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_3120282.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3120282.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3120282.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.23, per 1000 atoms: 0.66 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 312.7 milliseconds Time building geometry restraints manager: 0.81 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: 397 0.89 - 1.14: 1208 1.14 - 1.39: 565 1.39 - 1.64: 914 1.64 - 1.90: 69 Bond restraints: 3153 Sorted by residual: bond pdb=" ND1 HIS A 115 " pdb=" CE1 HIS A 115 " ideal model delta sigma weight residual 1.321 1.506 -0.185 1.00e-02 1.00e+04 3.42e+02 bond pdb=" N BLYS A 93 " pdb=" CA BLYS A 93 " ideal model delta sigma weight residual 1.459 1.670 -0.211 1.17e-02 7.31e+03 3.26e+02 bond pdb=" N AGLU A 94 " pdb=" CA AGLU A 94 " ideal model delta sigma weight residual 1.459 1.244 0.215 1.21e-02 6.83e+03 3.17e+02 bond pdb=" N TYR A 141 " pdb=" CA TYR A 141 " ideal model delta sigma weight residual 1.454 1.229 0.225 1.27e-02 6.20e+03 3.14e+02 bond pdb=" C ASN A 144 " pdb=" O ASN A 144 " ideal model delta sigma weight residual 1.234 1.031 0.203 1.22e-02 6.72e+03 2.76e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.77: 3188 4.77 - 9.53: 1877 9.53 - 14.30: 618 14.30 - 19.07: 88 19.07 - 23.83: 6 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 50 " pdb=" C VAL A 50 " pdb=" N VAL A 51 " ideal model delta sigma weight residual 122.67 140.42 -17.75 1.02e+00 9.61e-01 3.03e+02 angle pdb=" NE ARG A 98 " pdb=" CZ ARG A 98 " pdb=" NH1 ARG A 98 " ideal model delta sigma weight residual 121.50 136.53 -15.03 1.00e+00 1.00e+00 2.26e+02 angle pdb=" O HIS A 126 " pdb=" C HIS A 126 " pdb=" N PRO A 127 " ideal model delta sigma weight residual 121.30 134.92 -13.62 1.03e+00 9.43e-01 1.75e+02 angle pdb=" CA MET A 133 " pdb=" C MET A 133 " pdb=" O MET A 133 " ideal model delta sigma weight residual 120.55 134.31 -13.76 1.06e+00 8.90e-01 1.69e+02 angle pdb=" CA BGLU A 90 " pdb=" C BGLU A 90 " pdb=" O BGLU A 90 " ideal model delta sigma weight residual 120.55 134.06 -13.51 1.06e+00 8.90e-01 1.63e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 929 17.29 - 34.58: 127 34.58 - 51.88: 43 51.88 - 69.17: 9 69.17 - 86.46: 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 180.00 152.63 27.37 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual 180.00 -155.05 -24.95 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 156.43 23.57 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.222: 98 0.222 - 0.441: 79 0.441 - 0.660: 48 0.660 - 0.879: 16 0.879 - 1.099: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.49 -1.10 2.00e-01 2.50e+01 3.02e+01 chirality pdb=" CB THR A 154 " pdb=" CA THR A 154 " pdb=" OG1 THR A 154 " pdb=" CG2 THR A 154 " both_signs ideal model delta sigma weight residual False 2.55 1.57 0.98 2.00e-01 2.50e+01 2.39e+01 chirality pdb=" CA LEU A 58 " pdb=" N LEU A 58 " pdb=" C LEU A 58 " pdb=" CB LEU A 58 " both_signs ideal model delta sigma weight residual False 2.51 1.65 0.86 2.00e-01 2.50e+01 1.86e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.023 2.00e-02 2.50e+03 6.81e-02 1.39e+02 pdb=" CG TYR A 139 " 0.075 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.064 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.056 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.135 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.056 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.068 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.064 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.011 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 27 " -0.145 9.50e-02 1.11e+02 7.50e-02 7.62e+01 pdb=" NE ARG A 27 " -0.061 2.00e-02 2.50e+03 pdb=" CZ ARG A 27 " 0.126 2.00e-02 2.50e+03 pdb=" NH1 ARG A 27 " 0.037 2.00e-02 2.50e+03 pdb=" NH2 ARG A 27 " 0.048 2.00e-02 2.50e+03 pdb="HH11 ARG A 27 " -0.030 2.00e-02 2.50e+03 pdb="HH12 ARG A 27 " -0.032 2.00e-02 2.50e+03 pdb="HH21 ARG A 27 " -0.016 2.00e-02 2.50e+03 pdb="HH22 ARG A 27 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.010 2.00e-02 2.50e+03 4.87e-02 7.12e+01 pdb=" CG PHE A 162 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.071 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.075 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.066 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.055 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.016 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.036 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.051 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 1409 2.37 - 2.93: 8343 2.93 - 3.48: 10434 3.48 - 4.04: 15114 4.04 - 4.60: 21323 Nonbonded interactions: 