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

Date : 2024-03-29
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/6r35/wctemp_0cyc/6r35_0cyc.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.
 
# 2 # Warning: Class of conventional cell differs from CRYST1 cell
The crystal class of the conventional cell is different from the crystal
class of the cell given on the CRYST1 card. If the new class is supported
by the coordinates this is an indication of a wrong space group assignment.
 
The CRYST1 cell dimensions
    A    =  52.603  B   =  72.481  C    =  62.061
    Alpha=  90.000  Beta= 114.620  Gamma=  90.000
 
Dimensions of a reduced cell
    A    =  52.603  B   =  62.061  C    =  72.481
    Alpha=  90.000  Beta=  90.000  Gamma=  65.380
 
Dimensions of the conventional cell
    A    =  52.603  B   = 112.842  C    =  72.481
    Alpha=  90.000  Beta=  90.000  Gamma=  90.454
 
Transformation to conventional cell
  1.000000  0.000000  0.000000
 -1.000000  0.000000 -2.000000
  0.000000  1.000000  0.000000
 
Crystal class of the cell: MONOCLINIC
 
Crystal class of the conventional cell: ORTHORHOMBIC
 
Space group name: P 1 21 1
 
Bravais type of conventional cell is: C
WARNING. Date error on HEADER card:
HEADER                                                        6R35
 
# 3 # Note: Header records from PDB file
Header records from PDB file.
 
HEADER                                                        6R35
 
# 4 # Error: Missing unit cell information
No SCALE matrix is given in the PDB file.
 
# 5 # Note: Proposal for corrected SCALE matrix
A corrected SCALE matrix has been derived.
 
Proposed scale matrix
  0.019010  0.000000  0.008712
  0.000000  0.013797  0.000000
  0.000000  0.000000  0.017724
 
# 6 # Note: Non crystallographic symmetry RMS plot
The plot shows the RMS differences between two similar chains on a residue-
by-residue basis. Individual "spikes" can be indicative of interesting or
wrong residues. If all residues show a high RMS value, the structure could
be incorrectly refined.
 
In the TeX file, a plot has been inserted here
 
Chain identifiers of the two chains: D and A
 
 All-atom RMS fit for the two chains : 0.438
 CA-only RMS fit for the two chains : 0.139
 
# 7 # Note: Low non-crystallographic symmetry phi and psi differences
All comparable residues in the two chains mentioned below have comparable
backbone torsion angles
 
Chain identifiers of the two chains: D and A
 
# 8 # Note: Non crystallographic symmetry RMS plot
The plot shows the RMS differences between two similar chains on a residue-
by-residue basis. Individual "spikes" can be indicative of interesting or
wrong residues. If all residues show a high RMS value, the structure could
be incorrectly refined.
 
In the TeX file, a plot has been inserted here
 
Chain identifiers of the two chains: D and B
 
 All-atom RMS fit for the two chains : 0.362
 CA-only RMS fit for the two chains : 0.162
 
# 9 # Note: Low non-crystallographic symmetry phi and psi differences
All comparable residues in the two chains mentioned below have comparable
backbone torsion angles
 
Chain identifiers of the two chains: D and B
 
# 10 # Note: Non crystallographic symmetry RMS plot
The plot shows the RMS differences between two similar chains on a residue-
by-residue basis. Individual "spikes" can be indicative of interesting or
wrong residues. If all residues show a high RMS value, the structure could
be incorrectly refined.
 
In the TeX file, a plot has been inserted here
 
Chain identifiers of the two chains: D and C
 
 All-atom RMS fit for the two chains : 0.446
 CA-only RMS fit for the two chains : 0.199
 
# 11 # Note: Low non-crystallographic symmetry phi and psi differences
All comparable residues in the two chains mentioned below have comparable
backbone torsion angles
 
Chain identifiers of the two chains: D and C
 
# 12 # Note: Non crystallographic symmetry RMS plot
The plot shows the RMS differences between two similar chains on a residue-
by-residue basis. Individual "spikes" can be indicative of interesting or
wrong residues. If all residues show a high RMS value, the structure could
be incorrectly refined.
 
In the TeX file, a plot has been inserted here
 
Chain identifiers of the two chains: A and B
 
 All-atom RMS fit for the two chains : 0.469
 CA-only RMS fit for the two chains : 0.163
 
# 13 # Note: Non crystallographic symmetry backbone difference plot
The plot shows the differences in backbone torsion angles between two
similar chains on a residue-by-residue basis. Individual "spikes" can be
indicative of interesting or wrong residues. If all residues show high
differences, the structure could be incorrectly refined.
 
In the TeX file, a plot has been inserted here
 
Chain identifiers of the two chains: A and B
 
# 14 # Note: Non crystallographic symmetry RMS plot
The plot shows the RMS differences between two similar chains on a residue-
by-residue basis. Individual "spikes" can be indicative of interesting or
wrong residues. If all residues show a high RMS value, the structure could
be incorrectly refined.
 
