************************************************************************
********** REPORT OF PROTEIN ANALYSIS  by the WHAT IF program **********
************************************************************************

Date : 2025-04-11
This report was created by WHAT IF version WHATCHECK15.0

This document is a WHAT_CHECK 14.0 report for a PDB-file. Each reported
fact has an assigned severity, one of:

error  : 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 circumvents ambiguities in the
   many old PDB files in which DNA and RNA were both called A, C, G, and T.



=========================================
==== Compound code /zata/tempdir/5lad/wctemf/5lad_final.pdb         ====
=========================================
 
# 1 # Note: Introduction
WHAT CHECK needs to read a PDB file before it can check it. It does a
series of checks upon reading the file. The results of these checks are
reported in this section (section 2.1). The rest of the report will be more
systematic in that section 2.2 reports on administrative problems. Section
2.3 gives descriptive output that is not directly validating things but
more telling you how WHAT CHECK interpreted the input file. Section 2.4
looks at B-factors, occupancies, and the presence/absence of (spurious)
atoms. Section 2.5 deals with nomenclature problems. Section 2.6 deals with
geometric problems like bond lengths and bond angles. Section 2.7 deals with
torsion angle issues. Section 2.8 looks at atomic clashes. Section 2.9 deals
with packing, accessibility, etc, issues. Section 2.10 deals with hydrogen
bonds, ion packing, and other things that can be summarized under the common
name charge-charge interactions. Section 2.11 gives a summary of whole report
and tells you (if applicable) which symmetry matrices were used. Section 2.12
tells the crystallographer which are the things most in need of manual
correction. And the last section, section 2.13, lists all residues sorted
by their need for visual inspection in light of the electron density.
WARNING. Date error on HEADER card:
HEADER                                                        XXXX
 
# 2 # Note: Header records from PDB file
Header records from PDB file.
 
HEADER                                                        XXXX
 
# 3 # Error: Missing unit cell information
No SCALE matrix is given in the PDB file.
 
# 4 # Note: Proposal for corrected SCALE matrix
A corrected SCALE matrix has been derived.
 
Proposed scale matrix
  0.007928  0.000000  0.000000
  0.000000  0.007928  0.000000
  0.000000  0.000000  0.014526
 
# 5 # Warning: Problem detected upon counting molecules and matrices
The parameter Z as given on the CRYST card represents the molecular
multiplicity in the crystallographic cell. Normally, Z equals the number of
matrices of the space group multiplied by the number of NCS relations. The
value of Z is multiplied by the integrated molecular weight of the molecules
in the file to determine the Matthews coefficient. This relation is being
validated in this option. Be aware that the validation can get confused if
both multiple copies of the molecule are present in the ATOM records and
MTRIX records are present in the header of the PDB file.
 
 Space group as read from CRYST card: I 4
 Number of matrices in space group: 8
 Highest polymer chain multiplicity in structure: 1
 Highest polymer chain multiplicity according to SEQRES: 1
 No explicit MTRIX NCS matrices found in the input file
 Value of Z as found on the CRYST1 card: 0
 Z, symmetry, and molecular multiplicity disagree
 Could it be that Z must be: 8
 
# 6 # Error: Matthews Coefficient (Vm) very high
 
The Matthews coefficient [REF] is defined as the density of the protein
structure in cubic Angstroms per Dalton. Normal values are between 1.5
(tightly packed, little room for solvent) and 4.0 (loosely packed, much
space for solvent). Some very loosely packed structures can get values a bit
higher than that.
 
Numbers this high are almost always caused by giving the wrong value for Z
on the CRYST1 card (or not giving this number at all).
 
 Molecular weight of all polymer chains: 40106.156
 Volume of the Unit Cell V= 1095334.0
 Space group multiplicity: 8
 No NCS symmetry matrices (MTRIX records) found in PDB file
 Matthews coefficient for observed atoms and Z is high: Vm= 27.311
 No Matthews coefficient given in REMARK 280
 Could it be that Z must be: 8
 This number is the multiplication of the spacegroup and NCS symmetry count
 Matthews coefficient for observed atoms and corrected Z: Vm= 3.414
 
# 7 # Note: All atoms are sufficiently far away from symmetry axes
None of the atoms in the structure is closer than 0.77 Angstrom to a proper
symmetry axis.
 
# 8 # Note: No strange inter-chain connections detected
No covalent bonds have been detected between molecules with non-identical
chain identifiers.
 
# 9 # Note: No duplicate atom names in ligands
All atom names in ligands (if any) seem adequately unique.
 
# 10 # Note: In all cases the primary alternate atom was used
WHAT CHECK saw no need to make any alternate atom corrections (which means
they either are all correct, or there are none).
 
# 11 # Note: No residues detected inside ligands
Either this structure does not contain ligands with amino acid groups inside
it, or their naming is proper (enough).
 
# 12 # Note: No attached groups interfere with hydrogen bond calculations
It seems there are no sugars, lipids, etc., bound (or very close) to atoms
that otherwise could form hydrogen bonds.
 
# 13 # Note: No probable side chain atoms with zero occupancy detected.
Either there are no side chain atoms with zero occupancy, or the side chain
atoms with zero occupancy were not present in the input PDB file (in which
case they are listed as missing atoms), or their positions are sufficiently
improbable to warrant a zero occupancy.
 
# 14 # Note: No probable backbone atoms with zero occupancy detected.
Either there are no backbone atoms with zero occupancy, or the backbone
atoms with zero occupancy were left out of the input PDB file (in
which case they are listed as missing atoms), or their positions are
sufficiently improbable to warrant a zero occupancy.
 
# 15 # Note: All residues have a complete backbone.
No residues have missing backbone atoms.
 
# 16 # Note: No C-alpha only residues
There are no residues that consist of only an alpha carbon atom.
 
# 17 # Note: Content of the PDB file as interpreted by WHAT CHECK
Content of the PDB file as interpreted by WHAT CHECK.
WHAT CHECK has read your PDB file, and stored it internally in what is called
'the soup'. The content of this soup is listed here. An extensive explanation
of all frequently used WHAT CHECK output formats can be found at
swift.cmbi.ru.nl. Look under output formats. A course on reading this
'Molecules' table is part of the WHAT CHECK website.
 
     1     1 (    1)    22 (   22) A Protein             To check
     2    23 (   23)    96 (   96) B Protein             To check
     3    97 (   97)   123 (  123) C Protein             To check
     4   124 (  124)   268 (  268) D Protein             To check
     5   269 (  269)   359 (  359) E Protein             To check
MODELs skipped upon reading PDB file: 0
X-ray structure. No MODELs found
The total number of amino acids found is 359
of which 324 have poor or (essentially) missing atoms
No nucleic acids observed in input file
No sugars recognized in input file
No water observed in input file
Residue numbers increase monotonously OK
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
 
# 18 # Note: Ramachandran plot
In this Ramachandran plot x-signs represent glycines, squares represent
prolines, and plus-signs represent the other residues. If too many
plus-signs fall outside the contoured areas then the molecule is poorly
refined (or worse). Proline can only occur in the narrow region around
phi=-60 that also falls within the other contour islands.
 