56623 Sorted by model distance: nonbonded pdb=" H VAL A 35 " pdb=" OD2 ASP A 55 " model vdw 1.811 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.828 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.846 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.858 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.868 2.100 ... (remaining 56618 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_3120282_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= 0.2607 r_free= 0.1932 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789145 | | target function (ml) not normalized (work): 232352.472847 | | target function (ml) not normalized (free): 11822.019991 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3034 0.2137 7.054 4.9576| | 2: 3.57 - 2.84 1.00 2876 122 0.2443 0.1743 4.3523 4.3211| | 3: 2.84 - 2.48 1.00 2833 165 0.2356 0.1606 4.1316 4.1622| | 4: 2.47 - 2.25 1.00 2825 136 0.2338 0.1415 3.8342 3.8193| | 5: 2.25 - 2.09 1.00 2756 127 0.2482 0.1614 3.7975 3.8344| | 6: 2.09 - 1.97 1.00 2846 113 0.2547 0.1681 3.4736 3.5122| | 7: 1.97 - 1.87 1.00 2787 165 0.2488 0.1688 3.1201 3.1539| | 8: 1.87 - 1.79 1.00 2789 144 0.2476 0.1914 3.0574 3.1974| | 9: 1.79 - 1.72 1.00 2745 138 0.2399 0.1837 2.883 2.9101| | 10: 1.72 - 1.66 1.00 2789 158 0.2409 0.1938 2.7944 2.9247| | 11: 1.66 - 1.61 1.00 2740 147 0.2496 0.1823 2.7418 2.7453| | 12: 1.61 - 1.56 1.00 2787 146 0.2534 0.1940 2.6209 2.6264| | 13: 1.56 - 1.52 1.00 2745 130 0.2561 0.1841 2.5641 2.6238| | 14: 1.52 - 1.48 1.00 2803 134 0.2519 0.1901 2.494 2.5343| | 15: 1.48 - 1.45 1.00 2738 128 0.2611 0.2306 2.4279 2.5735| | 16: 1.45 - 1.42 1.00 2756 161 0.2645 0.2074 2.3775 2.4019| | 17: 1.42 - 1.39 1.00 2785 139 0.2690 0.2138 2.3339 2.3968| | 18: 1.39 - 1.36 1.00 2741 179 0.2711 0.2284 2.2965 2.3522| | 19: 1.36 - 1.34 1.00 2807 134 0.2684 0.2364 2.2627 2.32| | 20: 1.34 - 1.32 1.00 2696 147 0.2693 0.2200 2.2013 2.2105| | 21: 1.32 - 1.30 1.00 2785 112 0.2683 0.2359 2.1692 2.179| | 22: 1.29 - 1.27 1.00 2704 152 0.2700 0.2854 2.1261 2.2789| | 23: 1.27 - 1.26 1.00 2802 156 0.2761 0.2445 2.0977 2.1568| | 24: 1.26 - 1.24 1.00 2744 132 0.2800 0.2377 2.0624 2.1304| | 25: 1.24 - 1.22 1.00 2734 148 0.2870 0.2318 2.0553 2.02| | 26: 1.22 - 1.21 1.00 2727 135 0.2846 0.2435 2.0029 2.0955| | 27: 1.21 - 1.19 1.00 2814 148 0.2966 0.2573 2.0096 1.9638| | 28: 1.19 - 1.18 1.00 2671 147 0.2971 0.2779 1.9844 1.9983| | 29: 1.18 - 1.16 1.00 2800 134 0.2988 0.2795 1.97 2.0311| | 30: 1.16 - 1.15 1.00 2740 148 0.3041 0.2983 1.9213 1.9742| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.83 0.76 0.23 1494.09| | 2: 3.57 - 2.84 2876 122 0.80 26.12 1.27 0.23 1494.09| | 3: 2.84 - 2.48 2833 165 0.74 32.07 1.24 0.24 1239.15| | 4: 2.47 - 2.25 2825 136 0.81 25.73 1.26 0.25 577.54| | 5: 2.25 - 2.09 2756 127 0.77 29.52 1.29 0.25 577.54| | 6: 2.09 - 1.97 2846 113 0.83 22.87 1.29 0.25 316.03| | 7: 1.97 - 1.87 2787 165 0.90 16.79 1.28 0.26 93.01| | 8: 1.87 - 1.79 2789 144 0.85 21.38 1.25 0.26 93.01| | 9: 1.79 - 1.72 2745 138 0.88 18.91 1.23 0.25 56.50| | 10: 1.72 - 1.66 2789 158 0.86 20.69 1.22 0.25 49.19| | 11: 1.66 - 1.61 2740 147 0.86 21.46 1.24 0.25 47.37| | 12: 1.61 - 1.56 2787 146 0.89 18.20 1.24 0.25 28.97| | 13: 1.56 - 1.52 2745 130 0.87 20.33 1.25 0.25 28.97| | 14: 1.52 - 1.48 2803 134 0.87 20.47 1.23 0.25 26.07| | 15: 1.48 - 1.45 2738 128 0.87 20.13 1.24 0.25 20.76| | 16: 1.45 - 1.42 2756 161 0.86 21.57 1.23 0.25 20.76| | 17: 1.42 - 1.39 2785 139 0.86 20.98 1.23 0.25 17.84| | 18: 1.39 - 1.36 2741 179 0.86 21.23 1.22 0.25 16.15| | 19: 1.36 - 1.34 2807 134 0.85 22.20 1.22 0.25 16.15| | 20: 1.34 - 1.32 2696 147 0.87 21.13 1.22 0.25 13.55| | 21: 1.32 - 1.30 2785 112 0.86 22.21 1.20 0.25 13.37| | 22: 1.29 - 1.27 2704 152 0.85 22.66 1.22 0.25 13.04| | 23: 1.27 - 1.26 2802 156 0.85 22.48 1.21 0.24 11.38| | 24: 1.26 - 1.24 2744 132 0.84 23.42 1.22 0.24 11.38| | 25: 1.24 - 1.22 2734 148 0.84 24.00 1.21 0.24 10.76| | 26: 1.22 - 1.21 2727 135 0.84 24.32 1.21 0.23 10.07| | 27: 1.21 - 1.19 2814 148 0.83 25.17 1.20 0.23 10.07| | 28: 1.19 - 1.18 2671 147 0.82 25.71 1.18 0.23 9.51| | 29: 1.18 - 1.16 2800 134 0.82 26.17 1.16 0.22 9.29| | 30: 1.16 - 1.15 2740 148 0.80 27.90 1.16 0.22 9.29| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.29 max = 1494.09 mean = 217.10| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.95 mean = 22.82| |phase err.