============================== Collecting inputs ============================== ----------Processing X-ray data---------- I-obs: /nfs/staff/key/software_tests/PHENIX.ROSETTA.REFINE_linux/1I2T_F.mtz:IOBS,SIGIOBS Miller array info: /nfs/staff/key/software_tests/PHENIX.ROSETTA.REFINE_linux/1I2T_F.mtz:IOBS,SIGIOBS Observation type: xray.intensity Type of data: double, size=31449 Type of sigmas: double, size=31449 Number of Miller indices: 31449 Anomalous flag: False Unit cell: (32.969, 38.166, 51.062, 90, 90, 90) Space group: P 21 21 21 (No. 19) Systematic absences: 0 Centric reflections: 3439 Resolution range: 19.083 1.04105 Completeness in resolution range: 0.996609 Completeness with d_max=infinity: 0.996388 Wavelength: 1.1000 ----------Scaling input intensities via French-Wilson Method---------- Trying 60 bins... Number of bins = 60 ** Calculating bin mean intensity values for each intensity ** ** Total # rejected intensities: 0 ** Intensities converted to amplitudes for use in refinement. Number of F-obs in resolution range: 31449 Number of F-obs<0 (these reflections will be rejected): 0 Number of F-obs=0 (these reflections will be used in refinement): 0 Refinement resolution range: d_max = 19.0830 d_min = 1.0411 R-free flags: /nfs/staff/key/software_tests/PHENIX.ROSETTA.REFINE_linux/1I2T_F.mtz:FreeR_flag Miller array info: /nfs/staff/key/software_tests/PHENIX.ROSETTA.REFINE_linux/1I2T_F.mtz:FreeR_flag Observation type: None Type of data: int, size=31567 Type of sigmas: None Number of Miller indices: 31567 Anomalous flag: False Unit cell: (32.969, 38.166, 51.062, 90, 90, 90) Space group: P 21 21 21 (No. 19) Systematic absences: 0 Centric reflections: 3486 Resolution range: 30.5703 1.041 Completeness in resolution range: 1 Completeness with d_max=infinity: 1 Wavelength: 9.9990 Test (R-free flags) flag value: 0 Number of work/free reflections by resolution: work free %free bin 1: 19.0862 - 2.2418 [3340/3340] 3188 152 4.6% bin 2: 2.2418 - 1.7798 [3216/3217] 3050 166 5.2% bin 3: 1.7798 - 1.5549 [3147/3150] 2995 152 4.8% bin 4: 1.5549 - 1.4128 [3136/3137] 2983 153 4.9% bin 5: 1.4128 - 1.3116 [3144/3146] 2979 165 5.2% bin 6: 1.3116 - 1.2343 [3134/3134] 2981 153 4.9% bin 7: 1.2343 - 1.1725 [3107/3107] 2951 156 5.0% bin 8: 1.1725 - 1.1214 [3108/3114] 2950 158 5.1% bin 9: 1.1214 - 1.0783 [3103/3128] 2951 152 4.9% bin 10: 1.0783 - 1.0411 [3014/3083] 2860 154 5.1% overall 29888 1561 5.0% ----------Processing PDB file(s)---------- Monomer Library directory: "/programs/x86_64-linux/phenix/1.13-2998/phenix-1.13-2998/modules/chem_data/mon_lib" Total number of atoms: 602 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 472 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 57} Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 130 Classifications: {'water': 130} Link IDs: {None: 129} Time building chain proxies: 0.35, per 1000 atoms: 0.58 Number of scatterers: 602 At special positions: 0 Unit cell: (32.969, 38.166, 51.062, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 3 16.00 O 216 8.00 N 85 7.00 C 298 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: Warning: Ignoring bond with distance_ideal = None: atom_selection_1 = None atom_selection_2 = None Total number of custom bonds: 0 Custom angles: Warning: Ignoring angle with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None Total number of custom angles: 0 Custom dihedrals: Warning: Ignoring dihedral with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None atom_selection_4 = None Total number of custom dihedrals: 0 Custom planarities: Warning: Ignoring planarity with with sigma <= 0: atom_selection = None None Total number of custom planarities: 0 Custom parallelities: Warning: Ignoring parallelity with empty atom selection. Total number of custom parallelities: 0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : False - 3.50 Amimo acid : False - 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: 0.11 Conformation dependent library (CDL) restraints added in 24.