In a colour picture, the residues that are part of a helix are shown in blue,
strand residues in red. Preferred regions for helical residues are drawn in
blue, for strand residues in red, and for all other residues in green. A full
explanation of the Ramachandran plot together with a series of examples can
be found at the WHAT CHECK website [REF].
 
In the TeX file, a plot has been inserted here
 
Chain identifier: A
 
# 19 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 20 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: C
 
# 21 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 22 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: E
 
# 23 # Note: Secondary structure
This is the secondary structure according to DSSP. Only helix (H), overwound
or 3/10-helix (3), strand (S), turn (T) and coil (blank) are shown [REF].
All DSSP related information can be found at swift.cmbi.ru.nl/gv/dssp/
This is not really a structure validation option, but a very scattered
secondary structure (i.e. many strands of only a few residues length, many
Ts inside helices, etc) tends to indicate a poor structure. A full
explanation of the DSSP secondary structure determination program together
with a series of examples can be found at the WHAT CHECK website [REF].
 
Secondary structure assignment
                     10        20
                      |         |
    1 -   22 RRYIVVAGRRNVGKSSFMNALV
(   1)-(  22)
                   30        40        50        60        70        80
                    |         |         |         |         |         |
   23 -   82 VYKSMELYPVGPVTLVDTPGLDDVGELGRLRVEKARRVFYRADCGILVTDSEPTPYEDDV
(  23)-(  82)
                   90
                    |
   83 -   96 VNLFKEMEIPFVVV
(  83)-(  96)
              100       110       120
                |         |         |
   97 -  123 IDVLGEKAEELKGLYESRYEAKVLLVS
(  97)-( 123)
                 130       140       150       160       170       180
                   |         |         |         |         |         |
  124 -  183 GFDDIGKTISEILPGDEEIPYLGDLIDGGDLVILVVPIDLGAPKGRLIMPQVHAIREALD
( 124)-( 183)
                 190       200       210       220       230       240
                   |         |         |         |         |         |
  184 -  243 REAIALVVKERELRYVMENIGMKPKLVITDSQVVMKVASDVPEDVELTTFSIVESRYRGD
( 184)-( 243)
                 250       260
                   |         |
  244 -  268 LAYFVESVRKIEELEDGDTVVIMEG
( 244)-( 268)
            270       280       290       300       310       320
              |         |         |         |         |         |
  269 -  328 TEDIGRVKIPRWLVNHTGAQLNFKVIAGKDFPDLEEIEGAKLIIHCGGCVLNRAAMMRRV
( 269)-( 328)
            330       340       350
              |         |         |
  329 -  359 RMAKRLGIPMTNYGVTISYLHGVLDRAIRPF
( 329)-( 359)
 
 
 
 
# 24 # Note: No rounded coordinates detected
No significant rounding of atom coordinates has been detected.
 
# 25 # Note: No artificial side chains detected
No artificial side-chain positions characterized by chi-1=0.0 or chi-1=180.0
have been detected.
 
# 26 # Note: No missing atoms detected in residues
All expected atoms are present in residues. This validation option has not
looked at 'things' that can or should be attached to the elementary building
blocks (amino acids, nucleotides). Even the C-terminal oxygens are treated
separately.
 
# 27 # Warning: B-factors outside the range 0.0 - 100.0
In principle, B-factors can have a very wide range of values, but in
practice, B-factors should not be zero while B-factors above 100.0
are a good indicator that the location of that atom is meaningless. Be
aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms
with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with
a B-factor of zero were observed.
 
    1 ARG  (   1-) A  -   High
    2 ARG  (   2-) A  -   High
    3 TYR  (   3-) A  -   High
    4 ILE  (   4-) A  -   High
    5 VAL  (   5-) A  -   High
    6 VAL  (   6-) A  -   High
    7 ALA  (   7-) A  -   High
    8 GLY  (   8-) A  -   High
    9 ARG  (   9-) A  -   High
   10 ARG  (  10-) A  -   High
   11 ASN  (  11-) A  -   High
   12 VAL  (  12-) A  -   High
   13 GLY  (  13-) A  -   High
   14 LYS  (  14-) A  -   High
   15 SER  (  15-) A  -   High
And so on for a total of   324 lines.
 
# 28 # Note: C-terminus capping
The residues listed in the table below are either C-terminal or pseudo
C-terminal (i.e. last residue before a missing residue).
In X-ray the coordinates must be located in density. Mobility or disorder
sometimes cause this density to be so poor that the positions of the atoms
cannot be determined. Crystallographers tend to leave out the atoms in such
cases. In many cases the N- or C-terminal residues are too disordered to see.
In case of the N-terminus, you can often see from the residue numbers if
there are missing residues; at the C-terminus this is impossible. Therefore,
often the position of the backbone nitrogen of the first residue missing
at the C-terminal end is calculated and added to indicate that there
are missing residues. As a single N causes validation trouble, we remove
these single-N-residues before doing the validation. If this happened,
the label -N is added to the pseudo C-terminus. Other labels can be +X
in case something weird is bound to the backbone C, or +OXT if a spurious
OXT atom is found. -OXT indicates that an expected OXT is missing. 'Swap'
means that the O' and O'' (O and OXT in PDB files) have been swapped in
terms of nomenclature. 'Bad' means that something bad happened that WHAT IF
does not understand. In such cases you might get three residue numbers in
square brackets; one of those might be what WHAT IF had expected to find,
but then it also might not). In case of chain breaks the number of missing
residues is listen in round brackets. OK means what it suggests...
 
Be aware that we cannot easily see the difference between these errors and
errors in the chain and residue numbering schemes. So do not blindly trust
the table below. If you get weird errors at, or near, the left-over
incomplete C-terminal residue, please check by hand if a missing Oxt or
a removed single N is the cause. Also, many peptidic ligands get the same
chain identifier as the larger protein they are bound to. In such cases there
are more than one C-termini and OXTs with the same ID. WHAT IF gives some
random warnings about these cases. So, don't take everything at face value,
but think for yourself.
 
   22 VAL  (  22-) A  -        -OXT
   96 VAL  (  96-) B  -        OK
  123 SER  ( 123-) C  -        OK
  268 GLY  ( 268-) D  -        OK
  359 PHE  ( 359-) E  -        OK
 
# 29 # Note: Weights administratively correct
All atomic occupancy factors ('weights') fall in the 0.0--1.0 range, which
makes them administratively correct.
 
# 30 # Note: Normal distribution of occupancy values
 
The distribution of the occupancy values in this file seems 'normal'.
 
Be aware that this evaluation is merely the result of comparing this file
with about 500 well-refined high-resolution files in the PDB. If this file
has much higher or much lower resolution than the PDB files used
in WHAT CHECK's training set, non-normal values might very well be perfectly
fine, or normal values might actually be not so normal. So, this check is
actually more an indicator and certainly not a check in which I have great
confidence.
 
# 31 # Note: All occupancies seem to add up to 0.0 - 1.0.
In principle, the occupancy of all alternates of one atom should add up till
0.0 - 1.0. 0.0 is used for the missing atom (i.e. an atom not seen in the
electron density). Obviously, there is nothing terribly wrong when a few
occupancies add up to a bit more than 1.0, because the mathematics of
refinement allow for that. However, if it happens often, it seems worth
evaluating this in light of the refinement protocol used.
 