(test): min = 0.00 max = 89.85 mean = 22.89| |-----------------------------------------------------------------------------| ----------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 0.291 1557 Z= 5.341 Angle : 5.232 17.755 2118 Z= 3.705 Chirality : 0.382 1.099 243 Planarity : 0.029 0.073 284 Dihedral : 13.950 86.460 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 0.62 % Allowed : 4.97 % Favored : 94.41 % Cbeta Deviations : 31.89 % 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: -2.51 (0.47), residues: 224 helix: -2.60 (0.37), residues: 108 sheet: -0.34 (0.88), residues: 28 loop : -0.50 (0.57), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.112 0.034 ARG A 48 TYR 0.100 0.043 TYR A 139 PHE 0.073 0.033 PHE A 162 HIS 0.060 0.029 HIS A 115 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= 0.2607 r_free= 0.1932 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789145 | | target function (ml) not normalized (work): 232352.472847 | | target function (ml) not normalized (free): 11822.019991 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2607 0.1932 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2607 0.1932 n_refl.: 87602 remove outliers: r(all,work,free)=0.1979 0.1984 0.1932 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2004 0.2009 0.1946 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1641 0.1636 0.1743 n_refl.: 87594 remove outliers: r(all,work,free)=0.1640 0.1635 0.1743 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 0.3814 386.557 358.037 0.668 1.003 0.407 11.894-9.307 99.02 97 4 0.1793 614.028 594.853 0.929 1.004 0.390 9.237-7.194 100.00 213 7 0.2175 502.199 490.361 0.959 1.004 0.380 7.162-5.571 100.00 427 22 0.2317 376.872 362.064 0.927 1.004 0.320 5.546-4.326 100.00 867 58 0.1326 517.353 511.126 0.960 1.004 0.222 4.315-3.360 100.00 1859 96 0.1171 492.006 487.746 1.002 1.003 0.199 3.356-2.611 100.00 3867 181 0.1440 323.223 320.128 0.996 1.003 0.080 2.608-2.026 99.99 8198 413 0.1332 214.267 211.946 1.008 1.001 0.000 2.025-1.573 100.00 17313 902 0.1614 104.637 103.968 1.011 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2072 46.400 45.088 1.005 0.996 0.000 1.221-1.150 99.97 13689 708 0.2595 29.235 26.907 0.974 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0456 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1635 r_free=0.1743 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1643 r_free=0.1754 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.454909 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1983.061624 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 0.1467 0.0252 0.007 0.9 1.6 0.5 0.0 0 11.727 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.14 14.67 2.52 3.013 19.057 1983.062 0.017 12.42 15.36 2.94 3.176 19.538 1983.062 0.016 Individual atomic B min max mean iso aniso Overall: 8.55 118.46 21.00 2.88 0 1785 Protein: 8.55 118.46 17.87 2.88 0 1519 Water: 11.07 114.55 39.14 N/A 0 258 Other: 23.01 36.30 29.15 N/A 0 8 Chain A: 8.55 118.46 21.00 N/A 0 1785 Histogram: Values Number of atoms 8.55 - 19.54 1210 19.54 - 30.53 228 30.53 - 41.52 163 41.52 - 52.51 103 52.51 - 63.50 52 63.50 - 74.50 16 74.50 - 85.49 6 85.49 - 96.48 4 96.48 - 107.47 0 107.47 - 118.46 3 =========================== Idealize ADP of riding H ========================== r_work=0.1243 r_free=0.1536 r_work=0.1247 r_free=0.1539 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1247 r_free = 0.1539 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 = 0.1246 r_free = 0.1543 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1246 r_free= 0.1543 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015501 | | target function (ls_wunit_k1) not normalized (work): 1291.184834 | | target function (ls_wunit_k1) not normalized (free): 114.314990 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1260 0.1246 0.1543 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1704 0.1703 0.1764 n_refl.: 87593 remove outliers: r(all,work,free)=0.1704 0.1703 0.1764 n_refl.: 87593 overall B=0.14 to atoms: r(all,work,free)=0.1727 0.1727 0.1781 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1257 0.1243 0.1532 n_refl.: 87593 remove outliers: r(all,work,free)=0.1256 0.1242 0.1532 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 0.3643 298.450 278.099 0.687 0.922 0.380 11.894-9.307 99.02 97 4 0.1627 478.101 466.621 0.984 0.923 0.368 9.237-7.194 100.00 213 7 0.1838 391.028 385.853 1.028 0.923 0.340 7.162-5.571 100.00 427 22 0.1743 293.445 287.969 1.001 0.924 0.290 5.546-4.326 100.00 867 58 0.0929 402.827 399.930 1.028 0.924 0.204 4.315-3.360 100.00 1859 96 0.0775 383.091 382.119 1.076 0.926 0.190 3.356-2.611 100.00 3867 181 0.1022 251.671 250.950 1.078 0.928 0.048 2.608-2.026 99.99 8198 413 0.0975 166.835 166.265 1.087 0.931 0.000 2.025-1.573 100.00 17313 902 0.1206 81.474 81.653 1.086 0.936 0.000 1.573-1.221 100.00 36679 1900 0.1645 36.129 35.596 1.062 0.945 0.000 1.221-1.150 99.97 13689 708 0.2360 22.764 21.295 1.015 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0544 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1242 r_free=0.1532 