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

Date : 2024-12-06
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/3d0g/wctemp_besttls/3d0g_besttls.pd====
=========================================
 
# 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                                                        3D0G
ATOM  *****  C2  NDG A 616      28.614 -14.572 100.239  1.00 67.43       C2  C
ATOM  *****  C3  NDG A 616      28.980 -13.409 101.156  1.00 71.29       C3  C
ATOM  *****  C4  NDG A 616      29.292 -13.886 102.569  1.00 74.79       C4  C
ATOM  *****  C5  NDG A 616      30.319 -15.017 102.547  1.00 76.76       C5  C
ATOM  *****  C6  NDG A 616      30.527 -15.649 103.907  1.00 82.56       C6  C
ATOM  *****  C7  NDG A 616      28.182 -14.929  97.851  1.00 60.10       C7  C
ATOM  *****  C8  NDG A 616      26.780 -15.425  97.669  1.00 53.05       C8  C
ATOM  *****  O5  NDG A 616      29.877 -16.072 101.669  1.00 72.54       O5  O
ATOM  *****  O3  NDG A 616      27.903 -12.481 101.164  1.00 70.60       O3  O
ATOM  *****  O4  NDG A 616      29.819 -12.794 103.319  1.00 78.96       O4  O
ATOM  *****  O6  NDG A 616      31.912 -15.727 104.244  1.00 86.49       O6  O
ATOM  *****  O7  NDG A 616      29.093 -15.261  97.100  1.00 57.75       O7  O
ATOM  *****  N2  NDG A 616      28.386 -14.109  98.885  1.00 62.85       N2  N
ATOM  *****  O1  NDG A 616      30.871 -15.183  99.779  1.00 68.12       O1  O
ATOM  *****  C2  NDG B 616      52.382  24.252  34.848  1.00 80.97       C2  C
ATOM  *****  C3  NDG B 616      52.249  24.924  36.211  1.00 74.27       C3  C
ATOM  *****  C4  NDG B 616      51.504  26.243  36.059  1.00 74.71       C4  C
ATOM  *****  C5  NDG B 616      50.129  25.966  35.462  1.00 80.70       C5  C
ATOM  *****  C6  NDG B 616      49.321  27.226  35.235  1.00 80.54       C6  C
ATOM  *****  C7  NDG B 616      54.164  22.714  34.146  1.00 75.48       C7  C
ATOM  *****  C8  NDG B 616      55.523  23.044  34.685  1.00 68.23       C8  C
ATOM  *****  O5  NDG B 616      50.288  25.317  34.182  1.00 90.60       O5  O
ATOM  *****  O3  NDG B 616      53.533  25.118  36.786  1.00 71.13       O3  O
ATOM  *****  O4  NDG B 616      51.353  26.876  37.326  1.00 74.55       O4  O
ATOM  *****  O6  NDG B 616      48.701  27.239  33.951  1.00 84.18       O6  O
ATOM  *****  O7  NDG B 616      54.012  22.199  33.044  1.00 78.14       O7  O
ATOM  *****  N2  NDG B 616      53.127  23.011  34.935  1.00 80.57       N2  N
ATOM  *****  O1  NDG B 616      50.278  23.150  34.977  1.00 90.12       O1  O
ATOM  *****  C2  NDG B 617      51.064  41.131  66.600  1.00102.24       C2  C
ATOM  *****  C3  NDG B 617      51.692  41.419  67.963  1.00101.86       C3  C
ATOM  *****  C4  NDG B 617      51.507  42.883  68.343  1.00 98.10       C4  C
ATOM  *****  C5  NDG B 617      50.018  43.221  68.348  1.00100.70       C5  C
ATOM  *****  C6  NDG B 617      49.732  44.674  68.675  1.00 96.61       C6  C
ATOM  *****  C7  NDG B 617      51.849  39.261  65.179  1.00 80.36       C7  C
ATOM  *****  C8  NDG B 617      53.342  39.413  65.197  1.00 74.23       C8  C
ATOM  *****  O5  NDG B 617      49.465  42.969  67.040  1.00 95.72       O5  O
ATOM  *****  O3  NDG B 617      53.071  41.078  67.950  1.00111.14       O3  O
ATOM  *****  O4  NDG B 617      52.062  43.111  69.637  1.00 84.19       O4  O
ATOM  *****  O6  NDG B 617      49.241  45.398  67.542  1.00 78.78       O6  O
ATOM  *****  O7  NDG B 617      51.264  38.728  64.239  1.00 55.58       O7  O
ATOM  *****  N2  NDG B 617      51.189  39.727  66.248  1.00 87.88       N2  N
ATOM  *****  O1  NDG B 617      48.829  40.791  67.351  1.00103.34       O1  O
ATOM  *****  C2  NDG B 618      46.302  30.332  76.988  1.00 50.73       C2  C
ATOM  *****  C3  NDG B 618      46.307  31.469  78.004  1.00 55.44       C3  C
ATOM  *****  C4  NDG B 618      47.674  31.609  78.659  1.00 56.22       C4  C
ATOM  *****  C5  NDG B 618      48.677  31.970  77.567  1.00 63.42       C5  C
ATOM  *****  C6  NDG B 618      50.068  32.279  78.088  1.00 76.95       C6  C
ATOM  *****  C7  NDG B 618      44.181  29.492  76.042  1.00 46.80       C7  C
ATOM  *****  C8  NDG B 618      43.095  29.730  75.032  1.00 36.85       C8  C
ATOM  *****  O5  NDG B 618      48.812  30.848  76.671  1.00 55.20       O5  O
ATOM  *****  O3  NDG B 618      45.291  31.190  78.957  1.00 63.07       O3  O
ATOM  *****  O4  NDG B 618      47.650  32.610  79.676  1.00 43.86       O4  O
ATOM  *****  O6  NDG B 618      50.908  31.117  78.125  1.00 78.94       O6  O
ATOM  *****  O7  NDG B 618      44.204  28.481  76.737  1.00 48.23       O7  O
ATOM  *****  N2  NDG B 618      45.123  30.440  76.149  1.00 45.15       N2  N
ATOM  *****  O1  NDG B 618      47.341  30.897  74.969  1.00 55.38       O1  O
ATOM  *****  O   HOH B 904      29.532  29.159  52.828  1.00 74.81       904 O
ATOM  *****  O   HOH B 905      28.694  31.614  53.353  1.00 80.40       905 O
ATOM  *****  O   HOH B 906       2.843  34.034  54.524  1.00 51.37       906 O
ATOM  *****  O   HOH B 907      19.360  27.249  59.061  1.00 55.84       907 O
ATOM  *****  O   HOH B 908      25.220  42.405  62.176  1.00 74.85       908 O
ATOM  *****  O   HOH B 909       7.262  16.496  75.483  1.00 52.78       909 O
ATOM  *****  O   HOH B 910       9.489  14.405  70.592  1.00 50.17       910 O
ATOM  *****  O   HOH B 911      45.844  46.374  54.732  1.00 65.82       911 O
ATOM  *****  O   HOH B 912      43.990  40.505  68.620  1.00 58.86       912 O
ATOM  *****  O   HOH B 913      17.217  24.347  85.294  1.00 58.07       913 O
ATOM  *****  O   HOH B 914      14.518  25.163  82.295  1.00 53.55       914 O
ATOM  *****  O   HOH B 915      23.659  31.726  87.001  1.00 63.68       915 O
ATOM  *****  O   HOH B 916      23.974  35.546  79.800  1.00 60.89       916 O
ATOM  *****  O   HOH B 917      26.765  35.302  81.828  1.00 63.64       917 O
ATOM  *****  O   HOH B 918      34.333  30.432  90.929  1.00 84.17       918 O
ATOM  *****  O   HOH B 919      21.138  31.668  66.965  1.00 69.69       919 O
ATOM  *****  O   HOH B 920      13.566  36.160  64.619  1.00 53.76       920 O
ATOM  *****  O   HOH B 921      11.143  48.108  64.576  1.00 49.51       921 O
ATOM  *****  O   HOH B 922      18.715  41.251  41.092  1.00 67.97       922 O
ATOM  *****  O   HOH B 923      35.161  33.226  40.905  1.00 67.88       923 O
ATOM  *****  C2  NDG F  91      54.320  29.381  37.349  1.00 90.28       C2  C
ATOM  *****  C3  NDG F  91      55.546  30.149  37.840  1.00 93.00       C3  C
ATOM  *****  C4  NDG F  91      56.063  29.596  39.163  1.00 89.66       C4  C
ATOM  *****  C5  NDG F  91      56.335  28.102  39.020  1.00 84.15       C5  C
ATOM  *****  C6  NDG F  91      56.835  27.470  40.300  1.00 81.49       C6  C
ATOM  *****  C7  NDG F  91      52.765  30.217  35.629  1.00 89.43       C7  C
ATOM  *****  C8  NDG F  91      52.737  31.364  34.663  1.00 66.83       C8  C
ATOM  *****  O5  NDG F  91      55.105  27.438  38.669  1.00 83.13       O5  O
ATOM  *****  O3  NDG F  91      55.209  31.524  37.968  1.00 97.39       O3  O
ATOM  *****  O4  NDG F  91      57.271  30.260  39.524  1.00 81.99       O4  O
ATOM  *****  O6  NDG F  91      56.858  26.048  40.214  1.00 76.58       O6  O
ATOM  *****  O7  NDG F  91      51.735  29.695  36.049  1.00 83.39       O7  O
ATOM  *****  N2  NDG F  91      53.976  29.790  36.001  1.00 95.13       N2  N
ATOM  *****  O1  NDG F  91      55.385  27.469  36.400  1.00 88.78       O1  O
ATOM  *****  O   HOH F  11      57.261  42.453  47.063  1.00 53.63        11 O
ATOM  *****  O   HOH F  12      83.624  60.994  40.814  1.00 60.75        12 O
ATOM  *****  O   HOH F  24      56.345  36.161  33.603  1.00 77.62        24 O
ATOM  *****  O   HOH F  25      55.359  35.134  31.328  1.00 74.45        25 O
ATOM  *****  O   HOH F  26      48.017  52.814  38.312  1.00 60.40        26 O
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
 
