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

Date : 2024-04-18
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/5xc2/wctemp_0cyc/5xc2_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                                                        5XC2
 
# 2 # Note: Header records from PDB file
Header records from PDB file.
 
HEADER                                                        5XC2
 
# 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
  0.009200  0.000000  0.003596
  0.000000  0.010099  0.000000
  0.000000  0.000000  0.007756
 
# 5 # Warning: Problem detected upon counting molecules and matrices
The parameter Z as given on the CRYST card represents the molecular
multiplicity in the crystallographic cell. Normally, Z equals the number of
matrices of the space group multiplied by the number of NCS relations. The
value of Z is multiplied by the integrated molecular weight of the molecules
in the file to determine the Matthews coefficient. This relation is being
validated in this option. Be aware that the validation can get confused if
both multiple copies of the molecule are present in the ATOM records and
MTRIX records are present in the header of the PDB file.
 
 Space group as read from CRYST card: P 1 21 1
 Number of matrices in space group: 2
 Highest polymer chain multiplicity in structure: 2
 Highest polymer chain multiplicity according to SEQRES: 1
 No explicit MTRIX NCS matrices found in the input file
 Value of Z as found on the CRYST1 card: 0
 Polymer chain multiplicity and SEQRES multiplicity disagree 2 1
 Z agrees neither with the 3D multiplicity, nor with the SEQRES multiplicity
 It could be that Z must be one of: 2 4
 
# 6 # Warning: Matthews Coefficient (Vm) high
 
The Matthews coefficient [REF] is defined as the density of the protein
structure in cubic Angstroms per Dalton. Normal values are between 1.5
(tightly packed, little room for solvent) and 4.0 (loosely packed, much
space for solvent). Some very loosely packed structures can get values a bit
higher than that.
 
Very high numbers are most often caused by giving the wrong value for Z on
the CRYST1 card (or not giving this number at all), but can also result from
large fractions missing out of the molecular weight (e.g. a lot of UNK
residues, or DNA/RNA missing from virus structures).
 
 Molecular weight of all polymer chains: 314041.312
 Volume of the Unit Cell V= 1387735.5
 Space group multiplicity: 2
 No NCS symmetry matrices (MTRIX records) found in PDB file
 Matthews coefficient for observed atoms and Z is high: Vm= 4.419
 Be aware though that the number of residues with missing atoms is: 72
 No Matthews coefficient given in REMARK 280
 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
 (and the absence of MTRIX records doesn't help)
 Could it be that Z must be: 2
 This number is the multiplication of the spacegroup and NCS symmetry count
 Matthews coefficient for observed atoms and corrected Z: Vm= 2.209
 
# 7 # Note: Z missing on CRYST1 card
The messages above seem likely caused by the fact that Z is missing from the
CRYST1 card.
 
# 8 # 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.
 
# 9 # 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.
 
# 10 # Warning: Ligands for which a topology was generated automatically
The topology for the ligands in the table below were determined
automatically. WHAT CHECK uses a local copy of the CCP4 monomer library to
generate topology information for ligands. Be aware that automatic topology
generation is a complicated task. So, if you get messages that you fail to
understand or that you believe are wrong, and one of these ligands is
involved, then check the ligand topology entry first. This topology is either
present in the monomer library, or as a libcheck-generated file in the local
directory.
 
 2791 BGC  (   1-) E  -
 2792 BGC  (   2-) E  -
 2793 BGC  (   3-) E  -
 2794 BGC  (   4-) E  -
 2795 BGC  (   5-) E  -
 2796 BGC  (   6-) E  -
 2797 BGC  (   1-) F  -
 2798 BGC  (   2-) F  -
 2799 BGC  (   3-) F  -
 2800 BGC  (   4-) F  -
 2801 BGC  (   5-) F  -
 2802 BGC  (   1-) G  -
 2803 BGC  (   2-) G  -
 2804 BGC  (   3-) G  -
 2805 BGC  (   4-) G  -
And so on for a total of    52 lines.
 
# 11 # Warning: Covalently bound ligands
The ligands in this table are covalently bound to something else. It is
already difficult to automatically generate topologies for ligands,
but when they are covalently bound to something it becomes even more
complicated to do everything right. So, if you get weird error messages
that seem related to this covalent bond, then please feel free to
ignore those, or even better, make a topology entry by hand.
 
The comment `Other ligand` indicates that the covalent bond is to another
ligand. In that case you might want to convert the two ligands into one
bigger ligand.
 
 2791 BGC  (   1-) E  -          Other ligand
 2792 BGC  (   2-) E  -          Other ligand
 2793 BGC  (   3-) E  -          Other ligand
 2794 BGC  (   4-) E  -          Other ligand
 2795 BGC  (   5-) E  -          Other ligand
 2796 BGC  (   6-) E  -          Other ligand
 2797 BGC  (   1-) F  -          Other ligand
 2798 BGC  (   2-) F  -          Other ligand
 2799 BGC  (   3-) F  -          Other ligand
 2800 BGC  (   4-) F  -          Other ligand
 2801 BGC  (   5-) F  -          Other ligand
 2802 BGC  (   1-) G  -          Other ligand
 2803 BGC  (   2-) G  -          Other ligand
 2804 BGC  (   3-) G  -          Other ligand
 2805 BGC  (   4-) G  -          Other ligand
And so on for a total of    52 lines.
 
# 12 # Warning: Strange inter-chain connections detected
The pairs of residues listed in the table below seem covalently bound
while belonging to different chains in the PDB file.
 
Sometimes this is unavoidable (e.g. if two protein chains are covalently
connected via a Cys-Cys or other bond). But if it can be avoided (e.g.
often we observe sugars with one chain identifier connected to protein
chains with another chain identifier), it should be avoided. WHAT IF and
WHAT CHECK try to deal with all exceptions thrown at it, but if you want
these programs to work optimally (i.e. make as few false error messages as
is possible) you should help them by getting as much of the administration
correct as is humanly possible.
 
 2692 ASP  ( 624-) D  -    OD2  2837 BGC  (   2-) Q  -    O6
 2806 BGC  (   1-) H  -    C1   2811 BGC  (   3-) I  -    O3
 2806 BGC  (   1-) H  -    O5   2811 BGC  (   3-) I  -    O3
 2812 BGC  (   1-) J  -    C1   2815 BGC  (   2-) K  -    O3
 2812 BGC  (   1-) J  -    O5   2815 BGC  (   2-) K  -    O3
 
# 13 # Note: Strange inter-chain connections corrected
Chain identifiers modified to improve future validation options.
 
For the residues listed below, WHAT CHECK thinks that it could 'improve' the
chain-name. Often WHAT CHECK is rather smart about this, but if you find
strange
error messages related to this ligand, or related to the residues listed in
the previous section that it is bound to, then you better fix the chain
identifiers yourself, and run the validation again.
 
 2837 BGC  (   2-) D  -Q
Id: CORCNEU
 
# 14 # Note: No duplicate atom names in ligands
All atom names in ligands (if any) seem adequately unique.
 
# 15 # 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).
 
# 16 # 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).
 
# 17 # Warning: Groups attached to potentially hydrogen-bonding atoms
Residues were observed with groups attached to (or very near to) atoms that
potentially can form hydrogen bonds. WHAT CHECK is not very good at dealing
with such exceptional cases (Mainly because it's author is not...). So be
warned that the hydrogen-bonding related analyses of these residues
might be in error.
 
