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

Date : 2024-06-30
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/2z9j/wctemp_0cyc/2z9j_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.
WARNING. Date error on HEADER card:
HEADER                                                        2Z9J
 
# 2 # Note: Header records from PDB file
Header records from PDB file.
 
HEADER                                                        2Z9J
 
# 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
  0.019175  0.000000  0.004650
  0.000000  0.010384  0.000000
  0.000000  0.000000  0.015217
 
# 5 # 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 : 1.173
 CA-only RMS fit for the two chains : 0.873
 
# 6 # 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
 
# 7 # 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: 2
 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
 Polymer chain multiplicity and SEQRES multiplicity disagree 2 1
 Z agrees neither with the 3D multiplicity, nor with the SEQRES multiplicity
 It could be that Z must be one of: 2 4
 
# 8 # Warning: Matthews Coefficient (Vm) 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.
 
Very high numbers are most often caused by giving the wrong value for Z on
the CRYST1 card (or not giving this number at all), but can also result from
large fractions missing out of the molecular weight (e.g. a lot of UNK
residues, or DNA/RNA missing from virus structures).
 
 Molecular weight of all polymer chains: 66905.430
 Volume of the Unit Cell V= 330027.094
 Space group multiplicity: 2
 No NCS symmetry matrices (MTRIX records) found in PDB file
 Matthews coefficient for observed atoms and Z is high: Vm= 4.933
 No Matthews coefficient given in REMARK 280
 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
 (and the absence of MTRIX records doesn't help)
 Could it be that Z must be: 2
 This number is the multiplication of the spacegroup and NCS symmetry count
 Matthews coefficient for observed atoms and corrected Z: Vm= 2.466
 
# 9 # Note: Z missing on CRYST1 card
The messages above seem likely caused by the fact that Z is missing from the
CRYST1 card.
 
# 10 # 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.
 
# 11 # 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.
 
# 12 # 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.
 
  607 DMS  ( 802-) A  -
  608 DMS  ( 804-) A  -
  609 DTZ  ( 902-) A  -
  610 DMS  ( 801-) B  -
  611 DMS  ( 803-) B  -
  612 DTZ  ( 901-) B  -
 
# 13 # 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.
 
  609 DTZ  ( 902-) A  -
  612 DTZ  ( 901-) B  -
 
# 14 # Note: No strange inter-chain connections detected
No covalent bonds have been detected between molecules with non-identical
chain identifiers.
 
# 15 # Note: No duplicate atom names in ligands
All atom names in ligands (if any) seem adequately unique.
 
# 16 # 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).
 
# 17 # 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).
 
# 18 # 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.
 
   41 HIS  (  41-) A  -    NE2 bound to   609 DTZ  ( 902-) A  -   ZN
  343 HIS  (  41-) B  -    NE2 bound to   612 DTZ  ( 901-) B  -   ZN
 
# 19 # 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.
 
# 20 # 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.
 
# 21 # Note: All residues have a complete backbone.
No residues have missing backbone atoms.
 
# 22 # Note: No C-alpha only residues
There are no residues that consist of only an alpha carbon atom.
 
# 23 # 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)   302 (  302) A Protein             To check
     2   303 (    1)   606 (  304) B Protein             To check
     3   607 (  802)   607 (  802) A DMS                 To check
     4   608 (  804)   608 (  804) A DMS                 To check
     5   609 (  902)   609 (  902) A DTZ  <=             To check
     6   610 (  801)   610 (  801) B DMS                 To check
     7   611 (  803)   611 (  803) B DMS                 To check
     8   612 (  901)   612 (  901) B DTZ  <=             To check
     9   613 ( HOH )   613 ( HOH ) A water   (  381)     To check
    10   614 ( HOH )   614 ( HOH ) B water   (  351)     To check
MODELs skipped upon reading PDB file: 0
X-ray structure. No MODELs found
The total number of amino acids found is 606.
No nucleic acids observed in input file
No sugars recognized in input file
Number of water molecules: 732
Residue numbers increase monotonously OK
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
 