# 2 # Note: Header records from PDB file
Header records from PDB file.
 
HEADER                                                        3D0G
 
# 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
  0.012499  0.000000  0.001362
  0.000000  0.008350  0.000000
  0.000000  0.000000  0.009246
 
# 5 # Note: Non crystallographic symmetry RMS plot
The plot shows the RMS differences between two similar chains on a residue-
by-residue basis. Individual "spikes" can be indicative of interesting or
wrong residues. If all residues show a high RMS value, the structure could
be incorrectly refined.
 
In the TeX file, a plot has been inserted here
 
Chain identifiers of the two chains: E and F
 
 All-atom RMS fit for the two chains : 0.452
 CA-only RMS fit for the two chains : 0.300
 
# 6 # Note: Non crystallographic symmetry backbone difference plot
The plot shows the differences in backbone torsion angles between two
similar chains on a residue-by-residue basis. Individual "spikes" can be
indicative of interesting or wrong residues. If all residues show high
differences, the structure could be incorrectly refined.
 
In the TeX file, a plot has been inserted here
 
Chain identifiers of the two chains: E and F
 
# 7 # Warning: Problem detected upon counting molecules and matrices
The parameter Z as given on the CRYST card represents the molecular
multiplicity in the crystallographic cell. Normally, Z equals the number of
matrices of the space group multiplied by the number of NCS relations. The
value of Z is multiplied by the integrated molecular weight of the molecules
in the file to determine the Matthews coefficient. This relation is being
validated in this option. Be aware that the validation can get confused if
both multiple copies of the molecule are present in the ATOM records and
MTRIX records are present in the header of the PDB file.
 
 Space group as read from CRYST card: P 1 21 1
 Number of matrices in space group: 2
 Highest polymer chain multiplicity in structure: 2
 Highest polymer chain multiplicity according to SEQRES: 2
 No explicit MTRIX NCS matrices found in the input file
 Value of Z as found on the CRYST1 card: 0
 Z, symmetry, and molecular multiplicity disagree
 Could it be that Z must be: 4
 
# 8 # Error: Matthews Coefficient (Vm) very high
 
The Matthews coefficient [REF] is defined as the density of the protein
structure in cubic Angstroms per Dalton. Normal values are between 1.5
(tightly packed, little room for solvent) and 4.0 (loosely packed, much
space for solvent). Some very loosely packed structures can get values a bit
higher than that.
 
Numbers this high are almost always caused by giving the wrong value for Z
on the CRYST1 card (or not giving this number at all).
 
 Molecular weight of all polymer chains: 177634.953
 Volume of the Unit Cell V= 1036385.4
 Space group multiplicity: 2
 No NCS symmetry matrices (MTRIX records) found in PDB file
 Matthews coefficient for observed atoms and Z is high: Vm= 11.669
 No Matthews coefficient given in REMARK 280
 Or should we use the previously suggested Z = 4
 which would result in Vm= 2.917
 And remember, a matrix counting problem has been reported earlier already
 
# 9 # Note: Z missing on CRYST1 card
The messages above seem likely caused by the fact that Z is missing from the
CRYST1 card.
 
# 10 # Note: All atoms are sufficiently far away from symmetry axes
None of the atoms in the structure is closer than 0.77 Angstrom to a proper
symmetry axis.
 
# 11 # Note: Chain identifiers OK
WHAT CHECK has not detected any serious chain identifier problems. But be
aware that WHAT CHECK doesn't care about the chain identifiers of waters.
 
# 12 # Warning: Ligands for which a topology was generated automatically
The topology for the ligands in the table below were determined
automatically. WHAT CHECK uses a local copy of the CCP4 monomer library to
generate topology information for ligands. Be aware that automatic topology
generation is a complicated task. So, if you get messages that you fail to
understand or that you believe are wrong, and one of these ligands is
involved, then check the ligand topology entry first. This topology is either
present in the monomer library, or as a libcheck-generated file in the local
directory.
 
 1543 NDG  ( 616-) A  -
 1547 NDG  ( 616-) B  -
 1548 NDG  ( 617-) B  -
 1549 NDG  ( 618-) B  -
 1555 NDG  (  91-) F  -
 
# 13 # Note: Covalently bound ligands
No problems were detected that seem related to covalently bound ligands.
 
# 14 # Note: No strange inter-chain connections detected
No covalent bonds have been detected between molecules with non-identical
chain identifiers.
 
# 15 # Note: No duplicate atom names in ligands
All atom names in ligands (if any) seem adequately unique.
 
# 16 # Note: In all cases the primary alternate atom was used
WHAT CHECK saw no need to make any alternate atom corrections (which means
they either are all correct, or there are none).
 
# 17 # Note: No residues detected inside ligands
Either this structure does not contain ligands with amino acid groups inside
it, or their naming is proper (enough).
 
# 18 # Note: No attached groups interfere with hydrogen bond calculations
It seems there are no sugars, lipids, etc., bound (or very close) to atoms
that otherwise could form hydrogen bonds.
 