For example, an aspartic acid can be protonated on one of its delta
oxygens. This is possible because the one delta oxygen 'helps' the
other one holding that proton. However, if a delta oxygen has a group
bound to it, then it can no longer 'help' the other delta oxygen
bind the proton. However, both delta oxygens, in principle, can still
be hydrogen bond acceptors. Such problems can occur in the amino acids
Asp, Glu, and His. I have opted, for now to simply allow no hydrogen
bonds at all for any atom in any side chain that somewhere has a 'funny'
group attached to it. I know this is wrong, but there are only 12 hours
in a day.
 
 2692 ASP  ( 624-) D  -    OD2 bound to  2837 BGC  (   2-) D  -Q   O6
 
# 18 # 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.
 
# 19 # 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.
Residue with missing backbone atom(s)   270 ASP ( 277-)A  -
Residue with missing backbone atom(s)   990 ASP ( 277-)B  -
Residue with missing backbone atom(s)  1699 ASP ( 277-)C  -
Residue with missing backbone atom(s)  2345 ASP ( 277-)D  -
 
# 20 # Warning: Residues with missing backbone atoms.
Residues were detected with missing backbone atoms. This can be a normal
result of poor or missing density, but it can also be an error.
 
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. This is not an error, albeit that we would prefer them to give it
their best shot and provide coordinates with an occupancy of zero in cases
where only a few atoms are involved. Anyway, several checks depend on the
presence of the backbone atoms, so if you find errors in, or directly
adjacent to, residues with missing backbone atoms, then please check by hand
what is going on.
 
  270 ASP  ( 277-) A  -
  990 ASP  ( 277-) B  -
 1699 ASP  ( 277-) C  -
 2345 ASP  ( 277-) D  -
 
# 21 # Note: No C-alpha only residues
There are no residues that consist of only an alpha carbon atom.
 
# 22 # 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 (    5)   717 (  724) A Protein             To check
     2   718 (    5)  1437 (  724) B Protein             To check
     3  1438 (    5)  2142 (  722) C Protein             To check
     4  2143 (    5)  2790 (  722) D Protein             To check
     5  2791 (    1)  2791 (    1) E BGC  <-             To check
     6  2792 (    2)  2792 (    2) E BGC  <=             To check
     7  2793 (    3)  2793 (    3) E BGC  <=             To check
     8  2794 (    4)  2794 (    4) E BGC  <=             To check
     9  2795 (    5)  2795 (    5) E BGC  <=             To check
    10  2796 (    6)  2796 (    6) E BGC  <-             To check
    11  2797 (    1)  2797 (    1) F BGC  <-             To check
    12  2798 (    2)  2798 (    2) F BGC  <=             To check
    13  2799 (    3)  2799 (    3) F BGC  <=             To check
    14  2800 (    4)  2800 (    4) F BGC  <=             To check
    15  2801 (    5)  2801 (    5) F BGC  <-             To check
And so on for a total of    60 lines.
MODELs skipped upon reading PDB file: 0
X-ray structure. No MODELs found
The total number of amino acids found is 2790
of which 72 have poor or (essentially) missing atoms
No nucleic acids observed in input file
No sugars recognized in input file
Number of water molecules: 479
Residue numbers increase monotonously OK
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
 
