Luke-ebbis
commented
1 month ago The assembly log file when for the failing output is as follows
Details
```bash /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/CombinatorialAssembler.out chain.list /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/ 900 100 xlink_consts.txt -b 0.05 -t 80 Before process input PDBname A0_A.pdb:A0_A.pdb PDBname A0_B.pdb:A0_B.pdb PDBname A0_C.pdb:A0_C.pdb PDBname A0_D.pdb:A0_D.pdb PDBname A0_E.pdb:A0_E.pdb PDBname A0_F.pdb:A0_F.pdb PDBname G0_G.pdb:G0_G.pdb PDBname G0_H.pdb:G0_H.pdb PDBname G0_I.pdb:G0_I.pdb PDBname G0_J.pdb:G0_J.pdb PDBname G0_K.pdb:G0_K.pdb PDBname G0_L.pdb:G0_L.pdb Done reading ChemMolecule 3934 Number of vdW radius types: 14 Total number of atoms: 3934 Calculation of surface of 3934 atoms, with surface point density 10 and probe radius 1.8 917 yon and 2616 victim probes 1744 saddle and 2268 concave surface points removed during non-symmetry overlapping reentrant surface removal 60340 contact, 133877 reentrant, and 194217 total surface points Contact area: 6322.41; reentrant area: 13494.5; total area: 19816.9 Surface size 194217 In Layer 0 out of 11 curr->size() 88253 In Layer 1 out of 11 curr->size() 232921 In Layer 2 out of 11 curr->size() 218204 In Layer 3 out of 11 curr->size() 211651 In Layer 4 out of 11 curr->size() 194032 In Layer 5 out of 11 curr->size() 184058 In Layer 6 out of 11 curr->size() 175854 In Layer 7 out of 11 curr->size() 168792 In Layer 8 out of 11 curr->size() 164994 In Layer 9 out of 11 curr->size() 162563 In Layer 10 out of 11 curr->size() 161908 markTheInside: in Layer 1 out of 11 curr->size() 3934 markTheInside: in Layer 2 out of 11 curr->size() 88752 markTheInside: in Layer 3 out of 11 curr->size() 170832 markTheInside: in Layer 4 out of 11 curr->size() 130718 markTheInside: in Layer 5 out of 11 curr->size() 32850 markTheInside: in Layer 6 out of 11 curr->size() 2062 markTheInside: in Layer 7 out of 11 curr->size() 25 Done compute grid A0_A.pdb Fragment 0 chainId A range 1:510 Max radius: 51.9154 done reading BB A0_A.pdb Done reading ChemMolecule 3934 Number of vdW radius types: 14 Total number of atoms: 3934 Calculation of surface of 3934 atoms, with surface point density 10 and probe radius 1.8 917 yon and 2616 victim probes 1744 saddle and 2268 concave surface points removed during non-symmetry overlapping reentrant surface removal 60340 contact, 133877 reentrant, and 194217 total surface points Contact area: 6322.41; reentrant area: 13494.5; total area: 19816.9 Surface size 194217 In Layer 0 out of 11 curr->size() 88253 In Layer 1 out of 11 curr->size() 232921 In Layer 2 out of 11 curr->size() 218204 In Layer 3 out of 11 curr->size() 211651 In Layer 4 out of 11 curr->size() 194032 In Layer 5 out of 11 curr->size() 184058 In Layer 6 out of 11 curr->size() 175854 In Layer 7 out of 11 curr->size() 168792 In Layer 8 out of 11 curr->size() 164994 In Layer 9 out of 11 curr->size() 162563 In Layer 10 out of 11 curr->size() 161908 markTheInside: in Layer 1 out of 11 curr->size() 3934 markTheInside: in Layer 2 out of 11 curr->size() 88752 markTheInside: in Layer 3 out of 11 curr->size() 170832 markTheInside: in Layer 4 out of 11 curr->size() 130718 markTheInside: in Layer 5 out of 11 curr->size() 32850 markTheInside: in Layer 6 out of 11 curr->size() 2062 markTheInside: in Layer 7 out of 11 curr->size() 25 Done compute grid A0_B.pdb Fragment 0 chainId B range 1:510 Max radius: 51.9154 done reading BB A0_B.pdb Done reading ChemMolecule 3934 Number of vdW radius types: 14 Total number of atoms: 3934 Calculation of surface of 3934 atoms, with surface point density 10 and probe radius 1.8 917 yon and 2616 victim probes 1744 saddle and 2268 concave surface points removed during non-symmetry overlapping reentrant surface removal 60340 contact, 133877 reentrant, and 194217 total surface points Contact area: 6322.41; reentrant area: 13494.5; total area: 19816.9 Surface size 194217 In Layer 0 out of 11 curr->size() 88253 In Layer 1 out of 11 curr->size() 232921 In Layer 2 out of 11 curr->size() 218204 In Layer 3 out of 11 curr->size() 211651 In Layer 4 out of 11 curr->size() 194032 In Layer 5 out of 11 curr->size() 184058 In Layer 6 out of 11 curr->size() 175854 In Layer 7 out of 11 curr->size() 168792 In Layer 8 out of 11 curr->size() 164994 In Layer 9 out of 11 curr->size() 162563 In Layer 10 out of 11 curr->size() 161908 markTheInside: in Layer 1 out of 11 curr->size() 3934 markTheInside: in Layer 2 out of 11 curr->size() 88752 markTheInside: in Layer 3 out of 11 curr->size() 170832 markTheInside: in Layer 4 out of 11 curr->size() 130718 markTheInside: in Layer 5 out of 11 curr->size() 32850 markTheInside: in Layer 6 out of 11 curr->size() 2062 markTheInside: in Layer 7 out of 11 curr->size() 25 Done compute grid A0_C.pdb Fragment 0 chainId C range 1:510 Max radius: 51.9154 done reading BB A0_C.pdb Done reading ChemMolecule 3934 Number of vdW radius types: 14 Total number of atoms: 3934 Calculation of surface of 3934 atoms, with surface point density 10 and probe radius 1.8 917 yon and 2616 victim probes 1744 saddle and 2268 concave surface points removed during non-symmetry overlapping reentrant surface removal 60340 contact, 133877 reentrant, and 194217 total surface points Contact area: 6322.41; reentrant area: 13494.5; total area: 19816.9 Surface size 194217 In Layer 0 out of 11 curr->size() 88253 In Layer 1 out of 11 curr->size() 232921 In Layer 2 out of 11 curr->size() 218204 In Layer 3 out of 11 curr->size() 211651 In Layer 4 out of 11 curr->size() 194032 In Layer 5 out of 11 curr->size() 184058 In Layer 6 out of 11 curr->size() 175854 In Layer 7 out of 11 curr->size() 168792 In Layer 8 out of 11 curr->size() 164994 In Layer 9 out of 11 curr->size() 162563 In Layer 10 out of 11 curr->size() 161908 markTheInside: in Layer 1 out of 11 curr->size() 3934 markTheInside: in Layer 2 out of 11 curr->size() 88752 markTheInside: in Layer 3 out of 11 curr->size() 170832 markTheInside: in Layer 4 out of 11 curr->size() 130718 markTheInside: in Layer 5 out of 11 curr->size() 32850 markTheInside: in Layer 6 out of 11 curr->size() 2062 markTheInside: in Layer 7 out of 11 curr->size() 25 Done compute grid A0_D.pdb