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 116 Time building geometry restraints manager: 0.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 161 1.35 - 1.48: 94 1.48 - 1.61: 217 1.61 - 1.74: 0 1.74 - 1.87: 6 Bond restraints: 478 Sorted by residual: bond pdb=" C GLY A1069 " pdb=" OXT GLY A1069 " ideal model delta sigma weight residual 1.231 1.363 -0.132 2.00e-02 2.50e+03 4.36e+01 bond pdb=" CG MET A1024 " pdb=" SD MET A1024 " ideal model delta sigma weight residual 1.803 1.874 -0.071 2.50e-02 1.60e+03 8.11e+00 bond pdb=" CG MET A1035 " pdb=" SD MET A1035 " ideal model delta sigma weight residual 1.803 1.873 -0.070 2.50e-02 1.60e+03 7.94e+00 bond pdb=" SD MET A1035 " pdb=" CE MET A1035 " ideal model delta sigma weight residual 1.791 1.849 -0.058 2.50e-02 1.60e+03 5.41e+00 bond pdb=" SD MET A1024 " pdb=" CE MET A1024 " ideal model delta sigma weight residual 1.791 1.842 -0.051 2.50e-02 1.60e+03 4.10e+00 ... (remaining 473 not shown) Histogram of bond angle deviations from ideal: 96.82 - 105.53: 15 105.53 - 114.23: 281 114.23 - 122.94: 314 122.94 - 131.65: 32 131.65 - 140.35: 3 Bond angle restraints: 645 Sorted by residual: angle pdb=" CA GLY A1069 " pdb=" C GLY A1069 " pdb=" OXT GLY A1069 " ideal model delta sigma weight residual 121.00 140.35 -19.35 3.00e+00 1.11e-01 4.16e+01 angle pdb=" O GLY A1069 " pdb=" C GLY A1069 " pdb=" OXT GLY A1069 " ideal model delta sigma weight residual 118.00 99.51 18.49 3.00e+00 1.11e-01 3.80e+01 angle pdb=" CA HIS A1068 " pdb=" CB HIS A1068 " pdb=" CG HIS A1068 " ideal model delta sigma weight residual 113.80 118.12 -4.32 1.00e+00 1.00e+00 1.86e+01 angle pdb=" CB GLN A1011 " pdb=" CG GLN A1011 " pdb=" CD GLN A1011 " ideal model delta sigma weight residual 112.60 119.69 -7.09 1.70e+00 3.46e-01 1.74e+01 angle pdb=" OE1 GLN A1011 " pdb=" CD GLN A1011 " pdb=" NE2 GLN A1011 " ideal model delta sigma weight residual 122.60 119.13 3.47 1.00e+00 1.00e+00 1.21e+01 ... (remaining 640 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.59: 280 16.59 - 33.16: 16 33.16 - 49.74: 3 49.74 - 66.32: 1 66.32 - 82.89: 1 Dihedral angle restraints: 301 sinusoidal: 124 harmonic: 177 Sorted by residual: dihedral pdb=" CB MET A1062 " pdb=" CG MET A1062 " pdb=" SD MET A1062 " pdb=" CE MET A1062 " ideal model delta sinusoidal sigma weight residual -60.00 -108.96 48.96 3 1.50e+01 4.44e-03 8.71e+00 dihedral pdb=" CA PHE A1028 " pdb=" C PHE A1028 " pdb=" N ALA A1029 " pdb=" CA ALA A1029 " ideal model delta harmonic sigma weight residual -180.00 -167.77 -12.23 0 5.00e+00 4.00e-02 5.98e+00 dihedral pdb=" CB GLN A1011 " pdb=" CG GLN A1011 " pdb=" CD GLN A1011 " pdb=" OE1 GLN A1011 " ideal model delta sinusoidal sigma weight residual 180.00 97.11 82.89 2 3.00e+01 1.11e-03 5.25e+00 ... (remaining 298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 40 0.031 - 0.062: 21 0.062 - 0.094: 13 0.094 - 0.125: 1 0.125 - 0.156: 1 Chirality restraints: 76 Sorted by residual: chirality pdb=" CB ILE A1065 " pdb=" CA ILE A1065 " pdb=" CG1 ILE A1065 " pdb=" CG2 ILE A1065 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" CB ILE A1066 " pdb=" CA ILE A1066 " pdb=" CG1 ILE A1066 " pdb=" CG2 ILE A1066 " both_signs ideal model delta sigma weight residual False 2.64 2.53 0.11 2.00e-01 2.50e+01 3.06e-01 chirality pdb=" CA TYR A1018 " pdb=" N TYR A1018 " pdb=" C TYR A1018 " pdb=" CB TYR A1018 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.07e-01 ... (remaining 73 not shown) Planarity restraints: 84 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A1040 " 0.005 2.00e-02 2.50e+03 1.08e-02 1.17e+00 pdb=" C SER A1040 " -0.019 2.00e-02 2.50e+03 pdb=" O SER A1040 " 0.007 2.00e-02 2.50e+03 pdb=" N PRO A1041 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1020 " -0.010 2.00e-02 2.50e+03 9.40e-03 1.10e+00 pdb=" NE ARG A1020 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A1020 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A1020 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A1020 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A1043 " 0.005 2.00e-02 2.50e+03 9.14e-03 8.35e-01 pdb=" C GLN A1043 " -0.016 2.00e-02 2.50e+03 pdb=" O GLN A1043 " 0.006 2.00e-02 2.50e+03 pdb=" N LEU A1044 " 0.005 2.00e-02 2.50e+03 ... (remaining 81 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 225 2.81 - 3.33: 667 3.33 - 3.86: 1265 3.86 - 4.38: 1575 4.38 - 4.90: 2246 Nonbonded interactions: 5978 Sorted by model distance: nonbonded pdb=" O HOH A1131 " pdb=" O HOH A1149 " model vdw 2.288 2.440 nonbonded pdb=" O HOH A1146 " pdb=" O HOH A1151 " model vdw 2.297 2.440 nonbonded pdb=" O HOH A1130 " pdb=" O HOH A1177 " model vdw 2.297 2.440 nonbonded pdb=" O HOH A1139 " pdb=" O HOH A1143 " model vdw 2.298 2.440 nonbonded pdb=" OD2 ASP A1059 " pdb=" O HOH A1173 " model vdw 2.299 2.440 ... (remaining 5973 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: 4 Type Number sf(0) Gaussians S 3 15.96 2 O 216 7.97 2 N 85 6.97 2 C 298 5.97 2 sf(0) = scattering factor at diffraction angle 0. Number of scatterers: 602 At special positions: 0 Unit cell: (32.969, 38.166, 51.062, 90, 90, 90) Space group: P 21 21 21 (No. 19) ----------F(model) initialization---------- start: r(all,work,free)=0.2720 0.2733 0.2502 n_refl.: 31449 re-set all scales: r(all,work,free)=0.2720 0.2733 0.2502 n_refl.: 31449 remove outliers: r(all,work,free)=0.2722 0.2734 0.2502 n_refl.: 31445 bulk-solvent and scaling: r(all,work,free)=0.1978 0.1984 0.1864 n_refl.: 31445 remove outliers: r(all,work,free)=0.1977 0.1983 0.1864 n_refl.: 31444 |-Mask optimization: start----------------------------------------------------| | Solvent (probe) radius= 1.11 Shrink truncation radius= 0.90 | | all data: 500 lowest resolution reflections: | | r_work= 0.1983 r_free= 0.1864 r_work= 0.2432 | |-----------------------------------------------------------------------------| r_solv= 0.00 r_shrink= 0.00 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 r_solv= 0.10 r_shrink= 0.00 r_work=0.2008 r_free=0.1943 r_work_low=0.3020 r_solv= 0.20 r_shrink= 0.00 r_work=0.2000 r_free=0.1930 r_work_low=0.2725 r_solv= 0.30 r_shrink= 0.00 r_work=0.1992 r_free=0.1917 r_work_low=0.2512 r_solv= 0.40 r_shrink= 0.00 r_work=0.1985 r_free=0.1902 r_work_low=0.2362 r_solv= 0.50 r_shrink= 0.00 r_work=0.1982 r_free=0.1890 r_work_low=0.2416 r_solv= 0.60 r_shrink= 0.00 r_work=0.1983 r_free=0.1887 r_work_low=0.2547 r_solv= 0.70 r_shrink= 0.00 r_work=0.1987 r_free=0.1886 r_work_low=0.2696 r_solv= 0.80 r_shrink= 0.00 r_work=0.1992 r_free=0.1890 r_work_low=0.2839 r_solv= 0.90 r_shrink= 0.00 r_work=0.1998 r_free=0.1895 r_work_low=0.2974 r_solv= 1.00 r_shrink= 0.00 r_work=0.2004 r_free=0.1902 r_work_low=0.3092 r_solv= 1.10 r_shrink= 0.00 r_work=0.2009 r_free=0.1908 r_work_low=0.3185 r_solv= 1.20 r_shrink= 0.00 r_work=0.2013 r_free=0.1915 r_work_low=0.3244 r_solv= 1.30 r_shrink= 0.00 r_work=0.2017 r_free=0.1919 r_work_low=0.3282 r_solv= 1.40 r_shrink= 0.00 r_work=0.2021 r_free=0.1921 r_work_low=0.3301 r_solv= 0.00 r_shrink= 0.10 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 r_solv= 0.10 r_shrink= 0.10 r_work=0.2008 r_free=0.1943 r_work_low=0.3020 r_solv= 0.20 r_shrink= 0.10 r_work=0.2000 r_free=0.1930 r_work_low=0.2725 r_solv= 0.30 r_shrink= 0.10 r_work=0.1992 r_free=0.1917 r_work_low=0.2512 r_solv= 0.40 r_shrink= 0.10 