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

Date : 2025-02-02
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/3scj/wctemp_0cyc/3scj_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                                                        3SCJ
 
# 2 # Note: Header records from PDB file
Header records from PDB file.
 
HEADER                                                        3SCJ
 
# 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
  0.012312  0.000000  0.000471
  0.000000  0.008384  0.000000
  0.000000  0.000000  0.008838
 
# 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: E and F
 
 All-atom RMS fit for the two chains : 0.212
 CA-only RMS fit for the two chains : 0.158
 
# 6 # Note: Low non-crystallographic symmetry phi and psi differences
All comparable residues in the two chains mentioned below have comparable
backbone torsion angles
 
Chain identifiers of the two chains: E and F
 
# 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: 2
 No explicit MTRIX NCS matrices found in the input file
 Value of Z as found on the CRYST1 card: 0
 Z, symmetry, and molecular multiplicity disagree
 Could it be that Z must be: 4
 
# 8 # 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: 177839.391
 Volume of the Unit Cell V= 1096179.2
 Space group multiplicity: 2
 No NCS symmetry matrices (MTRIX records) found in PDB file
 Matthews coefficient for observed atoms and Z is high: Vm= 12.328
 No Matthews coefficient given in REMARK 280
 Or should we use the previously suggested Z = 4
 which would result in Vm= 3.082
 And remember, a matrix counting problem has been reported earlier already
 
# 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: No strange inter-chain connections detected
No covalent bonds have been detected between molecules with non-identical
chain identifiers.
 
# 12 # Note: No duplicate atom names in ligands
All atom names in ligands (if any) seem adequately unique.
 
# 13 # 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).
 
# 14 # 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).
 
# 15 # 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.
 
# 16 # 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.
 
# 17 # 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.
 
# 18 # Note: All residues have a complete backbone.
No residues have missing backbone atoms.
 
# 19 # Note: No C-alpha only residues
There are no residues that consist of only an alpha carbon atom.
 
# 20 # 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 (   19)   597 (  615) A Protein             /zata/tempdir/3sc...
     2   598 (   19)  1194 (  615) B Protein             /zata/tempdir/3sc...
     3  1195 (  323)  1368 (  502) E Protein             /zata/tempdir/3sc...
     4  1369 (  323)  1542 (  502) F Protein             /zata/tempdir/3sc...
     5  1543 (  901)  1543 (  901) A  ZN                 /zata/tempdir/3sc...
     6  1544 (  902)  1544 (  902) A  CL                 /zata/tempdir/3sc...
     7  1545 (  901)  1545 (  901) B  ZN                 /zata/tempdir/3sc...
     8  1546 (  902)  1546 (  902) B  CL                 /zata/tempdir/3sc...
MODELs skipped upon reading PDB file: 0
X-ray structure. No MODELs found
The total number of amino acids found is 1542
of which 1019 have poor or (essentially) missing atoms
No nucleic acids observed in input file
No sugars recognized in input file
No water observed in input file
Residue numbers increase monotonously OK
 
# 21 # Note: Chain identifiers seem OK
All ions seem to have a logical chain identifier, or there are no ions
present in the input file.
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
 
