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

Date : 2023-08-11
This report was created by WHAT IF version WHATCHECK15.0

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

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

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

Some remarks regarding the output:

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

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

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



=========================================
==== Compound code /zata/tempdir/1hr2/wctemp_0cyc/1hr2_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 # Note: Header records from PDB file
Header records from PDB file.
 
HEADER    RNA                                     20-DEC-00   1HR2
 TETRAHYMENA THEMOPHILA GROUP I INTRON.
 
# 3 # 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 21 21 21
 Number of matrices in space group: 4
 Highest polymer chain multiplicity in structure: 2
 Highest polymer chain multiplicity according to SEQRES: 2
 No explicit MTRIX NCS matrices found in the input file
 Value of Z as found on the CRYST1 card: 0
 BIOMT matrices have been found but not enough to explain the difference
 
# 4 # 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: 102934.664
 Volume of the Unit Cell V= 1375978.8
 Space group multiplicity: 4
 No NCS symmetry matrices (MTRIX records) found in PDB file
 Matthews coefficient for observed atoms and Z is high: Vm= 26.735
 BIOMT matrices observed in the PDB file: 2
 But accounting for these BIOMT matrices does not make Vm reasonable yet
 Matthews coefficient read from REMARK 280 Vm= 3.370
 Vm by authors and this calculated Vm do not agree very well
 
# 5 # Note: Z missing on CRYST1 card
The messages above seem likely caused by the fact that Z is missing from the
CRYST1 card.
 
# 6 # 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.
 
# 7 # 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.
 
# 8 # Note: No strange inter-chain connections detected
No covalent bonds have been detected between molecules with non-identical
chain identifiers.
 
# 9 # Note: No duplicate atom names in ligands
All atom names in ligands (if any) seem adequately unique.
 
# 10 # Note: In all cases the primary alternate atom was used
WHAT CHECK saw no need to make any alternate atom corrections (which means
they either are all correct, or there are none).
 
# 11 # Note: No residues detected inside ligands
Either this structure does not contain ligands with amino acid groups inside
it, or their naming is proper (enough).
 
# 12 # Note: No attached groups interfere with hydrogen bond calculations
It seems there are no sugars, lipids, etc., bound (or very close) to atoms
that otherwise could form hydrogen bonds.
 
# 13 # Note: No probable side chain atoms with zero occupancy detected.
Either there are no side chain atoms with zero occupancy, or the side chain
atoms with zero occupancy were not present in the input PDB file (in which
case they are listed as missing atoms), or their positions are sufficiently
improbable to warrant a zero occupancy.
 
# 14 # Note: No probable backbone atoms with zero occupancy detected.
Either there are no backbone atoms with zero occupancy, or the backbone
atoms with zero occupancy were left out of the input PDB file (in
which case they are listed as missing atoms), or their positions are
sufficiently improbable to warrant a zero occupancy.
 
# 15 # Note: All residues have a complete backbone.
No residues have missing backbone atoms.
 
# 16 # Note: No C-alpha only residues
There are no residues that consist of only an alpha carbon atom.
 
# 17 # Note: Content of the PDB file as interpreted by WHAT CHECK
Content of the PDB file as interpreted by WHAT CHECK.
WHAT CHECK has read your PDB file, and stored it internally in what is called
'the soup'. The content of this soup is listed here. An extensive explanation
of all frequently used WHAT CHECK output formats can be found at
swift.cmbi.ru.nl. Look under output formats. A course on reading this
'Molecules' table is part of the WHAT CHECK website.
 