In the TeX file, a plot has been inserted here
 
Chain identifiers of the two chains: A and C
 
 All-atom RMS fit for the two chains : 0.455
 CA-only RMS fit for the two chains : 0.195
 
# 15 # Note: Low non-crystallographic symmetry phi and psi differences
All comparable residues in the two chains mentioned below have comparable
backbone torsion angles
 
Chain identifiers of the two chains: A and C
 
# 16 # Note: NCS statistics suppressed
There are more pairs of NCS equivalent molecules, but the statistics
will not be shown.
 
# 17 # Warning: New symmetry found
Independent molecules in the asymmetric unit actually look like
symmetry relatives. This fact needs manual checking.
 
# 18 # 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: P 1 21 1
 Number of matrices in space group: 2
 Highest polymer chain multiplicity in structure: 4
 Highest polymer chain multiplicity according to SEQRES: 4
 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
 
# 19 # 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: 47304.301
 Volume of the Unit Cell V= 215110.062
 Space group multiplicity: 2
 No NCS symmetry matrices (MTRIX records) found in PDB file
 Matthews coefficient for observed atoms and Z is high: Vm= 18.189
 A few residues have missing atoms that did not enter the Vm calculation
 No Matthews coefficient given in REMARK 280
 Or should we use the previously suggested Z = 8
 which would result in Vm= 2.274
 And remember, a matrix counting problem has been reported earlier already
 
# 20 # Note: Z missing on CRYST1 card
The messages above seem likely caused by the fact that Z is missing from the
CRYST1 card.
 
# 21 # 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.
 
# 22 # Note: Chain identifiers OK
WHAT CHECK has not detected any serious chain identifier problems. But be
aware that WHAT CHECK doesn't care about the chain identifiers of waters.
 
# 23 # Warning: Ligands for which a topology was generated automatically
The topology for the ligands in the table below were determined
automatically. WHAT CHECK uses a local copy of the CCP4 monomer library to
generate topology information for ligands. Be aware that automatic topology
generation is a complicated task. So, if you get messages that you fail to
understand or that you believe are wrong, and one of these ligands is
involved, then check the ligand topology entry first. This topology is either
present in the monomer library, or as a libcheck-generated file in the local
directory.
 
  470 GAL  (   3-) E  -
  472 GAL  (   3-) F  -
  474 GAL  (   3-) G  -
  476 GAL  (   3-) H  -
 
# 24 # Warning: Covalently bound ligands
The ligands in this table are covalently bound to something else. It is
already difficult to automatically generate topologies for ligands,
but when they are covalently bound to something it becomes even more
complicated to do everything right. So, if you get weird error messages
that seem related to this covalent bond, then please feel free to
ignore those, or even better, make a topology entry by hand.
 
The comment `Other ligand` indicates that the covalent bond is to another
ligand. In that case you might want to convert the two ligands into one
bigger ligand.
 
  470 GAL  (   3-) E  -
  472 GAL  (   3-) F  -
  474 GAL  (   3-) G  -
  476 GAL  (   3-) H  -
 
# 25 # Note: No strange inter-chain connections detected
No covalent bonds have been detected between molecules with non-identical
chain identifiers.
 
# 26 # Note: No duplicate atom names in ligands
All atom names in ligands (if any) seem adequately unique.
 
# 27 # 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).
 
# 28 # 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).
 
# 29 # Warning: Groups attached to potentially hydrogen-bonding atoms
Residues were observed with groups attached to (or very near to) atoms that
potentially can form hydrogen bonds. WHAT CHECK is not very good at dealing
with such exceptional cases (Mainly because it's author is not...). So be
warned that the hydrogen-bonding related analyses of these residues
might be in error.
 
For example, an aspartic acid can be protonated on one of its delta
oxygens. This is possible because the one delta oxygen 'helps' the
other one holding that proton. However, if a delta oxygen has a group
bound to it, then it can no longer 'help' the other delta oxygen
bind the proton. However, both delta oxygens, in principle, can still
be hydrogen bond acceptors. Such problems can occur in the amino acids
Asp, Glu, and His. I have opted, for now to simply allow no hydrogen
bonds at all for any atom in any side chain that somewhere has a 'funny'
group attached to it. I know this is wrong, but there are only 12 hours
in a day.
 
  457 NAG  (   1-) E  -    O4  bound to   470 GAL  (   3-) E  -    C1
  459 NAG  (   1-) F  -    O4  bound to   472 GAL  (   3-) F  -    C1
  461 NAG  (   1-) G  -    O4  bound to   474 GAL  (   3-) G  -    C1
  463 NAG  (   1-) H  -    O4  bound to   476 GAL  (   3-) H  -    C1
 
