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

Date : 2024-12-18
This report was created by WHAT IF version WHATCHECK15.0

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

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

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

Some remarks regarding the output:

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

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

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



=========================================
==== Compound code /zata/tempdir/5mhp/wctemf/5mhp_final.pdb         ====
=========================================
 
# 1 # Note: Introduction
WHAT CHECK needs to read a PDB file before it can check it. It does a
series of checks upon reading the file. The results of these checks are
reported in this section (section 2.1). The rest of the report will be more
systematic in that section 2.2 reports on administrative problems. Section
2.3 gives descriptive output that is not directly validating things but
more telling you how WHAT CHECK interpreted the input file. Section 2.4
looks at B-factors, occupancies, and the presence/absence of (spurious)
atoms. Section 2.5 deals with nomenclature problems. Section 2.6 deals with
geometric problems like bond lengths and bond angles. Section 2.7 deals with
torsion angle issues. Section 2.8 looks at atomic clashes. Section 2.9 deals
with packing, accessibility, etc, issues. Section 2.10 deals with hydrogen
bonds, ion packing, and other things that can be summarized under the common
name charge-charge interactions. Section 2.11 gives a summary of whole report
and tells you (if applicable) which symmetry matrices were used. Section 2.12
tells the crystallographer which are the things most in need of manual
correction. And the last section, section 2.13, lists all residues sorted
by their need for visual inspection in light of the electron density.
WARNING. Date error on HEADER card:
HEADER                                                        5MHP
ATOM  *****  C2  BMA B   3      77.885  11.688  39.490  1.00 53.88       C2  C
ATOM  *****  C3  BMA B   3      78.139  12.796  40.505  1.00 58.48       C3  C
ATOM  *****  C4  BMA B   3      79.502  12.620  41.163  1.00 55.24       C4  C
ATOM  *****  C5  BMA B   3      80.589  12.472  40.102  1.00 53.93       C5  C
ATOM  *****  C6  BMA B   3      81.957  12.189  40.672  1.00 48.45       C6  C
ATOM  *****  O2  BMA B   3      77.633  10.451  40.149  1.00 44.98       O2  O
ATOM  *****  O3  BMA B   3      77.099  12.794  41.484  1.00 53.28       O3  O
ATOM  *****  O4  BMA B   3      79.806  13.752  41.964  1.00 62.05       O4  O
ATOM  *****  O5  BMA B   3      80.271  11.362  39.246  1.00 59.40       O5  O
ATOM  *****  O6  BMA B   3      82.906  11.947  39.613  1.00 47.69       O6  O
ATOM  *****  C2  MAN B   4      85.114  12.177  38.767  1.00 49.86       C2  C
ATOM  *****  C3  MAN B   4      85.108  10.903  37.919  1.00 50.07       C3  C
ATOM  *****  C4  MAN B   4      85.380   9.667  38.774  1.00 51.35       C4  C
ATOM  *****  C5  MAN B   4      84.484   9.641  40.024  1.00 50.77       C5  C
ATOM  *****  C6  MAN B   4      84.840   8.557  41.018  1.00 53.44       C6  C
ATOM  *****  O2  MAN B   4      86.436  12.549  39.151  1.00 47.35       O2  O
ATOM  *****  O3  MAN B   4      86.087  10.993  36.862  1.00 44.50       O3  O
ATOM  *****  O4  MAN B   4      85.131   8.496  37.996  1.00 45.21       O4  O
ATOM  *****  O5  MAN B   4      84.616  10.877  40.745  1.00 52.91       O5  O
ATOM  *****  O6  MAN B   4      85.636   7.523  40.425  1.00 58.90       O6  O
ATOM  *****  C2  MAN B   5      86.349  11.643  34.578  1.00 46.16       C2  C
ATOM  *****  C3  MAN B   5      87.843  11.415  34.404  1.00 46.40       C3  C
ATOM  *****  C4  MAN B   5      88.623  12.613  34.914  1.00 49.34       C4  C
ATOM  *****  C5  MAN B   5      88.238  12.879  36.363  1.00 46.64       C5  C
ATOM  *****  C6  MAN B   5      88.955  14.070  36.956  1.00 47.03       C6  C
ATOM  *****  O2  MAN B   5      85.901  12.638  33.626  1.00 45.03       O2  O
ATOM  *****  O3  MAN B   5      88.141  11.188  33.028  1.00 43.49       O3  O
ATOM  *****  O4  MAN B   5      90.025  12.373  34.822  1.00 47.00       O4  O
ATOM  *****  O5  MAN B   5      86.818  13.156  36.424  1.00 42.27       O5  O
ATOM  *****  O6  MAN B   5      88.034  15.040  37.441  1.00 55.71       O6  O
ATOM  *****  C2  MAN B   7      87.669   7.083  41.559  1.00 68.86       C2  C
ATOM  *****  C3  MAN B   7      88.486   6.945  40.276  1.00 69.52       C3  C
ATOM  *****  C4  MAN B   7      88.351   5.536  39.716  1.00 68.22       C4  C
ATOM  *****  C5  MAN B   7      86.875   5.218  39.510  1.00 71.52       C5  C
ATOM  *****  C6  MAN B   7      86.619   3.826  38.984  1.00 71.07       C6  C
ATOM  *****  O2  MAN B   7      88.237   6.337  42.632  1.00 72.28       O2  O
ATOM  *****  O3  MAN B   7      89.856   7.265  40.518  1.00 62.68       O3  O
ATOM  *****  O4  MAN B   7      89.033   5.423  38.470  1.00 63.34       O4  O
ATOM  *****  O5  MAN B   7      86.194   5.325  40.781  1.00 76.06       O5  O
ATOM  *****  O6  MAN B   7      85.221   3.563  38.891  1.00 71.47       O6  O
ATOM  *****  C2  MAN B   6      84.813  13.307  31.641  1.00 43.12       C2  C
ATOM  *****  C3  MAN B   6      84.593  14.749  32.027  1.00 40.87       C3  C
ATOM  *****  C4  MAN B   6      83.325  14.880  32.853  1.00 41.74       C4  C
ATOM  *****  C5  MAN B   6      83.398  13.950  34.068  1.00 44.12       C5  C
ATOM  *****  C6  MAN B   6      82.144  13.962  34.917  1.00 40.66       C6  C
ATOM  *****  O2  MAN B   6      83.829  12.922  30.686  1.00 41.60       O2  O
ATOM  *****  O3  MAN B   6      84.510  15.544  30.846  1.00 40.13       O3  O
ATOM  *****  O4  MAN B   6      83.168  16.228  33.289  1.00 41.70       O4  O
ATOM  *****  O5  MAN B   6      83.585  12.587  33.617  1.00 43.25       O5  O
ATOM  *****  O6  MAN B   6      82.333  13.234  36.132  1.00 42.49       O6  O
ATOM  *****  C   SCN A 917      79.332 -13.266  11.698  1.00 50.01       C   C
ATOM  *****  N   SCN A 917      79.163 -14.156  12.419  1.00 37.97       N   N
ATOM  *****  O1  PO4 A 918      41.051  23.363  18.874  1.00 76.59       O1  O
ATOM  *****  O2  PO4 A 918      40.543  23.940  21.238  1.00 71.88       O2  O
ATOM  *****  O3  PO4 A 918      42.299  25.200  20.005  1.00 76.17       O3  O
ATOM  *****  O4  PO4 A 918      42.694  22.837  20.661  1.00 85.85       O4  O
ATOM  *****  O1  PO4 A 919      99.958   7.290  13.991  1.00 49.37       O1  O
ATOM  *****  O2  PO4 A 919     101.459   7.612  15.954  1.00 62.74       O2  O
ATOM  *****  O3  PO4 A 919     100.525   5.355  15.415  1.00 52.86       O3  O
ATOM  *****  O4  PO4 A 919      99.045   7.142  16.318  1.00 50.27       O4  O
ATOM  *****  CAB 7NB A 920      95.968   5.219  35.499  1.00 78.87       CAB C
ATOM  *****  OAE 7NB A 920      95.451   5.795  36.677  1.00 65.83       OAE O
ATOM  *****  CAC 7NB A 920      96.982   4.035  35.726  1.00 85.39       CAC C
ATOM  *****  NAD 7NB A 920      97.940   4.937  35.074  1.00 87.79       NAD N
ATOM  *****  C   7NB A 920      99.282   4.771  34.850  1.00 88.38       C   C
ATOM  *****  O   7NB A 920      99.835   3.714  35.122  1.00 94.49       O   O
ATOM  *****  CA  7NB A 920     100.092   5.904  34.247  1.00 76.03       CA  C
ATOM  *****  N   7NB A 920     100.682   5.559  32.958  1.00 68.86       N   N
ATOM  *****  CAN 7NB A 920     101.621   6.588  32.523  1.00 69.70       CAN C
ATOM  *****  CAM 7NB A 920     102.392   6.136  31.305  1.00 64.78       CAM C
ATOM  *****  CAJ 7NB A 920      99.662   5.465  31.921  1.00 63.05       CAJ C
ATOM  *****  CAK 7NB A 920     100.246   4.938  30.632  1.00 58.38       CAK C
ATOM  *****  NAL 7NB A 920     101.565   5.492  30.268  1.00 56.34       NAL N
ATOM  *****  CAO 7NB A 920     102.083   5.263  28.980  1.00 48.03       CAO C
ATOM  *****  CAT 7NB A 920     101.371   4.446  28.107  1.00 42.27       CAT C
ATOM  *****  NAS 7NB A 920     101.884   4.192  26.859  1.00 38.66       NAS N
ATOM  *****  CAP 7NB A 920     103.306   5.789  28.570  1.00 43.55       CAP C
ATOM  *****  CAQ 7NB A 920     103.824   5.528  27.305  1.00 41.49       CAQ C
ATOM  *****  CAX 7NB A 920     105.140   6.108  26.870  1.00 37.50       CAX C
ATOM  *****  CAR 7NB A 920     103.097   4.715  26.448  1.00 38.94       CAR C
ATOM  *****  NAU 7NB A 920     103.370   4.320  25.204  1.00 39.56       NAU N