# 24 # 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
 
# 25 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 26 # 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 SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIR
(   1)-(  60)
                     70        80        90       100       110       120
                      |         |         |         |         |         |
   61 -  120 KSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNG
(  61)-( 120)
                    130       140       150       160       170       180
                      |         |         |         |         |         |
  121 -  180 SPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGK
( 121)-( 180)
                    190       200       210       220       230       240
                      |         |         |         |         |         |
  181 -  240 FYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
( 181)-( 240)
                    250       260       270       280       290       300
                      |         |         |         |         |         |
  241 -  302 PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQCSG
( 241)-( 302)
 
 
  301 -  302 SG
( 301)-( 302)
                  310       320       330       340       350       360
                    |         |         |         |         |         |
  303 -  362 SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIR
(   1)-(  60)
                  370       380       390       400       410       420
                    |         |         |         |         |         |
  363 -  422 KSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNG
(  61)-( 120)
                  430       440       450       460       470       480
                    |         |         |         |         |         |
  423 -  482 SPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGK
( 121)-( 180)
                  490       500       510       520       530       540
                    |         |         |         |         |         |
  483 -  542 FYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
( 181)-( 240)
                  550       560       570       580       590       600
                    |         |         |         |         |         |
  543 -  602 PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQC
( 241)-( 300)
 
 
  603 -  606 SGVT
( 301)-( 304)
 
 
 
 
# 27 # Note: No rounded coordinates detected
No significant rounding of atom coordinates has been detected.
 
# 28 # 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.
 
# 29 # 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.
 
# 30 # 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.
 
# 31 # 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.
 
  302 GLY  ( 302-) A  -        -OXT
  606 THR  ( 304-) B  -        OK
 
# 32 # Note: Weights administratively correct
All atomic occupancy factors ('weights') fall in the 0.0--1.0 range, which
makes them administratively correct.
 
# 33 # 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.
 
# 34 # 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.
 
# 35 # 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
 
# 36 # 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
 
# 37 # 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 :  0.455 over    4186 bonds
Average difference in B over a bond :    1.15
RMS difference in B over a bond :    1.55
 
# 38 # 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
 
# 39 # Note: B-factor plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 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 # Warning: Arginine nomenclature problem
The arginine residues listed in the table below have their NH1 and NH2
swapped.
 
    4 ARG  (   4-) A  -
  306 ARG  (   4-) B  -
 
# 46 # Note: Tyrosine torsion conventions OK
No errors were detected in tyrosine torsion angle conventions.
 
# 47 # Warning: Phenylalanine convention problem
The phenylalanine residues listed in the table below have their chi-2 not
between -90.0 and 90.0.
 
  112 PHE  ( 112-) A  -
 
# 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 # Note: All bond lengths OK
All bond lengths are in agreement with standard bond lengths using a
tolerance of 4 sigma (both standard values and sigma for amino acids
have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson
et al [REF]).
 
# 54 # Warning: Low bond length variability
Bond lengths were found to deviate less than normal from the mean Engh and
Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS
Z-score given below is expected to be near 1.0 for a normally restrained
data set. The fact that it is lower than 0.667 in this structure might
indicate that too-strong restraints have been used in the refinement. This
can only be a problem  for high resolution X-ray structures.
 