# 22 # 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
 
# 23 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 24 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: E
 
# 25 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: F
 
# 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 STIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQNMNNAGDKWSAFLKEQST
(  19)-(  78)
                     70        80        90       100       110       120
                      |         |         |         |         |         |
   61 -  120 LAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNP
(  79)-( 138)
                    130       140       150       160       170       180
                      |         |         |         |         |         |
  121 -  180 QECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYED
( 139)-( 198)
                    190       200       210       220       230       240
                      |         |         |         |         |         |
  181 -  240 YGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHLHAYVRAKLMNAYPSYISP
( 199)-( 258)
                    250       260       270       280       290       300
                      |         |         |         |         |         |
  241 -  300 IGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSV
( 259)-( 318)
                    310       320       330       340       350       360
                      |         |         |         |         |         |
  301 -  360 GLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILMCTKVTMDDFLTAHHEMGH
( 319)-( 378)
                    370       380       390       400       410       420
                      |         |         |         |         |         |
  361 -  420 IQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNETEINF
( 379)-( 438)
                    430       440       450       460       470       480
                      |         |         |         |         |         |
  421 -  480 LLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYC
( 439)-( 498)
                    490       500       510       520       530       540
                      |         |         |         |         |         |
  481 -  540 DPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLFNML
( 499)-( 558)
                    550       560       570       580       590
                      |         |         |         |         |
  541 -  597 RLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNKNSFVGWSTDWSPYAD
( 559)-( 615)
             600       610       620       630       640       650
               |         |         |         |         |         |
  598 -  657 STIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQNMNNAGDKWSAFLKEQST
(  19)-(  78)
             660       670       680       690       700       710
               |         |         |         |         |         |
  658 -  717 LAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNP
(  79)-( 138)
             720       730       740       750       760       770
               |         |         |         |         |         |
  718 -  777 QECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYED
( 139)-( 198)
             780       790       800       810       820       830
               |         |         |         |         |         |
  778 -  837 YGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHLHAYVRAKLMNAYPSYISP
( 199)-( 258)
             840       850       860       870       880       890
               |         |         |         |         |         |
  838 -  897 IGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSV
( 259)-( 318)
             900       910       920       930       940       950
               |         |         |         |         |         |
  898 -  957 GLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILMCTKVTMDDFLTAHHEMGH
( 319)-( 378)
             960       970       980       990      1000      1010
               |         |         |         |         |         |
  958 - 1017 IQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNETEINF
( 379)-( 438)
            1020      1030      1040      1050      1060      1070
               |         |         |         |         |         |
 1018 - 1077 LLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYC
( 439)-( 498)
            1080      1090      1100      1110      1120      1130
               |         |         |         |         |         |
 1078 - 1137 DPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLFNML
( 499)-( 558)
            1140      1150      1160      1170      1180      1190
               |         |         |         |         |         |
 1138 - 1194 RLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNKNSFVGWSTDWSPYAD
( 559)-( 615)
               1200      1210      1220      1230      1240      1250
                  |         |         |         |         |         |
 1195 - 1254 CPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNVYADSFV
( 323)-( 388)
               1260      1270      1280      1290      1300      1310
                  |         |         |         |         |         |
 1255 - 1314 VKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKL
( 389)-( 448)
               1320      1330      1340      1350      1360
                  |         |         |         |         |
 1315 - 1368 RPFERDISNVPFSPDGKPCTPPAPNCYWPLRGYGFYTTTGIGYQPYRVVVLSFE
( 449)-( 502)
           1370      1380      1390      1400      1410      1420
              |         |         |         |         |         |
 1369 - 1428 CPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNVYADSFV
( 323)-( 388)
           1430      1440      1450      1460      1470      1480
              |         |         |         |         |         |
 1429 - 1488 VKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKL
( 389)-( 448)
           1490      1500      1510      1520      1530      1540
              |         |         |         |         |         |
 1489 - 1542 RPFERDISNVPFSPDGKPCTPPAPNCYWPLRGYGFYTTTGIGYQPYRVVVLSFE
( 449)-( 502)
 
 
 
 
# 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 # 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 SER  (  19-) A  -   High
    2 THR  (  20-) A  -   High
    3 ILE  (  21-) A  -   High
    4 GLU  (  22-) A  -   High
    5 GLU  (  23-) A  -   High
    6 GLN  (  24-) A  -   High
    7 ALA  (  25-) A  -   High
    8 LYS  (  26-) A  -   High
    9 THR  (  27-) A  -   High
   10 PHE  (  28-) A  -   High
   11 LEU  (  29-) A  -   High
   20 ASP  (  38-) A  -   High
   31 ASN  (  49-) A  -   High
   32 TYR  (  50-) A  -   High
   33 ASN  (  51-) A  -   High
And so on for a total of  1017 lines.
 
# 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.
 
  597 ASP  ( 615-) A  -        OK
 1194 ASP  ( 615-) B  -        OK
 1247 ASN  ( 375-) E  -        OK (6)
 1368 GLU  ( 502-) E  -        OK
 1421 ASN  ( 375-) F  -        OK (6)
 1542 GLU  ( 502-) F  -        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: 1
 
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 :  0.372 over    4330 bonds
Average difference in B over a bond :    1.09
RMS difference in B over a bond :    1.42
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
 
# 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: B-factor plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: E
 
# 41 # Note: B-factor plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: F
 
# 42 # 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.
 
# 43 # Note: Valine nomenclature OK
No errors were detected in valine nomenclature.
 
# 44 # Note: Threonine nomenclature OK
No errors were detected in threonine nomenclature.
 
# 45 # Note: Isoleucine nomenclature OK
No errors were detected in isoleucine nomenclature.
 
# 46 # Note: Leucine nomenclature OK
No errors were detected in leucine nomenclature.
 
# 47 # Warning: Arginine nomenclature problem
The arginine residues listed in the table below have their NH1 and NH2
swapped.
 