# 23 # 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
 
# 24 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 25 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: C
 
# 26 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 27 # 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 GDDLFVPVSNFDPKSIFPEIKHPFEPMYANTENGKIVPTNSWISNLFYPSADNLAPTTPD
(   5)-(  64)
                     70        80        90       100       110       120
                      |         |         |         |         |         |
   61 -  120 PYTLRLLDGYGGNPGLTIRQPSAKVLGSYPPTNDVPYTDAGYMINSVVVDLRLTSSEWSD
(  65)-( 124)
                    130       140       150       160       170       180
                      |         |         |         |         |         |
  121 -  180 VVPDRQVTDWDHLSANLRLSTPQDSNSYIDFPIVRGMAYITANYNNLTPQFLSQHAIISV
( 125)-( 184)
                    190       200       210       220       230       240
                      |         |         |         |         |         |
  181 -  240 EADEKKNTSTFSGRKFKITMNDDPTSTFIIYSLGDKPLELRKQDNSNLVASKPYTGVIRV
( 185)-( 247)
                    250       260       270       280       290       300
                      |         |         |         |         |         |
  241 -  300 AKLPAPEFETLLDASRAVWPTGGDISARSDDNNGASYTIKWKTNSNEAPLLTYAYAHHLT
( 248)-( 307)
                    310       320       330       340       350       360
                      |         |         |         |         |         |
  301 -  360 SIDDSNVKRTDMTLQSATKGPMTALVGNEWTLRETELSPVEWLPLQAAPNPTTINEIMTE
( 308)-( 367)
                    370       380       390       400       410       420
                      |         |         |         |         |         |
  361 -  420 INKDIASNYTQETAKEDNYFSGKGLQKFAMLALILNKSDQTQLRNPELAQIALDKLKAAF
( 368)-( 427)
                    430       440       450       460       470       480
                      |         |         |         |         |         |
  421 -  480 LPYLQNEQADPFRYDTLYKGIVAKAGLPTSMGGTDDLSAEFGHSYYSDHHYHQGYFVVTA
( 428)-( 487)
                    490       500       510       520       530       540
                      |         |         |         |         |         |
  481 -  540 AIIHHLDPTWNADRLKAWTEALIRDVNNANDGDEYFAAFRNWDWFAGHSWAGGIKPDGAL
( 488)-( 547)
                    550       560       570       580       590       600
                      |         |         |         |         |         |
  541 -  600 DGRDQESVPESVNFYWGAKLWGLATGNTPLTKLASLQLAVTKRTTYEYFWMLDGNKNRPE
( 548)-( 607)
                    610       620       630       640       650       660
                      |         |         |         |         |         |
  601 -  660 NIVRNKVIGIYFEQKTDYTTYFGRFLEYIHGIQQLPMTPELMEYIRTPEFVSQEWDEKLG
( 608)-( 667)
                    670       680       690       700       710
                      |         |         |         |         |
  661 -  717 AIAPTVQSPWAGVLYLNYAIINPAEAYPALRKVQMDDGQTRSYSLYLTATRPHFFRR
( 668)-( 724)
             720       730       740       750       760       770
               |         |         |         |         |         |
  718 -  777 GDDLFVPVSNFDPKSIFPEIKHPFEPMYANTENGKIVPTNSWISNLFYPSADNLAPTTPD
(   5)-(  64)
             780       790       800       810       820       830
               |         |         |         |         |         |
  778 -  837 PYTLRLLDGYGGNPGLTIRQPSAKVLGSYPPTNDVPYTDAGYMINSVVVDLRLTSSEWSD
(  65)-( 124)
             840       850       860       870       880       890
               |         |         |         |         |         |
  838 -  897 VVPDRQVTDWDHLSANLRLSTPQDSNSYIDFPIVRGMAYITANYNNLTPQFLSQHAIISV
( 125)-( 184)
             900       910       920       930       940       950
               |         |         |         |         |         |
  898 -  957 EADEKKSDDNTSTFSGRKFKITMNDDPTSTFIIYSLGDKPLELRKQDNSNLVASKPYTGV
( 185)-( 244)
             960       970       980       990      1000      1010
               |         |         |         |         |         |
  958 - 1017 IRVAKLPAPEFETLLDASRAVWPTGGDISARSDDNNGASYTIKWKTNSNEAPLLTYAYAH
( 245)-( 304)
            1020      1030      1040      1050      1060      1070
               |         |         |         |         |         |
 1018 - 1077 HLTSIDDSNVKRTDMTLQSATKGPMTALVGNEWTLRETELSPVEWLPLQAAPNPTTINEI
( 305)-( 364)
            1080      1090      1100      1110      1120      1130
               |         |         |         |         |         |
 1078 - 1137 MTEINKDIASNYTQETAKEDNYFSGKGLQKFAMLALILNKSDQTQLRNPELAQIALDKLK
( 365)-( 424)
            1140      1150      1160      1170      1180      1190
               |         |         |         |         |         |
 1138 - 1197 AAFLPYLQNEQADPFRYDTLYKGIVAKAGLPTSMGGTDDLSAEFGHSYYSDHHYHQGYFV
( 425)-( 484)
            1200      1210      1220      1230      1240      1250
               |         |         |         |         |         |
 1198 - 1257 VTAAIIHHLDPTWNADRLKAWTEALIRDVNNANDGDEYFAAFRNWDWFAGHSWAGGIKPD
( 485)-( 544)
            1260      1270      1280      1290      1300      1310
               |         |         |         |         |         |
 1258 - 1317 GALDGRDQESVPESVNFYWGAKLWGLATGNTPLTKLASLQLAVTKRTTYEYFWMLDGNKN
( 545)-( 604)
            1320      1330      1340      1350      1360      1370
               |         |         |         |         |         |
 1318 - 1377 RPENIVRNKVIGIYFEQKTDYTTYFGRFLEYIHGIQQLPMTPELMEYIRTPEFVSQEWDE
( 605)-( 664)
            1380      1390      1400      1410      1420      1430
               |         |         |         |         |         |
 1378 - 1437 KLGAIAPTVQSPWAGVLYLNYAIINPAEAYPALRKVQMDDGQTRSYSLYLTATRPHFFRR
( 665)-( 724)
            1440      1450      1460      1470      1480      1490
               |         |         |         |         |         |
 1438 - 1497 GDDLFVPVSNFDPKSIFPEIKHPFEPMYANTENGKIVPTNSWISNLFYPSADNLAPTTPD
(   5)-(  64)
            1500      1510      1520      1530      1540      1550
               |         |         |         |         |         |
 1498 - 1557 PYTLRLLDGYGGNPGLTIRQPSAKVLGSYPPTNDVAGYMINSVVVDLRLTSSEWSDVVPD
(  65)-( 128)
            1560      1570      1580      1590      1600      1610
               |         |         |         |         |         |
 1558 - 1617 RQVTDWDHLSANLRLSTPQDSNSYIDFPIVRGMAYITANYNNLTPQFLSQHAIISVEADE
( 129)-( 188)
            1620      1630      1640      1650      1660      1670
               |         |         |         |         |         |
 1618 - 1677 KTFSGRKFKITMNDDPTSTFIIYSLGDKPLELRKQDNSNLVASKPYTGVIRVAKLPAPEF
( 189)-( 255)
            1680      1690      1700      1710      1720      1730
               |         |         |         |         |         |
 1678 - 1737 ETLLDASRAVWPTGGDISARSDDNNGASYTIKWKTNSNEAPLLTYAYAHHLTSIDDSNVK
( 256)-( 315)
            1740      1750      1760      1770      1780      1790
               |         |         |         |         |         |
 1738 - 1797 RTDMTLQSATKGPMTALVGNEWTLRETELSPVEWLPAAPNPTTINEIMTEINKDIASNYT
( 316)-( 377)
            1800      1810      1820      1830      1840      1850
               |         |         |         |         |         |
 1798 - 1857 QETAKEDNYFSGKGLQKFAMLALILNKSDQTQLRNPELAQIALDKLKAAFLPYLQNEQAD
( 378)-( 437)
            1860      1870      1880      1890      1900      1910
               |         |         |         |         |         |
 1858 - 1917 PFRYDTLYKGIVAKAGLPTSMGGTDDLSAEFGHSYYSDHHYHQGYFVVTAAIIHHLDPTW
( 438)-( 497)
            1920      1930      1940      1950      1960      1970
               |         |         |         |         |         |
 1918 - 1977 NADRLKAWTEALIRDVNNANDGDEYFAAFRNWDWFAGHSWAGGIKPDGALDGRDQESVPE
( 498)-( 557)
            1980      1990      2000      2010      2020      2030
               |         |         |         |         |         |
 1978 - 2037 SVNFYWGAKLWGLATGNTPLTKLASLQLAVTKRTTYEYFWMLDGNKNRPENIVRNKVIGI
( 558)-( 617)
            2040      2050      2060      2070      2080      2090
               |         |         |         |         |         |
 2038 - 2097 YFEQKTDYTTYFGRFLEYIHGIQQLPMTPELMEYIRTPEFVSQEWDEKLGAIAPTVQSPW
( 618)-( 677)
            2100      2110      2120      2130      2140
               |         |         |         |         |
 2098 - 2142 AGVLYLNYAIINPAEAYPALRKVQMDDGQTRSYSLYLTATRPHFF
( 678)-( 722)
                 2150      2160      2170      2180      2190      2200
                    |         |         |         |         |         |
 2143 - 2202 GDDLFVPVSNFDPKSIFPEIKHPFEPMYANTENGKIVPTNSWISNLFYPSADNLAPTTPD
(   5)-(  64)
                 2210      2220      2230      2240      2250      2260
                    |         |         |         |         |         |
 2203 - 2262 PYTLRLLGLTIRQPSAKVLGSYPAGYMINSVVVDLRLDRQVTDWDHLSANLRLSNSYIDF
(  65)-( 155)
                 2270      2280      2290      2300      2310      2320
                    |         |         |         |         |         |
 2263 - 2322 PIVRGMAYITANYNNLTPQFLSSGRKFKITSTFIIYSLGDKPLSKPYTGVIRVAKLPAPE
( 156)-( 254)
                 2330      2340      2350      2360      2370      2380
                    |         |         |         |         |         |
 2323 - 2382 FETLLDASRAVWPTGGDISARSDDNNGASYTIKWKTNSNEAPLLTYAYAHHLTSIDDSNV
( 255)-( 314)
                 2390      2400      2410      2420      2430      2440
                    |         |         |         |         |         |
 2383 - 2442 KRTDMTLQSATKGPMTALVGNEWTLRETELSPVEWLPLQAAPNPTTINEIMTEINKDIAS
( 315)-( 374)
                 2450      2460      2470      2480      2490      2500
                    |         |         |         |         |         |
 2443 - 2502 NYTQETAKEDNYFSGKGLQKFAMLALILNKSDQTQLRNPELAQIALDKLKAAFLPYLQNE
( 375)-( 434)
                 2510      2520      2530      2540      2550      2560
                    |         |         |         |         |         |
 2503 - 2562 QADPFRYDTLYKGIVAKAGLPTSMGGTDDLSAEFGHSYYSDHHYHQGYFVVTAAIIHHLD
( 435)-( 494)
                 2570      2580      2590      2600      2610      2620
                    |         |         |         |         |         |
 2563 - 2622 PTWNADRLKAWTEALIRDVNNANDGDEYFAAFRNWDWFAGHSWAGGIKPDGALDGRDQES
( 495)-( 554)
                 2630      2640      2650      2660      2670      2680
                    |         |         |         |         |         |
 2623 - 2682 VPESVNFYWGAKLWGLATGNTPLTKLASLQLAVTKRTTYEYFWMLDGNKNRPENIVRNKV
( 555)-( 614)
                 2690      2700      2710      2720      2730      2740
                    |         |         |         |         |         |
 2683 - 2742 IGIYFEQKTDYTTYFGRFLEYIHGIQQLPMTPELMEYIRTPEFVSQEWDEKLGAIAPTVQ
( 615)-( 674)
                 2750      2760      2770      2780      2790
                    |         |         |         |         |
 2743 - 2790 SPWAGVLYLNYAIINPAEAYPALRKVQMDDGQTRSYSLYLTATRPHFF
( 675)-( 722)
 
 
 
 
# 28 # Note: No rounded coordinates detected
No significant rounding of atom coordinates has been detected.
 
# 29 # 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.
 
# 30 # Warning: Missing atoms
The atoms listed in the table below are missing from the entry. If many atoms
are missing, the other checks can become less sensitive. Be aware that it
often happens that groups at the termini of DNA or RNA are really missing,
so that the absence of these atoms normally is neither an error nor the
result of poor electron density. Some of the atoms listed here might also be
listed by other checks, most noticeably by the options in the previous
section that list missing atoms in several categories. The plausible atoms
with zero occupancy are not listed here, as they already got assigned a
non-zero occupancy, and thus are no longer 'missing'.
 
