Alpha fold 2 multimer parameters used in example dataset
Luke-ebbis opened this issue · 12 comments
Luke-ebbis commented
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
--- 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?
Luke-ebbis commented
The assembly log file when for the failing output is as follows
Details
/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 /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_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_B_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_B_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_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 /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_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_B_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_B_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_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 /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_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_B_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_C_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_C_plus_A0_A
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_B
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_C_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_C_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_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 /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_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_C_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_C_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_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 /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_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_C_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_D_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_D_plus_A0_A
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_B
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_D_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_D_plus_A0_C
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_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 /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_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_D_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_E_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_E_plus_A0_A
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_B
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_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_E_plus_A0_C
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_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 /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_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_E_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_E_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_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 /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_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_E_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_E_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_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 /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_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_E_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_F_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_F_plus_A0_A
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_B
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_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_F_plus_A0_C
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_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 /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_E
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_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_F_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_F_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_F_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_F_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_F_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_F_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_F_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_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 /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_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_F_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/G0_G_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/G0_G_plus_A0_A
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_B
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_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/G0_G_plus_A0_C
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_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 /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_E
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_E
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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_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/G0_G_plus_G0_H
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_G0_H
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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_G0_I
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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_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/G0_G_plus_G0_K
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_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/G0_G_plus_G0_L
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_G0_L
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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_H_plus_A0_A
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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_H_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/G0_H_plus_A0_C
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_H_plus_A0_C
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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_H_plus_A0_D
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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_H_plus_A0_E
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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_H_plus_A0_F
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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_H_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/G0_H_plus_G0_I
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_H_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/G0_H_plus_G0_J
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_H_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/G0_H_plus_G0_K
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_H_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/G0_H_plus_G0_L
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_H_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/G0_I_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/G0_I_plus_A0_A
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_I_plus_A0_B
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_I_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/G0_I_plus_A0_C
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_I_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_I_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_I_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/G0_I_plus_A0_E
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_I_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/G0_I_plus_A0_F
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_I_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/G0_I_plus_G0_G
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_I_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/G0_I_plus_G0_H
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_I_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/G0_I_plus_G0_J
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_I_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/G0_I_plus_G0_K
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_I_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/G0_I_plus_G0_L
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_I_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/G0_J_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/G0_J_plus_A0_A
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_J_plus_A0_B
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_J_plus_A0_B
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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_J_plus_A0_C
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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_J_plus_A0_D
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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_J_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/G0_J_plus_A0_F
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_J_plus_A0_F
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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_J_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/G0_J_plus_G0_H
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_J_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/G0_J_plus_G0_I
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_J_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/G0_J_plus_G0_K
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_J_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/G0_J_plus_G0_L
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_J_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/G0_K_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/G0_K_plus_A0_A
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_K_plus_A0_B