   97 ARG  ( 115-) A  -
  151 ARG  ( 169-) A  -
  159 ARG  ( 177-) A  -
  174 ARG  ( 192-) A  -
  227 ARG  ( 245-) A  -
  255 ARG  ( 273-) A  -
  339 ARG  ( 357-) A  -
  500 ARG  ( 518-) A  -
  694 ARG  ( 115-) B  -
  748 ARG  ( 169-) B  -
  756 ARG  ( 177-) B  -
  771 ARG  ( 192-) B  -
  824 ARG  ( 245-) B  -
  852 ARG  ( 273-) B  -
  936 ARG  ( 357-) B  -
 1097 ARG  ( 518-) B  -
 
# 48 # Note: Tyrosine torsion conventions OK
No errors were detected in tyrosine torsion angle conventions.
 
# 49 # Warning: Phenylalanine convention problem
The phenylalanine residues listed in the table below have their chi-2 not
between -90.0 and 90.0.
 
 1500 PHE  ( 460-) F  -
 
# 50 # Note: Aspartic acid torsion conventions OK
No errors were detected in aspartic acid torsion angle conventions.
 
# 51 # Note: Glutamic acid torsion conventions OK
No errors were detected in glutamic acid torsion angle conventions.
 
# 52 # 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).
 
# 53 # 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.
 
# 54 # Note: No decreasing residue numbers
All residue numbers are strictly increasing within each chain.
 
# 55 # 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.
 
  869 ASN  ( 290-) B  -    N   -C     1.42    4.3
 
# 56 # 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: 0.454
 RMS-deviation in bond distances: 0.010
 
# 57 # Warning: Possible cell scaling problem
Comparison of bond distances with Engh and Huber [REF] standard values for
protein residues and Parkinson et al [REF] values for DNA/RNA shows a
significant systematic deviation. It could be that the unit cell used in
refinement was not accurate enough. The deformation matrix given below gives
the deviations found: the three numbers on the diagonal represent the
relative corrections needed along the A, B and C cell axis. These values are
1.000 in a normal case, but have significant deviations here (significant at
the 99.99 percent confidence level)
 
There are a number of different possible causes for the discrepancy. First
the cell used in refinement can be different from the best cell calculated.
Second, the value of the wavelength used for a synchrotron data set can be
miscalibrated. Finally, the discrepancy can be caused by a dataset that has
not been corrected for significant anisotropic thermal motion.
 
Please note that the proposed scale matrix has NOT been restrained to obey
the space group symmetry. This is done on purpose. The distortions can give
you an indication of the accuracy of the determination.
 
If you intend to use the result of this check to change the cell dimension
of your crystal, please read the extensive literature on this topic first.
This check depends on the wavelength, the cell dimensions, and on the
standard bond lengths and bond angles used by your refinement software.
 
SCALE matrix obtained from PDB file
  0.012312  0.000000  0.000471
  0.000000  0.008384  0.000000
  0.000000  0.000000  0.008838
Unit Cell deformation matrix
  1.000130 -0.000008  0.000589
 -0.000008  0.995570 -0.000214
  0.000589 -0.000214  0.996697
Proposed new scale matrix
  0.012311  0.000000  0.000465
  0.000000  0.008421  0.000002
 -0.000005  0.000002  0.008867
With corresponding cell
    A    =  81.230  B   = 118.749  C    = 112.857
    Alpha=  90.000  Beta=  92.130  Gamma=  90.000
 
The CRYST1 cell dimensions
    A    =  81.219  B   = 119.277  C    = 113.236
    Alpha=  90.000  Beta=  92.190  Gamma=  90.000
 
 Variance: 426.188
 (Under-)estimated Z-score: 15.215
 
# 58 # 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.
 
  399 HIS  ( 417-) A  -    CG   ND1  CE1 109.61    4.0
  475 HIS  ( 493-) A  -    CG   ND1  CE1 109.66    4.1
  996 HIS  ( 417-) B  -    CG   ND1  CE1 109.67    4.1
 1072 HIS  ( 493-) B  -    CG   ND1  CE1 109.77    4.2
 1202 ASN  ( 330-) E  -    N    CA   C    98.05   -4.7
 1376 ASN  ( 330-) F  -    N    CA   C    97.41   -4.9
 
# 59 # Warning: Low bond angle variability
Bond angles were found to deviate less than normal from the 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. 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 angles: 0.612
 RMS-deviation in bond angles: 1.316
 
