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_1522381.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 { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1522381.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1522381.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" } 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: 2.20, per 1000 atoms: 0.65 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: 0.84 Conformation dependent library (CDL) restraints added in 329.5 milliseconds Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 391 0.89 - 1.14: 1224 1.14 - 1.40: 582 1.40 - 1.66: 894 1.66 - 1.91: 62 Bond restraints: 3153 Sorted by residual: bond pdb=" C GLY A 159 " pdb=" O GLY A 159 " ideal model delta sigma weight residual 1.237 1.436 -0.199 1.07e-02 8.73e+03 3.47e+02 bond pdb=" C CYS A 106 " pdb=" O CYS A 106 " ideal model delta sigma weight residual 1.235 1.470 -0.234 1.26e-02 6.30e+03 3.46e+02 bond pdb=" N GLU A 176 " pdb=" CA GLU A 176 " ideal model delta sigma weight residual 1.459 1.240 0.220 1.19e-02 7.06e+03 3.41e+02 bond pdb=" C ALYS A 99 " pdb=" O ALYS A 99 " ideal model delta sigma weight residual 1.233 1.001 0.232 1.28e-02 6.10e+03 3.28e+02 bond pdb=" C ALA A 183 " pdb=" O ALA A 183 " ideal model delta sigma weight residual 1.244 1.064 0.180 1.00e-02 1.00e+04 3.23e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.91: 3295 4.91 - 9.83: 1855 9.83 - 14.74: 547 14.74 - 19.65: 71 19.65 - 24.57: 9 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA VAL A 25 " pdb=" C VAL A 25 " pdb=" N MET A 26 " ideal model delta sigma weight residual 117.15 134.91 -17.76 1.14e+00 7.69e-01 2.43e+02 angle pdb=" CA THR A 140 " pdb=" C THR A 140 " pdb=" O THR A 140 " ideal model delta sigma weight residual 120.36 104.85 15.51 1.07e+00 8.73e-01 2.10e+02 angle pdb=" CA ASN A 173 " pdb=" C ASN A 173 " pdb=" O ASN A 173 " ideal model delta sigma weight residual 119.05 133.57 -14.52 1.10e+00 8.26e-01 1.74e+02 angle pdb=" C VAL A 25 " pdb=" N MET A 26 " pdb=" CA MET A 26 " ideal model delta sigma weight residual 120.54 137.66 -17.12 1.35e+00 5.49e-01 1.61e+02 angle pdb=" C ASP A 42 " pdb=" N PRO A 43 " pdb=" CA PRO A 43 " ideal model delta sigma weight residual 120.03 107.87 12.16 9.90e-01 1.02e+00 1.51e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.32: 943 17.32 - 34.63: 116 34.63 - 51.95: 37 51.95 - 69.26: 12 69.26 - 86.57: 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 180.00 151.94 28.06 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA LYS A 182 " pdb=" C LYS A 182 " pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta harmonic sigma weight residual -180.00 -153.83 -26.17 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -154.83 -25.17 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.008 - 0.276: 120 0.276 - 0.544: 80 0.544 - 0.813: 34 0.813 - 1.081: 7 1.081 - 1.349: 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 -1.24 -1.35 2.00e-01 2.50e+01 4.55e+01 chirality pdb=" CA THR A 124 " pdb=" N THR A 124 " pdb=" C THR A 124 " pdb=" CB THR A 124 " both_signs ideal model delta sigma weight residual False 2.53 1.39 1.14 2.00e-01 2.50e+01 3.24e+01 chirality pdb=" CA ILE A 152 " pdb=" N ILE A 152 " pdb=" C ILE A 152 " pdb=" CB ILE A 152 " both_signs ideal model delta sigma weight residual False 2.43 3.42 -0.99 2.00e-01 2.50e+01 2.43e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.149 2.00e-02 2.50e+03 7.18e-02 1.55e+02 pdb=" CG TYR A 141 " -0.088 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.117 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.058 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.099 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.040 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.017 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.017 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.079 2.00e-02 2.50e+03 6.58e-02 1.30e+02 pdb=" CG PHE A 119 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.089 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.099 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.064 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.126 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.011 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.034 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.019 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.048 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BASN A 76 " -0.012 2.00e-02 2.50e+03 9.14e-02 1.25e+02 pdb=" CG BASN A 76 " 0.111 2.00e-02 2.50e+03 pdb=" OD1BASN A 76 " -0.086 2.00e-02 2.50e+03 pdb=" ND2BASN A 76 " 0.124 2.00e-02 2.50e+03 pdb="HD21BASN A 76 " -0.013 2.00e-02 2.50e+03 pdb="HD22BASN A 76 " -0.122 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1180 