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

Date : 2024-10-22
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/2g75/wctemp_besttls/2g75_besttls.pd====
=========================================
 
# 1 # Note: Introduction
WHAT CHECK needs to read a PDB file before it can check it. It does a
series of checks upon reading the file. The results of these checks are
reported in this section (section 2.1). The rest of the report will be more
systematic in that section 2.2 reports on administrative problems. Section
2.3 gives descriptive output that is not directly validating things but
more telling you how WHAT CHECK interpreted the input file. Section 2.4
looks at B-factors, occupancies, and the presence/absence of (spurious)
atoms. Section 2.5 deals with nomenclature problems. Section 2.6 deals with
geometric problems like bond lengths and bond angles. Section 2.7 deals with
torsion angle issues. Section 2.8 looks at atomic clashes. Section 2.9 deals
with packing, accessibility, etc, issues. Section 2.10 deals with hydrogen
bonds, ion packing, and other things that can be summarized under the common
name charge-charge interactions. Section 2.11 gives a summary of whole report
and tells you (if applicable) which symmetry matrices were used. Section 2.12
tells the crystallographer which are the things most in need of manual
correction. And the last section, section 2.13, lists all residues sorted
by their need for visual inspection in light of the electron density.
WARNING. Date error on HEADER card:
HEADER                                                        2G75
ATOM  *****  O   HOH A 242     -10.651 -33.196  20.100  1.00 45.77       242 O
ATOM  *****  O   HOH A 243     -10.548 -26.509   8.097  1.00 42.14       243 O
ATOM  *****  O   HOH A 244     -20.706 -23.190   9.363  1.00 49.77       244 O
ATOM  *****  O   HOH A 245     -17.882  -7.992  10.497  1.00 42.72       245 O
ATOM  *****  O   HOH A 246     -25.464 -19.014  11.754  1.00 47.66       246 O
ATOM  *****  O   HOH A 247     -21.020 -34.735  16.031  1.00 49.60       247 O
ATOM  *****  O   HOH A 248     -13.266 -38.720  16.948  1.00 61.94       248 O
ATOM  *****  O   HOH A 249     -17.367 -35.028  20.303  1.00 48.65       249 O
ATOM  *****  O   HOH A 250      -7.894 -11.102  21.878  1.00 47.04       250 O
ATOM  *****  O   HOH A 251     -10.196 -16.140  31.046  1.00 67.36       251 O
ATOM  *****  O   HOH A 252     -28.247 -23.889  18.818  1.00 61.36       252 O
ATOM  *****  O   HOH A 253     -28.970 -31.434  14.597  1.00 57.85       253 O
ATOM  *****  O   HOH A 254     -25.788   5.658  13.624  1.00 63.95       254 O
ATOM  *****  O   HOH A 255     -22.754   7.015  -1.189  1.00 39.11       255 O
ATOM  *****  O   HOH A 256     -19.520  10.731  -3.485  1.00 56.45       256 O
ATOM  *****  O   HOH A 257       1.021  13.617  -7.725  1.00 52.32       257 O
ATOM  *****  O   HOH A 258      11.696   9.558 -13.626  1.00 50.93       258 O
ATOM  *****  O   HOH A 259     -15.178  11.082  10.153  1.00 58.62       259 O
ATOM  *****  O   HOH A 260     -10.450   9.819   6.123  1.00 57.49       260 O
ATOM  *****  O   HOH A 261     -14.922  -1.617  -7.740  1.00 48.84       261 O
ATOM  *****  O   HOH A 262      -7.738  -1.476 -11.702  1.00 34.49       262 O
ATOM  *****  O   HOH A 263      -6.775  -2.570  -9.307  1.00 47.38       263 O
ATOM  *****  O   HOH A 264      -2.157  -1.915 -16.649  1.00 49.57       264 O
ATOM  *****  O   HOH A 265      -0.936  -5.396 -16.528  1.00 52.84       265 O
ATOM  *****  O   HOH A 266      -8.439  12.493 -15.513  1.00 48.89       266 O
ATOM  *****  O   HOH A 267      -7.968  14.622 -20.552  1.00 49.02       267 O
ATOM  *****  O   HOH A 268     -11.654  -5.326  19.002  1.00 37.66       268 O
ATOM  *****  O   HOH A 269     -29.170 -10.648  17.279  1.00 47.98       269 O
ATOM  *****  O   HOH A 270      -4.364  -9.450  13.400  1.00 52.14       270 O
ATOM  *****  O   HOH A 271       0.446  -8.193  14.296  1.00 49.30       271 O
ATOM  *****  O   HOH A 272     -24.135 -17.209  31.417  1.00 51.82       272 O
ATOM  *****  O   HOH A 273     -30.324 -19.450  17.411  1.00 46.82       273 O
ATOM  *****  O   HOH A 274     -18.807  -0.651  23.526  1.00 54.53       274 O
ATOM  *****  O   HOH A 275     -15.792   2.472  22.264  1.00 47.57       275 O
ATOM  *****  O   HOH A 276     -18.856   3.332  19.922  1.00 61.79       276 O
ATOM  *****  O   HOH A 277     -14.801  -1.281  16.639  1.00 53.03       277 O
ATOM  *****  O   HOH A 278      -8.740 -22.889   7.408  1.00 48.78       278 O
ATOM  *****  O   HOH A 279     -11.970 -14.490   8.216  1.00 38.71       279 O
ATOM  *****  O   HOH A 280     -16.690 -13.263   8.004  1.00 44.09       280 O
ATOM  *****  O   HOH A 281     -17.158  13.702   4.575  1.00 37.74       281 O
ATOM  *****  O   HOH A 282     -15.730  12.698   8.591  1.00 38.61       282 O
ATOM  *****  O   HOH A 283      -5.563   3.980 -19.293  1.00 48.32       283 O
ATOM  *****  O   HOH A 284     -29.238   3.142  14.059  1.00 44.83       284 O
ATOM  *****  O   HOH A 285     -29.736   1.753  12.393  1.00 50.61       285 O
ATOM  *****  O   HOH A 286     -23.417 -23.665  28.974  1.00 51.26       286 O
ATOM  *****  O   HOH A 287     -24.205 -15.768  25.473  1.00 43.22       287 O
ATOM  *****  O   HOH A 288     -22.740   9.093   2.087  1.00 55.71       288 O
ATOM  *****  O   HOH A 289     -21.642   3.389 -11.779  1.00 56.55       289 O
ATOM  *****  O   HOH A 290      -8.095  21.645 -11.036  1.00 72.49       290 O
ATOM  *****  O   HOH B 215      11.934   0.977  -3.216  1.00 57.99       215 O
ATOM  *****  O   HOH B 216      11.836  -8.359  18.895  1.00 49.64       216 O
ATOM  *****  O   HOH B 217      -1.676 -18.849   7.680  1.00 34.46       217 O
ATOM  *****  O   HOH B 218      -1.466 -14.489  21.919  1.00 47.64       218 O
ATOM  *****  O   HOH B 219      -1.149 -28.291  10.410  1.00 42.46       219 O
ATOM  *****  O   HOH B 220      -5.107 -24.383   9.583  1.00 61.04       220 O
ATOM  *****  O   HOH B 221       6.850  16.396  -5.363  1.00 45.94       221 O
ATOM  *****  O   HOH B 222       1.289  -2.327  -9.359  1.00 68.44       222 O
ATOM  *****  O   HOH B 223      -0.406  -1.098   2.417  1.00 48.19       223 O
ATOM  *****  O   HOH B 224      20.845 -16.031  11.229  1.00 52.31       224 O
ATOM  *****  O   HOH B 225      17.113 -16.231  14.687  1.00 37.61       225 O
ATOM  *****  O   HOH B 226      14.616 -16.207  19.027  1.00 53.21       226 O
ATOM  *****  O   HOH B 227       3.609 -16.674   2.350  1.00 61.56       227 O
ATOM  *****  O   HOH B 228      -2.205 -11.994   9.752  1.00 66.43       228 O
ATOM  *****  O   HOH B 229       4.140 -34.640   6.237  1.00 55.11       229 O
ATOM  *****  O   HOH B 230       1.074  -9.963  16.440  1.00 54.65       230 O
ATOM  *****  O   HOH B 231       5.212  -9.498  17.749  1.00 49.70       231 O
ATOM  *****  O   HOH B 232      11.361  -9.881   0.661  1.00 36.82       232 O
ATOM  *****  O   HOH B 233       4.001   7.448  -2.350  1.00 48.49       233 O
ATOM  *****  O   HOH B 234       9.280  -5.894   7.682  1.00 50.60       234 O
ATOM  *****  O   HOH B 235       3.179   6.137  12.703  1.00 54.15       235 O
ATOM  *****  O   HOH B 236      -8.990  10.793  14.328  1.00 79.58       236 O
ATOM  *****  O   HOH B 237      -1.134   0.308   5.275  1.00 45.33       237 O
ATOM  *****  O   HOH B 238      -3.733  -0.347  10.115  1.00 40.40       238 O
ATOM  *****  O   HOH B 239       0.048  -7.473   3.877  1.00 53.75       239 O
ATOM  *****  O   HOH B 240       5.734  -5.969   1.896  1.00 58.10       240 O
ATOM  *****  O   HOH B 241       6.643  -8.483  -7.522  1.00 53.51       241 O
ATOM  *****  O   HOH B 242       9.862  -9.668  -6.325  1.00 46.10       242 O
ATOM  *****  O   HOH B 243      11.183  -9.348  -3.851  1.00 51.36       243 O