# 30 # 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.
 
# 31 # 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.
 
# 32 # Note: All residues have a complete backbone.
No residues have missing backbone atoms.
 
# 33 # Note: No C-alpha only residues
There are no residues that consist of only an alpha carbon atom.
 
# 34 # 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)   114 (  114) D Protein             /zata/tempdir/6r3...
     2   115 (    1)   228 (  114) A Protein             /zata/tempdir/6r3...
     3   229 (    1)   342 (  114) B Protein             /zata/tempdir/6r3...
     4   343 (    1)   456 (  114) C Protein             /zata/tempdir/6r3...
     5   457 (    1)   457 (    1) E Sugar<=             /zata/tempdir/6r3...
     6   458 (    2)   458 (    2) E Sugar               /zata/tempdir/6r3...
     7   459 (    1)   459 (    1) F Sugar<=             /zata/tempdir/6r3...
     8   460 (    2)   460 (    2) F Sugar               /zata/tempdir/6r3...
     9   461 (    1)   461 (    1) G Sugar<=             /zata/tempdir/6r3...
    10   462 (    2)   462 (    2) G Sugar               /zata/tempdir/6r3...
    11   463 (    1)   463 (    1) H Sugar<=             /zata/tempdir/6r3...
    12   464 (    2)   464 (    2) H Sugar               /zata/tempdir/6r3...
    13   465 (  114)   465 (  114) D G O2 <-   114       /zata/tempdir/6r3...
    14   466 (  114)   466 (  114) A G O2 <-   228       /zata/tempdir/6r3...
    15   467 (  114)   467 (  114) B G O2 <-   342       /zata/tempdir/6r3...
And so on for a total of    46 lines.
MODELs skipped upon reading PDB file: 0
X-ray structure. No MODELs found
The total number of amino acids found is 456
of which 2 have poor or (essentially) missing atoms
No nucleic acids observed in input file
Number of (recognized) sugars: 8
Number of water molecules: 417
Residue numbers increase monotonously OK
 
# 35 # Warning: Ions bound to the wrong chain
The ions listed in the table have a chain identifier that is the same as one
of the protein, nucleic acid, or sugar chains. However, the ion seems bound
to protein, nucleic acid, or sugar, with another chain identifier.
 
Obviously, this is not wrong, but it is confusing for users of this PDB file.
 
  481  CA  ( 208-) D  -
  486  CA  ( 208-) A  -
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
 
# 36 # 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: D
 
# 37 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: A
 
# 38 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 39 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: C
 
# 40 # 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        30        40        50        60
                      |         |         |         |         |         |
    1 -   60 ATQGVFTLPANTRFGVTAFANSSGTQTVNVLVNNETAATFSGQSTNNAVIGTQVLNSGSS
(   1)-(  60)
                     70        80        90       100       110
                      |         |         |         |         |
   61 -  114 GKVQVQVSVNGRPSDLVSAQVILTNELNFALVGSEDGTDNDYNDAVVVINWPLG
(  61)-( 114)
                120       130       140       150       160       170
                  |         |         |         |         |         |
  115 -  174 ATQGVFTLPANTRFGVTAFANSSGTQTVNVLVNNETAATFSGQSTNNAVIGTQVLNSGSS
(   1)-(  60)
                180       190       200       210       220
                  |         |         |         |         |
  175 -  228 GKVQVQVSVNGRPSDLVSAQVILTNELNFALVGSEDGTDNDYNDAVVVINWPLG
(  61)-( 114)
            230       240       250       260       270       280
              |         |         |         |         |         |
  229 -  288 ATQGVFTLPANTRFGVTAFANSSGTQTVNVLVNNETAATFSGQSTNNAVIGTQVLNSGSS
(   1)-(  60)
            290       300       310       320       330       340
              |         |         |         |         |         |
  289 -  342 GKVQVQVSVNGRPSDLVSAQVILTNELNFALVGSEDGTDNDYNDAVVVINWPLG
(  61)-( 114)
                  350       360       370       380       390       400
                    |         |         |         |         |         |
  343 -  402 ATQGVFTLPANTRFGVTAFANSSGTQTVNVLVNNETAATFSGQSTNNAVIGTQVLNSGSS
(   1)-(  60)
                  410       420       430       440       450
                    |         |         |         |         |
  403 -  456 GKVQVQVSVNGRPSDLVSAQVILTNELNFALVGSEDGTDNDYNDAVVVINWPLG
(  61)-( 114)
 
 
 
 
# 41 # Note: No rounded coordinates detected
No significant rounding of atom coordinates has been detected.
 
# 42 # 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.
 
# 43 # Warning: Unexpected atoms encountered
While reading the PDB file, at least one atom was encountered that
was not expected in the residue. This might be caused by a naming
convention problem. It can also mean that a residue was found protonated
that normally is not (e.g. aspartic acid). The unexpected atoms have been
discarded; in case protons were deleted that actually might be needed, they
will later be put back by the hydrogen bond validation software.
This normally is not a warning you should worry too much about.
 
# 44 # Warning: Missing atoms
The atoms listed in the table below are missing from the entry. If many atoms
are missing, the other checks can become less sensitive. Be aware that it
often happens that groups at the termini of DNA or RNA are really missing,
so that the absence of these atoms normally is neither an error nor the
result of poor electron density. Some of the atoms listed here might also be
listed by other checks, most noticeably by the options in the previous
section that list missing atoms in several categories. The plausible atoms
with zero occupancy are not listed here, as they already got assigned a
non-zero occupancy, and thus are no longer 'missing'.
 
  300 ARG  (  72-) B  -    CG
  300 ARG  (  72-) B  -    CD
  300 ARG  (  72-) B  -    NE
  300 ARG  (  72-) B  -    CZ
  300 ARG  (  72-) B  -    NH1
  300 ARG  (  72-) B  -    NH2
  414 ARG  (  72-) C  -    CG
  414 ARG  (  72-) C  -    CD
  414 ARG  (  72-) C  -    NE
  414 ARG  (  72-) C  -    CZ
  414 ARG  (  72-) C  -    NH1
  414 ARG  (  72-) C  -    NH2
 
# 45 # Note: All B-factors fall in the range 0.0 - 100.0
All B-factors are larger than zero, and none are observed above 100.0.
 
