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_8565654.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" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8565654.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8565654.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 2.17, per 1000 atoms: 0.64 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: 0.95 Conformation dependent library (CDL) restraints added in 250.2 milliseconds Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.93: 605 0.93 - 1.19: 1066 1.19 - 1.46: 792 1.46 - 1.73: 674 1.73 - 2.00: 16 Bond restraints: 3153 Sorted by residual: bond pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " ideal model delta sigma weight residual 1.326 1.090 0.236 1.10e-02 8.26e+03 4.59e+02 bond pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " ideal model delta sigma weight residual 1.326 1.553 -0.227 1.10e-02 8.26e+03 4.25e+02 bond pdb=" N ALA A 129 " pdb=" CA ALA A 129 " ideal model delta sigma weight residual 1.456 1.213 0.243 1.31e-02 5.83e+03 3.45e+02 bond pdb=" N GLN A 95 " pdb=" CA GLN A 95 " ideal model delta sigma weight residual 1.459 1.676 -0.217 1.17e-02 7.31e+03 3.45e+02 bond pdb=" N GLU A 116 " pdb=" CA GLU A 116 " ideal model delta sigma weight residual 1.462 1.728 -0.266 1.46e-02 4.69e+03 3.33e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.95: 3279 4.95 - 9.89: 1859 9.89 - 14.84: 558 14.84 - 19.79: 75 19.79 - 24.73: 6 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 48 " pdb=" CZ ARG A 48 " pdb=" NH2 ARG A 48 " ideal model delta sigma weight residual 119.20 133.63 -14.43 9.00e-01 1.23e+00 2.57e+02 angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.29 111.06 11.23 8.10e-01 1.52e+00 1.92e+02 angle pdb=" O LEU A 7 " pdb=" C LEU A 7 " pdb=" N VAL A 8 " ideal model delta sigma weight residual 123.27 107.28 15.99 1.16e+00 7.43e-01 1.90e+02 angle pdb=" N ILE A 9 " pdb=" CA ILE A 9 " pdb=" CB ILE A 9 " ideal model delta sigma weight residual 111.21 126.28 -15.07 1.17e+00 7.31e-01 1.66e+02 angle pdb=" C GLY A 108 " pdb=" N PRO A 109 " pdb=" CA PRO A 109 " ideal model delta sigma weight residual 119.87 106.77 13.10 1.04e+00 9.25e-01 1.59e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 954 17.39 - 34.77: 102 34.77 - 52.15: 37 52.15 - 69.54: 14 69.54 - 86.92: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: 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 -149.99 -30.01 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ALYS A 41 " pdb=" C ALYS A 41 " pdb=" N ASP A 42 " pdb=" CA ASP A 42 " ideal model delta harmonic sigma weight residual -180.00 -152.38 -27.62 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA SER A 121 " pdb=" C SER A 121 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " ideal model delta harmonic sigma weight residual 180.00 156.60 23.40 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.242: 107 0.242 - 0.482: 79 0.482 - 0.723: 40 0.723 - 0.964: 14 0.964 - 1.204: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ALA A 104 " pdb=" N ALA A 104 " pdb=" C ALA A 104 " pdb=" CB ALA A 104 " both_signs ideal model delta sigma weight residual False 2.48 3.69 -1.20 2.00e-01 2.50e+01 3.63e+01 chirality pdb=" CB VAL A 186 " pdb=" CA VAL A 186 " pdb=" CG1 VAL A 186 " pdb=" CG2 VAL A 186 " both_signs ideal model delta sigma weight residual False -2.63 -1.56 -1.07 2.00e-01 2.50e+01 2.86e+01 chirality pdb=" CG LEU A 58 " pdb=" CB LEU A 58 " pdb=" CD1 LEU A 58 " pdb=" CD2 LEU A 58 " both_signs ideal model delta sigma weight residual False -2.59 -1.58 -1.01 2.00e-01 2.50e+01 2.53e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 28 " 0.166 9.50e-02 1.11e+02 9.29e-02 1.29e+02 pdb=" NE ARG A 28 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 28 " -0.104 2.00e-02 2.50e+03 pdb=" NH1 ARG A 28 " -0.038 2.00e-02 2.50e+03 pdb=" NH2 ARG A 28 " 0.057 2.00e-02 2.50e+03 pdb="HH11 ARG A 28 " 0.142 2.00e-02 2.50e+03 pdb="HH12 ARG A 28 " -0.047 2.00e-02 2.50e+03 pdb="HH21 ARG A 28 " 0.083 2.00e-02 2.50e+03 pdb="HH22 ARG A 28 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.021 2.00e-02 2.50e+03 6.00e-02 1.08e+02 pdb=" CG PHE A 119 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.074 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.117 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.120 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.051 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.048 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.007 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.034 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " -0.041 2.00e-02 2.50e+03 6.26e-02 8.81e+01 pdb=" CG HIS A 138 " 0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " 0.071 