2.33 - 2.90: 8113 2.90 - 3.47: 10476 3.47 - 4.03: 15204 4.03 - 4.60: 21599 Nonbonded interactions: 56572 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.764 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.769 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.795 2.450 nonbonded pdb=" H THR A 124 " pdb=" OG1 THR A 154 " model vdw 1.821 2.450 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.831 2.100 ... (remaining 56567 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_1522381_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= 0.2609 r_free= 0.1934 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792011 | | target function (ml) not normalized (work): 232591.308943 | | target function (ml) not normalized (free): 11792.018701 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3033 0.2094 7.0553 4.954| | 2: 3.57 - 2.84 1.00 2876 122 0.2440 0.1736 4.3522 4.3304| | 3: 2.84 - 2.48 1.00 2833 165 0.2346 0.1622 4.1283 4.1448| | 4: 2.47 - 2.25 1.00 2825 136 0.2332 0.1438 3.8347 3.8359| | 5: 2.25 - 2.09 1.00 2756 127 0.2472 0.1698 3.798 3.8329| | 6: 2.09 - 1.97 1.00 2846 113 0.2578 0.1869 3.4754 3.548| | 7: 1.97 - 1.87 1.00 2787 165 0.2552 0.1928 3.1425 3.2265| | 8: 1.87 - 1.79 1.00 2789 144 0.2402 0.1834 3.0656 3.1234| | 9: 1.79 - 1.72 1.00 2745 138 0.2439 0.1967 2.915 2.9377| | 10: 1.72 - 1.66 1.00 2789 158 0.2458 0.2029 2.7957 2.8935| | 11: 1.66 - 1.61 1.00 2740 147 0.2482 0.1718 2.7475 2.7401| | 12: 1.61 - 1.56 1.00 2787 146 0.2514 0.1908 2.6269 2.6354| | 13: 1.56 - 1.52 1.00 2745 130 0.2571 0.1906 2.5834 2.61| | 14: 1.52 - 1.48 1.00 2803 134 0.2570 0.1811 2.4963 2.4957| | 15: 1.48 - 1.45 1.00 2738 128 0.2637 0.2007 2.4351 2.4519| | 16: 1.45 - 1.42 1.00 2756 161 0.2672 0.2246 2.3881 2.5086| | 17: 1.42 - 1.39 1.00 2785 139 0.2632 0.2018 2.3352 2.3584| | 18: 1.39 - 1.36 1.00 2741 179 0.2656 0.2300 2.2923 2.3904| | 19: 1.36 - 1.34 1.00 2807 134 0.2681 0.2308 2.2447 2.2848| | 20: 1.34 - 1.32 1.00 2696 147 0.2659 0.2068 2.1907 2.1657| | 21: 1.32 - 1.30 1.00 2785 112 0.2698 0.2206 2.1542 2.1466| | 22: 1.29 - 1.27 1.00 2704 152 0.2774 0.2811 2.1253 2.2495| | 23: 1.27 - 1.26 1.00 2802 156 0.2792 0.2343 2.1167 2.1385| | 24: 1.26 - 1.24 1.00 2744 132 0.2746 0.2318 2.0695 2.126| | 25: 1.24 - 1.22 1.00 2734 148 0.2882 0.2321 2.0487 2.0213| | 26: 1.22 - 1.21 1.00 2727 135 0.2861 0.2164 2.0079 2.0493| | 27: 1.21 - 1.19 1.00 2814 148 0.2961 0.2644 1.9979 1.9889| | 28: 1.19 - 1.18 1.00 2671 147 0.2996 0.2465 1.9795 1.951| | 29: 1.18 - 1.16 1.00 2800 134 0.2995 0.2823 1.9683 2.0615| | 30: 1.16 - 1.15 1.00 2740 148 0.3040 0.2795 1.9333 1.9565| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.82 0.76 0.23 1475.89| | 2: 3.57 - 2.84 2876 122 0.80 26.03 1.27 0.23 1475.89| | 3: 2.84 - 2.48 2833 165 0.74 31.94 1.24 0.23 1224.00| | 4: 2.47 - 2.25 2825 136 0.81 25.47 1.25 0.25 570.30| | 5: 2.25 - 2.09 2756 127 0.77 29.33 1.28 0.25 570.30| | 6: 2.09 - 1.97 2846 113 0.84 22.61 1.29 0.25 312.12| | 7: 1.97 - 1.87 2787 165 0.90 16.50 1.28 0.26 91.93| | 8: 1.87 - 1.79 2789 144 0.86 20.99 1.24 0.26 91.93| | 9: 1.79 - 1.72 2745 138 0.88 18.46 1.23 0.25 55.12| | 10: 1.72 - 1.66 2789 158 0.86 20.28 1.23 0.25 47.75| | 11: 1.66 - 1.61 2740 147 0.86 21.21 1.23 0.25 46.05| | 12: 1.61 - 1.56 2787 146 0.89 18.20 1.23 0.25 28.87| | 13: 1.56 - 1.52 2745 130 0.87 19.90 1.24 0.25 28.87| | 14: 1.52 - 1.48 2803 134 0.86 20.81 1.24 0.25 25.83| | 15: 1.48 - 1.45 2738 128 0.87 20.04 1.24 0.25 20.27| | 16: 1.45 - 1.42 2756 161 0.86 21.37 1.23 0.25 20.27| | 17: 1.42 - 1.39 2785 139 0.87 20.46 1.23 0.25 17.42| | 18: 1.39 - 1.36 2741 179 0.87 20.72 1.22 0.25 15.78| | 19: 1.36 - 1.34 2807 134 0.85 22.03 1.22 0.25 15.78| | 20: 1.34 - 1.32 2696 147 0.87 20.53 1.21 0.24 12.89| | 21: 1.32 - 1.30 2785 112 0.86 21.57 1.20 0.24 12.69| | 22: 1.29 - 1.27 2704 152 0.85 22.29 1.22 0.24 12.38| | 23: 1.27 - 1.26 2802 156 0.86 21.87 1.21 0.24 10.81| | 24: 1.26 - 1.24 2744 132 0.86 22.32 1.20 0.24 10.81| | 25: 1.24 - 1.22 2734 148 0.85 23.35 1.21 0.24 10.19| | 26: 1.22 - 1.21 2727 135 0.84 23.57 1.20 0.23 9.49| | 27: 1.21 - 1.19 2814 148 0.84 24.19 1.20 0.23 9.49| | 28: 1.19 - 1.18 2671 147 0.83 24.74 1.19 0.23 8.91| | 29: 1.18 - 1.16 2800 134 0.83 25.24 1.17 0.23 8.69| | 30: 1.16 - 1.15 2740 148 0.81 26.53 1.15 0.23 8.69| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.69 max = 1475.89 mean = 214.18| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.38| |phase err.