# 46 # 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.
 
  114 GLY  ( 114-) D  -        OK
  228 GLY  ( 114-) A  -        OK
  342 GLY  ( 114-) B  -        OK
  456 GLY  ( 114-) C  -        OK
  457 NAG  (   1-) E  -        +X
  459 NAG  (   1-) F  -        +X
  461 NAG  (   1-) G  -        +X
  463 NAG  (   1-) H  -        +X
 
# 47 # Note: Weights administratively correct
All atomic occupancy factors ('weights') fall in the 0.0--1.0 range, which
makes them administratively correct.
 
# 48 # 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.
 
# 49 # Warning: Occupancy atoms do not add up to 1.0.
In principle, the occupancy of all alternates of one atom should add up till
1.0. A valid exception is the missing atom (i.e. an atom not seen in the
electron density) that is allowed to have a 0.0 occupancy. Sometimes this
even happens when there are no alternate atoms given...
 
Atoms want to move. That is the direct result of the second law of
thermodynamics, in a somewhat weird way of thinking. Any way, many atoms
seem to have more than one position where they like to sit, and they jump
between them. The population difference between those sites (which is related
to their energy differences) is seen in the occupancy factors. As also for
atoms it is 'to be or not to be', these occupancies should add up to 1.0.
Obviously, it is possible that they add up to a number less than 1.0, in
cases where there are yet more, but undetected' rotamers/positions in play,
but also in those cases a warning is in place as the information shown
in the PDB file is less certain than it could have been. The residues
listed below contain atoms that have an occupancy greater than zero, but
their alternates do not add up to one. 'Strange' is added as a comment when
we believe that the structure shows no obvious reasons why this residue
should have a reduced occupancy.
 
WARNING. Presently WHAT CHECK only deals with a maximum of two alternate
positions. A small number of atoms in the PDB has three alternates. In
those cases the warning given here should obviously be neglected!
In a next release we will try to fix this.
 
  241 ARG  (  13-) B  -   0.50
  314 GLU  (  86-) B  -   0.50
  412 ASN  (  70-) C  -   0.50
 
# 50 # 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: 0
 
Temperature not mentioned in PDB file. This most likely means
that the temperature record is absent.
Room temperature assumed
 
# 51 # 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
 
# 52 # 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 :  1.197 over    2880 bonds
Average difference in B over a bond :    2.63
RMS difference in B over a bond :    4.04
 
# 53 # 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: D
 
# 54 # Note: B-factor plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: A
 
# 55 # Note: B-factor plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 56 # Note: B-factor plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: C
 
# 57 # 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.
 
# 58 # Note: Valine nomenclature OK
No errors were detected in valine nomenclature.
 
# 59 # Note: Threonine nomenclature OK
No errors were detected in threonine nomenclature.
 
# 60 # Note: Isoleucine nomenclature OK
No errors were detected in isoleucine nomenclature.
 
# 61 # Note: Leucine nomenclature OK
No errors were detected in leucine nomenclature.
 
# 62 # Warning: Arginine nomenclature problem
The arginine residues listed in the table below have their NH1 and NH2
swapped.
 
   72 ARG  (  72-) D  -
  241 ARG  (  13-) B  -
 
# 63 # Note: Tyrosine torsion conventions OK
No errors were detected in tyrosine torsion angle conventions.
 
# 64 # Note: Phenylalanine torsion conventions OK
No errors were detected in phenylalanine torsion angle conventions.
 
# 65 # Note: Aspartic acid torsion conventions OK
No errors were detected in aspartic acid torsion angle conventions.
 
# 66 # Note: Glutamic acid torsion conventions OK
No errors were detected in glutamic acid torsion angle conventions.
 
# 67 # 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).
 
# 68 # Note: SO4/PO4 atom names OK
No errors were detected in SO4/PO4 atom naming conventions.
 
# 69 # 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.
 
# 70 # Note: No decreasing residue numbers
All residue numbers are strictly increasing within each chain.
 
# 71 # 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.
 
  241 ARG  (  13-) B  -    NE   CZ    1.39    4.1
 
# 72 # 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: 0.860
 RMS-deviation in bond distances: 0.018
 
# 73 # Warning: Possible cell scaling problem
Comparison of bond distances with Engh and Huber [REF] standard values for
protein residues and Parkinson et al [REF] values for DNA/RNA shows a
significant systematic deviation. It could be that the unit cell used in
refinement was not accurate enough. The deformation matrix given below gives
the deviations found: the three numbers on the diagonal represent the
relative corrections needed along the A, B and C cell axis. These values are
1.000 in a normal case, but have significant deviations here (significant at
the 99.99 percent confidence level)
 
There are a number of different possible causes for the discrepancy. First
the cell used in refinement can be different from the best cell calculated.
Second, the value of the wavelength used for a synchrotron data set can be
miscalibrated. Finally, the discrepancy can be caused by a dataset that has
not been corrected for significant anisotropic thermal motion.
 