ATOM  *****  CAV 7NB A 920     102.334   3.493  24.807  1.00 35.96       CAV C
ATOM  *****  CAY 7NB A 920     102.343   2.914  23.427  1.00 35.10       CAY C
ATOM  *****  CAZ 7NB A 920     101.713   3.800  22.378  1.00 37.10       CAZ C
ATOM  *****  CAW 7NB A 920     101.357   3.484  25.784  1.00 36.09       CAW C
ATOM  *****  NBA 7NB A 920     100.181   2.742  25.914  1.00 36.68       NBA N
ATOM  *****  CBB 7NB A 920      98.920   3.446  26.219  1.00 38.35       CBB C
ATOM  *****  CBC 7NB A 920     100.163   1.341  25.993  1.00 34.02       CBC C
ATOM  *****  NBG 7NB A 920      99.007   0.630  26.107  1.00 30.17       NBG N
ATOM  *****  SBD 7NB A 920     101.519   0.374  26.145  1.00 37.91       SBD S
ATOM  *****  CBE 7NB A 920     100.640  -1.042  26.256  1.00 35.22       CBE C
ATOM  *****  CBI 7NB A 920     101.299  -2.297  26.392  1.00 35.97       CBI C
ATOM  *****  N1  7NB A 920     101.826  -3.303  26.582  1.00 39.18       N1  N
ATOM  *****  CBF 7NB A 920      99.259  -0.744  26.196  1.00 31.61       CBF C
ATOM  *****  CBH 7NB A 920      98.099  -1.645  26.271  1.00 31.50       CBH C
ATOM  *****  CBJ 7NB A 920      96.854  -1.167  26.671  1.00 30.59       CBJ C
ATOM  *****  CBK 7NB A 920      95.757  -2.006  26.744  1.00 34.02       CBK C
ATOM  *****  CBL 7NB A 920      95.928  -3.327  26.430  1.00 36.07       CBL C
ATOM  *****  FBO 7NB A 920      94.856  -4.160  26.506  1.00 42.50       FBO F
ATOM  *****  CBM 7NB A 920      97.132  -3.847  26.040  1.00 34.90       CBM C
ATOM  *****  CBN 7NB A 920      98.223  -3.000  25.978  1.00 33.74       CBN C
ATOM  *****  O   HOH A1002      73.455  23.292   2.833  1.00 34.40      1002 O
ATOM  *****  O   HOH A1003      84.783   8.443  20.682  1.00 20.34      1003 O
ATOM  *****  O   HOH A1004      61.529  -0.830  15.742  1.00 21.47      1004 O
ATOM  *****  O   HOH A1005      79.300  13.672  24.141  1.00 22.29      1005 O
ATOM  *****  O   HOH A1006      79.835   3.234  20.611  1.00 23.73      1006 O
ATOM  *****  O   HOH A1007      63.981  -7.939   6.701  1.00 32.11      1007 O
ATOM  *****  O   HOH A1008      50.833  10.063  20.121  1.00 28.22      1008 O
ATOM  *****  O   HOH A1009      83.402  -2.677   7.063  1.00 32.40      1009 O
ATOM  *****  O   HOH A1010      57.790  -1.534  18.261  1.00 23.33      1010 O
ATOM  *****  O   HOH A1011      79.985   3.606  17.312  1.00 38.29      1011 O
ATOM  *****  O   HOH A1012      78.460   2.858  32.766  1.00 31.36      1012 O
ATOM  *****  O   HOH A1013      58.848  12.128  30.732  1.00 36.52      1013 O
ATOM  *****  O   HOH A1014      80.793   9.132  27.655  1.00 26.49      1014 O
ATOM  *****  O   HOH A1015     100.205   1.529  30.077  1.00 50.86      1015 O
ATOM  *****  O   HOH A1016      85.868   9.589   4.417  1.00 35.35      1016 O
ATOM  *****  O   HOH A1017      78.002  -0.519  24.689  1.00 25.34      1017 O
ATOM  *****  O   HOH A1018      82.842  -0.189  11.487  1.00 23.78      1018 O
ATOM  *****  O   HOH A1019      97.355 -24.708  22.114  1.00 29.85      1019 O
ATOM  *****  O   HOH A1020      55.598  14.717  10.401  1.00 32.13      1020 O
ATOM  *****  O   HOH A1021      44.757   7.026   4.313  1.00 50.70      1021 O
ATOM  *****  O   HOH A1022      73.994  11.493  15.052  1.00 25.10      1022 O
ATOM  *****  O   HOH A1023      70.581  -0.163  15.134  1.00 30.78      1023 O
ATOM  *****  O   HOH A1024      80.022 -10.100  18.408  1.00 31.60      1024 O
ATOM  *****  O   HOH A1025      87.983 -21.558  30.981  1.00 35.61      1025 O
ATOM  *****  O   HOH A1026      57.131   6.002   3.425  1.00 25.35      1026 O
ATOM  *****  O   HOH A1027      85.037   9.898  22.869  1.00 27.05      1027 O
ATOM  *****  O   HOH A1028      76.325  -6.168  18.132  1.00 42.09      1028 O
ATOM  *****  O   HOH A1029      66.318  12.714  25.625  1.00 29.02      1029 O
ATOM  *****  O   HOH A1030      92.956  19.272  22.610  1.00 28.01      1030 O
ATOM  *****  O   HOH A1031      82.054   5.076  18.358  1.00 32.68      1031 O
ATOM  *****  O   HOH A1032      71.765  19.064   6.843  1.00 18.47      1032 O
ATOM  *****  O   HOH A1033      86.450  17.458  31.048  1.00 43.63      1033 O
ATOM  *****  O   HOH A1034      82.184  10.750  31.313  1.00 28.09      1034 O
ATOM  *****  O   HOH A1035      78.323  15.608  19.069  1.00 15.27      1035 O
ATOM  *****  O   HOH A1036      91.267  12.529  32.413  1.00 29.73      1036 O
ATOM  *****  O   HOH A1037      46.675   7.289  11.663  1.00 34.62      1037 O
ATOM  *****  O   HOH A1038      80.835  23.734  21.455  1.00 40.52      1038 O
ATOM  *****  O   HOH A1039      48.539  11.021  19.316  1.00 32.39      1039 O
ATOM  *****  O   HOH A1040      55.257  -6.832   5.295  1.00 38.43      1040 O
ATOM  *****  O   HOH A1041      83.690  -3.249  28.228  1.00 22.47      1041 O
ATOM  *****  O   HOH A1042      77.866  21.464  11.274  1.00 37.76      1042 O
ATOM  *****  O   HOH A1043      56.573   3.030  27.512  1.00 36.59      1043 O
ATOM  *****  O   HOH A1044      81.362  -5.898  26.782  1.00 29.76      1044 O
ATOM  *****  O   HOH A1045      76.576  -1.679   6.406  1.00 32.89      1045 O
ATOM  *****  O   HOH A1046     102.891  -7.666  30.753  1.00 29.49      1046 O
ATOM  *****  O   HOH A1047      78.899  21.404   5.665  1.00 27.30      1047 O
ATOM  *****  O   HOH A1048      78.145  -3.150  14.242  1.00 31.94      1048 O
ATOM  *****  O   HOH A1049      89.618 -31.062  18.537  1.00 37.86      1049 O
ATOM  *****  O   HOH A1050      45.100  17.143  24.219  1.00 35.87      1050 O
ATOM  *****  O   HOH A1051      62.665   9.913  27.701  1.00 36.35      1051 O
ATOM  *****  O   HOH A1052      58.523   8.313  12.310  1.00 32.52      1052 O
ATOM  *****  O   HOH A1053      99.311  14.573  38.664  1.00 38.20      1053 O
ATOM  *****  O   HOH A1054      88.544  13.127  10.748  1.00 31.51      1054 O
ATOM  *****  O   HOH A1055      77.638   3.624  28.488  1.00 32.47      1055 O
ATOM  *****  O   HOH A1056      72.628   7.654   0.241  1.00 46.14      1056 O
ATOM  *****  O   HOH A1057      63.530  -9.672  24.746  1.00 28.41      1057 O
ATOM  *****  O   HOH A1058      81.739  22.305   4.599  1.00 32.29      1058 O
ATOM  *****  O   HOH A1059      44.514   5.103  24.319  1.00 35.27      1059 O
ATOM  *****  O   HOH A1060      87.371  -2.294  26.238  1.00 22.89      1060 O
ATOM  *****  O   HOH A1061      50.363  17.661  23.072  1.00 28.40      1061 O
ATOM  *****  O   HOH A1062      78.656  -2.510  17.229  1.00 38.84      1062 O
ATOM  *****  O   HOH A1063      65.731  -5.147  26.927  1.00 28.37      1063 O
ATOM  *****  O   HOH A1064      68.371  20.118   9.148  1.00 35.19      1064 O
ATOM  *****  O   HOH A1065      88.995  10.016  -0.453  1.00 33.09      1065 O
ATOM  *****  O   HOH A1066      79.062  29.847  11.905  1.00 42.97      1066 O
ATOM  *****  O   HOH A1067      83.002   0.001   8.614  1.00 31.83      1067 O
ATOM  *****  O   HOH A1069      89.030  -9.469  13.280  1.00 31.69      1069 O
ATOM  *****  O   HOH A1070      96.712  19.721  37.760  1.00 41.43      1070 O
ATOM  *****  O   HOH A1071      87.265   1.387  33.678  1.00 23.14      1071 O
ATOM  *****  O   HOH A1073      79.907  -3.603  19.619  1.00 25.32      1073 O
ATOM  *****  O   HOH A1074      77.928   4.375  18.686  1.00 25.71      1074 O
ATOM  *****  O   HOH A1075      55.163   4.674  38.421  1.00 43.97      1075 O
ATOM  *****  O   HOH A1076      64.607  26.266   9.711  1.00 33.04      1076 O
ATOM  *****  O   HOH A1077      87.438  19.537  18.129  1.00 34.45      1077 O
ATOM  *****  O   HOH A1078      83.984   6.476  18.986  1.00 27.05      1078 O
ATOM  *****  O   HOH A1079      71.541  -1.393  17.330  1.00 16.02      1079 O
ATOM  *****  O   HOH A1080      72.503   1.450  13.000  1.00 20.10      1080 O
ATOM  *****  O   HOH A1081      61.080  -8.724   7.857  1.00 25.66      1081 O
ATOM  *****  O   HOH A1082      53.031   7.706  34.150  1.00 43.27      1082 O
ATOM  *****  O   HOH A1083      86.952  11.563   9.543  1.00 16.34      1083 O
ATOM  *****  O   HOH A1084      75.041  18.251  12.832  1.00 25.02      1084 O
ATOM  *****  O   HOH A1086      79.302  -1.415  21.194  1.00 26.13      1086 O
ATOM  *****  O   HOH A1087      77.827   2.742  25.378  1.00 26.44      1087 O
ATOM  *****  O   HOH A1088      80.928   5.372  14.921  1.00 33.91      1088 O
ATOM  *****  O   HOH A1089      82.756   6.591  37.094  1.00 28.76      1089 O
ATOM  *****  O   HOH A1090      75.042   9.070  15.256  1.00 24.59      1090 O
ATOM  *****  O   HOH A1091      66.884 -17.328  21.234  1.00 53.10      1091 O
ATOM  *****  O   HOH A1092      99.320   2.264  37.327  1.00 50.23      1092 O