ATOM  *****  O   HOH B 244      16.070  10.740  10.820  1.00 45.43       244 O
ATOM  *****  O   HOH B 245      -7.943 -19.024  29.838  1.00 52.62       245 O
ATOM  *****  O   HOH B 246      -9.919 -14.042   7.821  1.00 55.42       246 O
ATOM  *****  O   HOH B 247      -9.212 -12.163   8.523  1.00 45.28       247 O
ATOM  *****  O   HOH B 248      14.571  -8.603  14.208  1.00 67.12       248 O
ATOM  *****  O   HOH B 249       7.285  -5.553  16.278  1.00 58.06       249 O
ATOM  *****  O   HOH B 250      10.180  -4.333  17.114  1.00 50.16       250 O
ATOM  *****  O   HOH B 251      20.429 -12.250   9.015  1.00 51.23       251 O
ATOM  *****  O   HOH B 252       1.543 -15.028   2.100  1.00 57.19       252 O
ATOM  *****  O   HOH B 253      -4.414 -13.423   8.857  1.00 48.81       253 O
ATOM  *****  O   HOH B 254      19.418  -8.482  -0.311  1.00 46.23       254 O
ATOM  *****  O   HOH B 255      19.875  -7.343   2.143  1.00 46.92       255 O
ATOM  *****  O   HOH B 256      15.258   4.489   4.462  1.00 33.31       256 O
ATOM  *****  O   HOH B 257       8.370  10.719  11.631  1.00 47.00       257 O
ATOM  *****  O   HOH C 242     -58.656  -7.992  28.635  1.00 47.17       242 O
ATOM  *****  O   HOH C 243     -28.827  -8.704  27.323  1.00 42.67       243 O
ATOM  *****  O   HOH C 244     -41.366 -16.021  31.856  1.00 39.30       244 O
ATOM  *****  O   HOH C 245     -54.040 -15.525  47.290  1.00 42.82       245 O
ATOM  *****  O   HOH C 246     -56.385 -15.830  35.448  1.00 65.35       246 O
ATOM  *****  O   HOH C 247     -61.200 -11.149  33.881  1.00 59.86       247 O
ATOM  *****  O   HOH C 248     -55.893 -12.566  31.000  1.00 50.75       248 O
ATOM  *****  O   HOH C 249     -40.515   8.532  30.728  1.00 46.32       249 O
ATOM  *****  O   HOH C 250     -38.763   7.515  38.237  1.00 40.90       250 O
ATOM  *****  O   HOH C 251     -39.467  10.436  38.327  1.00 57.48       251 O
ATOM  *****  O   HOH C 252     -42.013  12.739  37.228  1.00 37.36       252 O
ATOM  *****  O   HOH C 253     -43.139   3.579  20.373  1.00 70.46       253 O
ATOM  *****  O   HOH C 254     -35.564   1.260  22.918  1.00 58.39       254 O
ATOM  *****  O   HOH C 255     -55.089   3.480  40.386  1.00 49.93       255 O
ATOM  *****  O   HOH C 256     -16.634  -0.564  38.063  1.00 67.75       256 O
ATOM  *****  O   HOH C 257     -16.580   4.006  52.480  1.00 43.26       257 O
ATOM  *****  O   HOH C 258     -14.549   5.240  49.764  1.00 60.79       258 O
ATOM  *****  O   HOH C 259     -16.123   8.645  55.227  1.00 48.70       259 O
ATOM  *****  O   HOH C 260     -23.158  28.208  58.435  1.00 42.00       260 O
ATOM  *****  O   HOH C 261     -21.857  34.528  58.132  1.00 52.88       261 O
ATOM  *****  O   HOH C 262     -28.264  33.192  56.958  1.00 47.67       262 O
ATOM  *****  O   HOH C 263     -17.643  11.476  42.033  1.00 48.82       263 O
ATOM  *****  O   HOH C 264     -20.216  15.012  45.401  1.00 59.51       264 O
ATOM  *****  O   HOH C 265     -30.201   7.655  48.799  1.00 45.16       265 O
ATOM  *****  O   HOH C 266     -28.707  16.000  70.317  1.00 50.21       266 O
ATOM  *****  O   HOH C 267     -34.522  18.365  68.419  1.00 48.67       267 O
ATOM  *****  O   HOH C 268     -35.430  15.076  55.414  1.00 27.38       268 O
ATOM  *****  O   HOH C 269     -24.211  14.941  72.913  1.00 51.01       269 O
ATOM  *****  O   HOH C 270     -19.919   3.927  62.791  1.00 50.35       270 O
ATOM  *****  O   HOH C 271     -14.779  14.912  62.209  1.00 33.64       271 O
ATOM  *****  O   HOH C 272     -43.912 -12.471  23.687  1.00 64.02       272 O
ATOM  *****  O   HOH C 273     -33.896  -8.245  42.678  1.00 51.09       273 O
ATOM  *****  O   HOH C 274     -59.744  -5.766  28.077  1.00 65.91       274 O
ATOM  *****  O   HOH C 275     -49.331   0.252  43.813  1.00 59.71       275 O
ATOM  *****  O   HOH C 276     -43.670   4.748  42.789  1.00 38.39       276 O
ATOM  *****  O   HOH C 277     -39.527   1.763  44.198  1.00 46.92       277 O
ATOM  *****  O   HOH C 278     -19.177   6.038  34.308  1.00 51.82       278 O
ATOM  *****  O   HOH C 279     -22.662   4.133  32.152  1.00 50.21       279 O
ATOM  *****  O   HOH C 280     -16.948   1.609  52.741  1.00 36.69       280 O
ATOM  *****  O   HOH C 281     -18.146  16.625  44.222  1.00 45.70       281 O
ATOM  *****  O   HOH C 282     -17.378  14.159  41.998  1.00 45.82       282 O
ATOM  *****  O   HOH C 283     -36.944  18.350  60.287  1.00 40.96       283 O
ATOM  *****  O   HOH C 284     -24.954  23.235  75.070  1.00 46.76       284 O
ATOM  *****  O   HOH D 215     -29.771  27.412  53.729  1.00 42.45       215 O
ATOM  *****  O   HOH D 216     -45.755  11.489  29.437  1.00 47.63       216 O
ATOM  *****  O   HOH D 217     -38.803  31.578  55.180  1.00 41.32       217 O
ATOM  *****  O   HOH D 218     -38.948  30.989  40.958  1.00 33.85       218 O
ATOM  *****  O   HOH D 219     -17.195  34.814  42.866  1.00 38.42       219 O
ATOM  *****  O   HOH D 220     -43.704  15.968  34.915  1.00 65.09       220 O
ATOM  *****  O   HOH D 221     -44.957  18.296  33.749  1.00 62.18       221 O
ATOM  *****  O   HOH D 222     -42.800  11.323  42.089  1.00 68.57       222 O
ATOM  *****  O   HOH D 223     -42.839   9.241  41.623  1.00 50.51       223 O
ATOM  *****  O   HOH D 224     -52.842   3.238  41.454  1.00 44.19       224 O
ATOM  *****  O   HOH D 225     -24.345  34.438  55.991  1.00 69.59       225 O
ATOM  *****  O   HOH D 226     -35.127  18.975  49.350  1.00 49.11       226 O
ATOM  *****  O   HOH D 227     -48.263  26.341  32.515  1.00 62.01       227 O
ATOM  *****  O   HOH D 228     -48.933  27.339  36.997  1.00 63.10       228 O
ATOM  *****  O   HOH D 229     -56.163  30.260  42.577  1.00 56.52       229 O
ATOM  *****  O   HOH D 230     -55.585  24.666  32.387  1.00 53.18       230 O
ATOM  *****  O   HOH D 231     -50.328  15.507  48.774  1.00 53.98       231 O
ATOM  *****  O   HOH D 232     -66.477   5.572  45.509  1.00 61.53       232 O
ATOM  *****  O   HOH D 233     -66.961  24.864  40.671  1.00 57.15       233 O
ATOM  *****  O   HOH D 234     -10.354  18.705  58.842  1.00 46.70       234 O
ATOM  *****  O   HOH D 235     -44.746  25.341  42.819  1.00 49.27       235 O
ATOM  *****  O   HOH D 236     -36.818  31.238  39.198  1.00 46.94       236 O
ATOM  *****  O   HOH D 237     -33.546  16.050  42.824  1.00 55.39       237 O
ATOM  *****  O   HOH D 238     -33.956  18.827  46.651  1.00 41.54       238 O
ATOM  *****  O   HOH D 239     -43.768  20.975  49.568  1.00 53.78       239 O
ATOM  *****  O   HOH D 240     -46.365  21.498  49.050  1.00 51.97       240 O
ATOM  *****  O   HOH D 241     -57.205  -3.203  26.421  1.00 50.98       241 O
ATOM  *****  O   HOH D 242     -41.731   6.275  43.900  1.00 63.53       242 O
ATOM  *****  O   HOH D 243     -38.063  22.022  58.820  1.00 48.19       243 O
ATOM  *****  O   HOH D 244     -66.307  24.098  34.307  1.00 55.38       244 O
ATOM  *****  O   HOH D 245     -48.643  13.563  50.808  1.00 54.94       245 O
ATOM  *****  O   HOH D 246     -30.671  25.966  38.075  1.00 54.36       246 O
ATOM  *****  O   HOH D 247     -15.399  25.402  37.303  1.00 45.10       247 O
ATOM  *****  O   HOH D 248     -12.358  28.695  37.578  1.00 56.45       248 O
ATOM  *****  O   HOH D 249     -28.170  19.319  37.851  1.00 45.97       249 O
ATOM  *****  O   HOH D 250     -29.481  33.416  40.848  1.00 58.34       250 O
ATOM  *****  O   HOH D 251      -8.009  30.460  54.838  1.00 54.65       251 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.
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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:
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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:
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:
 
