Hi, If you checked the Ramachandran plot using PROCHECK, you may think almost all residues belong to the most favoured, additional allowed, or generously allowed regions of the Ramachandran plot that is the part 1 of the PROCHECK output PostScript file.
But if you checked the part 2 of the PROCHECK output PostScript file (Ramachandran plot by residue), you may find some unfavourable conformations. You can get the similar results as our validation letter. Please be informed that since August 1, 2007 we do not use PROCHECK values for the definition of the Ramachandran outliers. We define the Ramachandran outliers according to the following reference: GJ Kleywegt and TA Jones (1996). Phi/psi-chology: Ramachandran revisited. Structure 4, 1395 - 1400 As mentioned in the validation report. An additional information is available in the following website: http://xray.bmc.uu.se/gerard/supmat/ramarev.html If you want to check your coordinate before deposition, please use our validation server. http://deposit.pdb.org/validate/ http://pdbdep.protein.osaka-u.ac.jp/validate/ In the validation summary letter that is in the result page of our validation server, many of what we ask to depositors are written. Thanks, MATSUURA Takanori, Ph.D. Annotators' Leader, Group of Primary Annotation, Protein Data Bank Japan (PDBj) Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University 3-2 Yamadaoka, Suita, Osaka 565-0871, JAPAN Tel: +81-6-6879-8634 Fax: +81-6-6879-8636