   31 THR  (  35-) A  -    OG1
   31 THR  (  35-) A  -    CG2
   32 GLU  (  36-) A  -    CB
   32 GLU  (  36-) A  -    CG
   32 GLU  (  36-) A  -    CD
   32 GLU  (  36-) A  -    OE1
   32 GLU  (  36-) A  -    OE2
  120 ASP  ( 124-) A  -    CG
  120 ASP  ( 124-) A  -    OD1
  120 ASP  ( 124-) A  -    OD2
  125 ARG  ( 129-) A  -    CZ
  125 ARG  ( 129-) A  -    NH1
  125 ARG  ( 129-) A  -    NH2
  221 ARG  ( 228-) A  -    CG
  221 ARG  ( 228-) A  -    CD
And so on for a total of   218 lines.
 
# 31 # Note: All B-factors fall in the range 0.0 - 100.0
All B-factors are larger than zero, and none are observed above 100.0.
 
# 32 # 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.
 
  186 LYS  ( 190-) A  -        OK (3)
  717 ARG  ( 724-) A  -        OK
 1437 ARG  ( 724-) B  -        OK
 1532 VAL  (  99-) C  -        OK (4)
 1618 LYS  ( 189-) C  -        OK (7)
 1773 PRO  ( 351-) C  -        OK (2)
 2142 PHE  ( 722-) C  -        OK
 2209 LEU  (  71-) D  -        OK (7)
 2225 PRO  (  94-) D  -        OK (9)
 2239 LEU  ( 117-) D  -        OK (10)
 2255 LEU  ( 143-) D  -        OK (5)
 2284 SER  ( 177-) D  -        OK (21)
 2291 ILE  ( 205-) D  -        OK (6)
 2305 LEU  ( 225-) D  -        OK (12)
 2790 PHE  ( 722-) D  -        OK
 
# 33 # Note: Weights administratively correct
All atomic occupancy factors ('weights') fall in the 0.0--1.0 range, which
makes them administratively correct.
 
# 34 # 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.
 
# 35 # 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.
 
# 36 # Warning: What type of B-factor?
WHAT CHECK does not yet know well how to cope with B-factors in case TLS has
been used. It simply assumes that the B-factor listed on the ATOM and HETATM
cards are the total B-factors. When TLS refinement is used that assumption
sometimes is not correct. The header of the PDB file states that TLS groups
were used. So, if WHAT CHECK complains about your  B-factors, while you think
that they are OK, then check for TLS related B-factor problems first.
 
Number of TLS groups mentione in PDB file header: 0
 
Temperature not mentioned in PDB file. This most likely means
that the temperature record is absent.
Room temperature assumed
 
# 37 # Warning: More than 5 percent of buried atoms has low B-factor
For normal protein structures, no more than about 1 percent of the B factors
of buried atoms is below 5.0. The fact that this value is much higher in the
current structure could be a signal that the B-factors were restraints or
constraints to too-low values, misuse of B-factor field in the PDB file, or
a TLS/scaling problem. If the average B factor is low too, it is probably a
low temperature structure determination.  In liquid nitrogen this
percentage is allowed to be higher, of course.
 
Percentage of buried atoms with B less than 5 :   8.04
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
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
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 identifiers: A - D
 
# 39 # Note: B-factor plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifiers: A - D
 
# 40 # Note: B-factor plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifiers: A - D
 
# 41 # Note: B-factor plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifiers: A - D
 
Content of the SOUP. See the writeup for an explanation.
 Molecule      Range              Type              Set name
     1    1 (    5)  186 (  190)A Protein           To check
     2  187 (  194)  717 (  724)A Protein           To check
     3  718 (    5) 1437 (  724)B Protein           To check
     4 1438 (    5) 1532 (   99)C Protein           To check
     5 1533 (  104) 1618 (  189)C Protein           To check
     6 1619 (  197) 1773 (  351)C Protein           To check
     7 1774 (  354) 2142 (  722)C Protein           To check
     8 2143 (    5) 2209 (   71)D Protein           To check
     9 2210 (   79) 2225 (   94)D Protein           To check
    10 2226 (  104) 2239 (  117)D Protein           To check
    11 2240 (  128) 2255 (  143)D Protein           To check
    12 2256 (  149) 2284 (  177)D Protein           To check
    13 2285 (  199) 2291 (  205)D Protein           To check
    14 2292 (  212) 2305 (  225)D Protein           To check
    15 2306 (  238) 2790 (  722)D Protein           To check
    16 2791 (    1) 2791 (    1)E BGC  <-           To check
    17 2792 (    2) 2792 (    2)E BGC  <-           To check
    18 2793 (    3) 2793 (    3)E BGC  <-           To check
    19 2794 (    4) 2794 (    4)E BGC  <-           To check
    20 2795 (    5) 2795 (    5)E BGC  <-           To check
    21 2796 (    6) 2796 (    6)E BGC  <-           To check
    22 2797 (    1) 2797 (    1)F BGC  <-           To check
    23 2798 (    2) 2798 (    2)F BGC  <-           To check
    24 2799 (    3) 2799 (    3)F BGC  <-           To check
    25 2800 (    4) 2800 (    4)F BGC  <-           To check
    26 2801 (    5) 2801 (    5)F BGC  <-           To check
    27 2802 (    1) 2802 (    1)G BGC  <-           To check
    28 2803 (    2) 2803 (    2)G BGC  <-           To check
    29 2804 (    3) 2804 (    3)G BGC  <-           To check
    30 2805 (    4) 2805 (    4)G BGC  <-           To check
    31 2806 (    1) 2806 (    1)H BGC  <-           To check
    32 2807 (    2) 2807 (    2)H BGC  <-           To check
    33 2808 (    3) 2808 (    3)H BGC  <-           To check
    34 2809 (    1) 2809 (    1)I BGC  <-           To check
    35 2810 (    2) 2810 (    2)I BGC  <-           To check
    36 2811 (    3) 2811 (    3)I BGC  <-           To check
    37 2812 (    1) 2812 (    1)J BGC  <-           To check
    38 2813 (    2) 2813 (    2)J BGC  <-           To check
    39 2814 (    1) 2814 (    1)K BGC  <-           To check
    40 2815 (    2) 2815 (    2)K BGC  <-           To check
    41 2816 (    1) 2816 (    1)L BGC  <-           To check
    42 2817 (    2) 2817 (    2)L BGC  <-           To check
    43 2818 (    3) 2818 (    3)L BGC  <-           To check
    44 2819 (    4) 2819 (    4)L BGC  <-           To check
    45 2820 (    1) 2820 (    1)M BGC  <-           To check
    46 2821 (    2) 2821 (    2)M BGC  <-           To check
    47 2822 (    3) 2822 (    3)M BGC  <-           To check
    48 2823 (    4) 2823 (    4)M BGC  <-           To check
    49 2824 (    5) 2824 (    5)M BGC  <-           To check
    50 2825 (    1) 2825 (    1)N BGC  <-           To check
    51 2826 (    2) 2826 (    2)N BGC  <-           To check
    52 2827 (    3) 2827 (    3)N BGC  <-           To check
    53 2828 (    1) 2828 (    1)O BGC  <-           To check
    54 2829 (    2) 2829 (    2)O BGC  <-           To check
    55 2830 (    3) 2830 (    3)O BGC  <-           To check
    56 2831 (    4) 2831 (    4)O BGC  <-           To check
    57 2832 (    1) 2832 (    1)P BGC  <-           To check
    58 2833 (    2) 2833 (    2)P BGC  <-           To check
    59 2834 (    3) 2834 (    3)P BGC  <-           To check
    60 2835 (    4) 2835 (    4)P BGC  <-           To check
    61 2836 (    1) 2836 (    1)Q BGC  <-           To check
    62 2837 (    2) 2837 (    2)D BGC  <-           To check
    63 2838 (    3) 2838 (    3)Q BGC  <-           To check
    64 2839 (    4) 2839 (    4)Q BGC  <-           To check
    65 2840 (    1) 2840 (    1)R BGC  <-           To check
    66 2841 (    2) 2841 (    2)R BGC  <-           To check
    67 2842 (    3) 2842 (    3)R BGC  <-           To check
    68 2843 ( HOH ) 2843 ( HOH )A water   (  185)   To check
    69 2844 ( HOH ) 2844 ( HOH )B water   (  143)   To check
    70 2845 ( HOH ) 2845 ( HOH )C water   (   57)   To check
    71 2846 ( HOH ) 2846 ( HOH )D water   (   94)   To check
 