Please note that the proposed scale matrix has NOT been restrained to obey
the space group symmetry. This is done on purpose. The distortions can give
you an indication of the accuracy of the determination.
 
If you intend to use the result of this check to change the cell dimension
of your crystal, please read the extensive literature on this topic first.
This check depends on the wavelength, the cell dimensions, and on the
standard bond lengths and bond angles used by your refinement software.
 
SCALE matrix obtained from PDB file
  0.019010  0.000000  0.008712
  0.000000  0.013797  0.000000
  0.000000  0.000000  0.017724
Unit Cell deformation matrix
  0.994825  0.001541  0.000443
  0.001541  0.996760 -0.000794
  0.000443 -0.000794  0.997248
Proposed new scale matrix
  0.019105 -0.000023  0.008727
 -0.000021  0.013842  0.000011
 -0.000008  0.000014  0.017773
With corresponding cell
    A    =  52.331  B   =  72.246  C    =  61.843
    Alpha=  90.000  Beta= 114.525  Gamma=  90.000
 
The CRYST1 cell dimensions
    A    =  52.603  B   =  72.481  C    =  62.061
    Alpha=  90.000  Beta= 114.620  Gamma=  90.000
 
 Variance: 196.987
 (Under-)estimated Z-score: 10.344
 
# 74 # 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.
 
    2 THR  (   2-) D  -    CA   CB   OG1 102.96   -4.4
   72 ARG  (  72-) D  -    CA   CB   CG  123.27    4.6
   72 ARG  (  72-) D  -    CG   CD   NE  118.40    4.6
   73 PRO  (  73-) D  -    N    CA   CB  107.45    4.0
   84 THR  (  84-) D  -    C    CA   CB  119.26    4.8
   96 ASP  (  96-) D  -    CA   CB   CG  117.77    5.2
  101 ASP  ( 101-) D  -    CA   CB   CG  116.82    4.2
  210 ASP  (  96-) A  -    CA   CB   CG  117.93    5.3
  215 ASP  ( 101-) A  -    CA   CB   CG  118.71    6.1
  239 ASN  (  11-) B  -    CA   CB   CG  107.14   -5.5
  241 ARG  (  13-) B  -    CG   CD   NE  129.23   11.0
  241 ARG  (  13-) B  -    CD   NE   CZ  129.41    4.3
  329 ASP  ( 101-) B  -    CA   CB   CG  117.87    5.3
  344 THR  (   2-) C  -    CA   CB   OG1 102.66   -4.6
  355 ARG  (  13-) C  -    CG   CD   NE  120.12    5.7
  438 ASP  (  96-) C  -    CA   CB   CG  117.51    4.9
  440 THR  (  98-) C  -    CA   C    O   113.64   -4.2
  443 ASP  ( 101-) C  -    CA   CB   CG  119.60    7.0
 
# 75 # 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: 1.058
 RMS-deviation in bond angles: 1.993
 
# 76 # Error: Nomenclature error(s)
Checking for a hand-check. WHAT CHECK has over the course of this session
already corrected the handedness of atoms in several residues. These were
administrative corrections. These residues are listed here.
 
   72 ARG  (  72-) D  -
  241 ARG  (  13-) B  -
 
# 77 # 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.
 
Please also see the previous table that lists a series of administrative
chirality problems that were corrected automatically upon reading-in the
PDB file.
 
   86 GLU  (  86-) D  -    C     -6.1    -8.64     0.04
The average deviation= 1.738
 
# 78 # 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 : 1.505
 
# 79 # Note: Tau angles OK
All of the tau angles (N-C-alpha-C) of amino acids fall within expected
RMS deviations.
 
# 80 # 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 : 0.969
 
# 81 # 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.
 
   33 ASN  (  33-) D  -   6.46
  441 ASP  (  99-) C  -   5.23
   64 GLN  (  64-) D  -   5.09
  239 ASN  (  11-) B  -   5.07
  213 ASP  (  99-) A  -   4.69
   99 ASP  (  99-) D  -   4.52
 
# 82 # 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.
 
# 83 # Note: Ramachandran Z-score OK
The score expressing how well the backbone conformations of all residues
correspond to the known allowed areas in the Ramachandran plot is within
expected ranges for well-refined structures.
 
 Ramachandran Z-score : -1.966
 
# 84 # 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.
 
# 85 # 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.
 
  426 THR  (  84-) C  -   -3.4
  312 THR  (  84-) B  -   -3.4
  198 THR  (  84-) A  -   -3.3
   84 THR  (  84-) D  -   -3.3
  280 THR  (  52-) B  -   -2.2
  166 THR  (  52-) A  -   -2.2
   52 THR  (  52-) D  -   -2.1
  394 THR  (  52-) C  -   -2.0
 
# 86 # 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.
 
    4 GLY  (   4-) D  - Poor phi/psi
    8 LEU  (   8-) D  - Omega to (next) Pro poor
   11 ASN  (  11-) D  - Poor phi/psi
   34 ASN  (  34-) D  - Poor phi/psi
   42 GLY  (  42-) D  - Poor phi/psi
   44 SER  (  44-) D  - omega poor
   47 ASN  (  47-) D  - Poor phi/psi
   58 GLY  (  58-) D  - Poor phi/psi
   61 GLY  (  61-) D  - Poor phi/psi
   70 ASN  (  70-) D  - Poor phi/psi
   71 GLY  (  71-) D  - Poor phi/psi
   72 ARG  (  72-) D  - Omega to (next) Pro poor
   85 ASN  (  85-) D  - Poor phi/psi
   86 GLU  (  86-) D  - omega poor
   92 VAL  (  92-) D  - omega poor
And so on for a total of    81 lines.
 