 RMS Z-score for bond lengths: 0.382
 RMS-deviation in bond distances: 0.009
 
# 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.
 
  130 MET  ( 130-) A  -    N    CA   C    99.59   -4.1
  138 GLY  ( 138-) A  -    N    CA   C   127.97    5.3
  182 TYR  ( 182-) A  -    N    CA   C    98.86   -4.4
  307 LYS  (   5-) B  -    N    CA   C    98.84   -4.4
  484 TYR  ( 182-) B  -    N    CA   C    99.02   -4.3
 
# 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: 0.716
 RMS-deviation in bond angles: 1.594
 
# 58 # 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.
 
    4 ARG  (   4-) A  -
  306 ARG  (   4-) B  -
 
# 59 # Note: Chirality OK
All protein atoms have proper chirality. But, look at the previous table to
see a series of administrative chirality problems that were corrected
automatically upon reading-in the PDB file.
The average deviation= 0.826
 
# 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 : 0.677
 
# 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.
 
  138 GLY  ( 138-) A  -   5.17
  307 LYS  (   5-) B  -   4.80
  182 TYR  ( 182-) A  -   4.71
  484 TYR  ( 182-) B  -   4.64
 
# 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 : 1.387
 
# 63 # Note: Side chain planarity OK
All of the side chains of residues that have an intact planar group are
planar within expected RMS deviations.
 
# 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 # Warning: Ramachandran Z-score low
The score expressing how well the backbone conformations of all residues
correspond to the known allowed areas in the Ramachandran plot is a bit low.
 
 Ramachandran Z-score : -3.037
 
# 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.
 
  486 PRO  ( 184-) B  -   -2.6
  106 ILE  ( 106-) A  -   -2.5
  154 TYR  ( 154-) A  -   -2.4
  401 PRO  (  99-) B  -   -2.4
  456 TYR  ( 154-) B  -   -2.4
  184 PRO  ( 184-) A  -   -2.4
  526 THR  ( 224-) B  -   -2.4
  443 LEU  ( 141-) B  -   -2.3
  524 ARG  ( 222-) B  -   -2.3
  225 THR  ( 225-) A  -   -2.2
   99 PRO  (  99-) A  -   -2.2
   27 LEU  (  27-) A  -   -2.2
  403 TYR  ( 101-) B  -   -2.2
  329 LEU  (  27-) B  -   -2.2
  139 SER  ( 139-) A  -   -2.2
  408 ILE  ( 106-) B  -   -2.2
  414 PHE  ( 112-) B  -   -2.2
   45 THR  (  45-) A  -   -2.2
   86 LEU  (  86-) A  -   -2.1
  101 TYR  ( 101-) A  -   -2.1
  388 LEU  (  86-) B  -   -2.1
  588 ILE  ( 286-) B  -   -2.1
  479 LEU  ( 177-) B  -   -2.1
  177 LEU  ( 177-) A  -   -2.1
  471 THR  ( 169-) B  -   -2.1
   60 ARG  (  60-) A  -   -2.0
 
# 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.
 
    2 GLY  (   2-) A  - Poor phi/psi
    8 PHE  (   8-) A  - Omega to (next) Pro poor
   23 GLY  (  23-) A  - Poor phi/psi
   33 ASP  (  33-) A  - Poor phi/psi
   38 CYS  (  38-) A  - Omega to (next) Pro poor
   51 ASN  (  51-) A  - Omega to (next) Pro poor
   71 GLY  (  71-) A  - Poor phi/psi
   79 GLY  (  79-) A  - Poor phi/psi
   84 ASN  (  84-) A  - Poor phi/psi
   95 ASN  (  95-) A  - Omega to (next) Pro poor
   98 THR  (  98-) A  - Omega to (next) Pro poor
  107 GLN  ( 107-) A  - Omega to (next) Pro poor
  109 GLY  ( 109-) A  - Poor phi/psi
  120 GLY  ( 120-) A  - Poor phi/psi
  121 SER  ( 121-) A  - Omega to (next) Pro poor
And so on for a total of    75 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.
 