# 60 # 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.
 
   97 ARG  ( 115-) A  -
  151 ARG  ( 169-) A  -
  159 ARG  ( 177-) A  -
  174 ARG  ( 192-) A  -
  227 ARG  ( 245-) A  -
  255 ARG  ( 273-) A  -
  339 ARG  ( 357-) A  -
  500 ARG  ( 518-) A  -
  694 ARG  ( 115-) B  -
  748 ARG  ( 169-) B  -
  756 ARG  ( 177-) B  -
  771 ARG  ( 192-) B  -
  824 ARG  ( 245-) B  -
  852 ARG  ( 273-) B  -
  936 ARG  ( 357-) B  -
 1097 ARG  ( 518-) B  -
 
# 61 # 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= 0.645
 
# 62 # 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 : 0.552
 
# 63 # 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.
 
 1376 ASN  ( 330-) F  -   4.68
 1202 ASN  ( 330-) E  -   4.47
 
# 64 # 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 : 1.014
 
# 65 # Note: Side chain planarity OK
All of the side chains of residues that have an intact planar group are
planar within expected RMS deviations.
 
# 66 # 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.
 
# 67 # Error: Ramachandran Z-score very low
The score expressing how well the backbone conformations of all residues
correspond to the known allowed areas in the Ramachandran plot is very low.
 
 Ramachandran Z-score : -5.954
 
# 68 # 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.
 
# 69 # 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.
 
 1236 PHE  ( 364-) E  -   -3.7
 1410 PHE  ( 364-) F  -   -3.7
  271 PRO  ( 289-) A  -   -3.1
 1228 TYR  ( 356-) E  -   -3.1
  868 PRO  ( 289-) B  -   -3.0
 1201 PHE  ( 329-) E  -   -2.9
 1375 PHE  ( 329-) F  -   -2.9
 1052 TRP  ( 473-) B  -   -2.7
 1244 THR  ( 372-) E  -   -2.7
 1415 VAL  ( 369-) F  -   -2.6
 1241 VAL  ( 369-) E  -   -2.6
 1196 PRO  ( 324-) E  -   -2.5
 1499 PRO  ( 459-) F  -   -2.4
 1325 PRO  ( 459-) E  -   -2.4
  128 PRO  ( 146-) A  -   -2.4
And so on for a total of    66 lines.
 
# 70 # 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.
 
   65 TYR  (  83-) A  - Omega to (next) Pro poor
   86 GLY  ( 104-) A  - Poor phi/psi
  116 ASN  ( 134-) A  - Omega to (next) Pro poor
  118 ASP  ( 136-) A  - Poor phi/psi
  119 ASN  ( 137-) A  - Omega to (next) Pro poor
  127 GLU  ( 145-) A  - Omega to (next) Pro poor
  128 PRO  ( 146-) A  - Poor phi/psi
  129 GLY  ( 147-) A  - Poor phi/psi
  153 GLU  ( 171-) A  - Poor phi/psi
  159 ARG  ( 177-) A  - Omega to (next) Pro poor
  177 HIS  ( 195-) A  - Poor phi/psi
  180 ASP  ( 198-) A  - Poor phi/psi
  193 GLY  ( 211-) A  - Poor phi/psi
  196 GLY  ( 214-) A  - Poor phi/psi
  216 LYS  ( 234-) A  - Omega to (next) Pro poor
And so on for a total of   212 lines.
 
# 71 # 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.
 
   11 LEU  (  29-) A  -    -1.32
   21 LEU  (  39-) A  -    -1.31
   55 LEU  (  73-) A  -    -1.32
   67 LEU  (  85-) A  -    -1.32
   82 LEU  ( 100-) A  -    -1.32
  130 LEU  ( 148-) A  -    -1.31
  138 LEU  ( 156-) A  -    -1.30
  222 LEU  ( 240-) A  -    -1.32
  260 LEU  ( 278-) A  -    -1.31
  263 LEU  ( 281-) A  -    -1.32
  315 LEU  ( 333-) A  -    -1.32
  392 LEU  ( 410-) A  -    -1.32
  400 LEU  ( 418-) A  -    -1.32
  406 LEU  ( 424-) A  -    -1.30
  421 LEU  ( 439-) A  -    -1.32
And so on for a total of   877 lines.
 