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 180 GLN Total number of N/Q/H flips: 2 r_work=0.1245 r_free=0.1533 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1245 r_free=0.1533 | n_water=258 | time (s): 2.300 (total time: 2.300) Filter (dist) r_work=0.1254 r_free=0.1533 | n_water=252 | time (s): 27.330 (total time: 29.630) Filter (q & B) r_work=0.1257 r_free=0.1532 | n_water=249 | time (s): 3.690 (total time: 33.320) Compute maps r_work=0.1257 r_free=0.1532 | n_water=249 | time (s): 1.770 (total time: 35.090) Filter (map) r_work=0.1270 r_free=0.1539 | n_water=236 | time (s): 3.820 (total time: 38.910) Find peaks r_work=0.1270 r_free=0.1539 | n_water=236 | time (s): 0.740 (total time: 39.650) Add new water r_work=0.1426 r_free=0.1690 | n_water=452 | time (s): 3.840 (total time: 43.490) Refine new water occ: r_work=0.1339 r_free=0.1566 adp: r_work=0.1255 r_free=0.1511 occ: r_work=0.1269 r_free=0.1499 adp: r_work=0.1233 r_free=0.1486 occ: r_work=0.1236 r_free=0.1471 adp: r_work=0.1227 r_free=0.1472 ADP+occupancy (water only), MIN, final r_work=0.1227 r_free=0.1472 r_work=0.1227 r_free=0.1472 | n_water=452 | time (s): 73.020 (total time: 116.510) Filter (q & B) r_work=0.1232 r_free=0.1479 | n_water=434 | time (s): 3.920 (total time: 120.430) Filter (dist only) r_work=0.1232 r_free=0.1479 | n_water=434 | time (s): 40.490 (total time: 160.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.766116 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1528.993151 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1230 0.1515 0.0285 0.007 0.9 1.9 0.5 0.0 0 12.883 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.30 15.15 2.85 3.784 23.173 1528.993 0.015 12.06 15.03 2.97 4.065 23.030 1528.993 0.015 Individual atomic B min max mean iso aniso Overall: 8.57 115.12 23.25 2.60 198 1763 Protein: 8.57 115.12 17.74 2.61 0 1519 Water: 10.92 73.77 42.46 N/A 198 236 Other: 22.85 34.97 28.09 N/A 0 8 Chain A: 8.57 115.12 20.40 N/A 0 1763 Chain S: 16.68 68.05 48.69 N/A 198 0 Histogram: Values Number of atoms 8.57 - 19.22 1200 19.22 - 29.88 248 29.88 - 40.53 201 40.53 - 51.19 149 51.19 - 61.84 104 61.84 - 72.50 48 72.50 - 83.15 5 83.15 - 93.81 3 93.81 - 104.46 1 104.46 - 115.12 2 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1503 r_work=0.1206 r_free=0.1503 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1503 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 = 0.1206 r_free = 0.1496 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 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= 0.1206 r_free= 0.1496 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013979 | | target function (ls_wunit_k1) not normalized (work): 1164.358907 | | target function (ls_wunit_k1) not normalized (free): 105.972922 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1221 0.1206 0.1496 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1612 0.1608 0.1726 n_refl.: 87592 remove outliers: r(all,work,free)=0.1612 0.1608 0.1726 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1619 0.1615 0.1730 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1217 0.1203 0.1494 n_refl.: 87592 remove outliers: r(all,work,free)=0.1216 0.1201 0.1494 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 0.3241 293.844 272.845 0.628 0.938 0.360 11.894-9.307 99.02 97 4 0.1542 478.101 474.528 0.975 0.939 0.360 9.237-7.194 100.00 213 7 0.1626 391.028 392.106 1.044 0.940 0.270 7.162-5.571 100.00 427 22 0.1510 293.445 289.142 1.001 0.940 0.260 5.546-4.326 100.00 867 58 0.0818 402.827 400.051 1.019 0.940 0.210 4.315-3.360 100.00 1859 96 0.0711 383.091 381.897 1.066 0.941 0.210 3.356-2.611 100.00 3867 181 0.0951 251.671 251.035 1.074 0.941 0.150 2.608-2.026 99.99 8198 413 0.0961 166.835 166.519 1.081 0.942 0.000 2.025-1.573 100.00 17313 902 0.1189 81.474 81.694 1.087 0.944 0.000 1.573-1.221 100.00 36679 1900 0.1633 36.129 35.620 1.070 0.947 0.000 1.221-1.150 99.97 13689 708 0.2356 22.764 21.304 1.025 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0693 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1494 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1201 r_free=0.1494 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1494 | n_water=434 | time (s): 2.250 (total time: 2.250) Filter (dist) r_work=0.1201 r_free=0.1493 | n_water=432 | time (s): 38.950 (total time: 41.200) Filter (q & B) r_work=0.1201 r_free=0.1493 | n_water=432 | time (s): 1.350 (total time: 42.550) Compute maps r_work=0.1201 r_free=0.1493 | n_water=432 | time (s): 1.420 (total time: 43.970) Filter (map) r_work=0.1241 r_free=0.1487 | n_water=297 | time (s): 3.340 (total time: 47.310) Find peaks r_work=0.1241 r_free=0.1487 | n_water=297 | time (s): 0.650 (total time: 47.960) Add new water r_work=0.1371 r_free=0.1599 | n_water=496 | time (s): 3.350 (total time: 51.310) Refine new water occ: r_work=0.1264 r_free=0.1519 adp: r_work=0.1265 r_free=0.1522 occ: r_work=0.1241 r_free=0.1498 adp: r_work=0.1239 r_free=0.1500 occ: r_work=0.1226 r_free=0.1483 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=496 | time (s): 171.470 (total time: 222.780) Filter (q & B) r_work=0.1223 r_free=0.1487 | n_water=460 | time (s): 3.490 (total time: 226.270) Filter (dist only) r_work=0.1223 r_free=0.1487 | n_water=460 | time (s): 34.760 (total time: 261.