# 32 # Warning: What type of B-factor?
WHAT CHECK does not yet know well how to cope with B-factors in case TLS has
been used. It simply assumes that the B-factor listed on the ATOM and HETATM
cards are the total B-factors. When TLS refinement is used that assumption
sometimes is not correct. The header of the PDB file states that TLS groups
were used. So, if WHAT CHECK complains about your  B-factors, while you think
that they are OK, then check for TLS related B-factor problems first.
 
Number of TLS groups mentione in PDB file header: 1
 
Temperature not mentioned in PDB file. This most likely means
that the temperature record is absent.
Room temperature assumed
 
# 33 # Note: Number of buried atoms with low B-factor is OK
For protein structures determined at room temperature, no more than about 1
percent of the B factors of buried atoms is below 5.0. In liquid
nitrogen this percentage is allowed to be higher, of course.
 
Percentage of buried atoms with B less than 5 :   0.00
 
# 34 # Note: B-factor distribution normal
The distribution of B-factors within residues is within expected ranges.
A value over 1.5 here would mean that the B-factors show signs of
over-refinement.
 
RMS Z-score :  0.761 over     442 bonds
Average difference in B over a bond :    2.88
RMS difference in B over a bond :    3.72
 
# 35 # Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
number.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: A
 
# 36 # Note: B-factor plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 37 # Note: B-factor plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: C
 
# 38 # Note: B-factor plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 39 # Note: B-factor plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: E
 
# 40 # Note: Introduction to the nomenclature section.
Nomenclature problems seem, at first, rather unimportant. After all who
cares if we call the delta atoms in leucine delta2 and delta1 rather than
the other way around. Chemically speaking that is correct. But structures
have not been solved and deposited just for chemists to look at them. Most
times a structure is used, it is by software in a bioinformatics lab. And
if they compare structures in which the one used C delta1 and delta2 and the
other uses C delta2 and delta1, then that comparison will fail. Also, we
recalculate all structures every so many years to make sure that everybody
always can get access to the best coordinates that can be obtained from
the (your?) experimental data. These recalculations will be troublesome if
there are nomenclature problems.
 
Several nomenclature problems actually are worse than that. At the
WHAT CHECK website [REF] you can get an overview of the importance of all
nomenclature problems that we list.
 
# 41 # Note: Valine nomenclature OK
No errors were detected in valine nomenclature.
 
# 42 # Note: Threonine nomenclature OK
No errors were detected in threonine nomenclature.
 
# 43 # Note: Isoleucine nomenclature OK
No errors were detected in isoleucine nomenclature.
 
# 44 # Note: Leucine nomenclature OK
No errors were detected in leucine nomenclature.
 
# 45 # Note: Arginine nomenclature OK
No errors were detected in arginine nomenclature.
 
# 46 # Note: Tyrosine torsion conventions OK
No errors were detected in tyrosine torsion angle conventions.
 
# 47 # Note: Phenylalanine torsion conventions OK
No errors were detected in phenylalanine torsion angle conventions.
 
# 48 # Note: Aspartic acid torsion conventions OK
No errors were detected in aspartic acid torsion angle conventions.
 
# 49 # Note: Glutamic acid torsion conventions OK
No errors were detected in glutamic acid torsion angle conventions.
 
# 50 # Note: Phosphate group names OK in DNA/RNA
No errors were detected in nucleic acid phosphate group naming conventions
(or this structure contains no nucleic acids).
 
# 51 # Note: Heavy atom naming OK
No errors were detected in the atom names for non-hydrogen atoms. Please
be aware that the PDB wants us to deliberately make some nomenclature errors;
especially in non-canonical amino acids.
 
# 52 # Note: No decreasing residue numbers
All residue numbers are strictly increasing within each chain.
 
# 53 # Warning: Unusual bond lengths
The bond lengths listed in the table below were found to deviate more than 4
sigma from standard bond lengths (both standard values and sigmas for amino
acid residues have been taken from Engh and Huber [REF], for DNA they were
taken from Parkinson et al [REF]). In the table below for each unusual bond
the bond length and the number of standard deviations it differs from the
normal value is given.
 
Atom names starting with "-" belong to the previous residue in the chain. If
the second atom name is "-SG*", the disulphide bridge has a deviating length.
 
    4 ILE  (   4-) A  -    CG1  CD1   1.30   -5.4
   68 ILE  (  68-) B  -    CG1  CD1   1.09  -10.7
  235 ILE  ( 235-) D  -    CG1  CD1   1.34   -4.4
  277 ILE  ( 277-) E  -    CG1  CD1   1.32   -4.9
  312 ILE  ( 312-) E  -    CG1  CD1   1.35   -4.2
 
# 54 # Note: Normal bond length variability
Bond lengths were found to deviate normally from the standard bond lengths
(values for Protein residues were taken from Engh and Huber [REF], for
DNA/RNA from Parkinson et al [REF]).
 
 RMS Z-score for bond lengths: 0.584
 RMS-deviation in bond distances: 0.016
 
# 55 # Note: No bond length directionality
Comparison of bond distances with Engh and Huber [REF] standard values for
protein residues and Parkinson et al [REF] values for DNA/RNA does not show
significant systematic deviations.
 
# 56 # Warning: Unusual bond angles
The bond angles listed in the table below were found to deviate more than 4
sigma from standard bond angles (both standard values and sigma for protein
residues have been taken from Engh and Huber [REF], for DNA/RNA from
Parkinson et al [REF]). In the table below for each strange angle the bond
angle and the number of standard deviations it differs from the standard
values is given. Please note that disulphide bridges are neglected. Atoms
starting with "-" belong to the previous residue in the sequence.
 
    5 VAL  (   5-) A  -    N    CA   CB  119.45    5.3
   32 VAL  (  32-) B  -    C    CA   CB  119.33    4.9
   38 VAL  (  38-) B  -    C    CA   CB  118.71    4.5
   44 ASP  (  44-) B  -    CA   CB   CG  117.80    5.2
   80 ASP  (  80-) B  -    CA   CB   CG  116.74    4.1
   81 ASP  (  81-) B  -    CA   CB   CG  117.51    4.9
   98 ASP  (  98-) C  -    CA   CB   CG  120.06    7.5
  125 PHE  ( 125-) D  -    CA   CB   CG  121.36    7.6
  149 ILE  ( 149-) D  -    N    CA   CB  117.98    4.4
  158 VAL  ( 158-) D  -    N    CA   C    99.11   -4.3
  223 ASP  ( 223-) D  -    CA   CB   CG  118.27    5.7
  232 THR  ( 232-) D  -    C    CA   CB  118.02    4.2
  271 ASP  ( 271-) E  -    CA   CB   CG  117.31    4.7
  353 ASP  ( 353-) E  -    CA   CB   CG  118.12    5.5
 
# 57 # Note: Normal bond angle variability
Bond angles were found to deviate normally from the mean standard bond angles
(normal values for protein residues were taken from Engh and Huber [REF], for
DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected
to be near 1.0 for a normally restrained data set, and this is indeed
observed for very high resolution X-ray structures.
 
 RMS Z-score for bond angles: 0.929
 RMS-deviation in bond angles: 1.772
 
# 58 # Note: Residue hand check OK
No atoms are observed that have the wrong handedness. Be aware, though, that
WHAT CHECK might have corrected the handedness of some atoms already. The
handedness has not been corrected for any case where the problem is worse
than just an administrative discomfort.
 