# 19 # Note: No probable side chain atoms with zero occupancy detected.
Either there are no side chain atoms with zero occupancy, or the side chain
atoms with zero occupancy were not present in the input PDB file (in which
case they are listed as missing atoms), or their positions are sufficiently
improbable to warrant a zero occupancy.
 
# 20 # Note: No probable backbone atoms with zero occupancy detected.
Either there are no backbone atoms with zero occupancy, or the backbone
atoms with zero occupancy were left out of the input PDB file (in
which case they are listed as missing atoms), or their positions are
sufficiently improbable to warrant a zero occupancy.
 
# 21 # Note: All residues have a complete backbone.
No residues have missing backbone atoms.
 
# 22 # Note: No C-alpha only residues
There are no residues that consist of only an alpha carbon atom.
 
# 23 # Note: Content of the PDB file as interpreted by WHAT CHECK
Content of the PDB file as interpreted by WHAT CHECK.
WHAT CHECK has read your PDB file, and stored it internally in what is called
'the soup'. The content of this soup is listed here. An extensive explanation
of all frequently used WHAT CHECK output formats can be found at
swift.cmbi.ru.nl. Look under output formats. A course on reading this
'Molecules' table is part of the WHAT CHECK website.
 
     1     1 (   19)   597 (  615) A Protein             /zata/tempdir/3d0...
     2   598 (   19)  1194 (  615) B Protein             /zata/tempdir/3d0...
     3  1195 (  324)  1367 (  502) E Protein             /zata/tempdir/3d0...
     4  1368 (   91)  1368 (   91) E Sugar<-             /zata/tempdir/3d0...
     5  1369 (  324)  1541 (  502) F Protein             /zata/tempdir/3d0...
     6  1542 (  615)  1542 (  615) A D O2 <-   597       /zata/tempdir/3d0...
     7  1543 (  616)  1543 (  616) A NDG                 /zata/tempdir/3d0...
     8  1544 (  901)  1544 (  901) A  ZN                 /zata/tempdir/3d0...
     9  1545 (  902)  1545 (  902) A  CL                 /zata/tempdir/3d0...
    10  1546 (  615)  1546 (  615) B D O2 <-  1194       /zata/tempdir/3d0...
    11  1547 (  616)  1547 (  616) B NDG                 /zata/tempdir/3d0...
    12  1548 (  617)  1548 (  617) B NDG                 /zata/tempdir/3d0...
    13  1549 (  618)  1549 (  618) B NDG                 /zata/tempdir/3d0...
    14  1550 (  901)  1550 (  901) B  ZN                 /zata/tempdir/3d0...
    15  1551 (  902)  1551 (  902) B  CL                 /zata/tempdir/3d0...
    16  1552 (  502)  1552 (  502) E E O2 <-  1367       /zata/tempdir/3d0...
    17  1553 (   91)  1553 (   91) E NAG  <-             /zata/tempdir/3d0...
    18  1554 (  502)  1554 (  502) F E O2 <-  1541       /zata/tempdir/3d0...
    19  1555 (   91)  1555 (   91) F NDG                 /zata/tempdir/3d0...
    20  1556 ( HOH )  1556 ( HOH ) B water   (    1)     /zata/tempdir/3d0...
    21  1557 ( HOH )  1557 ( HOH ) F water   (    1)     /zata/tempdir/3d0...
MODELs skipped upon reading PDB file: 0
X-ray structure. No MODELs found
The total number of amino acids found is 1540
of which 40 have poor or (essentially) missing atoms
No nucleic acids observed in input file
Number of (recognized) sugars: 1
 of which one has poor or (essentially) missing atoms')
 
Number of water molecules: 2
Residue numbers increase monotonously OK
 
# 24 # Note: Chain identifiers seem OK
All ions seem to have a logical chain identifier, or there are no ions
present in the input file.
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
 
# 25 # 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
 
# 26 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 27 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: F
 
# 28 # 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 STTEELAKTFLETFNYEAQELSYQSSVASWNYNTNITEENVQNMNNAGDKWSAFLKEQST
(  19)-(  78)
                     70        80        90       100       110       120
                      |         |         |         |         |         |
   61 -  120 LAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNP
(  79)-( 138)
                    130       140       150       160       170       180
                      |         |         |         |         |         |
  121 -  180 QECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYED
( 139)-( 198)
                    190       200       210       220       230       240
                      |         |         |         |         |         |
  181 -  240 YGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHLHAYVRAKLMNAYPSYISP
( 199)-( 258)
                    250       260       270       280       290       300
                      |         |         |         |         |         |
  241 -  300 IGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSV
( 259)-( 318)
                    310       320       330       340       350       360
                      |         |         |         |         |         |
  301 -  360 GLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILMCTKVTMDDFLTAHHEMGH
( 319)-( 378)
                    370       380       390       400       410       420
                      |         |         |         |         |         |
  361 -  420 IQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNETEINF
( 379)-( 438)
                    430       440       450       460       470       480
                      |         |         |         |         |         |
  421 -  480 LLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYC
( 439)-( 498)
                    490       500       510       520       530       540
                      |         |         |         |         |         |
  481 -  540 DPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLFNML
( 499)-( 558)
                    550       560       570       580       590
                      |         |         |         |         |
  541 -  597 RLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNKNSFVGWSTDWSPYAD
( 559)-( 615)
             600       610       620       630       640       650
               |         |         |         |         |         |
  598 -  657 STTEELAKTFLETFNYEAQELSYQSSVASWNYNTNITEENVQNMNNAGDKWSAFLKEQST
(  19)-(  78)
             660       670       680       690       700       710
               |         |         |         |         |         |
  658 -  717 LAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNP
(  79)-( 138)
             720       730       740       750       760       770
               |         |         |         |         |         |
  718 -  777 QECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYED
( 139)-( 198)
             780       790       800       810       820       830
               |         |         |         |         |         |
  778 -  837 YGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHLHAYVRAKLMNAYPSYISP
( 199)-( 258)
             840       850       860       870       880       890
               |         |         |         |         |         |
  838 -  897 IGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSV
( 259)-( 318)
             900       910       920       930       940       950
               |         |         |         |         |         |
  898 -  957 GLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILMCTKVTMDDFLTAHHEMGH
( 319)-( 378)
             960       970       980       990      1000      1010
               |         |         |         |         |         |
  958 - 1017 IQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNETEINF
( 379)-( 438)
            1020      1030      1040      1050      1060      1070
               |         |         |         |         |         |
 1018 - 1077 LLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYC
( 439)-( 498)
            1080      1090      1100      1110      1120      1130
               |         |         |         |         |         |
 1078 - 1137 DPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLFNML
( 499)-( 558)
            1140      1150      1160      1170      1180      1190
               |         |         |         |         |         |
 1138 - 1194 RLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNKNSFVGWSTDWSPYAD
( 559)-( 615)
               1200      1210      1220      1230      1240      1250
                  |         |         |         |         |         |
 1195 - 1254 PFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNVYADSFVV
( 324)-( 389)
               1260      1270      1280      1290      1300      1310
                  |         |         |         |         |         |
 1255 - 1314 KGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLR
( 390)-( 449)
               1320      1330      1340      1350      1360
                  |         |         |         |         |
 1315 - 1367 PFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFE
( 450)-( 502)
           1370      1380      1390      1400      1410      1420
              |         |         |         |         |         |
 1369 - 1428 PFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNVYADSFVV
( 324)-( 389)
           1430      1440      1450      1460      1470      1480
              |         |         |         |         |         |
 1429 - 1488 KGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLR
( 390)-( 449)
           1490      1500      1510      1520      1530      1540
              |         |         |         |         |         |
 1489 - 1541 PFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFE
( 450)-( 502)
 
 
 
 
# 29 # Note: No rounded coordinates detected
No significant rounding of atom coordinates has been detected.
 
# 30 # 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.
 
# 31 # Warning: Unexpected atoms encountered
While reading the PDB file, at least one atom was encountered that
was not expected in the residue. This might be caused by a naming
convention problem. It can also mean that a residue was found protonated
that normally is not (e.g. aspartic acid). The unexpected atoms have been
discarded; in case protons were deleted that actually might be needed, they
will later be put back by the hydrogen bond validation software.
This normally is not a warning you should worry too much about.
 