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.046976 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 40.309066 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 0.1237 0.1457 0.0220 0.006 0.9 1.6 0.5 0.0 0 1.023 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.37 14.57 2.20 3.636 22.305 40.309 3.732 12.28 14.12 1.84 4.247 22.080 40.309 3.658 Individual atomic B min max mean iso aniso Overall: 9.25 110.16 21.84 2.30 226 1761 Protein: 9.25 110.16 17.22 2.30 0 1519 Water: 11.65 72.78 37.06 N/A 226 234 Other: 18.07 30.59 24.47 N/A 0 8 Chain A: 9.25 110.16 19.88 N/A 0 1761 Chain S: 15.84 64.98 37.13 N/A 226 0 Histogram: Values Number of atoms 9.25 - 19.34 1238 19.34 - 29.43 271 29.43 - 39.52 226 39.52 - 49.62 143 49.62 - 59.71 75 59.71 - 69.80 20 69.80 - 79.89 8 79.89 - 89.98 3 89.98 - 100.07 1 100.07 - 110.16 2 =========================== Idealize ADP of riding H ========================== r_work=0.1228 r_free=0.1412 r_work=0.1229 r_free=0.1413 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1229 r_free = 0.1413 target_work(ml) = 3.658 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1222 r_free = 0.1412 target_work(ml) = 3.656 | | occupancies: max = 1.00 min = 0.22 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= 0.1222 r_free= 0.1412 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.655717 | | target function (ml) not normalized (work): 304495.626688 | | target function (ml) not normalized (free): 16078.691980 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1222 0.1412 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1544 0.1543 0.1584 n_refl.: 87589 remove outliers: r(all,work,free)=0.1544 0.1543 0.1584 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1541 0.1541 0.1582 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1221 0.1212 0.1388 n_refl.: 87589 remove outliers: r(all,work,free)=0.1217 0.1208 0.1388 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3817 285.343 261.535 0.478 0.999 0.330 11.894-9.307 97.06 95 4 0.2373 471.500 454.687 0.854 1.001 0.272 9.237-7.194 98.18 209 7 0.2248 382.586 382.711 0.940 1.002 0.197 7.162-5.571 100.00 427 22 0.2086 293.445 282.057 0.912 1.002 0.170 5.546-4.326 100.00 867 58 0.1095 402.827 398.242 0.952 1.002 0.158 4.315-3.360 100.00 1859 96 0.0939 383.091 380.367 0.994 1.002 0.150 3.356-2.611 100.00 3867 181 0.1165 251.671 249.661 0.999 1.002 0.067 2.608-2.026 99.99 8198 413 0.1069 166.835 165.769 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1029 81.474 81.603 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1302 36.129 35.684 1.021 0.998 0.000 1.221-1.150 99.97 13689 708 0.2137 22.764 21.364 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=-0.0360 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1208 r_free=0.1388 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=0.1208 r_free=0.1388 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1208 r_free=0.1388 | n_water=460 | time (s): 1.710 (total time: 1.710) Filter (dist) r_work=0.1208 r_free=0.1388 | n_water=460 | time (s): 35.120 (total time: 36.830) Filter (q & B) r_work=0.1208 r_free=0.1388 | n_water=460 | time (s): 0.990 (total time: 37.820) Compute maps r_work=0.1208 r_free=0.1388 | n_water=460 | time (s): 1.640 (total time: 39.460) Filter (map) r_work=0.1229 r_free=0.1381 | n_water=311 | time (s): 3.140 (total time: 42.600) Find peaks r_work=0.1229 r_free=0.1381 | n_water=311 | time (s): 0.460 (total time: 43.060) Add new water r_work=0.1301 r_free=0.1450 | n_water=497 | time (s): 2.460 (total time: 45.520) Refine new water occ: r_work=0.1224 r_free=0.1384 adp: r_work=0.1225 r_free=0.1386 occ: r_work=0.1210 r_free=0.1374 adp: r_work=0.1209 r_free=0.1376 occ: r_work=0.1201 r_free=0.1368 adp: r_work=0.1197 r_free=0.1367 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1367 r_work=0.1197 r_free=0.1367 | n_water=497 | time (s): 129.430 (total time: 174.950) Filter (q & B) r_work=0.1207 r_free=0.1367 | n_water=449 | time (s): 3.320 (total time: 178.270) Filter (dist only) r_work=0.1206 r_free=0.1366 | n_water=448 | time (s): 39.000 (total time: 217.270) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.868867 