# 2 # Note: Header records from PDB file
Header records from PDB file.
 
HEADER                                                        2G75
 
# 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
  0.014479  0.008359  0.000000
  0.000000  0.016719  0.000000
  0.000000  0.000000  0.006000
 
# 5 # Note: Non crystallographic symmetry RMS plot
The plot shows the RMS differences between two similar chains on a residue-
by-residue basis. Individual "spikes" can be indicative of interesting or
wrong residues. If all residues show a high RMS value, the structure could
be incorrectly refined.
 
In the TeX file, a plot has been inserted here
 
Chain identifiers of the two chains: A and C
 
 All-atom RMS fit for the two chains : 0.401
 CA-only RMS fit for the two chains : 0.124
 
# 6 # Note: Non crystallographic symmetry backbone difference plot
The plot shows the differences in backbone torsion angles between two
similar chains on a residue-by-residue basis. Individual "spikes" can be
indicative of interesting or wrong residues. If all residues show high
differences, the structure could be incorrectly refined.
 
In the TeX file, a plot has been inserted here
 
Chain identifiers of the two chains: A and C
 
# 7 # Note: Non crystallographic symmetry RMS plot
The plot shows the RMS differences between two similar chains on a residue-
by-residue basis. Individual "spikes" can be indicative of interesting or
wrong residues. If all residues show a high RMS value, the structure could
be incorrectly refined.
 
In the TeX file, a plot has been inserted here
 
Chain identifiers of the two chains: B and D
 
 All-atom RMS fit for the two chains : 0.513
 CA-only RMS fit for the two chains : 0.097
 
# 8 # Note: Non crystallographic symmetry backbone difference plot
The plot shows the differences in backbone torsion angles between two
similar chains on a residue-by-residue basis. Individual "spikes" can be
indicative of interesting or wrong residues. If all residues show high
differences, the structure could be incorrectly refined.
 
In the TeX file, a plot has been inserted here
 
Chain identifiers of the two chains: B and D
 
# 9 # 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 31
 Number of matrices in space group: 3
 Highest polymer chain multiplicity in structure: 2
 Highest polymer chain multiplicity according to SEQRES: 2
 No explicit MTRIX NCS matrices found in the input file
 Value of Z as found on the CRYST1 card: 0
 Z, symmetry, and molecular multiplicity disagree
 Could it be that Z must be: 6
 
# 10 # Error: Matthews Coefficient (Vm) very high
 
The Matthews coefficient [REF] is defined as the density of the protein
structure in cubic Angstroms per Dalton. Normal values are between 1.5
(tightly packed, little room for solvent) and 4.0 (loosely packed, much
space for solvent). Some very loosely packed structures can get values a bit
higher than that.
 
Numbers this high are almost always caused by giving the wrong value for Z
on the CRYST1 card (or not giving this number at all).
 
 Molecular weight of all polymer chains: 90715.477
 Volume of the Unit Cell V= 688462.500
 Space group multiplicity: 3
 No NCS symmetry matrices (MTRIX records) found in PDB file
 Matthews coefficient for observed atoms and Z is high: Vm= 15.179
 No Matthews coefficient given in REMARK 280
 Or should we use the previously suggested Z = 6
 which would result in Vm= 2.530
 And remember, a matrix counting problem has been reported earlier already
 
# 11 # Note: Z missing on CRYST1 card
The messages above seem likely caused by the fact that Z is missing from the
CRYST1 card.
 
# 12 # 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.
 
# 13 # 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.
 
# 14 # Note: No strange inter-chain connections detected
No covalent bonds have been detected between molecules with non-identical
chain identifiers.
 
# 15 # Note: No duplicate atom names in ligands
All atom names in ligands (if any) seem adequately unique.
 
# 16 # Note: In all cases the primary alternate atom was used
WHAT CHECK saw no need to make any alternate atom corrections (which means
they either are all correct, or there are none).
 
# 17 # Note: No residues detected inside ligands
Either this structure does not contain ligands with amino acid groups inside
it, or their naming is proper (enough).
 
# 18 # Note: No attached groups interfere with hydrogen bond calculations
It seems there are no sugars, lipids, etc., bound (or very close) to atoms
that otherwise could form hydrogen bonds.
 
# 19 # Note: No probable side chain atoms with zero occupancy detected.
Either there are no side chain atoms with zero occupancy, or the side chain
atoms with zero occupancy were not present in the input PDB file (in which
case they are listed as missing atoms), or their positions are sufficiently
improbable to warrant a zero occupancy.
 
# 20 # Note: No probable backbone atoms with zero occupancy detected.
Either there are no backbone atoms with zero occupancy, or the backbone
atoms with zero occupancy were left out of the input PDB file (in
which case they are listed as missing atoms), or their positions are
sufficiently improbable to warrant a zero occupancy.
 
# 21 # Note: All residues have a complete backbone.
No residues have missing backbone atoms.
 
# 22 # Note: No C-alpha only residues
There are no residues that consist of only an alpha carbon atom.
 
# 23 # Note: Content of the PDB file as interpreted by WHAT CHECK
Content of the PDB file as interpreted by WHAT CHECK.
WHAT CHECK has read your PDB file, and stored it internally in what is called
'the soup'. The content of this soup is listed here. An extensive explanation
of all frequently used WHAT CHECK output formats can be found at
swift.cmbi.ru.nl. Look under output formats. A course on reading this
'Molecules' table is part of the WHAT CHECK website.
 