r_work=0.1985 r_free=0.1902 r_work_low=0.2362 r_solv= 0.50 r_shrink= 0.10 r_work=0.1982 r_free=0.1890 r_work_low=0.2416 r_solv= 0.60 r_shrink= 0.10 r_work=0.1983 r_free=0.1887 r_work_low=0.2547 r_solv= 0.70 r_shrink= 0.10 r_work=0.1987 r_free=0.1886 r_work_low=0.2696 r_solv= 0.80 r_shrink= 0.10 r_work=0.1992 r_free=0.1890 r_work_low=0.2839 r_solv= 0.90 r_shrink= 0.10 r_work=0.1998 r_free=0.1895 r_work_low=0.2974 r_solv= 1.00 r_shrink= 0.10 r_work=0.2004 r_free=0.1902 r_work_low=0.3092 r_solv= 1.10 r_shrink= 0.10 r_work=0.2009 r_free=0.1908 r_work_low=0.3185 r_solv= 1.20 r_shrink= 0.10 r_work=0.2013 r_free=0.1915 r_work_low=0.3244 r_solv= 1.30 r_shrink= 0.10 r_work=0.2017 r_free=0.1919 r_work_low=0.3282 r_solv= 1.40 r_shrink= 0.10 r_work=0.2021 r_free=0.1921 r_work_low=0.3301 r_solv= 0.00 r_shrink= 0.20 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 r_solv= 0.10 r_shrink= 0.20 r_work=0.2008 r_free=0.1943 r_work_low=0.3020 r_solv= 0.20 r_shrink= 0.20 r_work=0.2000 r_free=0.1930 r_work_low=0.2725 r_solv= 0.30 r_shrink= 0.20 r_work=0.1992 r_free=0.1917 r_work_low=0.2512 r_solv= 0.40 r_shrink= 0.20 r_work=0.1985 r_free=0.1902 r_work_low=0.2362 r_solv= 0.50 r_shrink= 0.20 r_work=0.1982 r_free=0.1890 r_work_low=0.2416 r_solv= 0.60 r_shrink= 0.20 r_work=0.1983 r_free=0.1887 r_work_low=0.2547 r_solv= 0.70 r_shrink= 0.20 r_work=0.1987 r_free=0.1886 r_work_low=0.2696 r_solv= 0.80 r_shrink= 0.20 r_work=0.1992 r_free=0.1890 r_work_low=0.2839 r_solv= 0.90 r_shrink= 0.20 r_work=0.1998 r_free=0.1895 r_work_low=0.2974 r_solv= 1.00 r_shrink= 0.20 r_work=0.2004 r_free=0.1902 r_work_low=0.3092 r_solv= 1.10 r_shrink= 0.20 r_work=0.2009 r_free=0.1908 r_work_low=0.3185 r_solv= 1.20 r_shrink= 0.20 r_work=0.2013 r_free=0.1915 r_work_low=0.3244 r_solv= 1.30 r_shrink= 0.20 r_work=0.2017 r_free=0.1919 r_work_low=0.3282 r_solv= 1.40 r_shrink= 0.20 r_work=0.2021 r_free=0.1921 r_work_low=0.3301 r_solv= 0.00 r_shrink= 0.30 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 r_solv= 0.10 r_shrink= 0.30 r_work=0.2016 r_free=0.1953 r_work_low=0.3304 r_solv= 0.20 r_shrink= 0.30 r_work=0.2016 r_free=0.1955 r_work_low=0.3276 r_solv= 0.30 r_shrink= 0.30 r_work=0.2010 r_free=0.1946 r_work_low=0.3013 r_solv= 0.40 r_shrink= 0.30 r_work=0.2000 r_free=0.1932 r_work_low=0.2660 r_solv= 0.50 r_shrink= 0.30 r_work=0.1990 r_free=0.1916 r_work_low=0.2412 r_solv= 0.60 r_shrink= 0.30 r_work=0.1982 r_free=0.1900 r_work_low=0.2313 r_solv= 0.70 r_shrink= 0.30 r_work=0.1981 r_free=0.1886 r_work_low=0.2402 r_solv= 0.80 r_shrink= 0.30 r_work=0.1983 r_free=0.1881 r_work_low=0.2578 r_solv= 0.90 r_shrink= 0.30 r_work=0.1988 r_free=0.1883 r_work_low=0.2731 r_solv= 1.00 r_shrink= 0.30 r_work=0.1994 r_free=0.1889 r_work_low=0.2870 r_solv= 1.10 r_shrink= 0.30 r_work=0.2000 r_free=0.1896 r_work_low=0.2997 r_solv= 1.20 r_shrink= 0.30 r_work=0.2006 r_free=0.1904 r_work_low=0.3110 r_solv= 1.30 r_shrink= 0.30 r_work=0.2010 r_free=0.1910 r_work_low=0.3207 r_solv= 1.40 r_shrink= 0.30 r_work=0.2014 r_free=0.1916 r_work_low=0.3262 r_solv= 0.00 r_shrink= 0.40 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 r_solv= 0.10 r_shrink= 0.40 r_work=0.2016 r_free=0.1952 r_work_low=0.3305 r_solv= 0.20 r_shrink= 0.40 r_work=0.2016 r_free=0.1953 r_work_low=0.3299 r_solv= 0.30 r_shrink= 0.40 r_work=0.2017 r_free=0.1956 r_work_low=0.3277 r_solv= 0.40 r_shrink= 0.40 r_work=0.2010 r_free=0.1948 r_work_low=0.2980 r_solv= 0.50 r_shrink= 0.40 r_work=0.1999 r_free=0.1930 r_work_low=0.2610 r_solv= 0.60 r_shrink= 0.40 r_work=0.1988 r_free=0.1914 r_work_low=0.2377 r_solv= 0.70 r_shrink= 0.40 r_work=0.1981 r_free=0.1896 r_work_low=0.2319 r_solv= 0.80 r_shrink= 0.40 r_work=0.1981 r_free=0.1880 r_work_low=0.2434 r_solv= 0.90 r_shrink= 0.40 r_work=0.1984 r_free=0.1879 r_work_low=0.2597 