# 59 # Warning: Chirality deviations detected
The atoms listed in the table below have an improper dihedral value
that is deviating from expected values. As the improper dihedral values
are all getting very close to ideal values in recent X-ray structures,
and as we actually do not know how big the spread around these values
should be, this check only warns for 6 sigma deviations.
 
Improper dihedrals are a measure of the chirality/planarity of the structure
at a specific atom. Values around -35 or +35 are expected for chiral atoms,
and values around 0 for planar atoms. Planar side chains are left out of the
calculations, these are better handled by the planarity checks.
 
Three numbers are given for each atom in the table. The first is the Z-score
for the improper dihedral. The second number is the measured improper
dihedral. The third number is the expected value for this atom type. A final
column contains an extra warning if the chirality for an atom is opposite
to the expected value.
 
    5 VAL  (   5-) A  -    CA   -39.1   -21.39    33.31 Wrong hand
   32 VAL  (  32-) B  -    CA   -37.8   -19.65    33.31 Wrong hand
   38 VAL  (  38-) B  -    CA   -33.9   -14.12    33.31 Wrong hand
  235 ILE  ( 235-) D  -    CA   -36.8   -23.86    33.22 Wrong hand
The average deviation= 0.899
 
# 60 # Note: Improper dihedral angle distribution OK
The RMS Z-score for all improper dihedrals in the structure is within normal
ranges.
 
 Improper dihedral RMS Z-score : 0.791
 
# 61 # Error: Tau angle problems
The side chains of the residues listed in the table below contain a tau
angle (N-C-alpha-C) that was found to deviate from te expected value by
more than 4.0 times the expected standard deviation. The number in the
table is the number of standard deviations this value deviates from
the expected value.
 
  158 VAL  ( 158-) D  -   4.22
 
# 62 # Note: Normal tau angle deviations
The RMS Z-score for the tau angles (N-C-alpha-C) in the structure falls
within the normal range that we guess to be 0.5 - 1.5. Be aware, we
determined the tau normal distributions from 500 high-resolution X-ray
structures, rather than from CSD data, so we cannot be 100 percent certain
about these numbers.
 
 Tau angle RMS Z-score : 1.106
 
# 63 # Error: Side chain planarity problems
The side chains of the residues listed in the table below contain a planar
group that was found to deviate from planarity by more than 4.0 times the
expected value. For an amino acid residue that has a side chain with a
planar group, the RMS deviation of the atoms to a least squares plane was
determined. The number in the table is the number of standard deviations
this RMS value deviates from the expected value. Not knowing better yet, we
assume that planarity of the groups analyzed should be perfect.
 
  354 ARG  ( 354-) E  -   5.64
  239 ARG  ( 239-) D  -   4.69
 
# 64 # Note: Atoms connected to aromatic rings OK
All of the atoms that are connected to planar aromatic rings in side chains
of amino-acid residues are in the plane within expected RMS deviations.
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 
# 65 # Error: Ramachandran Z-score very low
The score expressing how well the backbone conformations of all residues
correspond to the known allowed areas in the Ramachandran plot is very low.
 
 Ramachandran Z-score : -6.063
 
# 66 # Note: Ramachandran check
The list contains per-residue Z-scores describing how well each residue
fits into the allowed areas of the Ramachandran plot will not be printed
because WHAT CHECK found no reason to cry.
 
# 67 # Warning: Torsion angle evaluation shows unusual residues
The residues listed in the table below contain bad or abnormal
torsion angles.
 
These scores give an impression of how `normal' the torsion angles in
protein residues are. All torsion angles except omega are used for
calculating a `normality' score. Average values and standard deviations were
obtained from the residues in the WHAT CHECK database. These are used to
calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a
score of less than -3.0 is worrying. For such residues more than one torsion
angle is in a highly unlikely position.
 
   21 LEU  (  21-) A  -   -2.8
  318 VAL  ( 318-) E  -   -2.7
  160 PRO  ( 160-) D  -   -2.7
  232 THR  ( 232-) D  -   -2.6
  356 ILE  ( 356-) E  -   -2.6
  135 ILE  ( 135-) D  -   -2.5
  235 ILE  ( 235-) D  -   -2.5
  203 ILE  ( 203-) D  -   -2.5
  275 VAL  ( 275-) E  -   -2.5
  315 GLY  ( 315-) E  -   -2.4
  339 THR  ( 339-) E  -   -2.4
  270 GLU  ( 270-) E  -   -2.4
   76 THR  (  76-) B  -   -2.4
  128 ILE  ( 128-) D  -   -2.4
  100 LEU  ( 100-) C  -   -2.3
And so on for a total of    35 lines.
 
# 68 # Warning: Backbone evaluation reveals unusual conformations
The residues listed in the table below have abnormal backbone torsion
angles.
 
Residues with `forbidden' phi-psi combinations are listed, as well as
residues with unusual omega angles (deviating by more than 3 sigma from the
normal value). Please note that it is normal if about 5 percent of the
residues is listed here as having unusual phi-psi combinations.
 
    8 GLY  (   8-) A  - Poor phi/psi
    9 ARG  (   9-) A  - omega poor
   11 ASN  (  11-) A  - Poor phi/psi, omega poor
   12 VAL  (  12-) A  - omega poor
   13 GLY  (  13-) A  - Poor phi/psi
   18 MET  (  18-) A  - omega poor
   20 ALA  (  20-) A  - Poor phi/psi
   26 SER  (  26-) B  - omega poor
   30 TYR  (  30-) B  - Omega to (next) Pro poor
   33 GLY  (  33-) B  - Poor phi/psi, omega to (next)
   40 THR  (  40-) B  - Omega to (next) Pro poor
   47 GLY  (  47-) B  - Poor phi/psi
   50 GLY  (  50-) B  - Poor phi/psi
   63 ARG  (  63-) B  - omega poor
   73 SER  (  73-) B  - omega poor
And so on for a total of    74 lines.
 
# 69 # Error: Chi-1/chi-2 rotamer problems
List of residues with a poor chi-1/chi-2 combination. Be aware that for this
validation option the individual scores are far less important than the
overall score that is given below the table.
 
   21 LEU  (  21-) A  -    -1.32
   29 LEU  (  29-) B  -    -1.32
   37 LEU  (  37-) B  -    -1.32
   52 LEU  (  52-) B  -    -1.32
  100 LEU  ( 100-) C  -    -1.32
  120 LEU  ( 120-) C  -    -1.32
  136 LEU  ( 136-) D  -    -1.32
  148 LEU  ( 148-) D  -    -1.32
  157 LEU  ( 157-) D  -    -1.32
  163 LEU  ( 163-) D  -    -1.31
  189 LEU  ( 189-) D  -    -1.31
  230 LEU  ( 230-) D  -    -1.31
  319 LEU  ( 319-) E  -    -1.32
    4 ILE  (   4-) A  -    -1.25
   68 ILE  (  68-) B  -    -1.25
And so on for a total of   220 lines.
 