     1     1 (    2)   218 (  214) A Protein             To check
     2   219 (    2)   429 (  211) B Protein             To check
     3   430 (    2)   647 (  214) C Protein             To check
     4   648 (    2)   858 (  211) D Protein             To check
     5   859 ( HOH )   859 ( HOH ) A water   (    1)     To check
     6   860 ( HOH )   860 ( HOH ) B water   (    1)     To check
     7   861 ( HOH )   861 ( HOH ) C water   (    1)     To check
     8   862 ( HOH )   862 ( HOH ) D water   (    1)     To check
MODELs skipped upon reading PDB file: 0
X-ray structure. No MODELs found
The total number of amino acids found is 858
 of which one has poor or (essentially) missing atoms')
 
No nucleic acids observed in input file
No sugars recognized in input file
Number of water molecules: 4
Residue numbers increase monotonously OK
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
 
# 24 # 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
 
# 25 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 26 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: C
 
# 27 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 28 # Note: Secondary structure
This is the secondary structure according to DSSP. Only helix (H), overwound
or 3/10-helix (3), strand (S), turn (T) and coil (blank) are shown [REF].
All DSSP related information can be found at swift.cmbi.ru.nl/gv/dssp/
This is not really a structure validation option, but a very scattered
secondary structure (i.e. many strands of only a few residues length, many
Ts inside helices, etc) tends to indicate a poor structure. A full
explanation of the DSSP secondary structure determination program together
with a series of examples can be found at the WHAT CHECK website [REF].
 
Secondary structure assignment
                     10        20        30        40        50        60
                      |         |         |         |         |         |
    1 -   60 VQLQQSGAEVKKPGSSVKVSCKASGGTFSSYTISWVRQAPGQGLEWMGGITPILGIANYA
(   2)-(  60)
                     70        80        90       100       110       120
                      |         |         |         |         |         |
   61 -  120 QKFQGRVTITTDESTSTAYMELSSLRSEDTAVYYCARDTVMGGMDVWGQGTTVTVSSAST
(  61)-( 116)
                    130       140       150       160       170       180
                      |         |         |         |         |         |
  121 -  180 KGPSVFPLAPSSKSTSGGTSALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLY
( 117)-( 176)
                    190       200       210
                      |         |         |
  181 -  218 SLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK
( 177)-( 214)
            220       230       240       250       260       270
              |         |         |         |         |         |
  219 -  278 SYELTQPPSVSVAPGKTARITCGGNNIGSKSVHWYQQKPGQAPVLVVYDDSDRPSGIPER
(   2)-(  61)
            280       290       300       310       320       330
              |         |         |         |         |         |
  279 -  338 FSGSNSGNTATLTISRVEAGDEADYYCQVWDSSSDYVFGTGTKVTVLGQPKANPTVTLFP
(  62)-( 120)
            340       350       360       370       380       390
              |         |         |         |         |         |
  339 -  398 PSSEEFQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLS
( 121)-( 180)
            400       410       420
              |         |         |
  399 -  429 LTPEQWKSHRSYSCQVTHEGSTVEKTVAPTE
( 181)-( 211)
           430       440       450       460       470       480
             |         |         |         |         |         |
  430 -  489 VQLQQSGAEVKKPGSSVKVSCKASGGTFSSYTISWVRQAPGQGLEWMGGITPILGIANYA
(   2)-(  60)
           490       500       510       520       530       540
             |         |         |         |         |         |
  490 -  549 QKFQGRVTITTDESTSTAYMELSSLRSEDTAVYYCARDTVMGGMDVWGQGTTVTVSSAST
(  61)-( 116)
           550       560       570       580       590       600
             |         |         |         |         |         |
  550 -  609 KGPSVFPLAPSSKSTSGGTSALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLY
( 117)-( 176)
           610       620       630       640
             |         |         |         |
  610 -  647 SLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK
( 177)-( 214)
             650       660       670       680       690       700
               |         |         |         |         |         |
  648 -  707 SYELTQPPSVSVAPGKTARITCGGNNIGSKSVHWYQQKPGQAPVLVVYDDSDRPSGIPER
(   2)-(  61)
             710       720       730       740       750       760
               |         |         |         |         |         |
  708 -  767 FSGSNSGNTATLTISRVEAGDEADYYCQVWDSSSDYVFGTGTKVTVLGQPKANPTVTLFP
(  62)-( 120)
             770       780       790       800       810       820
               |         |         |         |         |         |
  768 -  827 PSSEEFQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLS
( 121)-( 180)
             830       840       850
               |         |         |
  828 -  858 LTPEQWKSHRSYSCQVTHEGSTVEKTVAPTE
( 181)-( 211)
 
 
 
 
# 29 # Note: No rounded coordinates detected
No significant rounding of atom coordinates has been detected.
 
# 30 # Note: No artificial side chains detected
No artificial side-chain positions characterized by chi-1=0.0 or chi-1=180.0
have been detected.
 
# 31 # 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.
 
# 32 # 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.
 
  562 LYS  ( 129-) C  -   High
 
# 33 # 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.
 
  218 LYS  ( 214-) A  -        OK
  429 GLU  ( 211-) B  -        OK
  647 LYS  ( 214-) C  -        OK
  858 GLU  ( 211-) D  -        OK
 
# 34 # Note: Weights administratively correct
All atomic occupancy factors ('weights') fall in the 0.0--1.0 range, which
makes them administratively correct.
 
# 35 # 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.
 
# 36 # 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.
 
# 37 # 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
 
# 38 # 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
 
# 39 # 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 :  0.671 over    5678 bonds
Average difference in B over a bond :    1.85
RMS difference in B over a bond :    2.43
 
# 40 # 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
 
# 41 # Note: B-factor plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 42 # Note: B-factor plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: C
 
# 43 # Note: B-factor plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 44 # Note: Introduction to the nomenclature section.
Nomenclature problems seem, at first, rather unimportant. After all who
cares if we call the delta atoms in leucine delta2 and delta1 rather than
the other way around. Chemically speaking that is correct. But structures
have not been solved and deposited just for chemists to look at them. Most
times a structure is used, it is by software in a bioinformatics lab. And
if they compare structures in which the one used C delta1 and delta2 and the
other uses C delta2 and delta1, then that comparison will fail. Also, we
recalculate all structures every so many years to make sure that everybody
always can get access to the best coordinates that can be obtained from
the (your?) experimental data. These recalculations will be troublesome if
there are nomenclature problems.
 
Several nomenclature problems actually are worse than that. At the
WHAT CHECK website [REF] you can get an overview of the importance of all
nomenclature problems that we list.
 
# 45 # Note: Valine nomenclature OK
No errors were detected in valine nomenclature.
 
# 46 # Note: Threonine nomenclature OK
No errors were detected in threonine nomenclature.
 
# 47 # Note: Isoleucine nomenclature OK
No errors were detected in isoleucine nomenclature.
 
# 48 # Note: Leucine nomenclature OK
No errors were detected in leucine nomenclature.
 
# 49 # Note: Arginine nomenclature OK
No errors were detected in arginine nomenclature.
 
# 50 # Warning: Tyrosine convention problem
The tyrosine residues listed in the table below have their chi-2 not between
-90.0 and 90.0
 
  303 TYR  (  86-) B  -
  314 TYR  (  96-) B  -
  359 TYR  ( 141-) B  -
  396 TYR  ( 178-) B  -
  732 TYR  (  86-) D  -
  743 TYR  (  96-) D  -
  788 TYR  ( 141-) D  -
  825 TYR  ( 178-) D  -
 
# 51 # Warning: Phenylalanine convention problem
The phenylalanine residues listed in the table below have their chi-2 not
between -90.0 and 90.0.
 
  150 PHE  ( 146-) A  -
  358 PHE  ( 140-) B  -
  579 PHE  ( 146-) C  -
  766 PHE  ( 119-) D  -
 
# 52 # Note: Aspartic acid torsion conventions OK
No errors were detected in aspartic acid torsion angle conventions.
 
# 53 # Note: Glutamic acid torsion conventions OK
No errors were detected in glutamic acid torsion angle conventions.
 
# 54 # Note: Phosphate group names OK in DNA/RNA
No errors were detected in nucleic acid phosphate group naming conventions
(or this structure contains no nucleic acids).
 