(test): min = 0.00 max = 89.71 mean = 22.25| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 0.253 1557 Z= 5.583 Angle : 5.316 19.200 2118 Z= 3.665 Chirality : 0.401 1.349 243 Planarity : 0.031 0.086 284 Dihedral : 13.837 86.569 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 1.08 % Allowed : 2.70 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 5.59 % Favored : 93.17 % Cbeta Deviations : 35.68 % 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: -2.36 (0.49), residues: 224 helix: -2.65 (0.39), residues: 103 sheet: -0.39 (0.73), residues: 38 loop : -0.27 (0.63), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.075 0.016 ARG A 156 TYR 0.143 0.050 TYR A 141 PHE 0.116 0.044 PHE A 119 HIS 0.047 0.028 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2609 r_free= 0.1934 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792011 | | target function (ml) not normalized (work): 232591.308943 | | target function (ml) not normalized (free): 11792.018701 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2567 0.2609 0.1934 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2567 0.2609 0.1934 n_refl.: 87602 remove outliers: r(all,work,free)=0.1985 0.1990 0.1934 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2008 0.2013 0.1947 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1648 0.1642 0.1756 n_refl.: 87594 remove outliers: r(all,work,free)=0.1647 0.1642 0.1756 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 0.3835 386.628 358.003 0.735 0.915 0.401 11.894-9.307 99.02 97 4 0.1808 614.139 593.788 1.020 0.915 0.370 9.237-7.194 100.00 213 7 0.2162 502.290 491.393 1.053 0.916 0.360 7.162-5.571 100.00 427 22 0.2125 376.941 365.920 1.018 0.917 0.330 5.546-4.326 100.00 867 58 0.1307 517.447 510.547 1.054 0.917 0.219 4.315-3.360 100.00 1859 96 0.1142 492.095 488.493 1.099 0.919 0.163 3.356-2.611 100.00 3867 181 0.1443 323.281 320.004 1.085 0.920 0.129 2.608-2.026 99.99 8198 413 0.1366 214.306 212.016 1.091 0.923 0.000 2.025-1.573 100.00 17313 902 0.1654 104.656 103.931 1.089 0.928 0.000 1.573-1.221 100.00 36679 1900 0.2065 46.409 45.173 1.069 0.936 0.000 1.221-1.150 99.97 13689 708 0.2586 29.241 27.019 1.031 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0438 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1642 r_free=0.1756 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1642 r_free=0.1756 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.522156 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2029.434230 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1210 0.1466 0.0256 0.007 0.9 1.0 0.5 0.0 0 11.761 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 14.66 2.56 3.013 19.050 2029.434 0.017 12.40 15.40 3.00 3.154 19.508 2029.434 0.016 Individual atomic B min max mean iso aniso Overall: 8.59 118.75 20.95 2.87 0 1785 Protein: 8.59 118.75 17.83 2.87 0 1519 Water: 11.09 114.93 39.04 N/A 0 258 Other: 22.49 36.09 28.80 N/A 0 8 Chain A: 8.59 118.75 20.95 N/A 0 1785 Histogram: Values Number of atoms 8.59 - 19.60 1212 19.60 - 30.62 226 30.62 - 41.64 169 41.64 - 52.65 95 52.65 - 63.67 54 63.67 - 74.68 17 74.68 - 85.70 5 85.70 - 96.72 4 96.72 - 107.73 0 107.73 - 118.75 3 =========================== Idealize ADP of riding H ========================== r_work=0.1241 r_free=0.1540 r_work=0.1245 r_free=0.1544 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1245 r_free = 0.1544 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 = 0.1245 r_free = 0.1549 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 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= 0.1245 r_free= 0.1549 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015478 | | target function (ls_wunit_k1) not normalized (work): 1289.237389 | | target function (ls_wunit_k1) not normalized (free): 112.954776 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1259 0.1245 0.1549 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1697 0.1695 0.1775 n_refl.: 87593 remove outliers: r(all,work,free)=0.1697 0.1695 0.1775 n_refl.: 87593 overall B=0.14 to atoms: r(all,work,free)=0.1720 0.1718 0.1791 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1258 0.1243 0.1541 n_refl.: 87593 remove outliers: r(all,work,free)=0.1257 0.1243 0.1541 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 0.3625 299.465 278.622 0.636 1.002 0.380 11.894-9.307 99.02 97 4 0.1613 479.727 467.870 0.910 1.003 0.380 9.237-7.194 100.00 213 7 0.1813 392.358 387.529 0.950 1.003 0.319 7.162-5.571 100.00 427 22 0.1708 294.443 288.705 0.923 1.003 0.263 5.546-4.326 100.00 867 58 0.0915 404.197 401.757 0.950 1.003 0.204 4.315-3.360 100.00 1859 96 0.0777 384.394 383.351 0.996 1.002 0.180 3.356-2.611 100.00 3867 181 0.1023 252.527 251.802 0.998 1.002 0.129 2.608-2.026 99.99 8198 413 0.0976 167.402 166.855 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1210 81.751 81.947 1.018 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1648 36.252 35.705 1.005 0.998 0.000 1.221-1.150 99.97 13689 708 0.2362 22.841 21.333 0.969 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0548 