Starting phenix.refine on Sat Dec 28 21:06:33 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6446528.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_6446528.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6446528.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" 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 3 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: 2.05, per 1000 atoms: 0.61 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 255.7 milliseconds Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.92: 547 0.92 - 1.19: 1123 1.19 - 1.46: 744 1.46 - 1.73: 724 1.73 - 1.99: 15 Bond restraints: 3153 Sorted by residual: bond pdb=" N LYS A 130 " pdb=" CA LYS A 130 " ideal model delta sigma weight residual 1.459 1.232 0.227 1.19e-02 7.06e+03 3.64e+02 bond pdb=" C SER A 121 " pdb=" O SER A 121 " ideal model delta sigma weight residual 1.234 1.455 -0.221 1.27e-02 6.20e+03 3.04e+02 bond pdb=" C ILE A 105 " pdb=" N CYS A 106 " ideal model delta sigma weight residual 1.332 1.574 -0.242 1.40e-02 5.10e+03 2.98e+02 bond pdb=" CA ALYS A 99 " pdb=" C ALYS A 99 " ideal model delta sigma weight residual 1.527 1.309 0.218 1.27e-02 6.20e+03 2.94e+02 bond pdb=" CA GLY A 174 " pdb=" C GLY A 174 " ideal model delta sigma weight residual 1.520 1.320 0.200 1.21e-02 6.83e+03 2.73e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.95: 3315 4.95 - 9.90: 1822 9.90 - 14.85: 544 14.85 - 19.80: 87 19.80 - 24.75: 9 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OE1BGLN A 80 " pdb=" CD BGLN A 80 " pdb=" NE2BGLN A 80 " ideal model delta sigma weight residual 122.60 141.59 -18.99 1.00e+00 1.00e+00 3.61e+02 angle pdb=" O VAL A 50 " pdb=" C VAL A 50 " pdb=" N VAL A 51 " ideal model delta sigma weight residual 122.67 106.92 15.75 1.09e+00 8.42e-01 2.09e+02 angle pdb=" O VAL A 8 " pdb=" C VAL A 8 " pdb=" N ILE A 9 " ideal model delta sigma weight residual 123.20 137.66 -14.46 1.06e+00 8.90e-01 1.86e+02 angle pdb=" CA GLN A 95 " pdb=" C GLN A 95 " pdb=" O GLN A 95 " ideal model delta sigma weight residual 120.55 134.58 -14.03 1.06e+00 8.90e-01 1.75e+02 angle pdb=" O ILE A 52 " pdb=" C ILE A 52 " pdb=" N ACYS A 53 " ideal model delta sigma weight residual 123.03 136.31 -13.28 1.11e+00 8.12e-01 1.43e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 18.03: 968 18.03 - 36.04: 86 36.04 - 54.05: 44 54.05 - 72.06: 10 72.06 - 90.07: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ARG A 48 " pdb=" C ARG A 48 " pdb=" N ASP A 49 " pdb=" CA ASP A 49 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA BGLY A 65 " pdb=" C BGLY A 65 " pdb=" N BPRO A 66 " pdb=" CA BPRO A 66 " ideal model delta harmonic sigma weight residual 0.00 -21.18 21.18 0 5.00e+00 4.00e-02 1.79e+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 -159.12 -20.88 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.231: 96 0.231 - 0.460: 75 0.460 - 0.690: 53 0.690 - 0.919: 13 0.919 - 1.149: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BLYS A 99 " pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CB BLYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.36 1.15 2.00e-01 2.50e+01 3.30e+01 chirality pdb=" CA PHE A 162 " pdb=" N PHE A 162 " pdb=" C PHE A 162 " pdb=" CB PHE A 162 " both_signs ideal model delta sigma weight residual False 2.51 1.38 1.13 2.00e-01 2.50e+01 3.18e+01 chirality pdb=" CA ALA A 183 " pdb=" N ALA A 183 " pdb=" C ALA A 183 " pdb=" CB ALA A 183 " both_signs ideal model delta sigma weight residual False 2.48 1.37 1.12 2.00e-01 2.50e+01 3.14e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 45 " 0.010 2.00e-02 2.50e+03 8.86e-02 1.18e+02 pdb=" CD GLN A 45 " -0.167 2.00e-02 2.50e+03 pdb=" OE1 GLN A 45 " 0.095 2.00e-02 2.50e+03 pdb=" NE2 GLN A 45 " 0.062 2.00e-02 2.50e+03 pdb="HE21 GLN A 45 " 0.057 2.00e-02 2.50e+03 pdb="HE22 GLN A 45 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.062 2.00e-02 2.50e+03 6.06e-02 1.10e+02 pdb=" CG PHE A 164 " 0.139 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.082 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.066 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.066 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.049 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.012 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.039 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.020 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.025 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.058 2.00e-02 2.50e+03 5.69e-02 9.71e+01 pdb=" CG PHE A 162 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.064 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.067 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.089 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.024 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.026 