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[INFO] Console - predicting pockets for proteins from dataset [il33.pdb] |
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[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_il33 |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Dataset - processing dataset [il33.pdb] using 0 threads |
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[INFO] Dataset - |
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processing [il33.pdb] (1/1) |
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[INFO] Console - processing [il33.pdb] (1/1) |
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[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/proteins/il33.pdb] |
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[INFO] PdbUtils - loading file [proteins/il33.pdb] |
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[INFO] Struct - groups in chain A: 270 |
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[INFO] Struct - groups in chain A: 270 |
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[INFO] Struct - 270 groups in chain A |
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[INFO] Protein - structure atoms: 2155 |
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[INFO] Protein - protein atoms: 2129 |
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[INFO] Protein - ignoring ligands |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Protein - SAS points: 7352 |
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[INFO] Protein - exposed protein atoms: 1743 of 2129 |
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[INFO] InstancePredictor - Creating WekaInstancePredictor |
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[INFO] SLinkClusterer - clustering [20] elements |
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[INFO] SLinkClusterer - clusters: [id:1( 2 ), id:2( 1 ), id:5( 1 ), id:11( 1 ), id:12( 1 ), id:16( 8 ), id:17( 4 ), id:18( 1 ), id:19( 1 )] |
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[INFO] SLinkClusterer - clusters together: 20 / 20 |
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[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
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[INFO] PocketPredictor - SAS POINTS: 7352 |
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[INFO] PocketPredictor - LIGANDABLE POINTS: 20 |
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[INFO] PocketPredictor - CLUSTERS: 9 |
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[INFO] PocketPredictor - FILTERED CLUSTERS: 2 |
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[INFO] PocketPredictor - pocket 1 - surf_atoms: 16 points: 8 score: 2.1 |
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[INFO] PocketPredictor - pocket 2 - surf_atoms: 10 points: 4 score: 1.5 |
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[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/proteins/il33.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_il33/visualizations/data/il33.pdb] |
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[INFO] Console - predicting pockets finished in 0 hours 0 minutes 10.379 seconds |
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[INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_il33] |
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[INFO] Console - |
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[INFO] Console - Finished successfully in 0 hours 0 minutes 11.873 seconds. |
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