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " -0.148 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " 0.013 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " 0.040 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " 0.015 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 716 2.26 - 2.85: 7771 2.85 - 3.43: 10628 3.43 - 4.02: 15312 4.02 - 4.60: 22148 Nonbonded interactions: 56575 Sorted by model distance: nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.681 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.808 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.810 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.813 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.833 2.450 ... (remaining 56570 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_8565654_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= 0.2598 r_free= 0.1946 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787316 | | target function (ml) not normalized (work): 232200.118767 | | target function (ml) not normalized (free): 11802.585392 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3024 0.2142 7.023 4.9604| | 2: 3.57 - 2.84 1.00 2876 122 0.2421 0.1707 4.3526 4.3208| | 3: 2.84 - 2.48 1.00 2833 165 0.2362 0.1681 4.1316 4.1602| | 4: 2.47 - 2.25 1.00 2825 136 0.2303 0.1514 3.8378 3.8499| | 5: 2.25 - 2.09 1.00 2756 127 0.2472 0.1611 3.8013 3.8362| | 6: 2.09 - 1.97 1.00 2846 113 0.2542 0.1801 3.4696 3.5433| | 7: 1.97 - 1.87 1.00 2787 165 0.2495 0.1809 3.1271 3.1989| | 8: 1.87 - 1.79 1.00 2789 144 0.2456 0.1888 3.0523 3.1192| | 9: 1.79 - 1.72 1.00 2745 138 0.2427 0.1969 2.8965 2.9568| | 10: 1.72 - 1.66 1.00 2789 158 0.2423 0.1806 2.8051 2.8389| | 11: 1.66 - 1.61 1.00 2740 147 0.2510 0.1902 2.7489 2.7482| | 12: 1.61 - 1.56 1.00 2787 146 0.2521 0.2122 2.6333 2.7213| | 13: 1.56 - 1.52 1.00 2745 130 0.2530 0.1919 2.5602 2.6354| | 14: 1.52 - 1.48 1.00 2803 134 0.2580 0.1795 2.5067 2.5139| | 15: 1.48 - 1.45 1.00 2738 128 0.2596 0.2171 2.4389 2.5198| | 16: 1.45 - 1.42 1.00 2756 161 0.2671 0.2031 2.3991 2.4184| | 17: 1.42 - 1.39 1.00 2785 139 0.2655 0.2343 2.3282 2.4425| | 18: 1.39 - 1.36 1.00 2741 179 0.2684 0.2247 2.2738 2.3654| | 19: 1.36 - 1.34 1.00 2807 134 0.2660 0.2270 2.2379 2.283| | 20: 1.34 - 1.32 1.00 2696 147 0.2637 0.2188 2.1835 2.1568| | 21: 1.32 - 1.30 1.00 2785 112 0.2767 0.2424 2.1685 2.2311| | 22: 1.29 - 1.27 1.00 2704 152 0.2699 0.2440 2.1249 2.1768| | 23: 1.27 - 1.26 1.00 2802 156 0.2695 0.2417 2.0861 2.1662| | 24: 1.26 - 1.24 1.00 2744 132 0.2754 0.2341 2.0674 2.1522| | 25: 1.24 - 1.22 1.00 2734 148 0.2816 0.2395 2.0361 2.0154| | 26: 1.22 - 1.21 1.00 2727 135 0.2843 0.2131 2.0058 2.0304| | 27: 1.21 - 1.19 1.00 2814 148 0.2994 0.2731 2.001 2.0289| | 28: 1.19 - 1.18 1.00 2671 147 0.3004 0.2508 1.9829 1.9276| | 29: 1.18 - 1.16 1.00 2800 134 0.3000 0.2606 1.9604 1.9988| | 30: 1.16 - 1.15 1.00 2740 148 0.3034 0.2918 1.9242 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 18.91 0.76 0.23 1504.75| | 2: 3.57 - 2.84 2876 122 0.80 26.32 1.27 0.23 1504.75| | 3: 2.84 - 2.48 2833 165 0.74 32.29 1.25 0.23 1247.77| | 4: 2.47 - 2.25 2825 136 0.81 25.81 1.25 0.25 580.84| | 5: 2.25 - 2.09 2756 127 0.77 29.61 1.28 0.25 580.84| | 6: 2.09 - 1.97 2846 113 0.83 22.87 1.29 0.25 317.77| | 7: 1.97 - 1.87 2787 165 0.90 16.86 1.27 0.25 93.41| | 8: 1.87 - 1.79 2789 144 0.85 21.57 1.25 0.25 93.41| | 9: 1.79 - 1.72 2745 138 0.88 18.59 1.23 0.25 55.67| | 10: 1.72 - 1.66 2789 158 0.87 20.10 1.22 0.25 48.11| | 11: 1.66 - 1.61 2740 147 0.85 21.49 1.24 0.25 46.45| | 12: 1.61 - 1.56 2787 146 0.88 18.51 1.23 0.25 29.58| | 13: 1.56 - 1.52 2745 130 0.87 20.41 1.24 0.25 29.58| | 14: 1.52 - 1.48 2803 134 0.87 20.59 1.24 0.25 26.37| | 15: 1.48 - 1.45 2738 128 0.87 20.08 1.22 0.25 20.49| | 16: 1.45 - 1.42 2756 161 0.86 21.54 1.24 0.25 20.49| | 17: 1.42 - 1.39 2785 139 0.86 20.90 1.23 0.25 17.57| | 18: 1.39 - 1.36 2741 179 0.86 21.34 1.23 0.25 15.87| | 19: 1.36 - 1.34 2807 134 0.85 22.29 1.22 0.25 15.87| | 20: 1.34 - 1.32 2696 147 0.87 20.99 1.21 0.25 13.06| | 21: 1.32 - 1.30 2785 112 0.86 22.08 1.21 0.25 12.86| | 22: 1.29 - 1.27 2704 152 0.86 22.24 1.21 0.25 12.53| | 23: 1.27 - 1.26 2802 156 0.86 21.56 1.21 0.24 10.84| | 24: 1.26 - 1.24 2744 132 0.85 22.45 1.20 0.24 10.84| | 25: 1.24 - 1.22 2734 148 0.85 23.00 1.20 0.24 10.11| | 26: 1.22 - 1.21 2727 135 0.85 23.02 1.20 0.23 9.30| | 27: 1.21 - 1.19 2814 148 0.84 23.87 1.21 0.23 9.30| | 28: 1.19 - 1.18 2671 147 0.84 24.21 1.19 0.23 8.57| | 29: 1.18 - 1.16 2800 134 0.84 24.54 1.16 0.23 8.29| | 30: 1.16 - 1.15 2740 148 0.82 25.73 1.15 0.23 8.29| |alpha: min = 0.23 max = 0.25 mean = 0.24| |beta: min = 8.29 max = 1504.75 mean = 218.10| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.46| |phase err.