Objective and steps

a) Select structure-candidates.

• Select 25 P1 structures from PDB and prepare them for quantum refinement.

b) Run cheap HF energy and gradients calculation using clustering.

• pick up results from "a)" and use it as input to run cheap HF calculation using clustering.

• write only gradient-based LBFGS (the line-search version)

c) Final HF based refinement.

• Analyse results of "b)" and pick one or two most favorable (showing most improvement) to run HF based refinements.

Details for each step a-b-c) follow below.

Structure preparation

1) Get structures from PDB.

• This is done manually using RCSB site. Selection criteria are: P1, not too many atoms, resolution ~3-4 Å, bad validation metrics. The criteria are rather arbitrary: we try to find low-resolution models that we believe can be improved by quantum refinement.

• File were downloaded using phenix.fetch_pdb PDB_CODE --mtz

• Some models have unknown to Phenix ligands. Corresponding CIF files were created using phenix.ready_set file_name.pdb This also adds hydrogens with are needed for the run_finalise.py script. The output is file_name.updated.pdb which needs to be renamed? We can use phenix.reduce which has it's own problems.

• Some data file were missing R-free flags. They were added at subsequent (re-refinement).

• .pdb, .mtz and .cif files are stored in 00 folder.

2) Phenix-Refine

• Refine structures from "1)" using phenix.refine. List of commands per each structure is in 01_run_phenix_refine file.

• Refinement results are stored in 01 folder. MTZ files from this folder are to be used in all subsequent refinements.

3) Finalize

• Run structure from "2)" through 02_run_update_pdb.py using command phenix.ready_set is used to add hydrogens to amino acids and ligands run_finalise.py is used to complete structures, remove altlocs and resset occupancies all completed structrues by 02_run_update_pdb.py are in 02

XXX This needs a careful and clear description what's being done and how. Adding H and missing non-H atoms? Remove altlocs? Reset occupancies? XXX

All PDBs in folder 01 have no errors in running 02_run_update_pdb.py are listed in folder 02.
9 out of 25 structures in folder 01 pass 02_run_update_pdb.py successfully.

Current issues to be resolved ASAP:

• Errors that have been postponed or manually resolved:

  • 1u0d - multiple models
  • 2jee - has a terminal amino acid with just a N

• Known errors:

  • 3kyi - nonstandard amino acid has strange charge
  • 4k2r - ANP does not have partial charges
  • 4rnf - bug in cctbx geometry restraints
  • 3oe9 - ITD
  • 3uds - ADP
  • 4ctd - C8E

• Unknown errors:

  • 2x10 - tardy errors, maximum charge error
  • 3nak - strange nonstandard amino acid

• No errors:

  • 1il5 - ✅
  • 1va7 - ✅
  • 1y1l - ✅
  • 1ok9 - ✅ ACT, GOL added to GeoStd
  • 2oeq - ✅
  • 2oy0 - ✅
  • 2ghj - ✅
  • 3tz9 - ✅ AQU added to GeoStd
  • 3dtj - ✅
  • 3uj4 - ✅
  • 4xa1 - ✅
  • 4drw - ✅
  • 4fsx - ✅
  • 4rnf - ✅
  • 4p7h - ✅
  • 5diz - ✅ Has S-S bond, better check them.
  • 5d12 - ✅ G97 added to GeoStd

• Hi/Lo pairs

  • 3dtj - works in my hands

• Waters

  • Do we make a policy about the inclusion of water below a certain resolution?

• Program completeness

  • need complete list of D-peptides
  • need complete list of nonstandard peptides

Testing

Testing is very simple. Run tests/run_tests.py and check for Sorry's.

• Tests to add:
  • Carbohydrates are correctly charged - taken from Chemical Components but polymerisation is not checked
  • Test that a ligand has partial charges

Structure refinement

XXX more results here, in folders 04, 05, etc.