# 87 # 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.
 
  259 LEU  (  31-) B  -    -1.31
    8 LEU  (   8-) D  -    -1.24
   31 LEU  (  31-) D  -    -1.28
  122 LEU  (   8-) A  -    -1.23
  145 LEU  (  31-) A  -    -1.28
  236 LEU  (   8-) B  -    -1.24
  350 LEU  (   8-) C  -    -1.24
  373 LEU  (  31-) C  -    -1.29
  298 ASN  (  70-) B  -    -1.11
   88 ASN  (  88-) D  -    -1.07
  111 TRP  ( 111-) D  -    -1.05
  202 ASN  (  88-) A  -    -1.05
  225 TRP  ( 111-) A  -    -1.03
  310 ILE  (  82-) B  -    -1.02
  316 ASN  (  88-) B  -    -1.06
And so on for a total of   148 lines.
 
# 88 # Note: chi-1/chi-2 angle correlation Z-score OK
The score expressing how well the chi-1/chi-2 angles of all residues
correspond to the populated areas in the database is
within expected ranges for well-refined structures.
 
 chi-1/chi-2 correlation Z-score : -2.292
 
# 89 # 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.
 
  167 GLN  (  53-) A  -   0.37
  281 GLN  (  53-) B  -   0.38
  383 SER  (  41-) C  -   0.39
 
# 90 # 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!
 
   84 THR  (  84-) D  -       1
  198 THR  (  84-) A  -       1
  312 THR  (  84-) B  -       1
  426 THR  (  84-) C  -       1
  447 ALA  ( 105-) C  -       1
 
# 91 # 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 : 0.177
 
# 92 # 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= 177.540 7.119
 
# 93 # Note: PRO puckering amplitude OK
Puckering amplitudes for all PRO residues are within normal ranges.
 
# 94 # Note: PRO puckering phases OK
Puckering phases for all PRO residues are normal
 
# 95 # Note: Backbone oxygen evaluation OK
All residues for which similar local backbone conformations could be found
in the WHAT CHECK database have a backbone oxygen position that has been
observed at least a few times in that database.
 
# 96 # Note: Peptide bond conformations
There was no need to complain about the peptide bond of a single amino acid.
 
# 97 # 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.
 
  457 NAG  (   1-) E  -    O3  <-->   458 FUC  (   2-) E  -    C1     1.28    1.42  INTRA
  459 NAG  (   1-) F  -    O3  <-->   460 FUC  (   2-) F  -    C1     1.28    1.42  INTRA
  461 NAG  (   1-) G  -    O3  <-->   462 FUC  (   2-) G  -    C1     1.26    1.44  INTRA
  463 NAG  (   1-) H  -    O3  <-->   464 FUC  (   2-) H  -    C1     1.25    1.45  INTRA
  457 NAG  (   1-) E  -    C3  <-->   458 FUC  (   2-) E  -    C1     0.74    2.36  INTRA
  459 NAG  (   1-) F  -    C3  <-->   460 FUC  (   2-) F  -    C1     0.67    2.43  INTRA
  463 NAG  (   1-) H  -    C3  <-->   464 FUC  (   2-) H  -    C1     0.63    2.47  INTRA
  461 NAG  (   1-) G  -    C3  <-->   462 FUC  (   2-) G  -    C1     0.61    2.49  INTRA
  459 NAG  (   1-) F  -    O3  <-->   460 FUC  (   2-) F  -    C2     0.30    2.40  INTRA
  461 NAG  (   1-) G  -    O3  <-->   462 FUC  (   2-) G  -    C2     0.29    2.41  INTRA
  457 NAG  (   1-) E  -    O3  <-->   458 FUC  (   2-) E  -    C2     0.28    2.42  INTRA
  463 NAG  (   1-) H  -    O3  <-->   464 FUC  (   2-) H  -    C2     0.28    2.42  INTRA
  115 ALA  (   1-) A  -    CB  <-->   419 VAL  (  77-) C  -  A CG1    0.17    3.03  INTRA BL
  457 NAG  (   1-) E  -    O3  <-->   458 FUC  (   2-) E  -    O5     0.12    2.28  INTRA
  459 NAG  (   1-) F  -    O3  <-->   460 FUC  (   2-) F  -    O5     0.08    2.32  INTRA
  158 SER  (  44-) A  -    OG  <-->   484 EDO  ( 203-) A  -    C1     0.06    2.74  INTRA
  457 NAG  (   1-) E  -    O3  <-->   458 FUC  (   2-) E  -    C5     0.03    2.77  INTRA
  463 NAG  (   1-) H  -    O3  <-->   464 FUC  (   2-) H  -    O5     0.02    2.38  INTRA
   75 ASP  (  75-) D  -    OD2 <-->   229 ALA  (   1-) B  -    N      0.02    2.68  INTRA
 
