Rosetta Enzyme Design: Warnings and Operations During Resfile Parsing and Interface Detection

This log file details the steps involved in a Rosetta enzyme design process. Here's a breakdown of the key events:

• Resfile Parsing Warnings:

  • 'Ignoring unknown one-letter amino acid code <' while parsing NOTAA mode for residue 167.
  • 'Ignoring unknown one-letter amino acid code >' while parsing NOTAA mode for residue 167.
  • 'Ignoring unknown one-letter amino acid code <' while parsing NOTAA mode for residue 224.
  • 'Ignoring unknown one-letter amino acid code >' while parsing NOTAA mode for residue 224. These messages indicate that the Resfile contained unknown single-letter amino acid codes, which were ignored.

• Interface Detection:

  • 'Choosing the following residues as targets for detecting interface: 17+120+164+307+372+421+463+'.
  • 'Design Interface: detected 6 design-shell residues and 77 repack-shell residues, shell sizes cut1-4 used were 0 0 8 10'. These lines describe the selection of residues for interface detection and the resulting shell sizes. Design-shell residues are directly involved in the interface, while repack-shell residues are adjacent and can be repacked to optimize interactions.

• Final Shell Residues:

  • 'Design-shell Residues(pose-numbering): 17+120+164+307+372+421+'.
  • 'Repack-shell Residues(pose-numbering): 12+13+14+15+16+18+19+43+44+45+52+53+55+75+77+78+79+80+117+118+119+121+122+161+162+163+165+166+167+168+169+171+177+178+221+222+223+224+225+226+227+303+304+305+306+308+309+321+344+345+346+348+352+370+371+373+374+375+376+412+413+414+415+416+417+419+420+422+423+424+425+426+427+428+429+430+463+'.
  • 'Final Design Shell Residues: 17, 44, 120, 165, 167, 168, 171, 178, 224, 225, 226, 305, 307, 308, 310, 319, 321, 344, 345, 372, 414, 419, 421, 422, 424, 430, '.
  • 'Final Repack Shell Residues: 12, 13, 14, 15, 16, 17, 18, 19, 43, 44, 45, 52, 53, 55, 75, 77, 78, 79, 80, 117, 118, 119, 120, 121, 122, 161, 162, 163, 164, 165, 166, 167, 168, 169, 171, 177, 178, 221, 222, 223, 224, 225, 226, 227, 303, 304, 305, 306, 307, 308, 309, 310, 319, 321, 344, 345, 346, 348, 352, 370, 371, 372, 373, 374, 375, 376, 412, 413, 414, 415, 416, 417, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 463, '.

• Catalytic Residue Behavior:

  • 'SetCatalyticResPackBehavior task operation touched the following catalytic residues: 17, 120, 164, 307, 372, 421, 463, '. This line indicates that specific residues were designated as catalytic and their packing behavior was adjusted accordingly.

• Constraint-Based Design (cst_design):

  • 'starting cst_design, 3 cycles of design/minimization ...'. Rosetta's cst_design protocol was initiated, involving 3 rounds of design and minimization to optimize the structure based on constraints.

• Rotamer Generation:

  • 'Using simple Rotamer generation logic for pdb_HIP'.
  • '[ WARNING ] including current in order to get at least 1 rotamer !!!!!! 429 pdb_HIP'.
  • '[ WARNING ] Subsampling proton chi expansion for LIG, as the estimated factor of 6561 exceeds 1139 proton rotamers per base residue!'.
  • 'Added 21641 rotamers for LIG'.
  • 'built 84462 rotamers at 85 positions'. These lines indicate the use of Rotamer generation for different residues. The warnings indicate that some residues had very large numbers of possible rotamers (conformations), leading to computational challenges. Subsampling was applied to reduce the number of rotamers considered.

This log file provides valuable insights into the steps involved in a Rosetta enzyme design run. It shows that the process involved warnings due to unknown amino acid codes and potential issues with Rotamer generation. The log also highlights the key stages of interface detection, shell residue identification, catalytic residue handling, and the use of constraint-based design to achieve a desired enzyme structure.