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********** REPORT OF PROTEIN ANALYSIS  by the WHAT IF program **********
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WHAT_CHECK is the name of the validation option in WHAT IF. It 
doesn't matter whether you use the WHAT_CHECK program or the
WHAT_CHECK program for validation. Both produce exactly the same
WHAT_CHECK-report.

This document is a WHAT_CHECK-report that holds the findings of 
the WHAT IF program
during the analysis of a PDB-file. Each reported fact has 
an assigned severity, one of:

error  : severe errors encountered during the analyses. Items marked as errors
         are considered severe problems requiring immediate attention.
warning: Either less severe problems or uncommon structural features. These
         still need special attention.
note   : Statistical values, plots, or other verbose results of tests and
         analyses that have been performed.

If alternate conformations are present, only the first is evaluated. Hydrogen 
atoms are only included if explicitly requested, and even then they are not 
used in all checks. The software functions less well for non-canonical amino 
acids and exotic ligands than for the 20 canonical residues and canonical 
nucleic acids.

Some remarks regarding the output:

Residues/atoms in tables are normally given in a few parts:

A number. This is the internal sequence number of the residue used
    by WHAT IF. The first residues in the file get number 1, 2, etc.
The residue type. Normally this is a three letter amino acid type.
The sequence number, between brackets. This is the residue number 
    as it was given in the input file. It can be followed by the insertion
    code.
The chain identifier. A single character. If no chain identifier
    was given in the input file, this will be a minus sign or a blank.
A model number. If no model number exists, like in most X-ray files,
    this will be a blank or occasionally a minus sign.
In case an atom is part of the output, the atom will be listed using 
    the PDB nomenclature for type and identifier.

To indicate the normality of a score, the score
   may be expressed as a Z-value or Z-score. This is just the number
   of standard deviations that the score deviates from the expected
   value.  A property of Z-values is that the root-mean-square of a
   group of Z-values (the RMS Z-value) is expected to be 1.0. Z-values
   above 4.0 and below $-4.0$ are very uncommon. If a Z-score is used
   in WHAT IF, the accompanying text will explain how the expected
   value and standard deviation were obtained.
The names of nucleic acids are DGUA, DTHY, OCYT, OADE, etc. The first
   character is a D or O for DNA or RNA respectively.
   This is done to circumvent ambiguities in the many old PDB files in which
   DNA and RNA were both called A, C, G, and T.