ATOM  *****  O   HOH A1093      78.317  22.845  13.681  1.00 36.27      1093 O
ATOM  *****  O   HOH A1094      74.153  22.751  23.309  1.00 33.61      1094 O
ATOM  *****  O   HOH A1095      58.531  -2.807  20.596  1.00 26.52      1095 O
ATOM  *****  O   HOH A1096      92.465 -24.844  20.569  1.00 53.69      1096 O
ATOM  *****  O   HOH A1097      65.187 -14.072  11.490  1.00 34.82      1097 O
ATOM  *****  O   HOH A1098      99.655  -0.559   8.982  1.00 38.57      1098 O
ATOM  *****  O   HOH A1099     104.737 -22.093  16.297  1.00 31.10      1099 O
ATOM  *****  O   HOH A1100      91.378   4.276  39.174  1.00 28.42      1100 O
ATOM  *****  O   HOH A1101      45.212   5.634  13.770  1.00 36.05      1101 O
ATOM  *****  O   HOH A1102      37.383  19.242   9.516  1.00 40.62      1102 O
ATOM  *****  O   HOH A1103      67.015  23.851   3.886  1.00 27.83      1103 O
ATOM  *****  O   HOH A1104     104.918  -0.561  25.384  1.00 31.22      1104 O
ATOM  *****  O   HOH A1105      72.721  15.299  30.855  1.00 39.89      1105 O
ATOM  *****  O   HOH A1106      94.036  10.512  37.077  1.00 40.22      1106 O
ATOM  *****  O   HOH A1107      99.746   1.563  -0.061  1.00 42.41      1107 O
ATOM  *****  O   HOH A1108      57.677  29.264  11.625  1.00 48.84      1108 O
ATOM  *****  O   HOH A1109     125.587   3.847  49.182  1.00 44.79      1109 O
ATOM  *****  O   HOH A1110      71.916  18.707   9.574  1.00 27.30      1110 O
ATOM  *****  O   HOH A1111     101.422   6.231  18.417  1.00 41.01      1111 O
ATOM  *****  O   HOH A1112      60.540  -2.827  24.542  1.00 40.39      1112 O
ATOM  *****  O   HOH A1113      78.719  -5.850  21.372  1.00 31.89      1113 O
ATOM  *****  O   HOH A1114      76.008 -12.298  23.622  1.00 29.09      1114 O
ATOM  *****  O   HOH A1115      74.776  16.993   0.687  1.00 32.03      1115 O
ATOM  *****  O   HOH A1116      76.619  14.897   6.928  1.00 33.47      1116 O
ATOM  *****  O   HOH A1117      62.469  10.320  24.441  1.00 34.82      1117 O
ATOM  *****  O   HOH A1118      82.788   2.966  19.697  1.00 42.24      1118 O
ATOM  *****  O   HOH A1119      99.539  11.503  16.022  1.00 26.81      1119 O
ATOM  *****  O   HOH A1120      77.451  14.862   3.952  1.00 41.30      1120 O
ATOM  *****  O   HOH A1121      72.959  21.084   9.108  1.00 27.09      1121 O
ATOM  *****  O   HOH A1122      88.989  13.720  31.644  1.00 20.39      1122 O
ATOM  *****  O   HOH A1123     101.527  -0.989  34.054  1.00 42.51      1123 O
ATOM  *****  O   HOH A1124      80.204  -8.528  27.386  1.00 34.76      1124 O
ATOM  *****  O   HOH A1126      40.456   5.449  13.857  1.00 38.28      1126 O
ATOM  *****  O   HOH A1127      51.195  -0.927   6.575  1.00 54.30      1127 O
ATOM  *****  O   HOH A1128      66.418  -0.049   6.216  1.00 43.27      1128 O
ATOM  *****  O   HOH A1129     109.611  10.977  25.138  1.00 40.19      1129 O
ATOM  *****  O   HOH A1130      66.360  -7.276   3.006  1.00 29.74      1130 O
ATOM  *****  O   HOH A1131      89.131 -24.616  22.113  1.00 38.13      1131 O
ATOM  *****  O   HOH A1132      70.924  -5.841  13.102  1.00 27.53      1132 O
ATOM  *****  O   HOH A1133      51.870  28.969  24.374  1.00 45.99      1133 O
ATOM  *****  O   HOH A1134      80.811 -11.015  27.902  1.00 43.72      1134 O
ATOM  *****  O   HOH A1135     101.183   1.687  33.090  1.00 46.29      1135 O
ATOM  *****  O   HOH A1136      86.344 -13.924   9.462  1.00 31.57      1136 O
ATOM  *****  O   HOH A1137      75.853  24.059   3.159  1.00 41.60      1137 O
ATOM  *****  O   HOH A1138      77.035  -2.767   8.904  1.00 36.88      1138 O
ATOM  *****  O   HOH A1139      98.936  25.516  14.800  1.00 35.59      1139 O
ATOM  *****  O   HOH A1140     106.237  17.055  27.871  1.00 38.06      1140 O
ATOM  *****  O   HOH A1141      88.402   2.772   3.419  1.00 33.42      1141 O
ATOM  *****  O   HOH A1142      55.071  31.027  12.657  1.00 46.01      1142 O
ATOM  *****  O   HOH A1143      58.341   6.973  39.468  1.00 37.87      1143 O
ATOM  *****  O   HOH A1144      54.961  27.841  12.247  1.00 43.58      1144 O
ATOM  *****  O   HOH A1145      88.920  -2.715   3.949  1.00 39.22      1145 O
ATOM  *****  O   HOH A1147      90.408  -3.277   6.603  1.00 36.04      1147 O
ATOM  *****  O   HOH A1148      60.874  -1.780  21.758  1.00 35.15      1148 O
ATOM  *****  O   HOH A1149      67.942  22.531  19.082  1.00 38.43      1149 O
ATOM  *****  O   HOH A1150      82.861 -24.013  21.914  1.00 29.11      1150 O
ATOM  *****  O   HOH A1151      97.426  20.237  21.253  1.00 14.19      1151 O
ATOM  *****  O   HOH A1153      88.538  16.327  32.636  1.00 20.09      1153 O
ATOM  *****  O   HOH A1154      83.098  36.255   2.477  1.00 45.07      1154 O
ATOM  *****  O   HOH A1155      78.517  -7.983  19.745  1.00 37.04      1155 O
ATOM  *****  O   HOH A1156      73.102  19.913  20.226  1.00 26.77      1156 O
ATOM  *****  O   HOH A1157     106.745   0.489  22.691  1.00 37.02      1157 O
ATOM  *****  O   HOH A1158      63.208  14.387  33.785  1.00 24.20      1158 O
ATOM  *****  O   HOH A1159      87.048  30.796  -0.393  1.00 37.71      1159 O
ATOM  *****  O   HOH A1160      66.411  -7.393   5.586  1.00 25.13      1160 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.
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.
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.
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:
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The line in the input file that created this problem is:
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The line in the input file that created this problem is:
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The line in the input file that created this problem is:
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The line in the input file that created this problem is:
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The line in the input file that created this problem is:
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The line in the input file that created this problem is:
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The line in the input file that created this problem is:
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The line in the input file that created this problem is:
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The line in the input file that created this problem is:
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The line in the input file that created this problem is:
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The line in the input file that created this problem is:
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The line in the input file that created this problem is:
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The line in the input file that created this problem is:
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The line in the input file that created this problem is:
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The line in the input file that created this problem is:
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The line in the input file that created this problem is:
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The line in the input file that created this problem is:
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The line in the input file that created this problem is:
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The line in the input file that created this problem is:
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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.
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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.
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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:
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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:
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The line in the input file that created this problem is:
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The line in the input file that created this problem is:
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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:
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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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# 2 # Note: Header records from PDB file
Header records from PDB file.
 