Fragment 0 chainId D range 1:510 Max radius: 51.9154 done reading BB A0_D.pdb Done reading ChemMolecule 3934 Number of vdW radius types: 14 Total number of atoms: 3934 Calculation of surface of 3934 atoms, with surface point density 10 and probe radius 1.8 917 yon and 2616 victim probes 1744 saddle and 2268 concave surface points removed during non-symmetry overlapping reentrant surface removal 60340 contact, 133877 reentrant, and 194217 total surface points Contact area: 6322.41; reentrant area: 13494.5; total area: 19816.9 Surface size 194217 In Layer 0 out of 11 curr->size() 88253 In Layer 1 out of 11 curr->size() 232921 In Layer 2 out of 11 curr->size() 218204 In Layer 3 out of 11 curr->size() 211651 In Layer 4 out of 11 curr->size() 194032 In Layer 5 out of 11 curr->size() 184058 In Layer 6 out of 11 curr->size() 175854 In Layer 7 out of 11 curr->size() 168792 In Layer 8 out of 11 curr->size() 164994 In Layer 9 out of 11 curr->size() 162563 In Layer 10 out of 11 curr->size() 161908 markTheInside: in Layer 1 out of 11 curr->size() 3934 markTheInside: in Layer 2 out of 11 curr->size() 88752 markTheInside: in Layer 3 out of 11 curr->size() 170832 markTheInside: in Layer 4 out of 11 curr->size() 130718 markTheInside: in Layer 5 out of 11 curr->size() 32850 markTheInside: in Layer 6 out of 11 curr->size() 2062 markTheInside: in Layer 7 out of 11 curr->size() 25 Done compute grid A0_E.pdb Fragment 0 chainId E range 1:510 Max radius: 51.9154 done reading BB A0_E.pdb Done reading ChemMolecule 3934 Number of vdW radius types: 14 Total number of atoms: 3934 Calculation of surface of 3934 atoms, with surface point density 10 and probe radius 1.8 917 yon and 2616 victim probes 1744 saddle and 2268 concave surface points removed during non-symmetry overlapping reentrant surface removal 60340 contact, 133877 reentrant, and 194217 total surface points Contact area: 6322.41; reentrant area: 13494.5; total area: 19816.9 Surface size 194217 In Layer 0 out of 11 curr->size() 88253 In Layer 1 out of 11 curr->size() 232921 In Layer 2 out of 11 curr->size() 218204 In Layer 3 out of 11 curr->size() 211651 In Layer 4 out of 11 curr->size() 194032 In Layer 5 out of 11 curr->size() 184058 In Layer 6 out of 11 curr->size() 175854 In Layer 7 out of 11 curr->size() 168792 In Layer 8 out of 11 curr->size() 164994 In Layer 9 out of 11 curr->size() 162563 In Layer 10 out of 11 curr->size() 161908 markTheInside: in Layer 1 out of 11 curr->size() 3934 markTheInside: in Layer 2 out of 11 curr->size() 88752 markTheInside: in Layer 3 out of 11 curr->size() 170832 markTheInside: in Layer 4 out of 11 curr->size() 130718 markTheInside: in Layer 5 out of 11 curr->size() 32850 markTheInside: in Layer 6 out of 11 curr->size() 2062 markTheInside: in Layer 7 out of 11 curr->size() 25 Done compute grid A0_F.pdb Fragment 0 chainId F range 1:510 Max radius: 51.9154 done reading BB A0_F.pdb Done reading ChemMolecule 5054 Number of vdW radius types: 14 Total number of atoms: 5054 Calculation of surface of 5054 atoms, with surface point density 10 and probe radius 1.8 1238 yon and 3826 victim probes 2020 saddle and 3572 concave surface points removed during non-symmetry overlapping reentrant surface removal 72783 contact, 172707 reentrant, and 245490 total surface points Contact area: 7623.02; reentrant area: 17400.7; total area: 25023.7 Surface size 245490 In Layer 0 out of 11 curr->size() 111240 In Layer 1 out of 11 curr->size() 292800 In Layer 2 out of 11 curr->size() 272702 In Layer 3 out of 11 curr->size() 261966 In Layer 4 out of 11 curr->size() 237072 In Layer 5 out of 11 curr->size() 223584 In Layer 6 out of 11 curr->size() 213037 In Layer 7 out of 11 curr->size() 202616 In Layer 8 out of 11 curr->size() 195165 In Layer 9 out of 11 curr->size() 189200 In Layer 10 out of 11 curr->size() 184693 markTheInside: in Layer 1 out of 11 curr->size() 5054 markTheInside: in Layer 2 out of 11 curr->size() 113588 markTheInside: in Layer 3 out of 11 curr->size() 218532 markTheInside: in Layer 4 out of 11 curr->size() 169180 markTheInside: in Layer 5 out of 11 curr->size() 44271 markTheInside: in Layer 6 out of 11 curr->size() 2442 markTheInside: in Layer 7 out of 11 curr->size() 20 Done compute grid G0_G.pdb Fragment 0 chainId G range 1:590 Fragment 1 chainId G range 612:665 Max radius: 56.9446 done reading BB G0_G.pdb Done reading ChemMolecule 5054 Number of vdW radius types: 14 Total number of atoms: 5054 Calculation of surface of 5054 atoms, with surface point density 10 and probe radius 1.8 1238 yon and 3826 victim probes 2020 saddle and 3572 concave surface points removed during non-symmetry overlapping reentrant surface removal 72783 contact, 172707 reentrant, and 245490 total surface points Contact area: 7623.02; reentrant area: 17400.7; total area: 25023.7 Surface size 245490 In Layer 0 out of 11 curr->size() 111240 In Layer 1 out of 11 curr->size() 292800 In Layer 2 out of 11 curr->size() 272702 In Layer 3 out of 11 curr->size() 261966 In Layer 4 out of 11 curr->size() 237072 In Layer 5 out of 11 curr->size() 223584 In Layer 6 out of 11 curr->size() 213037 In Layer 7 out of 11 curr->size() 202616 In Layer 8 out of 11 curr->size() 195165 In Layer 9 out of 11 curr->size() 189200 In Layer 10 out of 11 curr->size() 184693 markTheInside: in Layer 1 out of 11 curr->size() 5054 markTheInside: in Layer 2 out of 11 curr->size() 113588 markTheInside: in Layer 3 out of 11 curr->size() 218532 markTheInside: in Layer 4 out of 11 curr->size() 169180 markTheInside: in Layer 5 out of 11 curr->size() 44271 markTheInside: in Layer 6 out of 11 curr->size() 2442 markTheInside: in Layer 7 out of 11 curr->size() 20 Done compute grid G0_H.pdb Fragment 0 chainId H range 1:590 Fragment 1 chainId H range 612:665 Max radius: 56.9446 done reading BB G0_H.pdb Done reading ChemMolecule 5054 Number of vdW radius types: 14 Total number of atoms: 5054 Calculation of surface of 5054 atoms, with surface point density 10 and probe radius 1.8 1238 yon and 3826 victim probes 2020 saddle and 3572 concave surface points removed during non-symmetry overlapping reentrant surface removal 72783 contact, 172707 reentrant, and 245490 total surface points Contact