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

Date : 2025-03-09
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/6weu/wctemp_0cyc/6weu_0cyc.pdb     ====
=========================================
 
# 1 # Note: Introduction
WHAT CHECK needs to read a PDB file before it can check it. It does a
series of checks upon reading the file. The results of these checks are
reported in this section (section 2.1). The rest of the report will be more
systematic in that section 2.2 reports on administrative problems. Section
2.3 gives descriptive output that is not directly validating things but
more telling you how WHAT CHECK interpreted the input file. Section 2.4
looks at B-factors, occupancies, and the presence/absence of (spurious)
atoms. Section 2.5 deals with nomenclature problems. Section 2.6 deals with
geometric problems like bond lengths and bond angles. Section 2.7 deals with
torsion angle issues. Section 2.8 looks at atomic clashes. Section 2.9 deals
with packing, accessibility, etc, issues. Section 2.10 deals with hydrogen
bonds, ion packing, and other things that can be summarized under the common
name charge-charge interactions. Section 2.11 gives a summary of whole report
and tells you (if applicable) which symmetry matrices were used. Section 2.12
tells the crystallographer which are the things most in need of manual
correction. And the last section, section 2.13, lists all residues sorted
by their need for visual inspection in light of the electron density.
WARNING. Date error on HEADER card:
HEADER                                                        6WEU
ATOM  *****  OP1 SRA A1006      16.861 -31.753 -28.334  1.00 91.66       OP1 O
ATOM  *****  S2P SRA A1006      18.645 -31.437 -30.480  1.00 87.03       S2P S
ATOM  *****  OP3 SRA A1006      19.159 -31.227 -27.660  1.00 95.31       OP3 O
ATOM  *****  O5' SRA A1006      18.608 -33.613 -28.522  1.00105.28       O5' O
ATOM  *****  C5' SRA A1006      17.878 -34.532 -29.399  1.00103.02       C5' C
ATOM  *****  C4' SRA A1006      17.484 -35.810 -28.545  1.00102.84       C4' C
ATOM  *****  O4' SRA A1006      17.735 -36.863 -29.208  1.00101.75       O4' O
ATOM  *****  C3' SRA A1006      18.398 -35.916 -27.242  1.00101.61       C3' C
ATOM  *****  O3' SRA A1006      17.771 -35.365 -26.175  1.00107.08       O3' O
ATOM  *****  C2' SRA A1006      18.609 -37.397 -27.026  1.00100.37       C2' C
ATOM  *****  C1' SRA A1006      18.101 -38.017 -28.105  1.00 94.44       C1' C
ATOM  *****  N9  SRA A1006      19.057 -38.914 -28.656  1.00 81.33       N9  N
ATOM  *****  C8  SRA A1006      20.371 -38.881 -28.480  1.00 76.02       C8  C
ATOM  *****  N7  SRA A1006      20.946 -39.873 -29.140  1.00 69.99       N7  N
ATOM  *****  C5  SRA A1006      19.975 -40.582 -29.773  1.00 77.45       C5  C
ATOM  *****  C6  SRA A1006      19.944 -41.723 -30.616  1.00 78.39       C6  C
ATOM  *****  N6  SRA A1006      21.118 -42.368 -30.950  1.00 67.37       N6  N
ATOM  *****  N1  SRA A1006      18.776 -42.170 -31.081  1.00 77.48       N1  N
ATOM  *****  C2  SRA A1006      17.647 -41.569 -30.771  1.00 69.67       C2  C
ATOM  *****  N3  SRA A1006      17.637 -40.486 -29.977  1.00 72.27       N3  N
ATOM  *****  C4  SRA A1006      18.788 -39.974 -29.466  1.00 79.25       C4  C
ATOM  *****  O2' SRA A1006      17.888 -37.874 -25.743  1.00 95.76       O2' O
ATOM  *****  C1  EDO A1007      21.845 -20.397 -57.367  1.00 69.72       C1  C