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.083 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.058 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.044 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.018 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1017 2.32 - 2.89: 8108 2.89 - 3.46: 10552 3.46 - 4.03: 15217 4.03 - 4.60: 21670 Nonbonded interactions: 56564 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.747 2.100 nonbonded pdb=" O LEU A 166 " pdb=" H GLU A 170 " model vdw 1.820 2.450 nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.841 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.844 2.450 nonbonded pdb=" O GLU A 16 " pdb=" H VAL A 20 " model vdw 1.852 2.450 ... (remaining 56559 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_6446528_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2608 r_free= 0.1926 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.784748 | | target function (ml) not normalized (work): 231986.208295 | | target function (ml) not normalized (free): 11772.415375 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3032 0.2105 7.0587 4.95| | 2: 3.57 - 2.84 1.00 2876 122 0.2457 0.1792 4.3496 4.3486| | 3: 2.84 - 2.48 1.00 2833 165 0.2335 0.1646 4.136 4.1621| | 4: 2.47 - 2.25 1.00 2825 136 0.2325 0.1417 3.8367 3.8321| | 5: 2.25 - 2.09 1.00 2756 127 0.2506 0.1666 3.8014 3.829| | 6: 2.09 - 1.97 1.00 2846 113 0.2542 0.1673 3.4617 3.5493| | 7: 1.97 - 1.87 1.00 2787 165 0.2550 0.1801 3.1368 3.1773| | 8: 1.87 - 1.79 1.00 2789 144 0.2513 0.1760 3.0394 3.0944| | 9: 1.79 - 1.72 1.00 2745 138 0.2430 0.2040 2.8816 3.0192| | 10: 1.72 - 1.66 1.00 2789 158 0.2349 0.1718 2.7889 2.7968| | 11: 1.66 - 1.61 1.00 2740 147 0.2525 0.1888 2.7308 2.7255| | 12: 1.61 - 1.56 1.00 2787 146 0.2549 0.1862 2.6311 2.5902| | 13: 1.56 - 1.52 1.00 2745 130 0.2536 0.1896 2.5616 2.5921| | 14: 1.52 - 1.48 1.00 2803 134 0.2594 0.1967 2.4899 2.5235| | 15: 1.48 - 1.45 1.00 2738 128 0.2532 0.1853 2.4507 2.3522| | 16: 1.45 - 1.42 1.00 2756 161 0.2650 0.2159 2.3697 2.4337| | 17: 1.42 - 1.39 1.00 2785 139 0.2633 0.2126 2.3148 2.3757| | 18: 1.39 - 1.36 1.00 2741 179 0.2629 0.2305 2.2494 2.381| | 19: 1.36 - 1.34 1.00 2807 134 0.2640 0.2093 2.2312 2.2269| | 20: 1.34 - 1.32 1.00 2696 147 0.2679 0.2473 2.1943 2.2749| | 21: 1.32 - 1.30 1.00 2785 112 0.2654 0.2248 2.1446 2.1713| | 22: 1.29 - 1.27 1.00 2704 152 0.2714 0.2552 2.1263 2.2166| | 23: 1.27 - 1.26 1.00 2802 156 0.2754 0.2291 2.104 2.1256| | 24: 1.26 - 1.24 1.00 2744 132 0.2782 0.2590 2.0739 2.2022| | 25: 1.24 - 1.22 1.00 2734 148 0.2847 0.2256 2.0308 2.0587| | 26: 1.22 - 1.21 1.00 2727 135 0.2906 0.2300 2.0156 2.0661| | 27: 1.21 - 1.19 1.00 2814 148 0.2981 0.2590 2.0143 1.994| | 28: 1.19 - 1.18 1.00 2671 147 0.2989 0.2715 1.9878 1.9747| | 29: 1.18 - 1.16 1.00 2800 134 0.2959 0.2801 1.9534 2.0404| | 30: 1.16 - 1.15 1.00 2740 148 0.3062 0.2953 1.9207 1.9655| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.94 0.76 0.23 1508.99| | 2: 3.57 - 2.84 2876 122 0.80 26.32 1.27 0.23 1508.99| | 3: 2.84 - 2.48 2833 165 0.74 32.11 1.24 0.24 1249.81| | 4: 2.47 - 2.25 2825 136 0.81 25.53 1.26 0.25 577.20| | 5: 2.25 - 2.09 2756 127 0.77 29.43 1.28 0.25 577.20| | 6: 2.09 - 1.97 2846 113 0.84 22.51 1.29 0.25 312.54| | 7: 1.97 - 1.87 2787 165 0.90 16.13 1.28 0.26 86.83| | 8: 1.87 - 1.79 2789 144 0.86 20.78 1.26 0.26 86.83| | 9: 1.79 - 1.72 2745 138 0.88 18.13 1.23 0.25 52.54| | 10: 1.72 - 1.66 2789 158 0.87 19.47 1.21 0.25 45.68| | 11: 1.66 - 1.61 2740 147 0.86 20.91 1.25 0.25 44.06| | 12: 1.61 - 1.56 2787 146 0.89 17.72 1.24 0.25 27.62| | 13: 1.56 - 1.52 2745 130 0.87 19.57 1.24 0.25 27.62| | 14: 1.52 - 1.48 2803 134 0.87 20.07 1.23 0.25 24.97| | 15: 1.48 - 1.45 2738 128 0.88 19.34 1.21 0.25 20.11| | 16: 1.45 - 1.42 2756 161 0.86 21.19 1.24 0.25 20.11| | 17: 1.42 - 1.39 2785 139 0.87 20.62 1.23 0.25 17.43| | 18: 1.39 - 1.36 2741 179 0.86 21.08 1.23 0.25 15.88| | 19: 1.36 - 1.34 2807 134 0.86 21.90 1.22 0.25 15.88| | 20: 1.34 - 1.32 2696 147 0.86 21.27 1.21 0.25 13.32| | 21: 1.32 - 1.30 2785 112 0.86 21.95 1.20 0.25 13.15| | 22: 1.29 - 1.27 2704 152 0.85 22.42 1.21 0.25 12.84| | 23: 1.27 - 1.26 2802 156 0.86 22.09 1.21 0.24 11.26| | 24: 1.26 - 1.24 2744 132 0.85 22.83 1.21 0.24 11.26| | 25: 1.24 - 1.22 2734 148 0.84 23.95 1.20 0.24 10.65| | 26: 1.22 - 1.21 2727 135 0.84 24.07 1.20 0.23 9.97| | 27: 1.21 - 1.19 2814 148 0.83 24.84 1.21 0.23 9.97| | 28: 1.19 - 1.18 2671 147 0.83 25.35 1.18 0.23 9.39| | 29: 1.18 - 1.16 2800 134 0.82 25.82 1.16 0.23 9.17| | 30: 1.16 - 1.15 2740 148 0.80 27.67 1.16 0.23 9.17| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 9.17 max = 1508.99 mean = 217.34| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 22.47| |phase err.