# 32 # Note: No missing atoms detected in residues
All expected atoms are present in residues. This validation option has not
looked at 'things' that can or should be attached to the elementary building
blocks (amino acids, nucleotides). Even the C-terminal oxygens are treated
separately.
 
# 33 # Warning: B-factors outside the range 0.0 - 100.0
In principle, B-factors can have a very wide range of values, but in
practice, B-factors should not be zero while B-factors above 100.0
are a good indicator that the location of that atom is meaningless. Be
aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms
with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with
a B-factor of zero were observed.
 
   59 SER  (  77-) A  -   High
   85 ASN  ( 103-) A  -   High
   86 GLY  ( 104-) A  -   High
   87 SER  ( 105-) A  -   High
   88 SER  ( 106-) A  -   High
  384 GLU  ( 402-) A  -   High
  401 LYS  ( 419-) A  -   High
  402 SER  ( 420-) A  -   High
  405 LEU  ( 423-) A  -   High
  406 LEU  ( 424-) A  -   High
  407 SER  ( 425-) A  -   High
  408 PRO  ( 426-) A  -   High
  409 ASP  ( 427-) A  -   High
  410 PHE  ( 428-) A  -   High
  411 GLN  ( 429-) A  -   High
And so on for a total of    40 lines.
 
# 34 # Note: C-terminus capping
The residues listed in the table below are either C-terminal or pseudo
C-terminal (i.e. last residue before a missing residue).
In X-ray the coordinates must be located in density. Mobility or disorder
sometimes cause this density to be so poor that the positions of the atoms
cannot be determined. Crystallographers tend to leave out the atoms in such
cases. In many cases the N- or C-terminal residues are too disordered to see.
In case of the N-terminus, you can often see from the residue numbers if
there are missing residues; at the C-terminus this is impossible. Therefore,
often the position of the backbone nitrogen of the first residue missing
at the C-terminal end is calculated and added to indicate that there
are missing residues. As a single N causes validation trouble, we remove
these single-N-residues before doing the validation. If this happened,
the label -N is added to the pseudo C-terminus. Other labels can be +X
in case something weird is bound to the backbone C, or +OXT if a spurious
OXT atom is found. -OXT indicates that an expected OXT is missing. 'Swap'
means that the O' and O'' (O and OXT in PDB files) have been swapped in
terms of nomenclature. 'Bad' means that something bad happened that WHAT IF
does not understand. In such cases you might get three residue numbers in
square brackets; one of those might be what WHAT IF had expected to find,
but then it also might not). In case of chain breaks the number of missing
residues is listen in round brackets. OK means what it suggests...
 
Be aware that we cannot easily see the difference between these errors and
errors in the chain and residue numbering schemes. So do not blindly trust
the table below. If you get weird errors at, or near, the left-over
incomplete C-terminal residue, please check by hand if a missing Oxt or
a removed single N is the cause. Also, many peptidic ligands get the same
chain identifier as the larger protein they are bound to. In such cases there
are more than one C-termini and OXTs with the same ID. WHAT IF gives some
random warnings about these cases. So, don't take everything at face value,
but think for yourself.
 
  597 ASP  ( 615-) A  -        +OXT [ 597 ; 597 ; 615]
 1194 ASP  ( 615-) B  -        +OXT [1194 ; 597 ; 615]
 1246 ASN  ( 375-) E  -        OK (6)
 1367 GLU  ( 502-) E  -        +OXT [1367 ; 597 ; 502]
 1368 NAG  (  91-) E  -        +X
 1420 ASN  ( 375-) F  -        OK (6)
 1541 GLU  ( 502-) F  -        +OXT [1541 ; 597 ; 502]
 
# 35 # Note: Weights administratively correct
All atomic occupancy factors ('weights') fall in the 0.0--1.0 range, which
makes them administratively correct.
 
# 36 # 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.
 
# 37 # 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.
 
# 38 # Warning: What type of B-factor?
WHAT CHECK does not yet know well how to cope with B-factors in case TLS has
been used. It simply assumes that the B-factor listed on the ATOM and HETATM
cards are the total B-factors. When TLS refinement is used that assumption
sometimes is not correct. The header of the PDB file states that TLS groups
were used. So, if WHAT CHECK complains about your  B-factors, while you think
that they are OK, then check for TLS related B-factor problems first.
 
Number of TLS groups mentione in PDB file header: 1
 
Temperature not mentioned in PDB file. This most likely means
that the temperature record is absent.
Room temperature assumed
 
# 39 # Note: Number of buried atoms with low B-factor is OK
For protein structures determined at room temperature, no more than about 1
percent of the B factors of buried atoms is below 5.0. In liquid
nitrogen this percentage is allowed to be higher, of course.
 
Percentage of buried atoms with B less than 5 :   0.00
 
# 40 # Note: B-factor distribution normal
The distribution of B-factors within residues is within expected ranges.
A value over 1.5 here would mean that the B-factors show signs of
over-refinement.
 
RMS Z-score :  0.910 over   11188 bonds
Average difference in B over a bond :    3.00
RMS difference in B over a bond :    4.05
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
 
# 41 # Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
number.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: A
 
# 42 # Note: B-factor plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 43 # Note: B-factor plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: F
 
# 44 # 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.
 
# 45 # Note: Valine nomenclature OK
No errors were detected in valine nomenclature.
 
# 46 # Note: Threonine nomenclature OK
No errors were detected in threonine nomenclature.
 
# 47 # Note: Isoleucine nomenclature OK
No errors were detected in isoleucine nomenclature.
 
# 48 # Note: Leucine nomenclature OK
No errors were detected in leucine nomenclature.
 
# 49 # Warning: Arginine nomenclature problem
The arginine residues listed in the table below have their NH1 and NH2
swapped.
 
   97 ARG  ( 115-) A  -
  151 ARG  ( 169-) A  -
  159 ARG  ( 177-) A  -
  174 ARG  ( 192-) A  -
  227 ARG  ( 245-) A  -
  255 ARG  ( 273-) A  -
  339 ARG  ( 357-) A  -
  500 ARG  ( 518-) A  -
  694 ARG  ( 115-) B  -
  748 ARG  ( 169-) B  -
  756 ARG  ( 177-) B  -
  771 ARG  ( 192-) B  -
  824 ARG  ( 245-) B  -
  852 ARG  ( 273-) B  -
 1097 ARG  ( 518-) B  -
 
# 50 # Warning: Tyrosine convention problem
The tyrosine residues listed in the table below have their chi-2 not between
-90.0 and 90.0
 