# 72 # Error: chi-1/chi-2 angle correlation Z-score very low
The score expressing how well the chi-1/chi-2 angles of all residues
correspond to the populated areas in the database is
very low.
 
 chi-1/chi-2 correlation Z-score : -6.468
 
# 73 # 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.
 
  548 TRP  ( 566-) A  -   0.33
  812 ILE  ( 233-) B  -   0.36
  393 SER  ( 411-) A  -   0.36
  703 SER  ( 124-) B  -   0.36
  313 SER  ( 331-) A  -   0.36
  414 ASN  ( 432-) A  -   0.37
 1252 SER  ( 386-) E  -   0.37
 1426 SER  ( 386-) F  -   0.37
  152 SER  ( 170-) A  -   0.38
  649 SER  (  70-) B  -   0.38
  692 SER  ( 113-) B  -   0.38
  749 SER  ( 170-) B  -   0.38
 1145 TRP  ( 566-) B  -   0.38
   95 SER  ( 113-) A  -   0.39
  106 SER  ( 124-) A  -   0.39
  262 SER  ( 280-) A  -   0.39
  720 CYS  ( 141-) B  -   0.39
 
# 74 # 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!
 
   85 ASN  ( 103-) A  -       0
  127 GLU  ( 145-) A  -       0
  271 PRO  ( 289-) A  -       0
  272 ASN  ( 290-) A  -       0
  320 ASN  ( 338-) A  -       0
  321 VAL  ( 339-) A  -       0
  412 GLU  ( 430-) A  -       0
  413 ASP  ( 431-) A  -       0
  582 LYS  ( 600-) A  -       0
  682 ASN  ( 103-) B  -       0
  724 GLU  ( 145-) B  -       0
  869 ASN  ( 290-) B  -       0
  870 ILE  ( 291-) B  -       0
  917 ASN  ( 338-) B  -       0
  918 VAL  ( 339-) B  -       0
And so on for a total of    82 lines.
 
# 75 # 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 : -0.872
 
# 76 # 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= 179.750 3.320
 
# 77 # Note: PRO puckering amplitude OK
Puckering amplitudes for all PRO residues are within normal ranges.
 
# 78 # 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].
 
  271 PRO  ( 289-) A  -  -15.1 half-chair C-alpha/N (-18 degrees)
  868 PRO  ( 289-) B  -   44.0 envelop C-delta (36 degrees)
 1079 PRO  ( 500-) B  - -117.5 half-chair C-delta/C-gamma (-126 degrees)
 1265 PRO  ( 399-) E  - -117.4 half-chair C-delta/C-gamma (-126 degrees)
 1316 PRO  ( 450-) E  - -115.1 envelop C-gamma (-108 degrees)
 1325 PRO  ( 459-) E  - -124.9 half-chair C-delta/C-gamma (-126 degrees)
 1359 PRO  ( 493-) E  -   34.6 envelop C-delta (36 degrees)
 1439 PRO  ( 399-) F  - -117.3 half-chair C-delta/C-gamma (-126 degrees)
 1490 PRO  ( 450-) F  - -122.8 half-chair C-delta/C-gamma (-126 degrees)
 1499 PRO  ( 459-) F  - -121.9 half-chair C-delta/C-gamma (-126 degrees)
 1533 PRO  ( 493-) F  -   26.7 half-chair N/C-delta (18 degrees)
 
# 79 # 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!
 
 1440 GLY  ( 400-) F  -  3.20   58
 1266 GLY  ( 400-) E  -  3.16   52
 1045 GLY  ( 466-) B  -  1.68   80
  916 GLY  ( 337-) B  -  1.59   20
  319 GLY  ( 337-) A  -  1.59   31
  482 PRO  ( 500-) A  -  1.57   11
  445 VAL  ( 463-) A  -  1.55   80
   63 GLN  (  81-) A  -  1.55   28
 
# 80 # 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.
 
  234 TYR  ( 252-) A  - TT+   Highly likely
  236 SER  ( 254-) A  - TT+   Highly likely
  253 TRP  ( 271-) A  - TT+   Highly likely
  264 THR  ( 282-) A  - TT+   Highly likely
  267 PHE  ( 285-) A  - TT+   Highly likely
  367 TYR  ( 385-) A  - TT+   Highly likely
  833 SER  ( 254-) B  - TT+   Highly likely
  864 PHE  ( 285-) B  - TT+   Highly likely
 1120 LYS  ( 541-) B  - TT+   Highly likely
 1211 ALA  ( 339-) E  - TT+   Highly likely
 1317 PHE  ( 451-) E  - TT+   Highly likely
 1339 ASN  ( 473-) E  - TT+   Highly likely
   69 GLU  (  87-) A  - TT+   Likely
   89 VAL  ( 107-) A  - TT+   Likely
  136 ASN  ( 154-) A  - TT+   Likely
And so on for a total of    89 lines.
 