# 70 # Error: chi-1/chi-2 angle correlation Z-score very low
The score expressing how well the chi-1/chi-2 angles of all residues
correspond to the populated areas in the database is
very low.
 
 chi-1/chi-2 correlation Z-score : -7.742
 
# 71 # Warning: Unusual rotamers
The residues listed in the table below have a rotamer that is not seen very
often in the database of solved protein structures. This option determines
for every residue the position specific chi-1 rotamer distribution.
Thereafter it verified whether the actual residue in the molecule has the
most preferred rotamer or not. If the actual rotamer is the preferred one,
the score is 1.0. If the actual rotamer is unique, the score is 0.0. If
there are two preferred rotamers, with a population distribution of 3:2 and
your rotamer sits in the lesser populated rotamer, the score will be 0.667.
No value will be given if insufficient hits are found in the database.
 
It is not necessarily an error if a few residues have rotamer values below
0.3, but careful inspection of all residues with these low values could be
worth it.
 
   15 SER  (  15-) A  -   0.36
   16 SER  (  16-) A  -   0.38
  346 SER  ( 346-) E  -   0.38
   94 VAL  (  94-) B  -   0.39
 
# 72 # Warning: Unusual backbone conformations
For the residues listed in the table below, the backbone formed by itself and
two neighbouring residues on either side is in a conformation that is not
seen very often in the database of solved protein structures. The number
given in the table is the number of similar backbone conformations in the
database with the same amino acid in the centre.
 
For this check, backbone conformations are compared with database structures
using C-alpha superpositions with some restraints on the backbone oxygen
positions.
 
A residue mentioned in the table can be part of a strange loop, or there
might be something wrong with it or its directly surrounding residues. There
are a few of these in every protein, but in any case it is worth looking at,
especially if a regular DSSP secondary structure (H or S for helix or strand,
respectively) is indicated!
 
    5 VAL  (   5-) A  -       0
   11 ASN  (  11-) A  -       0
   12 VAL  (  12-) A  -       0
   19 ASN  (  19-) A  -       0
   32 VAL  (  32-) B  -       0
   38 VAL  (  38-) B  -       0
  100 LEU  ( 100-) C  -       0
  102 GLU  ( 102-) C  -       0
  139 ASP  ( 139-) D  -       0
  148 LEU  ( 148-) D  -       0
  161 ILE  ( 161-) D  -       0
  162 ASP  ( 162-) D  -       0
  203 ILE  ( 203-) D  -       0
  222 SER  ( 222-) D  -       0
  223 ASP  ( 223-) D  -       0
  235 ILE  ( 235-) D  -       0
  297 LYS  ( 297-) E  -       0
  317 CYS  ( 317-) E  -       0
  318 VAL  ( 318-) E  -       0
  356 ILE  ( 356-) E  -       0
   10 ARG  (  10-) A  -       1
  145 LEU  ( 145-) D  -       1
  296 GLY  ( 296-) E  -       1
  355 ALA  ( 355-) E  -       1
  140 GLU  ( 140-) D  -       2
 
# 73 # Note: Backbone conformation Z-score OK
The backbone conformation analysis gives a score that is normal for well
refined protein structures.
 
 Backbone conformation Z-score : -1.225
 
# 74 # Warning: Omega angle restraints not strong enough
The omega angles for trans-peptide bonds in a structure is expected to give
a gaussian distribution with the average around +178 degrees, and a standard
deviation around 5.5. In the current structure the standard deviation of
this distribution is above 7.0, which indicates that the omega values have
been under-restrained.
 
Omega average and std. deviation= 178.900 9.737
 
# 75 # Warning: Unusual PRO puckering amplitudes
The proline residues listed in the table below have a puckering amplitude
that is outside of normal ranges. Puckering parameters were calculated by
the method of Cremer and Pople [REF]. Normal PRO rings have a puckering
amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom
for a PRO residue, this could indicate disorder between the two different
normal ring forms (with C-gamma below and above the ring, respectively). If
Q is higher than 0.45 Angstrom something could have gone wrong during the
refinement. Be aware that this is a warning with a low confidence level. See:
Who checks the checkers? Four validation tools applied to eight atomic
resolution structures [REF]
 
  337 PRO  ( 337-) E  -   0.19 LOW
 
# 76 # Warning: Unusual PRO puckering phases
The proline residues listed in the table below have a puckering phase that is
not expected to occur in protein structures. Puckering parameters were
calculated by the method of Cremer and Pople [REF]. Normal PRO rings
approximately show a so-called envelope conformation with the C-gamma atom
above the plane of the ring (phi=+72 degrees), or a half-chair conformation
with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees).
If phi deviates strongly from these values, this is indicative of a very
strange conformation for a PRO residue, and definitely requires a manual
check of the data. Be aware that this is a warning with a low confidence
level. See: Who checks the checkers? Four validation tools applied to eight
atomic resolution structures [REF].
 
   31 PRO  (  31-) B  -   46.5 half-chair C-delta/C-gamma (54 degrees)
  160 PRO  ( 160-) D  -  -61.8 half-chair C-beta/C-alpha (-54 degrees)
  278 PRO  ( 278-) E  -  115.2 envelop C-beta (108 degrees)
 
# 77 # Warning: Backbone oxygen evaluation
The residues listed in the table below have an unusual backbone oxygen
position.
 
For each of the residues in the structure, a search was performed to find
5-residue stretches in the WHAT CHECK database with superposable C-alpha
coordinates, and some restraints on the neighbouring backbone oxygens.
 
In the following table the RMS distance between the backbone oxygen positions
of these matching structures in the database and the position of the backbone
oxygen atom in the current residue is given. If this number is larger than
1.5 a significant number of structures in the database show an alternative
position for the backbone oxygen. If the number is larger than 2.0 most
matching backbone fragments in the database have the peptide plane flipped.
A manual check needs to be performed to assess whether the experimental data
can support that alternative as well. The number in the last column is the
number of database hits (maximum 80) used in the calculation. It is "normal"
that some glycine residues show up in this list, but they are still worth
checking!
 
  152 GLY  ( 152-) D  -  2.83   40
  241 ARG  ( 241-) D  -  2.24   27
  350 GLY  ( 350-) E  -  1.66   80
  225 PRO  ( 225-) D  -  1.57   32
 
# 78 # Warning: Possible peptide flips
For the residues listed in the table below, the backbone formed by the
residue mentioned and the one N-terminal of it show systematic deviations
from normality that are consistent with a peptide flip. This can either
be a 180 degree flip of the entire peptide plane or a trans to cis flip.
(Cis to trans flips cannot be detected yet). The type can be TT+, TC-,
or TC+:
TT+ indicates a 180 degree flip of the entire peptide plane.
TC- indicates a trans to cis conversion that requires a flip of the N atom.
TC+ indicates a trans to cis conversion that requires a flip of the O atom.
Note that the method will only work correctly for PDB files with full
isotropic B-factors.
 
   53 ARG  (  53-) B  - TT+   Likely
  115 TYR  ( 115-) C  - TT+   Likely
  153 ASP  ( 153-) D  - TT+   Likely
  185 GLU  ( 185-) D  - TT+   Likely
  223 ASP  ( 223-) D  - TT+   Likely
  243 ASP  ( 243-) D  - TT+   Likely
  297 LYS  ( 297-) E  - TT+   Likely
  334 LEU  ( 334-) E  - TT+   Likely
  349 HIS  ( 349-) E  - TT+   Likely
 
# 79 # Error: Abnormally short interatomic distances
The pairs of atoms listed in the table below have an unusually short
interactomic distance; each bump is listed in only one direction.
 