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.012101 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1209 0.1373 0.0164 0.006 0.9 2.2 0.5 0.0 0 0.934 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.09 13.73 1.64 3.416 21.492 44.012 3.642 11.87 13.61 1.74 3.704 21.408 44.012 3.624 Individual atomic B min max mean iso aniso Overall: 9.29 105.51 21.31 2.17 218 1757 Protein: 9.29 105.51 17.03 2.17 0 1519 Water: 11.34 71.87 35.77 N/A 218 230 Other: 17.77 27.67 22.88 N/A 0 8 Chain A: 9.29 105.51 19.58 N/A 0 1757 Chain S: 16.00 59.02 35.21 N/A 218 0 Histogram: Values Number of atoms 9.29 - 18.91 1229 18.91 - 28.53 285 28.53 - 38.16 217 38.16 - 47.78 136 47.78 - 57.40 69 57.40 - 67.02 24 67.02 - 76.65 10 76.65 - 86.27 2 86.27 - 95.89 1 95.89 - 105.51 2 =========================== Idealize ADP of riding H ========================== r_work=0.1187 r_free=0.1361 r_work=0.1187 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1187 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 = 0.1360 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.13 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= 0.1182 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.622447 | | target function (ml) not normalized (work): 301688.272595 | | target function (ml) not normalized (free): 15941.601913 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1182 0.1360 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1504 0.1504 0.1560 n_refl.: 87579 remove outliers: r(all,work,free)=0.1504 0.1504 0.1560 n_refl.: 87579 overall B=-0.02 to atoms: r(all,work,free)=0.1502 0.1501 0.1558 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1182 0.1361 n_refl.: 87579 remove outliers: r(all,work,free)=0.1189 0.1180 0.1361 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 87.50 79 5 0.4144 280.558 254.706 0.422 0.999 0.269 11.894-9.307 94.12 92 4 0.2473 471.697 450.481 0.832 1.001 0.221 9.237-7.194 97.73 208 7 0.2433 383.659 375.139 0.910 1.001 0.175 7.162-5.571 100.00 427 22 0.2193 293.445 281.745 0.906 1.002 0.156 5.546-4.326 100.00 867 58 0.1122 402.827 398.391 0.953 1.002 0.123 4.315-3.360 100.00 1859 96 0.0935 383.091 380.791 0.995 1.002 0.117 3.356-2.611 100.00 3867 181 0.1157 251.671 249.770 1.002 1.001 0.090 2.608-2.026 99.99 8198 413 0.1019 166.835 166.004 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0969 81.474 81.755 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1247 36.129 35.758 1.022 0.998 0.000 1.221-1.150 99.97 13689 708 0.2129 22.764 21.391 0.980 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0436 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1180 r_free=0.1361 After: r_work=0.1180 r_free=0.1361 ================================== NQH flips ================================== r_work=0.1180 r_free=0.1361 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=0.1180 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1180 r_free=0.1361 | n_water=448 | time (s): 1.790 (total time: 1.790) Filter (dist) r_work=0.1180 r_free=0.1361 | n_water=448 | time (s): 34.140 (total time: 35.930) Filter (q & B) r_work=0.1181 r_free=0.1362 | n_water=446 | time (s): 2.570 (total time: 38.500) Compute maps r_work=0.1181 r_free=0.1362 | n_water=446 | time (s): 1.110 (total time: 39.610) Filter (map) r_work=0.1201 r_free=0.1362 | n_water=339 | time (s): 3.010 (total time: 42.620) Find peaks r_work=0.1201 r_free=0.1362 | n_water=339 | time (s): 0.660 (total time: 43.280) Add new water r_work=0.1250 r_free=0.1402 | n_water=495 | time (s): 3.000 (total time: 46.280) Refine new water occ: r_work=0.1187 r_free=0.1336 adp: r_work=0.1187 r_free=0.1339 occ: r_work=0.1176 r_free=0.1331 adp: r_work=0.1174 r_free=0.1332 occ: r_work=0.1168 r_free=0.1331 adp: r_work=0.1165 r_free=0.1329 ADP+occupancy (water only), MIN, final r_work=0.1165 r_free=0.1329 r_work=0.1165 r_free=0.1329 | n_water=495 | time (s): 149.330 (total time: 195.610) Filter (q & B) r_work=0.1173 r_free=0.1338 | n_water=457 | time (s): 2.980 (total time: 198.590) Filter (dist only) r_work=0.1173 r_free=0.1337 | n_water=456 | time (s): 37.520 (total time: 236.110) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.960193 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.479497 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 0.1365 0.0165 0.007 1.1 4.5 0.5 0.0 0 0.980 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.65 1.65 3.312 21.301 41.479 3.627 12.04 13.66 1.61 3.553 21.224 41.479 3.621 Individual atomic B min max mean iso aniso Overall: 9.31 101.30 21.20 2.03 226 1757 Protein: 9.31 101.30 16.82 2.03 0 1519 Water: 11.48 71.13 35.80 N/A 226 230 Other: 17.26 24.84 21.65 N/A 0 8 Chain A: 9.31 101.30 19.36 N/A 0 1757 Chain S: 15.87 58.25 35.53 N/A 226 0 Histogram: Values Number of atoms 