     1     1 (  103)   157 (  260) A DNA/RNA             /zata/tempdir/1hr...
     2   158 (  102)   315 (  260) B DNA/RNA             /zata/tempdir/1hr...
     3   316 (   51)   316 (   51) A MG                  /zata/tempdir/1hr...
     4   317 (   53)   317 (   53) A MG                  /zata/tempdir/1hr...
     5   318 (   55)   318 (   55) A MG                  /zata/tempdir/1hr...
     6   319 (   57)   319 (   57) A MG                  /zata/tempdir/1hr...
     7   320 (   58)   320 (   58) A MG                  /zata/tempdir/1hr...
     8   321 (   59)   321 (   59) A MG                  /zata/tempdir/1hr...
     9   322 (   60)   322 (   60) A MG                  /zata/tempdir/1hr...
    10   323 (   61)   323 (   61) A MG                  /zata/tempdir/1hr...
    11   324 (   62)   324 (   62) A MG                  /zata/tempdir/1hr...
    12   325 (   64)   325 (   64) A MG                  /zata/tempdir/1hr...
    13   326 (    1)   326 (    1) A MG                  /zata/tempdir/1hr...
    14   327 (    3)   327 (    3) A MG                  /zata/tempdir/1hr...
    15   328 (    5)   328 (    5) A MG                  /zata/tempdir/1hr...
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 nucleic acids found is 315.
No sugars recognized in input file
Number of water molecules: 265
of which 6 are poor
Residue numbers increase monotonously OK
 
# 18 # Note: Chain identifiers seem OK
All ions seem to have a logical chain identifier, or there are no ions
present in the input file.
 
# 19 # Note: No rounded coordinates detected
No significant rounding of atom coordinates has been detected.
 
# 20 # 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.
 
# 21 # Warning: B-factors outside the range 0.0 - 100.0
In principle, B-factors can have a very wide range of values, but in
practice, B-factors should not be zero while B-factors above 100.0
are a good indicator that the location of that atom is meaningless. Be
aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms
with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with
a B-factor of zero were observed.
 
    1 OGUA ( 103-) A  -   High
    2 OADE ( 104-) A  -   High
    3 OADE ( 105-) A  -   High
    4 OURA ( 106-) A  -   High
    5 OURA ( 107-) A  -   High
    6 OGUA ( 108-) A  -   High
    7 OCYT ( 109-) A  -   High
   20 OADE ( 122-) A  -   High
   21 OADE ( 123-) A  -   High
   22 OCYT ( 124-) A  -   High
   23 OADE ( 125-) A  -   High
   27 OGUA ( 129-) A  -   High
   28 OURA ( 130-) A  -   High
   29 OURA ( 131-) A  -   High
   30 OCYT ( 132-) A  -   High
And so on for a total of    71 lines.
Since there is no protein, no test for the presence of C-terminal oxygens
was performed.
 
# 22 # Note: Weights administratively correct
All atomic occupancy factors ('weights') fall in the 0.0--1.0 range, which
makes them administratively correct.
 
# 23 # 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.
 
# 24 # 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.
 
# 25 # 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
 
Crystal temperature (K) :100.000
 
# 26 # Note: Insufficient residues for statistics
Not enough (intact) amino acids were observed to reliably evaluate the
percentage of buried residues with a low B-factor as a function of the
temperature during X-ray data collection.
 
Number of (intact) amino acids observed :    0
 
# 27 # 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
 
# 28 # 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.
Since there is no protein, no amino acid name convention check was performed.
 
# 29 # Note: No decreasing residue numbers
All residue numbers are strictly increasing within each chain.
 
# 30 # 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.
 
    3 OADE ( 105-) A  -    O5'  C5'   1.34   -6.2
  303 OADE ( 248-) B  -    O5'  C5'   1.38   -4.0
 
# 31 # 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: 0.489
 RMS-deviation in bond distances: 0.006
 
# 32 # 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.
 
    1 OGUA ( 103-) A  -    O3'  C3'  C2' 122.96    4.3
    1 OGUA ( 103-) A  -    C2'  C1'  N9  120.88    4.7
    1 OGUA ( 103-) A  -    N9   C8   N7  113.49    4.8
    2 OADE ( 104-) A  -    O5*  P   -O3* 126.87   12.0
    2 OADE ( 104-) A  -    P   -C3* -O3* 172.86   44.3
    2 OADE ( 104-) A  -    C3'  C4'  C5' 122.67    4.8
    3 OADE ( 105-) A  -    C3'  C4'  C5' 108.48   -4.7
    4 OURA ( 106-) A  -    C3'  C4'  C5' 109.04   -4.3
    6 OGUA ( 108-) A  -    N9   C8   N7  113.26    4.3
    8 OGUA ( 110-) A  -    N9   C8   N7  113.12    4.0
   14 OGUA ( 116-) A  -    N9   C8   N7  113.23    4.3
   15 OGUA ( 117-) A  -    N9   C8   N7  113.11    4.0
   16 OGUA ( 118-) A  -    N9   C8   N7  113.13    4.1
   20 OADE ( 122-) A  -    O3'  C3'  C4' 121.31    4.1
   20 OADE ( 122-) A  -    O3'  C3'  C2' 127.81    6.0
And so on for a total of    84 lines.
 