(test): min = 0.00 max = 89.62 mean = 22.48| |-----------------------------------------------------------------------------| ----------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 0.242 1557 Z= 5.374 Angle : 5.219 18.992 2118 Z= 3.663 Chirality : 0.412 1.149 243 Planarity : 0.032 0.167 284 Dihedral : 13.668 90.066 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 32.43 % 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: -2.24 (0.49), residues: 224 helix: -2.46 (0.40), residues: 109 sheet: -1.52 (0.69), residues: 30 loop : 0.37 (0.64), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.068 0.013 ARG A 145 TYR 0.134 0.039 TYR A 141 PHE 0.134 0.055 PHE A 164 HIS 0.055 0.031 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2608 r_free= 0.1926 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.784748 | | target function (ml) not normalized (work): 231986.208295 | | target function (ml) not normalized (free): 11772.415375 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2608 0.1927 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2608 0.1927 n_refl.: 87602 remove outliers: r(all,work,free)=0.1976 0.1981 0.1927 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2000 0.2005 0.1940 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1641 0.1635 0.1740 n_refl.: 87594 remove outliers: r(all,work,free)=0.1640 0.1635 0.1740 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 0.3857 386.284 355.918 0.668 1.003 0.402 11.894-9.307 99.02 97 4 0.1876 613.594 594.747 0.922 1.003 0.380 9.237-7.194 100.00 213 7 0.2167 501.844 490.365 0.960 1.004 0.344 7.162-5.571 100.00 427 22 0.2227 376.606 363.891 0.933 1.004 0.273 5.546-4.326 100.00 867 58 0.1267 516.987 510.346 0.962 1.004 0.214 4.315-3.360 100.00 1859 96 0.1177 491.658 487.345 1.004 1.003 0.199 3.356-2.611 100.00 3867 181 0.1442 322.994 319.438 0.997 1.003 0.052 2.608-2.026 99.99 8198 413 0.1353 214.116 212.038 1.006 1.002 0.000 2.025-1.573 100.00 17313 902 0.1639 104.563 103.895 1.013 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2040 46.367 45.070 1.002 0.997 0.000 1.221-1.150 99.97 13689 708 0.2587 29.215 26.960 0.977 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0445 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1635 r_free=0.1740 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 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1640 r_free=0.1751 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.368852 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1996.617701 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 0.1215 0.1468 0.0253 0.007 1.0 1.3 0.5 0.0 0 12.684 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.15 14.68 2.53 3.013 19.053 1996.618 0.017 12.41 15.38 2.97 3.130 19.503 1996.618 0.016 Individual atomic B min max mean iso aniso Overall: 8.41 118.35 20.93 2.88 0 1785 Protein: 8.41 118.35 17.82 2.88 0 1519 Water: 10.99 114.60 39.05 N/A 0 258 Other: 22.81 35.56 28.61 N/A 0 8 Chain A: 8.41 118.35 20.93 N/A 0 1785 Histogram: Values Number of atoms 8.41 - 19.41 1208 19.41 - 30.40 230 30.40 - 41.40 165 41.40 - 52.39 99 52.39 - 63.38 54 63.38 - 74.38 17 74.38 - 85.37 5 85.37 - 96.37 4 96.37 - 107.36 0 107.36 - 118.35 3 =========================== Idealize ADP of riding H ========================== r_work=0.1241 r_free=0.1538 r_work=0.1245 r_free=0.1542 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1245 r_free = 0.1542 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 = 0.1545 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.29 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= 0.1545 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015341 | | target function (ls_wunit_k1) not normalized (work): 1277.876461 | | target function (ls_wunit_k1) not normalized (free): 113.931973 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1259 0.1245 0.1545 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1695 0.1694 0.1764 n_refl.: 87593 remove outliers: r(all,work,free)=0.1695 0.1694 0.1764 n_refl.: 87593 overall B=0.14 to atoms: r(all,work,free)=0.1718 0.1717 0.1780 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1257 0.1243 0.1539 n_refl.: 87593 remove outliers: r(all,work,free)=0.1257 0.1242 0.1539 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 0.3593 299.246 278.537 0.692 0.923 0.380 11.894-9.307 99.02 97 4 0.1612 479.376 467.999 0.987 0.923 0.380 9.237-7.194 100.00 213 7 0.1824 392.071 386.780 1.031 0.924 0.340 7.162-5.571 100.00 427 22 0.1729 294.227 288.910 1.001 0.924 0.248 5.546-4.326 100.00 867 58 0.0920 403.901 401.142 1.031 0.925 0.209 4.315-3.360 100.00 1859 96 0.0779 384.113 383.132 1.077 0.927 0.199 3.356-2.611 100.00 3867 181 0.1021 252.342 251.630 1.077 0.929 0.052 2.608-2.026 99.99 8198 413 0.0974 167.280 166.684 1.083 0.933 0.000 2.025-1.573 100.00 17313 902 0.1208 