Quality Control Check

The QC server reports the stereochemical quality of the model using AutoDepInputTool1, MolProbity2, and Phenix3, the agreement between the atomic model and the data using Resolve4, the agreement between the model and protein sequences using Clustalw5, the ADP distribution using Phenix, differences in Rcryst/Rfree and expected Rfree/Rcryst, and various other items including nomenclature issues, atom occupancies, consistency of NCS pairs, ligand interactions, special positions, presence of CIS-peptides, waters with no interactions, etc. using in-house scripts and analyzing refinement log file and PDB header.

The Quality Control Check was developed at the Joint Center for Structural Genomics. If you use this tool in preparing a structure, please acknowledge the JCSG.

1. Usage:
  1. The interface allows the input of necessary files and allows the user to select which checks to run
    1. pdb_file, mtz_file, and refmac_log are the most recent files from the refinement
    2. sequence is the sequence file in FASTA format
    3. It is only necessary to upload the files that correspond to the selected job requests. For example, selecting molprobity requires only the pdb file, while the sequence check requires the pdb and sequence files. Most browsers will list the required input files if the mouse is held over the check-boxes.
2. Output:
  1. All results are output to the screen. Use the links at the top of the page to jump to a specific section.
  2. Saving results: Under the "Input Comments and Save Results" section (located at the bottom of the page) there is a box in which the user can optionally add comments. The entire output can then be saved using the "Save comments and QC output" box. It will automatically be saved as qc_check.html, though the name can be changed. It is important, however, to retain the ".html" to facilitate later viewing in a web browser. Note that the file will be saved even if no comments are entered.
3. Checks:
  1. Refinement Statistics
    1. The space group and unit cell parameters are presented.
    2. The resolution limits are checked and the nominal resolution is calculated.
    3. The Rwork and Rfree stats are presented and the gap between them is calculated. Flagged if the gap is over 5%.
    4. Expectation values calculated based on Tickle (1998, 2000). Flagged if the standard deviation from the expectation value is greater than three.
    5. If the Fo-Fc map correlation is below 0.9, it is flagged.
    6. Check for the addition of hydrogens during refinement.
    7. The number of NCS groups is compared to the number of molecules in the ASU. If the resolution is worse than 2.0 and there are no NCS restraints, then it is flagged.
    8. The number of TLS groups is presented. The presence of MAKE_U_POSITIVE errors is flagged.
  2. PDB Checks
    1. Verify that REMARKs 300, 350, and 999 are present (does not check that content is correct).
    2. Model geometry indicators (various RMSDs) are printed from the PDB header as well as calculated by Phenix.
    3. Presence of CIS-peptides is checked.
    4. Occupancy is checked; any atoms that do not have occ = 1.0 are listed.
    5. MSE occupancy is listed seperately from the other atoms, and the file is checked for the presence of MET.
    6. Atoms on crystallographic special positions are listed and their occupancies verified.
    7. Model ADP distribution is listed and plotted. Significant B-factor variations in alternate conformation residues and anisotropies are flagged.
    8. Check chain ID's. Specifically look for the presence of chain ID "X", which is typically inserted by refmac. Breaks in the chains are listed.
    9. Ligand interactions are listed. Torsion angle range for EDO and GOL are also listed and flaggged if found beyond acceptable range.
    10. Waters without any direct/indirect interactions with proteins are listed.
  3. Sequence Alignment
    1. Sequence alignment is presented and any gaps and/or mismatches are highlighted.
  4. NCS Outliers
    1. Possible residue "flips" between different chains are flagged.
    2. Residues that are in different conformations between different chains are flagged.
    3. An aligned pdb file and a coot script that lists and residues flagged from 1 or 2 above are generated.
  5. Molprobity Checks
    1. Check for, and generate, REMARK 40 using MolProbity.
    2. The clash, rotamer, and ramachandran scores from molprobity are presented.
    3. If present, ramachandran outliers are listed.
    4. If present, rotamer outliers are listed.
    5. If present, Cβ deviations and bond length/angle outliers listed.
    6. If present, flips to check are listed.
    7. A script compatible with Coot is available for download. Open in Coot with 'Calculate/Run Script'.
  6. Nomenclature Check
    1. Model is checked for various nomenclature errors.
    2. An option is provided to fix the selected errors and save into a new file.
  7. ADIT Check
    1. ADIT is run and results from pdb_file.letter are included.
  8. Resolve Evaluate
    1. Resolve_evaluate is run to check fit of atoms in electron density and residues with weak density are listed.
4. References:
  1. Yang H, Guranovic V, Dutta S, Feng Z, Berman HM, Westbrook JD. 2004. Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank. Acta Crystallogr. Sect. D. Biol. Crystallogr. 60:1833-1839.
  2. Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB, 3rd, Snoeyink J, Richardson JS, Richardson DC. 2007. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 35:375-383.
  3. Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH. 2010. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66:213-221.
  4. Terwilliger TC. 2003. Statistical density modification using local pattern matching. Acta Crystallogr D Biol Crystallogr 59:1688-1701.
  5. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948.

Technical questions: Webmaster, Content questions: Abhinav Kumar
Last modified: Tuesday, 10 September 2013