r_solv= 1.00 r_shrink= 0.40 r_work=0.1990 r_free=0.1882 r_work_low=0.2751 r_solv= 1.10 r_shrink= 0.40 r_work=0.1995 r_free=0.1889 r_work_low=0.2880 r_solv= 1.20 r_shrink= 0.40 r_work=0.2001 r_free=0.1897 r_work_low=0.3000 r_solv= 1.30 r_shrink= 0.40 r_work=0.2006 r_free=0.1904 r_work_low=0.3123 r_solv= 1.40 r_shrink= 0.40 r_work=0.2011 r_free=0.1911 r_work_low=0.3218 r_solv= 0.00 r_shrink= 0.50 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 r_solv= 0.10 r_shrink= 0.50 r_work=0.2016 r_free=0.1952 r_work_low=0.3305 r_solv= 0.20 r_shrink= 0.50 r_work=0.2016 r_free=0.1953 r_work_low=0.3301 r_solv= 0.30 r_shrink= 0.50 r_work=0.2017 r_free=0.1956 r_work_low=0.3301 r_solv= 0.40 r_shrink= 0.50 r_work=0.2014 r_free=0.1957 r_work_low=0.3131 r_solv= 0.50 r_shrink= 0.50 r_work=0.2004 r_free=0.1938 r_work_low=0.2737 r_solv= 0.60 r_shrink= 0.50 r_work=0.1992 r_free=0.1921 r_work_low=0.2436 r_solv= 0.70 r_shrink= 0.50 r_work=0.1983 r_free=0.1900 r_work_low=0.2321 r_solv= 0.80 r_shrink= 0.50 r_work=0.1981 r_free=0.1883 r_work_low=0.2383 r_solv= 0.90 r_shrink= 0.50 r_work=0.1983 r_free=0.1877 r_work_low=0.2530 r_solv= 1.00 r_shrink= 0.50 r_work=0.1988 r_free=0.1878 r_work_low=0.2690 r_solv= 1.10 r_shrink= 0.50 r_work=0.1993 r_free=0.1885 r_work_low=0.2827 r_solv= 1.20 r_shrink= 0.50 r_work=0.1999 r_free=0.1894 r_work_low=0.2945 r_solv= 1.30 r_shrink= 0.50 r_work=0.2004 r_free=0.1901 r_work_low=0.3078 r_solv= 1.40 r_shrink= 0.50 r_work=0.2009 r_free=0.1909 r_work_low=0.3188 r_solv= 0.00 r_shrink= 0.60 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 r_solv= 0.10 r_shrink= 0.60 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 r_solv= 0.20 r_shrink= 0.60 r_work=0.2016 r_free=0.1952 r_work_low=0.3304 r_solv= 0.30 r_shrink= 0.60 r_work=0.2017 r_free=0.1955 r_work_low=0.3325 r_solv= 0.40 r_shrink= 0.60 r_work=0.2018 r_free=0.1962 r_work_low=0.3309 r_solv= 0.50 r_shrink= 0.60 r_work=0.2014 r_free=0.1959 r_work_low=0.3076 r_solv= 0.60 r_shrink= 0.60 r_work=0.2005 r_free=0.1946 r_work_low=0.2727 r_solv= 0.70 r_shrink= 0.60 r_work=0.1993 r_free=0.1918 r_work_low=0.2444 r_solv= 0.80 r_shrink= 0.60 r_work=0.1984 r_free=0.1898 r_work_low=0.2395 r_solv= 0.90 r_shrink= 0.60 r_work=0.1981 r_free=0.1881 r_work_low=0.2414 r_solv= 1.00 r_shrink= 0.60 r_work=0.1984 r_free=0.1870 r_work_low=0.2535 r_solv= 1.10 r_shrink= 0.60 r_work=0.1988 r_free=0.1876 r_work_low=0.2667 r_solv= 1.20 r_shrink= 0.60 r_work=0.1994 r_free=0.1885 r_work_low=0.2799 r_solv= 1.30 r_shrink= 0.60 r_work=0.1999 r_free=0.1892 r_work_low=0.2932 r_solv= 1.40 r_shrink= 0.60 r_work=0.2004 r_free=0.1902 r_work_low=0.3069 r_solv= 0.00 r_shrink= 0.70 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 r_solv= 0.10 r_shrink= 0.70 r_work=0.2016 r_free=0.1952 r_work_low=0.3306 r_solv= 0.20 r_shrink= 0.70 r_work=0.2016 r_free=0.1952 r_work_low=0.3305 r_solv= 0.30 r_shrink= 0.70 r_work=0.2017 r_free=0.1954 r_work_low=0.3325 r_solv= 0.40 r_shrink= 0.70 r_work=0.2018 r_free=0.1962 r_work_low=0.3342 r_solv= 0.50 r_shrink= 0.70 r_work=0.2016 r_free=0.1961 r_work_low=0.3168 r_solv= 0.60 r_shrink= 0.70 r_work=0.2009 r_free=0.1956 r_work_low=0.2864 r_solv= 0.70 r_shrink= 0.70 r_work=0.1997 r_free=0.1925 r_work_low=0.2547 r_solv= 0.80 r_shrink= 0.70 r_work=0.1987 r_free=0.1904 r_work_low=0.2429 r_solv= 0.90 r_shrink= 0.70 r_work=0.1982 r_free=0.1885 r_work_low=0.2420 r_solv= 1.00 r_shrink= 0.70 r_work=0.1983 r_free=0.1868 r_work_low=0.2488 r_solv= 1.10 r_shrink= 0.70 r_work=0.1987 r_free=0.1873 r_work_low=0.2599 r_solv= 1.20 r_shrink= 0.70 r_work=0.1992 r_free=0.1882 r_work_low=0.2745 r_solv= 1.30 r_shrink= 0.70 r_work=0.1997 r_free=0.1889 r_work_low=0.2882 r_solv= 1.40 r_shrink= 0.70 r_work=0.2002 r_free=0.1898 r_work_low=0.3019 r_solv= 0.00 r_shrink= 0.80 