81.691 81.863 1.082 0.940 0.000 1.573-1.221 100.00 36679 1900 0.1649 36.225 35.688 1.055 0.951 0.000 1.221-1.150 99.97 13689 708 0.2359 22.824 21.361 1.008 0.960 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0551 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1242 r_free=0.1539 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1242 r_free=0.1540 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1242 r_free=0.1540 | n_water=258 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1252 r_free=0.1540 | n_water=251 | time (s): 26.330 (total time: 28.810) Filter (q & B) r_work=0.1255 r_free=0.1539 | n_water=248 | time (s): 3.890 (total time: 32.700) Compute maps r_work=0.1255 r_free=0.1539 | n_water=248 | time (s): 1.880 (total time: 34.580) Filter (map) r_work=0.1269 r_free=0.1539 | n_water=237 | time (s): 3.910 (total time: 38.490) Find peaks r_work=0.1269 r_free=0.1539 | n_water=237 | time (s): 0.710 (total time: 39.200) Add new water r_work=0.1425 r_free=0.1709 | n_water=452 | time (s): 3.790 (total time: 42.990) Refine new water occ: r_work=0.1338 r_free=0.1575 adp: r_work=0.1256 r_free=0.1522 occ: r_work=0.1269 r_free=0.1510 adp: r_work=0.1232 r_free=0.1498 occ: r_work=0.1236 r_free=0.1487 adp: r_work=0.1225 r_free=0.1487 ADP+occupancy (water only), MIN, final r_work=0.1225 r_free=0.1487 r_work=0.1225 r_free=0.1487 | n_water=452 | time (s): 118.220 (total time: 161.210) Filter (q & B) r_work=0.1230 r_free=0.1490 | n_water=430 | time (s): 4.000 (total time: 165.210) Filter (dist only) r_work=0.1230 r_free=0.1489 | n_water=429 | time (s): 44.510 (total time: 209.720) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.513222 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1591.954205 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1224 0.1508 0.0284 0.007 0.9 1.6 0.5 0.0 0 13.257 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.24 15.08 2.84 3.778 23.114 1591.954 0.015 11.94 14.76 2.82 4.195 22.922 1591.954 0.015 Individual atomic B min max mean iso aniso Overall: 8.71 113.50 23.10 2.62 192 1764 Protein: 8.71 113.50 17.57 2.62 0 1519 Water: 11.20 73.29 42.54 N/A 192 237 Other: 26.11 37.46 30.96 N/A 0 8 Chain A: 8.71 113.50 20.31 N/A 0 1764 Chain S: 17.36 71.79 48.73 N/A 192 0 Histogram: Values Number of atoms 8.71 - 19.19 1208 19.19 - 29.67 244 29.67 - 40.15 187 40.15 - 50.63 136 50.63 - 61.10 116 61.10 - 71.58 52 71.58 - 82.06 7 82.06 - 92.54 3 92.54 - 103.02 1 103.02 - 113.50 2 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1476 r_work=0.1194 r_free=0.1476 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1476 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 = 0.1195 r_free = 0.1465 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.23 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= 0.1195 r_free= 0.1465 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013912 | | target function (ls_wunit_k1) not normalized (work): 1158.775307 | | target function (ls_wunit_k1) not normalized (free): 104.700089 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1208 0.1195 0.1465 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1602 0.1599 0.1702 n_refl.: 87592 remove outliers: r(all,work,free)=0.1602 0.1599 0.1702 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1608 0.1605 0.1705 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1193 0.1456 n_refl.: 87592 remove outliers: r(all,work,free)=0.1204 0.1191 0.1456 n_refl.: 87588 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3319 291.936 271.784 0.571 1.002 0.340 11.894-9.307 99.02 97 4 0.1536 479.376 477.974 0.913 1.003 0.333 9.237-7.194 100.00 213 7 0.1683 392.071 392.661 0.982 1.003 0.280 7.162-5.571 100.00 427 22 0.1516 294.227 290.339 0.937 1.003 0.224 5.546-4.326 100.00 867 58 0.0828 403.901 401.138 0.957 1.003 0.210 4.315-3.360 100.00 1859 96 0.0706 384.113 383.147 1.002 1.003 0.210 3.356-2.611 100.00 3867 181 0.0952 252.342 251.727 1.009 1.002 0.067 2.608-2.026 99.99 8198 413 0.0961 167.280 166.894 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1169 81.691 81.904 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1603 36.225 35.731 1.017 0.998 0.000 1.221-1.150 99.97 13689 708 0.2333 22.824 21.355 0.977 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0534 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1456 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1192 r_free=0.1458 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1458 | n_water=429 | time (s): 2.030 (total time: 2.030) Filter (dist) r_work=0.1192 r_free=0.1458 | n_water=429 | time (s): 32.420 (total time: 34.450) Filter (q & B) r_work=0.1192 r_free=0.1458 | n_water=429 | time (s): 1.300 (total time: 35.750) Compute maps r_work=0.1192 r_free=0.1458 | n_water=429 | time (s): 1.520 (total time: 