HEADER                                                        5MHP
 
# 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
  0.012948  0.000000  0.002465
  0.000000  0.012574  0.000000
  0.000000  0.000000  0.012766
 
# 5 # Warning: Problem detected upon counting molecules and matrices
The parameter Z as given on the CRYST card represents the molecular
multiplicity in the crystallographic cell. Normally, Z equals the number of
matrices of the space group multiplied by the number of NCS relations. The
value of Z is multiplied by the integrated molecular weight of the molecules
in the file to determine the Matthews coefficient. This relation is being
validated in this option. Be aware that the validation can get confused if
both multiple copies of the molecule are present in the ATOM records and
MTRIX records are present in the header of the PDB file.
 
 Space group as read from CRYST card: P 1 21 1
 Number of matrices in space group: 2
 Highest polymer chain multiplicity in structure: 1
 Highest polymer chain multiplicity according to SEQRES: 1
 No explicit MTRIX NCS matrices found in the input file
 Value of Z as found on the CRYST1 card: 0
 Z, symmetry, and molecular multiplicity disagree
 Could it be that Z must be: 2
 
# 6 # Warning: Matthews Coefficient (Vm) high
 
The Matthews coefficient [REF] is defined as the density of the protein
structure in cubic Angstroms per Dalton. Normal values are between 1.5
(tightly packed, little room for solvent) and 4.0 (loosely packed, much
space for solvent). Some very loosely packed structures can get values a bit
higher than that.
 
Very high numbers are most often caused by giving the wrong value for Z on
the CRYST1 card (or not giving this number at all), but can also result from
large fractions missing out of the molecular weight (e.g. a lot of UNK
residues, or DNA/RNA missing from virus structures).
 
 Molecular weight of all polymer chains: 88857.688
 Volume of the Unit Cell V= 481128.031
 Space group multiplicity: 2
 No NCS symmetry matrices (MTRIX records) found in PDB file
 Matthews coefficient for observed atoms and Z is high: Vm= 5.415
 No Matthews coefficient given in REMARK 280
 Could it be that Z must be: 2
 This number is the multiplication of the spacegroup and NCS symmetry count
 Matthews coefficient for observed atoms and corrected Z: Vm= 2.707
 
# 7 # 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.
 
# 8 # 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.
 
# 9 # 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.
 
  772 BMA  (   3-) B  -
  773 MAN  (   4-) B  -
  774 MAN  (   5-) B  -
  775 MAN  (   7-) B  -
  776 MAN  (   6-) B  -
  785 SCN  ( 917-) A  -
  788 7NB  ( 920-) A  -
 
# 10 # Warning: Covalently bound ligands
The ligands in this table are covalently bound to something else. It is
already difficult to automatically generate topologies for ligands,
but when they are covalently bound to something it becomes even more
complicated to do everything right. So, if you get weird error messages
that seem related to this covalent bond, then please feel free to
ignore those, or even better, make a topology entry by hand.
 
The comment `Other ligand` indicates that the covalent bond is to another
ligand. In that case you might want to convert the two ligands into one
bigger ligand.
 
  772 BMA  (   3-) B  -
 
# 11 # Note: No strange inter-chain connections detected
No covalent bonds have been detected between molecules with non-identical
chain identifiers.
 
# 12 # Note: No duplicate atom names in ligands
All atom names in ligands (if any) seem adequately unique.
 
# 13 # Note: In all cases the primary alternate atom was used
WHAT CHECK saw no need to make any alternate atom corrections (which means
they either are all correct, or there are none).
 
# 14 # Note: No residues detected inside ligands
Either this structure does not contain ligands with amino acid groups inside
it, or their naming is proper (enough).
 
# 15 # Warning: Groups attached to potentially hydrogen-bonding atoms
Residues were observed with groups attached to (or very near to) atoms that
potentially can form hydrogen bonds. WHAT CHECK is not very good at dealing
with such exceptional cases (Mainly because it's author is not...). So be
warned that the hydrogen-bonding related analyses of these residues
might be in error.
 
For example, an aspartic acid can be protonated on one of its delta
oxygens. This is possible because the one delta oxygen 'helps' the
other one holding that proton. However, if a delta oxygen has a group
bound to it, then it can no longer 'help' the other delta oxygen
bind the proton. However, both delta oxygens, in principle, can still
be hydrogen bond acceptors. Such problems can occur in the amino acids
Asp, Glu, and His. I have opted, for now to simply allow no hydrogen
bonds at all for any atom in any side chain that somewhere has a 'funny'
group attached to it. I know this is wrong, but there are only 12 hours
in a day.
 