# 55 # Note: Heavy atom naming OK
No errors were detected in the atom names for non-hydrogen atoms. Please
be aware that the PDB wants us to deliberately make some nomenclature errors;
especially in non-canonical amino acids.
 
# 56 # Note: No decreasing residue numbers
All residue numbers are strictly increasing within each chain.
 
# 57 # Warning: Unusual bond lengths
The bond lengths listed in the table below were found to deviate more than 4
sigma from standard bond lengths (both standard values and sigmas for amino
acid residues have been taken from Engh and Huber [REF], for DNA they were
taken from Parkinson et al [REF]). In the table below for each unusual bond
the bond length and the number of standard deviations it differs from the
normal value is given.
 
Atom names starting with "-" belong to the previous residue in the chain. If
the second atom name is "-SG*", the disulphide bridge has a deviating length.
 
   56 ILE  (  56-) A  -    CG1  CD1   1.68    4.2
  199 ILE  ( 195-) A  -    CG1  CD1   1.31   -5.3
  275 ILE  (  58-) B  -    CG1  CD1   1.73    5.7
  292 ILE  (  75-) B  -    CG1  CD1   1.69    4.5
  485 ILE  (  56-) C  -    CG1  CD1   1.71    5.1
  628 ILE  ( 195-) C  -    CG1  CD1   1.31   -5.3
  704 ILE  (  58-) D  -    CG1  CD1   1.74    5.9
  783 LEU  ( 136-) D  -    CG   CD1   1.39   -4.0
 
# 58 # 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: 0.680
 RMS-deviation in bond distances: 0.018
 
# 59 # Warning: Possible cell scaling problem
Comparison of bond distances with Engh and Huber [REF] standard values for
protein residues and Parkinson et al [REF] values for DNA/RNA shows a
significant systematic deviation. It could be that the unit cell used in
refinement was not accurate enough. The deformation matrix given below gives
the deviations found: the three numbers on the diagonal represent the
relative corrections needed along the A, B and C cell axis. These values are
1.000 in a normal case, but have significant deviations here (significant at
the 99.99 percent confidence level)
 
There are a number of different possible causes for the discrepancy. First
the cell used in refinement can be different from the best cell calculated.
Second, the value of the wavelength used for a synchrotron data set can be
miscalibrated. Finally, the discrepancy can be caused by a dataset that has
not been corrected for significant anisotropic thermal motion.
 
Please note that the proposed scale matrix has NOT been restrained to obey
the space group symmetry. This is done on purpose. The distortions can give
you an indication of the accuracy of the determination.
 
If you intend to use the result of this check to change the cell dimension
of your crystal, please read the extensive literature on this topic first.
This check depends on the wavelength, the cell dimensions, and on the
standard bond lengths and bond angles used by your refinement software.
 
SCALE matrix obtained from PDB file
  0.014479  0.008359  0.000000
  0.000000  0.016719  0.000000
  0.000000  0.000000  0.006000
Unit Cell deformation matrix
  1.001577 -0.000768 -0.000699
 -0.000768  1.000640  0.000346
 -0.000699  0.000346  1.002093
Proposed new scale matrix
  0.014463  0.008365  0.000007
  0.000013  0.016708 -0.000006
  0.000004 -0.000002  0.005988
With corresponding cell
    A    =  69.175  B   =  69.172  C    = 167.005
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000
 
The CRYST1 cell dimensions
    A    =  69.066  B   =  69.066  C    = 166.656
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000
 
 Variance: 69.849
 (Under-)estimated Z-score: 6.160
 
# 60 # Warning: Unusual bond angles
The bond angles listed in the table below were found to deviate more than 4
sigma from standard bond angles (both standard values and sigma for protein
residues have been taken from Engh and Huber [REF], for DNA/RNA from
Parkinson et al [REF]). In the table below for each strange angle the bond
angle and the number of standard deviations it differs from the standard
values is given. Please note that disulphide bridges are neglected. Atoms
starting with "-" belong to the previous residue in the sequence.
 
   61 GLN  (  61-) A  -    CB   CG   CD  102.61   -5.9
  105 ASP  ( 101-) A  -    C    CA   CB   96.66   -7.1
  105 ASP  ( 101-) A  -    CA   CB   CG  122.94   10.3
  126 PHE  ( 122-) A  -    CA   CB   CG  109.43   -4.4
  309 ASP  (  92-) B  -    CA   CB   CG  117.36    4.8
  321 LYS  ( 103-) B  -    N    CA   CB  117.74    4.3
  370 ASP  ( 152-) B  -    CA   CB   CG  117.73    5.1
  420 THR  ( 202-) B  -    C    CA   CB  101.35   -4.6
  738 ASP  (  92-) D  -    CA   CB   CG  117.04    4.4
  799 ASP  ( 152-) D  -    CA   CB   CG  116.94    4.3
  818 ASN  ( 171-) D  -    ND2  CG   OD1 118.52   -4.1
  849 THR  ( 202-) D  -    CA   CB   OG1 102.51   -4.7
 
# 61 # 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: 0.918
 RMS-deviation in bond angles: 1.772
 
# 62 # 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.
 
# 63 # Note: Chirality OK
All protein atoms have proper chirality, or there is no intact protein
present in the PDB file.
The average deviation= 1.168
 
# 64 # Note: Improper dihedral angle distribution OK
The RMS Z-score for all improper dihedrals in the structure is within normal
ranges.
 
 Improper dihedral RMS Z-score : 0.971
 
# 65 # Note: Tau angles OK
All of the tau angles (N-C-alpha-C) of amino acids fall within expected
RMS deviations.
 
# 66 # Note: Normal tau angle deviations
The RMS Z-score for the tau angles (N-C-alpha-C) in the structure falls
within the normal range that we guess to be 0.5 - 1.5. Be aware, we
determined the tau normal distributions from 500 high-resolution X-ray
structures, rather than from CSD data, so we cannot be 100 percent certain
about these numbers.
 
 Tau angle RMS Z-score : 1.044
 
# 67 # Error: Side chain planarity problems
The side chains of the residues listed in the table below contain a planar
group that was found to deviate from planarity by more than 4.0 times the
expected value. For an amino acid residue that has a side chain with a
planar group, the RMS deviation of the atoms to a least squares plane was
determined. The number in the table is the number of standard deviations
this RMS value deviates from the expected value. Not knowing better yet, we
assume that planarity of the groups analyzed should be perfect.
 
  271 ARG  (  54-) B  -   4.77
  700 ARG  (  54-) D  -   4.48
 
# 68 # Note: Atoms connected to aromatic rings OK
All of the atoms that are connected to planar aromatic rings in side chains
of amino-acid residues are in the plane within expected RMS deviations.
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 
# 69 # Warning: Ramachandran Z-score low
The score expressing how well the backbone conformations of all residues
correspond to the known allowed areas in the Ramachandran plot is a bit low.
 
 Ramachandran Z-score : -3.937
 
# 70 # Note: Ramachandran check
The list contains per-residue Z-scores describing how well each residue
fits into the allowed areas of the Ramachandran plot will not be printed
because WHAT CHECK found no reason to cry.
 
# 71 # Warning: Torsion angle evaluation shows unusual residues
The residues listed in the table below contain bad or abnormal
torsion angles.
 
These scores give an impression of how `normal' the torsion angles in
protein residues are. All torsion angles except omega are used for
calculating a `normality' score. Average values and standard deviations were
obtained from the residues in the WHAT CHECK database. These are used to
calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a
score of less than -3.0 is worrying. For such residues more than one torsion
angle is in a highly unlikely position.
 