area: 7623.02; reentrant area: 17400.7; total area: 25023.7 Surface size 245490 In Layer 0 out of 11 curr->size() 111240 In Layer 1 out of 11 curr->size() 292800 In Layer 2 out of 11 curr->size() 272702 In Layer 3 out of 11 curr->size() 261966 In Layer 4 out of 11 curr->size() 237072 In Layer 5 out of 11 curr->size() 223584 In Layer 6 out of 11 curr->size() 213037 In Layer 7 out of 11 curr->size() 202616 In Layer 8 out of 11 curr->size() 195165 In Layer 9 out of 11 curr->size() 189200 In Layer 10 out of 11 curr->size() 184693 markTheInside: in Layer 1 out of 11 curr->size() 5054 markTheInside: in Layer 2 out of 11 curr->size() 113588 markTheInside: in Layer 3 out of 11 curr->size() 218532 markTheInside: in Layer 4 out of 11 curr->size() 169180 markTheInside: in Layer 5 out of 11 curr->size() 44271 markTheInside: in Layer 6 out of 11 curr->size() 2442 markTheInside: in Layer 7 out of 11 curr->size() 20 Done compute grid G0_I.pdb Fragment 0 chainId I range 1:590 Fragment 1 chainId I range 612:665 Max radius: 56.9446 done reading BB G0_I.pdb Done reading ChemMolecule 5054 Number of vdW radius types: 14 Total number of atoms: 5054 Calculation of surface of 5054 atoms, with surface point density 10 and probe radius 1.8 1238 yon and 3826 victim probes 2020 saddle and 3572 concave surface points removed during non-symmetry overlapping reentrant surface removal 72783 contact, 172707 reentrant, and 245490 total surface points Contact area: 7623.02; reentrant area: 17400.7; total area: 25023.7 Surface size 245490 In Layer 0 out of 11 curr->size() 111240 In Layer 1 out of 11 curr->size() 292800 In Layer 2 out of 11 curr->size() 272702 In Layer 3 out of 11 curr->size() 261966 In Layer 4 out of 11 curr->size() 237072 In Layer 5 out of 11 curr->size() 223584 In Layer 6 out of 11 curr->size() 213037 In Layer 7 out of 11 curr->size() 202616 In Layer 8 out of 11 curr->size() 195165 In Layer 9 out of 11 curr->size() 189200 In Layer 10 out of 11 curr->size() 184693 markTheInside: in Layer 1 out of 11 curr->size() 5054 markTheInside: in Layer 2 out of 11 curr->size() 113588 markTheInside: in Layer 3 out of 11 curr->size() 218532 markTheInside: in Layer 4 out of 11 curr->size() 169180 markTheInside: in Layer 5 out of 11 curr->size() 44271 markTheInside: in Layer 6 out of 11 curr->size() 2442 markTheInside: in Layer 7 out of 11 curr->size() 20 Done compute grid G0_J.pdb Fragment 0 chainId J range 1:590 Fragment 1 chainId J range 612:665 Max radius: 56.9446 done reading BB G0_J.pdb Done reading ChemMolecule 5054 Number of vdW radius types: 14 Total number of atoms: 5054 Calculation of surface of 5054 atoms, with surface point density 10 and probe radius 1.8 1238 yon and 3826 victim probes 2020 saddle and 3572 concave surface points removed during non-symmetry overlapping reentrant surface removal 72783 contact, 172707 reentrant, and 245490 total surface points Contact area: 7623.02; reentrant area: 17400.7; total area: 25023.7 Surface size 245490 In Layer 0 out of 11 curr->size() 111240 In Layer 1 out of 11 curr->size() 292800 In Layer 2 out of 11 curr->size() 272702 In Layer 3 out of 11 curr->size() 261966 In Layer 4 out of 11 curr->size() 237072 In Layer 5 out of 11 curr->size() 223584 In Layer 6 out of 11 curr->size() 213037 In Layer 7 out of 11 curr->size() 202616 In Layer 8 out of 11 curr->size() 195165 In Layer 9 out of 11 curr->size() 189200 In Layer 10 out of 11 curr->size() 184693 markTheInside: in Layer 1 out of 11 curr->size() 5054 markTheInside: in Layer 2 out of 11 curr->size() 113588 markTheInside: in Layer 3 out of 11 curr->size() 218532 markTheInside: in Layer 4 out of 11 curr->size() 169180 markTheInside: in Layer 5 out of 11 curr->size() 44271 markTheInside: in Layer 6 out of 11 curr->size() 2442 markTheInside: in Layer 7 out of 11 curr->size() 20 Done compute grid G0_K.pdb Fragment 0 chainId K range 1:590 Fragment 1 chainId K range 612:665 Max radius: 56.9446 done reading BB G0_K.pdb Done reading ChemMolecule 5054 Number of vdW radius types: 14 Total number of atoms: 5054 Calculation of surface of 5054 atoms, with surface point density 10 and probe radius 1.8 1238 yon and 3826 victim probes 2020 saddle and 3572 concave surface points removed during non-symmetry overlapping reentrant surface removal 72783 contact, 172707 reentrant, and 245490 total surface points Contact area: 7623.02; reentrant area: 17400.7; total area: 25023.7 Surface size 245490 In Layer 0 out of 11 curr->size() 111240 In Layer 1 out of 11 curr->size() 292800 In Layer 2 out of 11 curr->size() 272702 In Layer 3 out of 11 curr->size() 261966 In Layer 4 out of 11 curr->size() 237072 In Layer 5 out of 11 curr->size() 223584 In Layer 6 out of 11 curr->size() 213037 In Layer 7 out of 11 curr->size() 202616 In Layer 8 out of 11 curr->size() 195165 In Layer 9 out of 11 curr->size() 189200 In Layer 10 out of 11 curr->size() 184693 markTheInside: in Layer 1 out of 11 curr->size() 5054 markTheInside: in Layer 2 out of 11 curr->size() 113588 markTheInside: in Layer 3 out of 11 curr->size() 218532 markTheInside: in Layer 4 out of 11 curr->size() 169180 markTheInside: in Layer 5 out of 11 curr->size() 44271 markTheInside: in Layer 6 out of 11 curr->size() 2442 markTheInside: in Layer 7 out of 11 curr->size() 20 Done compute grid G0_L.pdb Fragment 0 chainId L range 1:590 Fragment 1 chainId L range 612:665 Max radius: 56.9446 done reading BB G0_L.pdb Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_A_plus_A0_B loaded score: 90.2638 loaded score: 89.8996 loaded score: 89.264 loaded score: 86.896 loaded score: 85.3017 5 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_A_plus_A0_B Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_A_plus_A0_C loaded score: 90.2638 loaded score: 89.8996 loaded score: 89.264 loaded score: 86.896 loaded score: 85.3017 5 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_A_plus_A0_C Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_A_plus_A0_D loaded score: 90.2638 loaded score: 89.8996 loaded score: 89.264 loaded score: 86.896 loaded score: 85.3017 5 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_A_plus_A0_D Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_A_plus_A0_E loaded