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[INFO] Console - predicting pockets for proteins from dataset [pcsk9.pdb] |
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[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_pcsk9 |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Dataset - processing dataset [pcsk9.pdb] using 0 threads |
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[INFO] Dataset - |
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processing [pcsk9.pdb] (1/1) |
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[INFO] Console - processing [pcsk9.pdb] (1/1) |
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[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/pcsk9.pdb] |
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[INFO] PdbUtils - loading file [../proteins/pcsk9.pdb] |
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[INFO] Struct - groups in chain A: 692 |
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[INFO] Struct - groups in chain A: 692 |
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[INFO] Struct - 692 groups in chain A |
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[INFO] Protein - structure atoms: 5208 |
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[INFO] Protein - protein atoms: 5094 |
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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: 11398 |
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[INFO] Protein - exposed protein atoms: 3365 of 5094 |
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[INFO] InstancePredictor - Creating WekaInstancePredictor |
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[INFO] SLinkClusterer - clustering [100] elements |
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[INFO] SLinkClusterer - clusters: [id:13( 8 ), id:18( 3 ), id:20( 3 ), id:23( 6 ), id:24( 1 ), id:27( 7 ), id:29( 1 ), id:32( 4 ), id:33( 1 ), id:37( 2 ), id:38( 1 ), id:39( 1 ), id:52( 1 ), id:73( 14 ), id:80( 4 ), id:91( 33 ), id:94( 1 ), id:95( 1 ), id:96( 2 ), id:99( 6 )] |
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[INFO] SLinkClusterer - clusters together: 100 / 100 |
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[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
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[INFO] PocketPredictor - SAS POINTS: 11398 |
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[INFO] PocketPredictor - LIGANDABLE POINTS: 100 |
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[INFO] PocketPredictor - CLUSTERS: 20 |
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[INFO] PocketPredictor - FILTERED CLUSTERS: 10 |
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[INFO] PocketPredictor - pocket 1 - surf_atoms: 34 points: 33 score: 9.9 |
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[INFO] PocketPredictor - pocket 2 - surf_atoms: 33 points: 14 score: 4.6 |
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[INFO] PocketPredictor - pocket 3 - surf_atoms: 19 points: 8 score: 2.1 |
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[INFO] PocketPredictor - pocket 4 - surf_atoms: 19 points: 7 score: 1.9 |
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[INFO] PocketPredictor - pocket 5 - surf_atoms: 12 points: 4 score: 1.7 |
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[INFO] PocketPredictor - pocket 6 - surf_atoms: 19 points: 6 score: 1.5 |
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[INFO] PocketPredictor - pocket 7 - surf_atoms: 23 points: 4 score: 1.5 |
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[INFO] PocketPredictor - pocket 8 - surf_atoms: 17 points: 3 score: 1.5 |
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[INFO] PocketPredictor - pocket 9 - surf_atoms: 12 points: 6 score: 1.2 |
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[INFO] PocketPredictor - pocket10 - surf_atoms: 11 points: 3 score: 0.9 |
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[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/pcsk9.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_pcsk9/visualizations/data/pcsk9.pdb] |
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[INFO] Console - predicting pockets finished in 0 hours 0 minutes 19.067 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_pcsk9] |
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[INFO] Console - |
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[INFO] Console - Finished successfully in 0 hours 0 minutes 20.776 seconds. |
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