  504 THR  (  75-) C  -   -3.5
  571 LEU  ( 138-) C  -   -2.6
  142 LEU  ( 138-) A  -   -2.6
  399 LEU  ( 181-) B  -   -2.6
  582 PRO  ( 149-) C  -   -2.6
  828 LEU  ( 181-) D  -   -2.5
   75 THR  (  75-) A  -   -2.5
   29 SER  (  30-) A  -   -2.5
  566 GLY  ( 133-) C  -   -2.5
  137 GLY  ( 133-) A  -   -2.4
   84 SER  (  82B) A  -   -2.4
  153 PRO  ( 149-) A  -   -2.4
  792 VAL  ( 145-) D  -   -2.4
  611 LEU  ( 178-) C  -   -2.4
  513 SER  (  82B) C  -   -2.3
  557 LEU  ( 124-) C  -   -2.3
  182 LEU  ( 178-) A  -   -2.2
  128 LEU  ( 124-) A  -   -2.2
  808 GLU  ( 161-) D  -   -2.2
  363 VAL  ( 145-) B  -   -2.2
  659 VAL  (  13-) D  -   -2.1
  230 VAL  (  13-) B  -   -2.1
   86 ARG  (  83-) A  -   -2.1
  471 GLN  (  43-) C  -   -2.1
  269 SER  (  52-) B  -   -2.1
  485 ILE  (  56-) C  -   -2.1
  379 GLU  ( 161-) B  -   -2.0
  674 ILE  (  28-) D  -   -2.0
 
# 72 # Warning: Backbone evaluation reveals unusual conformations
The residues listed in the table below have abnormal backbone torsion
angles.
 
Residues with `forbidden' phi-psi combinations are listed, as well as
residues with unusual omega angles (deviating by more than 3 sigma from the
normal value). Please note that it is normal if about 5 percent of the
residues is listed here as having unusual phi-psi combinations.
 
   12 LYS  (  13-) A  - Omega to (next) Pro poor
   14 GLY  (  15-) A  - Poor phi/psi
   22 LYS  (  23-) A  - omega poor
   26 GLY  (  27-) A  - Poor phi/psi
   29 SER  (  30-) A  - Poor phi/psi
   31 TYR  (  32-) A  - omega poor
   39 ALA  (  40-) A  - Omega to (next) Pro poor
   41 GLY  (  42-) A  - Poor phi/psi
   48 GLY  (  49-) A  - Poor phi/psi
   51 THR  (  52-) A  - Omega to (next) Pro poor
   63 PHE  (  63-) A  - omega poor
   64 GLN  (  64-) A  - Poor phi/psi
   65 GLY  (  65-) A  - Poor phi/psi
   75 THR  (  75-) A  - Poor phi/psi
   91 ALA  (  88-) A  - omega poor
And so on for a total of   163 lines.
 
# 73 # Error: Chi-1/chi-2 rotamer problems
List of residues with a poor chi-1/chi-2 combination. Be aware that for this
validation option the individual scores are far less important than the
overall score that is given below the table.
 
  128 LEU  ( 124-) A  -    -1.32
  142 LEU  ( 138-) A  -    -1.32
  145 LEU  ( 141-) A  -    -1.32
  182 LEU  ( 178-) A  -    -1.32
  399 LEU  ( 181-) B  -    -1.32
  557 LEU  ( 124-) C  -    -1.32
  571 LEU  ( 138-) C  -    -1.32
  574 LEU  ( 141-) C  -    -1.32
  611 LEU  ( 178-) C  -    -1.31
  622 LEU  ( 189-) C  -    -1.31
  780 LEU  ( 133-) D  -    -1.32
  828 LEU  ( 181-) D  -    -1.32
   56 ILE  (  56-) A  -    -1.24
   98 ASP  (  95-) A  -    -1.22
  193 LEU  ( 189-) A  -    -1.30
And so on for a total of   346 lines.
 
# 74 # Warning: chi-1/chi-2 angle correlation Z-score low
The score expressing how well the chi-1/chi-2 angles of all residues
correspond to the populated areas in the database is
a bit low.
 
 chi-1/chi-2 correlation Z-score : -3.879
 
# 75 # Warning: Unusual rotamers
The residues listed in the table below have a rotamer that is not seen very
often in the database of solved protein structures. This option determines
for every residue the position specific chi-1 rotamer distribution.
Thereafter it verified whether the actual residue in the molecule has the
most preferred rotamer or not. If the actual rotamer is the preferred one,
the score is 1.0. If the actual rotamer is unique, the score is 0.0. If
there are two preferred rotamers, with a population distribution of 3:2 and
your rotamer sits in the lesser populated rotamer, the score will be 0.667.
No value will be given if insufficient hits are found in the database.
 
It is not necessarily an error if a few residues have rotamer values below
0.3, but careful inspection of all residues with these low values could be
worth it.
 
  425 VAL  ( 207-) B  -   0.34
  613 SER  ( 180-) C  -   0.34
  184 SER  ( 180-) A  -   0.35
  183 SER  ( 179-) A  -   0.38
  854 VAL  ( 207-) D  -   0.38
  280 SER  (  63-) B  -   0.38
  740 SER  (  94-) D  -   0.39
 
# 76 # Warning: Unusual backbone conformations
For the residues listed in the table below, the backbone formed by itself and
two neighbouring residues on either side is in a conformation that is not
seen very often in the database of solved protein structures. The number
given in the table is the number of similar backbone conformations in the
database with the same amino acid in the centre.
 
For this check, backbone conformations are compared with database structures
using C-alpha superpositions with some restraints on the backbone oxygen
positions.
 
A residue mentioned in the table can be part of a strange loop, or there
might be something wrong with it or its directly surrounding residues. There
are a few of these in every protein, but in any case it is worth looking at,
especially if a regular DSSP secondary structure (H or S for helix or strand,
respectively) is indicated!
 
  134 SER  ( 130-) A  -       0
  136 SER  ( 132-) A  -       0
  268 ASP  (  51-) B  -       0
  294 ARG  (  77-) B  -       0
  313 ASP  (  95A) B  -       0
  563 SER  ( 130-) C  -       0
  565 SER  ( 132-) C  -       0
  697 ASP  (  51-) D  -       0
  713 SER  (  67-) D  -       0
  723 ARG  (  77-) D  -       0
  742 ASP  (  95A) D  -       0
  133 LYS  ( 129-) A  -       1
  318 THR  ( 100-) B  -       1
  376 ALA  ( 158-) B  -       1
  457 PHE  (  29-) C  -       1
  562 LYS  ( 129-) C  -       1
  743 TYR  (  96-) D  -       1
  747 THR  ( 100-) D  -       1
  805 ALA  ( 158-) D  -       1
   28 PHE  (  29-) A  -       2
  150 PHE  ( 146-) A  -       2
  152 GLU  ( 148-) A  -       2
  243 ASN  (  26-) B  -       2
  270 ASP  (  53-) B  -       2
  284 SER  (  67-) B  -       2
  314 TYR  (  96-) B  -       2
  579 PHE  ( 146-) C  -       2
  581 GLU  ( 148-) C  -       2
  672 ASN  (  26-) D  -       2
  699 ASP  (  53-) D  -       2
 
# 77 # Note: Backbone conformation Z-score OK
The backbone conformation analysis gives a score that is normal for well
refined protein structures.
 
 Backbone conformation Z-score : 0.105
 
# 78 # Warning: Omega angle restraints not strong enough
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 of
this distribution is above 7.0, which indicates that the omega values have
been under-restrained.
 
Omega average and std. deviation= 178.260 7.296
 
# 79 # Warning: Unusual PRO puckering amplitudes
The proline residues listed in the table below have a puckering amplitude
that is outside of normal ranges. Puckering parameters were calculated by
the method of Cremer and Pople [REF]. Normal PRO rings have a puckering
amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom
for a PRO residue, this could indicate disorder between the two different
normal ring forms (with C-gamma below and above the ring, respectively). If
Q is higher than 0.45 Angstrom something could have gone wrong during the
refinement. Be aware that this is a warning with a low confidence level. See:
Who checks the checkers? Four validation tools applied to eight atomic
resolution structures [REF]
 
  171 PRO  ( 167-) A  -   0.16 LOW
  189 PRO  ( 185-) A  -   0.05 LOW
  232 PRO  (  15-) B  -   0.17 LOW
  272 PRO  (  55-) B  -   0.11 LOW
  276 PRO  (  59-) B  -   0.19 LOW
  360 PRO  ( 142-) B  -   0.20 LOW
  383 PRO  ( 165-) B  -   0.11 LOW
  618 PRO  ( 185-) C  -   0.04 LOW
  655 PRO  (   9-) D  -   0.20 LOW
  701 PRO  (  55-) D  -   0.10 LOW
  812 PRO  ( 165-) D  -   0.06 LOW
 
# 80 # Warning: Unusual PRO puckering phases
The proline residues listed in the table below have a puckering phase that is
not expected to occur in protein structures. Puckering parameters were
calculated by the method of Cremer and Pople [REF]. Normal PRO rings
approximately show a so-called envelope conformation with the C-gamma atom
above the plane of the ring (phi=+72 degrees), or a half-chair conformation
with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees).
If phi deviates strongly from these values, this is indicative of a very
strange conformation for a PRO residue, and definitely requires a manual
check of the data. Be aware that this is a warning with a low confidence
level. See: Who checks the checkers? Four validation tools applied to eight
atomic resolution structures [REF].
 