(test): min = 0.00 max = 89.65 mean = 22.21| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.266 1557 Z= 5.534 Angle : 5.258 23.015 2118 Z= 3.666 Chirality : 0.408 1.204 243 Planarity : 0.033 0.139 284 Dihedral : 14.100 86.919 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Cbeta Deviations : 36.22 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.48), residues: 224 helix: -3.20 (0.32), residues: 109 sheet: -0.60 (0.84), residues: 38 loop : -1.00 (0.67), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.090 0.021 ARG A 98 TYR 0.083 0.039 TYR A 141 PHE 0.141 0.039 PHE A 119 HIS 0.104 0.040 HIS A 138 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= 0.2598 r_free= 0.1946 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787316 | | target function (ml) not normalized (work): 232200.118767 | | target function (ml) not normalized (free): 11802.585392 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2557 0.2599 0.1946 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2557 0.2599 0.1946 n_refl.: 87602 remove outliers: r(all,work,free)=0.1970 0.1974 0.1946 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.1994 0.1998 0.1958 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1633 0.1626 0.1765 n_refl.: 87594 remove outliers: r(all,work,free)=0.1632 0.1626 0.1765 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 0.3841 386.325 356.727 0.723 0.913 0.401 11.894-9.307 99.02 97 4 0.1797 613.658 592.762 1.015 0.914 0.375 9.237-7.194 100.00 213 7 0.2199 501.897 490.401 1.055 0.915 0.370 7.162-5.571 100.00 427 22 0.2126 376.646 364.898 1.023 0.916 0.310 5.546-4.326 100.00 867 58 0.1287 517.041 511.674 1.054 0.917 0.214 4.315-3.360 100.00 1859 96 0.1152 491.710 488.246 1.097 0.918 0.189 3.356-2.611 100.00 3867 181 0.1431 323.028 319.349 1.088 0.920 0.109 2.608-2.026 99.99 8198 413 0.1328 214.138 211.996 1.093 0.923 0.000 2.025-1.573 100.00 17313 902 0.1627 104.574 103.786 1.089 0.928 0.000 1.573-1.221 100.00 36679 1900 0.2056 46.372 45.138 1.067 0.936 0.000 1.221-1.150 99.97 13689 708 0.2598 29.218 27.049 1.032 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0446 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1626 r_free=0.1765 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1626 r_free=0.1765 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.896203 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2013.235035 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 0.1208 0.1456 0.0249 0.007 0.9 1.6 0.5 0.0 0 11.948 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 14.56 2.49 3.012 19.053 2013.235 0.017 12.39 15.33 2.94 3.128 19.496 2013.235 0.016 Individual atomic B min max mean iso aniso Overall: 8.50 118.75 20.92 2.87 0 1785 Protein: 8.50 118.75 17.82 2.87 0 1519 Water: 10.97 114.92 38.95 N/A 0 258 Other: 22.50 35.90 28.58 N/A 0 8 Chain A: 8.50 118.75 20.92 N/A 0 1785 Histogram: Values Number of atoms 8.50 - 19.52 1211 19.52 - 30.55 227 30.55 - 41.57 169 41.57 - 52.60 97 52.60 - 63.62 52 63.62 - 74.65 18 74.65 - 85.67 4 85.67 - 96.70 4 96.70 - 107.72 0 107.72 - 118.75 3 =========================== Idealize ADP of riding H ========================== r_work=0.1239 r_free=0.1533 r_work=0.1243 r_free=0.1537 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1243 r_free = 0.1537 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1243 r_free = 0.1542 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1243 r_free= 0.1542 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015443 | | target function (ls_wunit_k1) not normalized (work): 1286.351864 | | target function (ls_wunit_k1) not normalized (free): 111.655426 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1257 0.1243 0.1542 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1699 0.1698 0.1770 n_refl.: 87593 remove outliers: r(all,work,free)=0.1699 0.1698 0.1770 n_refl.: 87593 overall B=0.13 to atoms: r(all,work,free)=0.1720 0.1719 0.1785 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1256 0.1242 0.1535 n_refl.: 87593 remove outliers: r(all,work,free)=0.1255 0.1241 0.1535 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 0.3632 299.325 278.467 0.634 1.002 0.380 11.894-9.307 99.02 97 4 0.1609 479.501 467.627 0.908 1.003 0.380 9.237-7.194 100.00 213 7 0.1829 392.173 386.994 0.950 1.003 0.340 7.162-5.571 100.00 427 22 0.1717 294.304 288.675 0.926 1.003 0.258 5.546-4.326 100.00 867 58 0.0913 404.007 401.520 0.950 1.003 0.214 4.315-3.360 100.00 1859 96 0.0776 384.213 383.142 0.995 1.003 0.200 3.356-2.611 100.00 3867 181 0.1022 252.408 251.693 0.999 1.002 0.110 2.608-2.026 99.99 8198 413 0.0973 167.324 166.792 1.010 1.002 0.000 2.025-1.573 100.00 17313 902 0.1204 81.712 81.910 1.017 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1650 