# 98 # 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: 9.398
Total bump value per residue: 0.041
Total number of bumps: 19
Total squared bump value: 8.598
Total number of bumps in the mildest bin: 7
Total number of bumps in the second bin: 4
Total number of bumps in the middle bin: 4
Total number of bumps in the fourth bin: 0
Total number of bumps in the worst bin: 4
 
# 99 # 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.
 
# 100 # 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 : 0.928
 
# 101 # 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: D
 
# 102 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: A
 
# 103 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 104 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: C
 
# 105 # 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.
 
  412 ASN  (  70-) C  -  -5.78
  298 ASN  (  70-) B  -  -5.69
 
# 106 # Note: No series of residues with bad packing environment
There are no stretches of three or more residues each having a packing score
worse than -4.0.
 
# 107 # Note: Structural average packing environment OK
The structural average packing score is within normal ranges.
 
 
Average for range     1 -  464 :   0.106
 
# 108 # 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
 
# 109 # 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
 
# 110 # 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
 
# 111 # 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
 
# 112 # 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.
 
  300 ARG  (  72-) B  -  -2.84
  414 ARG  (  72-) C  -  -2.82
  328 ASN  ( 100-) B  -  -2.73
  100 ASN  ( 100-) D  -  -2.64
 
# 113 # 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
 
# 114 # 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: D
 
# 115 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: A
 
# 116 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 117 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: C
 
# 118 # 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.
 
# 119 # Note: Water contacts OK
All water clusters make at least one contact with a non-water atom.
 
# 120 # Note: No waters need moving
All water molecules are sufficiently close to the asymmetric unit given in
the input file.
 
# 121 # Error: Water molecules without hydrogen bonds
The water molecules listed in the table below do not form any hydrogen bonds,
neither with the protein or DNA/RNA, nor with other water molecules. This is
a strong indication of a refinement problem.
 
  496 HOH  ( 328 ) A  -    O
  497 HOH  ( 310 ) B  -    O
  498 HOH  ( 330 ) C  -    O
  498 HOH  ( 373 ) C  -  B O
 
# 122 # Error: His, Asn, Gln side chain flips
Listed here are Histidine, Asparagine or Glutamine residues for
which the orientation determined from hydrogen bonding analysis are
different from the assignment given in the input. Either they could
form energetically more favourable hydrogen bonds if the terminal
group was rotated by 180 degrees, or there is no assignment in the
input file (atom type 'A') but an assignment could be made. Be aware,
though, that if the topology could not be determined for one or more
ligands, then this option will make errors.
 
   11 ASN  (  11-) D  -
   29 ASN  (  29-) D  -
   33 ASN  (  33-) D  -
  125 ASN  (  11-) A  -
  143 ASN  (  29-) A  -
  178 GLN  (  64-) A  -
  184 ASN  (  70-) A  -
  199 ASN  (  85-) A  -
  281 GLN  (  53-) B  -
 
# 123 # 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.
 
    4 GLY  (   4-) D  -    N
    7 THR  (   7-) D  -    N
   11 ASN  (  11-) D  -    ND2
   17 THR  (  17-) D  -    OG1
   22 SER  (  22-) D  -    OG
   24 GLY  (  24-) D  -    N
   46 ASN  (  46-) D  -  A N
   60 SER  (  60-) D  -    OG
   62 LYS  (  62-) D  -    N
   94 SER  (  94-) D  -    OG
  103 ASN  ( 103-) D  -    ND2
  115 ALA  (   1-) A  -    N
  158 SER  (  44-) A  -    OG
  217 ASN  ( 103-) A  -    ND2
  331 ASN  ( 103-) B  -    ND2
  445 ASN  ( 103-) C  -    ND2
  447 ALA  ( 105-) C  -    N
  484 EDO  ( 203-) A  -    O2
  492 EDO  ( 203-) C  -    O1
 
# 124 # 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.
 
   96 ASP  (  96-) D  -    OD1
  254 GLN  (  26-) B  -    OE1
  368 GLN  (  26-) C  -    OE1
 
# 125 # 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: 655
- of which buried: 384
Total number of acceptors: 713
- of which buried: 333
Total number of donor+acceptors: 105
  (e.g. the Ser Ogamma that can donate and accept)
- of which buried: 28
Buried donors: 384
- without H-bond: 12
- essentially without H-bond: 0
- with only a very poor H-bond: 1
- with a poor H-bond: 2
- with a H-bond: 369
Buried acceptors: 333
- without H-bond: 34
- essentially without H-bond: 0
- with only a very poor H-bond: 2
- with a poor H-bond: 18
- with a H-bond: 279
 