# 42 # Note: B-factor plot
A large B-factor difference was observed between individual chains. This is
not wrong or so, but it is a bit strange...
 
In the TeX file, a plot has been inserted here
 
Chain identifiers: A - D
 
# 43 # 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.
 
# 44 # Note: Valine nomenclature OK
No errors were detected in valine nomenclature.
 
# 45 # Note: Threonine nomenclature OK
No errors were detected in threonine nomenclature.
 
# 46 # Note: Isoleucine nomenclature OK
No errors were detected in isoleucine nomenclature.
 
# 47 # Note: Leucine nomenclature OK
No errors were detected in leucine nomenclature.
 
# 48 # Warning: Arginine nomenclature problem
The arginine residues listed in the table below have their NH1 and NH2
swapped.
 
  194 ARG  ( 201-) A  -
  333 ARG  ( 340-) A  -
  494 ARG  ( 501-) A  -
  504 ARG  ( 511-) A  -
  520 ARG  ( 527-) A  -
  604 ARG  ( 611-) A  -
  691 ARG  ( 698-) A  -
  701 ARG  ( 708-) A  -
  914 ARG  ( 201-) B  -
  941 ARG  ( 228-) B  -
 1053 ARG  ( 340-) B  -
 1214 ARG  ( 501-) B  -
 1224 ARG  ( 511-) B  -
 1240 ARG  ( 527-) B  -
 1324 ARG  ( 611-) B  -
And so on for a total of    35 lines.
 
# 49 # Note: Tyrosine torsion conventions OK
No errors were detected in tyrosine torsion angle conventions.
 
# 50 # Note: Phenylalanine torsion conventions OK
No errors were detected in phenylalanine torsion angle conventions.
 
# 51 # Note: Aspartic acid torsion conventions OK
No errors were detected in aspartic acid torsion angle conventions.
 
# 52 # Note: Glutamic acid torsion conventions OK
No errors were detected in glutamic acid torsion angle conventions.
 
# 53 # 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).
 
# 54 # 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.
 
# 55 # Note: No decreasing residue numbers
All residue numbers are strictly increasing within each chain.
 
# 56 # Note: All bond lengths OK
All bond lengths are in agreement with standard bond lengths using a
tolerance of 4 sigma (both standard values and sigma for amino acids
have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson
et al [REF]).
 
# 57 # 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: 0.430
 RMS-deviation in bond distances: 0.010
 
# 58 # Note: No bond length directionality
Comparison of bond distances with Engh and Huber [REF] standard values for
protein residues and Parkinson et al [REF] values for DNA/RNA does not show
significant systematic deviations.
 
# 59 # 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.
 
  470 HIS  ( 477-) A  -    CG   ND1  CE1 109.73    4.1
  849 HIS  ( 136-) B  -    CG   ND1  CE1 109.73    4.1
 1248 HIS  ( 535-) B  -    CG   ND1  CE1 109.74    4.1
 1324 ARG  ( 611-) B  -    CB   CG   CD  105.80   -4.1
 1411 ARG  ( 698-) B  -    CG   CD   NE  117.59    4.2
 1653 ASP  ( 231-) C  -    C    CA   CB  118.76    4.6
 2164 HIS  (  26-) D  -    CG   ND1  CE1 109.61    4.0
 2545 HIS  ( 477-) D  -    CG   ND1  CE1 109.61    4.0
 
# 60 # 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: 0.676
 RMS-deviation in bond angles: 1.421
 
# 61 # 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.
 
  194 ARG  ( 201-) A  -
  333 ARG  ( 340-) A  -
  494 ARG  ( 501-) A  -
  504 ARG  ( 511-) A  -
  520 ARG  ( 527-) A  -
  604 ARG  ( 611-) A  -
  691 ARG  ( 698-) A  -
  701 ARG  ( 708-) A  -
  914 ARG  ( 201-) B  -
  941 ARG  ( 228-) B  -
 1053 ARG  ( 340-) B  -
 1214 ARG  ( 501-) B  -
 1224 ARG  ( 511-) B  -
 1240 ARG  ( 527-) B  -
 1324 ARG  ( 611-) B  -
And so on for a total of    35 lines.
 
# 62 # 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= 1.071
 
# 63 # 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 : 0.880
 
# 64 # Note: Tau angles OK
All of the tau angles (N-C-alpha-C) of amino acids fall within expected
RMS deviations.
 
# 65 # Note: Normal tau angle deviations
The RMS Z-score for the tau angles (N-C-alpha-C) in the structure falls
within the normal range that we guess to be 0.5 - 1.5. Be aware, we
determined the tau normal distributions from 500 high-resolution X-ray
structures, rather than from CSD data, so we cannot be 100 percent certain
about these numbers.
 
 Tau angle RMS Z-score : 0.913
 
# 66 # Note: Side chain planarity OK
All of the side chains of residues that have an intact planar group are
planar within expected RMS deviations.
 
# 67 # 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.
 
# 68 # Warning: Ramachandran Z-score low
The score expressing how well the backbone conformations of all residues
correspond to the known allowed areas in the Ramachandran plot is a bit low.
 
