============================== Collecting inputs ============================== ----------Processing X-ray data---------- ----------Processing PDB file(s)---------- Symmetric amino acids flipped Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/dev/shm/nigel/phenix-1.20.1-4487/modules/chem_data/mon_lib" Total number of atoms: 8966 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 4483 Classifications: {'peptide': 276} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "B" Number of atoms: 4483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 4483 Classifications: {'peptide': 276} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 264} Time building chain proxies: 1.85, per 1000 atoms: 0.21 Number of scatterers: 8966 At special positions: 0 Unit cell: (58.37, 58.37, 212.61, 90, 90, 90) Space group: P 41 (No. 76) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 O 850 8.00 N 744 7.00 C 2876 6.00 H 4488 1.00 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 added/changed 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 new custom angles: 0 Total number of changed 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 Custom bonds: Warning: Ignoring bond with distance_ideal = None: atom_selection_1 = None atom_selection_2 = None Total number of added/changed 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 new custom angles: 0 Total number of changed 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 : Auto - 3.50 Amino 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: 2.63 Conformation dependent library (CDL) restraints added in 228.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 1044 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.16: 4486 1.16 - 1.34: 1456 1.34 - 1.52: 2031 1.52 - 1.70: 1071 1.70 - 1.89: 14 Bond restraints: 9058 Sorted by residual: bond pdb=" N PHE A 162 " pdb=" H PHE A 162 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N GLN A 38 " pdb=" H GLN A 38 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLU B 192 " pdb=" H GLU B 192 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 GLN A 271 " pdb="HE22 GLN A 271 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N LEU A 111 " pdb=" H LEU A 111 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 9053 not shown) Histogram of bond angle deviations from ideal: 94.75 - 102.61: 90 102.61 - 110.47: 9016 110.47 - 118.34: 3303 118.34 - 126.20: 3941 126.20 - 134.06: 78 Bond angle restraints: 16428 Sorted by residual: angle pdb=" N LEU B 196 " pdb=" CA LEU B 196 " pdb=" C LEU B 196 " ideal model delta sigma weight residual 113.18 99.40 13.78 1.21e+00 6.83e-01 1.30e+02 angle pdb=" N PHE B 183 " pdb=" CA PHE B 183 " pdb=" C PHE B 183 " ideal model delta sigma weight residual 112.87 125.82 -12.95 1.20e+00 6.94e-01 1.16e+02 angle pdb=" N PHE A 178 " pdb=" CA PHE A 178 " pdb=" C PHE A 178 " ideal model delta sigma weight residual 110.17 126.12 -15.95 1.51e+00 4.39e-01 1.12e+02 angle pdb=" N LEU A 196 " pdb=" CA LEU A 196 " pdb=" C LEU A 196 " ideal model delta sigma weight residual 113.18 100.49 12.69 1.21e+00 6.83e-01 1.10e+02 angle pdb=" N PHE B 104 " pdb=" CA PHE B 104 " pdb=" C PHE B 104 " ideal model delta sigma weight residual 113.97 101.08 12.89 1.28e+00 6.10e-01 1.01e+02 ... (remaining 16423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 3139 17.98 - 35.97: 297 35.97 - 53.95: 128 53.95 - 71.94: 47 71.94 - 89.92: 17 Dihedral angle restraints: 3628 sinusoidal: 1712 harmonic: 1916 Sorted by residual: dihedral pdb=" N THR B 180 " pdb=" C THR B 180 " pdb=" CA THR B 180 " pdb=" CB THR B 180 " ideal model delta harmonic sigma weight residual 123.40 133.58 -10.18 0 2.50e+00 1.60e-01 1.66e+01 dihedral pdb=" C THR B 180 " pdb=" N THR B 180 " pdb=" CA THR B 180 " pdb=" CB THR B 180 " ideal model delta harmonic sigma weight residual -122.00 -132.09 10.09 0 2.50e+00 1.60e-01 1.63e+01 dihedral pdb=" C LYS A 175 " pdb=" N LYS A 175 " pdb=" CA LYS A 175 " pdb=" CB LYS A 175 " ideal model delta harmonic sigma weight residual -122.60 -132.24 9.64 0 2.50e+00 1.60e-01 1.49e+01 ... (remaining 3625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 524 0.131 - 0.262: 137 0.262 - 0.393: 16 0.393 - 0.524: 6 0.524 - 0.655: 3 Chirality restraints: 686 Sorted by residual: chirality pdb=" CA LYS A 175 " pdb=" N LYS A 175 " pdb=" C LYS A 175 " pdb=" CB LYS A 175 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CA THR B 180 " pdb=" N THR B 180 " pdb=" C THR B 180 " pdb=" CB THR B 180 " both_signs ideal model delta sigma weight residual False 2.53 1.92 0.61 2.00e-01 2.50e+01 9.27e+00 chirality pdb=" CA GLU A 192 " pdb=" N GLU A 192 " pdb=" C GLU A 192 " pdb=" CB GLU A 192 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.34e+00 ... (remaining 683 not shown) Planarity restraints: 1326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 234 " 0.133 2.00e-02 2.50e+03 5.31e-02 8.47e+01 pdb=" CG TYR A 234 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR A 234 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR A 234 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR A 234 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR A 234 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 234 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 234 " 0.094 2.00e-02 2.50e+03 pdb=" HD1 TYR A 234 " -0.052 2.00e-02 2.50e+03 pdb=" HD2 TYR A 234 " -0.041 2.00e-02 2.50e+03 