The contact distances of all atom pairs have been checked. Two atoms are
said to `bump' if they are closer than the sum of their Van der Waals radii
minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom
is used. The first number in the table tells you how much shorter that
specific contact is than the acceptable limit. The second distance is the
distance between the centres of the two atoms. Although we believe that two
water atoms at 2.4 A distance are too close, we only report water pairs that
are closer than this rather short distance.
 
INTRA and INTER indicate whether the clashes are between atoms in the same
asymmetric unit, or atoms in symmetry related asymmetric units, respectively.
The last text-item on each line represents the status of the atom pair. If
the final column contains the text 'HB', the bump criterion was relaxed
because there could be a hydrogen bond. Similarly relaxed criteria are used
for 1--3 and 1--4 interactions (listed as 'B2' and 'B3', respectively).
If the last column is 'BF', the sum of the B-factors of the atoms is higher
than 80, which makes the appearance of the bump somewhat less severe because
the atoms probably are not there anyway. BL, on the other hand, indicates
that the bumping atoms both have a low B-factor, and that makes the bumps
more worrisome.
 
Bumps between atoms for which the sum of their occupancies is lower than one
are not reported. If the MODEL number does not exist (as is the case in most
X-ray files), a minus sign is printed instead.
 
  222 SER  ( 222-) D  -    O   <-->   224 VAL  ( 224-) D  -    N      0.51    2.19  INTRA BL
    6 VAL  (   6-) A  -    CA  <-->    68 ILE  (  68-) B  -    CD1    0.45    2.75  INTRA BF
  233 PHE  ( 233-) D  -    CE1 <-->   235 ILE  ( 235-) D  -    CA     0.45    2.75  INTRA BF
  112 GLU  ( 112-) C  -    CD  <-->   118 LYS  ( 118-) C  -    NZ     0.44    2.66  INTRA BF
  235 ILE  ( 235-) D  -    CD1 <-->   238 SER  ( 238-) D  -    N      0.38    2.72  INTRA BF
  351 VAL  ( 351-) E  -    O   <-->   354 ARG  ( 354-) E  -    CD     0.36    2.44  INTRA BF
  107 LEU  ( 107-) C  -    O   <-->   110 LEU  ( 110-) C  -    N      0.33    2.37  INTRA BL
  112 GLU  ( 112-) C  -    CD  <-->   118 LYS  ( 118-) C  -    CE     0.33    2.87  INTRA BF
  239 ARG  ( 239-) D  -    CD  <-->   340 ASN  ( 340-) E  -    ND2    0.33    2.77  INTRA BF
  161 ILE  ( 161-) D  -    O   <-->   162 ASP  ( 162-) D  -    CG     0.33    2.37  INTRA BF
   24 TYR  (  24-) B  -    CD2 <-->    38 VAL  (  38-) B  -    CG2    0.32    2.88  INTRA BF
  233 PHE  ( 233-) D  -    C   <-->   237 GLU  ( 237-) D  -    OE2    0.30    2.50  INTRA BF
  235 ILE  ( 235-) D  -    CD1 <-->   239 ARG  ( 239-) D  -    N      0.30    2.80  INTRA BF
  107 LEU  ( 107-) C  -    O   <-->   108 LYS  ( 108-) C  -    C      0.30    2.30  INTRA BL
  235 ILE  ( 235-) D  -    CD1 <-->   238 SER  ( 238-) D  -    CA     0.29    2.91  INTRA BF
And so on for a total of   130 lines.
 
# 80 # Note: Some notes regarding these bumps
The bumps have been binned in 5 categories ranging from 'please look at'
till 'must fix'. Additionally, the integrated sum of all bumps, the squared
sum of all bumps, and these latter two values normalized by the number of
contacts are listed too for comparison purposes between, for example, small
and large proteins.
 
Total bump value: 17.915
Total bump value per residue: 0.362
Total number of bumps: 130
Total squared bump value: 4.008
Total number of bumps in the mildest bin: 110
Total number of bumps in the second bin: 19
Total number of bumps in the middle bin: 1
Total number of bumps in the fourth bin: 0
Total number of bumps in the worst bin: 0
 
# 81 # Note: Inside/outside distribution check
The following list contains per-residue Z-scores describing how well the
residue's observed accessibility fits the expected one. A positive Z-score
indicates "more exposure than usual", whereas a negative Z-score means
"more buried than usual". The absolute value of the Z-score must be used to
judge the quality. Today WHAT CHECK saw no reason to complain.
 
# 82 # Note: Inside/Outside residue distribution normal
The distribution of residue types over the inside and the outside of the
protein is normal.
 
inside/outside RMS Z-score : 1.070
 
# 83 # Note: Inside/Outside RMS Z-score plot
The Inside/Outside distribution normality RMS Z-score over a 15 residue
window is plotted as function of the residue number. High areas in the plot
(above 1.5) indicate unusual inside/outside patterns.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: A
 
# 84 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 85 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: C
 
# 86 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 87 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: E
 
# 88 # Warning: Abnormal packing environment for some residues
The residues listed in the table below have an unusual packing environment.
 
The packing environment of the residues is compared with the average packing
environment for all residues of the same type in good PDB files. A low
packing score can indicate one of several things: Poor packing, misthreading
of the sequence through the density, crystal contacts, contacts with a
co-factor, or the residue is part of the active site. It is not uncommon to
see a few of these, but in any case this requires further inspection of the
residue.
 
   30 TYR  (  30-) B  -  -7.09
  169 ARG  ( 169-) D  -  -6.82
  205 MET  ( 205-) D  -  -6.19
  357 ARG  ( 357-) E  -  -6.04
  297 LYS  ( 297-) E  -  -6.03
  144 TYR  ( 144-) D  -  -6.03
  115 TYR  ( 115-) C  -  -5.98
  148 LEU  ( 148-) D  -  -5.66
   49 LEU  (  49-) B  -  -5.40
  274 ARG  ( 274-) E  -  -5.22
  241 ARG  ( 241-) D  -  -5.20
  122 VAL  ( 122-) C  -  -5.13
  215 GLN  ( 215-) D  -  -5.09
   10 ARG  (  10-) A  -  -5.05
 
# 89 # Warning: Abnormal packing environment for sequential residues
A stretch of at least three sequential residues with a questionable packing
environment was found. This could indicate that these residues are part
of a strange loop. It might also be an indication of misthreading in the
density. However, it can also indicate that one or more residues in this
stretch have other problems such as, for example, missing atoms, very
weird angles or bond lengths, etc.
 
The table below lists the first and last residue in each stretch found,
as well as the average residue score of the series.
 