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_K_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/G0_K_plus_A0_C
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_K_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_K_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_K_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/G0_K_plus_A0_E
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_K_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/G0_K_plus_A0_F
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_K_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/G0_K_plus_G0_G
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_K_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/G0_K_plus_G0_H
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_K_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/G0_K_plus_G0_I
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_K_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/G0_K_plus_G0_J
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_K_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/G0_K_plus_G0_L
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_K_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/G0_L_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/G0_L_plus_A0_A
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_L_plus_A0_B
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_L_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/G0_L_plus_A0_C
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_L_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_L_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_L_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/G0_L_plus_A0_E
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_L_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/G0_L_plus_A0_F
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_L_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/G0_L_plus_G0_G
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_L_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/G0_L_plus_G0_H
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_L_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/G0_L_plus_G0_I
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_L_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/G0_L_plus_G0_J
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_L_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/G0_L_plus_G0_K
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_L_plus_G0_K
Starting HierarchicalFold
SBB 0 set 1 isEmpty 0
SBB 0 size 1
0 1 trans size 5 10
0 2 trans size 5 100
0 3 trans size 5 1000
0 4 trans size 5 10000
0 5 trans size 5 100000
0 6 trans size 6 1000000
0 7 trans size 6 10000000
0 8 trans size 6 100000000
0 9 trans size 6 1000000000
0 10 trans size 6 10000000000
0 11 trans size 6 100000000000
SBB 1 set 10 isEmpty 0
SBB 1 size 1
1 2 trans size 5 100
1 3 trans size 5 1000
1 4 trans size 5 10000
1 5 trans size 5 100000
1 6 trans size 6 1000000
1 7 trans size 6 10000000
1 8 trans size 6 100000000
1 9 trans size 6 1000000000
1 10 trans size 6 10000000000
1 11 trans size 6 100000000000
SBB 2 set 100 isEmpty 0
SBB 2 size 1
2 3 trans size 5 1000
2 4 trans size 5 10000
2 5 trans size 5 100000
2 6 trans 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
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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
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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
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5 6 trans size 6
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5 7 trans size 6
done add_edge
5 8 trans size 6
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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
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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
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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
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7 4 trans size 6
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7 5 trans size 6
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7 6 trans size 0
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7 7 trans size 0
done add_edge
7 8 trans size 0
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7 9 trans size 0
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7 10 trans size 0
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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
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8 2 trans size 6
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8 3 trans size 6
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8 4 trans size 6
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8 5 trans size 6
done add_edge
8 6 trans size 0
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8 7 trans size 0
done add_edge
8 8 trans size 0
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8 9 trans size 0
done add_edge
8 10 trans size 0
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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
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9 2 trans size 6
done add_edge
9 3 trans size 6
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9 4 trans size 6
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9 5 trans size 6
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9 6 trans size 0
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9 7 trans size 0
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9 10 trans size 0
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isEmpty 10 0
SBB 10 size 1
10 0 trans size 6
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10 1 trans size 6
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10 2 trans size 6
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10 3 trans size 6
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10 4 trans size 6
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10 5 trans size 6
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10 6 trans size 0
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10 7 trans size 0
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10 8 trans size 0
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10 9 trans size 0
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10 10 trans size 0
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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
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11 4 trans size 6
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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
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Overall time 20.7175 s
only fold time 0.313187 s
countResults_ 5
timer_ 00:00:00.31
timerAll_ 00:00:20.19The log files notes that there are problems opening the transformation files
ben-shor commented
Hi!
Thanks for the well-formatted question!
From your logs, it seems that the issue is that you computed 5 models, but only from one type of subcomplex (A-A-G). However, it is most likely that necessary transformations are not present in these models. For example, you do not supply any model with two G subunits. I would recommend you to compute other types of subcomplexes (like in the example): A-A-A, G-G,A-G. The more types of subcomplexes you compute, the more you are likely that the correct transformations will be there and then CombFold will be able to assemble.
Let me know if that helped.
Ben
Luke-ebbis commented
This is what I suspected, but I have troubles getting the scripts/prepare_fastas.py produce the right combinations of subunits.
I have the following pair pdb files (predicted using default AF (
results/data/6ybq/subunits/pdb-pairs/A0_A0_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
results/data/6ybq/subunits/pdb-pairs/A0_A0_unrelaxed_rank_002_alphafold2_multimer_v3_model_2_seed_000.pdb
results/data/6ybq/subunits/pdb-pairs/A0_A0_unrelaxed_rank_003_alphafold2_multimer_v3_model_1_seed_000.pdb
results/data/6ybq/subunits/pdb-pairs/A0_A0_unrelaxed_rank_004_alphafold2_multimer_v3_model_3_seed_000.pdb
results/data/6ybq/subunits/pdb-pairs/A0_A0_unrelaxed_rank_005_alphafold2_multimer_v3_model_4_seed_000.pdb
results/data/6ybq/subunits/pdb-pairs/A0_G0_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
results/data/6ybq/subunits/pdb-pairs/A0_G0_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb
results/data/6ybq/subunits/pdb-pairs/A0_G0_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb
results/data/6ybq/subunits/pdb-pairs/A0_G0_unrelaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb
results/data/6ybq/subunits/pdb-pairs/A0_G0_unrelaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb
results/data/6ybq/subunits/pdb-pairs/G0_G0_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
results/data/6ybq/subunits/pdb-pairs/G0_G0_unrelaxed_rank_002_alphafold2_multimer_v3_model_5_seed_000.pdb
results/data/6ybq/subunits/pdb-pairs/G0_G0_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb
results/data/6ybq/subunits/pdb-pairs/G0_G0_unrelaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb
results/data/6ybq/subunits/pdb-pairs/G0_G0_unrelaxed_rank_005_alphafold2_multimer_v3_model_2_seed_000.pdb
Then I run the scripts/prepare_fastas.py script and only one type of grouping is produced:
-rw-r--r-- 1 bakker6625 domain users 1700 May 16 13:46 A0_A0_G0.fasta
I call the prepare_fastas.py as follows:
python3 scripts/prepare_fastas.py ../../../../results/data/test_sub_unit/test_sub_unit.json --stage groups --output-fasta-folder ../../../../results/data/test_sub_unit/subunits/fasta-groups --max-af-size 1800 --input-pairs-results ../../../../results/data/test_sub_unit/subunits/pdb-pairsWhy does it not produce the required larger pairs (as also made in the examples)?