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 r_solv= 0.10 r_shrink= 0.80 r_work=0.2016 r_free=0.1952 r_work_low=0.3306 r_solv= 0.20 r_shrink= 0.80 r_work=0.2016 r_free=0.1952 r_work_low=0.3306 r_solv= 0.30 r_shrink= 0.80 r_work=0.2017 r_free=0.1953 r_work_low=0.3325 r_solv= 0.40 r_shrink= 0.80 r_work=0.2019 r_free=0.1961 r_work_low=0.3376 r_solv= 0.50 r_shrink= 0.80 r_work=0.2018 r_free=0.1962 r_work_low=0.3280 r_solv= 0.60 r_shrink= 0.80 r_work=0.2013 r_free=0.1965 r_work_low=0.3023 r_solv= 0.70 r_shrink= 0.80 r_work=0.2006 r_free=0.1946 r_work_low=0.2769 r_solv= 0.80 r_shrink= 0.80 r_work=0.1996 r_free=0.1917 r_work_low=0.2647 r_solv= 0.90 r_shrink= 0.80 r_work=0.1986 r_free=0.1894 r_work_low=0.2530 r_solv= 1.00 r_shrink= 0.80 r_work=0.1983 r_free=0.1870 r_work_low=0.2479 r_solv= 1.10 r_shrink= 0.80 r_work=0.1984 r_free=0.1866 r_work_low=0.2483 r_solv= 1.20 r_shrink= 0.80 r_work=0.1988 r_free=0.1873 r_work_low=0.2619 r_solv= 1.30 r_shrink= 0.80 r_work=0.1994 r_free=0.1881 r_work_low=0.2782 r_solv= 1.40 r_shrink= 0.80 r_work=0.1999 r_free=0.1891 r_work_low=0.2922 r_solv= 0.00 r_shrink= 0.90 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 r_solv= 0.10 r_shrink= 0.90 r_work=0.2016 r_free=0.1952 r_work_low=0.3306 r_solv= 0.20 r_shrink= 0.90 r_work=0.2016 r_free=0.1952 r_work_low=0.3306 r_solv= 0.30 r_shrink= 0.90 r_work=0.2016 r_free=0.1953 r_work_low=0.3318 r_solv= 0.40 r_shrink= 0.90 r_work=0.2019 r_free=0.1960 r_work_low=0.3386 r_solv= 0.50 r_shrink= 0.90 r_work=0.2019 r_free=0.1963 r_work_low=0.3345 r_solv= 0.60 r_shrink= 0.90 r_work=0.2016 r_free=0.1968 r_work_low=0.3126 r_solv= 0.70 r_shrink= 0.90 r_work=0.2011 r_free=0.1955 r_work_low=0.2890 r_solv= 0.80 r_shrink= 0.90 r_work=0.2002 r_free=0.1933 r_work_low=0.2820 r_solv= 0.90 r_shrink= 0.90 r_work=0.1991 r_free=0.1904 r_work_low=0.2658 r_solv= 1.00 r_shrink= 0.90 r_work=0.1984 r_free=0.1873 r_work_low=0.2538 r_solv= 1.10 r_shrink= 0.90 r_work=0.1983 r_free=0.1866 r_work_low=0.2429 r_solv= 1.20 r_shrink= 0.90 r_work=0.1986 r_free=0.1869 r_work_low=0.2538 r_solv= 1.30 r_shrink= 0.90 r_work=0.1991 r_free=0.1875 r_work_low=0.2702 r_solv= 1.40 r_shrink= 0.90 r_work=0.1996 r_free=0.1886 r_work_low=0.2851 r_solv= 0.00 r_shrink= 1.00 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 r_solv= 0.10 r_shrink= 1.00 r_work=0.2016 r_free=0.1952 r_work_low=0.3306 r_solv= 0.20 r_shrink= 1.00 r_work=0.2016 r_free=0.1952 r_work_low=0.3306 r_solv= 0.30 r_shrink= 1.00 r_work=0.2016 r_free=0.1953 r_work_low=0.3312 r_solv= 0.40 r_shrink= 1.00 r_work=0.2019 r_free=0.1960 r_work_low=0.3388 r_solv= 0.50 r_shrink= 1.00 r_work=0.2019 r_free=0.1962 r_work_low=0.3390 r_solv= 0.60 r_shrink= 1.00 r_work=0.2017 r_free=0.1970 r_work_low=0.3216 r_solv= 0.70 r_shrink= 1.00 r_work=0.2014 r_free=0.1961 r_work_low=0.3012 r_solv= 0.80 r_shrink= 1.00 r_work=0.2007 r_free=0.1945 r_work_low=0.2936 r_solv= 0.90 r_shrink= 1.00 r_work=0.1997 r_free=0.1917 r_work_low=0.2852 r_solv= 1.00 r_shrink= 1.00 r_work=0.1988 r_free=0.1878 r_work_low=0.2655 r_solv= 1.10 r_shrink= 1.00 r_work=0.1984 r_free=0.1868 r_work_low=0.2433 r_solv= 1.20 r_shrink= 1.00 r_work=0.1985 r_free=0.1865 r_work_low=0.2470 r_solv= 1.30 r_shrink= 1.00 r_work=0.1989 r_free=0.1869 r_work_low=0.2628 r_solv= 1.40 r_shrink= 1.00 r_work=0.1994 r_free=0.1881 r_work_low=0.2771 r_solv= 0.00 r_shrink= 1.10 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 r_solv= 0.10 r_shrink= 1.10 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 r_solv= 0.20 r_shrink= 1.10 r_work=0.2016 r_free=0.1952 r_work_low=0.3306 r_solv= 0.30 r_shrink= 1.10 r_work=0.2016 r_free=0.1952 r_work_low=0.3308 r_solv= 0.40 r_shrink= 1.10 r_work=0.2018 r_free=0.1959 r_work_low=0.3383 r_solv= 0.50 r_shrink= 1.10 r_work=0.2020 r_free=0.1962 