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1243 r_free=0.1541 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1244 r_free=0.1543 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1244 r_free=0.1543 | n_water=258 | time (s): 2.400 (total time: 2.400) Filter (dist) r_work=0.1254 r_free=0.1539 | n_water=252 | time (s): 26.350 (total time: 28.750) Filter (q & B) r_work=0.1257 r_free=0.1538 | n_water=249 | time (s): 3.720 (total time: 32.470) Compute maps r_work=0.1257 r_free=0.1538 | n_water=249 | time (s): 1.780 (total time: 34.250) Filter (map) r_work=0.1278 r_free=0.1548 | n_water=234 | time (s): 3.570 (total time: 37.820) Find peaks r_work=0.1278 r_free=0.1548 | n_water=234 | time (s): 0.730 (total time: 38.550) Add new water r_work=0.1431 r_free=0.1708 | n_water=453 | time (s): 3.840 (total time: 42.390) Refine new water occ: r_work=0.1329 r_free=0.1572 adp: r_work=0.1254 r_free=0.1524 occ: r_work=0.1267 r_free=0.1516 adp: r_work=0.1233 r_free=0.1505 occ: r_work=0.1237 r_free=0.1493 adp: r_work=0.1226 r_free=0.1493 ADP+occupancy (water only), MIN, final r_work=0.1226 r_free=0.1493 r_work=0.1226 r_free=0.1493 | n_water=453 | time (s): 84.050 (total time: 126.440) Filter (q & B) r_work=0.1233 r_free=0.1499 | n_water=431 | time (s): 4.120 (total time: 130.560) Filter (dist only) r_work=0.1233 r_free=0.1499 | n_water=431 | time (s): 41.010 (total time: 171.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.733816 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1488.641892 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 0.1518 0.0288 0.007 0.9 2.2 0.5 0.0 0 12.367 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.30 15.18 2.88 3.781 23.131 1488.642 0.015 12.02 14.88 2.87 4.159 22.944 1488.642 0.015 Individual atomic B min max mean iso aniso Overall: 8.78 114.79 23.12 2.60 197 1761 Protein: 8.78 114.79 17.63 2.60 0 1519 Water: 10.81 73.18 42.34 N/A 197 234 Other: 25.35 35.92 30.47 N/A 0 8 Chain A: 8.78 114.79 20.33 N/A 0 1761 Chain S: 18.29 69.49 48.11 N/A 197 0 Histogram: Values Number of atoms 8.78 - 19.38 1210 19.38 - 29.98 251 29.98 - 40.58 189 40.58 - 51.19 146 51.19 - 61.79 103 61.79 - 72.39 47 72.39 - 82.99 6 82.99 - 93.59 3 93.59 - 104.19 1 104.19 - 114.79 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1489 r_work=0.1202 r_free=0.1488 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1488 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1487 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.19 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= 0.1204 r_free= 0.1487 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014209 | | target function (ls_wunit_k1) not normalized (work): 1183.558333 | | target function (ls_wunit_k1) not normalized (free): 103.844019 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1218 0.1204 0.1487 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1607 0.1602 0.1741 n_refl.: 87592 remove outliers: r(all,work,free)=0.1607 0.1602 0.1741 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1613 0.1608 0.1745 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1214 0.1201 0.1483 n_refl.: 87592 remove outliers: r(all,work,free)=0.1213 0.1199 0.1483 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 0.3400 295.396 271.115 0.626 0.939 0.364 11.894-9.307 99.02 97 4 0.1513 479.727 478.865 0.985 0.940 0.360 9.237-7.194 100.00 213 7 0.1692 392.358 392.688 1.044 0.940 0.280 7.162-5.571 100.00 427 22 0.1512 294.443 290.428 1.003 0.940 0.225 5.546-4.326 100.00 867 58 0.0841 404.197 401.877 1.020 0.940 0.206 4.315-3.360 100.00 1859 96 0.0725 384.394 383.170 1.067 0.941 0.200 3.356-2.611 100.00 3867 181 0.0966 252.527 251.870 1.073 0.941 0.072 2.608-2.026 99.99 8198 413 0.0966 167.402 167.028 1.081 0.943 0.000 2.025-1.573 100.00 17313 902 0.1177 81.751 81.959 1.086 0.945 0.000 1.573-1.221 100.00 36679 1900 0.1605 36.252 35.769 1.068 0.949 0.000 1.221-1.150 99.97 13689 708 0.2335 22.841 21.389 1.023 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0652 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1483 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1483 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1483 | n_water=431 | time (s): 1.910 (total time: 1.910) Filter (dist) r_work=0.1198 r_free=0.1483 | n_water=429 | time (s): 38.000 (total time: 39.910) Filter (q & B) r_work=0.1198 r_free=0.1483 | n_water=429 | time (s): 1.490 (total time: 41.400) Compute maps r_work=0.1198 r_free=0.1483 | n_water=429 | time (s): 1.790 (total time: 43.190) Filter (map) r_work=0.1243 r_free=0.1469 | n_water=290 | time (s): 2.930 (total time: 46.120) Find peaks r_work=0.1243 r_free=0.1469 | n_water=290 | time (s): 0.460 (total time: 46.580) Add new water r_work=0.1370 r_free=0.1609 | n_water=493 | time (s): 2.930 (total time: 49.510) Refine new water occ: r_work=0.1266 r_free=0.1527 adp: r_work=0.1268 r_free=0.1529 occ: r_work=0.1245 r_free=0.1503 adp: r_work=0.1243 r_free=0.1506 occ: r_work=0.1231 r_free=0.1487 adp: r_work=0.1224 r_free=0.1487 ADP+occupancy (water only), MIN, final r_work=0.1224 r_free=0.1487 r_work=0.1224 r_free=0.1487 | n_water=493 | time (s): 337.240 (total time: 386.750) Filter (q & B) r_work=0.1229 r_free=0.1483 | n_water=448 | time (s): 2.980 (total time: 389.730) Filter (dist only) r_work=0.1229 r_free=0.1483 | n_water=448 | time (s): 36.090 (total time: 425.