  737 TYR  ( 158-) B  -
  762 TYR  ( 183-) B  -
 1076 TYR  ( 497-) B  -
 1166 TYR  ( 587-) B  -
 1301 TYR  ( 436-) E  -
 
# 51 # Note: Phenylalanine torsion conventions OK
No errors were detected in phenylalanine torsion angle conventions.
 
# 52 # Note: Aspartic acid torsion conventions OK
No errors were detected in aspartic acid torsion angle conventions.
 
# 53 # Note: Glutamic acid torsion conventions OK
No errors were detected in glutamic acid torsion angle conventions.
 
# 54 # 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).
 
# 55 # 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.
 
# 56 # Note: No decreasing residue numbers
All residue numbers are strictly increasing within each chain.
 
# 57 # 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]).
 
# 58 # 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: 0.376
 RMS-deviation in bond distances: 0.009
 
# 59 # 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.
 
# 60 # 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.
 
  251 ASP  ( 269-) A  -    CA   CB   CG  117.46    4.9
  317 ASP  ( 335-) A  -    CA   CB   CG  116.85    4.3
  332 ASP  ( 350-) A  -    CA   CB   CG  116.88    4.3
  379 ASN  ( 397-) A  -    CA   CB   CG  116.86    4.3
  507 PHE  ( 525-) A  -    CA   CB   CG  118.16    4.4
  848 ASP  ( 269-) B  -    CA   CB   CG  117.61    5.0
  914 ASP  ( 335-) B  -    CA   CB   CG  117.13    4.5
  929 ASP  ( 350-) B  -    CA   CB   CG  117.21    4.6
 1231 PHE  ( 360-) E  -    CA   CB   CG  118.43    4.6
 1279 ASP  ( 414-) E  -    CA   CB   CG  116.75    4.2
 
# 61 # Warning: Low bond angle variability
Bond angles were found to deviate less than normal from the standard bond
angles (normal values for protein residues were taken from Engh and Huber
[REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below
is expected to be near 1.0 for a normally restrained data set. The fact that
it is lower than 0.667 in this structure might indicate that too-strong
restraints have been used in the refinement. This can only be a problem for
high resolution X-ray structures.
 
 RMS Z-score for bond angles: 0.634
 RMS-deviation in bond angles: 1.159
 
# 62 # Error: Nomenclature error(s)
Checking for a hand-check. WHAT CHECK has over the course of this session
already corrected the handedness of atoms in several residues. These were
administrative corrections. These residues are listed here.
 
   97 ARG  ( 115-) A  -
  151 ARG  ( 169-) A  -
  159 ARG  ( 177-) A  -
  174 ARG  ( 192-) A  -
  227 ARG  ( 245-) A  -
  255 ARG  ( 273-) A  -
  339 ARG  ( 357-) A  -
  500 ARG  ( 518-) A  -
  694 ARG  ( 115-) B  -
  748 ARG  ( 169-) B  -
  756 ARG  ( 177-) B  -
  771 ARG  ( 192-) B  -
  824 ARG  ( 245-) B  -
  852 ARG  ( 273-) B  -
 1097 ARG  ( 518-) B  -
 
# 63 # Note: Chirality OK
All protein atoms have proper chirality. But, look at the previous table to
see a series of administrative chirality problems that were corrected
automatically upon reading-in the PDB file.
The average deviation= 0.593
 
# 64 # 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 : 0.532
 
# 65 # Note: Tau angles OK
All of the tau angles (N-C-alpha-C) of amino acids fall within expected
RMS deviations.
 
# 66 # 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 : 0.671
 
# 67 # Error: Side chain planarity problems
The side chains of the residues listed in the table below contain a planar
group that was found to deviate from planarity by more than 4.0 times the
expected value. For an amino acid residue that has a side chain with a
planar group, the RMS deviation of the atoms to a least squares plane was
determined. The number in the table is the number of standard deviations
this RMS value deviates from the expected value. Not knowing better yet, we
assume that planarity of the groups analyzed should be perfect.
 
  936 ARG  ( 357-) B  -   7.85
  500 ARG  ( 518-) A  -   7.76
 1097 ARG  ( 518-) B  -   7.65
   97 ARG  ( 115-) A  -   7.62
  339 ARG  ( 357-) A  -   7.55
  227 ARG  ( 245-) A  -   6.85
  694 ARG  ( 115-) B  -   6.71
  852 ARG  ( 273-) B  -   6.32
  255 ARG  ( 273-) A  -   6.29
  159 ARG  ( 177-) A  -   6.08
  756 ARG  ( 177-) B  -   6.07
  151 ARG  ( 169-) A  -   5.95
  748 ARG  ( 169-) B  -   5.72
  771 ARG  ( 192-) B  -   5.61
  824 ARG  ( 245-) B  -   5.48
  174 ARG  ( 192-) A  -   4.93
 
# 68 # 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.
 
# 69 # Error: Ramachandran Z-score very low
The score expressing how well the backbone conformations of all residues
correspond to the known allowed areas in the Ramachandran plot is very low.
 
 Ramachandran Z-score : -4.191
 
# 70 # 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.
 
# 71 # 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.
 
 1507 THR  ( 468-) F  -   -3.0
 1333 THR  ( 468-) E  -   -2.9
  271 PRO  ( 289-) A  -   -2.8
 1414 VAL  ( 369-) F  -   -2.7
 1240 VAL  ( 369-) E  -   -2.7
 1409 PHE  ( 364-) F  -   -2.7
 1235 PHE  ( 364-) E  -   -2.7
 1417 THR  ( 372-) F  -   -2.5
  194 VAL  ( 212-) A  -   -2.5
  316 THR  ( 334-) A  -   -2.4
  791 VAL  ( 212-) B  -   -2.4
 1509 PRO  ( 470-) F  -   -2.3
 1455 PHE  ( 416-) F  -   -2.3
 1204 LYS  ( 333-) E  -   -2.3
  913 THR  ( 334-) B  -   -2.3
And so on for a total of    50 lines.
 
# 72 # Warning: Backbone evaluation reveals unusual conformations
The residues listed in the table below have abnormal backbone torsion
angles.
 
Residues with `forbidden' phi-psi combinations are listed, as well as
residues with unusual omega angles (deviating by more than 3 sigma from the
normal value). Please note that it is normal if about 5 percent of the
residues is listed here as having unusual phi-psi combinations.
 
    2 THR  (  20-) A  - Poor phi/psi
   65 TYR  (  83-) A  - Omega to (next) Pro poor
   66 PRO  (  84-) A  - omega poor
   83 GLN  ( 101-) A  - Poor phi/psi, omega poor
   86 GLY  ( 104-) A  - Poor phi/psi
  116 ASN  ( 134-) A  - Omega to (next) Pro poor
  119 ASN  ( 137-) A  - Omega to (next) Pro poor
  127 GLU  ( 145-) A  - Omega to (next) Pro poor
  136 ASN  ( 154-) A  - Poor phi/psi
  159 ARG  ( 177-) A  - Omega to (next) Pro poor
  177 HIS  ( 195-) A  - Poor phi/psi
  193 GLY  ( 211-) A  - Poor phi/psi
  194 VAL  ( 212-) A  - Poor phi/psi
  195 ASP  ( 213-) A  - Poor phi/psi
  196 GLY  ( 214-) A  - Poor phi/psi
And so on for a total of   192 lines.
 
# 73 # Error: Chi-1/chi-2 rotamer problems
List of residues with a poor chi-1/chi-2 combination. Be aware that for this
validation option the individual scores are far less important than the
overall score that is given below the table.
 
   11 LEU  (  29-) A  -    -1.32
   67 LEU  (  85-) A  -    -1.32
   77 LEU  (  95-) A  -    -1.32
   82 LEU  ( 100-) A  -    -1.32
  125 LEU  ( 143-) A  -    -1.30
  130 LEU  ( 148-) A  -    -1.32
  138 LEU  ( 156-) A  -    -1.32
  161 LEU  ( 179-) A  -    -1.31
  222 LEU  ( 240-) A  -    -1.32
  263 LEU  ( 281-) A  -    -1.32
  315 LEU  ( 333-) A  -    -1.32
  341 LEU  ( 359-) A  -    -1.30
  374 LEU  ( 392-) A  -    -1.31
  392 LEU  ( 410-) A  -    -1.32
  400 LEU  ( 418-) A  -    -1.32
And so on for a total of   759 lines.
 