  153 PRO  ( 149-) A  -  -47.2 half-chair C-beta/C-alpha (-54 degrees)
  582 PRO  ( 149-) C  -  -46.4 half-chair C-beta/C-alpha (-54 degrees)
  600 PRO  ( 167-) C  -   39.2 envelop C-delta (36 degrees)
  661 PRO  (  15-) D  - -129.3 half-chair C-delta/C-gamma (-126 degrees)
 
# 81 # Warning: Backbone oxygen evaluation
The residues listed in the table below have an unusual backbone oxygen
position.
 
For each of the residues in the structure, a search was performed to find
5-residue stretches in the WHAT CHECK database with superposable C-alpha
coordinates, and some restraints on the neighbouring backbone oxygens.
 
In the following table the RMS distance between the backbone oxygen positions
of these matching structures in the database and the position of the backbone
oxygen atom in the current residue is given. If this number is larger than
1.5 a significant number of structures in the database show an alternative
position for the backbone oxygen. If the number is larger than 2.0 most
matching backbone fragments in the database have the peptide plane flipped.
A manual check needs to be performed to assess whether the experimental data
can support that alternative as well. The number in the last column is the
number of database hits (maximum 80) used in the calculation. It is "normal"
that some glycine residues show up in this list, but they are still worth
checking!
 
  566 GLY  ( 133-) C  -  2.39   11
  137 GLY  ( 133-) A  -  2.39   11
 
# 82 # Warning: Possible peptide flips
For the residues listed in the table below, the backbone formed by the
residue mentioned and the one N-terminal of it show systematic deviations
from normality that are consistent with a peptide flip. This can either
be a 180 degree flip of the entire peptide plane or a trans to cis flip.
(Cis to trans flips cannot be detected yet). The type can be TT+, TC-,
or TC+:
TT+ indicates a 180 degree flip of the entire peptide plane.
TC- indicates a trans to cis conversion that requires a flip of the N atom.
TC+ indicates a trans to cis conversion that requires a flip of the O atom.
Note that the method will only work correctly for PDB files with full
isotropic B-factors.
 
  136 SER  ( 132-) A  - TT+   Likely
  312 SER  (  95-) B  - TT+   Likely
 
# 83 # Error: Abnormally short interatomic distances
The pairs of atoms listed in the table below have an unusually short
interactomic distance; each bump is listed in only one direction.
 
The contact distances of all atom pairs have been checked. Two atoms are
said to `bump' if they are closer than the sum of their Van der Waals radii
minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom
is used. The first number in the table tells you how much shorter that
specific contact is than the acceptable limit. The second distance is the
distance between the centres of the two atoms. Although we believe that two
water atoms at 2.4 A distance are too close, we only report water pairs that
are closer than this rather short distance.
 
INTRA and INTER indicate whether the clashes are between atoms in the same
asymmetric unit, or atoms in symmetry related asymmetric units, respectively.
The last text-item on each line represents the status of the atom pair. If
the final column contains the text 'HB', the bump criterion was relaxed
because there could be a hydrogen bond. Similarly relaxed criteria are used
for 1--3 and 1--4 interactions (listed as 'B2' and 'B3', respectively).
If the last column is 'BF', the sum of the B-factors of the atoms is higher
than 80, which makes the appearance of the bump somewhat less severe because
the atoms probably are not there anyway. BL, on the other hand, indicates
that the bumping atoms both have a low B-factor, and that makes the bumps
more worrisome.
 
Bumps between atoms for which the sum of their occupancies is lower than one
are not reported. If the MODEL number does not exist (as is the case in most
X-ray files), a minus sign is printed instead.
 
  185 VAL  ( 181-) A  -    CG1 <-->   354 LEU  ( 136-) B  -    CD1    0.33    2.87  INTRA BF
  327 GLN  ( 109-) B  -    NE2 <-->   359 TYR  ( 141-) B  -    CD1    0.32    2.78  INTRA
  763 VAL  ( 116-) D  -    O   <-->   852 LYS  ( 205-) D  -    NZ     0.28    2.42  INTRA BF
  614 VAL  ( 181-) C  -    CG1 <-->   783 LEU  ( 136-) D  -    CD1    0.28    2.92  INTRA
  205 LYS  ( 201-) A  -    N   <-->   206 PRO  ( 202-) A  -    CD     0.24    2.76  INTRA BL
  634 LYS  ( 201-) C  -    N   <-->   635 PRO  ( 202-) C  -    CD     0.24    2.76  INTRA BF
   98 ASP  (  95-) A  -    OD2 <-->   314 TYR  (  96-) B  -    OH     0.23    2.17  INTRA BF
  738 ASP  (  92-) D  -    O   <-->   742 ASP  (  95A) D  -    N      0.20    2.50  INTRA BF
  309 ASP  (  92-) B  -    O   <-->   313 ASP  (  95A) B  -    N      0.20    2.50  INTRA BF
  102 GLY  (  99-) A  -    O   <-->   314 TYR  (  96-) B  -    CE2    0.16    2.64  INTRA BF
  278 ARG  (  61-) B  -    CG  <-->   294 ARG  (  77-) B  -    NH2    0.15    2.95  INTRA BF
  738 ASP  (  92-) D  -    N   <-->   742 ASP  (  95A) D  -    O      0.15    2.55  INTRA BF
  309 ASP  (  92-) B  -    N   <-->   313 ASP  (  95A) B  -    O      0.15    2.55  INTRA BF
  413 GLN  ( 195-) B  -    NE2 <-->   422 GLU  ( 204-) B  -    OE1    0.15    2.55  INTRA BF
  855 ALA  ( 208-) D  -    N   <-->   858 GLU  ( 211-) D  -    OE2    0.14    2.56  INTRA BF
And so on for a total of   104 lines.
 
# 84 # Note: Some notes regarding these bumps
The bumps have been binned in 5 categories ranging from 'please look at'
till 'must fix'. Additionally, the integrated sum of all bumps, the squared
sum of all bumps, and these latter two values normalized by the number of
contacts are listed too for comparison purposes between, for example, small
and large proteins.
 
Total bump value: 7.976
Total bump value per residue: 0.121
Total number of bumps: 104
Total squared bump value: 1.121
Total number of bumps in the mildest bin: 100
Total number of bumps in the second bin: 4
Total number of bumps in the middle bin: 0
Total number of bumps in the fourth bin: 0
Total number of bumps in the worst bin: 0
 
# 85 # Note: Inside/outside distribution check
The following list contains per-residue Z-scores describing how well the
residue's observed accessibility fits the expected one. A positive Z-score
indicates "more exposure than usual", whereas a negative Z-score means
"more buried than usual". The absolute value of the Z-score must be used to
judge the quality. Today WHAT CHECK saw no reason to complain.
 