  770 NAG  (   2-) B  -    O4  bound to   772 BMA  (   3-) B  -    C1
 
# 16 # Note: No probable side chain atoms with zero occupancy detected.
Either there are no side chain atoms with zero occupancy, or the side chain
atoms with zero occupancy were not present in the input PDB file (in which
case they are listed as missing atoms), or their positions are sufficiently
improbable to warrant a zero occupancy.
 
# 17 # Note: No probable backbone atoms with zero occupancy detected.
Either there are no backbone atoms with zero occupancy, or the backbone
atoms with zero occupancy were left out of the input PDB file (in
which case they are listed as missing atoms), or their positions are
sufficiently improbable to warrant a zero occupancy.
 
# 18 # Note: All residues have a complete backbone.
No residues have missing backbone atoms.
 
# 19 # Note: No C-alpha only residues
There are no residues that consist of only an alpha carbon atom.
 
# 20 # Note: Content of the PDB file as interpreted by WHAT CHECK
Content of the PDB file as interpreted by WHAT CHECK.
WHAT CHECK has read your PDB file, and stored it internally in what is called
'the soup'. The content of this soup is listed here. An extensive explanation
of all frequently used WHAT CHECK output formats can be found at
swift.cmbi.ru.nl. Look under output formats. A course on reading this
'Molecules' table is part of the WHAT CHECK website.
 
     1     1 (   52)   768 (  860) A Protein             /zata/tempdir/5mh...
     2   769 (    1)   769 (    1) B Sugar               /zata/tempdir/5mh...
     3   770 (    2)   770 (    2) B Sugar<-             /zata/tempdir/5mh...
     4   771 (  908)   771 (  908) A Sugar               /zata/tempdir/5mh...
     5   772 (    3)   772 (    3) B BMA  <-             /zata/tempdir/5mh...
     6   773 (    4)   773 (    4) B MAN                 /zata/tempdir/5mh...
     7   774 (    5)   774 (    5) B MAN                 /zata/tempdir/5mh...
     8   775 (    7)   775 (    7) B MAN                 /zata/tempdir/5mh...
     9   776 (    6)   776 (    6) B MAN                 /zata/tempdir/5mh...
    10   777 (  909)   777 (  909) A  ZN                 /zata/tempdir/5mh...
    11   778 (  910)   778 (  910) A  ZN                 /zata/tempdir/5mh...
    12   779 (  911)   779 (  911) A  CA                 /zata/tempdir/5mh...
    13   780 (  912)   780 (  912) A  MG                 /zata/tempdir/5mh...
    14   781 (  913)   781 (  913) A IOD                 /zata/tempdir/5mh...
    15   782 (  914)   782 (  914) A  CL                 /zata/tempdir/5mh...
    16   783 (  915)   783 (  915) A  CL                 /zata/tempdir/5mh...
    17   784 (  916)   784 (  916) A  CL                 /zata/tempdir/5mh...
    18   785 (  917)   785 (  917) A SCN                 /zata/tempdir/5mh...
    19   786 (  918)   786 (  918) A PO4                 /zata/tempdir/5mh...
    20   787 (  919)   787 (  919) A PO4                 /zata/tempdir/5mh...
    21   788 (  920)   788 (  920) A 7NB                 /zata/tempdir/5mh...
    22   789 ( HOH )   789 ( HOH ) A water   (    1)     /zata/tempdir/5mh...
MODELs skipped upon reading PDB file: 0
X-ray structure. No MODELs found
The total number of amino acids found is 768
of which 11 have poor or (essentially) missing atoms
No nucleic acids observed in input file
Number of (recognized) sugars: 3
Number of water molecules: 1
Residue numbers increase monotonously OK
 
# 21 # Note: Chain identifiers seem OK
All ions seem to have a logical chain identifier, or there are no ions
present in the input file.
ERROR. File not found:
TAPEOUT.DAT
 
# 22 # Note: Ramachandran plot
In this Ramachandran plot x-signs represent glycines, squares represent
prolines, and plus-signs represent the other residues. If too many
plus-signs fall outside the contoured areas then the molecule is poorly
refined (or worse). Proline can only occur in the narrow region around
phi=-60 that also falls within the other contour islands.
 
In a colour picture, the residues that are part of a helix are shown in blue,
strand residues in red. Preferred regions for helical residues are drawn in
blue, for strand residues in red, and for all other residues in green. A full
explanation of the Ramachandran plot together with a series of examples can
be found at the WHAT CHECK website [REF].
 
In the TeX file, a plot has been inserted here
 
Chain identifier: A
 
# 23 # Note: 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 WTNISGSCKGRCFELCRCDNLCKSYTSCCHDFDELCLKTARGWECTKDRCGEVRNEENAC
(  52)-( 118)
                     70        80        90       100       110       120
                      |         |         |         |         |         |
   61 -  120 HCSEDCLARGDCCTNYQVVCKGESHWVDDDCEEIKAAECPAGFVRPPLIIFSVDGFRASY
( 119)-( 178)
                    130       140       150       160       170       180
                      |         |         |         |         |         |
  121 -  180 MKKGSKVMPNIEKLRSCGTHSPYMRPVYPTKTFPNLYTLATGLYPESHGIVGNSMYDPVF
( 179)-( 238)
                    190       200       210       220       230       240
                      |         |         |         |         |         |
  181 -  240 DATFHLRGREKFNHRWWGGQPLWITATKQGVKAGTFFWSVVIPHERRILTILQWLTLPDH
( 239)-( 298)
                    250       260       270       280       290       300
                      |         |         |         |         |         |
  241 -  300 ERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKIVGQLMDGLKQLKLHRCVNVIFVG
( 299)-( 358)
                    310       320       330       340       350       360
                      |         |         |         |         |         |
  301 -  360 DHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRSKFSNNAKYDPKAIIANLTCKKPD
( 359)-( 418)
                    370       380       390       400       410       420
                      |         |         |         |         |         |
  361 -  420 QHFKPYLKQHLPKRLHYANNRRIEDIHLLVERRWHVARKPCFFQGDHGFDNKVNSMQTVF
( 419)-( 488)
                    430       440       450       460       470       480
                      |         |         |         |         |         |
  421 -  480 VGYGPTFKYKTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTFRPTMPEEVTR
( 489)-( 550)
                    490       500       510       520       530       540
                      |         |         |         |         |         |
  481 -  540 PNYPGIMYLQSDFDLGCTCTEERHLLYGRPAVLYRTRYDILYHTDFESGYSEIFLMPLWT
( 551)-( 632)
                    550       560       570       580       590       600
                      |         |         |         |         |         |
  541 -  600 SYTVSKQAEVSSVPDHLTSCVRPDVRVSPSFSQNCLAYKNDKQMSYGFLFPPYLSSSPEA
( 633)-( 692)
                    610       620       630       640       650       660
                      |         |         |         |         |         |
  601 -  660 KYDAFLVTNMVPMYPAFKRVWNYFQRVLVKKYASERNGVNVISGPIFDYDYDGLHDTEDK
( 693)-( 752)
                    670       680       690       700       710       720
                      |         |         |         |         |         |
  661 -  720 IKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNEESCNSSEDE
( 753)-( 812)
                    730       740       750       760
                      |         |         |         |
  721 -  768 SKWVEELMKMHTARVRDIEHLTSLDFFRKTSRSYPEILTLKTYLHTYE
( 813)-( 860)
 
 
 
 
# 24 # Note: No rounded coordinates detected
No significant rounding of atom coordinates has been detected.
 
# 25 # 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.
 
# 26 # 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.
 
# 27 # 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.
 
   48 ASP  ( 106-) A  -   High
   50 CYS  ( 108-) A  -   High
   52 GLU  ( 110-) A  -   High
   57 GLU  ( 115-) A  -   High
   91 CYS  ( 149-) A  -   High
  137 CYS  ( 195-) A  -   High
  341 ASN  ( 399-) A  -   High
  497 CYS  ( 567-) A  -   High
  499 CYS  ( 569-) A  -   High
  549 GLU  ( 641-) A  -   High
  557 LEU  ( 649-) A  -   High
 
# 28 # 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.
 
   15 LEU  (  66-) A  -        OK (7)
  400 PRO  ( 458-) A  -        OK (10)
  469 THR  ( 537-) A  -        OK (2)
  499 CYS  ( 569-) A  -        OK (22)
  768 GLU  ( 860-) A  -        OK
 
# 29 # Note: Weights administratively correct
All atomic occupancy factors ('weights') fall in the 0.0--1.0 range, which
makes them administratively correct.
 