 Ramachandran Z-score : -3.936
 
# 69 # 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.
 
# 70 # 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.
 
  619 THR  ( 626-) A  -   -3.3
 2393 THR  ( 325-) D  -   -3.2
 2046 THR  ( 626-) C  -   -3.2
 1339 THR  ( 626-) B  -   -3.2
 2694 THR  ( 626-) D  -   -3.2
  831 THR  ( 118-) B  -   -3.1
  114 THR  ( 118-) A  -   -3.1
 1547 THR  ( 118-) C  -   -3.0
  188 THR  ( 195-) A  -   -2.8
  104 ILE  ( 108-) A  -   -2.5
 2683 ILE  ( 615-) D  -   -2.5
 1610 ILE  ( 181-) C  -   -2.4
 1824 LYS  ( 404-) C  -   -2.4
  635 LEU  ( 642-) A  -   -2.4
 2788 HIS  ( 720-) D  -   -2.4
And so on for a total of    48 lines.
 
# 71 # 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.
 
    6 VAL  (  10-) A  - Omega to (next) Pro poor
   12 ASP  (  16-) A  - Omega to (next) Pro poor
   17 PHE  (  21-) A  - Omega to (next) Pro poor
   22 HIS  (  26-) A  - Omega to (next) Pro poor
   25 GLU  (  29-) A  - Omega to (next) Pro poor
   34 GLY  (  38-) A  - Poor phi/psi
   37 VAL  (  41-) A  - Omega to (next) Pro poor
   48 TYR  (  52-) A  - Omega to (next) Pro poor
   52 ASP  (  56-) A  - Poor phi/psi
   55 ALA  (  59-) A  - Omega to (next) Pro poor
   58 THR  (  62-) A  - Omega to (next) Pro poor
   60 ASP  (  64-) A  - Poor phi/psi, omega to (next)
   67 LEU  (  71-) A  - Poor phi/psi
   71 GLY  (  75-) A  - Poor phi/psi
   72 GLY  (  76-) A  - Poor phi/psi
And so on for a total of   351 lines.
 
# 72 # 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.
 
  137 LEU  ( 141-) A  -    -1.32
  172 LEU  ( 176-) A  -    -1.32
  218 LEU  ( 225-) A  -    -1.32
  332 LEU  ( 339-) A  -    -1.31
  457 LEU  ( 464-) A  -    -1.31
  592 LEU  ( 599-) A  -    -1.31
  626 LEU  ( 633-) A  -    -1.32
  635 LEU  ( 642-) A  -    -1.31
  674 LEU  ( 681-) A  -    -1.31
  783 LEU  (  70-) B  -    -1.32
  854 LEU  ( 141-) B  -    -1.32
  889 LEU  ( 176-) B  -    -1.32
  938 LEU  ( 225-) B  -    -1.32
 1052 LEU  ( 339-) B  -    -1.32
 1177 LEU  ( 464-) B  -    -1.30
And so on for a total of  1123 lines.
 
# 73 # Warning: chi-1/chi-2 angle correlation Z-score low
The score expressing how well the chi-1/chi-2 angles of all residues
correspond to the populated areas in the database is
a bit low.
 
 chi-1/chi-2 correlation Z-score : -3.573
 
# 74 # 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.
 
 1630 ASN  ( 208-) C  -   0.33
  696 ASP  ( 703-) A  -   0.35
 2373 HIS  ( 305-) D  -   0.35
  551 SER  ( 558-) A  -   0.36
 2079 SER  ( 659-) C  -   0.36
 1559 GLN  ( 130-) C  -   0.36
  292 THR  ( 299-) A  -   0.38
  732 SER  (  19-) B  -   0.38
 1372 SER  ( 659-) B  -   0.38
 1621 SER  ( 199-) C  -   0.38
 1978 SER  ( 558-) C  -   0.38
 2157 SER  (  19-) D  -   0.38
  652 SER  ( 659-) A  -   0.39
 1271 SER  ( 558-) B  -   0.39
 1452 SER  (  19-) C  -   0.39
 2129 SER  ( 709-) C  -   0.39
 2367 THR  ( 299-) D  -   0.39
 2626 SER  ( 558-) D  -   0.39
 2727 SER  ( 659-) D  -   0.39
 2777 SER  ( 709-) D  -   0.39
 2242 GLN  ( 130-) D  -   0.39
  976 ARG  ( 263-) B  -   0.40
 
# 75 # 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!
 
   32 GLU  (  36-) A  -       0
   60 ASP  (  64-) A  -       0
  270 ASP  ( 277-) A  -       0
  319 LYS  ( 326-) A  -       0
  341 GLU  ( 348-) A  -       0
  342 TRP  ( 349-) A  -       0
  404 ARG  ( 411-) A  -       0
  490 TRP  ( 497-) A  -       0
  537 ASP  ( 544-) A  -       0
  610 ILE  ( 617-) A  -       0
  637 MET  ( 644-) A  -       0
  749 GLU  (  36-) B  -       0
  777 ASP  (  64-) B  -       0
  990 ASP  ( 277-) B  -       0
 1038 THR  ( 325-) B  -       0
And so on for a total of    87 lines.
 
# 76 # 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 : -0.825
 
# 77 # Note: Omega angle restraint OK
The omega angles for trans-peptide bonds in a structure is expected to give a
gaussian distribution with the average around +178 degrees, and a standard
deviation around 5.5. In the current structure the standard deviation agrees
with this expectation.
 
Omega average and std. deviation= 179.540 5.426
 
# 78 # Note: PRO puckering amplitude OK
Puckering amplitudes for all PRO residues are within normal ranges.
 
# 79 # 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].
 
   56 PRO  (  60-) A  -  -56.4 half-chair C-beta/C-alpha (-54 degrees)
   90 PRO  (  94-) A  - -113.4 envelop C-gamma (-108 degrees)
  169 PRO  ( 173-) A  -   99.8 envelop C-beta (108 degrees)
  233 PRO  ( 240-) A  - -114.5 envelop C-gamma (-108 degrees)
  246 PRO  ( 253-) A  - -122.7 half-chair C-delta/C-gamma (-126 degrees)
  344 PRO  ( 351-) A  - -120.3 half-chair C-delta/C-gamma (-126 degrees)
  349 PRO  ( 356-) A  -   48.3 half-chair C-delta/C-gamma (54 degrees)
  406 PRO  ( 413-) A  -  101.6 envelop C-beta (108 degrees)
  422 PRO  ( 429-) A  - -114.6 envelop C-gamma (-108 degrees)
  648 PRO  ( 655-) A  -  105.6 envelop C-beta (108 degrees)
  669 PRO  ( 676-) A  -  110.0 envelop C-beta (108 degrees)
  773 PRO  (  60-) B  -  -56.8 half-chair C-beta/C-alpha (-54 degrees)
  966 PRO  ( 253-) B  - -122.0 half-chair C-delta/C-gamma (-126 degrees)
 1064 PRO  ( 351-) B  - -120.8 half-chair C-delta/C-gamma (-126 degrees)
 1069 PRO  ( 356-) B  -   49.3 half-chair C-delta/C-gamma (54 degrees)
And so on for a total of    32 lines.
 