score: 90.2638 loaded score: 89.8996 loaded score: 89.264 loaded score: 86.896 loaded score: 85.3017 5 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_A_plus_A0_E Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_A_plus_A0_F loaded score: 90.2638 loaded score: 89.8996 loaded score: 89.264 loaded score: 86.896 loaded score: 85.3017 5 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_A_plus_A0_F Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_A_plus_G0_G loaded score: 91.8348 loaded score: 90.919 loaded score: 89.2002 loaded score: 88.6655 loaded score: 86.9096 loaded score: 62.1667 6 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_A_plus_G0_G Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_A_plus_G0_H loaded score: 91.8348 loaded score: 90.919 loaded score: 89.2002 loaded score: 88.6655 loaded score: 86.9096 loaded score: 62.1667 6 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_A_plus_G0_H Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_A_plus_G0_I loaded score: 91.8348 loaded score: 90.919 loaded score: 89.2002 loaded score: 88.6655 loaded score: 86.9096 loaded score: 62.1667 6 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_A_plus_G0_I Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_A_plus_G0_J loaded score: 91.8348 loaded score: 90.919 loaded score: 89.2002 loaded score: 88.6655 loaded score: 86.9096 loaded score: 62.1667 6 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_A_plus_G0_J Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_A_plus_G0_K loaded score: 91.8348 loaded score: 90.919 loaded score: 89.2002 loaded score: 88.6655 loaded score: 86.9096 loaded score: 62.1667 6 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_A_plus_G0_K Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_A_plus_G0_L loaded score: 91.8348 loaded score: 90.919 loaded score: 89.2002 loaded score: 88.6655 loaded score: 86.9096 loaded score: 62.1667 6 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_A_plus_G0_L Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_B_plus_A0_A Problem opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_B_plus_A0_A Opening transformation file 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/home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_B_plus_A0_D Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_B_plus_A0_E loaded score: 90.2638 loaded score: 89.8996 loaded score: 89.264 loaded score: 86.896 loaded score: 85.3017 5 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_B_plus_A0_E Opening transformation file 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file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_B_plus_G0_G Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_B_plus_G0_H loaded score: 91.8348 loaded score: 90.919 loaded score: 89.2002 loaded score: 88.6655 loaded score: 86.9096 loaded score: 62.1667 6 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_B_plus_G0_H Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_B_plus_G0_I loaded score: 91.8348 loaded score: 90.919 loaded score: 89.2002 loaded score: 88.6655 loaded score: 86.9096 loaded score: 62.1667 6 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_B_plus_G0_I Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_B_plus_G0_J loaded score: 91.8348 loaded score: 90.919 loaded score: 89.2002 loaded score: 88.6655 loaded score: 86.9096 loaded score: 62.1667 6 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_B_plus_G0_J Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_B_plus_G0_K loaded score: 91.8348 loaded score: 90.919 loaded score: 89.2002 loaded score: 88.6655 loaded score: 86.9096 loaded score: 62.1667 6 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_B_plus_G0_K Opening transformation file 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score: 90.2638 loaded score: 89.8996 loaded score: 89.264 loaded score: 86.896 loaded score: 85.3017 5 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_C_plus_A0_D Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_C_plus_A0_E loaded score: 90.2638 loaded score: 89.8996 loaded score: 89.264 loaded score: 86.896 loaded score: 85.3017 5 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_C_plus_A0_E Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_C_plus_A0_F loaded score: 90.2638 loaded score: 89.8996 loaded score: 89.264 loaded score: 86.896 loaded score: 85.3017 5 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_C_plus_A0_F Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_C_plus_G0_G loaded score: 91.8348 loaded score: 90.919 loaded score: 89.2002 loaded score: 88.6655 loaded score: 86.9096 loaded score: 62.1667 6 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_C_plus_G0_G Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_C_plus_G0_H loaded score: 91.8348 loaded score: 90.919 loaded score: 89.2002 loaded score: 88.6655 loaded score: 86.9096 loaded score: 62.1667 6 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_C_plus_G0_H Opening transformation file 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transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_C_plus_G0_J Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_C_plus_G0_K loaded score: 91.8348 loaded score: 90.919 loaded score: 89.2002 loaded score: 88.6655 loaded score: 86.9096 loaded score: 62.1667 6 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_C_plus_G0_K Opening transformation file 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opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_D_plus_A0_C Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_D_plus_A0_E loaded score: 90.2638 loaded score: 89.8996 loaded score: 89.264 loaded score: 86.896 loaded score: 85.3017 5 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_D_plus_A0_E Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_D_plus_A0_F loaded score: 90.2638 loaded score: 89.8996 loaded score: 89.264 loaded score: 86.896 loaded score: 85.3017 5 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_D_plus_A0_F Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_D_plus_G0_G loaded score: 91.8348 loaded score: 90.919 loaded score: 89.2002 loaded score: 88.6655 loaded