r_work_low=0.3411 r_solv= 0.60 r_shrink= 1.10 r_work=0.2018 r_free=0.1971 r_work_low=0.3285 r_solv= 0.70 r_shrink= 1.10 r_work=0.2017 r_free=0.1966 r_work_low=0.3122 r_solv= 0.80 r_shrink= 1.10 r_work=0.2011 r_free=0.1954 r_work_low=0.3052 r_solv= 0.90 r_shrink= 1.10 r_work=0.2002 r_free=0.1932 r_work_low=0.3026 r_solv= 1.00 r_shrink= 1.10 r_work=0.1994 r_free=0.1883 r_work_low=0.2830 r_solv= 1.10 r_shrink= 1.10 r_work=0.1986 r_free=0.1868 r_work_low=0.2513 r_solv= 1.20 r_shrink= 1.10 r_work=0.1984 r_free=0.1868 r_work_low=0.2434 r_solv= 1.30 r_shrink= 1.10 r_work=0.1987 r_free=0.1866 r_work_low=0.2542 r_solv= 1.40 r_shrink= 1.10 r_work=0.1992 r_free=0.1873 r_work_low=0.2684 r_solv= 0.00 r_shrink= 1.20 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 r_solv= 0.10 r_shrink= 1.20 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 r_solv= 0.20 r_shrink= 1.20 r_work=0.2016 r_free=0.1952 r_work_low=0.3306 r_solv= 0.30 r_shrink= 1.20 r_work=0.2016 r_free=0.1952 r_work_low=0.3307 r_solv= 0.40 r_shrink= 1.20 r_work=0.2018 r_free=0.1957 r_work_low=0.3374 r_solv= 0.50 r_shrink= 1.20 r_work=0.2020 r_free=0.1961 r_work_low=0.3417 r_solv= 0.60 r_shrink= 1.20 r_work=0.2019 r_free=0.1970 r_work_low=0.3333 r_solv= 0.70 r_shrink= 1.20 r_work=0.2019 r_free=0.1968 r_work_low=0.3196 r_solv= 0.80 r_shrink= 1.20 r_work=0.2013 r_free=0.1960 r_work_low=0.3114 r_solv= 0.90 r_shrink= 1.20 r_work=0.2005 r_free=0.1942 r_work_low=0.3138 r_solv= 1.00 r_shrink= 1.20 r_work=0.1997 r_free=0.1889 r_work_low=0.2941 r_solv= 1.10 r_shrink= 1.20 r_work=0.1989 r_free=0.1870 r_work_low=0.2617 r_solv= 1.20 r_shrink= 1.20 r_work=0.1985 r_free=0.1871 r_work_low=0.2457 r_solv= 1.30 r_shrink= 1.20 r_work=0.1985 r_free=0.1864 r_work_low=0.2471 r_solv= 1.40 r_shrink= 1.20 r_work=0.1991 r_free=0.1870 r_work_low=0.2634 r_solv= 0.00 r_shrink= 1.30 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 r_solv= 0.10 r_shrink= 1.30 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 r_solv= 0.20 r_shrink= 1.30 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 r_solv= 0.30 r_shrink= 1.30 r_work=0.2016 r_free=0.1952 r_work_low=0.3307 r_solv= 0.40 r_shrink= 1.30 r_work=0.2018 r_free=0.1957 r_work_low=0.3370 r_solv= 0.50 r_shrink= 1.30 r_work=0.2020 r_free=0.1960 r_work_low=0.3418 r_solv= 0.60 r_shrink= 1.30 r_work=0.2019 r_free=0.1970 r_work_low=0.3358 r_solv= 0.70 r_shrink= 1.30 r_work=0.2019 r_free=0.1970 r_work_low=0.3237 r_solv= 0.80 r_shrink= 1.30 r_work=0.2015 r_free=0.1965 r_work_low=0.3155 r_solv= 0.90 r_shrink= 1.30 r_work=0.2007 r_free=0.1950 r_work_low=0.3221 r_solv= 1.00 r_shrink= 1.30 r_work=0.1999 r_free=0.1895 r_work_low=0.3035 r_solv= 1.10 r_shrink= 1.30 r_work=0.1991 r_free=0.1872 r_work_low=0.2676 r_solv= 1.20 r_shrink= 1.30 r_work=0.1986 r_free=0.1874 r_work_low=0.2504 r_solv= 1.30 r_shrink= 1.30 r_work=0.1984 r_free=0.1864 r_work_low=0.2449 r_solv= 1.40 r_shrink= 1.30 r_work=0.1990 r_free=0.1868 r_work_low=0.2594 r_solv= 0.00 r_shrink= 1.40 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 r_solv= 0.10 r_shrink= 1.40 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 r_solv= 0.20 r_shrink= 1.40 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 r_solv= 0.30 r_shrink= 1.40 r_work=0.2016 r_free=0.1952 r_work_low=0.3306 r_solv= 0.40 r_shrink= 1.40 r_work=0.2017 r_free=0.1955 r_work_low=0.3357 r_solv= 0.50 r_shrink= 1.40 r_work=0.2019 r_free=0.1959 r_work_low=0.3411 r_solv= 0.60 r_shrink= 1.40 r_work=0.2019 r_free=0.1968 r_work_low=0.3389 r_solv= 0.70 r_shrink= 1.40 r_work=0.2020 r_free=0.1972 r_work_low=0.3300 r_solv= 0.80 r_shrink= 1.40 r_work=0.2017 r_free=0.1971 r_work_low=0.3218 r_solv= 0.90 r_shrink= 1.40 r_work=0.2011 r_free=0.1960 r_work_low=0.3323 r_solv= 1.00 r_shrink= 1.40 r_work=0.2003 r_free=0.1905 