   27 LEU  (  27-) A  -    -1.32
   86 LEU  (  86-) A  -    -1.32
   87 LEU  (  87-) A  -    -1.32
  177 LEU  ( 177-) A  -    -1.30
  268 LEU  ( 268-) A  -    -1.32
  329 LEU  (  27-) B  -    -1.32
  352 LEU  (  50-) B  -    -1.31
  377 LEU  (  75-) B  -    -1.32
  388 LEU  (  86-) B  -    -1.32
  389 LEU  (  87-) B  -    -1.32
  443 LEU  ( 141-) B  -    -1.32
  479 LEU  ( 177-) B  -    -1.31
  522 LEU  ( 220-) B  -    -1.32
  529 LEU  ( 227-) B  -    -1.32
  570 LEU  ( 268-) B  -    -1.32
And so on for a total of   256 lines.
 
# 70 # Warning: chi-1/chi-2 angle correlation Z-score low
The score expressing how well the chi-1/chi-2 angles of all residues
correspond to the populated areas in the database is
a bit low.
 
 chi-1/chi-2 correlation Z-score : -3.282
 
# 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.
 
  527 THR  ( 225-) B  -   0.35
  404 LYS  ( 102-) B  -   0.35
  344 VAL  (  42-) B  -   0.36
  102 LYS  ( 102-) A  -   0.37
  198 THR  ( 198-) A  -   0.39
  225 THR  ( 225-) A  -   0.39
  464 MET  ( 162-) 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!
 
  139 SER  ( 139-) A  -       0
  154 TYR  ( 154-) A  -       0
  182 TYR  ( 182-) A  -       0
  276 MET  ( 276-) A  -       0
  456 TYR  ( 154-) B  -       0
  467 MET  ( 165-) B  -       0
  484 TYR  ( 182-) B  -       0
  578 MET  ( 276-) B  -       0
   85 CYS  (  85-) A  -       1
  165 MET  ( 165-) A  -       1
  352 LEU  (  50-) B  -       1
  387 CYS  (  85-) B  -       1
  131 ARG  ( 131-) A  -       2
  145 CYS  ( 145-) A  -       2
  217 ARG  ( 217-) A  -       2
  433 ARG  ( 131-) B  -       2
  447 CYS  ( 145-) B  -       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 : -0.282
 
# 74 # Warning: Omega angles too tightly restrained
The omega angles for trans-peptide bonds in a structure are expected to give
a gaussian distribution with the average around +178 degrees and a standard
deviation around 5.5 degrees. These expected values were obtained from very
accurately determined structures. Many protein structures are too tightly
restrained. This seems to be the case with the current structure too, as the
observed standard deviation is below 4.0 degrees.
 
Omega average and std. deviation= 179.720 1.722
 
# 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]
 
  241 PRO  ( 241-) A  -   0.46 HIGH
  293 PRO  ( 293-) A  -   0.46 HIGH
  554 PRO  ( 252-) B  -   0.45 HIGH
 
# 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].
 
  470 PRO  ( 168-) B  - -120.9 half-chair C-delta/C-gamma (-126 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!
 
  138 GLY  ( 138-) A  -  3.26   41
 
# 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.
 
  139 SER  ( 139-) A  - TT+   Highly likely
  275 GLY  ( 275-) A  - TT+   Highly likely
  374 ASN  (  72-) B  - TT+   Highly likely
  155 ASP  ( 155-) A  - TT+   Likely
  170 GLY  ( 170-) A  - TT+   Likely
  353 ASN  (  51-) B  - 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.
 