# 80 # 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!
 
 1820 LEU  ( 400-) C  -  1.75   80
  403 LEU  ( 410-) A  -  1.71   21
 1509 GLY  (  76-) C  -  1.67   28
 2607 GLY  ( 539-) D  -  1.61   14
 1830 LEU  ( 410-) C  -  1.57   23
  789 GLY  (  76-) B  -  1.54   33
 1123 LEU  ( 410-) B  -  1.50   28
 
# 81 # 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.
 
 1993 GLY  ( 573-) C  - TT+   Highly likely
   97 TYR  ( 101-) A  - TT+   Likely
  814 TYR  ( 101-) B  - TT+   Likely
 1510 ASN  (  77-) C  - TT+   Likely
 1577 ASP  ( 148-) C  - TT+   Likely
 1616 ASP  ( 187-) C  - TT+   Likely
 1811 GLY  ( 391-) C  - TT+   Likely
 1823 ASN  ( 403-) C  - TT+   Likely
 1828 THR  ( 408-) C  - TT+   Likely
 1829 GLN  ( 409-) C  - TT+   Likely
 1914 ASP  ( 494-) C  - TT+   Likely
 1918 ASN  ( 498-) C  - TT+   Likely
 2166 PHE  (  28-) D  - TT+   Likely
 2526 MET  ( 458-) D  - TT+   Likely
 2528 GLY  ( 460-) D  - TT+   Likely
 
# 82 # Error: Abnormally short interatomic distances
The pairs of atoms listed in the table below have an unusually short
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.
 
The last text-item on each line represents the status of the atom pair. The
text `INTRA' means that the bump is between atoms that are explicitly listed
in the PDB file. `INTER' means it is an inter-symmetry bump. 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.
 
It seems likely that at least some of the reported bumps are caused by
administrative errors in the chain names. I.e. covalently bound atoms with
different non-blank chain-names are reported as bumps. In rare cases this is
not an error.
 
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.
 
 1497 ASP  (  64-) C  -    OD2  <-->   1724 TYR  ( 302-) C  -    OH   0.70    1.70  INTRA BL
 1076 GLU  ( 363-) B  -    OE2  <-->   1411 ARG  ( 698-) B  -    NH1  0.63    2.07  INTRA BF
 2064 MET  ( 644-) C  -    CG   <-->   2069 MET  ( 649-) C  -    CE   0.60    2.60  INTRA BF
 1066 GLN  ( 353-) B  -    NE2  <-->   1068 ALA  ( 355-) B  -    O    0.58    2.12  INTRA
  787 TYR  (  74-) B  -    O    <-->    829 ARG  ( 116-) B  -    NH1  0.45    2.25  INTRA
 2045 TYR  ( 625-) C  -    OH   <-->   2057 HIS  ( 637-) C  -    NE2  0.43    2.27  INTRA
 2492 LYS  ( 424-) D  -    NZ   <-->   2562 ASP  ( 494-) D  -    OD2  0.43    2.27  INTRA BL
 1405 GLU  ( 692-) B  -    OE1  <-->   1437 ARG  ( 724-) B  -    NH1  0.41    2.29  INTRA
   77 THR  (  81-) A  -    OG1  <-->    112 ARG  ( 116-) A  -    NE   0.40    2.30  INTRA
 1137 LYS  ( 424-) B  -    NZ   <-->   1207 ASP  ( 494-) B  -    OD2  0.39    2.31  INTRA
 2214 ARG  (  83-) D  -    NH2  <-->   2232 SER  ( 110-) D  -    OG   0.35    2.35  INTRA BF
 1820 LEU  ( 400-) C  -    O    <-->   1823 ASN  ( 403-) C  -    N    0.34    2.36  INTRA BF
 1644 ASP  ( 222-) C  -    OD1  <-->   1645 LYS  ( 223-) C  -    N    0.33    2.27  INTRA BF
  319 LYS  ( 326-) A  -    NZ   <-->    528 HIS  ( 535-) A  -    NE2  0.33    2.67  INTRA BL
 1624 LYS  ( 202-) C  -    NZ   <-->   1682 ASP  ( 260-) C  -    OD1  0.30    2.40  INTRA BF
And so on for a total of   243 lines.
 
# 83 # 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: 26.106
Total bump value per residue: 0.087
Total number of bumps: 243
Total squared bump value: 5.971
Total number of bumps in the mildest bin: 218
Total number of bumps in the second bin: 21
Total number of bumps in the middle bin: 4
Total number of bumps in the fourth bin: 0
Total number of bumps in the worst bin: 0
 
# 84 # 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.
 
# 85 # 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 : 1.038
 
# 86 # 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
 
# 87 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 88 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: C
 
# 89 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 90 # 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.
 
   70 TYR  (  74-) A  -  -7.95
  404 ARG  ( 411-) A  -  -7.87
 1124 ARG  ( 411-) B  -  -7.58
 1507 TYR  (  74-) C  -  -7.57
 2224 TYR  (  93-) D  -  -7.53
 1831 ARG  ( 411-) C  -  -7.45
 1526 TYR  (  93-) C  -  -7.33
  806 TYR  (  93-) B  -  -7.27
 2479 ARG  ( 411-) D  -  -7.25
   89 TYR  (  93-) A  -  -7.07
 1436 ARG  ( 723-) B  -  -6.91
  787 TYR  (  74-) B  -  -6.81
  716 ARG  ( 723-) A  -  -6.79
 2696 TYR  ( 628-) D  -  -6.55
  903 LYS  ( 190-) B  -  -6.52
And so on for a total of    50 lines.
 
# 91 # 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.
 
 2223 SER  (  92-) D  -     2225 --- PRO    94- (D ) -       -5.36
 
# 92 # Note: Structural average packing environment OK
The structural average packing score is within normal ranges.
 
 
Average for range     1 - 2790 :  -0.461
 
# 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: A
 
# 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: B
 
# 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: C
 
# 96 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as function
of the residue number. Low areas in the plot (below -2.0) indicate unusual
packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 97 # 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.
 
 2138 ARG  ( 718-) C  -  -3.86
  314 LEU  ( 321-) A  -  -2.78
 1645 LYS  ( 223-) C  -  -2.75
  622 PHE  ( 629-) A  -  -2.72
 2389 LEU  ( 321-) D  -  -2.69
 2697 PHE  ( 629-) D  -  -2.68
 1034 LEU  ( 321-) B  -  -2.68
 2049 PHE  ( 629-) C  -  -2.67
  749 GLU  (  36-) B  -  -2.67
 2347 ASN  ( 279-) D  -  -2.66
  272 ASN  ( 279-) A  -  -2.64
 1341 TYR  ( 628-) B  -  -2.64
 1342 PHE  ( 629-) B  -  -2.63
 1743 LEU  ( 321-) C  -  -2.51
 
# 98 # 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
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
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
 
# 99 # 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
 
# 100 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 101 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: C
 
# 102 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 103 # Warning: No crystallisation information
No, or very inadequate, crystallisation information was observed upon
reading the PDB file header records. This information should be available
in the form of a series of REMARK 280 lines. Without this information a
few things, such as checking ions in the structure, cannot be performed
optimally.
 
# 104 # 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.
 
 2843 HOH  (1085 ) A  -    O
 2844 HOH  (1036 ) B  -    O
 2845 HOH  ( 957 ) C  -    O
 2846 HOH  ( 992 ) D  -    O
 2846 HOH  ( 993 ) D  -    O
 2846 HOH  ( 994 ) D  -    O
 
# 105 # Note: No waters need moving
All water molecules are sufficiently close to the asymmetric unit given in
the input file.
 