ATOM  *****  C2  EDO A1007      20.543 -19.777 -57.717  1.00 70.59       C2  C
ATOM  *****  O2  EDO A1007      19.507 -20.720 -57.915  1.00 67.36       O2  O
ATOM  *****  O   HOH A1102      55.179 -19.561 -58.589  1.00 54.39      1102 O
ATOM  *****  O   HOH A1103      36.256 -26.182 -23.247  1.00 35.39      1103 O
ATOM  *****  O   HOH A1104      43.691 -45.980 -31.564  1.00 32.64      1104 O
ATOM  *****  O   HOH A1105      33.356 -22.501 -40.642  1.00 33.51      1105 O
ATOM  *****  O   HOH A1106      23.455 -13.097 -49.574  1.00 53.04      1106 O
ATOM  *****  O   HOH A1107      35.520 -44.073 -10.478  1.00 46.55      1107 O
ATOM  *****  O   HOH A1108      35.336 -19.785 -12.428  1.00 38.39      1108 O
ATOM  *****  O   HOH A1109      19.749 -52.496 -27.602  1.00 50.45      1109 O
ATOM  *****  O   HOH A1110      41.993 -32.532 -11.647  1.00 39.82      1110 O
ATOM  *****  O   HOH A1111      25.712 -34.031  -9.371  1.00 37.27      1111 O
ATOM  *****  O   HOH A1112      40.816  -6.569 -54.769  1.00 49.07      1112 O
ATOM  *****  O   HOH A1113      28.755 -25.962 -49.386  1.00 44.09      1113 O
ATOM  *****  O   HOH A1114      45.481 -44.280 -22.916  1.00 41.94      1114 O
ATOM  *****  O   HOH A1115      26.504 -47.156   0.957  1.00 43.43      1115 O
ATOM  *****  O   HOH A1116      26.172 -52.615 -18.226  1.00 36.65      1116 O
ATOM  *****  O   HOH A1117      46.637 -43.022 -18.178  1.00 28.33      1117 O
ATOM  *****  O   HOH A1118      -2.139 -37.903 -46.666  1.00 57.79      1118 O
ATOM  *****  O   HOH A1119      41.851 -28.377 -39.390  1.00 28.00      1119 O
ATOM  *****  O   HOH A1120      35.683 -28.636 -46.298  1.00 41.35      1120 O
ATOM  *****  O   HOH A1121      19.881 -17.763 -32.229  1.00 31.70      1121 O
ATOM  *****  O   HOH A1122      48.138 -38.052 -40.008  1.00 35.16      1122 O
ATOM  *****  O   HOH A1123      20.263 -19.214 -37.717  1.00 31.34      1123 O
ATOM  *****  O   HOH A1124      44.098 -26.428 -34.239  1.00 45.68      1124 O
ATOM  *****  O   HOH A1125      25.442 -48.768 -39.126  1.00 43.40      1125 O
ATOM  *****  O   HOH A1126      32.259 -53.710 -16.516  1.00 35.52      1126 O
ATOM  *****  O   HOH A1127      38.583 -44.971  -7.877  1.00 34.96      1127 O
ATOM  *****  O   HOH A1128      27.917 -43.667  -9.568  1.00 35.78      1128 O
ATOM  *****  O   HOH A1129      37.739 -35.622 -41.326  1.00 33.79      1129 O
ATOM  *****  O   HOH A1130      20.746 -19.905 -17.432  1.00 40.14      1130 O
ATOM  *****  O   HOH A1131      22.109 -18.059 -35.880  1.00 33.39      1131 O
ATOM  *****  O   HOH A1132      38.223 -29.104 -44.166  1.00 34.43      1132 O
ATOM  *****  O   HOH A1133      38.502 -55.045 -34.102  1.00 43.36      1133 O
ATOM  *****  O   HOH A1134      47.655 -49.451 -20.615  1.00 31.63      1134 O
ATOM  *****  O   HOH A1135      14.658 -50.854   4.609  1.00 37.74      1135 O
ATOM  *****  O   HOH A1136      27.841 -57.368  -1.868  1.00 44.68      1136 O
ATOM  *****  O   HOH A1137      37.977 -17.697 -59.462  1.00 37.36      1137 O
ATOM  *****  O   HOH A1138      43.939 -50.827 -38.621  1.00 46.45      1138 O
ATOM  *****  O   HOH A1139      23.947 -18.676 -22.051  1.00 36.85      1139 O
ATOM  *****  O   HOH A1140      35.090 -31.167 -48.939  1.00 42.78      1140 O
ATOM  *****  O   HOH A1141      29.027 -30.352 -49.020  1.00 44.43      1141 O
