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[INFO] Console - predicting pockets for proteins from dataset [il4r.pdb] |
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[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_il4r |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Dataset - processing dataset [il4r.pdb] using 0 threads |
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[INFO] Dataset - |
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processing [il4r.pdb] (1/1) |
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[INFO] Console - processing [il4r.pdb] (1/1) |
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[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/il4r.pdb] |
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[INFO] PdbUtils - loading file [../proteins/il4r.pdb] |
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[INFO] Struct - groups in chain A: 825 |
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[INFO] Struct - groups in chain A: 825 |
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[INFO] Struct - 825 groups in chain A |
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[INFO] Protein - structure atoms: 6290 |
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[INFO] Protein - protein atoms: 6198 |
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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: 29317 |
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[INFO] Protein - exposed protein atoms: 5672 of 6198 |
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[INFO] InstancePredictor - Creating WekaInstancePredictor |
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[INFO] SLinkClusterer - clustering [8] elements |
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[INFO] SLinkClusterer - clusters: [id:0( 1 ), id:1( 1 ), id:3( 2 ), id:4( 1 ), id:5( 1 ), id:6( 1 ), id:7( 1 )] |
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[INFO] SLinkClusterer - clusters together: 8 / 8 |
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[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
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[INFO] PocketPredictor - SAS POINTS: 29317 |
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[INFO] PocketPredictor - LIGANDABLE POINTS: 8 |
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[INFO] PocketPredictor - CLUSTERS: 7 |
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[INFO] PocketPredictor - FILTERED CLUSTERS: 0 |
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[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/il4r.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_il4r/visualizations/data/il4r.pdb] |
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[INFO] Console - predicting pockets finished in 0 hours 0 minutes 13.629 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_il4r] |
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[INFO] Console - |
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[INFO] Console - Finished successfully in 0 hours 0 minutes 15.090 seconds. |
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