# 33 # 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: 0.774
 RMS-deviation in bond angles: 1.226
Since there is no protein, no tau anglecheck was performed.
Since there is no protein, no calibrated planarity check was performed.
 
# 34 # Note: Uncalibrated side chain planarity OK
All of the side chains of DNA/RNA residues (and groups in proteins that
contain a proton and are supposed to be planar) are planar within 0.10
Angstrom RMS (or no intact DNA/RNA was found...). Please be aware that
this check cannot be callibrated and that the cutoff of 0.10 Angstrom thus
is a wild guess.
Since there is no protein, no Ramachandran check was performed.
Since there is no protein, no torsion angle evaluation was performed.
Since there is no protein, no chi1-chi2 check was performed.
Since there is no protein, no rotamer check was performed.
Since there is no protein, no backbone conformation check was performed.
Since there is no protein, no omega check was performed.
 
# 35 # Note: No prolines in structure
Since there are no proline residues in the structure, the PRO puckering
check was skipped.
Since there is no protein, no backbone oxygen evaluation was performed.
 
# 36 # Note: Peptide bond conformations
There was no need to complain about the peptide bond of a single amino acid.
 
# 37 # 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.
 
    5 OURA ( 107-) A  -    C5  <-->   157 OCYT ( 260-) A  -    N3     0.64    2.46  INTRA BF
    1 OGUA ( 103-) A  -    C5' <-->   116 OADE ( 219-) A  -    N3     0.59    2.51  INTRA BF
  115 OADE ( 218-) A  -    C2' <-->   116 OADE ( 219-) A  -    C5'    0.50    2.70  INTRA BF
    3 OADE ( 105-) A  -    C5' <-->     4 OURA ( 106-) A  -    P      0.48    2.82  INTRA BF
    1 OGUA ( 103-) A  -    C5' <-->   115 OADE ( 218-) A  -    N1     0.47    2.63  INTRA BF
  189 OADE ( 133-) B  -    N1  <-->   246 OURA ( 190-) B  -    N3     0.41    2.59  INTRA BF
    9 OGUA ( 111-) A  -    N1  <-->   107 OADE ( 210-) A  -    N1     0.40    2.60  INTRA BL
    4 OURA ( 106-) A  -    C4  <-->   157 OCYT ( 260-) A  -    C2     0.39    2.81  INTRA BF
  273 OADE ( 218-) B  -    C2  <-->   274 OADE ( 219-) B  -    N6     0.36    2.74  INTRA BF
    5 OURA ( 107-) A  -    C5  <-->   157 OCYT ( 260-) A  -    C2     0.34    2.86  INTRA BF
   82 OADE ( 184-) A  -    N3  <-->   109 OGUA ( 212-) A  -    N2     0.34    2.66  INTRA BL
  283 OURA ( 228-) B  -    N3  <-->   301 OADE ( 246-) B  -    N1     0.33    2.67  INTRA BL
   44 OADE ( 146-) A  -    N1  <-->    55 OURA ( 157-) A  -    N3     0.33    2.67  INTRA BF
  201 OCYT ( 145-) B  -    N3  <-->   214 OGUA ( 158-) B  -    N1     0.33    2.67  INTRA BL
    2 OADE ( 104-) A  -    P   <-->   115 OADE ( 218-) A  -    N6     0.32    2.98  INTRA BF
And so on for a total of   206 lines.
 
# 38 # 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: 28.113
Total bump value per residue: 0.654
Total number of bumps: 206
Total squared bump value: 6.445
Total number of bumps in the mildest bin: 173
Total number of bumps in the second bin: 30
Total number of bumps in the middle bin: 3
Total number of bumps in the fourth bin: 0
Total number of bumps in the worst bin: 0
There is not enough protein in the PDB file to perform either the
inside/outside distribution check, or the packing normality checks.
 
# 39 # 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 this output 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.
 