ATOM  *****  O   HOH A1142      15.089 -17.118 -27.395  1.00 46.79      1142 O
ATOM  *****  O   HOH A1143      47.258 -50.425 -14.238  0.50 11.60      1143 O
ATOM  *****  O   HOH A1144      34.511 -35.549 -38.452  1.00 30.98      1144 O
ATOM  *****  O   HOH A1145      30.472 -30.713 -32.353  1.00 29.42      1145 O
ATOM  *****  O   HOH A1146      39.452 -41.115 -11.754  1.00 39.28      1146 O
ATOM  *****  O   HOH A1147      30.646 -21.271 -40.194  1.00 34.93      1147 O
ATOM  *****  O   HOH A1148      21.935 -38.510 -14.717  1.00 29.90      1148 O
ATOM  *****  O   HOH A1149      27.510 -43.444  -5.446  1.00 35.73      1149 O
ATOM  *****  O   HOH A1150      23.824 -27.792 -21.569  1.00 32.47      1150 O
ATOM  *****  O   HOH A1151      26.926 -51.721  -5.210  1.00 39.02      1151 O
ATOM  *****  O   HOH A1152      24.540 -20.783 -49.039  1.00 47.67      1152 O
ATOM  *****  O   HOH A1153      37.956 -26.972 -40.874  1.00 37.58      1153 O
ATOM  *****  O   HOH A1154      32.433 -28.128 -37.803  1.00 42.70      1154 O
ATOM  *****  O   HOH A1155      16.439 -10.441 -49.157  1.00 50.46      1155 O
ATOM  *****  O   HOH A1156      31.509 -49.940 -10.105  1.00 38.19      1156 O
ATOM  *****  O   HOH A1157      21.745 -45.116 -30.721  1.00 57.04      1157 O
ATOM  *****  O   HOH A1158      36.478 -27.446 -25.742  1.00 26.84      1158 O
ATOM  *****  O   HOH A1159      33.367 -23.886 -50.235  1.00 40.24      1159 O
ATOM  *****  O   HOH A1160      39.251  -2.864 -57.019  1.00 40.84      1160 O
ATOM  *****  O   HOH A1161      19.063 -34.399 -23.744  1.00 44.94      1161 O
ATOM  *****  O   HOH A1162      25.629 -22.249 -46.707  1.00 34.73      1162 O
ATOM  *****  O   HOH A1163      24.336 -48.157 -30.268  1.00 42.76      1163 O
ATOM  *****  O   HOH A1164      34.643 -36.356 -10.544  1.00 40.38      1164 O
ATOM  *****  O   HOH A1165      39.396 -26.997 -38.536  1.00 33.87      1165 O
ATOM  *****  O   HOH A1166      21.907 -42.106 -15.841  1.00 47.28      1166 O
ATOM  *****  O   HOH A1167      41.725 -34.104 -47.322  1.00 25.96      1167 O
ATOM  *****  O   HOH A1168      -2.804  -8.183 -46.002  1.00 62.85      1168 O
ATOM  *****  O   HOH A1169      26.747 -44.839  -7.502  1.00 30.43      1169 O
ATOM  *****  O   HOH A1170      39.781 -47.839  -7.643  1.00 45.64      1170 O
ATOM  *****  O   HOH A1171      47.743 -37.721 -24.765  1.00 38.05      1171 O
ATOM  *****  O   HOH A1172      30.774 -22.690 -25.362  1.00 33.58      1172 O
ATOM  *****  O   HOH A1173      17.258 -26.086 -28.876  1.00 39.32      1173 O
ATOM  *****  O   HOH A1174      39.050 -21.759 -36.767  1.00 42.00      1174 O
ATOM  *****  O   HOH A1175      26.736 -39.127  -9.988  1.00 40.41      1175 O
ATOM  *****  O   HOH A1176      25.488 -15.543 -65.816  1.00 44.10      1176 O
ATOM  *****  O   HOH A1177      28.876 -15.124 -30.057  1.00 51.51      1177 O
ATOM  *****  O   HOH A1178      15.434 -12.779 -51.596  1.00 44.23      1178 O
ATOM  *****  O   HOH A1179      17.054 -14.129 -49.619  1.00 45.33      1179 O
ATOM  *****  O   HOH A1180      45.809 -47.279 -43.682  1.00 47.36      1180 O
ATOM  *****  O   HOH A1181      35.454 -34.931 -50.689  1.00 38.09      1181 O
ATOM  *****  O   HOH A1182      31.290 -52.454 -11.008  1.00 43.05      1182 O
ATOM  *****  O   HOH A1183      21.425 -55.715 -31.479  1.00 50.00      1183 O
ATOM  *****  O   HOH A1184      37.687 -39.749 -10.351  1.00 49.37      1184 O