r_work_low=0.3169 r_solv= 1.10 r_shrink= 1.40 r_work=0.1995 r_free=0.1881 r_work_low=0.2785 r_solv= 1.20 r_shrink= 1.40 r_work=0.1989 r_free=0.1874 r_work_low=0.2593 r_solv= 1.30 r_shrink= 1.40 r_work=0.1984 r_free=0.1866 r_work_low=0.2447 r_solv= 1.40 r_shrink= 1.40 r_work=0.1989 r_free=0.1866 r_work_low=0.2549 |-Mask optimization: final----------------------------------------------------| | Solvent (probe) radius= 0.70 Shrink truncation radius= 0.30 | | all data: 500 lowest resolution reflections: | | r_work= 0.1981 r_free= 0.1886 r_work= 0.2402 | |-----------------------------------------------------------------------------| |--(resolution: 1.04 - 19.08 A, n_refl.=31444 (all), 4.96 % free)------------| | | | r_work= 0.1981 r_free= 0.1886 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.640880 | | target function (ml) not normalized (work): 138683.431375 | | target function (ml) not normalized (free): 7189.821067 | |-----------------------------------------------------------------------------| End of input processing ======================= ROSETTA/PHENIX X-ray refinement ======================= Output directory: /nfs/staff/key/software_tests/PHENIX.ROSETTA.REFINE_linux/rosetta_refine_4 ----------Setting up input files for Rosetta---------- |-starting model--------------------------------------------------------------| | target_work(ml) = 4.64088 r_work = 0.1981 r_free = 0.1886 | |-----------------------------------------------------------------------------| Validation statistics (starting model): Ramachandran outliers = 0.00 % favored = 100.00 % Rotamer outliers = 2.04 % C-beta deviations = 0 Clashscore = 4.15 RMS(bonds) = 0.0000 RMS(angles) = 0.00 MolProbity score = 1.43 Rosetta command-line arguments: -parser:protocol /programs/x86_64-linux/rosetta/3.8/main/source/src/apps/public/crystal_refinement/low_resolution_refine.xml -s 1I2T_modified_rosetta_in.pdb -mtzfile 1I2T_modified_rosetta_data.mtz -run:preserve_header -crystal_refine -parser:script_vars symmdef=1I2T_modified_rosetta.symm -parser:script_vars bfactstrat=individual -parser:script_vars map_type=Auto -score:weights talaris2013_cart -nstruct 1 -database /programs/x86_64-linux/rosetta/3.8/main/database Generating 5 models on 1 processors... 1: r_work = 0.2200 r_free = 0.2181 energy = -694.96 rmsd = 0.946 *** 2: r_work = 0.2207 r_free = 0.2171 energy = -698.52 rmsd = 1.065 *** 3: r_work = 0.2206 r_free = 0.2139 energy = -704.21 rmsd = 0.970 *** 4: r_work = 0.2199 r_free = 0.2152 energy = -711.36 rmsd = 1.001 5: r_work = 0.2231 r_free = 0.2205 energy = -703.18 rmsd = 1.156 |-after ROSETTA---------------------------------------------------------------| | target_work(ml) = 4.64366 r_work = 0.2206 r_free = 0.2139 | |-----------------------------------------------------------------------------| Validation statistics after ROSETTA: Ramachandran outliers = 0.00 % favored = 100.00 % Rotamer outliers = 0.00 % C-beta deviations = 0 Clashscore = 0.00 RMS(bonds) = 0.0000 RMS(angles) = 0.00 MolProbity score = 0.50 ----------Running phenix.refine (with null strategy)---------- start r_work=0.2898 r_free=0.2737 1_bss r_work=0.2120 r_free=0.2065 end r_work=0.2120 r_free=0.2065 Ramachandran outliers = 0.00 % favored = 100.00 % Rotamer outliers = 0.00 % C-beta deviations = 0 Clashscore = 9.34 RMS(bonds) = 0.1003 RMS(angles) = 1.77 MolProbity score = 1.49 Resolution = 1.04 R-work = 0.2120 R-free = 0.2065 ----------Final results---------- Refined model: 1I2T_modified_rosetta_phenix_001.pdb Final maps: 1I2T_modified_rosetta_phenix_001.mtz Elapsed time: 9291.2s Citation: DiMaio F., Echols N., Headd J.J., Terwilliger T.C., Adams P.D., and Baker D. (2013). Improved low-resolution crystallographic refinement with Phenix and Rosetta. Nat Methods 10, 1102-4.