[INFO] Console - predicting pockets for proteins from dataset [ankh.pdb]
[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_ankh
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Dataset - processing dataset [ankh.pdb] using 0 threads
[INFO] Dataset - 
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processing [ankh.pdb] (1/1)
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[INFO] Console - processing [ankh.pdb] (1/1)
[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/ankh.pdb]
[INFO] PdbUtils - loading file [../proteins/ankh.pdb]
[INFO] Struct - groups in chain A: 492
[INFO] Struct - groups in chain A: 492
[INFO] Struct - 492 groups in chain A
[INFO] Protein - structure atoms: 3816
[INFO] Protein - protein   atoms: 3754
[INFO] Protein - ignoring ligands
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Protein - SAS points: 8101
[INFO] Protein - exposed protein atoms: 2480 of 3754
[INFO] InstancePredictor - Creating WekaInstancePredictor
[INFO] SLinkClusterer - clustering [167] elements
[INFO] SLinkClusterer - clusters: [id:4( 1 ), id:13( 2 ), id:44( 1 ), id:48( 25 ), id:50( 1 ), id:53( 13 ), id:67( 39 ), id:74( 1 ), id:81( 1 ), id:87( 1 ), id:90( 1 ), id:129( 8 ), id:133( 4 ), id:134( 1 ), id:136( 1 ), id:137( 2 ), id:145( 3 ), id:151( 4 ), id:154( 3 ), id:162( 44 ), id:166( 11 )]
[INFO] SLinkClusterer - clusters together: 167 / 167
[INFO] PocketPredictor - PREDICTING POCKETS.... ====================================
[INFO] PocketPredictor - SAS POINTS: 8101
[INFO] PocketPredictor - LIGANDABLE POINTS: 167
[INFO] PocketPredictor - CLUSTERS: 21
[INFO] PocketPredictor - FILTERED CLUSTERS: 10
[INFO] PocketPredictor - pocket 1 -  surf_atoms:  41   points:  44   score:   16.1
[INFO] PocketPredictor - pocket 2 -  surf_atoms:  47   points:  39   score:   15.5
[INFO] PocketPredictor - pocket 3 -  surf_atoms:  32   points:  25   score:    8.4
[INFO] PocketPredictor - pocket 4 -  surf_atoms:  24   points:  13   score:    7.0
[INFO] PocketPredictor - pocket 5 -  surf_atoms:  20   points:   8   score:    4.1
[INFO] PocketPredictor - pocket 6 -  surf_atoms:  25   points:  11   score:    3.7
[INFO] PocketPredictor - pocket 7 -  surf_atoms:  19   points:   4   score:    2.6
[INFO] PocketPredictor - pocket 8 -  surf_atoms:  17   points:   3   score:    1.4
[INFO] PocketPredictor - pocket 9 -  surf_atoms:   9   points:   4   score:    1.3
[INFO] PocketPredictor - pocket10 -  surf_atoms:   8   points:   3   score:    1.0
[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/ankh.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_ankh/visualizations/data/ankh.pdb]
[INFO] Console - predicting pockets finished in 0 hours 0 minutes 10.626 seconds
[INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_ankh]
[INFO] Console - 
[INFO] Console - Finished successfully in 0 hours 0 minutes 12.089 seconds.