36.234 35.693 1.006 0.999 0.000 1.221-1.150 99.97 13689 708 0.2363 22.830 21.333 0.970 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0495 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1241 r_free=0.1535 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1241 r_free=0.1535 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1241 r_free=0.1535 | n_water=258 | time (s): 2.330 (total time: 2.330) Filter (dist) r_work=0.1251 r_free=0.1533 | n_water=252 | time (s): 27.060 (total time: 29.390) Filter (q & B) r_work=0.1254 r_free=0.1532 | n_water=249 | time (s): 3.660 (total time: 33.050) Compute maps r_work=0.1254 r_free=0.1532 | n_water=249 | time (s): 1.820 (total time: 34.870) Filter (map) r_work=0.1266 r_free=0.1547 | n_water=237 | time (s): 3.850 (total time: 38.720) Find peaks r_work=0.1266 r_free=0.1547 | n_water=237 | time (s): 0.730 (total time: 39.450) Add new water r_work=0.1424 r_free=0.1697 | n_water=457 | time (s): 3.860 (total time: 43.310) Refine new water occ: r_work=0.1332 r_free=0.1544 adp: r_work=0.1252 r_free=0.1501 occ: r_work=0.1264 r_free=0.1491 adp: r_work=0.1230 r_free=0.1482 occ: r_work=0.1234 r_free=0.1468 adp: r_work=0.1223 r_free=0.1470 ADP+occupancy (water only), MIN, final r_work=0.1223 r_free=0.1470 r_work=0.1223 r_free=0.1470 | n_water=457 | time (s): 90.470 (total time: 133.780) Filter (q & B) r_work=0.1230 r_free=0.1475 | n_water=436 | time (s): 3.840 (total time: 137.620) Filter (dist only) r_work=0.1230 r_free=0.1475 | n_water=436 | time (s): 41.400 (total time: 179.020) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.065349 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1476.564705 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 0.1226 0.1520 0.0294 0.007 0.9 2.9 0.5 0.0 0 13.533 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.26 15.20 2.94 3.773 23.075 1476.565 0.015 11.98 14.94 2.97 4.139 22.918 1476.565 0.015 Individual atomic B min max mean iso aniso Overall: 8.68 114.43 23.11 2.59 199 1764 Protein: 8.68 114.43 17.63 2.59 0 1519 Water: 11.02 72.13 42.07 N/A 199 237 Other: 24.57 36.53 29.96 N/A 0 8 Chain A: 8.68 114.43 20.33 N/A 0 1764 Chain S: 19.07 71.70 47.70 N/A 199 0 Histogram: Values Number of atoms 8.68 - 19.25 1204 19.25 - 29.83 258 29.83 - 40.40 189 40.40 - 50.98 154 50.98 - 61.55 94 61.55 - 72.13 52 72.13 - 82.70 6 82.70 - 93.28 3 93.28 - 103.85 1 103.85 - 114.43 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1494 r_work=0.1197 r_free=0.1493 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1493 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1486 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.15 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= 0.1198 r_free= 0.1486 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013927 | | target function (ls_wunit_k1) not normalized (work): 1160.095552 | | target function (ls_wunit_k1) not normalized (free): 102.050087 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1212 0.1198 0.1486 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1605 0.1601 0.1719 n_refl.: 87592 remove outliers: r(all,work,free)=0.1605 0.1601 0.1719 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1611 0.1607 0.1722 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1195 0.1483 n_refl.: 87592 remove outliers: r(all,work,free)=0.1207 0.1193 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 0.3420 295.257 271.666 0.633 0.937 0.370 11.894-9.307 99.02 97 4 0.1468 479.501 477.194 0.986 0.937 0.360 9.237-7.194 100.00 213 7 0.1633 392.173 393.198 1.048 0.938 0.280 7.162-5.571 100.00 427 22 0.1510 294.304 291.254 1.008 0.938 0.229 5.546-4.326 100.00 867 58 0.0842 404.007 401.630 1.024 0.938 0.219 4.315-3.360 100.00 1859 96 0.0717 384.213 382.884 1.069 0.939 0.218 3.356-2.611 100.00 3867 181 0.0960 252.408 251.647 1.075 0.940 0.067 2.608-2.026 99.99 8198 413 0.0952 167.324 166.921 1.083 0.941 0.000 2.025-1.573 100.00 17313 902 0.1174 81.712 81.903 1.088 0.944 0.000 1.573-1.221 100.00 36679 1900 0.1605 36.234 35.741 1.071 0.947 0.000 1.221-1.150 99.97 13689 708 0.2334 22.830 21.381 1.026 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0570 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1483 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1194 r_free=0.1486 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1486 | n_water=436 | time (s): 1.700 (total time: 1.700) Filter (dist) r_work=0.1194 r_free=0.1486 | n_water=434 | time (s): 36.850 (total time: 38.550) Filter (q & B) r_work=0.1194 r_free=0.1486 | n_water=434 | time (s): 1.630 (total time: 40.180) Compute maps r_work=0.1194 r_free=0.1486 | n_water=434 | time (s): 1.140 (total time: 41.320) Filter (map) r_work=0.1235 r_free=0.1484 | n_water=301 | time (s): 2.560 (total time: 43.880) Find peaks r_work=0.1235 r_free=0.1484 | n_water=301 | time (s): 0.560 (total time: 44.440) Add new water r_work=0.1359 r_free=0.1592 | n_water=491 | time (s): 3.140 (total time: 47.580) Refine new water occ: r_work=0.1258 r_free=0.1522 adp: r_work=0.1260 r_free=0.1521 occ: r_work=0.1236 r_free=0.1509 adp: r_work=0.1235 r_free=0.1505 occ: r_work=0.1222 r_free=0.1499 adp: r_work=0.1215 r_free=0.1494 ADP+occupancy (water only), MIN, final r_work=0.1215 r_free=0.1494 r_work=0.1215 r_free=0.1494 | n_water=491 | time (s): 200.200 (total time: 247.780) Filter (q & B) r_work=0.1221 r_free=0.1494 | n_water=453 | time (s): 3.190 (total time: 250.970) Filter (dist only) r_work=0.1221 r_free=0.1494 | n_water=453 | time (s): 33.800 (total time: 284.770) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.163499 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.328868 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 0.1225 0.1448 0.0223 0.006 0.9 2.6 0.5 0.0 0 1.082 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.25 14.48 2.23 3.610 22.091 50.329 3.725 12.06 14.03 1.98 4.156 21.888 50.329 3.652 Individual atomic B min max mean iso aniso Overall: 9.13 109.89 21.64 2.32 217 1763 Protein: 9.13 109.89 17.14 2.32 0 1519 Water: 11.44 70.89 36.62 N/A 217 236 Other: 20.15 32.17 26.36 N/A 0 8 Chain A: 9.13 109.89 19.84 N/A 0 1763 Chain S: 15.97 65.17 36.26 N/A 217 0 Histogram: Values Number of atoms 9.13 - 19.20 1234 19.20 - 29.28 277 29.28 - 39.36 225 39.36 - 49.43 133 49.43 - 59.51 78 59.51 - 69.59 21 69.59 - 79.66 6 79.66 - 89.74 3 89.74 - 99.82 1 99.82 - 109.89 2 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1403 r_work=0.1206 r_free=0.1404 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1404 target_work(ml) = 3.652 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1407 target_work(ml) = 3.652 | | occupancies: max = 1.00 min = 0.14 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= 0.1204 r_free= 0.1407 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.651919 | | target function (ml) not normalized (work): 304179.307095 | | target function (ml) not normalized (free): 16072.419803 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1214 0.1204 0.1407 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1530 0.1528 0.1592 n_refl.: 87589 remove outliers: r(all,work,free)=0.1530 0.1528 0.1592 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1529 0.1527 0.1591 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1194 0.1377 n_refl.: 87589 remove outliers: r(all,work,free)=0.1200 0.1191 0.1377 n_refl.: 87582 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.4005 292.003 258.351 0.472 0.999 0.330 11.894-9.307 97.06 95 4 0.2521 472.881 458.860 0.836 1.001 0.330 9.237-7.194 98.64 210 7 0.2439 385.721 386.164 0.944 1.002 0.190 7.162-5.571 100.00 427 22 0.2073 294.304 283.431 0.912 1.002 0.167 5.546-4.326 100.00 867 58 0.1099 404.007 399.645 0.953 1.002 0.158 4.315-3.360 100.00 1859 96 0.0927 384.213 381.338 0.992 1.002 0.153 3.356-2.611 100.00 3867 181 0.1139 252.408 250.619 0.999 1.002 0.067 2.608-2.026 99.99 8198 413 0.1033 167.324 166.432 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.1000 81.712 81.865 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1286 36.234 35.807 1.018 0.999 0.000 1.221-1.150 99.97 13689 708 0.2125 22.830 21.441 0.977 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0246 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1377 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1377 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1377 | n_water=453 | time (s): 2.210 (total time: 2.210) Filter (dist) r_work=0.1191 r_free=0.1377 | n_water=452 | time (s): 39.370 (total time: 41.580) Filter (q & B) r_work=0.1191 r_free=0.1377 | n_water=452 | time (s): 0.840 (total time: 42.420) Compute maps r_work=0.1191 r_free=0.1377 | n_water=452 | time (s): 1.300 (total time: 43.720) Filter (map) r_work=0.1217 r_free=0.1376 | n_water=315 | time (s): 2.580 (total time: 46.300) Find peaks r_work=0.1217 r_free=0.1376 | n_water=315 | time (s): 0.500 (total time: 46.800) Add new water r_work=0.1278 r_free=0.1439 | n_water=482 | time (s): 3.210 (total time: 50.010) Refine new water occ: r_work=0.1206 r_free=0.1375 adp: r_work=0.1206 r_free=0.1375 occ: r_work=0.1193 r_free=0.1368 adp: r_work=0.1191 r_free=0.1366 occ: r_work=0.1184 r_free=0.1364 adp: r_work=0.1180 r_free=0.1360 ADP+occupancy (water only), MIN, final r_work=0.1180 r_free=0.1360 r_work=0.1180 r_free=0.1360 | n_water=482 | time (s): 186.480 (total time: 236.490) Filter (q & B) r_work=0.1188 r_free=0.1367 | n_water=444 | time (s): 2.650 (total time: 239.140) Filter (dist only) r_work=0.1188 r_free=0.1365 | n_water=443 | time (s): 37.210 (total time: 276.350) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.972716 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.691162 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 0.1196 0.1372 0.0177 0.006 0.9 1.9 0.5 0.0 0 0.986 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.72 1.77 3.412 21.364 49.691 3.640 11.85 13.66 1.81 3.740 21.259 49.691 3.624 Individual atomic B min max mean iso aniso Overall: 9.22 105.71 21.10 2.17 210 1760 Protein: 9.22 105.71 16.91 2.17 0 1519 Water: 11.48 69.78 35.40 N/A 210 233 Other: 20.67 29.68 25.28 N/A 0 8 Chain A: 9.22 105.71 19.51 N/A 0 1760 Chain S: 15.05 60.92 34.46 N/A 210 0 Histogram: Values Number of atoms 9.22 - 18.87 1230 18.87 - 28.52 287 28.52 - 38.17 217 38.17 - 47.82 132 47.82 - 57.47 67 57.47 - 67.11 24 67.11 - 76.76 8 76.76 - 86.41 2 86.41 - 96.06 1 96.06 - 105.71 2 =========================== Idealize ADP of riding H ========================== r_work=0.1185 r_free=0.1366 r_work=0.1186 r_free=0.1367 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1186 r_free = 0.1367 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1183 r_free = 0.1364 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87582 (all), 4.91 % free)------------| | | | r_work= 0.1183 r_free= 0.1364 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.623372 | | target function (ml) not normalized (work): 301776.158139 | | target function (ml) not normalized (free): 15955.828933 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1183 0.1364 n_refl.: 87582 re-set all scales: r(all,work,free)=0.1508 0.1508 0.1544 n_refl.: 87582 remove outliers: r(all,work,free)=0.1508 0.1508 0.1544 n_refl.: 87582 overall B=-0.01 to atoms: r(all,work,free)=0.1506 0.1506 0.1543 n_refl.: 87582 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1183 0.1362 n_refl.: 87582 remove outliers: r(all,work,free)=0.1189 0.1180 0.1362 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 0.3992 289.979 257.475 0.456 0.999 0.299 11.894-9.307 94.12 92 4 0.2363 481.292 450.624 0.826 1.002 0.277 9.237-7.194 98.18 209 7 0.2570 383.706 377.905 0.920 1.002 0.160 7.162-5.571 100.00 427 22 0.2225 294.304 282.906 0.905 1.002 0.160 5.546-4.326 100.00 867 58 0.1154 404.007 399.432 0.953 1.002 0.128 4.315-3.360 100.00 1859 96 0.0956 384.213 381.635 0.993 1.002 0.120 3.356-2.611 100.00 3867 181 0.1156 252.408 250.689 1.001 1.002 0.053 2.608-2.026 99.99 8198 413 0.1022 167.324 166.588 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0956 81.712 82.010 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1235 36.234 35.873 1.021 0.998 0.000 1.221-1.150 99.97 13689 708 0.2119 22.830 21.462 0.979 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0362 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1180 r_free=0.1362 After: r_work=0.1181 r_free=0.1362 ================================== NQH flips ================================== r_work=0.1181 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1181 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1181 r_free=0.1362 | n_water=443 | time (s): 1.540 (total time: 1.540) Filter (dist) r_work=0.1181 r_free=0.1362 | n_water=443 | time (s): 35.100 (total time: 36.640) Filter (q & B) r_work=0.1181 r_free=0.1362 | n_water=442 | time (s): 3.520 (total time: 40.160) Compute maps r_work=0.1181 r_free=0.1362 | n_water=442 | time (s): 1.730 (total time: 41.890) Filter (map) r_work=0.1208 r_free=0.1378 | n_water=325 | time (s): 3.090 (total time: 44.980) Find peaks r_work=0.1208 r_free=0.1378 | n_water=325 | time (s): 0.490 (total time: 45.470) Add new water r_work=0.1262 r_free=0.1418 | n_water=494 | time (s): 2.850 (total time: 48.320) Refine new water occ: r_work=0.1190 r_free=0.1346 adp: r_work=0.1191 r_free=0.1350 occ: r_work=0.1177 r_free=0.1335 adp: r_work=0.1176 r_free=0.1338 occ: r_work=0.1168 r_free=0.1330 adp: r_work=0.1164 r_free=0.1331 ADP+occupancy (water only), MIN, final r_work=0.1164 r_free=0.1331 r_work=0.1164 r_free=0.1331 | n_water=494 | time (s): 224.670 (total time: 272.990) Filter (q & B) r_work=0.1174 r_free=0.1340 | n_water=448 | time (s): 2.710 (total time: 275.700) Filter (dist only) r_work=0.1174 r_free=0.1339 | n_water=447 | time (s): 37.890 (total time: 313.