    9 ARG  (   9-) A  -       12 --- VAL    12- (A ) -       -4.62
  297 LYS  ( 297-) E  -      299 --- PHE   299- (E ) -       -5.03
 
# 90 # Note: Structural average packing environment OK
The structural average packing score is within normal ranges.
 
 
Average for range     1 -  359 :  -0.907
 
# 91 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as function
of the residue number. Low areas in the plot (below -2.0) indicate unusual
packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: A
 
# 92 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as function
of the residue number. Low areas in the plot (below -2.0) indicate unusual
packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 93 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as function
of the residue number. Low areas in the plot (below -2.0) indicate unusual
packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: C
 
# 94 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as function
of the residue number. Low areas in the plot (below -2.0) indicate unusual
packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 95 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as function
of the residue number. Low areas in the plot (below -2.0) indicate unusual
packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: E
 
# 96 # Warning: Low packing Z-score for some residues
The residues listed in the table below have an unusual packing
environment according to the 2nd generation packing check. The score
listed in the table is a packing normality Z-score: positive means
better than average, negative means worse than average. Only residues
scoring less than -2.50 are listed here. These are the unusual
residues in the structure, so it will be interesting to take a
special look at them.
 
   10 ARG  (  10-) A  -  -2.79
 
# 97 # Note: No series of residues with abnormal new packing environment
There are no stretches of four or more residues each having a packing
Z-score worse than -1.75.
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
 
# 98 # Note: Second generation quality Z-score plot
The second generation quality Z-score smoothed over a 10 residue window
is plotted as function of the residue number. Low areas in the plot (below
-1.3) indicate unusual packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: A
 
# 99 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 100 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: C
 
# 101 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 102 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: E
 
# 103 # Warning: No crystallisation information
No, or very inadequate, crystallisation information was observed upon
reading the PDB file header records. This information should be available
in the form of a series of REMARK 280 lines. Without this information a
few things, such as checking ions in the structure, cannot be performed
optimally.
 
# 104 # Note: His, Asn, Gln side chains OK
All of the side chain conformations of Histidine, Asparagine and Glutamine
residues were found to be optimal for hydrogen bonding.
 
# 105 # Note: Histidine type assignments
For all complete HIS residues in the structure a tentative assignment to
HIS-D (protonated on ND1), HIS-E (protonated on NE2), or HIS-H (protonated
on both ND1 and NE2, positively charged) is made based on the hydrogen bond
network. A second assignment is made based on which of the Engh and Huber
[REF] histidine geometries fits best to the structure.
 
In the table below all normal histidine residues are listed. The assignment
based on the geometry of the residue is listed first, together with the RMS
Z-score for the fit to the Engh and Huber parameters. For all residues where
the H-bond assignment is different, the assignment is listed in the last
columns, together with its RMS Z-score to the Engh and Huber parameters.
 
As always, the RMS Z-scores should be close to 1.0 if the residues were
restrained to the Engh and Huber parameters during refinement, and if
enough (high resolution) data is available.
 
Please note that because the differences between the geometries of the
different types are small it is possible that the geometric assignment given
here does not correspond to the type used in refinement. This is especially
true if the RMS Z-scores are much higher than 1.0.
 
If the two assignments differ, or the `geometry' RMS Z-score is high, it is
advisable to verify the hydrogen bond assignment, check the HIS type used
during the refinement and possibly adjust it.
 
  176 HIS  ( 176-) D  -   HIS-E   0.61
  284 HIS  ( 284-) E  -   HIS-E   0.40
  313 HIS  ( 313-) E  -   HIS-E   0.52 HIS-D   0.86
  349 HIS  ( 349-) E  -   HIS-E   0.58
 
# 106 # Warning: Buried unsatisfied hydrogen bond donors
The buried hydrogen bond donors listed in the table below have a hydrogen
atom that is not involved in a hydrogen bond in the optimized hydrogen bond
network.
 
Hydrogen bond donors that are buried inside the protein normally use all of
their hydrogens to form hydrogen bonds within the protein. If there are any
non hydrogen bonded buried hydrogen bond donors in the structure they will
be listed here. In very good structures the number of listed atoms will tend
to zero.
 
Waters are not listed by this option.
 
    1 ARG  (   1-) A  -    NE
    8 GLY  (   8-) A  -    N
    9 ARG  (   9-) A  -    N
    9 ARG  (   9-) A  -    NH1
   10 ARG  (  10-) A  -    N
   10 ARG  (  10-) A  -    NE
   10 ARG  (  10-) A  -    NH2
   11 ASN  (  11-) A  -    N
   30 TYR  (  30-) B  -    N
   40 THR  (  40-) B  -    N
   53 ARG  (  53-) B  -    N
   63 ARG  (  63-) B  -    N
   98 ASP  (  98-) C  -    N
  114 ARG  ( 114-) C  -    NE
  116 GLU  ( 116-) C  -    N
And so on for a total of    39 lines.
 
# 107 # Warning: Buried unsatisfied hydrogen bond acceptors
The buried side-chain hydrogen bond acceptors listed in the table below are
not involved in a hydrogen bond in the optimized hydrogen bond network.
 
Side-chain hydrogen bond acceptors buried inside the protein normally form
hydrogen bonds within the protein. If there are any not hydrogen bonded in
the optimized hydrogen bond network they will be listed here.
 
Waters are not listed by this option.
 
   39 ASP  (  39-) B  -    OD1
   79 GLU  (  79-) B  -    OE2
  140 GLU  ( 140-) D  -    OE1
  150 ASP  ( 150-) D  -    OD1
  150 ASP  ( 150-) D  -    OD2
  174 GLN  ( 174-) D  -    OE1
  229 GLU  ( 229-) D  -    OE1
  237 GLU  ( 237-) D  -    OE1
  237 GLU  ( 237-) D  -    OE2
 
# 108 # Note: Some notes regarding these donors and acceptors
The donors and acceptors have been counted, also as function of their
accessibility. The buried donors and acceptors have been binned in five
categories ranging from not forming any hydrogen bond till forming a poor
till perfect hydrogen bond. Obviously, the buried donors and acceptors
with no or just a poor hydrogen bond should be a topic of concern. As every
protein contains more acceptors than donors, unsatisfied donors are more in
need of attention than unsatisfied acceptors.
 
Total number of donors: 497
- of which buried: 241
Total number of acceptors: 544
- of which buried: 203
Total number of donor+acceptors: 39
  (e.g. the Ser Ogamma that can donate and accept)
- of which buried: 10
Buried donors: 241
- without H-bond: 39
- essentially without H-bond: 0
- with only a very poor H-bond: 5
- with a poor H-bond: 2
- with a H-bond: 195
Buried acceptors: 203
- without H-bond: 42
- essentially without H-bond: 0
- with only a very poor H-bond: 0
- with a poor H-bond: 7
- with a H-bond: 154
 
# 109 # Note: Content of the PDB file as interpreted by WHAT CHECK
Content of the PDB file as interpreted by WHAT CHECK.
WHAT CHECK has read your PDB file, and stored it internally in what is called
'the soup'. The content of this soup is listed here. An extensive explanation
of all frequently used WHAT CHECK output formats can be found at
swift.cmbi.ru.nl. Look under output formats. A course on reading this
'Molecules' table is part of the WHAT CHECK website.
 
     1     1 (    1)    22 (   22) A Protein             To check
     2    23 (   23)    96 (   96) B Protein             To check
     3    97 (   97)   123 (  123) C Protein             To check
     4   124 (  124)   268 (  268) D Protein             To check
     5   269 (  269)   359 (  359) E Protein             To check
 
# 110 # Note: Summary report
This is an overall summary of the quality of the structure as compared with
current reliable structures. Numbers in brackets are the average and standard
deviation observed for a large number of files determined with a similar
resolution.
 