ben-shor commented
I am not sure, I will take a look at the script, perhaps changes in the code caused it to limit the amount of created groups.
In any case, I would suggest that when assembling complexes with a low number of unique subunits, you would compute all possible triplets in addition to the prepare_fastas output. This script is meant mainly for large heteromers and is used to limit and rank the many possible combinations, but it is possible that when there is a low number of subunits it limits the number of combinations too much and not all possibilities are present.
Luke-ebbis commented
Oke @ben-shor, thanks for the response. Just to confirm my understanding, you did not use your scripts/prepare_fastas.py ... --stage groups for the complex in the example/ folder?
ben-shor commented
Hi, I suspected before that something meaningful changed in the scripts since using them for the example and so they can not recreate the example, but I just tried running
python3 scripts/prepare_fastas.py --stage groups --output-fasta-folder <output_folder> --input-pairs-<pairs_pdbs_folder> example/subunits.json
Using the 5 pairs PDB files and I see that fastas are created both for AAA and AAG, just like in the example.
When you run on those 5 PDBs, do you still get only AAG?
Luke-ebbis commented
Alright, I will run the prepare_fastas.py again on the pair PDBs and the json file given as the example.
Luke-ebbis commented
So when running the command, I do get the correct output (in terms of the fasta files generated).
├── fasta-groups
│ ├── A0_A0_A0.fasta
│ └── A0_A0_G0.fasta
├── fasta-pairs
│ ├── A0_A0.fasta
│ ├── A0_G0.fasta
│ └── G0_G0.fasta
└── pdb-pairs
├── AFM_A0_A0_unrelaxed_rank_1_model_1.pdb
├── AFM_A0_A0_unrelaxed_rank_2_model_4.pdb
├── AFM_A0_G0_unrelaxed_rank_1_model_2.pdb
├── AFM_A0_G0_unrelaxed_rank_2_model_3.pdb
└── AFM_G0_G0_unrelaxed_rank_1_model_4.pdb
So I think it is down to my usage of colabfold. Which version are you using? I am using ">=1.5.5,<1.6".
ben-shor commented
I don't know the specific version of ColabFold, but it was AlphaFold2 with no templates.
Why are you trying to recreate the example? what is your end goal?
Luke-ebbis commented
To see whether I set up the colabfold and combfold programme correctly
ben-shor commented
It seems that the CombFold pipeline is working well for you(as all scripts and assembly seem to work), and the only issue is the specific models outputted by ColabFold that may be a bit different from the example. This can happen for example if the MSA used for this sample has changed, or maybe previously I used the original AlphaFold2 weights, and currently ColabFold defaults to AFMv2.3.
I would suggest you look at the generated PDB files, and if they seem to be valid and close to the PDB files in the example, it is likely small changes so you should not worry about that for the sanity check, and you can move to compute your target assemblies.
Luke-ebbis commented
Hey @ben-shor, I will give that a go then. Thank you for your help.