# 81 # 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.
 
  481 ASP  ( 499-) A  -    O   <-->   483 ALA  ( 501-) A  -    N      0.47    2.23  INTRA BL
  243 CYS  ( 261-) A  -    CB  <-->   470 VAL  ( 488-) A  -    CG2    0.39    2.81  INTRA BL
  159 ARG  ( 177-) A  -    NH2 <-->   452 LYS  ( 470-) A  -    O      0.37    2.33  INTRA BF
  957 HIS  ( 378-) B  -    ND1 <-->   980 HIS  ( 401-) B  -    ND1    0.37    2.63  INTRA BL
  439 GLU  ( 457-) A  -    OE1 <-->   442 ARG  ( 460-) A  -    NH1    0.34    2.36  INTRA BL
  527 SER  ( 545-) A  -    O   <-->   529 SER  ( 547-) A  -    N      0.33    2.37  INTRA BL
  595 TYR  ( 613-) A  -    O   <-->   597 ASP  ( 615-) A  -    N      0.33    2.37  INTRA BL
  513 GLN  ( 531-) A  -    O   <-->   516 LYS  ( 534-) A  -    N      0.32    2.38  INTRA BL
  945 MET  ( 366-) B  -    CE  <-->  1020 LYS  ( 441-) B  -    NZ     0.32    2.78  INTRA BL
  953 HIS  ( 374-) B  -    NE2 <-->   957 HIS  ( 378-) B  -    NE2    0.31    2.69  INTRA BL
  869 ASN  ( 290-) B  -    C   <-->   871 ASP  ( 292-) B  -    N      0.30    2.60  INTRA BL
  272 ASN  ( 290-) A  -    C   <-->   274 ASP  ( 292-) A  -    N      0.30    2.60  INTRA BL
 1376 ASN  ( 330-) F  -    N   <-->  1377 ALA  ( 331-) F  -    N      0.29    2.31  INTRA BL
  844 HIS  ( 265-) B  -    ND1 <-->  1069 PRO  ( 490-) B  -    CG     0.29    2.81  INTRA BF
 1060 LYS  ( 481-) B  -    O   <-->  1066 VAL  ( 487-) B  -    N      0.27    2.43  INTRA BL
And so on for a total of   289 lines.
 
# 82 # 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: 26.576
Total bump value per residue: 0.187
Total number of bumps: 289
Total squared bump value: 4.425
Total number of bumps in the mildest bin: 272
Total number of bumps in the second bin: 17
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
 
# 83 # 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.
 
# 84 # Note: Inside/Outside residue distribution normal
The distribution of residue types over the inside and the outside of the
protein is normal.
 
inside/outside RMS Z-score : 1.044
 
# 85 # 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
 
# 86 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 87 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: E
 
# 88 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: F
 
# 89 # 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.
 
 1456 PHE  ( 416-) F  -  -7.27
 1282 PHE  ( 416-) E  -  -7.16
  866 GLN  ( 287-) B  -  -6.55
  661 MET  (  82-) B  -  -6.55
   64 MET  (  82-) A  -  -6.37
 1379 LYS  ( 333-) F  -  -6.37
  269 GLN  ( 287-) A  -  -6.25
 1205 LYS  ( 333-) E  -  -6.21
 1441 GLN  ( 401-) F  -  -6.10
 1367 PHE  ( 501-) E  -  -6.05
 1267 GLN  ( 401-) E  -  -5.95
 1413 TYR  ( 367-) F  -  -5.83
  518 GLU  ( 536-) A  -  -5.81
 1115 GLU  ( 536-) B  -  -5.79
 1192 TYR  ( 613-) B  -  -5.61
And so on for a total of    34 lines.
 
# 90 # Warning: Abnormal packing environment for sequential residues
A stretch of at least three sequential residues with a questionable packing
environment was found. This could indicate that these residues are part
of a strange loop. It might also be an indication of misthreading in the
density. However, it can also indicate that one or more residues in this
stretch have other problems such as, for example, missing atoms, very
weird angles or bond lengths, etc.
 
The table below lists the first and last residue in each stretch found,
as well as the average residue score of the series.
 
  409 ASP  ( 427-) A  -      412 --- GLU   430- (A ) -       -4.43
 1239 TYR  ( 367-) E  -     1242 --- SER   370- (E ) -       -4.62
 1280 ASP  ( 414-) E  -     1283 --- MET   417- (E ) -       -5.08
 1413 TYR  ( 367-) F  -     1416 --- SER   370- (F ) -       -4.69
 1454 ASP  ( 414-) F  -     1457 --- MET   417- (F ) -       -5.12
 
# 91 # Note: Structural average packing environment OK
The structural average packing score is within normal ranges.
 
 
Average for range     1 - 1542 :  -0.541
 
# 92 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as function
of the residue number. Low areas in the plot (below -2.0) indicate unusual
packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: A
 