37.270) Filter (map) r_work=0.1231 r_free=0.1477 | n_water=292 | time (s): 3.920 (total time: 41.190) Find peaks r_work=0.1231 r_free=0.1477 | n_water=292 | time (s): 0.710 (total time: 41.900) Add new water r_work=0.1358 r_free=0.1607 | n_water=482 | time (s): 3.710 (total time: 45.610) Refine new water occ: r_work=0.1258 r_free=0.1522 adp: r_work=0.1259 r_free=0.1523 occ: r_work=0.1236 r_free=0.1501 adp: r_work=0.1233 r_free=0.1500 occ: r_work=0.1221 r_free=0.1485 adp: r_work=0.1214 r_free=0.1482 ADP+occupancy (water only), MIN, final r_work=0.1214 r_free=0.1482 r_work=0.1214 r_free=0.1482 | n_water=482 | time (s): 181.930 (total time: 227.540) Filter (q & B) r_work=0.1218 r_free=0.1480 | n_water=448 | time (s): 3.310 (total time: 230.850) Filter (dist only) r_work=0.1218 r_free=0.1479 | n_water=447 | time (s): 39.050 (total time: 269.900) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.136182 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 40.863814 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 0.1221 0.1445 0.0224 0.006 1.0 1.9 0.5 0.0 0 1.068 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.21 14.45 2.24 3.612 22.064 40.864 3.720 12.16 14.04 1.88 4.004 21.908 40.864 3.658 Individual atomic B min max mean iso aniso Overall: 9.21 109.79 21.72 2.29 211 1763 Protein: 9.21 109.79 17.23 2.29 0 1519 Water: 11.55 72.54 36.87 N/A 211 236 Other: 21.44 33.81 27.99 N/A 0 8 Chain A: 9.21 109.79 19.96 N/A 0 1763 Chain S: 15.43 69.23 36.43 N/A 211 0 Histogram: Values Number of atoms 9.21 - 19.27 1236 19.27 - 29.33 268 29.33 - 39.39 224 39.39 - 49.45 134 49.45 - 59.50 80 59.50 - 69.56 19 69.56 - 79.62 7 79.62 - 89.68 3 89.68 - 99.74 1 99.74 - 109.79 2 =========================== Idealize ADP of riding H ========================== r_work=0.1216 r_free=0.1404 r_work=0.1217 r_free=0.1405 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1217 r_free = 0.1405 target_work(ml) = 3.658 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1210 r_free = 0.1403 target_work(ml) = 3.655 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1210 r_free= 0.1403 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.655489 | | target function (ml) not normalized (work): 304472.982596 | | target function (ml) not normalized (free): 16070.759902 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1220 0.1210 0.1403 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1539 0.1538 0.1591 n_refl.: 87588 remove outliers: r(all,work,free)=0.1539 0.1538 0.1591 n_refl.: 87588 overall B=-0.01 to atoms: r(all,work,free)=0.1538 0.1537 0.1590 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1211 0.1203 0.1382 n_refl.: 87588 remove outliers: r(all,work,free)=0.1209 0.1200 0.1382 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 0.3743 288.570 261.224 0.468 1.001 0.312 11.894-9.307 98.04 96 4 0.2464 479.500 461.800 0.849 1.002 0.300 9.237-7.194 98.18 209 7 0.2386 383.606 384.714 0.947 1.002 0.200 7.162-5.571 100.00 427 22 0.2078 294.227 282.939 0.907 1.002 0.158 5.546-4.326 100.00 867 58 0.1070 403.901 399.588 0.952 1.002 0.150 4.315-3.360 100.00 1859 96 0.0915 384.113 381.651 0.993 1.002 0.143 3.356-2.611 100.00 3867 181 0.1147 252.342 250.565 1.000 1.002 0.120 2.608-2.026 99.99 8198 413 0.1049 167.280 166.329 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1030 81.691 81.857 1.025 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1299 36.225 35.804 1.018 0.999 0.000 1.221-1.150 99.97 13689 708 0.2134 22.824 21.435 0.976 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0241 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1382 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1382 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1382 | n_water=447 | time (s): 2.060 (total time: 2.060) Filter (dist) r_work=0.1200 r_free=0.1382 | n_water=447 | time (s): 36.550 (total time: 38.610) Filter (q & B) r_work=0.1200 r_free=0.1382 | n_water=447 | time (s): 1.040 (total time: 39.650) Compute maps r_work=0.1200 r_free=0.1382 | n_water=447 | time (s): 1.790 (total time: 41.440) Filter (map) r_work=0.1224 r_free=0.1379 | n_water=311 | time (s): 3.480 (total time: 44.920) Find peaks r_work=0.1224 r_free=0.1379 | n_water=311 | time (s): 0.680 (total time: 45.600) Add new water r_work=0.1291 r_free=0.1431 | n_water=470 | time (s): 3.350 (total time: 48.950) Refine new water occ: r_work=0.1216 r_free=0.1370 adp: r_work=0.1216 r_free=0.1371 occ: r_work=0.1201 r_free=0.1361 adp: r_work=0.1199 r_free=0.1361 occ: r_work=0.1191 r_free=0.1359 adp: r_work=0.1186 r_free=0.1355 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1355 r_work=0.1186 r_free=0.1355 | n_water=470 | time (s): 235.480 (total time: 284.430) Filter (q & B) r_work=0.1193 r_free=0.1356 | n_water=439 | time (s): 3.280 (total time: 287.710) Filter (dist only) r_work=0.1193 r_free=0.1355 | n_water=438 | time (s): 39.530 (total time: 327.