ATOM  *****  O   HOH A1185      34.697 -53.127 -15.009  1.00 40.02      1185 O
ATOM  *****  O   HOH A1186      11.242 -56.303 -12.096  1.00 57.90      1186 O
ATOM  *****  OP1 SRA B1005      35.034  -1.789   0.567  1.00 99.65       OP1 O
ATOM  *****  S2P SRA B1005      33.229  -0.557   2.358  1.00 90.03       S2P S
ATOM  *****  OP3 SRA B1005      32.852  -2.888   0.727  1.00 77.67       OP3 O
ATOM  *****  O5' SRA B1005      34.560  -3.172   2.655  1.00 91.46       O5' O
ATOM  *****  C5' SRA B1005      34.634  -4.603   2.357  1.00 90.27       C5' C
ATOM  *****  C4' SRA B1005      35.631  -5.266   3.402  1.00 91.00       C4' C
ATOM  *****  O4' SRA B1005      35.667  -4.589   4.482  1.00 80.99       O4' O
ATOM  *****  C3' SRA B1005      35.106  -6.694   3.863  1.00 87.17       C3' C
ATOM  *****  O3' SRA B1005      35.517  -7.658   3.001  1.00 93.18       O3' O
ATOM  *****  C2' SRA B1005      35.731  -6.885   5.225  1.00 86.07       C2' C
ATOM  *****  C1' SRA B1005      36.085  -5.660   5.655  1.00 82.98       C1' C
ATOM  *****  N9  SRA B1005      35.408  -5.352   6.870  1.00 85.09       N9  N
ATOM  *****  C8  SRA B1005      34.171  -5.703   7.199  1.00 84.73       C8  C
ATOM  *****  N7  SRA B1005      33.877  -5.250   8.406  1.00 76.56       N7  N
ATOM  *****  C5  SRA B1005      34.957  -4.582   8.888  1.00 77.88       C5  C
ATOM  *****  C6  SRA B1005      35.260  -3.889  10.086  1.00 76.84       C6  C
ATOM  *****  N6  SRA B1005      34.315  -3.797  11.086  1.00 71.59       N6  N
ATOM  *****  N1  SRA B1005      36.456  -3.327  10.243  1.00 75.32       N1  N
ATOM  *****  C2  SRA B1005      37.364  -3.405   9.298  1.00 78.21       C2  C
ATOM  *****  N3  SRA B1005      37.112  -4.054   8.148  1.00 79.90       N3  N
ATOM  *****  C4  SRA B1005      35.916  -4.650   7.920  1.00 80.41       C4  C
ATOM  *****  O2' SRA B1005      36.978  -7.792   5.135  1.00 87.54       O2' O
ATOM  *****  O   HOH B1102      12.382 -10.654  18.501  1.00 36.84      1102 O
ATOM  *****  O   HOH B1103      15.914 -18.890  30.878  1.00 45.20      1103 O
ATOM  *****  O   HOH B1104      36.651 -23.033 -12.242  1.00 36.35      1104 O
ATOM  *****  O   HOH B1105      19.235 -22.047 -11.423  1.00 32.60      1105 O
ATOM  *****  O   HOH B1106      13.246   1.637   9.583  1.00 33.48      1106 O
ATOM  *****  O   HOH B1107      32.172 -24.859   0.452  1.00 43.68      1107 O
ATOM  *****  O   HOH B1108      12.550 -19.496  15.418  1.00 42.44      1108 O
ATOM  *****  O   HOH B1109      11.933 -26.790  12.440  1.00 53.98      1109 O
ATOM  *****  O   HOH B1110      12.223 -23.211  20.204  1.00 28.97      1110 O
ATOM  *****  O   HOH B1111      36.167 -31.981  16.000  1.00 44.55      1111 O
ATOM  *****  O   HOH B1112      37.917 -16.471 -11.241  1.00 37.27      1112 O
ATOM  *****  O   HOH B1113      35.890 -20.045  -2.336  1.00 42.57      1113 O
ATOM  *****  O   HOH B1114      27.740   1.458  20.046  1.00 44.97      1114 O
ATOM  *****  O   HOH B1115       9.972 -24.356   9.608  1.00 30.09      1115 O
ATOM  *****  O   HOH B1116      30.205 -11.898  -4.041  1.00 34.91      1116 O
ATOM  *****  O   HOH B1117      25.417 -26.986   7.924  1.00 38.03      1117 O
ATOM  *****  O   HOH B1118      11.589   2.264   1.283  1.00 43.20      1118 O
ATOM  *****  O   HOH B1119      -0.372 -23.801  20.978  1.00 51.12      1119 O
ATOM  *****  O   HOH B1120      17.224   0.017   8.505  1.00 35.83      1120 O