# 30 # 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.
 
# 31 # 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.
 
# 32 # Warning: What type of B-factor?
WHAT CHECK does not yet know well how to cope with B-factors in case TLS has
been used. It simply assumes that the B-factor listed on the ATOM and HETATM
cards are the total B-factors. When TLS refinement is used that assumption
sometimes is not correct. The header of the PDB file states that TLS groups
were used. So, if WHAT CHECK complains about your  B-factors, while you think
that they are OK, then check for TLS related B-factor problems first.
 
Number of TLS groups mentione in PDB file header: 0
 
Temperature not mentioned in PDB file. This most likely means
that the temperature record is absent.
Room temperature assumed
 
# 33 # 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
 
# 34 # 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 :  0.749 over    5624 bonds
Average difference in B over a bond :    2.41
RMS difference in B over a bond :    3.42
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
 
# 35 # 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
 
# 36 # 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.
 
# 37 # Note: Valine nomenclature OK
No errors were detected in valine nomenclature.
 
# 38 # Note: Threonine nomenclature OK
No errors were detected in threonine nomenclature.
 
# 39 # Note: Isoleucine nomenclature OK
No errors were detected in isoleucine nomenclature.
 
# 40 # Note: Leucine nomenclature OK
No errors were detected in leucine nomenclature.
 
# 41 # Note: Arginine nomenclature OK
No errors were detected in arginine nomenclature.
 
# 42 # Note: Tyrosine torsion conventions OK
No errors were detected in tyrosine torsion angle conventions.
 
# 43 # Note: Phenylalanine torsion conventions OK
No errors were detected in phenylalanine torsion angle conventions.
 
# 44 # Note: Aspartic acid torsion conventions OK
No errors were detected in aspartic acid torsion angle conventions.
 
# 45 # Note: Glutamic acid torsion conventions OK
No errors were detected in glutamic acid torsion angle conventions.
 
# 46 # 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).
 
# 47 # Note: SO4/PO4 atom names OK
No errors were detected in SO4/PO4 atom naming conventions.
 
# 48 # 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.
 
# 49 # Note: No decreasing residue numbers
All residue numbers are strictly increasing within each chain.
 
# 50 # 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]).
 
# 51 # Note: Normal bond length variability
Bond lengths were found to deviate normally from the standard bond lengths
(values for Protein residues were taken from Engh and Huber [REF], for
DNA/RNA from Parkinson et al [REF]).
 
 RMS Z-score for bond lengths: 0.345
 RMS-deviation in bond distances: 0.008
 
# 52 # 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.
 
# 53 # 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.
 
   48 ASP  ( 106-) A  -    CA   CB   CG  116.66    4.1
  168 HIS  ( 226-) A  -    CA   CB   CG  118.13    4.3
  180 PHE  ( 238-) A  -    CA   CB   CG  118.48    4.7
  184 PHE  ( 242-) A  -    CA   CB   CG  118.84    5.0
  254 ASP  ( 312-) A  -    CA   CB   CG  117.52    4.9
  410 ASP  ( 478-) A  -    CA   CB   CG  116.72    4.1
  656 ASP  ( 748-) A  -    CA   CB   CG  117.77    5.2
 
# 54 # Note: Normal bond angle variability
Bond angles were found to deviate normally from the mean standard bond angles
(normal values for protein residues were taken from Engh and Huber [REF], for
DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected
to be near 1.0 for a normally restrained data set, and this is indeed
observed for very high resolution X-ray structures.
 
 RMS Z-score for bond angles: 0.606
 RMS-deviation in bond angles: 1.120
 
# 55 # Note: Residue hand check OK
No atoms are observed that have the wrong handedness. Be aware, though, that
WHAT CHECK might have corrected the handedness of some atoms already. The
handedness has not been corrected for any case where the problem is worse
than just an administrative discomfort.
 
# 56 # Note: Chirality OK
All protein atoms have proper chirality, or there is no intact protein
present in the PDB file.
The average deviation= 0.540
 
# 57 # 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 : 0.427
 
# 58 # Note: Tau angles OK
All of the tau angles (N-C-alpha-C) of amino acids fall within expected
RMS deviations.
 
# 59 # 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 : 0.704
 
# 60 # Note: Side chain planarity OK
All of the side chains of residues that have an intact planar group are
planar within expected RMS deviations.
 
# 61 # 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.
 
# 62 # Note: Ramachandran Z-score OK
The score expressing how well the backbone conformations of all residues
correspond to the known allowed areas in the Ramachandran plot is within
expected ranges for well-refined structures.
 
 Ramachandran Z-score : -2.262
 
# 63 # 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.
 
# 64 # 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.
 
  516 THR  ( 608-) A  -   -3.3
   26 THR  (  84-) A  -   -3.1
  329 PRO  ( 387-) A  -   -2.7
  332 LEU  ( 390-) A  -   -2.7
  253 PRO  ( 311-) A  -   -2.7
   13 PHE  (  64-) A  -   -2.4
    2 THR  (  53-) A  -   -2.2
  418 THR  ( 486-) A  -   -2.1
  505 LEU  ( 597-) A  -   -2.1
  171 VAL  ( 229-) A  -   -2.0
  170 ILE  ( 228-) A  -   -2.0
   10 GLY  (  61-) A  -   -2.0
 
# 65 # 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.
 
   13 PHE  (  64-) A  - Poor phi/psi
   25 TYR  (  83-) A  - Poor phi/psi
   26 THR  (  84-) A  - Poor phi/psi
   41 ARG  (  99-) A  - Poor phi/psi
   42 GLY  ( 100-) A  - Poor phi/psi
   51 GLY  ( 109-) A  - Poor phi/psi
   70 GLY  ( 128-) A  - Poor phi/psi
   72 CYS  ( 130-) A  - omega poor
   99 CYS  ( 157-) A  - Omega to (next) Pro poor
  105 ARG  ( 163-) A  - Omega to (next) Pro poor
  106 PRO  ( 164-) A  - Omega to (next) Pro poor
  115 GLY  ( 173-) A  - Poor phi/psi
  124 GLY  ( 182-) A  - Poor phi/psi
  128 MET  ( 186-) A  - Omega to (next) Pro poor
  138 GLY  ( 196-) A  - Poor phi/psi
And so on for a total of    98 lines.
 
# 66 # 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.
 
  332 LEU  ( 390-) A  -    -1.32
  489 LEU  ( 559-) A  -    -1.30
   19 ASP  (  77-) A  -    -1.21
   33 ASP  (  91-) A  -    -1.21
   67 LEU  ( 125-) A  -    -1.29
  466 LEU  ( 534-) A  -    -1.24
  486 ILE  ( 556-) A  -    -1.23
  505 LEU  ( 597-) A  -    -1.25
  555 ASP  ( 647-) A  -    -1.21
   65 ASP  ( 123-) A  -    -1.14
  114 ASP  ( 172-) A  -    -1.19
  175 MET  ( 233-) A  -    -1.14
  235 LEU  ( 293-) A  -    -1.19
  321 ASN  ( 379-) A  -    -1.12
  327 LEU  ( 385-) A  -    -1.12
And so on for a total of   295 lines.
 
# 67 # Note: chi-1/chi-2 angle correlation Z-score OK
The score expressing how well the chi-1/chi-2 angles of all residues
correspond to the populated areas in the database is
within expected ranges for well-refined structures.
 
 chi-1/chi-2 correlation Z-score : -2.224
 
# 68 # 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.
 
  305 GLU  ( 363-) A  -   0.35
   30 HIS  (  88-) A  -   0.36
  411 ASN  ( 479-) A  -   0.36
   86 TRP  ( 144-) A  -   0.38
  167 SER  ( 225-) A  -   0.39
  634 SER  ( 726-) A  -   0.39
  698 SER  ( 790-) A  -   0.39
 
# 69 # 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!
 
   24 SER  (  82-) A  -       0
   25 TYR  (  83-) A  -       0
   41 ARG  (  99-) A  -       0
   60 CYS  ( 118-) A  -       0
  150 THR  ( 208-) A  -       0
  187 ARG  ( 245-) A  -       0
  252 GLN  ( 310-) A  -       0
  356 CYS  ( 414-) A  -       0
  377 TYR  ( 435-) A  -       0
  407 HIS  ( 475-) A  -       0
  486 ILE  ( 556-) A  -       0
    8 CYS  (  59-) A  -       1
   12 CYS  (  63-) A  -       1
  123 LYS  ( 181-) A  -       1
  137 CYS  ( 195-) A  -       1
  329 PRO  ( 387-) A  -       1
  355 THR  ( 413-) A  -       1
  378 ALA  ( 436-) A  -       1
  487 MET  ( 557-) A  -       1
  535 LEU  ( 627-) A  -       1
  637 ASN  ( 729-) A  -       1
   43 TRP  ( 101-) A  -       2
   50 CYS  ( 108-) A  -       2
  331 THR  ( 389-) A  -       2
  429 TYR  ( 497-) A  -       2
  460 HIS  ( 528-) A  -       2
 
# 70 # 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 : -0.812
 
# 71 # 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= 178.830 6.077
 
# 72 # Note: PRO puckering amplitude OK
Puckering amplitudes for all PRO residues are within normal ranges.
 
# 73 # 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].
 
  329 PRO  ( 387-) A  -  -54.0 half-chair C-beta/C-alpha (-54 degrees)
  372 PRO  ( 430-) A  -   99.9 envelop C-beta (108 degrees)
  645 PRO  ( 737-) A  -  -62.8 half-chair C-beta/C-alpha (-54 degrees)
 
# 74 # Note: Backbone oxygen evaluation OK
All residues for which similar local backbone conformations could be found
in the WHAT CHECK database have a backbone oxygen position that has been
observed at least a few times in that database.
 