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.819490 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.498285 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 0.1199 0.1370 0.0172 0.006 0.9 1.6 0.5 0.0 0 0.910 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.70 1.72 3.420 21.542 46.498 3.643 11.84 13.63 1.79 3.952 21.368 46.498 3.627 Individual atomic B min max mean iso aniso Overall: 9.24 105.44 21.20 2.16 205 1760 Protein: 9.24 105.44 16.84 2.16 0 1519 Water: 11.61 70.87 36.25 N/A 205 233 Other: 19.78 30.44 25.03 N/A 0 8 Chain A: 9.24 105.44 19.47 N/A 0 1760 Chain S: 16.32 69.68 36.05 N/A 205 0 Histogram: Values Number of atoms 9.24 - 18.86 1233 18.86 - 28.48 277 28.48 - 38.10 204 38.10 - 47.72 140 47.72 - 57.34 71 57.34 - 66.96 28 66.96 - 76.58 7 76.58 - 86.20 2 86.20 - 95.82 1 95.82 - 105.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1184 r_free=0.1363 r_work=0.1184 r_free=0.1363 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1184 r_free = 0.1363 target_work(ml) = 3.627 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1180 r_free = 0.1358 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.22 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= 0.1180 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.625209 | | target function (ml) not normalized (work): 301925.559372 | | target function (ml) not normalized (free): 15950.737597 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1188 0.1180 0.1358 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1503 0.1503 0.1554 n_refl.: 87581 remove outliers: r(all,work,free)=0.1503 0.1503 0.1554 n_refl.: 87581 overall B=-0.01 to atoms: r(all,work,free)=0.1501 0.1501 0.1553 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1189 0.1180 0.1361 n_refl.: 87581 remove outliers: r(all,work,free)=0.1187 0.1178 0.1361 n_refl.: 87576 ======================== 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 0.3990 283.857 260.167 0.443 1.000 0.273 11.894-9.307 94.12 92 4 0.2319 473.471 467.825 0.853 1.001 0.253 9.237-7.194 98.18 209 7 0.2479 383.606 378.183 0.918 1.001 0.175 7.162-5.571 100.00 427 22 0.2099 294.227 284.369 0.905 1.001 0.150 5.546-4.326 100.00 867 58 0.1122 403.901 399.504 0.954 1.001 0.150 4.315-3.360 100.00 1859 96 0.0938 384.113 381.245 0.994 1.001 0.140 3.356-2.611 100.00 3867 181 0.1158 252.342 250.413 1.001 1.002 0.053 2.608-2.026 99.99 8198 413 0.1020 167.280 166.391 1.011 1.002 0.000 2.025-1.573 100.00 17313 902 0.0972 81.691 81.968 1.025 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1244 36.225 35.855 1.017 1.002 0.000 1.221-1.150 99.97 13689 708 0.2123 22.824 21.396 0.971 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0293 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1178 r_free=0.1361 After: r_work=0.1178 r_free=0.1361 ================================== NQH flips ================================== r_work=0.1178 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1178 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1178 r_free=0.1361 | n_water=438 | time (s): 1.570 (total time: 1.570) Filter (dist) r_work=0.1178 r_free=0.1361 | n_water=438 | time (s): 35.350 (total time: 36.920) Filter (q & B) r_work=0.1178 r_free=0.1361 | n_water=438 | time (s): 1.280 (total time: 38.200) Compute maps r_work=0.1178 r_free=0.1361 | n_water=438 | time (s): 1.370 (total time: 39.570) Filter (map) r_work=0.1202 r_free=0.1370 | n_water=331 | time (s): 2.470 (total time: 42.040) Find peaks r_work=0.1202 r_free=0.1370 | n_water=331 | time (s): 0.430 (total time: 42.470) Add new water r_work=0.1255 r_free=0.1419 | n_water=488 | time (s): 3.220 (total time: 45.690) Refine new water occ: r_work=0.1190 r_free=0.1350 adp: r_work=0.1190 r_free=0.1352 occ: r_work=0.1179 r_free=0.1342 adp: r_work=0.1177 r_free=0.1342 occ: r_work=0.1170 r_free=0.1337 adp: r_work=0.1167 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1167 r_free=0.1335 r_work=0.1167 r_free=0.1335 | n_water=488 | time (s): 205.450 (total time: 251.140) Filter (q & B) r_work=0.1173 r_free=0.1345 | n_water=450 | time (s): 3.210 (total time: 254.350) Filter (dist only) r_work=0.1173 r_free=0.1343 | n_water=448 | time (s): 39.370 (total time: 293.720) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.923140 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 51.036054 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 0.1385 0.0175 0.007 1.1 5.1 0.5 0.0 0 0.962 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 13.85 1.75 3.274 21.040 51.036 3.636 12.08 13.82 1.74 3.431 21.003 51.036 3.626 Individual atomic B min max mean iso aniso Overall: 9.29 101.45 21.00 2.03 217 1758 Protein: 9.29 101.45 16.71 2.03 0 1519 Water: 11.44 70.11 35.50 N/A 217 231 Other: 20.44 28.94 24.89 N/A 0 8 Chain A: 9.29 101.45 19.30 N/A 0 1758 Chain S: 15.58 56.76 34.82 N/A 217 0 Histogram: Values Number of atoms 9.29 - 18.50 1227 18.50 - 27.72 275 27.72 - 36.94 213 36.94 - 46.15 147 46.15 - 55.37 73 55.37 - 64.59 24 64.59 - 73.80 12 73.80 - 83.02 1 83.02 - 92.23 1 92.23 - 101.