score: 86.9096 loaded score: 62.1667 6 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_D_plus_G0_G Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_D_plus_G0_H loaded score: 91.8348 loaded score: 90.919 loaded score: 89.2002 loaded score: 88.6655 loaded score: 86.9096 loaded score: 62.1667 6 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_D_plus_G0_H Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_D_plus_G0_I loaded score: 91.8348 loaded score: 90.919 loaded score: 89.2002 loaded score: 88.6655 loaded score: 86.9096 loaded score: 62.1667 6 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_D_plus_G0_I Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_D_plus_G0_J loaded score: 91.8348 loaded score: 90.919 loaded score: 89.2002 loaded score: 88.6655 loaded score: 86.9096 loaded score: 62.1667 6 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_D_plus_G0_J Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_D_plus_G0_K loaded score: 91.8348 loaded score: 90.919 loaded score: 89.2002 loaded score: 88.6655 loaded score: 86.9096 loaded score: 62.1667 6 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_D_plus_G0_K Opening transformation file 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opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_E_plus_A0_C Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_E_plus_A0_D Problem opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_E_plus_A0_D Opening transformation file 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file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_E_plus_G0_G Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_E_plus_G0_H loaded score: 91.8348 loaded score: 90.919 loaded score: 89.2002 loaded score: 88.6655 loaded score: 86.9096 loaded score: 62.1667 6 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_E_plus_G0_H Opening transformation file 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transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_E_plus_G0_J Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_E_plus_G0_K loaded score: 91.8348 loaded score: 90.919 loaded score: 89.2002 loaded score: 88.6655 loaded score: 86.9096 loaded score: 62.1667 6 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_E_plus_G0_K Opening transformation file 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opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_F_plus_A0_C Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_F_plus_A0_D Problem opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_F_plus_A0_D Opening transformation file 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transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_F_plus_G0_J Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_F_plus_G0_K loaded score: 91.8348 loaded score: 90.919 loaded score: 89.2002 loaded score: 88.6655 loaded score: 86.9096 loaded score: 62.1667 6 transforms were read from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/A0_F_plus_G0_K Opening transformation file 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opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/G0_G_plus_A0_C Opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/G0_G_plus_A0_D Problem opening transformation file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/G0_G_plus_A0_D Opening transformation file 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size 6 1000000 2 7 trans size 6 10000000 2 8 trans size 6 100000000 2 9 trans size 6 1000000000 2 10 trans size 6 10000000000 2 11 trans size 6 100000000000 SBB 3 set 1000 isEmpty 0 SBB 3 size 1 3 4 trans size 5 10000 3 5 trans size 5 100000 3 6 trans size 6 1000000 3 7 trans size 6 10000000 3 8 trans size 6 100000000 3 9 trans size 6 1000000000 3 10 trans size 6 10000000000 3 11 trans size 6 100000000000 SBB 4 set 10000 isEmpty 0 SBB 4 size 1 4 5 trans size 5 100000 4 6 trans size 6 1000000 4 7 trans size 6 10000000 4 8 trans size 6 100000000 4 9 trans size 6 1000000000 4 10 trans size 6 10000000000 4 11 trans size 6 100000000000 SBB 5 set 100000 isEmpty 0 SBB 5 size 1 5 6 trans size 6 1000000 5 7 trans size 6 10000000 5 8 trans size 6 100000000 5 9 trans size 6 1000000000 5 10 trans size 6 10000000000 5 11 trans size 6 100000000000 SBB 6 set 1000000 isEmpty 0 SBB 6 size 1 6 7 trans size 0 10000000 6 8 trans size 0 100000000 6 9 trans size 0 1000000000 6 10 trans size 0 10000000000 6 11 trans size 0 100000000000 SBB 7 set 10000000 isEmpty 0 SBB 7 size 1 7 8 trans size 0 100000000 7 9 trans size 0 1000000000 7 10 trans size 0 10000000000 7 11 trans size 0 100000000000 SBB 8 set 100000000 isEmpty 0 SBB 8 size 1 8 9 trans size 0 1000000000 8 10 trans size 0 10000000000 8 11 trans size 0 100000000000 SBB 9 set 1000000000 isEmpty 0 SBB 9 size 1 9 10 trans size 0 10000000000 9 11 trans size 0 100000000000 SBB 10 set 10000000000 isEmpty 0 SBB 10 size 1 10 11 trans size 0 100000000000 SBB 11 set 100000000000 isEmpty 0 SBB 11 size 1 isEmpty 0 0 SBB 0 size 1 0 0 trans size 0 done add_edge 0 1 trans size 5 done add_edge 0 2 trans size 5 done add_edge 0 3 trans size 5 done add_edge 0 4 trans size 5 done add_edge 0 5 trans size 5 done add_edge 0 6 trans size 6 done add_edge 0 7 trans size 6 done add_edge 0 8 trans size 6 done add_edge 0 9 trans size 6 done add_edge 0 10 trans size 6 done add_edge 0 11 trans size 6 done add_edge isEmpty 1 0 SBB 1 size 1 1 0 trans size 5 done add_edge 1 1 trans size 0 done add_edge 1 2 trans size 5 done add_edge 1 3 trans size 5 done add_edge 1 4 trans size 5 done add_edge 1 5 trans size 5 done add_edge 1 6 trans size 6 done add_edge 1 7 trans size 6 done add_edge 1 8 trans size 6 done add_edge 1 9 trans size 6 done add_edge 1 10 trans size 6 done add_edge 1 11 trans size 6 done add_edge isEmpty 2 0 SBB 2 size 1 2 0 trans size 5 done add_edge 2 1 trans size 5 done add_edge 2 2 trans size 0 done add_edge 2 3 trans size 5 done add_edge 2 4 trans size 5 done add_edge 2 5 trans size 5 done add_edge 2 6 trans size 6 done add_edge 2 7 trans size 6 done add_edge 2 8 trans size 6 done add_edge 2 9 trans size 6 done add_edge 2 10 trans size 6 done add_edge 2 11 trans size 6 done add_edge isEmpty 3 0 SBB 3 size 