# 75 # 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.
 
   25 TYR  (  83-) A  - TT+   Likely
   31 ASP  (  89-) A  - TT+   Likely
   37 LEU  (  95-) A  - TT+   Likely
   41 ARG  (  99-) A  - TT+   Likely
   57 GLU  ( 115-) A  - TT+   Likely
   81 LYS  ( 139-) A  - TT+   Likely
  321 ASN  ( 379-) A  - TT+   Likely
  341 ASN  ( 399-) A  - TT+   Likely
  360 ASP  ( 418-) A  - TT+   Likely
  557 LEU  ( 649-) A  - TT+   Likely
  559 SER  ( 651-) A  - TT+   Likely
 
# 76 # Error: Abnormally short interatomic distances
The pairs of atoms listed in the table below have an unusually short
distance; each bump is listed in only one direction,
 
The contact distances of all atom pairs have been checked. Two atoms are
said to `bump' if they are closer than the sum of their Van der Waals radii
minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom
is used. The first number in the table tells you how much shorter that
specific contact is than the acceptable limit. The second distance is the
distance between the centres of the two atoms.
 
The last text-item on each line represents the status of the atom pair. The
text `INTRA' means that the bump is between atoms that are explicitly listed
in the PDB file. `INTER' means it is an inter-symmetry bump. If the final
column contains the text 'HB', the bump criterion was relaxed because there
could be a hydrogen bond. Similarly relaxed criteria are used for 1--3 and
1--4 interactions (listed as 'B2' and 'B3', respectively). If the last column
is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes
the appearance of the bump somewhat less severe because the atoms probably
are not there anyway. BL, on the other hand, indicates that the bumping atoms
both have a low B-factor, and that makes the bumps more worrisome.
 
It seems likely that at least some of the reported bumps are caused by
administrative errors in the chain names. I.e. covalently bound atoms with
different non-blank chain-names are reported as bumps. In rare cases this is
not an error.
 
Bumps between atoms for which the sum of their occupancies is lower than one
are not reported. If the MODEL number does not exist (as is the case in most
X-ray files), a minus sign is printed instead.
 
  353 ASN  ( 411-) A  -    ND2  <-->    771 NAG  ( 908-) A  -    C1   1.67    1.43  INTRA BF
  457 ASN  ( 525-) A  -    ND2  <-->    769 NAG  (   1-) B  -    C1   1.67    1.43  INTRA BL
  769 NAG  (   1-) B  -    O4   <-->    770 NAG  (   2-) B  -    C1   1.21    1.39  INTRA BL
  457 ASN  ( 525-) A  -    CG   <-->    769 NAG  (   1-) B  -    C1   0.79    2.41  INTRA BL
  353 ASN  ( 411-) A  -    CG   <-->    771 NAG  ( 908-) A  -    C1   0.76    2.44  INTRA BF
  353 ASN  ( 411-) A  -    ND2  <-->    771 NAG  ( 908-) A  -    C2   0.68    2.42  INTRA BF
  457 ASN  ( 525-) A  -    ND2  <-->    769 NAG  (   1-) B  -    C2   0.60    2.50  INTRA BL
  769 NAG  (   1-) B  -    C4   <-->    770 NAG  (   2-) B  -    C1   0.58    2.42  INTRA BL
  457 ASN  ( 525-) A  -    ND2  <-->    769 NAG  (   1-) B  -    O5   0.40    2.30  INTRA BL
  353 ASN  ( 411-) A  -    ND2  <-->    771 NAG  ( 908-) A  -    O5   0.38    2.32  INTRA BF
  769 NAG  (   1-) B  -    O4   <-->    770 NAG  (   2-) B  -    C2   0.32    2.38  INTRA BL
   66 CYS  ( 124-) A  -    C    <-->     72 CYS  ( 130-) A  -    SG   0.23    3.17  INTRA BF
   22 CYS  (  80-) A  -    C    <-->     28 CYS  (  86-) A  -    SG   0.19    3.21  INTRA BF
  322 VAL  ( 380-) A  -    O    <-->    398 ARG  ( 456-) A  -    NH1  0.18    2.52  INTRA BF
   86 TRP  ( 144-) A  -    O    <-->    133 LYS  ( 191-) A  -    NZ   0.15    2.55  INTRA BL
And so on for a total of    52 lines.
 
# 77 # 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: 11.985
Total bump value per residue: 0.067
Total number of bumps: 52
Total squared bump value: 10.131
Total number of bumps in the mildest bin: 41
Total number of bumps in the second bin: 3
Total number of bumps in the middle bin: 3
Total number of bumps in the fourth bin: 2
Total number of bumps in the worst bin: 3
 
# 78 # 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.
 
# 79 # 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 : 1.060
 
# 80 # 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
 
# 81 # 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.
 
  187 ARG  ( 245-) A  -  -7.91
  263 PHE  ( 321-) A  -  -7.53
   41 ARG  (  99-) A  -  -7.20
  483 TYR  ( 553-) A  -  -7.13
  515 ARG  ( 607-) A  -  -6.84
  105 ARG  ( 163-) A  -  -6.81
   25 TYR  (  83-) A  -  -6.40
  767 TYR  ( 859-) A  -  -6.23
   95 LYS  ( 153-) A  -  -6.13
  480 ARG  ( 550-) A  -  -6.10
  471 ARG  ( 541-) A  -  -5.84
  509 ARG  ( 601-) A  -  -5.82
  468 ARG  ( 536-) A  -  -5.79
  186 LEU  ( 244-) A  -  -5.62
  402 PHE  ( 470-) A  -  -5.57
  487 MET  ( 557-) A  -  -5.50
  104 VAL  ( 162-) A  -  -5.45
  522 TYR  ( 614-) A  -  -5.31
  432 LYS  ( 500-) A  -  -5.31
  260 TYR  ( 318-) A  -  -5.18
  392 ARG  ( 450-) A  -  -5.15
  474 MET  ( 544-) A  -  -5.13
  357 LYS  ( 415-) A  -  -5.03
  749 LYS  ( 841-) A  -  -5.01
 
# 82 # 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.
 
  103 PHE  ( 161-) A  -      105 --- ARG   163- (A ) -       -5.48
 
# 83 # Note: Structural average packing environment OK
The structural average packing score is within normal ranges.
 
 
Average for range     1 -  771 :  -0.922
 
# 84 # 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
 
# 85 # 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.
 
  433 VAL  ( 501-) A  -  -2.56
  375 LEU  ( 433-) A  -  -2.52
 
# 86 # Note: No series of residues with abnormal new packing environment
There are no stretches of four or more residues each having a packing
Z-score worse than -1.75.
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
 
# 87 # 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
 
# 88 # 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.
 
# 89 # Note: Water contacts OK
All water clusters make at least one contact with a non-water atom.
 
# 90 # Note: No waters need moving
All water molecules are sufficiently close to the asymmetric unit given in
the input file.
 