ATOM  *****  O   HOH B1121       9.402 -17.198  27.374  1.00 50.02      1121 O
ATOM  *****  O   HOH B1122      16.929 -11.420  -1.688  1.00 44.99      1122 O
ATOM  *****  O   HOH B1123      35.778 -19.454   4.188  1.00 41.42      1123 O
ATOM  *****  O   HOH B1124      35.007  -2.318 -14.115  1.00 52.94      1124 O
ATOM  *****  O   HOH B1125      11.206 -26.635  10.079  1.00 39.76      1125 O
ATOM  *****  O   HOH B1126       9.918 -23.053  25.648  1.00 61.75      1126 O
ATOM  *****  O   HOH B1127      21.559  -4.047   2.110  1.00 41.49      1127 O
ATOM  *****  O   HOH B1128      10.866  -0.109   0.657  1.00 34.96      1128 O
ATOM  *****  O   HOH B1129      35.285 -19.225   1.612  1.00 42.45      1129 O
ATOM  *****  O   HOH B1130       7.199  -1.239  -1.407  1.00 41.89      1130 O
ATOM  *****  O   HOH B1131      27.205   5.309  -9.803  1.00 53.39      1131 O
ATOM  *****  O   HOH B1132      36.331 -18.694   8.211  1.00 39.83      1132 O
ATOM  *****  O   HOH B1133       8.645 -17.476   9.618  1.00 40.02      1133 O
ATOM  *****  O   HOH B1134      34.366 -28.892   9.551  1.00 36.96      1134 O
ATOM  *****  O   HOH B1135       2.175  -3.241   4.889  1.00 46.81      1135 O
ATOM  *****  O   HOH B1136      30.653 -28.196  -5.439  1.00 45.66      1136 O
ATOM  *****  C2  MAN C   3      28.332 -38.579 -58.189  1.00106.97       C2  C
ATOM  *****  C3  MAN C   3      26.938 -38.476 -58.804  1.00105.85       C3  C
ATOM  *****  C4  MAN C   3      26.784 -37.082 -59.390  1.00105.22       C4  C
ATOM  *****  C5  MAN C   3      28.130 -36.652 -59.982  1.00104.38       C5  C
ATOM  *****  C6  MAN C   3      28.024 -35.385 -60.816  1.00 99.65       C6  C
ATOM  *****  O2  MAN C   3      28.329 -39.504 -57.103  1.00114.35       O2  O
ATOM  *****  O3  MAN C   3      25.939 -38.697 -57.805  1.00 93.63       O3  O
ATOM  *****  O4  MAN C   3      25.777 -37.087 -60.387  1.00103.37       O4  O
ATOM  *****  O5  MAN C   3      29.087 -36.457 -58.933  1.00105.07       O5  O
ATOM  *****  O6  MAN C   3      28.475 -35.685 -62.138  1.00 93.52       O6  O
ATOM  *****  C2  BMA E   3      16.289  20.926  12.899  1.00120.62       C2  C
ATOM  *****  C3  BMA E   3      16.958  22.285  12.700  1.00119.63       C3  C
ATOM  *****  C4  BMA E   3      18.417  22.313  13.168  1.00115.55       C4  C
ATOM  *****  C5  BMA E   3      19.183  21.026  12.865  1.00114.39       C5  C
ATOM  *****  C6  BMA E   3      20.506  20.979  13.612  1.00110.41       C6  C
ATOM  *****  O2  BMA E   3      15.960  20.726  14.274  1.00123.53       O2  O
ATOM  *****  O3  BMA E   3      16.211  23.282  13.403  1.00114.58       O3  O
ATOM  *****  O4  BMA E   3      19.072  23.390  12.491  1.00107.56       O4  O
ATOM  *****  O5  BMA E   3      18.413  19.888  13.234  1.00117.33       O5  O
ATOM  *****  O6  BMA E   3      20.298  20.308  14.853  1.00105.84       O6  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.
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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:
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.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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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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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                                                        6WEU
 