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.118711 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.826419 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 0.1233 0.1444 0.0210 0.006 0.9 1.6 0.5 0.0 0 1.059 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.33 14.44 2.10 3.614 22.063 49.826 3.727 12.24 14.05 1.81 4.107 21.871 49.826 3.656 Individual atomic B min max mean iso aniso Overall: 9.21 110.31 21.60 2.33 218 1757 Protein: 9.21 110.31 17.20 2.33 0 1519 Water: 11.45 72.23 36.43 N/A 218 230 Other: 21.06 32.25 27.35 N/A 0 8 Chain A: 9.21 110.31 19.82 N/A 0 1757 Chain S: 16.75 66.18 35.93 N/A 218 0 Histogram: Values Number of atoms 9.21 - 19.32 1235 19.32 - 29.43 279 29.43 - 39.54 224 39.54 - 49.65 132 49.65 - 59.76 73 59.76 - 69.87 19 69.87 - 79.98 7 79.98 - 90.09 3 90.09 - 100.20 1 100.20 - 110.31 2 =========================== Idealize ADP of riding H ========================== r_work=0.1224 r_free=0.1405 r_work=0.1225 r_free=0.1406 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1225 r_free = 0.1406 target_work(ml) = 3.656 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1218 r_free = 0.1401 target_work(ml) = 3.654 | | 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= 0.1218 r_free= 0.1401 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.653974 | | target function (ml) not normalized (work): 304350.477322 | | target function (ml) not normalized (free): 16075.144077 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1227 0.1218 0.1401 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1539 0.1539 0.1572 n_refl.: 87589 remove outliers: r(all,work,free)=0.1539 0.1539 0.1572 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1537 0.1537 0.1571 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1216 0.1208 0.1372 n_refl.: 87589 remove outliers: r(all,work,free)=0.1212 0.1204 0.1372 n_refl.: 87581 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.4026 294.761 256.985 0.463 1.000 0.322 11.894-9.307 97.06 95 4 0.2538 477.391 462.593 0.838 1.002 0.316 9.237-7.194 98.64 210 7 0.2436 385.903 385.239 0.941 1.002 0.160 7.162-5.571 100.00 427 22 0.2139 294.443 283.850 0.906 1.002 0.148 5.546-4.326 100.00 867 58 0.1127 404.197 399.305 0.951 1.002 0.140 4.315-3.360 100.00 1859 96 0.0955 384.394 381.597 0.992 1.002 0.133 3.356-2.611 100.00 3867 181 0.1154 252.527 250.631 0.999 1.002 0.053 2.608-2.026 99.99 8198 413 0.1049 167.402 166.408 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1010 81.751 81.898 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1287 36.252 35.831 1.019 0.999 0.000 1.221-1.150 99.97 13689 708 0.2123 22.841 21.457 0.977 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0248 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1204 r_free=0.1372 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1204 r_free=0.1372 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1204 r_free=0.1372 | n_water=448 | time (s): 1.880 (total time: 1.880) Filter (dist) r_work=0.1204 r_free=0.1372 | n_water=448 | time (s): 37.770 (total time: 39.650) Filter (q & B) r_work=0.1204 r_free=0.1371 | n_water=446 | time (s): 2.960 (total time: 42.610) Compute maps r_work=0.1204 r_free=0.1371 | n_water=446 | time (s): 1.890 (total time: 44.500) Filter (map) r_work=0.1230 r_free=0.1385 | n_water=306 | time (s): 3.540 (total time: 48.040) Find peaks r_work=0.1230 r_free=0.1385 | n_water=306 | time (s): 0.700 (total time: 48.740) Add new water r_work=0.1289 r_free=0.1445 | n_water=473 | time (s): 3.260 (total time: 52.000) Refine new water occ: r_work=0.1215 r_free=0.1378 adp: r_work=0.1216 r_free=0.1381 occ: r_work=0.1201 r_free=0.1369 adp: r_work=0.1200 r_free=0.1371 occ: r_work=0.1190 r_free=0.1365 adp: r_work=0.1187 r_free=0.1365 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1365 r_work=0.1187 r_free=0.1365 | n_water=473 | time (s): 170.960 (total time: 222.960) Filter (q & B) r_work=0.1194 r_free=0.1371 | n_water=440 | time (s): 3.460 (total time: 226.420) Filter (dist only) r_work=0.1194 r_free=0.1370 | n_water=439 | time (s): 39.520 (total time: 265.940) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.848596 