# 86 # Note: Inside/Outside residue distribution normal
The distribution of residue types over the inside and the outside of the
protein is normal.
 
inside/outside RMS Z-score : 0.937
 
# 87 # Note: Inside/Outside RMS Z-score plot
The Inside/Outside distribution normality RMS Z-score over a 15 residue
window is plotted as function of the residue number. High areas in the plot
(above 1.5) indicate unusual inside/outside patterns.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: A
 
# 88 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 89 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: C
 
# 90 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 91 # 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.
 
  375 LYS  ( 157-) B  -  -6.45
  688 GLN  (  42-) D  -  -6.36
  259 GLN  (  42-) B  -  -6.32
  804 LYS  ( 157-) D  -  -6.27
  837 ARG  ( 190-) D  -  -5.91
  133 LYS  ( 129-) A  -  -5.87
  471 GLN  (  43-) C  -  -5.72
  562 LYS  ( 129-) C  -  -5.70
  109 GLN  ( 105-) A  -  -5.69
  538 GLN  ( 105-) C  -  -5.68
  408 ARG  ( 190-) B  -  -5.67
  101 MET  (  98-) A  -  -5.65
  530 MET  (  98-) C  -  -5.52
   42 GLN  (  43-) A  -  -5.41
  152 GLU  ( 148-) A  -  -5.24
  529 VAL  (  97-) C  -  -5.20
  581 GLU  ( 148-) C  -  -5.19
  100 VAL  (  97-) A  -  -5.14
 
# 92 # Note: No series of residues with bad packing environment
There are no stretches of three or more residues each having a packing score
worse than -4.0.
 
# 93 # Note: Structural average packing environment OK
The structural average packing score is within normal ranges.
 
 
Average for range     1 -  858 :  -0.522
 
# 94 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as function
of the residue number. Low areas in the plot (below -2.0) indicate unusual
packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: A
 
# 95 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as function
of the residue number. Low areas in the plot (below -2.0) indicate unusual
packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 96 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as function
of the residue number. Low areas in the plot (below -2.0) indicate unusual
packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: C
 
# 97 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as function
of the residue number. Low areas in the plot (below -2.0) indicate unusual
packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 98 # Note: Second generation packing environment OK
None of the individual amino acid residues has a bad packing environment.
 
# 99 # 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
 
# 100 # 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
 
# 101 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 102 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: C
 
# 103 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 104 # 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.
 
# 105 # Note: Water contacts OK
All water clusters make at least one contact with a non-water atom.
 
# 106 # Note: No waters need moving
All water molecules are sufficiently close to the asymmetric unit given in
the input file.
 
# 107 # Note: Water hydrogen bonds OK
All water molecules can form hydrogen bonds.
 
# 108 # 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.
 
  244 ASN  (  27-) B  -
  251 HIS  (  34-) B  -
  680 HIS  (  34-) D  -
  836 HIS  ( 189-) D  -
 
# 109 # 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.
 
  168 HIS  ( 164-) A  -   HIS-D   0.76 HIS-E   1.00
  204 HIS  ( 200-) A  -   HIS-D   0.55 HIS-E   1.00
  251 HIS  (  34-) B  -   HIS-E   1.01
  407 HIS  ( 189-) B  -   HIS-H   0.68 HIS-D   0.77
  416 HIS  ( 198-) B  -   HIS-E   1.07
  597 HIS  ( 164-) C  -   HIS-D   0.90 HIS-E   1.10
  633 HIS  ( 200-) C  -   HIS-E   0.65
  680 HIS  (  34-) D  -   HIS-E   0.94
  836 HIS  ( 189-) D  -   HIS-E   0.49 HIS-D   0.83
  845 HIS  ( 198-) D  -   HIS-E   0.40
 
# 110 # 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.
 
    5 GLN  (   6-) A  -    N
   25 GLY  (  26-) A  -    N
   26 GLY  (  27-) A  -    N
   30 SER  (  31-) A  -    N
   35 TRP  (  36-) A  -    NE1
   44 LEU  (  45-) A  -    N
   71 THR  (  71-) A  -    OG1
   88 GLU  (  85-) A  -    N
  101 MET  (  98-) A  -    N
  103 GLY  ( 100-) A  -    N
  106 VAL  ( 102-) A  -    N
  110 GLY  ( 106-) A  -    N
  133 LYS  ( 129-) A  -    N
  140 SER  ( 136-) A  -    OG
  168 HIS  ( 164-) A  -    NE2
And so on for a total of    50 lines.
 
# 111 # 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.
 
  283 ASN  (  66-) B  -    OD1
  416 HIS  ( 198-) B  -    ND1
  712 ASN  (  66-) D  -    OD1
  774 GLN  ( 127-) D  -    OE1
  845 HIS  ( 198-) D  -    ND1
  851 GLU  ( 204-) D  -    OE1
 
# 112 # 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: 1244
- of which buried: 582
Total number of acceptors: 1334
- of which buried: 474
Total number of donor+acceptors: 244
  (e.g. the Ser Ogamma that can donate and accept)
- of which buried: 44
Buried donors: 582
- without H-bond: 47
- essentially without H-bond: 0
- with only a very poor H-bond: 4
- with a poor H-bond: 10
- with a H-bond: 521
Buried acceptors: 474
- without H-bond: 64
- essentially without H-bond: 0
- with only a very poor H-bond: 4
- with a poor H-bond: 9
- with a H-bond: 397
 
# 113 # 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 (    2)   218 (  214) A Protein             To check
     2   219 (    2)   429 (  211) B Protein             To check
     3   430 (    2)   647 (  214) C Protein             To check
     4   648 (    2)   858 (  211) D Protein             To check
     5   859 ( HOH )   859 ( HOH ) A water   (    1)     To check
     6   860 ( HOH )   860 ( HOH ) B water   (    1)     To check
     7   861 ( HOH )   861 ( HOH ) C water   (    1)     To check
     8   862 ( HOH )   862 ( HOH ) D water   (    1)     To check
 
# 114 # 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  :   2.280
  1st generation packing quality :  -0.054 (          (  -0.3,  2.5))
  2nd generation packing quality :   0.373 (          (  -1.2,  1.3))
  Ramachandran plot appearance   :  -3.937 (poor      (  -1.8,  1.3))
  chi-1/chi-2 rotamer normality  :  -3.879 (poor      (  -3.5,  1.6))
  Backbone conformation          :   0.105 (          (  -0.7,  3.5))
  Inside/Outside distribution    :   0.937
 
 RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.680
  Bond angles                    :   0.918
  Omega angle restraints         :   1.327 (loose)
  Side chain planarity           :   1.269
  Improper dihedral distribution :   0.971
  B-factor distribution          :   0.671
 
# 115 # 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.
 
# 116 # 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.
 
# 117 # Note: Cell parameter anomaly
WHAT CHECK has compared the observed bond lengths with the Engh and Huber
parameters, and has done this as function of the direction of the bond
relative to the cell axes. From this analysis it was concluded that the
cell dimensions are probably not entirely perfect. The problem is not very
big, so you do not need to fix this before you start dealing with the other
suggestions, but you better fix this.
 
If this problem is caused by refining with another set of target values
than the Engh and Huber values, then WHAT CHECK cannot help you because
systematic target value deviations can also cause this message to pop up.
 
# 118 # Error: Bumps in your structure
Upon analysing the bumps in your structure, WHAT CHECK got a bit
worried. Sometimes this means that you have forgotten to lower the
occupancy of overlapping ligands, residues, or water molecules. But,
whatever is the origin of this problem, you have to analyse it and
fix it.
 
# 119 # Note: Omega angles insufficiently restraint
Omega angles tend to fall around 178 degrees with a standard deviation of 5.5
degrees. Even with a resolution of 1.5-2.5 Angstrom, you dont have enough
data to warrant the omega angle variability that we observed. The variability
is larger than 7.0 degrees. So, especially if your resolution is closer to
2.5 than to 1.5 Angstrom, you might want to tighten the screws on the
omega angle target values a bit.
 
# 120 # 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.
 
# 121 # 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.
 
  647 LYS  ( 214-) C  -     13.95
  218 LYS  ( 214-) A  -     13.53
  105 ASP  ( 101-) A  -     13.10
  375 LYS  ( 157-) B  -     12.90
  133 LYS  ( 129-) A  -     12.74
  688 GLN  (  42-) D  -     12.71
  259 GLN  (  42-) B  -     12.64
  804 LYS  ( 157-) D  -     12.54
  562 LYS  ( 129-) C  -     12.41
  101 MET  (  98-) A  -     12.30
  837 ARG  ( 190-) D  -     11.88
  471 GLN  (  43-) C  -     11.55
  408 ARG  ( 190-) B  -     11.40
  109 GLN  ( 105-) A  -     11.37
  538 GLN  ( 105-) C  -     11.36
And so on for a total of    89 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.