# 126 # 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)   114 (  114) D Protein             /zata/tempdir/6r3...
     2   115 (    1)   228 (  114) A Protein             /zata/tempdir/6r3...
     3   229 (    1)   342 (  114) B Protein             /zata/tempdir/6r3...
     4   343 (    1)   456 (  114) C Protein             /zata/tempdir/6r3...
     5   457 (    1)   457 (    1) E Sugar<=             /zata/tempdir/6r3...
     6   458 (    2)   458 (    2) E Sugar               /zata/tempdir/6r3...
     7   459 (    1)   459 (    1) F Sugar<=             /zata/tempdir/6r3...
     8   460 (    2)   460 (    2) F Sugar               /zata/tempdir/6r3...
     9   461 (    1)   461 (    1) G Sugar<=             /zata/tempdir/6r3...
    10   462 (    2)   462 (    2) G Sugar               /zata/tempdir/6r3...
    11   463 (    1)   463 (    1) H Sugar<=             /zata/tempdir/6r3...
    12   464 (    2)   464 (    2) H Sugar               /zata/tempdir/6r3...
    13   465 (  114)   465 (  114) D G O2 <-   114       /zata/tempdir/6r3...
    14   466 (  114)   466 (  114) A G O2 <-   228       /zata/tempdir/6r3...
    15   467 (  114)   467 (  114) B G O2 <-   342       /zata/tempdir/6r3...
And so on for a total of    46 lines.
 
# 127 # 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  :   1.800
  1st generation packing quality :   1.515 (          (   0.0,  2.5))
  2nd generation packing quality :   1.862 (          (  -1.1,  1.4))
  Ramachandran plot appearance   :  -1.966 (          (  -0.5,  1.1))
  chi-1/chi-2 rotamer normality  :  -2.292 (          (  -1.8,  1.3))
  Backbone conformation          :   0.177 (          (  -0.3,  2.9))
  Inside/Outside distribution    :   0.928
 
 RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.860
  Bond angles                    :   1.058
  Omega angle restraints         :   1.294 (loose)
  Side chain planarity           :   2.023 (loose)
  Improper dihedral distribution :   1.505 (loose)
  B-factor distribution          :   1.197
 
# 128 # 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.
 
# 129 # 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.
 
# 130 # Note: Cell parameter anomaly
WHAT CHECK has compared the observed bond lengths with the Engh and Huber
parameters, and has done this as function of the direction of the bond
relative to the cell axes. From this analysis it was concluded that the
cell dimensions are probably not entirely perfect. The problem is not very
big, so you do not need to fix this before you start dealing with the other
suggestions, but you better fix this.
 
If this problem is caused by refining with another set of target values
than the Engh and Huber values, then WHAT CHECK cannot help you because
systematic target value deviations can also cause this message to pop up.
 
# 131 # Error: Bumps in your structure
Upon analysing the bumps in your structure, WHAT CHECK got very, very
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.
 
# 132 # Error: Water bumps in your structure
WHAT CHECK had to delete several water molecules because they overlapped
so badly that things like hydrogen bond calculations were not possible.
Obviously WHAT CHECK is not as smart as you in dealing with this problem,
so you better do something about the overlapping waters.
Often this problem is caused by having alternate water locations that
did not get a reduced occupancy.
 
# 133 # Note: Bond angle variabilty Z-score high
With a resolution of 1.5-2.5 Angstrom, you dont have enough data to warrant
the bond angle variability that we observed (more than 1.0). So, you better
tighten the screws on the bond angle target values a bit.
 
# 134 # Note: Omega angles insufficiently restraint
Omega angles tend to fall around 178 degrees with a standard deviation of 5.5
degrees. Even with a resolution of 1.5-2.5 Angstrom, you dont have enough
data to warrant the omega angle variability that we observed. The variability
is larger than 7.0 degrees. So, especially if your resolution is closer to
2.5 than to 1.5 Angstrom, you might want to tighten the screws on the
omega angle target values a bit.
 
# 135 # Note: His, Asn, Gln side chain flips.
His, Asn, and Gln have an asymmetry in their side chain that is hard to
detect unless you have data at much better than 1.0 Angstrom resolution.
WHAT CHECK thinks that your structure contains His, Asn, or Gln residues that
will make better hydrogen bonds when flipped around their chi-2, chi-2, or
chi-3 side chain torsion angle, respectively. You better
check these Asn, His, and Gln residues, and if you use a refinement program
that includes molecular dynamics, then you must (after the
flips were made) refine a bit further before running WHAT CHECK again.
 
# 136 # Note: Free floating waters
Your structure contains a few water molecules that make no hydrogen bonds at
all. These waters must be removed, and you must then refine a bit further
before running WHAT CHECK again.
 
# 137 # 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.
 
  241 ARG  (  13-) B  -     13.52
  412 ASN  (  70-) C  -     11.56
  298 ASN  (  70-) B  -     11.37
  457 NAG  (   1-) E  -      9.82
  458 FUC  (   2-) E  -      9.82
  459 NAG  (   1-) F  -      9.35
  460 FUC  (   2-) F  -      9.35
  463 NAG  (   1-) H  -      8.73
  464 FUC  (   2-) H  -      8.73
  461 NAG  (   1-) G  -      8.65
  462 FUC  (   2-) G  -      8.65
   72 ARG  (  72-) D  -      6.96
  443 ASP  ( 101-) C  -      5.25
   96 ASP  (  96-) D  -      4.87
  239 ASN  (  11-) B  -      4.64
And so on for a total of    44 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.
