18 - 1.16 2800 134 0.88 20.52 0.99 0.92 90.18| | 30: 1.16 - 1.15 2739 148 0.86 21.93 0.98 0.92 90.18| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 81.99 max = 5991.50 mean = 943.60| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.95 mean = 14.02| |phase err.(test): min = 0.00 max = 89.44 mean = 14.14| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1192 0.1362 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1506 0.1506 0.1546 n_refl.: 87575 remove outliers: r(all,work,free)=0.1506 0.1506 0.1546 n_refl.: 87575 overall B=-0.01 to atoms: r(all,work,free)=0.1505 0.1505 0.1545 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1192 0.1364 n_refl.: 87575 remove outliers: r(all,work,free)=0.1200 0.1191 0.1364 n_refl.: 87574 ======================== 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 0.4132 289.268 249.926 0.434 1.001 0.299 11.894-9.307 93.14 91 4 0.2327 471.385 453.539 0.854 1.002 0.204 9.237-7.194 97.73 208 7 0.2477 383.839 376.393 0.903 1.002 0.130 7.162-5.571 100.00 427 22 0.2204 293.583 284.238 0.898 1.002 0.130 5.546-4.326 100.00 867 58 0.1185 403.017 398.349 0.954 1.002 0.130 4.315-3.360 100.00 1859 96 0.0989 383.272 380.540 0.994 1.002 0.120 3.356-2.611 100.00 3867 181 0.1179 251.790 249.936 1.000 1.002 0.110 2.608-2.026 99.99 8198 413 0.1041 166.914 165.931 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0972 81.512 81.762 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1222 36.146 35.778 1.021 0.996 0.000 1.221-1.150 99.97 13689 708 0.2112 22.774 21.401 0.979 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0209 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2606 0.1951 0.081 5.237 8.8 119.3 19.9 258 0.000 1_bss: 0.1640 0.1774 0.081 5.237 9.1 119.5 20.1 258 0.000 1_settarget: 0.1640 0.1774 0.081 5.237 9.1 119.5 20.1 258 0.000 1_nqh: 0.1643 0.1772 0.081 5.237 9.1 119.5 20.1 258 0.006 1_weight: 0.1643 0.1772 0.081 5.237 9.1 119.5 20.1 258 0.006 1_xyzrec: 0.1214 0.1469 0.007 0.971 9.1 119.5 20.1 258 0.127 1_adp: 0.1242 0.1541 0.007 0.971 8.6 118.4 20.9 258 0.127 1_regHadp: 0.1246 0.1546 0.007 0.971 8.6 118.4 20.9 258 0.127 1_occ: 0.1243 0.1547 0.007 0.971 8.6 118.4 20.9 258 0.127 2_bss: 0.1239 0.1536 0.007 0.971 8.7 118.5 21.0 258 0.127 2_settarget: 0.1239 0.1536 0.007 0.971 8.7 118.5 21.0 258 0.127 2_updatecdl: 0.1239 0.1536 0.007 0.973 8.7 118.5 21.0 258 0.127 2_nqh: 0.1240 0.1537 0.007 0.973 8.7 118.5 21.0 258 0.124 2_sol: 0.1224 0.1487 0.007 0.973 8.7 118.5 23.4 434 n/a 2_weight: 0.1224 0.1487 0.007 0.973 8.7 118.5 23.4 434 n/a 2_xyzrec: 0.1224 0.1518 0.007 0.881 8.7 118.5 23.4 434 n/a 2_adp: 0.1193 0.1492 0.007 0.881 8.8 114.5 23.1 434 n/a 2_regHadp: 0.1192 0.1492 0.007 0.881 8.8 114.5 23.1 434 n/a 2_occ: 0.1196 0.1484 0.007 0.881 8.8 114.5 23.1 434 n/a 3_bss: 0.1193 0.1485 0.007 0.881 8.8 114.6 23.1 434 n/a 3_settarget: 0.1193 0.1485 0.007 0.881 8.8 114.6 23.1 434 n/a 3_updatecdl: 0.1193 0.1485 0.007 0.882 8.8 114.6 23.1 434 n/a 3_nqh: 0.1193 0.1485 0.007 0.882 8.8 114.6 23.1 434 n/a 3_sol: 0.1216 0.1479 0.007 0.882 8.8 114.6 21.9 444 n/a 3_weight: 0.1216 0.1479 0.007 0.882 8.8 114.6 21.9 444 n/a 3_xyzrec: 0.1217 0.1439 0.006 0.918 8.8 114.6 21.9 444 n/a 3_adp: 0.1217 0.1399 0.006 0.918 9.2 110.1 21.6 444 n/a 3_regHadp: 0.1218 0.1400 0.006 0.918 9.2 110.1 21.6 444 n/a 3_occ: 0.1210 0.1398 0.006 0.918 9.2 110.1 21.6 444 n/a 4_bss: 0.1200 0.1374 0.006 0.918 9.2 110.1 21.6 444 n/a 4_settarget: 0.1200 0.1374 0.006 0.918 9.2 110.1 21.6 444 n/a 4_updatecdl: 0.1200 0.1374 0.006 0.915 9.2 110.1 21.6 444 n/a 4_nqh: 0.1200 0.1374 0.006 0.915 9.2 110.1 21.6 444 n/a 4_sol: 0.1198 0.1362 0.006 0.915 9.2 110.1 21.5 456 n/a 4_weight: 0.1198 0.1362 0.006 0.915 9.2 110.1 21.5 456 n/a 4_xyzrec: 0.1211 0.1369 0.006 0.953 9.2 110.1 21.5 456 n/a 4_adp: 0.1189 0.1361 0.006 0.953 9.2 105.1 21.3 456 n/a 4_regHadp: 0.1189 0.1361 0.006 0.953 9.2 105.1 21.3 456 n/a 4_occ: 0.1182 0.1357 0.006 0.953 9.2 105.1 21.3 456 n/a 5_bss: 0.1176 0.1357 0.006 0.953 9.2 105.1 21.3 456 n/a 5_settarget: 0.1176 0.1357 0.006 0.953 9.2 105.1 21.3 456 n/a 5_updatecdl: 0.1176 0.1357 0.006 0.954 9.2 105.1 21.3 456 n/a 5_setrh: 0.1177 0.1357 0.006 0.954 9.2 105.1 21.3 456 n/a 5_nqh: 0.1177 0.1357 0.006 0.954 9.2 105.1 21.3 456 n/a 5_sol: 0.1175 0.1348 0.006 0.954 9.2 105.1 21.2 451 n/a 5_weight: 0.1175 0.1348 0.006 0.954 9.2 105.1 21.2 451 n/a 5_xyzrec: 0.1193 0.1366 0.008 1.022 9.2 105.1 21.2 451 n/a 5_adp: 0.1196 0.1364 0.008 1.022 9.2 102.2 21.1 451 n/a 5_regHadp: 0.1196 0.1364 0.008 1.022 9.2 102.2 21.1 451 n/a 5_occ: 0.1192 0.1362 0.008 1.022 9.2 102.2 21.1 451 n/a end: 0.1191 0.1364 0.008 1.022 9.2 102.2 21.1 451 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6727304_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6727304_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7900 Refinement macro-cycles (run) : 3607.2200 Write final files (write_after_run_outputs) : 57.0100 Total : 3669.0200 Total CPU time: 61.78 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:12:44 PST -0800 (1735452764.99 s) Start R-work = 0.1640, R-free = 0.1774 Final R-work = 0.1191, R-free = 0.1364 =============================================================================== Job complete usr+sys time: 3801.06 seconds wall clock time: 67 minutes 50.79 seconds (4070.79 seconds total)