  465 HIS  ( 163-) B  -    NE2 <-->   610 DMS  ( 801-) B  -    C2     0.43    2.67  INTRA
  294 PHE  ( 294-) A  -    CD1 <-->   298 ARG  ( 298-) A  -    NH2    0.36    2.74  INTRA BF
    5 LYS  (   5-) A  -    NZ  <-->   290 GLU  ( 290-) A  -    OE1    0.29    2.41  INTRA
  166 GLU  ( 166-) A  -    OE1 <-->   303 SER  (   1-) B  -    N      0.27    2.43  INTRA BF
  298 ARG  ( 298-) A  -    NH1 <-->   607 DMS  ( 802-) A  -    S      0.26    3.04  INTRA BF
  294 PHE  ( 294-) A  -    CE1 <-->   298 ARG  ( 298-) A  -    NH2    0.26    2.84  INTRA BF
   44 CYS  (  44-) A  -    SG  <-->    54 TYR  (  54-) A  -    CE1    0.25    3.15  INTRA
  347 THR  (  45-) B  -    CG2 <-->   348 ALA  (  46-) B  -    N      0.25    2.75  INTRA BF
  597 ASP  ( 295-) B  -    OD1 <-->   600 ARG  ( 298-) B  -    NH1    0.22    2.48  INTRA
  221 ASN  ( 221-) A  -    ND2 <-->   270 GLU  ( 270-) A  -    OE1    0.22    2.48  INTRA
  596 PHE  ( 294-) B  -    CD2 <-->   600 ARG  ( 298-) B  -    NH2    0.19    2.91  INTRA BF
  338 VAL  (  36-) B  -    CG1 <-->   391 LEU  (  89-) B  -    CB     0.17    3.03  INTRA
   11 GLY  (  11-) A  -    N   <-->   316 GLU  (  14-) B  -    OE2    0.17    2.53  INTRA BL
   21 THR  (  21-) A  -    CG2 <-->    26 THR  (  26-) A  -    OG1    0.17    2.63  INTRA
  351 MET  (  49-) B  -    O   <-->   353 ASN  (  51-) B  -    N      0.17    2.53  INTRA BF
And so on for a total of    76 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: 7.812
Total bump value per residue: 0.125
Total number of bumps: 76
Total squared bump value: 1.384
Total number of bumps in the mildest bin: 69
Total number of bumps in the second bin: 7
Total number of bumps in the middle bin: 0
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 : 0.987
 
# 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 # 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.
 
  456 TYR  ( 154-) B  -  -7.35
  154 TYR  ( 154-) A  -  -7.17
  524 ARG  ( 222-) B  -  -7.07
  222 ARG  ( 222-) A  -  -6.81
   97 LYS  (  97-) A  -  -5.95
  399 LYS  (  97-) B  -  -5.88
  491 GLN  ( 189-) B  -  -5.61
  189 GLN  ( 189-) A  -  -5.56
  581 ARG  ( 279-) B  -  -5.43
  409 GLN  ( 107-) B  -  -5.35
  107 GLN  ( 107-) A  -  -5.32
  105 ARG  ( 105-) A  -  -5.28
  279 ARG  ( 279-) A  -  -5.17
  525 PHE  ( 223-) B  -  -5.03
 
# 86 # 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.
 
# 87 # Note: Structural average packing environment OK
The structural average packing score is within normal ranges.
 
 
Average for range     1 -  606 :  -0.460
 
# 88 # 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
 
# 89 # 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
 
# 90 # 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.
 
  435 ASN  ( 133-) B  -  -2.72
  351 MET  (  49-) B  -  -2.69
  223 PHE  ( 223-) A  -  -2.63
  276 MET  ( 276-) A  -  -2.59
  399 LYS  (  97-) B  -  -2.55
  578 MET  ( 276-) B  -  -2.54
  133 ASN  ( 133-) A  -  -2.51
 
# 91 # 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
 
# 92 # 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
 
# 93 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 94 # 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.
 
# 95 # Error: Water clusters without contacts with non-water atoms
The water molecules listed in the table below are part of water molecule
clusters that do not make contacts with non-waters. These water molecules are
part of clusters that have a distance at least 1 Angstrom larger than the
sum of the Van der Waals radii to the nearest non-solvent atom. Because
these kinds of water clusters usually are not observed with X-ray diffraction
their presence could indicate a refinement artifact. The number in brackets
is the identifier of the water molecule in the input file.
 