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.862544 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 0.1201 0.1366 0.0164 0.006 0.9 1.6 0.5 0.0 0 0.924 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.66 1.64 3.428 21.428 47.863 3.639 11.88 13.59 1.71 3.831 21.305 47.863 3.626 Individual atomic B min max mean iso aniso Overall: 9.26 105.64 21.12 2.16 210 1756 Protein: 9.26 105.64 16.90 2.16 0 1519 Water: 11.52 70.81 35.62 N/A 210 229 Other: 21.13 30.12 25.64 N/A 0 8 Chain A: 9.26 105.64 19.48 N/A 0 1756 Chain S: 15.60 61.58 34.82 N/A 210 0 Histogram: Values Number of atoms 9.26 - 18.90 1230 18.90 - 28.54 284 28.54 - 38.18 213 38.18 - 47.81 132 47.81 - 57.45 66 57.45 - 67.09 27 67.09 - 76.73 9 76.73 - 86.37 2 86.37 - 96.01 1 96.01 - 105.64 2 =========================== Idealize ADP of riding H ========================== r_work=0.1188 r_free=0.1359 r_work=0.1188 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1188 r_free = 0.1359 target_work(ml) = 3.626 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1185 r_free = 0.1357 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1185 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.624839 | | target function (ml) not normalized (work): 301894.719118 | | target function (ml) not normalized (free): 15933.436609 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1185 0.1357 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1509 0.1509 0.1543 n_refl.: 87581 remove outliers: r(all,work,free)=0.1509 0.1509 0.1543 n_refl.: 87581 overall B=-0.01 to atoms: r(all,work,free)=0.1507 0.1507 0.1542 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1185 0.1355 n_refl.: 87581 remove outliers: r(all,work,free)=0.1191 0.1183 0.1355 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 0.4013 290.115 258.139 0.453 1.000 0.291 11.894-9.307 93.14 91 4 0.2348 476.446 454.524 0.835 1.002 0.270 9.237-7.194 98.18 209 7 0.2577 383.887 377.506 0.915 1.002 0.150 7.162-5.571 100.00 427 22 0.2229 294.443 284.833 0.903 1.002 0.120 5.546-4.326 100.00 867 58 0.1151 404.197 399.704 0.951 1.002 0.118 4.315-3.360 100.00 1859 96 0.0976 384.394 381.629 0.993 1.002 0.117 3.356-2.611 100.00 3867 181 0.1151 252.527 250.737 1.001 1.002 0.053 2.608-2.026 99.99 8198 413 0.1012 167.402 166.561 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0960 81.751 82.036 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1247 36.252 35.881 1.021 0.998 0.000 1.221-1.150 99.97 13689 708 0.2124 22.841 21.473 0.979 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0339 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1183 r_free=0.1355 After: r_work=0.1183 r_free=0.1355 ================================== NQH flips ================================== r_work=0.1183 r_free=0.1355 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=0.1183 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1183 r_free=0.1355 | n_water=439 | time (s): 1.990 (total time: 1.990) Filter (dist) r_work=0.1183 r_free=0.1355 | n_water=439 | time (s): 37.880 (total time: 39.870) Filter (q & B) r_work=0.1184 r_free=0.1354 | n_water=438 | time (s): 3.530 (total time: 43.400) Compute maps r_work=0.1184 r_free=0.1354 | n_water=438 | time (s): 1.280 (total time: 44.680) Filter (map) r_work=0.1207 r_free=0.1381 | n_water=337 | time (s): 3.070 (total time: 47.750) Find peaks r_work=0.1207 r_free=0.1381 | n_water=337 | time (s): 0.700 (total time: 48.450) Add new water r_work=0.1249 r_free=0.1426 | n_water=484 | time (s): 3.560 (total time: 52.010) Refine new water occ: r_work=0.1193 r_free=0.1360 adp: r_work=0.1193 r_free=0.1362 occ: r_work=0.1183 r_free=0.1350 adp: r_work=0.1182 r_free=0.1351 occ: r_work=0.1176 r_free=0.1344 adp: r_work=0.1173 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1173 r_free=0.1344 r_work=0.1173 r_free=0.1344 | n_water=484 | time (s): 113.760 (total time: 165.770) Filter (q & B) r_work=0.1180 r_free=0.1351 | n_water=440 | time (s): 3.400 (total time: 169.170) Filter (dist only) r_work=0.1180 r_free=0.1350 | n_water=439 | time (s): 38.200 (total time: 207.370) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.873036 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 38.603074 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 0.1201 0.1369 0.0168 0.007 1.0 4.5 0.5 0.0 0 0.937 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.69 1.68 3.287 21.054 38.603 3.630 12.09 13.75 1.67 3.462 20.997 38.603 3.627 Individual atomic B min max mean iso aniso Overall: 9.26 101.88 20.92 2.01 211 1755 Protein: 9.26 101.88 16.75 2.01 0 1519 Water: 11.52 70.22 35.28 N/A 211 228 Other: 21.18 29.26 25.36 N/A 0 8 Chain A: 9.26 101.88 19.30 N/A 0 1755 Chain S: 14.96 60.05 34.40 N/A 211 0 Histogram: Values Number of atoms 9.26 - 18.52 1222 18.52 - 27.78 282 27.78 - 37.05 206 37.05 - 46.31 148 46.31 - 55.57 66 55.57 - 64.83 26 64.83 - 74.09 11 74.09 - 83.36 2 83.36 - 92.62 1 92.62 - 101.88 2 =========================== Idealize ADP of riding H ========================== r_work=0.1209 r_free=0.1375 r_work=0.1209 r_free=0.1375 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1209 r_free = 0.1375 target_work(ml) = 3.628 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1207 r_free = 0.1373 target_work(ml) = 3.627 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1207 r_free= 0.1373 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.626690 | | target function (ml) not normalized (work): 302027.081498 | | target function (ml) not normalized (free): 15942.454697 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1444 0.1445 5.7204 5.629| | 2: 3.57 - 2.84 1.00 2888 124 0.1130 0.1460 5.2029 5.2609| | 3: 2.83 - 2.48 1.00 2820 163 0.1232 0.1275 5.0043 5.0127| | 4: 2.47 - 2.25 1.00 2825 136 0.1026 0.1155 4.7055 4.7463| | 5: 2.25 - 2.09 1.00 2756 127 0.1010 0.1065 4.6487 4.712| | 6: 2.09 - 1.97 1.00 2846 113 0.0979 0.1172 4.3514 4.4714| | 7: 1.97 - 1.87 1.00 2787 165 0.0993 0.1234 4.0714 4.1771| | 8: 1.87 - 1.79 1.00 2789 144 0.1025 0.1205 3.9894 4.0606| | 9: 1.79 - 1.72 1.00 2745 138 0.0956 0.1262 3.7173 3.8944| | 10: 1.72 - 1.66 1.00 2831 160 0.1011 0.1247 3.6392 3.7684| | 11: 1.66 - 1.61 1.00 2712 147 0.0968 0.1098 3.5723 3.6111| | 12: 1.61 - 1.56 1.00 2773 144 0.0927 0.1216 3.3593 3.4957| | 13: 1.56 - 1.52 1.00 2745 130 0.0987 0.1101 3.3456 3.4459| | 14: 1.52 - 1.48 1.00 2803 134 0.1003 0.1164 3.2706 3.3553| | 15: 1.48 - 1.45 1.00 2738 128 0.1022 0.1368 3.179 3.331| | 16: 1.45 - 1.42 1.00 2756 161 0.1076 0.1277 3.1615 3.2604| | 17: 1.42 - 1.39 1.00 2785 139 0.1126 0.1303 3.1214 3.2411| | 18: 1.39 - 1.36 1.00 2741 179 0.1161 0.1386 3.0936 3.2723| | 19: 1.36 - 1.34 1.00 2807 134 0.1227 0.1602 3.0997 3.2738| | 20: 1.34 - 1.32 1.00 2696 147 0.1321 0.1467 3.0916 3.1336| | 21: 1.32 - 1.30 1.00 2785 112 0.1416 0.1624 3.0905 3.1598| | 22: 1.29 - 1.27 1.00 2704 152 0.1481 0.1917 3.0902 3.2887| | 23: 1.27 - 1.26 1.00 2802 156 0.1584 0.1842 3.1065 3.2053| | 24: 1.26 - 1.24 1.00 2744 132 0.1627 0.1780 3.0967 3.2045| | 25: 1.24 - 1.22 1.00 2733 148 0.1800 0.2293 3.1123 3.2899| | 26: 1.22 - 1.21 1.00 2727 135 0.1861 0.1790 3.1269 3.1991| | 27: 1.21 - 1.19 1.00 2814 148 0.2016 0.2092 3.1444 3.1495| | 28: 1.19 - 1.18 1.00 2671 147 0.2149 0.2319 3.1439 3.1672| | 29: 1.18 - 1.16 1.00 2800 134 0.2224 0.2365 3.1312 3.2295| | 30: 1.16 - 1.15 1.00 2739 148 0.2379 0.2475 3.119 3.1642| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.93 1.00 0.97 6182.76| | 2: 3.57 - 2.84 2888 124 0.92 13.18 1.01 0.97 6182.76| | 3: 2.83 - 2.48 2820 163 0.89 17.30 0.98 0.97 5182.89| | 4: 2.47 - 2.25 2825 136 0.91 14.39 1.00 0.98 2604.56| | 5: 2.25 - 2.09 2756 127 0.90 16.65 1.01 0.98 2604.56| | 6: 2.09 - 1.97 2846 113 0.92 13.45 1.02 0.98 1531.71| | 7: 1.97 - 1.87 2787 165 0.94 10.64 1.02 0.98 616.70| | 8: 1.87 - 1.79 2789 144 0.92 14.19 1.00 0.98 616.70| | 9: 1.79 - 1.72 2745 138 0.93 11.33 0.98 0.97 336.96| | 10: 1.72 - 1.66 2831 160 0.93 12.20 0.98 0.97 280.94| | 11: 1.66 - 1.61 2712 147 0.93 12.82 0.98 0.97 268.37| | 12: 1.61 - 1.56 2773 144 0.95 9.60 0.99 0.97 149.79| | 13: 1.56 - 1.52 2745 130 0.94 11.18 1.02 0.97 149.79| | 14: 1.52 - 1.48 2803 134 0.94 11.41 1.02 0.98 134.00| | 15: 1.48 - 1.45 2738 128 0.95 10.53 1.02 0.98 105.06| | 16: 1.45 - 1.42 2756 161 0.94 11.67 1.02 0.98 105.06| | 17: 1.42 - 1.39 2785 139 0.94 11.60 1.01 0.98 94.56| | 18: 1.39 - 1.36 2741 179 0.94 11.82 1.01 0.98 88.48| | 19: 1.36 - 1.34 2807 134 0.94 12.37 1.00 0.98 88.48| | 20: 1.34 - 1.32 2696 147 0.94 12.45 0.99 0.97 82.87| | 21: 1.32 - 1.30 2785 112 0.94 13.39 0.99 0.97 82.48| | 22: 1.29 - 1.27 2704 152 0.93 13.91 0.98 0.96 82.55| | 23: 1.27 - 1.26 2802 156 0.92 14.81 0.98 0.95 82.95| | 24: 1.26 - 1.24 2744 132 0.92 14.94 0.97 0.95 82.95| | 25: 1.24 - 1.22 2733 148 0.91 16.34 0.96 0.94 84.53| | 26: 1.22 - 1.21 2727 135 0.90 18.06 1.02 0.93 86.28| | 27: 1.21 - 1.19 2814 148 0.89 18.73 1.02 0.93 86.28| | 28: 1.19 - 1.18 2671 147 0.88 20.22 1.01 0.93 89.77| | 29: 1.18 - 1.16 2800 134 0.88 20.56 0.99 0.93 91.08| | 30: 1.16 - 1.15 2739 148 0.86 21.99 0.98 0.93 91.08| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 82.48 max = 6182.76 mean = 965.57| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 14.01| |phase err.