1 3 0 trans size 5 done add_edge 3 1 trans size 5 done add_edge 3 2 trans size 5 done add_edge 3 3 trans size 0 done add_edge 3 4 trans size 5 done add_edge 3 5 trans size 5 done add_edge 3 6 trans size 6 done add_edge 3 7 trans size 6 done add_edge 3 8 trans size 6 done add_edge 3 9 trans size 6 done add_edge 3 10 trans size 6 done add_edge 3 11 trans size 6 done add_edge isEmpty 4 0 SBB 4 size 1 4 0 trans size 5 done add_edge 4 1 trans size 5 done add_edge 4 2 trans size 5 done add_edge 4 3 trans size 5 done add_edge 4 4 trans size 0 done add_edge 4 5 trans size 5 done add_edge 4 6 trans size 6 done add_edge 4 7 trans size 6 done add_edge 4 8 trans size 6 done add_edge 4 9 trans size 6 done add_edge 4 10 trans size 6 done add_edge 4 11 trans size 6 done add_edge isEmpty 5 0 SBB 5 size 1 5 0 trans size 5 done add_edge 5 1 trans size 5 done add_edge 5 2 trans size 5 done add_edge 5 3 trans size 5 done add_edge 5 4 trans size 5 done add_edge 5 5 trans size 0 done add_edge 5 6 trans size 6 done add_edge 5 7 trans size 6 done add_edge 5 8 trans size 6 done add_edge 5 9 trans size 6 done add_edge 5 10 trans size 6 done add_edge 5 11 trans size 6 done add_edge isEmpty 6 0 SBB 6 size 1 6 0 trans size 6 done add_edge 6 1 trans size 6 done add_edge 6 2 trans size 6 done add_edge 6 3 trans size 6 done add_edge 6 4 trans size 6 done add_edge 6 5 trans size 6 done add_edge 6 6 trans size 0 done add_edge 6 7 trans size 0 done add_edge 6 8 trans size 0 done add_edge 6 9 trans size 0 done add_edge 6 10 trans size 0 done add_edge 6 11 trans size 0 done add_edge isEmpty 7 0 SBB 7 size 1 7 0 trans size 6 done add_edge 7 1 trans size 6 done add_edge 7 2 trans size 6 done add_edge 7 3 trans size 6 done add_edge 7 4 trans size 6 done add_edge 7 5 trans size 6 done add_edge 7 6 trans size 0 done add_edge 7 7 trans size 0 done add_edge 7 8 trans size 0 done add_edge 7 9 trans size 0 done add_edge 7 10 trans size 0 done add_edge 7 11 trans size 0 done add_edge isEmpty 8 0 SBB 8 size 1 8 0 trans size 6 done add_edge 8 1 trans size 6 done add_edge 8 2 trans size 6 done add_edge 8 3 trans size 6 done add_edge 8 4 trans size 6 done add_edge 8 5 trans size 6 done add_edge 8 6 trans size 0 done add_edge 8 7 trans size 0 done add_edge 8 8 trans size 0 done add_edge 8 9 trans size 0 done add_edge 8 10 trans size 0 done add_edge 8 11 trans size 0 done add_edge isEmpty 9 0 SBB 9 size 1 9 0 trans size 6 done add_edge 9 1 trans size 6 done add_edge 9 2 trans size 6 done add_edge 9 3 trans size 6 done add_edge 9 4 trans size 6 done add_edge 9 5 trans size 6 done add_edge 9 6 trans size 0 done add_edge 9 7 trans size 0 done add_edge 9 8 trans size 0 done add_edge 9 9 trans size 0 done add_edge 9 10 trans size 0 done add_edge 9 11 trans size 0 done add_edge isEmpty 10 0 SBB 10 size 1 10 0 trans size 6 done add_edge 10 1 trans size 6 done add_edge 10 2 trans size 6 done add_edge 10 3 trans size 6 done add_edge 10 4 trans size 6 done add_edge 10 5 trans size 6 done add_edge 10 6 trans size 0 done add_edge 10 7 trans size 0 done add_edge 10 8 trans size 0 done add_edge 10 9 trans size 0 done add_edge 10 10 trans size 0 done add_edge 10 11 trans size 0 done add_edge isEmpty 11 0 SBB 11 size 1 11 0 trans size 6 done add_edge 11 1 trans size 6 done add_edge 11 2 trans size 6 done add_edge 11 3 trans size 6 done add_edge 11 4 trans size 6 done add_edge 11 5 trans size 6 done add_edge 11 6 trans size 0 done add_edge 11 7 trans size 0 done add_edge 11 8 trans size 0 done add_edge 11 9 trans size 0 done add_edge 11 10 trans size 0 done add_edge 11 11 trans size 0 done add_edge Num of components 1 checking ident 0 & 1 checking transforms found ident 0 1 checking ident 0 & 2 checking transforms found ident 0 2 checking ident 0 & 3 checking transforms found ident 0 3 checking ident 0 & 4 checking transforms found ident 0 4 checking ident 0 & 5 checking transforms found ident 0 5 checking ident 0 & 6 different num of atoms checking ident 0 & 7 different num of atoms checking ident 0 & 8 different num of atoms checking ident 0 & 9 different num of atoms checking ident 0 & 10 different num of atoms checking ident 0 & 11 different num of atoms checking ident 6 & 7 checking transforms found ident 6 7 checking ident 6 & 8 checking transforms found ident 6 8 checking ident 6 & 9 checking transforms found ident 6 9 checking ident 6 & 10 checking transforms found ident 6 10 checking ident 6 & 11 checking transforms found ident 6 11 ---- ident groups ident group: 0 1 2 3 4 5 ident group: 6 7 8 9 10 11 ---- assembly groups assembly group 0:0 1 2 3 4 5 6 7 8 9 10 11 searching for size 6 has 1 started trans check, bb_size:6 number of transformations:5 checking trans indexed0 adding trans -1.602 0.476 -2.649 -5.322 -29.31 -24.22 **** 90.2638 adding trans 0.000958817 0.00185881 0.00203345 -0.0367236 -0.0364056 0.0520153 **** 90.2638 adding trans -1.60196 0.473909 -2.64698 -5.25408 -29.3338 -24.2059 **** 90.2638 adding trans 0.00191386 0.00371956 0.00406514 -0.0734696 -0.0729351 0.103926 **** 90.2638 adding trans -1.60192 0.471818 -2.64497 -5.18614 -29.3576 -24.1918 **** 90.2638 created possibly symSBB dropping 6 because penetration 1 checking trans indexed1 adding trans -1.603 0.4777 -2.65 -5.439 -29.26 -24.14 **** 89.8996 adding trans -0.00051879 -0.00100168 -0.00109649 0.0428133 -0.0251217 0.0207443 **** 89.8996 adding trans -1.60302 0.478828 -2.65109 -5.45244 -29.2916 -24.0986 **** 89.8996 adding trans -0.00103869 -0.00200279 -0.00219349 0.0856214 -0.0502815 0.04146 **** 89.8996 adding trans -1.60303 0.479956 -2.65218 -5.46588 -29.3232 -24.0572 **** 89.8996 created possibly symSBB dropping 6 because penetration 1 checking trans indexed2 adding trans -1.605 0.4779 -2.649 -5.39 -29.27 -24.2 **** 89.264 adding trans -0.000589539 -0.00113765 -0.00124329 0.0523601 -0.0356636 0.0313702 **** 89.264 adding trans -1.60502 0.479181 -2.65023 -5.40155 -29.3132 -24.1452 **** 89.264 adding trans -0.00118049 -0.00227455 -0.00248725 0.104711 -0.071373 0.0627022 **** 89.264 adding trans -1.60504 0.480462 -2.65147 -5.4131 -29.3563 -24.0904 **** 89.264 created possibly symSBB dropping 6 because penetration 1 checking trans indexed3 adding trans -1.609 0.4697 -2.655 -5.403 -29.07 -24.29 **** 86.896 adding trans -0.000317 -0.000624097 -0.000676662 0.0178747 0.00110626 -0.00530624 **** 86.896 adding trans -1.60901 0.4704 -2.65567 -5.41995 -29.0729 -24.2827 **** 86.896 adding trans -0.00063441 -0.00124797 -0.00135353 0.0357461 0.00219917 -0.0106239 **** 86.896 adding trans -1.60903 0.4711 -2.65634 -5.4369 -29.0758 -24.2754 **** 86.896 created possibly symSBB dropping 6 because penetration 1 checking trans indexed4 adding trans -1.602 0.4668 -2.662 -5.317 -29.04 -24.29 **** 85.3017 adding trans -0.000652193 -0.00129355 -0.00140929 0.00256491 0.0709209 -0.0856037 **** 85.3017 adding trans -1.60202 0.468249 -2.6634 -5.38677 -28.9774 -24.3498 **** 85.3017 adding trans -0.00130621 -0.0025862 -0.00281946 0.00512075 0.141783 -0.171257 **** 85.3017 adding trans -1.60204 0.469697 -2.6648 -5.45653 -28.9146 -24.4095 **** 85.3017 created possibly symSBB dropping 6 because penetration 1 Created 0 Symmetrical for 111111 searching for size 6 has 1 started trans check, bb_size:6 number of transformations:0 Created 0 Symmetrical for 111111000000 *** running iteration 2 prev kept results: 12 ** running sub-iteration 1 1 counters 0/0 found more for 11 based on 1 and 10 before: 0 after: 1 scores 90.2638:90.2638 found more for 1000001 based on 1 and 1000000 before: 0 after: 1 scores 91.8348:91.8348 clustering resSet 1000001 before: 1 after 1 scores -1:91.8348 clustering resSet 11 before: 1 after 1 scores -1:90.2638 scores of saved -1:91.8348 new kept results by chain 0:5, 1:2, 2:0, 3:0, 4:0, 5:0, 6:3, 7:0, 8:0, 9:0, 10:0, 11:0, new kept results by resSet 1000001:3, 11:2, *** running iteration 3 prev kept results: 5 ** running sub-iteration 1 2 counters 0/2 found more for 1000011 based on 1 and 1000010 before: 0 after: 1 scores 182.099:182.099 found more for 11000001 based on 1000000 and 10000001 before: 0 after: 1 scores 154.001:154.001 clustering resSet 11000001 before: 1 after 1 scores -1:154.001 clustering resSet 1000011 before: 1 after 1 scores -1:182.099 scores of saved -1:182.099 new kept results by chain 0:6, 1:4, 2:0, 3:0, 4:0, 5:0, 6:6, 7:2, 8:0, 9:0, 10:0, 11:0, new kept results by resSet 1000011:4, 11000001:2, *** running iteration 4 prev kept results: 6 ** running sub-iteration 1 3 counters 0/88 found more for 11000011 based on 1 and 11000010 before: 0 after: 1 scores 245.836:245.836 found more for 11000011 based on 1000000 and 10000011 before: 1 after: 1 scores 273.933:273.933 ** running sub-iteration 2 2 counters 0/258 clustering resSet 11000011 before: 1 after 1 scores -1:273.933 scores of saved -1:273.933 new kept results by chain 0:5, 1:5, 2:0, 3:0, 4:0, 5:0, 6:5, 7:5, 8:0, 9:0, 10:0, 11:0, new kept results by resSet 11000011:5, *** running iteration 5 prev kept results: 5 ** running sub-iteration 1 4 counters 0/660 ** running sub-iteration 2 3 counters 0/1085 scores of saved -1:0 new kept results by chain 0:0, 1:0, 2:0, 3:0, 4:0, 5:0, 6:0, 7:0, 8:0, 9:0, 10:0, 11:0, new kept results by resSet *** running iteration 6 prev kept results: 0 ** running sub-iteration 1 5 counters 0/2893 ** running sub-iteration 2 4 counters 0/2893 ** running sub-iteration 3 3 counters 0/5268 scores of saved -1:0 new kept results by chain 0:0, 1:0, 2:0, 3:0, 4:0, 5:0, 6:0, 7:0, 8:0, 9:0, 10:0, 11:0, new kept results by resSet *** running iteration 7 prev kept results: 0 ** running sub-iteration 1 6 counters 0/7429 ** running sub-iteration 2 5 counters 0/7429 ** running sub-iteration 3 4 counters 0/7429 scores of saved -1:0 new kept results by chain 0:0, 1:0, 2:0, 3:0, 4:0, 5:0, 6:0, 7:0, 8:0, 9:0, 10:0, 11:0, new kept results by resSet *** running iteration 8 prev kept results: 0 ** running sub-iteration 1 7 counters 0/11379 ** running sub-iteration 2 6 counters 0/11379 ** running sub-iteration 3 5 counters 0/11379 ** running sub-iteration 4 4 counters 0/11379 scores of saved -1:0 new kept results by chain 0:0, 1:0, 2:0, 3:0, 4:0, 5:0, 6:0, 7:0, 8:0, 9:0, 10:0, 11:0, new kept results by resSet *** running iteration 9 prev kept results: 0 ** running sub-iteration 1 8 counters 0/13929 ** running sub-iteration 2 7 counters 0/13929 ** running sub-iteration 3 6 counters 0/13929 ** running sub-iteration 4 5 counters 0/13929 scores of saved -1:0 new kept results by chain 0:0, 1:0, 2:0, 3:0, 4:0, 5:0, 6:0, 7:0, 8:0, 9:0, 10:0, 11:0, new kept results by resSet *** running iteration 10 prev kept results: 0 ** running sub-iteration 1 9 counters 0/13929 ** running sub-iteration 2 8 counters 0/13929 ** running sub-iteration 3 7 counters 0/13929 ** running sub-iteration 4 6 counters 0/13929 ** running sub-iteration 5 5 counters 0/13929 scores of saved -1:0 new kept results by chain 0:0, 1:0, 2:0, 3:0, 4:0, 5:0, 6:0, 7:0, 8:0, 9:0, 10:0, 11:0, new kept results by resSet *** running iteration 11 prev kept results: 0 ** running sub-iteration 1 10 counters 0/13929 ** running sub-iteration 2 9 counters 0/13929 ** running sub-iteration 3 8 counters 0/13929 ** running sub-iteration 4 7 counters 0/13929 ** running sub-iteration 5 6 counters 0/13929 scores of saved -1:0 new kept results by chain 0:0, 1:0, 2:0, 3:0, 4:0, 5:0, 6:0, 7:0, 8:0, 9:0, 10:0, 11:0, new kept results by resSet *** running iteration 12 prev kept results: 0 ** running sub-iteration 1 11 counters 0/13929 ** running sub-iteration 2 10 counters 0/13929 ** running sub-iteration 3 9 counters 0/13929 ** running sub-iteration 4 8 counters 0/13929 ** running sub-iteration 5 7 counters 0/13929 ** running sub-iteration 6 6 counters 0/13929 scores of saved -1:0 new kept results by chain 0:0, 1:0, 2:0, 3:0, 4:0, 5:0, 6:0, 7:0, 8:0, 9:0, 10:0, 11:0, new kept results by resSet Overall time 20.7175 s only fold time 0.313187 s countResults_ 5 timer_ 00:00:00.31 timerAll_ 00:00:20.19 ```
The log files notes that there are problems opening the transformation files
ben-shor
Hey @ben-shor and @duhovka , thank you for providing the combfold algorithm. I have been able to get it to work locally, but I am having issues reproducing the output for 6YBQ you give in the
example/folder. I think it is an issue with how I pick the parameters for AM.Applying Combfold on the example data directly I get the following output which I think is correct?
