[INFO] Console - predicting pockets for proteins from dataset [map3k15.pdb]
[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_map3k15
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Dataset - processing dataset [map3k15.pdb] using 0 threads
[INFO] Dataset - 
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processing [map3k15.pdb] (1/1)
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[INFO] Console - processing [map3k15.pdb] (1/1)
[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/map3k15.pdb]
[INFO] PdbUtils - loading file [../proteins/map3k15.pdb]
[INFO] Struct - groups in chain A: 1313
[INFO] Struct - groups in chain A: 1313
[INFO] Struct - 1313 groups in chain A
[INFO] Protein - structure atoms: 10370
[INFO] Protein - protein   atoms: 10154
[INFO] Protein - ignoring ligands
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Protein - SAS points: 28287
[INFO] Protein - exposed protein atoms: 7499 of 10154
[INFO] InstancePredictor - Creating WekaInstancePredictor
[INFO] SLinkClusterer - clustering [143] elements
[INFO] SLinkClusterer - clusters: [id:0( 1 ), id:1( 1 ), id:3( 2 ), id:4( 1 ), id:7( 3 ), id:8( 1 ), id:42( 5 ), id:53( 2 ), id:58( 47 ), id:75( 3 ), id:76( 9 ), id:78( 4 ), id:82( 1 ), id:83( 1 ), id:84( 2 ), id:105( 2 ), id:108( 7 ), id:120( 20 ), id:123( 3 ), id:128( 4 ), id:133( 2 ), id:141( 21 ), id:142( 1 )]
[INFO] SLinkClusterer - clusters together: 143 / 143
[INFO] PocketPredictor - PREDICTING POCKETS.... ====================================
[INFO] PocketPredictor - SAS POINTS: 28287
[INFO] PocketPredictor - LIGANDABLE POINTS: 143
[INFO] PocketPredictor - CLUSTERS: 23
[INFO] PocketPredictor - FILTERED CLUSTERS: 11
[INFO] PocketPredictor - pocket 1 -  surf_atoms:  58   points:  47   score:   16.0
[INFO] PocketPredictor - pocket 2 -  surf_atoms:  52   points:  20   score:    8.6
[INFO] PocketPredictor - pocket 3 -  surf_atoms:  40   points:  21   score:    6.6
[INFO] PocketPredictor - pocket 4 -  surf_atoms:  20   points:   9   score:    2.7
[INFO] PocketPredictor - pocket 5 -  surf_atoms:  18   points:   4   score:    2.7
[INFO] PocketPredictor - pocket 6 -  surf_atoms:  21   points:   7   score:    2.6
[INFO] PocketPredictor - pocket 7 -  surf_atoms:  17   points:   5   score:    1.9
[INFO] PocketPredictor - pocket 8 -  surf_atoms:  13   points:   4   score:    1.4
[INFO] PocketPredictor - pocket 9 -  surf_atoms:  14   points:   3   score:    1.2
[INFO] PocketPredictor - pocket10 -  surf_atoms:  17   points:   3   score:    1.0
[INFO] PocketPredictor - pocket11 -  surf_atoms:   9   points:   3   score:    0.8
[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/map3k15.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_map3k15/visualizations/data/map3k15.pdb]
[INFO] Console - predicting pockets finished in 0 hours 0 minutes 13.170 seconds
[INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_map3k15]
[INFO] Console - 
[INFO] Console - Finished successfully in 0 hours 0 minutes 14.607 seconds.