# 93 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as function
of the residue number. Low areas in the plot (below -2.0) indicate unusual
packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 94 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as function
of the residue number. Low areas in the plot (below -2.0) indicate unusual
packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: E
 
# 95 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as function
of the residue number. Low areas in the plot (below -2.0) indicate unusual
packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: F
 
# 96 # Warning: Low packing Z-score for some residues
The residues listed in the table below have an unusual packing
environment according to the 2nd generation packing check. The score
listed in the table is a packing normality Z-score: positive means
better than average, negative means worse than average. Only residues
scoring less than -2.50 are listed here. These are the unusual
residues in the structure, so it will be interesting to take a
special look at them.
 
  542 LEU  ( 560-) A  -  -3.00
 
# 97 # Note: No series of residues with abnormal new packing environment
There are no stretches of four or more residues each having a packing
Z-score worse than -1.75.
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
 
# 98 # Note: Second generation quality Z-score plot
The second generation quality Z-score smoothed over a 10 residue window
is plotted as function of the residue number. Low areas in the plot (below
-1.3) indicate unusual packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: A
 
# 99 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 100 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: E
 
# 101 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: F
 
# 102 # 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.
 
# 103 # 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.
 
    6 GLN  (  24-) A  -
   33 ASN  (  51-) A  -
   45 ASN  (  63-) A  -
   83 GLN  ( 101-) A  -
  131 ASN  ( 149-) A  -
  192 ASN  ( 210-) A  -
  259 ASN  ( 277-) A  -
  282 GLN  ( 300-) A  -
  312 ASN  ( 330-) A  -
  320 ASN  ( 338-) A  -
  355 HIS  ( 373-) A  -
  376 ASN  ( 394-) A  -
  411 GLN  ( 429-) A  -
  475 HIS  ( 493-) A  -
  487 HIS  ( 505-) A  -
And so on for a total of    42 lines.
 
# 104 # 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.
 
   16 HIS  (  34-) A  -   HIS-H   0.24 HIS-E   0.48
  177 HIS  ( 195-) A  -   HIS-H   0.29 HIS-E   0.63
  210 HIS  ( 228-) A  -   HIS-E   0.64
  221 HIS  ( 239-) A  -   HIS-H   0.26 HIS-E   0.58
  223 HIS  ( 241-) A  -   HIS-H   0.29 HIS-E   0.50
  247 HIS  ( 265-) A  -   HIS-H   0.22 HIS-E   0.54
  327 HIS  ( 345-) A  -   HIS-H   0.35 HIS-E   0.58
  355 HIS  ( 373-) A  -   HIS-H   0.25 HIS-D   0.45
  356 HIS  ( 374-) A  -   HIS-H   0.45 HIS-D   0.49
  360 HIS  ( 378-) A  -   HIS-H   0.21 HIS-D   0.60
  383 HIS  ( 401-) A  -   HIS-H   0.16 HIS-E   0.57
  399 HIS  ( 417-) A  -   HIS-H   0.32 HIS-D   0.44
  475 HIS  ( 493-) A  -   HIS-H   0.16
  487 HIS  ( 505-) A  -   HIS-H   0.19 HIS-E   0.56
  517 HIS  ( 535-) A  -   HIS-H   0.18 HIS-E   0.59
And so on for a total of    34 lines.
 
# 105 # 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.
 
   15 ASN  (  33-) A  -    ND2
   16 HIS  (  34-) A  -    N
   40 ASN  (  58-) A  -    N
   64 MET  (  82-) A  -    N
   68 GLN  (  86-) A  -    N
   89 VAL  ( 107-) A  -    N
   90 LEU  ( 108-) A  -    N
  126 LEU  ( 144-) A  -    N
  147 TRP  ( 165-) A  -    NE1
  154 VAL  ( 172-) A  -    N
  161 LEU  ( 179-) A  -    N
  180 ASP  ( 198-) A  -    N
  186 ARG  ( 204-) A  -    NH1
  197 TYR  ( 215-) A  -    N
  211 THR  ( 229-) A  -    OG1
And so on for a total of   193 lines.
 