(test): min = 0.00 max = 88.98 mean = 14.10| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1207 0.1373 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1519 0.1519 0.1566 n_refl.: 87575 remove outliers: r(all,work,free)=0.1519 0.1519 0.1566 n_refl.: 87575 overall B=-0.01 to atoms: r(all,work,free)=0.1517 0.1516 0.1564 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1215 0.1207 0.1378 n_refl.: 87575 remove outliers: r(all,work,free)=0.1215 0.1207 0.1378 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 0.4328 290.115 245.964 0.437 1.000 0.314 11.894-9.307 93.14 91 4 0.2425 476.446 461.147 0.851 1.002 0.216 9.237-7.194 98.18 209 7 0.2643 383.887 374.983 0.900 1.002 0.130 7.162-5.571 100.00 427 22 0.2292 294.443 283.816 0.897 1.002 0.120 5.546-4.326 100.00 867 58 0.1193 404.197 399.820 0.953 1.002 0.110 4.315-3.360 100.00 1859 96 0.1009 384.394 381.415 0.993 1.002 0.100 3.356-2.611 100.00 3867 181 0.1195 252.527 250.632 1.000 1.002 0.043 2.608-2.026 99.99 8198 413 0.1048 167.402 166.442 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0981 81.751 82.016 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1233 36.252 35.877 1.022 0.997 0.000 1.221-1.150 99.97 13689 708 0.2119 22.841 21.462 0.980 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0358 ================= 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 : 0.2609 0.1934 0.084 5.316 8.8 119.3 19.9 258 0.000 1_bss: 0.1642 0.1756 0.084 5.316 9.0 119.5 20.1 258 0.000 1_settarget: 0.1642 0.1756 0.084 5.316 9.0 119.5 20.1 258 0.000 1_nqh: 0.1642 0.1756 0.084 5.316 9.0 119.5 20.1 258 0.000 1_weight: 0.1642 0.1756 0.084 5.316 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1210 0.1466 0.007 0.941 9.0 119.5 20.1 258 0.125 1_adp: 0.1241 0.1540 0.007 0.941 8.6 118.7 20.9 258 0.125 1_regHadp: 0.1245 0.1544 0.007 0.941 8.6 118.7 20.9 258 0.125 1_occ: 0.1245 0.1549 0.007 0.941 8.6 118.7 20.9 258 0.125 2_bss: 0.1243 0.1541 0.007 0.941 8.7 118.9 21.1 258 0.125 2_settarget: 0.1243 0.1541 0.007 0.941 8.7 118.9 21.1 258 0.125 2_updatecdl: 0.1243 0.1541 0.007 0.941 8.7 118.9 21.1 258 0.125 2_nqh: 0.1244 0.1543 0.007 0.941 8.7 118.9 21.1 258 0.128 2_sol: 0.1233 0.1499 0.007 0.941 8.7 118.9 23.5 431 n/a 2_weight: 0.1233 0.1499 0.007 0.941 8.7 118.9 23.5 431 n/a 2_xyzrec: 0.1230 0.1518 0.007 0.864 8.7 118.9 23.5 431 n/a 2_adp: 0.1202 0.1489 0.007 0.864 8.8 114.8 23.1 431 n/a 2_regHadp: 0.1202 0.1488 0.007 0.864 8.8 114.8 23.1 431 n/a 2_occ: 0.1204 0.1487 0.007 0.864 8.8 114.8 23.1 431 n/a 3_bss: 0.1199 0.1483 0.007 0.864 8.8 114.8 23.2 431 n/a 3_settarget: 0.1199 0.1483 0.007 0.864 8.8 114.8 23.2 431 n/a 3_updatecdl: 0.1199 0.1483 0.007 0.865 8.8 114.8 23.2 431 n/a 3_nqh: 0.1199 0.1483 0.007 0.865 8.8 114.8 23.2 431 n/a 3_sol: 0.1229 0.1483 0.007 0.865 8.8 114.8 21.9 448 n/a 3_weight: 0.1229 0.1483 0.007 0.865 8.8 114.8 21.9 448 n/a 3_xyzrec: 0.1233 0.1444 0.006 0.923 8.8 114.8 21.9 448 n/a 3_adp: 0.1224 0.1405 0.006 0.923 9.2 110.3 21.6 448 n/a 3_regHadp: 0.1225 0.1406 0.006 0.923 9.2 110.3 21.6 448 n/a 3_occ: 0.1218 0.1401 0.006 0.923 9.2 110.3 21.6 448 n/a 4_bss: 0.1204 0.1372 0.006 0.923 9.2 110.3 21.6 448 n/a 4_settarget: 0.1204 0.1372 0.006 0.923 9.2 110.3 21.6 448 n/a 4_updatecdl: 0.1204 0.1372 0.006 0.921 9.2 110.3 21.6 448 n/a 4_nqh: 0.1204 0.1372 0.006 0.921 9.2 110.3 21.6 448 n/a 4_sol: 0.1194 0.1370 0.006 0.921 9.2 110.3 21.3 439 n/a 4_weight: 0.1194 0.1370 0.006 0.921 9.2 110.3 21.3 439 n/a 4_xyzrec: 0.1201 0.1366 0.006 0.939 9.2 110.3 21.3 439 n/a 4_adp: 0.1188 0.1359 0.006 0.939 9.3 105.6 21.1 439 n/a 4_regHadp: 0.1188 0.1359 0.006 0.939 9.3 105.6 21.1 439 n/a 4_occ: 0.1185 0.1357 0.006 0.939 9.3 105.6 21.1 439 n/a 5_bss: 0.1183 0.1355 0.006 0.939 9.2 105.6 21.1 439 n/a 5_settarget: 0.1183 0.1355 0.006 0.939 9.2 105.6 21.1 439 n/a 5_updatecdl: 0.1183 0.1355 0.006 0.941 9.2 105.6 21.1 439 n/a 5_setrh: 0.1183 0.1355 0.006 0.941 9.2 105.6 21.1 439 n/a 5_nqh: 0.1183 0.1355 0.006 0.941 9.2 105.6 21.1 439 n/a 5_sol: 0.1180 0.1350 0.006 0.941 9.2 105.6 21.0 439 n/a 5_weight: 0.1180 0.1350 0.006 0.941 9.2 105.6 21.0 439 n/a 5_xyzrec: 0.1201 0.1369 0.007 1.020 9.2 105.6 21.0 439 n/a 5_adp: 0.1209 0.1375 0.007 1.020 9.3 101.9 20.9 439 n/a 5_regHadp: 0.1209 0.1375 0.007 1.020 9.3 101.9 20.9 439 n/a 5_occ: 0.1207 0.1373 0.007 1.020 9.3 101.9 20.9 439 n/a end: 0.1207 0.1378 0.007 1.020 9.2 101.9 20.9 439 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_1522381_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_1522381_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7700 Refinement macro-cycles (run) : 3584.5100 Write final files (write_after_run_outputs) : 61.3400 Total : 3650.6200 Total CPU time: 61.46 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:12:20 PST -0800 (1735452740.39 s) Start R-work = 0.1642, R-free = 0.1756 Final R-work = 0.1207, R-free = 0.1378 =============================================================================== Job complete usr+sys time: 3786.77 seconds wall clock time: 67 minutes 32.97 seconds (4052.97 seconds total)