The second table mostly gives an impression of how well the model conforms
to common refinement restraint values. These numbers are less than 1.0 if the
spread in data is too little, and larger than 1.0 when the spread is too
large. The former does not need to be a problem, the latter always is bad.
 
 Structure Z-scores, positive is better than average:
  Resolution read from PDB file  :   3.000
  1st generation packing quality :  -1.018 (          (  -1.0,  2.5))
  2nd generation packing quality :  -2.458 (          (  -1.9,  1.4))
  Ramachandran plot appearance   :  -6.063 (bad       (  -4.1,  2.0))
  chi-1/chi-2 rotamer normality  :  -7.742 (bad       (  -5.6,  2.0))
  Backbone conformation          :  -1.225 (          (  -1.4,  3.9))
  Inside/Outside distribution    :   1.070
 
 RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.584 (tight)
  Bond angles                    :   0.929
  Omega angle restraints         :   1.770 (loose)
  Side chain planarity           :   1.162
  Improper dihedral distribution :   0.791
  B-factor distribution          :   0.761
 
# 111 # Note: Introduction to refinement recommendations
First, be aware that the recommendations for crystallographers listed below
are produced by a computer program that was written by a guy who got his
PhD in NMR...
 
We have tried to convert the messages written in this report into a small
set of things you can do with your refinement software to get a better
structure. The things you should do first are listed first. And in some
cases you should first fix that problem, then refine a bit further, and
then run WHAT CHECK again before looking at other problems. If, for example,
WHAT CHECK has found a problem with the SCALE and CRYST cards, then you must
first fix that problem, refine the structure a bit further, and run WHAT
CHECK again because errors in the SCALE and or CRYST card can lead to many
problems elsewhere in the validation process.
 
It is also important to keep in mind that WHAT CHECK is software and that it
occasionally totally misunderstands what is the cause of a problem. But, if
WHAT CHECK lists a problem there normally is a problem albeit that it not
always is the actual problem that gets listed.
 
# 112 # Note: Matthews coefficient problem
WHAT CHECK detected a Matthews coefficient problem. Most times this is an
administrative problem caused by typing the wrong cell multiplicity number
on the CRYST card (or not typing it at all). Occasionally it is caused by
typing the wrong space group on the CRYST card. You better fix this problem,
but normally this problem does not cause WHAT CHECK to give any erroneous
error messages further down in the report.
 
# 113 # Note: Hand problems
Your structure contains several residues with a reported hand problem (a
hand problem means that an atom was found with inverted chirality).
Obviously, things like D-amino acids exist, and if you know that your
molecule has groups with an inverted chirality, you can neglect this
message. If, however, this message comes as a surprise to you, then
you should correct the problems and do some serious refinement again
before you run WHAT CHECK again.
 
# 114 # Error: Bumps in your structure
Upon analysing the bumps in your structure, WHAT CHECK got a bit
worried. Sometimes this means that you have forgotten to lower the
occupancy of overlapping ligands, residues, or water molecules. But,
whatever is the origin of this problem, you have to analyse it and
fix it.
 
# 115 # Note: Bond angle variabilty Z-score high
With a resolution of 2.5-3.0 Angstrom, you dont have enough data to warrant
the bond angle variability that we observed (almost 1.0). So, you better
tighten
the screws on the bond angle target values a bit.
 
# 116 # Note: Omega angles insufficiently restraint
Omega angles tend to fall around 178 degrees with a standard deviation of 5.5
degrees. With a resolution of 2.5-3.0 Angstrom, you dont have enough data to
warrant the omega angle variability that we observed. The variability is
larger than 7.0 degrees. So, tighten the screws on the omega angle target
values a bit.
 
# 117 # Warning: Troublesome residues
The residues listed in the table below need to be inspected
 
This table is a very rough attempt to sort the residues according to how
badly they need your attention. The idea is that when you sit in  in front
of the graphics screen and study the residues with the electron density
present that you improve the structure most by dealing with the top residues
in this list first.
 
  107 LEU  ( 107-) C  -     17.34
  359 PHE  ( 359-) E  -     16.26
  357 ARG  ( 357-) E  -     16.20
   30 TYR  (  30-) B  -     15.27
   10 ARG  (  10-) A  -     15.18
  235 ILE  ( 235-) D  -     14.86
  169 ARG  ( 169-) D  -     13.66
  205 MET  ( 205-) D  -     12.37
  148 LEU  ( 148-) D  -     12.36
  297 LYS  ( 297-) E  -     12.10
  224 VAL  ( 224-) D  -     12.06
  144 TYR  ( 144-) D  -     12.05
  115 TYR  ( 115-) C  -     12.00
  354 ARG  ( 354-) E  -     11.63
   49 LEU  (  49-) B  -     10.80
And so on for a total of    99 lines.
==============
 
 
WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).
 
WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra
    information)
 
PDB facilities
    Touw WG, Baakman C, Black J, te Beek TA, Krieger E, Joosten RP, Vriend G.
      A series of PDB-related databanks for everyday needs.
    Nucleic Acids Research D364-368 Database issue (2015).
 
Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991) and
    R.Engh and R.Huber,
    International Tables for Crystallography (2001)
 
 
Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).
 
DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).
 
Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).
 
Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).
 
Peptide flips
    Touw WG, Joosten RP, Vriend G.
      Detection of trans-cis flips and peptide-plane flips in protein
      structures.
    Acta Crystallogr D Biological Crystallograhy 71, 1604-1614 (2015).
 
Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).
 
Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).
 
Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).
 
Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).
    R.W.W. Hooft, C.Sander and G.Vriend,
      Objectively judging the quality of a protein structure from a
      Ramachandran plot
    CABIOS (1997), 13, 425--430.
 
Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).
 
Tau angle
    W.G.Touw and G.Vriend
      On the complexity of Engh and Huber refinement restraints: the angle
      tau as example.
    Acta Crystallogr D 66, 1341--1350 (2010).
 
Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).
 
    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).
 
    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).
 
Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.
==============
 
 
WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).
 
WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra
    information)
 
PDB facilities
    Touw WG, Baakman C, Black J, te Beek TA, Krieger E, Joosten RP, Vriend G.
      A series of PDB-related databanks for everyday needs.
    Nucleic Acids Research D364-368 Database issue (2015).
 
Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991) and
    R.Engh and R.Huber,
    International Tables for Crystallography (2001)
 
 
Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).
 
DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).
 
Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).
 
Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).
 
Peptide flips
    Touw WG, Joosten RP, Vriend G.
      Detection of trans-cis flips and peptide-plane flips in protein
      structures.
    Acta Crystallogr D Biological Crystallograhy 71, 1604-1614 (2015).
 
Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).
 
Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).
 
Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).
 
Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).
    R.W.W. Hooft, C.Sander and G.Vriend,
      Objectively judging the quality of a protein structure from a
      Ramachandran plot
    CABIOS (1997), 13, 425--430.
 
Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).
 
Tau angle
    W.G.Touw and G.Vriend
      On the complexity of Engh and Huber refinement restraints: the angle
      tau as example.
    Acta Crystallogr D 66, 1341--1350 (2010).
 
Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).
 
    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).
 
    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).
 
Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.