  613 HOH  (1046 ) A  -    O
  613 HOH  (1050 ) A  -    O
  613 HOH  (1087 ) A  -    O
  613 HOH  (1090 ) A  -    O
  613 HOH  (1116 ) A  -    O
  613 HOH  (1137 ) A  -    O
  613 HOH  (1147 ) A  -    O
  613 HOH  (1153 ) A  -    O
  613 HOH  (1191 ) A  -    O
  613 HOH  (1192 ) A  -    O
  613 HOH  (1196 ) A  -    O
  613 HOH  (1199 ) A  -    O
  613 HOH  (1202 ) A  -    O
  613 HOH  (1205 ) A  -    O
  613 HOH  (1206 ) A  -    O
And so on for a total of    42 lines.
 
# 96 # Note: No waters need moving
All water molecules are sufficiently close to the asymmetric unit given in
the input file.
 
# 97 # 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.
 
  613 HOH  (1018 ) A  -    O
  613 HOH  (1046 ) A  -    O
  613 HOH  (1084 ) A  -    O
  613 HOH  (1087 ) A  -    O
  613 HOH  (1116 ) A  -    O
  613 HOH  (1117 ) A  -    O
  613 HOH  (1128 ) A  -    O
  613 HOH  (1137 ) A  -    O
  613 HOH  (1153 ) A  -    O
  613 HOH  (1156 ) A  -    O
  613 HOH  (1191 ) A  -    O
  613 HOH  (1200 ) A  -    O
  613 HOH  (1205 ) A  -    O
  613 HOH  (1206 ) A  -    O
  613 HOH  (1211 ) A  -    O
And so on for a total of    41 lines.
 
# 98 # 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.
 
   41 HIS  (  41-) A  -
   95 ASN  (  95-) A  -
  134 HIS  ( 134-) A  -
  151 ASN  ( 151-) A  -
  192 GLN  ( 192-) A  -
  256 GLN  ( 256-) A  -
  343 HIS  (  41-) B  -
  421 ASN  ( 119-) B  -
  436 HIS  ( 134-) B  -
  516 ASN  ( 214-) B  -
  523 ASN  ( 221-) B  -
  548 HIS  ( 246-) B  -
  575 GLN  ( 273-) B  -
Atom is not a donor    41 HIS (  41-)A  -    ND1
Atom is not a donor   343 HIS (  41-)B  -    ND1
 
# 99 # 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.
 
   64 HIS  (  64-) A  -   HIS-H   0.11 HIS-E   0.58
   80 HIS  (  80-) A  -   HIS-H   0.11
  134 HIS  ( 134-) A  -   HIS-H   0.12 HIS-E   0.62
  163 HIS  ( 163-) A  -   HIS-H   0.09 HIS-E   0.56
  164 HIS  ( 164-) A  -   HIS-H   0.14 HIS-D   0.62
  172 HIS  ( 172-) A  -   HIS-H   0.24 HIS-D   0.51
  246 HIS  ( 246-) A  -   HIS-H   0.10 HIS-D   0.56
  366 HIS  (  64-) B  -   HIS-H   0.10 HIS-E   0.57
  382 HIS  (  80-) B  -   HIS-H   0.07
  436 HIS  ( 134-) B  -   HIS-H   0.19 HIS-D   0.60
  465 HIS  ( 163-) B  -   HIS-H   0.20 HIS-D   0.65
  466 HIS  ( 164-) B  -   HIS-H   0.08 HIS-E   0.60
  474 HIS  ( 172-) B  -   HIS-H   0.06 HIS-E   0.58
  548 HIS  ( 246-) B  -   HIS-H   0.11 HIS-E   0.58
 
# 100 # 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.
 
   45 THR  (  45-) A  -    N
   60 ARG  (  60-) A  -    N
   93 THR  (  93-) A  -    N
  113 SER  ( 113-) A  -    OG
  127 GLN  ( 127-) A  -    NE2
  138 GLY  ( 138-) A  -    N
  140 PHE  ( 140-) A  -    N
  145 CYS  ( 145-) A  -    N
  152 ILE  ( 152-) A  -    N
  169 THR  ( 169-) A  -    OG1
  185 PHE  ( 185-) A  -    N
  198 THR  ( 198-) A  -    N
  214 ASN  ( 214-) A  -    ND2
  219 PHE  ( 219-) A  -    N
  225 THR  ( 225-) A  -    N
And so on for a total of    39 lines.
 