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1208 r_free=0.1383 r_work=0.1209 r_free=0.1383 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1209 r_free = 0.1383 target_work(ml) = 3.626 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1206 r_free = 0.1379 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1206 r_free= 0.1379 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.625390 | | target function (ml) not normalized (work): 301922.494157 | | target function (ml) not normalized (free): 15961.867917 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2918 171 0.1408 0.1397 5.6665 5.6354| | 2: 3.57 - 2.84 1.00 2888 124 0.1150 0.1474 5.212 5.2854| | 3: 2.83 - 2.48 1.00 2820 163 0.1249 0.1294 5.0191 5.0409| | 4: 2.47 - 2.25 1.00 2825 136 0.1054 0.1169 4.7228 4.7621| | 5: 2.25 - 2.09 1.00 2756 127 0.1015 0.1126 4.6605 4.7323| | 6: 2.09 - 1.97 1.00 2846 113 0.0989 0.1311 4.3697 4.5261| | 7: 1.97 - 1.87 1.00 2787 165 0.1027 0.1266 4.1064 4.2059| | 8: 1.87 - 1.79 1.00 2789 144 0.1038 0.1286 4.0148 4.1117| | 9: 1.79 - 1.72 1.00 2745 138 0.0956 0.1322 3.7287 3.9259| | 10: 1.72 - 1.66 1.00 2831 160 0.1000 0.1271 3.6466 3.7785| | 11: 1.66 - 1.61 1.00 2712 147 0.0964 0.1102 3.5788 3.6197| | 12: 1.61 - 1.56 1.00 2773 144 0.0921 0.1163 3.3512 3.4902| | 13: 1.56 - 1.52 1.00 2745 130 0.0983 0.1050 3.3439 3.4248| | 14: 1.52 - 1.48 1.00 2803 134 0.0985 0.1140 3.2618 3.3465| | 15: 1.48 - 1.45 1.00 2738 128 0.1003 0.1311 3.1632 3.3195| | 16: 1.45 - 1.42 1.00 2756 161 0.1068 0.1230 3.15 3.2326| | 17: 1.42 - 1.39 1.00 2785 139 0.1111 0.1240 3.108 3.2032| | 18: 1.39 - 1.36 1.00 2741 179 0.1138 0.1390 3.0769 3.2718| | 19: 1.36 - 1.34 1.00 2807 134 0.1206 0.1581 3.0874 3.2681| | 20: 1.34 - 1.32 1.00 2696 147 0.1315 0.1469 3.0843 3.1363| | 21: 1.32 - 1.30 1.00 2785 112 0.1410 0.1625 3.0848 3.1558| | 22: 1.29 - 1.27 1.00 2704 152 0.1469 0.1895 3.0805 3.2798| | 23: 1.27 - 1.26 1.00 2802 156 0.1571 0.1866 3.1004 3.2127| | 24: 1.26 - 1.24 1.00 2744 132 0.1618 0.1749 3.0915 3.1847| | 25: 1.24 - 1.22 1.00 2733 148 0.1785 0.2319 3.1065 3.2933| | 26: 1.22 - 1.21 1.00 2727 135 0.1859 0.1804 3.1251 3.2061| | 27: 1.21 - 1.19 1.00 2814 148 0.2008 0.2089 3.1424 3.1462| | 28: 1.19 - 1.18 1.00 2671 147 0.2144 0.2319 3.1406 3.167| | 29: 1.18 - 1.16 1.00 2800 134 0.2218 0.2340 3.127 3.2188| | 30: 1.16 - 1.15 1.00 2739 148 0.2369 0.2495 3.116 3.168| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2918 171 0.95 9.14 1.00 0.97 6311.37| | 2: 3.57 - 2.84 2888 124 0.92 13.41 1.01 0.97 6311.37| | 3: 2.83 - 2.48 2820 163 0.89 17.53 0.99 0.97 5301.13| | 4: 2.47 - 2.25 2825 136 0.91 14.71 1.00 0.98 2696.06| | 5: 2.25 - 2.09 2756 127 0.89 17.01 1.01 0.98 2696.06| | 6: 2.09 - 1.97 2846 113 0.91 13.92 1.02 0.98 1600.88| | 7: 1.97 - 1.87 2787 165 0.94 11.25 1.02 0.97 666.83| | 8: 1.87 - 1.79 2789 144 0.91 14.91 1.00 0.97 666.83| | 9: 1.79 - 1.72 2745 138 0.93 11.78 0.98 0.97 356.06| | 10: 1.72 - 1.66 2831 160 0.93 12.55 0.98 0.97 293.83| | 11: 1.66 - 1.61 2712 147 0.93 13.16 0.98 0.97 280.02| | 12: 1.61 - 1.56 2773 144 0.95 9.64 0.99 0.97 149.75| | 13: 1.56 - 1.52 2745 130 0.94 11.23 1.02 0.97 149.75| | 14: 1.52 - 1.48 2803 134 0.94 11.29 1.02 0.98 133.11| | 15: 1.48 - 1.45 2738 128 0.95 10.31 1.01 0.98 102.64| | 16: 1.45 - 1.42 2756 161 0.94 11.51 1.02 0.98 102.64| | 17: 1.42 - 1.39 2785 139 0.94 11.37 1.01 0.98 92.22| | 18: 1.39 - 1.36 2741 179 0.94 11.56 1.01 0.98 86.19| | 19: 1.36 - 1.34 2807 134 0.94 12.14 1.00 0.98 86.19| | 20: 1.34 - 1.32 2696 147 0.94 12.28 0.99 0.97 81.16| | 21: 1.32 - 1.30 2785 112 0.94 13.19 0.98 0.96 80.81| | 22: 1.29 - 1.27 2704 152 0.93 13.77 0.98 0.96 81.03| | 23: 1.27 - 1.26 2802 156 0.93 14.72 0.98 0.95 82.15| | 24: 1.26 - 1.24 2744 132 0.93 14.83 0.97 0.95 82.15| | 25: 1.24 - 1.22 2733 148 0.91 16.25 0.96 0.94 83.91| | 26: 1.22 - 1.21 2727 135 0.90 18.05 1.03 0.93 85.86| | 27: 1.21 - 1.19 2814 148 0.89 18.68 1.02 0.93 85.86| | 28: 1.19 - 1.18 2671 147 0.88 20.18 1.01 0.93 89.39| | 29: 1.18 - 1.16 2800 134 0.88 20.50 0.99 0.93 90.72| | 30: 1.16 - 1.15 2739 148 0.86 21.92 0.99 0.93 90.72| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 80.81 max = 6311.37 mean = 991.19| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 14.08| |phase err.