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.985893 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.921220 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 0.1198 0.1359 0.0161 0.006 1.1 3.2 0.5 0.0 0 0.993 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.59 1.61 3.294 21.081 45.921 3.629 12.03 13.66 1.63 3.527 21.004 45.921 3.625 Individual atomic B min max mean iso aniso Overall: 9.10 101.65 20.92 2.03 216 1758 Protein: 9.10 101.65 16.71 2.03 0 1519 Water: 11.52 68.94 35.19 N/A 216 231 Other: 20.16 28.55 24.56 N/A 0 8 Chain A: 9.10 101.65 19.26 N/A 0 1758 Chain S: 14.06 60.90 34.44 N/A 216 0 Histogram: Values Number of atoms 9.10 - 18.36 1214 18.36 - 27.61 287 27.61 - 36.87 219 36.87 - 46.12 147 46.12 - 55.38 64 55.38 - 64.63 27 64.63 - 73.89 11 73.89 - 83.14 2 83.14 - 92.40 1 92.40 - 101.65 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1366 r_work=0.1203 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1366 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1363 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1199 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.624473 | | target function (ml) not normalized (work): 301846.087903 | | target function (ml) not normalized (free): 15964.282155 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1441 0.1401 5.71 5.6655| | 2: 3.57 - 2.84 1.00 2888 124 0.1127 0.1411 5.2099 5.2619| | 3: 2.83 - 2.48 1.00 2820 163 0.1220 0.1260 5.0153 5.0342| | 4: 2.47 - 2.25 1.00 2825 136 0.1024 0.1127 4.7137 4.7613| | 5: 2.25 - 2.09 1.00 2756 127 0.0987 0.1101 4.6552 4.7302| | 6: 2.09 - 1.97 1.00 2846 113 0.0977 0.1185 4.3549 4.4754| | 7: 1.97 - 1.87 1.00 2787 165 0.0978 0.1274 4.0697 4.2075| | 8: 1.87 - 1.79 1.00 2789 144 0.1025 0.1252 3.9916 4.0821| | 9: 1.79 - 1.72 1.00 2745 138 0.0949 0.1291 3.7139 3.8981| | 10: 1.72 - 1.66 1.00 2831 160 0.0997 0.1278 3.6329 3.773| | 11: 1.66 - 1.61 1.00 2712 147 0.0966 0.1091 3.5714 3.6117| | 12: 1.61 - 1.56 1.00 2773 144 0.0916 0.1226 3.3496 3.4944| | 13: 1.56 - 1.52 1.00 2745 130 0.0981 0.1068 3.3406 3.4337| | 14: 1.52 - 1.48 1.00 2803 134 0.0991 0.1169 3.2654 3.3706| | 15: 1.48 - 1.45 1.00 2738 128 0.1012 0.1356 3.173 3.3312| | 16: 1.45 - 1.42 1.00 2756 161 0.1068 0.1228 3.1552 3.2448| | 17: 1.42 - 1.39 1.00 2785 139 0.1121 0.1288 3.1188 3.2365| | 18: 1.39 - 1.36 1.00 2741 179 0.1143 0.1388 3.0875 3.2727| | 19: 1.36 - 1.34 1.00 2807 134 0.1212 0.1610 3.0957 3.2828| | 20: 1.34 - 1.32 1.00 2696 147 0.1317 0.1472 3.0878 3.1421| | 21: 1.32 - 1.30 1.00 2785 112 0.1403 0.1629 3.0848 3.1547| | 22: 1.29 - 1.27 1.00 2704 152 0.1475 0.1919 3.0865 3.289| | 23: 1.27 - 1.26 1.00 2802 156 0.1569 0.1844 3.1026 3.2078| | 24: 1.26 - 1.24 1.00 2744 132 0.1621 0.1769 3.0952 3.1964| | 25: 1.24 - 1.22 1.00 2733 148 0.1790 0.2313 3.1094 3.2849| | 26: 1.22 - 1.21 1.00 2727 135 0.1854 0.1788 3.1213 3.2068| | 27: 1.21 - 1.19 1.00 2814 148 0.2014 0.2084 3.1421 3.1494| | 28: 1.19 - 1.18 1.00 2671 147 0.2142 0.2326 3.1409 3.1682| | 29: 1.18 - 1.16 1.00 2800 134 0.2213 0.2377 3.1269 3.2253| | 30: 1.16 - 1.15 1.00 2739 148 0.2376 0.2466 3.1168 3.1593| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.94 9.28 1.00 0.97 6433.26| | 2: 3.57 - 2.84 2888 124 0.92 13.54 1.01 0.97 6433.26| | 3: 2.83 - 2.48 2820 163 0.89 17.62 0.99 0.98 5389.96| | 4: 2.47 - 2.25 2825 136 0.91 14.75 1.00 0.98 2699.64| | 5: 2.25 - 2.09 2756 127 0.89 17.00 1.01 0.98 2699.64| | 6: 2.09 - 1.97 2846 113 0.92 13.73 1.02 0.97 1581.92| | 7: 1.97 - 1.87 2787 165 0.94 10.82 1.02 0.97 628.66| | 8: 1.87 - 1.79 2789 144 0.91 14.44 1.00 0.97 628.66| | 9: 1.79 - 1.72 2745 138 0.93 11.46 0.98 0.97 341.08| | 10: 1.72 - 1.66 2831 160 0.93 12.31 0.98 0.97 283.49| | 11: 1.66 - 1.61 2712 147 0.93 12.91 0.98 0.97 270.70| | 12: 1.61 - 1.56 2773 144 0.95 9.66 0.99 0.97 150.09| | 13: 1.56 - 1.52 2745 130 0.94 11.20 1.02 0.97 150.09| | 14: 1.52 - 1.48 2803 134 0.94 11.39 1.02 0.98 134.17| | 15: 1.48 - 1.45 2738 128 0.95 10.55 1.01 0.98 105.03| | 16: 1.45 - 1.42 2756 161 0.94 11.72 1.02 0.98 105.03| | 17: 1.42 - 1.39 2785 139 0.94 11.53 1.01 0.98 94.74| | 18: 1.39 - 1.36 2741 179 0.94 11.88 1.01 0.98 88.78| | 19: 1.36 - 1.34 2807 134 0.94 12.44 1.00 0.98 88.78| | 20: 1.34 - 1.32 2696 147 0.94 12.52 0.99 0.97 83.28| | 21: 1.32 - 1.30 2785 112 0.94 13.41 0.98 0.96 82.89| | 22: 1.29 - 1.27 2704 152 0.93 13.96 0.98 0.96 82.97| | 23: 1.27 - 1.26 2802 156 0.92 14.84 0.97 0.95 83.35| | 24: 1.26 - 1.24 2744 132 0.92 15.01 0.97 0.95 83.35| | 25: 1.24 - 1.22 2733 148 0.91 16.37 0.96 0.94 84.77| | 26: 1.22 - 1.21 2727 135 0.90 18.04 1.02 0.93 86.36| | 27: 1.21 - 1.19 2814 148 0.89 18.71 1.02 0.93 86.36| | 28: 1.19 - 1.18 2671 147 0.88 20.23 1.01 0.93 89.47| | 29: 1.18 - 1.16 2800 134 0.88 20.50 0.99 0.93 90.64| | 30: 1.16 - 1.15 2739 148 0.86 21.90 0.98 0.93 90.64| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 82.89 max = 6433.26 mean = 999.39| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 14.11| |phase err.