9.31 - 18.51 1221 18.51 - 27.71 281 27.71 - 36.90 213 36.90 - 46.10 136 46.10 - 55.30 86 55.30 - 64.50 30 64.50 - 73.70 11 73.70 - 82.90 2 82.90 - 92.10 1 92.10 - 101.30 2 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1366 r_work=0.1205 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1365 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1363 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87574 (all), 4.91 % free)------------| | | | r_work= 0.1200 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.620017 | | target function (ml) not normalized (work): 301467.765541 | | target function (ml) not normalized (free): 15927.244411 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2916 171 0.1406 0.1373 5.6714 5.5947| | 2: 3.57 - 2.84 1.00 2888 124 0.1116 0.1429 5.181 5.2479| | 3: 2.83 - 2.48 1.00 2820 163 0.1239 0.1333 4.9901 5.0169| | 4: 2.47 - 2.25 1.00 2825 136 0.1037 0.1236 4.694 4.7693| | 5: 2.25 - 2.09 1.00 2756 127 0.1011 0.1075 4.6316 4.6881| | 6: 2.09 - 1.97 1.00 2846 113 0.0971 0.1148 4.3386 4.4548| | 7: 1.97 - 1.87 1.00 2787 165 0.0999 0.1166 4.073 4.1571| | 8: 1.87 - 1.79 1.00 2789 144 0.1022 0.1251 3.9841 4.0824| | 9: 1.79 - 1.72 1.00 2745 138 0.0961 0.1284 3.7159 3.9061| | 10: 1.72 - 1.66 1.00 2831 160 0.1007 0.1218 3.6371 3.7604| | 11: 1.66 - 1.61 1.00 2712 147 0.0975 0.1101 3.5722 3.6102| | 12: 1.61 - 1.56 1.00 2773 144 0.0929 0.1206 3.3559 3.5079| | 13: 1.56 - 1.52 1.00 2745 130 0.0994 0.1051 3.3468 3.4284| | 14: 1.52 - 1.48 1.00 2803 134 0.0998 0.1084 3.2653 3.3158| | 15: 1.48 - 1.45 1.00 2738 128 0.1024 0.1337 3.1717 3.3309| | 16: 1.45 - 1.42 1.00 2756 161 0.1080 0.1254 3.1541 3.2488| | 17: 1.42 - 1.39 1.00 2785 139 0.1134 0.1314 3.1193 3.2415| | 18: 1.39 - 1.36 1.00 2741 179 0.1156 0.1388 3.0883 3.2659| | 19: 1.36 - 1.34 1.00 2807 134 0.1228 0.1570 3.0965 3.2671| | 20: 1.34 - 1.32 1.00 2696 147 0.1325 0.1524 3.0889 3.1426| | 21: 1.32 - 1.30 1.00 2785 112 0.1415 0.1605 3.0886 3.159| | 22: 1.29 - 1.27 1.00 2704 152 0.1491 0.1940 3.0893 3.2926| | 23: 1.27 - 1.26 1.00 2802 156 0.1572 0.1875 3.103 3.2157| | 24: 1.26 - 1.24 1.00 2744 132 0.1633 0.1755 3.0966 3.1956| | 25: 1.24 - 1.22 1.00 2733 148 0.1792 0.2307 3.1098 3.29| | 26: 1.22 - 1.21 1.00 2727 135 0.1872 0.1838 3.1264 3.2174| | 27: 1.21 - 1.19 1.00 2814 148 0.2016 0.2047 3.1411 3.1426| | 28: 1.19 - 1.18 1.00 2671 147 0.2148 0.2345 3.1396 3.1676| | 29: 1.18 - 1.16 1.00 2800 134 0.2212 0.2356 3.1243 3.2183| | 30: 1.16 - 1.15 1.00 2739 148 0.2384 0.2499 3.1166 3.1686| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2916 171 0.95 8.65 1.00 0.98 5809.90| | 2: 3.57 - 2.84 2888 124 0.92 12.74 1.01 0.98 5809.90| | 3: 2.83 - 2.48 2820 163 0.89 16.96 0.99 0.98 4878.70| | 4: 2.47 - 2.25 2825 136 0.91 14.04 1.00 0.98 2477.42| | 5: 2.25 - 2.09 2756 127 0.90 16.22 1.01 0.98 2477.42| | 6: 2.09 - 1.97 2846 113 0.92 13.27 1.02 0.98 1471.93| | 7: 1.97 - 1.87 2787 165 0.94 10.68 1.02 0.97 614.39| | 8: 1.87 - 1.79 2789 144 0.91 14.27 1.00 0.97 614.39| | 9: 1.79 - 1.72 2745 138 0.93 11.41 0.98 0.97 337.49| | 10: 1.72 - 1.66 2831 160 0.93 12.30 0.98 0.97 282.04| | 11: 1.66 - 1.61 2712 147 0.93 13.00 0.98 0.97 269.30| | 12: 1.61 - 1.56 2773 144 0.95 9.61 0.99 0.97 149.11| | 13: 1.56 - 1.52 2745 130 0.94 11.21 1.02 0.97 149.11| | 14: 1.52 - 1.48 2803 134 0.94 11.32 1.02 0.98 132.91| | 15: 1.48 - 1.45 2738 128 0.95 10.43 1.02 0.98 103.25| | 16: 1.45 - 1.42 2756 161 0.94 11.57 1.02 0.98 103.25| | 17: 1.42 - 1.39 2785 139 0.94 11.44 1.01 0.99 93.25| | 18: 1.39 - 1.36 2741 179 0.94 11.72 1.01 0.99 87.47| | 19: 1.36 - 1.34 2807 134 0.94 12.33 1.00 0.99 87.47| | 20: 1.34 - 1.32 2696 147 0.94 12.46 0.99 0.97 82.37| | 21: 1.32 - 1.30 2785 112 0.93 13.41 0.99 0.97 82.02| | 22: 1.29 - 1.27 2704 152 0.93 13.98 0.99 0.96 82.22| | 23: 1.27 - 1.26 2802 156 0.92 14.88 0.98 0.95 83.28| | 24: 1.26 - 1.24 2744 132 0.92 14.98 0.97 0.95 83.28| | 25: 1.24 - 1.22 2733 148 0.91 16.39 0.96 0.94 84.76| | 26: 1.22 - 1.21 2727 135 0.90 18.16 1.03 0.93 86.40| | 27: 1.21 - 1.19 2814 148 0.89 18.76 1.02 0.93 86.40| | 28: 1.19 - 1.18 2671 147 0.88 20.24 1.01 0.93 89.58| | 29: 1.18 - 1.16 2800 134 0.88 20.55 0.99 0.93 90.77| | 30: 1.16 - 1.15 2739 148 0.86 21.99 0.98 0.93 90.77| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 82.02 max = 5809.90 mean = 918.25| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.95 mean = 13.95| |phase err.