# 106 # 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.
 
 2843 HOH  ( 936 ) A  -    O
 2843 HOH  (1076 ) A  -    O
 2843 HOH  (1085 ) A  -    O
 2844 HOH  ( 901 ) B  -    O
 2844 HOH  (1003 ) B  -    O
 2844 HOH  (1036 ) B  -    O
 2845 HOH  ( 903 ) C  -    O
 2845 HOH  ( 957 ) C  -    O
 2846 HOH  ( 971 ) D  -    O
 2846 HOH  ( 975 ) D  -    O
 2846 HOH  ( 992 ) D  -    O
 2846 HOH  ( 993 ) D  -    O
 2846 HOH  ( 994 ) D  -    O
 
# 107 # 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.
 
   73 ASN  (  77-) A  -
  136 ASN  ( 140-) A  -
  507 ASN  ( 514-) A  -
  577 GLN  ( 584-) A  -
 1066 GLN  ( 353-) B  -
 1190 HIS  ( 477-) B  -
 1228 ASN  ( 515-) B  -
 1265 GLN  ( 552-) B  -
 1447 ASN  (  14-) C  -
 1569 ASN  ( 140-) C  -
 1837 GLN  ( 417-) C  -
 
# 108 # 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.
 
   22 HIS  (  26-) A  -   HIS-H   0.16 HIS-E   0.56
  132 HIS  ( 136-) A  -   HIS-H   0.40 HIS-D   0.45
  175 HIS  ( 179-) A  -   HIS-H   0.08 HIS-E   0.59
  297 HIS  ( 304-) A  -   HIS-H   0.22 HIS-E   0.65
  298 HIS  ( 305-) A  -   HIS-H   0.19 HIS-E   0.59
  463 HIS  ( 470-) A  -   HIS-H   0.31 HIS-E   0.50
  469 HIS  ( 476-) A  -   HIS-H   0.20
  470 HIS  ( 477-) A  -   HIS-H   0.29 HIS-E   0.57
  472 HIS  ( 479-) A  -   HIS-H   0.28 HIS-E   0.61
  484 HIS  ( 491-) A  -   HIS-H   0.15
  485 HIS  ( 492-) A  -   HIS-H   0.23 HIS-D   0.64
  528 HIS  ( 535-) A  -   HIS-H   0.16 HIS-D   0.58
  630 HIS  ( 637-) A  -   HIS-H   0.13 HIS-D   0.59
  713 HIS  ( 720-) A  -   HIS-H   0.34 HIS-E   0.61
  739 HIS  (  26-) B  -   HIS-H   0.16 HIS-E   0.61
And so on for a total of    55 lines.
 
# 109 # 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.
 
    6 VAL  (  10-) A  -    N
    8 VAL  (  12-) A  -    N
    9 SER  (  13-) A  -    N
   29 ALA  (  33-) A  -    N
   33 ASN  (  37-) A  -    N
   33 ASN  (  37-) A  -    ND2
   45 ASN  (  49-) A  -    N
   75 GLY  (  79-) A  -    N
   97 TYR  ( 101-) A  -    N
   98 THR  ( 102-) A  -    OG1
  112 ARG  ( 116-) A  -    NE
  115 SER  ( 119-) A  -    OG
  133 LEU  ( 137-) A  -    N
  155 ARG  ( 159-) A  -    NE
  159 TYR  ( 163-) A  -    N
And so on for a total of   246 lines.
 
# 110 # 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.
 
  304 ASP  ( 311-) A  -    OD1
  521 ASN  ( 528-) A  -    OD1
  546 GLU  ( 553-) A  -    OE1
  550 GLU  ( 557-) A  -    OE2
  634 GLN  ( 641-) A  -    OE1
  822 ASN  ( 109-) B  -    OD1
 1024 ASP  ( 311-) B  -    OD1
 1150 ASP  ( 437-) B  -    OD2
 1204 HIS  ( 491-) B  -    ND1
 1228 ASN  ( 515-) B  -    OD1
 1241 ASN  ( 528-) B  -    OD1
 1264 ASP  ( 551-) B  -    OD2
 1334 GLN  ( 621-) B  -    OE1
 1337 ASP  ( 624-) B  -    OD2
 1354 GLN  ( 641-) B  -    OE1
And so on for a total of    32 lines.
 
# 111 # 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: 3977
- of which buried: 2328
Total number of acceptors: 4271
- of which buried: 1923
Total number of donor+acceptors: 549
  (e.g. the Ser Ogamma that can donate and accept)
- of which buried: 171
Buried donors: 2328
- without H-bond: 206
- essentially without H-bond: 1
- with only a very poor H-bond: 20
- with a poor H-bond: 45
- with a H-bond: 2056
Buried acceptors: 1923
- without H-bond: 261
- essentially without H-bond: 0
- with only a very poor H-bond: 15
- with a poor H-bond: 52
- with a H-bond: 1595
 
# 112 # 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 (    5)   186 (  190) A Protein             To check
     2   187 (  194)   717 (  724) A Protein             To check
     3   718 (    5)  1437 (  724) B Protein             To check
     4  1438 (    5)  1532 (   99) C Protein             To check
     5  1533 (  104)  1618 (  189) C Protein             To check
     6  1619 (  197)  1773 (  351) C Protein             To check
     7  1774 (  354)  2142 (  722) C Protein             To check
     8  2143 (    5)  2209 (   71) D Protein             To check
     9  2210 (   79)  2225 (   94) D Protein             To check
    10  2226 (  104)  2239 (  117) D Protein             To check
    11  2240 (  128)  2255 (  143) D Protein             To check
    12  2256 (  149)  2284 (  177) D Protein             To check
    13  2285 (  199)  2291 (  205) D Protein             To check
    14  2292 (  212)  2305 (  225) D Protein             To check
    15  2306 (  238)  2790 (  722) D Protein             To check
And so on for a total of    71 lines.
 
# 113 # 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  :   2.700
  1st generation packing quality :   0.099 (          (  -0.8,  2.5))
  2nd generation packing quality :  -1.804 (          (  -1.6,  1.2))
  Ramachandran plot appearance   :  -3.936 (poor      (  -2.9,  1.6))
  chi-1/chi-2 rotamer normality  :  -3.573 (poor      (  -4.7,  1.8))
  Backbone conformation          :  -0.825 (          (  -0.9,  3.7))
  Inside/Outside distribution    :   1.038
 
 RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.430 (tight)
  Bond angles                    :   0.676
  Omega angle restraints         :   0.986
  Side chain planarity           :   0.670
  Improper dihedral distribution :   0.880
 
# 114 # 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.
 
# 115 # 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.
 
# 116 # 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.
 
# 117 # Error: Water bumps in your structure
WHAT CHECK had to delete several water molecules because they overlapped
so badly that things like hydrogen bond calculations were not possible.
Obviously WHAT CHECK is not as smart as you in dealing with this problem,
so you better do something about the overlapping waters.
Often this problem is caused by having alternate water locations that
did not get a reduced occupancy.
 
# 118 # 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.
 
# 119 # Note: Free floating waters
Your structure contains many water molecules that make no hydrogen bonds at
all. These waters must be removed, and you must then refine a bit further
before running WHAT CHECK again.
 
# 120 # 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.
 
 1437 ARG  ( 724-) B  -     16.74
 1724 TYR  ( 302-) C  -     15.98
   70 TYR  (  74-) A  -     15.90
  404 ARG  ( 411-) A  -     15.73
  787 TYR  (  74-) B  -     15.43
 1507 TYR  (  74-) C  -     15.20
 1411 ARG  ( 698-) B  -     15.18
 1124 ARG  ( 411-) B  -     15.15
 2224 TYR  (  93-) D  -     15.09
 1831 ARG  ( 411-) C  -     14.90
 1526 TYR  (  93-) C  -     14.70
  806 TYR  (  93-) B  -     14.59
 2479 ARG  ( 411-) D  -     14.50
   89 TYR  (  93-) A  -     14.17
 1436 ARG  ( 723-) B  -     13.93
And so on for a total of   291 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.