# 74 # Error: chi-1/chi-2 angle correlation Z-score very low
The score expressing how well the chi-1/chi-2 angles of all residues
correspond to the populated areas in the database is
very low.
 
 chi-1/chi-2 correlation Z-score : -4.889
 
# 75 # 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.
 
   26 SER  (  44-) A  -   0.35
   52 SER  (  70-) A  -   0.35
  106 SER  ( 124-) A  -   0.35
  623 SER  (  44-) B  -   0.35
  649 SER  (  70-) B  -   0.35
 1259 VAL  ( 394-) E  -   0.35
   95 SER  ( 113-) A  -   0.36
  703 SER  ( 124-) B  -   0.36
  990 SER  ( 411-) B  -   0.36
 1456 MET  ( 417-) F  -   0.36
  692 SER  ( 113-) B  -   0.38
  152 SER  ( 170-) A  -   0.39
 1365 SER  ( 500-) E  -   0.39
 
# 76 # 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!
 
  127 GLU  ( 145-) A  -       0
  194 VAL  ( 212-) A  -       0
  195 ASP  ( 213-) A  -       0
  320 ASN  ( 338-) A  -       0
  321 VAL  ( 339-) A  -       0
  322 GLN  ( 340-) A  -       0
  724 GLU  ( 145-) B  -       0
  791 VAL  ( 212-) B  -       0
  792 ASP  ( 213-) B  -       0
  917 ASN  ( 338-) B  -       0
  918 VAL  ( 339-) B  -       0
  919 GLN  ( 340-) B  -       0
 1266 GLN  ( 401-) E  -       0
 1267 THR  ( 402-) E  -       0
 1269 VAL  ( 404-) E  -       0
And so on for a total of    54 lines.
 
# 77 # 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 : -0.402
 
# 78 # 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= 179.330 5.708
 
# 79 # Warning: Unusual PRO puckering amplitudes
The proline residues listed in the table below have a puckering amplitude
that is outside of normal ranges. Puckering parameters were calculated by
the method of Cremer and Pople [REF]. Normal PRO rings have a puckering
amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom
for a PRO residue, this could indicate disorder between the two different
normal ring forms (with C-gamma below and above the ring, respectively). If
Q is higher than 0.45 Angstrom something could have gone wrong during the
refinement. Be aware that this is a warning with a low confidence level. See:
Who checks the checkers? Four validation tools applied to eight atomic
resolution structures [REF]
 
   66 PRO  (  84-) A  -   0.17 LOW
  240 PRO  ( 258-) A  -   0.18 LOW
  837 PRO  ( 258-) B  -   0.15 LOW
 
# 80 # 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].
 
  128 PRO  ( 146-) A  -    1.4 envelop N (0 degrees)
  271 PRO  ( 289-) A  -  -31.6 envelop C-alpha (-36 degrees)
  482 PRO  ( 500-) A  - -132.9 half-chair C-delta/C-gamma (-126 degrees)
  725 PRO  ( 146-) B  -  -56.8 half-chair C-beta/C-alpha (-54 degrees)
 1079 PRO  ( 500-) B  - -133.0 half-chair C-delta/C-gamma (-126 degrees)
 1195 PRO  ( 324-) E  -  -58.4 half-chair C-beta/C-alpha (-54 degrees)
 1264 PRO  ( 399-) E  - -117.2 half-chair C-delta/C-gamma (-126 degrees)
 1334 PRO  ( 469-) E  - -119.7 half-chair C-delta/C-gamma (-126 degrees)
 1335 PRO  ( 470-) E  -   30.2 envelop C-delta (36 degrees)
 1369 PRO  ( 324-) F  - -123.2 half-chair C-delta/C-gamma (-126 degrees)
 1438 PRO  ( 399-) F  - -121.0 half-chair C-delta/C-gamma (-126 degrees)
 1508 PRO  ( 469-) F  - -115.6 envelop C-gamma (-108 degrees)
 1509 PRO  ( 470-) F  -   24.0 half-chair N/C-delta (18 degrees)
 
# 81 # 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!
 
 1439 GLY  ( 400-) F  -  3.36   40
 1265 GLY  ( 400-) E  -  3.35   40
 1329 GLY  ( 464-) E  -  3.17   80
 1503 GLY  ( 464-) F  -  3.05   80
 1442 GLY  ( 403-) F  -  2.76   16
 1521 GLY  ( 482-) F  -  1.63   16
 
# 82 # 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.
 
 1201 ASN  ( 330-) E  - TT+   Highly likely
 1338 ASN  ( 473-) E  - TT+   Highly likely
 1375 ASN  ( 330-) F  - TT+   Highly likely
   35 ASN  (  53-) A  - TT+   Likely
  195 ASP  ( 213-) A  - TT+   Likely
  267 PHE  ( 285-) A  - TT+   Likely
  282 GLN  ( 300-) A  - TT+   Likely
  321 VAL  ( 339-) A  - TT+   Likely
  322 GLN  ( 340-) A  - TT+   Likely
  367 TYR  ( 385-) A  - TT+   Likely
  528 ASN  ( 546-) A  - TT+   Likely
  792 ASP  ( 213-) B  - TT+   Likely
  918 VAL  ( 339-) B  - TT+   Likely
  919 GLN  ( 340-) B  - TT+   Likely
 1223 TYR  ( 352-) E  - TT+   Likely
 1228 ASN  ( 357-) E  - TT+   Likely
 1266 GLN  ( 401-) E  - TT+   Likely
 1330 LYS  ( 465-) E  - TT+   Likely
 1397 TYR  ( 352-) F  - TT+   Likely
 1402 ASN  ( 357-) F  - TT+   Likely
 1440 GLN  ( 401-) F  - TT+   Likely
 1502 ASP  ( 463-) F  - TT+   Likely
 1504 LYS  ( 465-) F  - TT+   Likely
 1512 ASN  ( 473-) F  - TT+   Likely
 
# 83 # Error: Abnormally short interatomic distances
The pairs of atoms listed in the table below have an unusually short
interactomic distance; each bump is listed in only one direction.
 
The contact distances of all atom pairs have been checked. Two atoms are
said to `bump' if they are closer than the sum of their Van der Waals radii
minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom
is used. The first number in the table tells you how much shorter that
specific contact is than the acceptable limit. The second distance is the
distance between the centres of the two atoms. Although we believe that two
water atoms at 2.4 A distance are too close, we only report water pairs that
are closer than this rather short distance.
 
INTRA and INTER indicate whether the clashes are between atoms in the same
asymmetric unit, or atoms in symmetry related asymmetric units, respectively.
The last text-item on each line represents the status of the atom pair. If
the final column contains the text 'HB', the bump criterion was relaxed
because there could be a hydrogen bond. Similarly relaxed criteria are used
for 1--3 and 1--4 interactions (listed as 'B2' and 'B3', respectively).
If the last column is 'BF', the sum of the B-factors of the atoms is higher
than 80, which makes the appearance of the bump somewhat less severe because
the atoms probably are not there anyway. BL, on the other hand, indicates
that the bumping atoms both have a low B-factor, and that makes the bumps
more worrisome.
 
Bumps between atoms for which the sum of their occupancies is lower than one
are not reported. If the MODEL number does not exist (as is the case in most
X-ray files), a minus sign is printed instead.
 