pdb=" HE1 TYR A 234 " -0.010 2.00e-02 2.50e+03 pdb=" HE2 TYR A 234 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 191 " 0.113 2.00e-02 2.50e+03 4.82e-02 6.98e+01 pdb=" CG TYR B 191 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 191 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR B 191 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR B 191 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR B 191 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 191 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 191 " 0.099 2.00e-02 2.50e+03 pdb=" HD1 TYR B 191 " -0.036 2.00e-02 2.50e+03 pdb=" HD2 TYR B 191 " -0.035 2.00e-02 2.50e+03 pdb=" HE1 TYR B 191 " -0.023 2.00e-02 2.50e+03 pdb=" HE2 TYR B 191 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 208 " 0.113 2.00e-02 2.50e+03 4.57e-02 6.26e+01 pdb=" CG TYR A 208 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 208 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 208 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR A 208 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR A 208 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 208 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 208 " 0.085 2.00e-02 2.50e+03 pdb=" HD1 TYR A 208 " -0.032 2.00e-02 2.50e+03 pdb=" HD2 TYR A 208 " -0.043 2.00e-02 2.50e+03 pdb=" HE1 TYR A 208 " -0.021 2.00e-02 2.50e+03 pdb=" HE2 TYR A 208 " -0.009 2.00e-02 2.50e+03 ... (remaining 1323 not shown) Histogram of nonbonded interaction distances: 0.78 - 1.54: 133 1.54 - 2.31: 2854 2.31 - 3.07: 28771 3.07 - 3.84: 38164 3.84 - 4.60: 61883 Warning: very small nonbonded interaction distances. Nonbonded interactions: 131805 Sorted by model distance: nonbonded pdb=" HA LYS A 276 " pdb=" HZ2 LYS A 276 " model vdw 0.775 2.270 nonbonded pdb="HD12 LEU B 218 " pdb=" H GLY B 219 " model vdw 0.996 2.270 nonbonded pdb=" H ASN A 75 " pdb="HD22 ASN A 75 " model vdw 1.050 2.100 nonbonded pdb=" O THR A 225 " pdb=" H ASN A 228 " model vdw 1.052 1.850 nonbonded pdb=" HA ILE A 252 " pdb="HD12 LEU A 255 " model vdw 1.091 2.440 ... (remaining 131800 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: 5 Type Number sf(0) Gaussians S 8 15.91 1 O 850 7.97 1 N 744 6.97 1 C 2876 5.97 1 H 4488 1.00 1 sf(0) = scattering factor at diffraction angle 0. Number of scatterers: 8966 At special positions: 0 Unit cell: (58.37, 58.37, 212.61, 90, 90, 90) Space group: P 41 (No. 76) ----------F(model) initialization---------- Twinning will be detected automatically. start: r(all,work,free)=0.3476 0.3408 0.4051 n_refl.: 8549 re-set all scales: r(all,work,free)=0.3476 0.3408 0.4051 n_refl.: 8549 remove outliers: r(all,work,free)=0.3469 0.3400 0.4051 n_refl.: 8544 bulk-solvent and scaling: r(all,work,free)=0.2829 0.2738 0.3589 n_refl.: 8544 add H (0.00, 0.00): r(all,work,free)=0.3223 0.3141 0.3896 n_refl.: 8544 remove outliers: r(all,work,free)=0.3223 0.3141 0.3896 n_refl.: 8544 |--(resolution: 3.49 - 19.81 A, n_refl.=8544 (all), 10.57 % free)-------------| | | | r_work= 0.3141 r_free= 0.3896 coordinate error (max.-lik. estimate): 0.71 A | | | | normalized target function (ml) (work): 6.723006 | | target function (ml) not normalized (work): 51370.489545 | | target function (ml) not normalized (free): 6175.931881 | |-----------------------------------------------------------------------------| End of input processing ======================= ROSETTA/PHENIX X-ray refinement ======================= Output directory: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/rosetta_3 ----------Setting up input files for Rosetta---------- |-starting model--------------------------------------------------------------| | target_work(ml) = 6.72301 r_work = 0.3141 r_free = 0.3896 | |-----------------------------------------------------------------------------| Validation statistics (starting model): Ramachandran outliers = 16.42 % favored = 61.13 % Rotamer outliers = 17.07 % C-beta deviations = 0 Clashscore = 93.32 RMS(bonds) = 0.0099 RMS(angles) = 1.83 MolProbity score = 4.28 Rosetta command-line arguments: -parser:protocol /dev/shm/bkpoon/software/rosetta_src_2021.16.61629_bundle/main/source/src/apps/public/crystal_refinement/low_resolution_refine.xml -s 1jkt_rosetta_in.pdb -mtzfile 1jkt_rosetta_data.mtz -run:preserve_header -crystal_refine -parser:script_vars symmdef=1jkt_rosetta.symm -parser:script_vars bfactstrat=individual -parser:script_vars map_type=Auto -nstruct 1 Generating 5 models on 1 processors... 1: r_work = 0.3204 r_free = 0.4089 energy = -2009.28 rmsd = 1.558 *** 2: r_work = 0.3124 r_free = 0.3950 energy = -2208.27 rmsd = 1.729 *** 3: r_work = 0.3133 r_free = 0.3979 energy = -1945.84 rmsd = 2.446 4: r_work = 0.3149 r_free = 0.3957 energy = -1935.15 rmsd = 1.717 DEBUG dumping error message ERROR: Rosetta exited with status 1 stderr output: ERROR: error computing X-ray target ERROR:: Exit from: src/core/scoring/cryst/PhenixInterface.cc line: 158 [ ERROR ]: Caught exception: File: src/core/scoring/cryst/PhenixInterface.cc:158 [ ERROR ] UtilityExitException ERROR: error computing X-ray target AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS. --------------------------------------------------------------- [ ERROR ]: Error(s) were encountered when running jobs. 1 jobs failed; Check the output further up for additional error messages. ---------------------------------------------------------------