# 101 # 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.
 
  172 HIS  ( 172-) A  -    NE2
  376 GLN  (  74-) B  -    OE1
  465 HIS  ( 163-) B  -    NE2
 
# 102 # 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: 865
- of which buried: 457
Total number of acceptors: 933
- of which buried: 388
Total number of donor+acceptors: 105
  (e.g. the Ser Ogamma that can donate and accept)
- of which buried: 28
Buried donors: 457
- without H-bond: 35
- essentially without H-bond: 0
- with only a very poor H-bond: 0
- with a poor H-bond: 6
- with a H-bond: 416
Buried acceptors: 388
- without H-bond: 56
- essentially without H-bond: 0
- with only a very poor H-bond: 4
- with a poor H-bond: 5
- with a H-bond: 323
 
# 103 # 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)   302 (  302) A Protein             To check
     2   303 (    1)   606 (  304) B Protein             To check
     3   607 (  802)   607 (  802) A DMS                 To check
     4   608 (  804)   608 (  804) A DMS                 To check
     5   609 (  902)   609 (  902) A DTZ  <=             To check
     6   610 (  801)   610 (  801) B DMS                 To check
     7   611 (  803)   611 (  803) B DMS                 To check
     8   612 (  901)   612 (  901) B DTZ  <=             To check
     9   613 ( HOH )   613 ( HOH ) A water   (  381)     To check
    10   614 ( HOH )   614 ( HOH ) B water   (  351)     To check
 
# 104 # 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  :   1.950
  1st generation packing quality :   0.101 (          (  -0.3,  2.5))
  2nd generation packing quality :  -1.997 (          (  -1.1,  1.4))
  Ramachandran plot appearance   :  -3.037 (poor      (  -0.9,  1.2))
  chi-1/chi-2 rotamer normality  :  -3.282 (poor      (  -2.5,  1.4))
  Backbone conformation          :  -0.282 (          (  -0.5,  3.3))
  Inside/Outside distribution    :   0.987
 
 RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.382 (tight)
  Bond angles                    :   0.716
  Omega angle restraints         :   0.313 (tight)
  Side chain planarity           :   0.281 (tight)
  Improper dihedral distribution :   0.677
  B-factor distribution          :   0.455
 
# 105 # 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.
 
# 106 # 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.
 
# 107 # 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.
 
# 108 # Note: Bond length variabilty Z-score low
With a resolution of 1.5-2.5 Angstrom, you might have enough data to warrant
more bond length variability that we observed (less than 0.5). If your
resolution is close to 1.5 Angstrom, you can consider allowing the refinement
software more freedom when it comes to applying the bond length target
restraints. If your resolution is close to 2.5 Angstrom, you can do this too,
but you might want to be a bit careful.
 
# 109 # 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.
 
# 110 # Note: Free floating waters
Your structure contains many 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.
 
# 111 # 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.
 
  456 TYR  ( 154-) B  -     14.88
  154 TYR  ( 154-) A  -     14.48
  524 ARG  ( 222-) B  -     14.22
  222 ARG  ( 222-) A  -     13.62
   97 LYS  (  97-) A  -     11.91
  399 LYS  (  97-) B  -     11.77
  409 GLN  ( 107-) B  -     11.75
  491 GLN  ( 189-) B  -     11.22
  189 GLN  ( 189-) A  -     11.12
  107 GLN  ( 107-) A  -     11.02
  581 ARG  ( 279-) B  -     10.86
  105 ARG  ( 105-) A  -     10.57
  279 ARG  ( 279-) A  -     10.34
  525 PHE  ( 223-) B  -     10.07
  138 GLY  ( 138-) A  -      6.81
And so on for a total of    62 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.
