[INFO] Console - predicting pockets for proteins from dataset [ifih1.pdb]
[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_ifih1
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Dataset - processing dataset [ifih1.pdb] using 0 threads
[INFO] Dataset - 
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processing [ifih1.pdb] (1/1)
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[INFO] Console - processing [ifih1.pdb] (1/1)
[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/ifih1.pdb]
[INFO] PdbUtils - loading file [../proteins/ifih1.pdb]
[INFO] Struct - groups in chain A: 921
[INFO] Struct - groups in chain A: 921
[INFO] Struct - 921 groups in chain A
[INFO] Protein - structure atoms: 7353
[INFO] Protein - protein   atoms: 7244
[INFO] Protein - ignoring ligands
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Protein - SAS points: 18250
[INFO] Protein - exposed protein atoms: 5205 of 7244
[INFO] InstancePredictor - Creating WekaInstancePredictor
[INFO] SLinkClusterer - clustering [123] elements
[INFO] SLinkClusterer - clusters: [id:1( 2 ), id:25( 31 ), id:32( 4 ), id:33( 3 ), id:47( 1 ), id:52( 1 ), id:58( 2 ), id:73( 1 ), id:81( 25 ), id:86( 1 ), id:87( 2 ), id:89( 2 ), id:90( 1 ), id:95( 12 ), id:98( 4 ), id:100( 5 ), id:109( 15 ), id:111( 2 ), id:112( 1 ), id:117( 4 ), id:118( 1 ), id:120( 1 ), id:121( 1 ), id:122( 1 )]
[INFO] SLinkClusterer - clusters together: 123 / 123
[INFO] PocketPredictor - PREDICTING POCKETS.... ====================================
[INFO] PocketPredictor - SAS POINTS: 18250
[INFO] PocketPredictor - LIGANDABLE POINTS: 123
[INFO] PocketPredictor - CLUSTERS: 24
[INFO] PocketPredictor - FILTERED CLUSTERS: 9
[INFO] PocketPredictor - pocket 1 -  surf_atoms:  34   points:  31   score:   11.0
[INFO] PocketPredictor - pocket 2 -  surf_atoms:  37   points:  25   score:    8.6
[INFO] PocketPredictor - pocket 3 -  surf_atoms:  31   points:  15   score:    5.8
[INFO] PocketPredictor - pocket 4 -  surf_atoms:  26   points:  12   score:    4.3
[INFO] PocketPredictor - pocket 5 -  surf_atoms:  34   points:   5   score:    2.6
[INFO] PocketPredictor - pocket 6 -  surf_atoms:  16   points:   4   score:    1.8
[INFO] PocketPredictor - pocket 7 -  surf_atoms:  18   points:   4   score:    1.5
[INFO] PocketPredictor - pocket 8 -  surf_atoms:   9   points:   4   score:    1.4
[INFO] PocketPredictor - pocket 9 -  surf_atoms:   8   points:   3   score:    0.6
[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/ifih1.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_ifih1/visualizations/data/ifih1.pdb]
[INFO] Console - predicting pockets finished in 0 hours 0 minutes 12.392 seconds
[INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_ifih1]
[INFO] Console - 
[INFO] Console - Finished successfully in 0 hours 0 minutes 13.975 seconds.