Details
```bash --- Searching for subunits in supplied PDB files found full A0 in AFM_A0_G0_unrelaxed_rank_1_model_2.pdb chain B found full G0 in AFM_A0_G0_unrelaxed_rank_1_model_2.pdb chain C found full A0 in AFM_A0_G0_unrelaxed_rank_2_model_3.pdb chain B found full G0 in AFM_A0_G0_unrelaxed_rank_2_model_3.pdb chain C found full A0 in AFM_A0_A0_A0_unrelaxed_rank_1_model_3.pdb chain B found full A0 in AFM_A0_A0_A0_unrelaxed_rank_1_model_3.pdb chain C found full A0 in AFM_A0_A0_A0_unrelaxed_rank_1_model_3.pdb chain D found full A0 in AFM_A0_A0_unrelaxed_rank_1_model_1.pdb chain B found full A0 in AFM_A0_A0_unrelaxed_rank_1_model_1.pdb chain C found full A0 in AFM_A0_A0_G0_unrelaxed_rank_1_model_1.pdb chain B found full A0 in AFM_A0_A0_G0_unrelaxed_rank_1_model_1.pdb chain C found full G0 in AFM_A0_A0_G0_unrelaxed_rank_1_model_1.pdb chain D found full A0 in AFM_A0_A0_unrelaxed_rank_2_model_4.pdb chain B found full A0 in AFM_A0_A0_unrelaxed_rank_2_model_4.pdb chain C found full G0 in AFM_G0_G0_unrelaxed_rank_2_model_5.pdb chain B found full G0 in AFM_G0_G0_unrelaxed_rank_2_model_5.pdb chain C found full G0 in AFM_G0_G0_unrelaxed_rank_1_model_4.pdb chain B found full G0 in AFM_G0_G0_unrelaxed_rank_1_model_4.pdb chain C found full A0 in AFM_A0_A0_A0_unrelaxed_rank_2_model_1.pdb chain B found full A0 in AFM_A0_A0_A0_unrelaxed_rank_2_model_1.pdb chain C found full A0 in AFM_A0_A0_A0_unrelaxed_rank_2_model_1.pdb chain D found full A0 in AFM_A0_A0_G0_unrelaxed_rank_2_model_3.pdb chain B found full A0 in AFM_A0_A0_G0_unrelaxed_rank_2_model_3.pdb chain C found full G0 in AFM_A0_A0_G0_unrelaxed_rank_2_model_3.pdb chain D --- Extracting representative subunits (for each subunit, its best scored model in the PDBs folder) rep A0 has plddt score 96.00915686274507 rep G0 has plddt score 89.0577211394304 --- Extracting pairwise transformations between subunits (from each PDB file with 2 or more subunits) - Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/example/pdbs/AFM_A0_G0_unrelaxed_rank_1_model_2.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_G0.pdb - Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/example/pdbs/AFM_A0_G0_unrelaxed_rank_2_model_3.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_G0.pdb - Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/example/pdbs/AFM_A0_A0_A0_unrelaxed_rank_1_model_3.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_A0.pdb Skipping transformation, missing interface between A0 A0 - Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/example/pdbs/AFM_A0_A0_unrelaxed_rank_1_model_1.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_A0.pdb - Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/example/pdbs/AFM_A0_A0_G0_unrelaxed_rank_1_model_1.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_G0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_G0.pdb - Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/example/pdbs/AFM_A0_A0_unrelaxed_rank_2_model_4.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_A0.pdb - Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/example/pdbs/AFM_G0_G0_unrelaxed_rank_2_model_5.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_G0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_G0.pdb - Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/example/pdbs/AFM_G0_G0_unrelaxed_rank_1_model_4.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_G0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_G0.pdb - Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/example/pdbs/AFM_A0_A0_A0_unrelaxed_rank_2_model_1.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_A0.pdb Skipping transformation, missing interface between A0 A0 - Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/example/pdbs/AFM_A0_A0_G0_unrelaxed_rank_2_model_3.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_G0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/programmes/CombFold/test_example/_unified_representation/transformations/temp_transformations/sample2_G0.pdb found 6 transformations between A0 and G0 found 8 transformations between A0 and A0 found 2 transformations between G0 and G0 --- Finished building unified representation --- Running combinatorial assembly algorithm, may take a while --- Finished combinatorial assembly, writing output models --- Assembled 3 complexes, confidence: 88.9885-88.9885 ```
however, when I fold pairs of subunits locally I get the following output
Details
--- Searching for subunits in supplied PDB files found full A0 in A0_A0_G0_unrelaxed_rank_005_alphafold2_multimer_v3_model_1_seed_000.pdb chain A found full A0 in A0_A0_G0_unrelaxed_rank_005_alphafold2_multimer_v3_model_1_seed_000.pdb chain B found full G0 in A0_A0_G0_unrelaxed_rank_005_alphafold2_multimer_v3_model_1_seed_000.pdb chain C found full A0 in A0_A0_G0_unrelaxed_rank_004_alphafold2_multimer_v3_model_3_seed_000.pdb chain A found full A0 in A0_A0_G0_unrelaxed_rank_004_alphafold2_multimer_v3_model_3_seed_000.pdb chain B found full G0 in A0_A0_G0_unrelaxed_rank_004_alphafold2_multimer_v3_model_3_seed_000.pdb chain C found full A0 in A0_A0_G0_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb chain A found full A0 in A0_A0_G0_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb chain B found full G0 in A0_A0_G0_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb chain C found full A0 in A0_A0_G0_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb chain A found full A0 in A0_A0_G0_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb chain B found full G0 in A0_A0_G0_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb chain C found full A0 in A0_A0_G0_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb chain A found full A0 in A0_A0_G0_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb chain B found full G0 in A0_A0_G0_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb chain C --- Extracting representative subunits (for each subunit, its best scored model in the PDBs folder) rep A0 has plddt score 92.55382352941182 rep G0 has plddt score 89.27013493253367 --- Extracting pairwise transformations between subunits (from each PDB file with 2 or more subunits) - Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/results/data/subunits/subunits/pdb/A0_A0_G0_unrelaxed_rank_005_alphafold2_multimer_v3_model_1_seed_000.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_A0.pdb Skipping transformation, missing interface between A0 G0 /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_G0.pdb - Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/results/data/subunits/subunits/pdb/A0_A0_G0_unrelaxed_rank_004_alphafold2_multimer_v3_model_3_seed_000.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_A0.pdb Skipping transformation, missing interface between A0 G0 /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_G0.pdb - Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/results/data/subunits/subunits/pdb/A0_A0_G0_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_G0.pdb Skipping transformation, missing interface between A0 G0 - Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/results/data/subunits/subunits/pdb/A0_A0_G0_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_G0.pdb Skipping transformation, missing interface between A0 G0 - Extracting pairwise transformations from file /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/results/data/subunits/subunits/pdb/A0_A0_G0_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_G0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/CombinatorialAssembler/AF2trans.out /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/A0_1_510.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/G0_1_667.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample1_A0.pdb /home/mpimp-golm.mpg.de/bakker6625/Documents/experiments/complex_prediction_pipeline/complex-prediction-test-runs/workflow/scripts/dependencies/CombFold/output-subunits/_unified_representation/transformations/temp_transformations/sample2_G0.pdb found 5 transformations between A0 and A0 found 6 transformations between A0 and G0 --- Finished building unified representation --- Running combinatorial assembly algorithm, may take a while --- Finished combinatorial assembly, writing output models Could not assemble, exiting made the following files in output
I am unsure what AM parameters I should use to obtain the same structures as in the example folder. Currently I am using the default colabfold parameters, but with 5 models.
Can you help me in finding the correct AM parameters?