|
|
[INFO] Console - predicting pockets for proteins from dataset [cfhr5.pdb] |
|
|
[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_cfhr5 |
|
|
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
|
|
[INFO] Dataset - processing dataset [cfhr5.pdb] using 0 threads |
|
|
[INFO] Dataset - |
|
|
------------------------------------------------------------------------------------------------------------------------ |
|
|
processing [cfhr5.pdb] (1/1) |
|
|
------------------------------------------------------------------------------------------------------------------------ |
|
|
|
|
|
[INFO] Console - processing [cfhr5.pdb] (1/1) |
|
|
[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/cfhr5.pdb] |
|
|
[INFO] PdbUtils - loading file [../proteins/cfhr5.pdb] |
|
|
[INFO] Struct - groups in chain A: 569 |
|
|
[INFO] Struct - groups in chain A: 569 |
|
|
[INFO] Struct - 569 groups in chain A |
|
|
[INFO] Protein - structure atoms: 4513 |
|
|
[INFO] Protein - protein atoms: 4433 |
|
|
[INFO] Protein - ignoring ligands |
|
|
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
|
|
[INFO] Protein - SAS points: 11807 |
|
|
[INFO] Protein - exposed protein atoms: 3475 of 4433 |
|
|
[INFO] InstancePredictor - Creating WekaInstancePredictor |
|
|
[INFO] SLinkClusterer - clustering [62] elements |
|
|
[INFO] SLinkClusterer - clusters: [id:1( 31 ), id:28( 5 ), id:32( 4 ), id:45( 10 ), id:46( 2 ), id:48( 4 ), id:49( 5 ), id:61( 1 )] |
|
|
[INFO] SLinkClusterer - clusters together: 62 / 62 |
|
|
[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
|
|
[INFO] PocketPredictor - SAS POINTS: 11807 |
|
|
[INFO] PocketPredictor - LIGANDABLE POINTS: 62 |
|
|
[INFO] PocketPredictor - CLUSTERS: 8 |
|
|
[INFO] PocketPredictor - FILTERED CLUSTERS: 6 |
|
|
[INFO] PocketPredictor - pocket 1 - surf_atoms: 54 points: 31 score: 10.1 |
|
|
[INFO] PocketPredictor - pocket 2 - surf_atoms: 26 points: 10 score: 3.1 |
|
|
[INFO] PocketPredictor - pocket 3 - surf_atoms: 22 points: 4 score: 1.7 |
|
|
[INFO] PocketPredictor - pocket 4 - surf_atoms: 28 points: 5 score: 1.7 |
|
|
[INFO] PocketPredictor - pocket 5 - surf_atoms: 16 points: 5 score: 1.4 |
|
|
[INFO] PocketPredictor - pocket 6 - surf_atoms: 18 points: 4 score: 1.3 |
|
|
[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/cfhr5.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_cfhr5/visualizations/data/cfhr5.pdb] |
|
|
[INFO] Console - predicting pockets finished in 0 hours 0 minutes 11.148 seconds |
|
|
[INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_cfhr5] |
|
|
[INFO] Console - |
|
|
[INFO] Console - Finished successfully in 0 hours 0 minutes 12.587 seconds. |
|
|
|