  439 GLU  ( 457-) A  -    OE2 <-->   442 ARG  ( 460-) A  -    NH1    0.51    2.19  INTRA BF
  957 HIS  ( 378-) B  -    ND1 <-->   980 HIS  ( 401-) B  -    ND1    0.24    2.76  INTRA BL
  360 HIS  ( 378-) A  -    ND1 <-->   383 HIS  ( 401-) A  -    ND1    0.23    2.77  INTRA BF
  442 ARG  ( 460-) A  -    NH2 <-->   492 TYR  ( 510-) A  -    O      0.23    2.47  INTRA BF
  744 TRP  ( 165-) B  -    CD1 <-->   748 ARG  ( 169-) B  -    NH1    0.15    2.95  INTRA BL
  147 TRP  ( 165-) A  -    CD1 <-->   151 ARG  ( 169-) A  -    NH1    0.13    2.97  INTRA BL
 1039 ARG  ( 460-) B  -    NH2 <-->  1089 TYR  ( 510-) B  -    O      0.13    2.57  INTRA BF
 1061 ARG  ( 482-) B  -    NH1 <-->  1187 THR  ( 608-) B  -    O      0.13    2.57  INTRA BF
 1219 CYS  ( 348-) E  -    SG  <-->  1220 VAL  ( 349-) E  -    N      0.12    3.08  INTRA BF
  518 GLU  ( 536-) A  -    CD  <-->   998 LYS  ( 419-) B  -    NZ     0.12    2.98  INTRA BF
  564 ARG  ( 582-) A  -    N   <-->   565 PRO  ( 583-) A  -    CD     0.11    2.89  INTRA BF
 1161 ARG  ( 582-) B  -    N   <-->  1162 PRO  ( 583-) B  -    CD     0.11    2.89  INTRA BF
   20 GLU  (  38-) A  -    OE2 <-->   335 LYS  ( 353-) A  -    NZ     0.11    2.59  INTRA BF
  848 ASP  ( 269-) B  -    OD1 <-->   851 GLY  ( 272-) B  -    N      0.11    2.59  INTRA BF
  216 LYS  ( 234-) A  -    N   <-->   217 PRO  ( 235-) A  -    CD     0.10    2.90  INTRA BF
And so on for a total of    77 lines.
 
# 84 # 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: 5.867
Total bump value per residue: 0.050
Total number of bumps: 77
Total squared bump value: 0.799
Total number of bumps in the mildest bin: 76
Total number of bumps in the second bin: 0
Total number of bumps in the middle bin: 1
Total number of bumps in the fourth bin: 0
Total number of bumps in the worst bin: 0
 
# 85 # 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.
 
# 86 # 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 : 1.033
 
# 87 # 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
 
# 88 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 89 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: F
 
# 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.
 
 1455 PHE  ( 416-) F  -  -7.16
 1281 PHE  ( 416-) E  -  -7.14
  866 GLN  ( 287-) B  -  -6.50
  269 GLN  ( 287-) A  -  -6.46
  665 GLN  (  86-) B  -  -6.24
 1204 LYS  ( 333-) E  -  -6.02
 1378 LYS  ( 333-) F  -  -5.99
 1115 GLU  ( 536-) B  -  -5.89
 1530 TYR  ( 491-) F  -  -5.83
   71 GLN  (  89-) A  -  -5.78
  972 ARG  ( 393-) B  -  -5.78
  375 ARG  ( 393-) A  -  -5.76
 1266 GLN  ( 401-) E  -  -5.74
 1218 ASN  ( 347-) E  -  -5.70
  518 GLU  ( 536-) A  -  -5.70
And so on for a total of    39 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.
 
  320 ASN  ( 338-) A  -      322 --- GLN   340- (A ) -       -4.82
  917 ASN  ( 338-) B  -      919 --- GLN   340- (B ) -       -4.85
 1244 LYS  ( 373-) E  -     1246 --- ASN   375- (E ) -       -4.83
 1279 ASP  ( 414-) E  -     1282 --- MET   417- (E ) -       -4.97
 1418 LYS  ( 373-) F  -     1420 --- ASN   375- (F ) -       -4.71
 1453 ASP  ( 414-) F  -     1456 --- MET   417- (F ) -       -5.05
 
# 92 # Note: Structural average packing environment OK
The structural average packing score is within normal ranges.
 
 
Average for range     1 - 1541 :  -0.341
 
# 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: F
 
# 96 # Warning: Low packing Z-score for some residues
The residues listed in the table below have an unusual packing
environment according to the 2nd generation packing check. The score
listed in the table is a packing normality Z-score: positive means
better than average, negative means worse than average. Only residues
scoring less than -2.50 are listed here. These are the unusual
residues in the structure, so it will be interesting to take a
special look at them.
 
  542 LEU  ( 560-) A  -  -2.97
 1139 LEU  ( 560-) B  -  -2.56
  897 VAL  ( 318-) B  -  -2.53
  300 VAL  ( 318-) A  -  -2.50
 
# 97 # Warning: Abnormal packing Z-score for sequential residues
A stretch of at least four sequential residues with a 2nd generation packing
Z-score below -1.75 was found. This could indicate that these residues are
part of a strange loop or that the residues in this range are incomplete,
but it might also be an indication of misthreading.
 
The table below lists the first and last residue in each stretch found,
as well as the average residue Z-score of the series.
 
  854 TRP  ( 275-) B  -   ---   857 LEU  ( 278-) B  -      -1.66
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
 
# 98 # Note: Second generation quality Z-score plot
The second generation quality Z-score smoothed over a 10 residue window
is plotted as function of the residue number. Low areas in the plot (below
-1.3) indicate unusual packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: A
 
# 99 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 100 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: F
 
# 101 # 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.
 
# 102 # Note: Water contacts OK
All water clusters make at least one contact with a non-water atom.
 
# 103 # Note: No waters need moving
All water molecules are sufficiently close to the asymmetric unit given in
the input file.
 
# 104 # Note: Water hydrogen bonds OK
All water molecules can form hydrogen bonds.
 
# 105 # 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.
 
   45 ASN  (  63-) A  -
  119 ASN  ( 137-) A  -
  131 ASN  ( 149-) A  -
  136 ASN  ( 154-) A  -
  192 ASN  ( 210-) A  -
  203 GLN  ( 221-) A  -
  259 ASN  ( 277-) A  -
  282 GLN  ( 300-) A  -
  362 GLN  ( 380-) A  -
  411 GLN  ( 429-) A  -
  475 HIS  ( 493-) A  -
  487 HIS  ( 505-) A  -
  506 GLN  ( 524-) A  -
  568 ASN  ( 586-) A  -
  581 ASN  ( 599-) A  -
And so on for a total of    37 lines.
 
# 106 # 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.
 
  177 HIS  ( 195-) A  -   HIS-E   0.45
  210 HIS  ( 228-) A  -   HIS-E   0.56
  221 HIS  ( 239-) A  -   HIS-E   0.52
  223 HIS  ( 241-) A  -   HIS-E   0.44
  247 HIS  ( 265-) A  -   HIS-E   0.49
  327 HIS  ( 345-) A  -   HIS-E   0.56
  355 HIS  ( 373-) A  -   HIS-E   0.56 HIS-D   0.75
  356 HIS  ( 374-) A  -   HIS-E   0.62 HIS-D   0.86
  360 HIS  ( 378-) A  -   HIS-E   0.70 HIS-D   1.37
  383 HIS  ( 401-) A  -   HIS-E   0.45
  399 HIS  ( 417-) A  -   HIS-E   0.70 HIS-D   1.04
  475 HIS  ( 493-) A  -   HIS-H   0.44 HIS-E   0.53
  487 HIS  ( 505-) A  -   HIS-E   0.54
  517 HIS  ( 535-) A  -   HIS-E   0.46
  522 HIS  ( 540-) A  -   HIS-E   0.47
And so on for a total of    32 lines.
 