(test): min = 0.00 max = 89.83 mean = 14.24| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1199 0.1363 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1515 0.1514 0.1555 n_refl.: 87576 remove outliers: r(all,work,free)=0.1515 0.1514 0.1555 n_refl.: 87576 overall B=-0.01 to atoms: r(all,work,free)=0.1513 0.1512 0.1554 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1209 0.1200 0.1366 n_refl.: 87576 remove outliers: r(all,work,free)=0.1208 0.1200 0.1366 n_refl.: 87574 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.4192 286.517 251.433 0.422 1.001 0.272 11.894-9.307 93.14 91 4 0.2470 481.412 457.821 0.843 1.002 0.252 9.237-7.194 98.18 209 7 0.2620 383.706 375.218 0.907 1.002 0.155 7.162-5.571 100.00 427 22 0.2304 294.304 282.574 0.898 1.002 0.130 5.546-4.326 100.00 867 58 0.1216 404.007 398.696 0.954 1.002 0.120 4.315-3.360 100.00 1859 96 0.0994 384.213 381.369 0.994 1.002 0.113 3.356-2.611 100.00 3867 181 0.1184 252.408 250.487 1.001 1.002 0.073 2.608-2.026 99.99 8198 413 0.1040 167.324 166.464 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0973 81.712 81.974 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1225 36.234 35.866 1.021 0.997 0.000 1.221-1.150 99.97 13689 708 0.2115 22.830 21.452 0.979 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0318 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2598 0.1946 0.083 5.258 8.8 119.3 19.9 258 0.000 1_bss: 0.1626 0.1765 0.083 5.258 9.0 119.5 20.1 258 0.000 1_settarget: 0.1626 0.1765 0.083 5.258 9.0 119.5 20.1 258 0.000 1_nqh: 0.1626 0.1765 0.083 5.258 9.0 119.5 20.1 258 0.000 1_weight: 0.1626 0.1765 0.083 5.258 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1208 0.1456 0.007 0.941 9.0 119.5 20.1 258 0.125 1_adp: 0.1239 0.1533 0.007 0.941 8.5 118.7 20.9 258 0.125 1_regHadp: 0.1243 0.1537 0.007 0.941 8.5 118.7 20.9 258 0.125 1_occ: 0.1243 0.1542 0.007 0.941 8.5 118.7 20.9 258 0.125 2_bss: 0.1241 0.1535 0.007 0.941 8.6 118.9 21.0 258 0.125 2_settarget: 0.1241 0.1535 0.007 0.941 8.6 118.9 21.0 258 0.125 2_updatecdl: 0.1241 0.1535 0.007 0.948 8.6 118.9 21.0 258 0.125 2_nqh: 0.1241 0.1535 0.007 0.948 8.6 118.9 21.0 258 0.125 2_sol: 0.1230 0.1475 0.007 0.948 8.6 118.9 23.4 436 n/a 2_weight: 0.1230 0.1475 0.007 0.948 8.6 118.9 23.4 436 n/a 2_xyzrec: 0.1226 0.1520 0.007 0.887 8.6 118.9 23.4 436 n/a 2_adp: 0.1198 0.1494 0.007 0.887 8.7 114.4 23.1 436 n/a 2_regHadp: 0.1197 0.1493 0.007 0.887 8.7 114.4 23.1 436 n/a 2_occ: 0.1198 0.1486 0.007 0.887 8.7 114.4 23.1 436 n/a 3_bss: 0.1193 0.1483 0.007 0.887 8.7 114.5 23.1 436 n/a 3_settarget: 0.1193 0.1483 0.007 0.887 8.7 114.5 23.1 436 n/a 3_updatecdl: 0.1193 0.1483 0.007 0.889 8.7 114.5 23.1 436 n/a 3_nqh: 0.1194 0.1486 0.007 0.889 8.7 114.5 23.1 436 n/a 3_sol: 0.1221 0.1494 0.007 0.889 8.7 114.5 22.0 453 n/a 3_weight: 0.1221 0.1494 0.007 0.889 8.7 114.5 22.0 453 n/a 3_xyzrec: 0.1225 0.1448 0.006 0.925 8.7 114.5 22.0 453 n/a 3_adp: 0.1206 0.1403 0.006 0.925 9.1 109.9 21.6 453 n/a 3_regHadp: 0.1206 0.1404 0.006 0.925 9.1 109.9 21.6 453 n/a 3_occ: 0.1204 0.1407 0.006 0.925 9.1 109.9 21.6 453 n/a 4_bss: 0.1191 0.1377 0.006 0.925 9.1 109.9 21.6 453 n/a 4_settarget: 0.1191 0.1377 0.006 0.925 9.1 109.9 21.6 453 n/a 4_updatecdl: 0.1191 0.1377 0.006 0.923 9.1 109.9 21.6 453 n/a 4_nqh: 0.1191 0.1377 0.006 0.923 9.1 109.9 21.6 453 n/a 4_sol: 0.1188 0.1365 0.006 0.923 9.1 109.9 21.3 443 n/a 4_weight: 0.1188 0.1365 0.006 0.923 9.1 109.9 21.3 443 n/a 4_xyzrec: 0.1196 0.1372 0.006 0.950 9.1 109.9 21.3 443 n/a 4_adp: 0.1185 0.1366 0.006 0.950 9.2 105.7 21.1 443 n/a 4_regHadp: 0.1186 0.1367 0.006 0.950 9.2 105.7 21.1 443 n/a 4_occ: 0.1183 0.1364 0.006 0.950 9.2 105.7 21.1 443 n/a 5_bss: 0.1180 0.1362 0.006 0.950 9.2 105.7 21.1 443 n/a 5_settarget: 0.1180 0.1362 0.006 0.950 9.2 105.7 21.1 443 n/a 5_updatecdl: 0.1180 0.1362 0.006 0.951 9.2 105.7 21.1 443 n/a 5_setrh: 0.1181 0.1362 0.006 0.951 9.2 105.7 21.1 443 n/a 5_nqh: 0.1181 0.1362 0.006 0.951 9.2 105.7 21.1 443 n/a 5_sol: 0.1174 0.1339 0.006 0.951 9.2 105.7 21.1 447 n/a 5_weight: 0.1174 0.1339 0.006 0.951 9.2 105.7 21.1 447 n/a 5_xyzrec: 0.1198 0.1359 0.006 1.060 9.2 105.7 21.1 447 n/a 5_adp: 0.1203 0.1366 0.006 1.060 9.1 101.7 20.9 447 n/a 5_regHadp: 0.1203 0.1366 0.006 1.060 9.1 101.7 20.9 447 n/a 5_occ: 0.1199 0.1363 0.006 1.060 9.1 101.7 20.9 447 n/a end: 0.1200 0.1366 0.006 1.060 9.1 101.6 20.9 447 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8565654_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8565654_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7300 Refinement macro-cycles (run) : 3434.4000 Write final files (write_after_run_outputs) : 69.6000 Total : 3508.7300 Total CPU time: 59.08 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:10:53 PST -0800 (1735452653.13 s) Start R-work = 0.1626, R-free = 0.1765 Final R-work = 0.1200, R-free = 0.1366 =============================================================================== Job complete usr+sys time: 3646.16 seconds wall clock time: 66 minutes 6.65 seconds (3966.65 seconds total)