# 91 # Note: Water hydrogen bonds OK
All water molecules can form hydrogen bonds.
 
# 92 # 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.
 
   58 ASN  ( 116-) A  -
  341 ASN  ( 399-) A  -
  395 HIS  ( 453-) A  -
  460 HIS  ( 528-) A  -
 
# 93 # 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.
 
   30 HIS  (  88-) A  -   HIS-E   0.55 HIS-D   0.88
   61 HIS  ( 119-) A  -   HIS-E   0.41 HIS-H   0.67
   85 HIS  ( 143-) A  -   HIS-E   0.41 HIS-D   0.76
  140 HIS  ( 198-) A  -   HIS-E   0.47
  168 HIS  ( 226-) A  -   HIS-E   0.56
  185 HIS  ( 243-) A  -   HIS-E   0.52
  194 HIS  ( 252-) A  -   HIS-E   0.50
  224 HIS  ( 282-) A  -   HIS-E   0.44
  240 HIS  ( 298-) A  -   HIS-E   0.51
  258 HIS  ( 316-) A  -   HIS-E   0.50 HIS-D   0.69
  291 HIS  ( 349-) A  -   HIS-E   0.47
  302 HIS  ( 360-) A  -   HIS-E   0.41 HIS-D   1.03
  362 HIS  ( 420-) A  -   HIS-E   0.52 HIS-D   0.82
  370 HIS  ( 428-) A  -   HIS-E   0.41
  376 HIS  ( 434-) A  -   HIS-E   0.39 HIS-D   0.79
  387 HIS  ( 445-) A  -   HIS-E   0.40 HIS-D   0.85
  395 HIS  ( 453-) A  -   HIS-E   0.44
  407 HIS  ( 475-) A  -   HIS-E   0.44 HIS-D   0.88
  460 HIS  ( 528-) A  -   HIS-E   0.42
  465 HIS  ( 533-) A  -   HIS-E   0.55
  504 HIS  ( 596-) A  -   HIS-E   0.51
  523 HIS  ( 615-) A  -   HIS-E   0.52 HIS-D   0.69
  556 HIS  ( 648-) A  -   HIS-E   0.52
  655 HIS  ( 747-) A  -   HIS-E   0.40
  675 HIS  ( 767-) A  -   HIS-E   0.53 HIS-D   0.90
  706 HIS  ( 798-) A  -   HIS-E   0.43 HIS-D   0.95
  731 HIS  ( 823-) A  -   HIS-E   0.38
  740 HIS  ( 832-) A  -   HIS-E   0.40
  765 HIS  ( 857-) A  -   HIS-E   0.47
 
# 94 # 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.
 
   19 ASP  (  77-) A  -    N
   26 THR  (  84-) A  -    N
   38 LYS  (  96-) A  -    N
   46 THR  ( 104-) A  -    N
   49 ARG  ( 107-) A  -    NE
   49 ARG  ( 107-) A  -    NH1
   54 ARG  ( 112-) A  -    NH1
   54 ARG  ( 112-) A  -    NH2
   55 ASN  ( 113-) A  -    N
   60 CYS  ( 118-) A  -    N
   64 GLU  ( 122-) A  -    N
   67 LEU  ( 125-) A  -    N
   78 VAL  ( 136-) A  -    N
  116 PHE  ( 174-) A  -    N
  117 ARG  ( 175-) A  -    NH1
And so on for a total of    69 lines.
 
# 95 # 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.
 
   20 ASN  (  78-) A  -    OD1
  417 GLN  ( 485-) A  -    OE1
  519 ASP  ( 611-) A  -    OD2
  527 GLU  ( 619-) A  -    OE1
  740 HIS  ( 832-) A  -    ND1
  765 HIS  ( 857-) A  -    ND1
 
# 96 # 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: 1135
- of which buried: 557
Total number of acceptors: 1235
- of which buried: 457
Total number of donor+acceptors: 150
  (e.g. the Ser Ogamma that can donate and accept)
- of which buried: 30
Buried donors: 557
- without H-bond: 63
- essentially without H-bond: 2
- with only a very poor H-bond: 3
- with a poor H-bond: 6
- with a H-bond: 483
Buried acceptors: 457
- without H-bond: 98
- essentially without H-bond: 0
- with only a very poor H-bond: 4
- with a poor H-bond: 11
- with a H-bond: 344
 
# 97 # 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 (   52)    15 (   66) A Protein             /zata/tempdir/5mh...
     2    16 (   74)   400 (  458) A Protein             /zata/tempdir/5mh...
     3   401 (  469)   469 (  537) A Protein             /zata/tempdir/5mh...
     4   470 (  540)   499 (  569) A Protein             /zata/tempdir/5mh...
     5   500 (  592)   768 (  860) A Protein             /zata/tempdir/5mh...
     6   769 (    1)   769 (    1) B Sugar               /zata/tempdir/5mh...
     7   770 (    2)   770 (    2) B Sugar<-             /zata/tempdir/5mh...
     8   771 (  908)   771 (  908) A Sugar               /zata/tempdir/5mh...
     9   772 (    3)   772 (    3) B BMA  <-             /zata/tempdir/5mh...
    10   773 (    4)   773 (    4) B MAN                 /zata/tempdir/5mh...
    11   774 (    5)   774 (    5) B MAN                 /zata/tempdir/5mh...
    12   775 (    7)   775 (    7) B MAN                 /zata/tempdir/5mh...
    13   776 (    6)   776 (    6) B MAN                 /zata/tempdir/5mh...
    14   777 (  909)   777 (  909) A  ZN                 /zata/tempdir/5mh...
    15   778 (  910)   778 (  910) A  ZN                 /zata/tempdir/5mh...
    16   779 (  911)   779 (  911) A  CA                 /zata/tempdir/5mh...
    17   780 (  912)   780 (  912) A  MG                 /zata/tempdir/5mh...
    18   781 (  913)   781 (  913) A IOD                 /zata/tempdir/5mh...
    19   782 (  914)   782 (  914) A  CL                 /zata/tempdir/5mh...
    20   783 (  915)   783 (  915) A  CL                 /zata/tempdir/5mh...
    21   784 (  916)   784 (  916) A  CL                 /zata/tempdir/5mh...
    22   785 (  917)   785 (  917) A SCN                 /zata/tempdir/5mh...
    23   786 (  918)   786 (  918) A PO4                 /zata/tempdir/5mh...
    24   787 (  919)   787 (  919) A PO4                 /zata/tempdir/5mh...
    25   788 (  920)   788 (  920) A 7NB                 /zata/tempdir/5mh...
    26   789 ( HOH )   789 ( HOH ) A water   (    1)     /zata/tempdir/5mh...
 
# 98 # 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  :   2.430
  1st generation packing quality :  -1.054 (          (  -0.3,  2.5))
  2nd generation packing quality :  -2.184 (          (  -1.4,  1.2))
  Ramachandran plot appearance   :  -2.262 (          (  -2.4,  1.5))
  chi-1/chi-2 rotamer normality  :  -2.224 (          (  -4.2,  1.7))
  Backbone conformation          :  -0.812 (          (  -0.7,  3.6))
  Inside/Outside distribution    :   1.060
 
 RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.345 (tight)
  Bond angles                    :   0.606 (tight)
  Omega angle restraints         :   1.105
  Side chain planarity           :   0.621 (tight)
  Improper dihedral distribution :   0.427
  B-factor distribution          :   0.749
 
# 99 # 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.
 
# 100 # 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.
 
# 101 # Error: Bumps in your structure
Upon analysing the bumps in your structure, WHAT CHECK got very, very
worried. Sometimes this means that you have forgotten to lower the
occupancy of overlapping ligands, residues, or water molecules. But,
whatever is the origin of this problem, you have to analyse it and
fix it.
 
# 102 # Note: Bond length variabilty Z-score low
With a resolution of 1.5-2.5 Angstrom, you might have enough data to warrant
more bond length variability that we observed (less than 0.5). If your
resolution is close to 1.5 Angstrom, you can consider allowing the refinement
software more freedom when it comes to applying the bond length target
restraints. If your resolution is close to 2.5 Angstrom, you can do this too,
but you might want to be a bit careful.
 
# 103 # 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.
 
# 104 # 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.
 
  769 NAG  (   1-) B  -     91.09
  457 ASN  ( 525-) A  -     57.25
  770 NAG  (   2-) B  -     33.84
  187 ARG  ( 245-) A  -     15.82
  263 PHE  ( 321-) A  -     15.07
   41 ARG  (  99-) A  -     14.44
  483 TYR  ( 553-) A  -     14.31
  515 ARG  ( 607-) A  -     13.68
  105 ARG  ( 163-) A  -     13.67
   25 TYR  (  83-) A  -     12.84
  470 PHE  ( 540-) A  -     12.78
  767 TYR  ( 859-) A  -     12.50
   95 LYS  ( 153-) A  -     12.26
  480 ARG  ( 550-) A  -     12.23
  471 ARG  ( 541-) A  -     11.72
And so on for a total of    81 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.
