PROCHECK is a suite of programs to assess the "stereochemical quality" of a given protein structure.

You can obtain the latest online manual or print the local postscript file:

/joule2/programs/procheck30/manual/manual.ps 

To run PROCHECK type: procheck PDBFILENAME resolution(A)

Example:

procheck  pdb1xls.ent  2.0

You can filter residues with more than 3 standard deviations from ideal values with this awk filter:

# file procheck.filter
#  USAGE:
#  unix> awk -f procheck.filter procheck.out > 3sigma.txt
# This script pulls out residues with more than 3 std. from ideal values  
{ if ( NR <= 38 ) print }
$2 ~ /[A-Z][A-Z][A-Z]/ && NF == 19 { prev = $0; rec = NR; next }
( $0 ~ /\*\*\*/ || $0 ~ /\*[1-9]/ ) && NR == rec + 1 { print prev; print $0 }
/Max dev/ { exit }