(test): min = 0.00 max = 89.51 mean = 14.01| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1208 0.1200 0.1363 n_refl.: 87574 re-set all scales: r(all,work,free)=0.1507 0.1506 0.1560 n_refl.: 87574 remove outliers: r(all,work,free)=0.1507 0.1506 0.1560 n_refl.: 87574 overall B=-0.02 to atoms: r(all,work,free)=0.1504 0.1502 0.1557 n_refl.: 87574 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1199 0.1367 n_refl.: 87574 remove outliers: r(all,work,free)=0.1206 0.1198 0.1367 n_refl.: 87572 ======================== 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 87.50 79 5 0.4142 280.558 248.153 0.424 0.999 0.307 11.894-9.307 92.16 90 4 0.2412 467.335 444.190 0.832 1.001 0.206 9.237-7.194 97.73 208 7 0.2415 383.659 377.012 0.911 1.002 0.130 7.162-5.571 100.00 427 22 0.2216 293.445 281.724 0.900 1.002 0.120 5.546-4.326 100.00 867 58 0.1187 402.827 398.333 0.951 1.002 0.116 4.315-3.360 100.00 1859 96 0.0974 383.091 380.564 0.995 1.002 0.114 3.356-2.611 100.00 3867 181 0.1192 251.671 249.805 1.001 1.002 0.053 2.608-2.026 99.99 8198 413 0.1051 166.835 165.832 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0981 81.474 81.740 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1235 36.129 35.760 1.025 0.996 0.000 1.221-1.150 99.97 13689 708 0.2119 22.764 21.399 0.984 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0466 ================= 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 : 0.2607 0.1932 0.081 5.232 8.8 119.3 19.9 258 0.000 1_bss: 0.1635 0.1743 0.081 5.232 9.0 119.5 20.1 258 0.000 1_settarget: 0.1635 0.1743 0.081 5.232 9.0 119.5 20.1 258 0.000 1_nqh: 0.1643 0.1754 0.081 5.232 9.0 119.5 20.1 258 0.003 1_weight: 0.1643 0.1754 0.081 5.232 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1214 0.1467 0.007 0.928 9.0 119.5 20.1 258 0.127 1_adp: 0.1243 0.1536 0.007 0.928 8.6 118.5 21.0 258 0.127 1_regHadp: 0.1247 0.1539 0.007 0.928 8.6 118.5 21.0 258 0.127 1_occ: 0.1246 0.1543 0.007 0.928 8.6 118.5 21.0 258 0.127 2_bss: 0.1242 0.1532 0.007 0.928 8.7 118.6 21.1 258 0.127 2_settarget: 0.1242 0.1532 0.007 0.928 8.7 118.6 21.1 258 0.127 2_updatecdl: 0.1242 0.1532 0.007 0.931 8.7 118.6 21.1 258 0.127 2_nqh: 0.1245 0.1533 0.007 0.931 8.7 118.6 21.1 258 0.128 2_sol: 0.1232 0.1479 0.007 0.931 8.7 118.6 23.5 434 n/a 2_weight: 0.1232 0.1479 0.007 0.931 8.7 118.6 23.5 434 n/a 2_xyzrec: 0.1230 0.1515 0.007 0.876 8.7 118.6 23.5 434 n/a 2_adp: 0.1206 0.1503 0.007 0.876 8.6 115.1 23.3 434 n/a 2_regHadp: 0.1206 0.1503 0.007 0.876 8.6 115.1 23.3 434 n/a 2_occ: 0.1206 0.1496 0.007 0.876 8.6 115.1 23.3 434 n/a 3_bss: 0.1201 0.1494 0.007 0.876 8.6 115.2 23.3 434 n/a 3_settarget: 0.1201 0.1494 0.007 0.876 8.6 115.2 23.3 434 n/a 3_updatecdl: 0.1201 0.1494 0.007 0.876 8.6 115.2 23.3 434 n/a 3_nqh: 0.1201 0.1494 0.007 0.876 8.6 115.2 23.3 434 n/a 3_sol: 0.1223 0.1487 0.007 0.876 8.6 115.2 22.2 460 n/a 3_weight: 0.1223 0.1487 0.007 0.876 8.6 115.2 22.2 460 n/a 3_xyzrec: 0.1237 0.1457 0.006 0.913 8.6 115.2 22.2 460 n/a 3_adp: 0.1228 0.1412 0.006 0.913 9.3 110.2 21.8 460 n/a 3_regHadp: 0.1229 0.1413 0.006 0.913 9.3 110.2 21.8 460 n/a 3_occ: 0.1222 0.1412 0.006 0.913 9.3 110.2 21.8 460 n/a 4_bss: 0.1208 0.1388 0.006 0.913 9.2 110.1 21.8 460 n/a 4_settarget: 0.1208 0.1388 0.006 0.913 9.2 110.1 21.8 460 n/a 4_updatecdl: 0.1208 0.1388 0.006 0.912 9.2 110.1 21.8 460 n/a 4_nqh: 0.1208 0.1388 0.006 0.912 9.2 110.1 21.8 460 n/a 4_sol: 0.1206 0.1366 0.006 0.912 9.2 110.1 21.5 448 n/a 4_weight: 0.1206 0.1366 0.006 0.912 9.2 110.1 21.5 448 n/a 4_xyzrec: 0.1209 0.1373 0.006 0.939 9.2 110.1 21.5 448 n/a 4_adp: 0.1187 0.1361 0.006 0.939 9.3 105.5 21.3 448 n/a 4_regHadp: 0.1187 0.1361 0.006 0.939 9.3 105.5 21.3 448 n/a 4_occ: 0.1182 0.1360 0.006 0.939 9.3 105.5 21.3 448 n/a 5_bss: 0.1180 0.1361 0.006 0.939 9.3 105.5 21.3 448 n/a 5_settarget: 0.1180 0.1361 0.006 0.939 9.3 105.5 21.3 448 n/a 5_updatecdl: 0.1180 0.1361 0.006 0.941 9.3 105.5 21.3 448 n/a 5_setrh: 0.1180 0.1361 0.006 0.941 9.3 105.5 21.3 448 n/a 5_nqh: 0.1180 0.1361 0.006 0.941 9.3 105.5 21.3 448 n/a 5_sol: 0.1173 0.1337 0.006 0.941 9.3 105.5 21.3 456 n/a 5_weight: 0.1173 0.1337 0.006 0.941 9.3 105.5 21.3 456 n/a 5_xyzrec: 0.1200 0.1365 0.007 1.051 9.3 105.5 21.3 456 n/a 5_adp: 0.1204 0.1366 0.007 1.051 9.3 101.3 21.2 456 n/a 5_regHadp: 0.1205 0.1365 0.007 1.051 9.3 101.3 21.2 456 n/a 5_occ: 0.1200 0.1363 0.007 1.051 9.3 101.3 21.2 456 n/a end: 0.1198 0.1367 0.007 1.051 9.3 101.3 21.2 456 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_3120282_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_3120282_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7900 Refinement macro-cycles (run) : 3282.9900 Write final files (write_after_run_outputs) : 67.7200 Total : 3355.5000 Total CPU time: 56.54 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:07:25 PST -0800 (1735452445.17 s) Start R-work = 0.1635, R-free = 0.1743 Final R-work = 0.1198, R-free = 0.1367 =============================================================================== Job complete usr+sys time: 3510.27 seconds wall clock time: 62 minutes 55.30 seconds (3775.30 seconds total)