# 106 # 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.
 
  223 HIS  ( 241-) A  -    ND1
  355 HIS  ( 373-) A  -    NE2
  481 ASP  ( 499-) A  -    OD1
  504 GLN  ( 522-) A  -    OE1
  506 GLN  ( 524-) A  -    OE1
  560 ASN  ( 578-) A  -    OD1
  760 GLU  ( 181-) B  -    OE1
  777 ASP  ( 198-) B  -    OD1
  820 HIS  ( 241-) B  -    ND1
  952 HIS  ( 373-) B  -    NE2
  996 HIS  ( 417-) B  -    NE2
 1078 ASP  ( 499-) B  -    OD1
 1103 GLN  ( 524-) B  -    OE1
 
# 107 # 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: 2224
- of which buried: 1143
Total number of acceptors: 2454
- of which buried: 913
Total number of donor+acceptors: 266
  (e.g. the Ser Ogamma that can donate and accept)
- of which buried: 53
Buried donors: 1143
- without H-bond: 179
- essentially without H-bond: 2
- with only a very poor H-bond: 13
- with a poor H-bond: 29
- with a H-bond: 920
Buried acceptors: 913
- without H-bond: 192
- essentially without H-bond: 1
- with only a very poor H-bond: 15
- with a poor H-bond: 39
- with a H-bond: 666
 
# 108 # 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 (   19)   597 (  615) A Protein             /zata/tempdir/3sc...
     2   598 (   19)  1194 (  615) B Protein             /zata/tempdir/3sc...
     3  1195 (  323)  1247 (  375) E Protein             /zata/tempdir/3sc...
     4  1248 (  382)  1368 (  502) E Protein             /zata/tempdir/3sc...
     5  1369 (  323)  1421 (  375) F Protein             /zata/tempdir/3sc...
     6  1422 (  382)  1542 (  502) F Protein             /zata/tempdir/3sc...
     7  1543 (  901)  1543 (  901) A  ZN                 /zata/tempdir/3sc...
     8  1544 (  902)  1544 (  902) A  CL                 /zata/tempdir/3sc...
     9  1545 (  901)  1545 (  901) B  ZN                 /zata/tempdir/3sc...
    10  1546 (  902)  1546 (  902) B  CL                 /zata/tempdir/3sc...
 
# 109 # Note: Summary report
This is an overall summary of the quality of the structure as compared with
current reliable structures. Numbers in brackets are the average and standard
deviation observed for a large number of files determined with a similar
resolution.
 
The second table mostly gives an impression of how well the model conforms
to common refinement restraint values. These numbers are less than 1.0 if the
spread in data is too little, and larger than 1.0 when the spread is too
large. The former does not need to be a problem, the latter always is bad.
 
 Structure Z-scores, positive is better than average:
  Resolution read from PDB file  :   3.000
  1st generation packing quality :  -0.103 (          (  -1.0,  2.5))
  2nd generation packing quality :  -2.292 (          (  -1.9,  1.4))
  Ramachandran plot appearance   :  -5.954 (bad       (  -4.1,  2.0))
  chi-1/chi-2 rotamer normality  :  -6.468 (bad       (  -5.6,  2.0))
  Backbone conformation          :  -0.872 (          (  -1.4,  3.9))
  Inside/Outside distribution    :   1.044
 
 RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.454 (tight)
  Bond angles                    :   0.612 (tight)
  Omega angle restraints         :   0.604 (tight)
  Side chain planarity           :   0.291 (tight)
  Improper dihedral distribution :   0.552
  B-factor distribution          :   0.372
 
# 110 # 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.
 
# 111 # 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.
 
# 112 # Note: Cell parameter anomaly
WHAT CHECK has compared the observed bond lengths with the Engh and Huber
parameters, and has done this as function of the direction of the bond
relative to the cell axes. From this analysis it was concluded that the
cell dimensions are probably not entirely perfect. The problem is not very
big, so you do not need to fix this before you start dealing with the other
suggestions, but you better fix this.
 
If this problem is caused by refining with another set of target values
than the Engh and Huber values, then WHAT CHECK cannot help you because
systematic target value deviations can also cause this message to pop up.
 
# 113 # 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.
 
# 114 # 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.
 
# 115 # 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.
 
   64 MET  (  82-) A  -     16.81
  957 HIS  ( 378-) B  -     15.98
 1456 PHE  ( 416-) F  -     15.62
 1282 PHE  ( 416-) E  -     15.40
  661 MET  (  82-) B  -     14.91
  481 ASP  ( 499-) A  -     14.34
  972 ARG  ( 393-) B  -     14.32
  866 GLN  ( 287-) B  -     14.10
  483 ALA  ( 501-) A  -     13.67
  269 GLN  ( 287-) A  -     13.51
  320 ASN  ( 338-) A  -     13.46
 1239 TYR  ( 367-) E  -     13.44
 1379 LYS  ( 333-) F  -     12.74
  869 ASN  ( 290-) B  -     12.65
 1205 LYS  ( 333-) E  -     12.41
And so on for a total of   315 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.