(test): min = 0.00 max = 88.17 mean = 14.13| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1206 0.1379 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1519 0.1518 0.1565 n_refl.: 87576 remove outliers: r(all,work,free)=0.1519 0.1518 0.1565 n_refl.: 87576 overall B=-0.01 to atoms: r(all,work,free)=0.1517 0.1516 0.1563 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1214 0.1205 0.1381 n_refl.: 87576 remove outliers: r(all,work,free)=0.1213 0.1205 0.1381 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 0.4023 283.857 249.759 0.430 1.001 0.292 11.894-9.307 93.14 91 4 0.2196 475.457 453.283 0.840 1.002 0.280 9.237-7.194 98.18 209 7 0.2469 383.606 377.712 0.909 1.002 0.140 7.162-5.571 100.00 427 22 0.2177 294.227 283.620 0.895 1.002 0.120 5.546-4.326 100.00 867 58 0.1183 403.901 399.803 0.954 1.002 0.120 4.315-3.360 100.00 1859 96 0.1010 384.113 381.103 0.994 1.002 0.120 3.356-2.611 100.00 3867 181 0.1220 252.342 250.268 1.000 1.002 0.120 2.608-2.026 99.99 8198 413 0.1062 167.280 166.354 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0990 81.691 81.975 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1221 36.225 35.875 1.021 0.998 0.000 1.221-1.150 99.97 13689 708 0.2112 22.824 21.469 0.979 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0330 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2608 0.1926 0.081 5.219 8.8 119.3 19.9 258 0.000 1_bss: 0.1635 0.1740 0.081 5.219 9.0 119.5 20.1 258 0.000 1_settarget: 0.1635 0.1740 0.081 5.219 9.0 119.5 20.1 258 0.000 1_nqh: 0.1640 0.1751 0.081 5.219 9.0 119.5 20.1 258 0.006 1_weight: 0.1640 0.1751 0.081 5.219 9.0 119.5 20.1 258 0.006 1_xyzrec: 0.1215 0.1468 0.007 0.951 9.0 119.5 20.1 258 0.130 1_adp: 0.1241 0.1538 0.007 0.951 8.4 118.4 20.9 258 0.130 1_regHadp: 0.1245 0.1542 0.007 0.951 8.4 118.4 20.9 258 0.130 1_occ: 0.1245 0.1545 0.007 0.951 8.4 118.4 20.9 258 0.130 2_bss: 0.1242 0.1539 0.007 0.951 8.6 118.5 21.1 258 0.130 2_settarget: 0.1242 0.1539 0.007 0.951 8.6 118.5 21.1 258 0.130 2_updatecdl: 0.1242 0.1539 0.007 0.957 8.6 118.5 21.1 258 0.130 2_nqh: 0.1242 0.1540 0.007 0.957 8.6 118.5 21.1 258 0.127 2_sol: 0.1230 0.1489 0.007 0.957 8.6 118.5 23.5 429 n/a 2_weight: 0.1230 0.1489 0.007 0.957 8.6 118.5 23.5 429 n/a 2_xyzrec: 0.1224 0.1508 0.007 0.890 8.6 118.5 23.5 429 n/a 2_adp: 0.1194 0.1476 0.007 0.890 8.7 113.5 23.1 429 n/a 2_regHadp: 0.1194 0.1476 0.007 0.890 8.7 113.5 23.1 429 n/a 2_occ: 0.1195 0.1465 0.007 0.890 8.7 113.5 23.1 429 n/a 3_bss: 0.1191 0.1456 0.007 0.890 8.7 113.5 23.1 429 n/a 3_settarget: 0.1191 0.1456 0.007 0.890 8.7 113.5 23.1 429 n/a 3_updatecdl: 0.1191 0.1456 0.007 0.891 8.7 113.5 23.1 429 n/a 3_nqh: 0.1192 0.1458 0.007 0.891 8.7 113.5 23.1 429 n/a 3_sol: 0.1218 0.1479 0.007 0.891 8.7 113.5 22.0 447 n/a 3_weight: 0.1218 0.1479 0.007 0.891 8.7 113.5 22.0 447 n/a 3_xyzrec: 0.1221 0.1445 0.006 0.952 8.7 113.5 22.0 447 n/a 3_adp: 0.1216 0.1404 0.006 0.952 9.2 109.8 21.7 447 n/a 3_regHadp: 0.1217 0.1405 0.006 0.952 9.2 109.8 21.7 447 n/a 3_occ: 0.1210 0.1403 0.006 0.952 9.2 109.8 21.7 447 n/a 4_bss: 0.1200 0.1382 0.006 0.952 9.2 109.8 21.7 447 n/a 4_settarget: 0.1200 0.1382 0.006 0.952 9.2 109.8 21.7 447 n/a 4_updatecdl: 0.1200 0.1382 0.006 0.950 9.2 109.8 21.7 447 n/a 4_nqh: 0.1200 0.1382 0.006 0.950 9.2 109.8 21.7 447 n/a 4_sol: 0.1193 0.1355 0.006 0.950 9.2 109.8 21.5 438 n/a 4_weight: 0.1193 0.1355 0.006 0.950 9.2 109.8 21.5 438 n/a 4_xyzrec: 0.1199 0.1370 0.006 0.940 9.2 109.8 21.5 438 n/a 4_adp: 0.1184 0.1363 0.006 0.940 9.2 105.4 21.2 438 n/a 4_regHadp: 0.1184 0.1363 0.006 0.940 9.2 105.4 21.2 438 n/a 4_occ: 0.1180 0.1358 0.006 0.940 9.2 105.4 21.2 438 n/a 5_bss: 0.1178 0.1361 0.006 0.940 9.2 105.4 21.2 438 n/a 5_settarget: 0.1178 0.1361 0.006 0.940 9.2 105.4 21.2 438 n/a 5_updatecdl: 0.1178 0.1361 0.006 0.942 9.2 105.4 21.2 438 n/a 5_setrh: 0.1178 0.1361 0.006 0.942 9.2 105.4 21.2 438 n/a 5_nqh: 0.1178 0.1361 0.006 0.942 9.2 105.4 21.2 438 n/a 5_sol: 0.1173 0.1343 0.006 0.942 9.2 105.4 21.1 448 n/a 5_weight: 0.1173 0.1343 0.006 0.942 9.2 105.4 21.1 448 n/a 5_xyzrec: 0.1210 0.1385 0.007 1.057 9.2 105.4 21.1 448 n/a 5_adp: 0.1208 0.1383 0.007 1.057 9.3 101.5 21.0 448 n/a 5_regHadp: 0.1209 0.1383 0.007 1.057 9.3 101.5 21.0 448 n/a 5_occ: 0.1206 0.1379 0.007 1.057 9.3 101.5 21.0 448 n/a end: 0.1205 0.1381 0.007 1.057 9.3 101.4 21.0 448 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6446528_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6446528_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.9100 Refinement macro-cycles (run) : 3591.8900 Write final files (write_after_run_outputs) : 59.6700 Total : 3656.4700 Total CPU time: 61.56 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:12:18 PST -0800 (1735452738.16 s) Start R-work = 0.1635, R-free = 0.1740 Final R-work = 0.1205, R-free = 0.1381 =============================================================================== Job complete usr+sys time: 3790.75 seconds wall clock time: 67 minutes 27.70 seconds (4047.70 seconds total)