# 107 # Warning: Buried unsatisfied hydrogen bond donors
The buried hydrogen bond donors listed in the table below have a hydrogen
atom that is not involved in a hydrogen bond in the optimized hydrogen bond
network.
 
Hydrogen bond donors that are buried inside the protein normally use all of
their hydrogens to form hydrogen bonds within the protein. If there are any
non hydrogen bonded buried hydrogen bond donors in the structure they will
be listed here. In very good structures the number of listed atoms will tend
to zero.
 
Waters are not listed by this option.
 
   15 ASN  (  33-) A  -    ND2
   40 ASN  (  58-) A  -    N
   97 ARG  ( 115-) A  -    NE
  141 ASN  ( 159-) A  -    N
  159 ARG  ( 177-) A  -    NE
  162 TYR  ( 180-) A  -    OH
  176 ASN  ( 194-) A  -    ND2
  180 ASP  ( 198-) A  -    N
  186 ARG  ( 204-) A  -    NH1
  197 TYR  ( 215-) A  -    N
  214 GLU  ( 232-) A  -    N
  239 SER  ( 257-) A  -    N
  243 CYS  ( 261-) A  -    N
  247 HIS  ( 265-) A  -    NE2
  249 LEU  ( 267-) A  -    N
And so on for a total of   134 lines.
 
# 108 # Warning: Buried unsatisfied hydrogen bond acceptors
The buried side-chain hydrogen bond acceptors listed in the table below are
not involved in a hydrogen bond in the optimized hydrogen bond network.
 
Side-chain hydrogen bond acceptors buried inside the protein normally form
hydrogen bonds within the protein. If there are any not hydrogen bonded in
the optimized hydrogen bond network they will be listed here.
 
Waters are not listed by this option.
 
  223 HIS  ( 241-) A  -    ND1
  362 GLN  ( 380-) A  -    OE1
  481 ASP  ( 499-) A  -    OD1
  506 GLN  ( 524-) A  -    OE1
  612 ASN  (  33-) B  -    OD1
  660 GLN  (  81-) B  -    OE1
  820 HIS  ( 241-) B  -    ND1
  952 HIS  ( 373-) B  -    NE2
  959 GLN  ( 380-) B  -    OE1
 1078 ASP  ( 499-) B  -    OD1
 1103 GLN  ( 524-) B  -    OE1
 1446 ASP  ( 407-) F  -    OD1
 
# 109 # 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: 2227
- of which buried: 1137
Total number of acceptors: 2452
- of which buried: 933
Total number of donor+acceptors: 275
  (e.g. the Ser Ogamma that can donate and accept)
- of which buried: 55
Buried donors: 1137
- without H-bond: 129
- essentially without H-bond: 1
- with only a very poor H-bond: 11
- with a poor H-bond: 15
- with a H-bond: 981
Buried acceptors: 933
- without H-bond: 155
- essentially without H-bond: 0
- with only a very poor H-bond: 5
- with a poor H-bond: 38
- with a H-bond: 735
 
# 110 # Note: Content of the PDB file as interpreted by WHAT CHECK
Content of the PDB file as interpreted by WHAT CHECK.
WHAT CHECK has read your PDB file, and stored it internally in what is called
'the soup'. The content of this soup is listed here. An extensive explanation
of all frequently used WHAT CHECK output formats can be found at
swift.cmbi.ru.nl. Look under output formats. A course on reading this
'Molecules' table is part of the WHAT CHECK website.
 
     1     1 (   19)   597 (  615) A Protein             /zata/tempdir/3d0...
     2   598 (   19)  1194 (  615) B Protein             /zata/tempdir/3d0...
     3  1195 (  324)  1246 (  375) E Protein             /zata/tempdir/3d0...
     4  1247 (  382)  1367 (  502) E Protein             /zata/tempdir/3d0...
     5  1368 (   91)  1368 (   91) E Sugar<-             /zata/tempdir/3d0...
     6  1369 (  324)  1420 (  375) F Protein             /zata/tempdir/3d0...
     7  1421 (  382)  1541 (  502) F Protein             /zata/tempdir/3d0...
     8  1542 (  615)  1542 (  615) A D O2 <-   597       /zata/tempdir/3d0...
     9  1543 (  616)  1543 (  616) A NDG                 /zata/tempdir/3d0...
    10  1544 (  901)  1544 (  901) A  ZN                 /zata/tempdir/3d0...
    11  1545 (  902)  1545 (  902) A  CL                 /zata/tempdir/3d0...
    12  1546 (  615)  1546 (  615) B D O2 <-  1194       /zata/tempdir/3d0...
    13  1547 (  616)  1547 (  616) B NDG                 /zata/tempdir/3d0...
    14  1548 (  617)  1548 (  617) B NDG                 /zata/tempdir/3d0...
    15  1549 (  618)  1549 (  618) B NDG                 /zata/tempdir/3d0...
    16  1550 (  901)  1550 (  901) B  ZN                 /zata/tempdir/3d0...
    17  1551 (  902)  1551 (  902) B  CL                 /zata/tempdir/3d0...
    18  1552 (  502)  1552 (  502) E E O2 <-  1367       /zata/tempdir/3d0...
    19  1553 (   91)  1553 (   91) E NAG  <-             /zata/tempdir/3d0...
    20  1554 (  502)  1554 (  502) F E O2 <-  1541       /zata/tempdir/3d0...
    21  1555 (   91)  1555 (   91) F NDG                 /zata/tempdir/3d0...
    22  1556 ( HOH )  1556 ( HOH ) B water   (    1)     /zata/tempdir/3d0...
    23  1557 ( HOH )  1557 ( HOH ) F water   (    1)     /zata/tempdir/3d0...
 
# 111 # 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  :   2.790
  1st generation packing quality :   0.397 (          (  -0.8,  2.5))
  2nd generation packing quality :  -1.443 (          (  -1.7,  1.3))
  Ramachandran plot appearance   :  -4.191 (bad       (  -3.4,  1.7))
  chi-1/chi-2 rotamer normality  :  -4.889 (bad       (  -5.0,  1.9))
  Backbone conformation          :  -0.402 (          (  -1.0,  3.7))
  Inside/Outside distribution    :   1.033
 
 RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.376 (tight)
  Bond angles                    :   0.634 (tight)
  Omega angle restraints         :   1.038
  Side chain planarity           :   1.189
  Improper dihedral distribution :   0.532
  B-factor distribution          :   0.910
 
# 112 # 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.
 
# 113 # 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.
 
# 114 # Error: Bumps in your structure
Upon analysing the bumps in your structure, WHAT CHECK got a bit
worried. Sometimes this means that you have forgotten to lower the
occupancy of overlapping ligands, residues, or water molecules. But,
whatever is the origin of this problem, you have to analyse it and
fix it.
 
# 115 # 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.
 
# 116 # 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.
 
 1455 PHE  ( 416-) F  -     14.51
 1281 PHE  ( 416-) E  -     14.45
 1204 LYS  ( 333-) E  -     13.12
 1378 LYS  ( 333-) F  -     13.06
  866 GLN  ( 287-) B  -     13.01
  269 GLN  ( 287-) A  -     12.91
 1115 GLU  ( 536-) B  -     12.82
  665 GLN  (  86-) B  -     12.52
 1530 TYR  ( 491-) F  -     11.66
   71 GLN  (  89-) A  -     11.57
  972 ARG  ( 393-) B  -     11.55
 1266 GLN  ( 401-) E  -     11.53
  375 ARG  ( 393-) A  -     11.51
  518 GLU  ( 536-) A  -     11.49
 1440 GLN  ( 401-) F  -     11.41
And so on for a total of   170 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.