Many hydrogen bond related checks skipped.
 
The content of the PDB file makes most hydrogen bond related checks rather
useless. For just nucleic acids these checks do not add much value and when
there are either no amino acids, or too many broken amino acids the outcome
of this set of checks cannot be trusted. So, please keep your brain switched
on while looking at the validation results in this section.
 
     1     1 (  103)   157 (  260) A DNA/RNA             /zata/tempdir/1hr...
     2   158 (  102)   315 (  260) B DNA/RNA             /zata/tempdir/1hr...
     3   316 (   51)   316 (   51) A MG                  /zata/tempdir/1hr...
     4   317 (   53)   317 (   53) A MG                  /zata/tempdir/1hr...
     5   318 (   55)   318 (   55) A MG                  /zata/tempdir/1hr...
     6   319 (   57)   319 (   57) A MG                  /zata/tempdir/1hr...
     7   320 (   58)   320 (   58) A MG                  /zata/tempdir/1hr...
     8   321 (   59)   321 (   59) A MG                  /zata/tempdir/1hr...
     9   322 (   60)   322 (   60) A MG                  /zata/tempdir/1hr...
    10   323 (   61)   323 (   61) A MG                  /zata/tempdir/1hr...
    11   324 (   62)   324 (   62) A MG                  /zata/tempdir/1hr...
    12   325 (   64)   325 (   64) A MG                  /zata/tempdir/1hr...
    13   326 (    1)   326 (    1) A MG                  /zata/tempdir/1hr...
    14   327 (    3)   327 (    3) A MG                  /zata/tempdir/1hr...
    15   328 (    5)   328 (    5) A MG                  /zata/tempdir/1hr...
And so on for a total of    46 lines.
 
# 40 # Note: Crystallisation conditions from REMARK 280
Crystallisation conditions as found in the PDB file header.
 
CRYSTAL
SOLVENT CONTENT, VS   (%): 63.46
MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.37
CRYSTALLIZATION CONDITIONS: MPD, MAGNESIUM CHLORIDE, SODIUM
CACODYLATE, SPERMINE, SODIUM CHLORIDE, PH 6.5, VAPOR DIFFUSION,
SITTING DROP, TEMPERATURE 293K
 
# 41 # 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.
 
  359 HOH  ( 306 ) B  -    O
 
# 42 # Note: No waters need moving
All water molecules are sufficiently close to the asymmetric unit given in
the input file.
 
# 43 # 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.
 
  359 HOH  ( 306 ) B  -    O
 
# 44 # Note: Summary report about a structure
This is an overall summary of the quality of the structure as
compared with currently accepted standard values. This structure does
not contain any (recognizable) protein. As this software is specialized
in checking protein structures, this summary is of limited value.
 
  Resolution read from PDB file  :   2.250
 
 RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.489 (tight)
  Bond angles                    :   0.774
 
# 45 # 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.
 
# 46 # Warning: Validation report has little value
WHAT CHECK was designed to validate normal protein structures. It is
neither the ideal validation tool for nucleic acid structures, nor for
protein structures of which you already know that there is trouble. For
example, if you only deposit coordinates for the alpha carbons, this
report becomes nearly meaningless.
Number of amino acids in the PDB file : 0
The number of nucleic acids is : 315
which is much more even than the number of amino acids
 
# 47 # 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.
 
# 48 # 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.
 
# 49 # 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.
 
# 50 # 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.
 
# 51 # 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.
 
    1 OGUA ( 103-) A  -     36.70
    2 OADE ( 104-) A  -     21.02
  303 OADE ( 248-) B  -     19.79
   23 OADE ( 125-) A  -     16.66
  146 OURA ( 249-) A  -     15.58
  109 OGUA ( 212-) A  -     12.20
   20 OADE ( 122-) A  -     11.62
  244 OGUA ( 188-) B  -     10.81
  189 OADE ( 133-) B  -     10.50
  147 OGUA ( 250-) A  -     10.38
   82 OADE ( 184-) A  -     10.05
  179 OADE ( 123-) B  -      8.88
  145 OADE ( 248-) A  -      8.62
   77 OURA ( 179-) A  -      8.53
  214 OGUA ( 158-) B  -      8.47
And so on for a total of   155 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.