# 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
  0.012047  0.000000  0.000000
  0.000000  0.006244  0.000000
  0.000000  0.000000  0.004770
 
# 5 # Warning: Problem detected upon counting molecules and matrices
The parameter Z as given on the CRYST card represents the molecular
multiplicity in the crystallographic cell. Normally, Z equals the number of
matrices of the space group multiplied by the number of NCS relations. The
value of Z is multiplied by the integrated molecular weight of the molecules
in the file to determine the Matthews coefficient. This relation is being
validated in this option. Be aware that the validation can get confused if
both multiple copies of the molecule are present in the ATOM records and
MTRIX records are present in the header of the PDB file.
 
 Space group as read from CRYST card: P 21 21 21
 Number of matrices in space group: 4
 Highest polymer chain multiplicity in structure: 1
 Highest polymer chain multiplicity according to SEQRES: 1
 No explicit MTRIX NCS matrices found in the input file
 Value of Z as found on the CRYST1 card: 0
 Z, symmetry, and molecular multiplicity disagree
 Could it be that Z must be: 4
 
# 6 # 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: 185574.391
 Volume of the Unit Cell V= 2786737.0
 Space group multiplicity: 4
 No NCS symmetry matrices (MTRIX records) found in PDB file
 Matthews coefficient for observed atoms and Z is high: Vm= 15.017
 Be aware though that the number of residues with missing atoms is: 95
 No Matthews coefficient given in REMARK 280
 Could it be that Z must be: 4
 This number is the multiplication of the spacegroup and NCS symmetry count
 Matthews coefficient for observed atoms and corrected Z: Vm= 3.754
 
# 7 # Note: Z missing on CRYST1 card
The messages above seem likely caused by the fact that Z is missing from the
CRYST1 card.
 
# 8 # Note: All atoms are sufficiently far away from symmetry axes
None of the atoms in the structure is closer than 0.77 Angstrom to a proper
symmetry axis.
 
# 9 # Note: Chain identifiers OK
WHAT CHECK has not detected any serious chain identifier problems. But be
aware that WHAT CHECK doesn't care about the chain identifiers of waters.
 
# 10 # Warning: Ligands for which a topology was generated automatically
The topology for the ligands in the table below were determined
automatically. WHAT CHECK uses a local copy of the CCP4 monomer library to
generate topology information for ligands. Be aware that automatic topology
generation is a complicated task. So, if you get messages that you fail to
understand or that you believe are wrong, and one of these ligands is
involved, then check the ligand topology entry first. This topology is either
present in the monomer library, or as a libcheck-generated file in the local
directory.
 
 1631 SRA  (1006-) A  -
 1635 SRA  (1005-) B  -
 1636 MAN  (   3-) C  -
 1637 BMA  (   3-) E  -
 
# 11 # Warning: Covalently bound ligands
The ligands in this table are covalently bound to something else. It is
already difficult to automatically generate topologies for ligands,
but when they are covalently bound to something it becomes even more
complicated to do everything right. So, if you get weird error messages
that seem related to this covalent bond, then please feel free to
ignore those, or even better, make a topology entry by hand.
 
The comment `Other ligand` indicates that the covalent bond is to another
ligand. In that case you might want to convert the two ligands into one
bigger ligand.
 
 1636 MAN  (   3-) C  -
 1637 BMA  (   3-) E  -
 
# 12 # Note: No strange inter-chain connections detected
No covalent bonds have been detected between molecules with non-identical
chain identifiers.
 
# 13 # Note: No duplicate atom names in ligands
All atom names in ligands (if any) seem adequately unique.
 
# 14 # 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).
 
# 15 # 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).
 
# 16 # Warning: Groups attached to potentially hydrogen-bonding atoms
Residues were observed with groups attached to (or very near to) atoms that
potentially can form hydrogen bonds. WHAT CHECK is not very good at dealing
with such exceptional cases (Mainly because it's author is not...). So be
warned that the hydrogen-bonding related analyses of these residues
might be in error.
 
For example, an aspartic acid can be protonated on one of its delta
oxygens. This is possible because the one delta oxygen 'helps' the
other one holding that proton. However, if a delta oxygen has a group
bound to it, then it can no longer 'help' the other delta oxygen
bind the proton. However, both delta oxygens, in principle, can still
be hydrogen bond acceptors. Such problems can occur in the amino acids
Asp, Glu, and His. I have opted, for now to simply allow no hydrogen
bonds at all for any atom in any side chain that somewhere has a 'funny'
group attached to it. I know this is wrong, but there are only 12 hours
in a day.
 
 1622 NAG  (   2-) C  -    O4  bound to  1636 MAN  (   3-) C  -    C1
 1626 NAG  (   2-) E  -    O4  bound to  1637 BMA  (   3-) E  -    C1
 
# 17 # 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.
 
# 18 # 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.
 
# 19 # Note: All residues have a complete backbone.
No residues have missing backbone atoms.
 
# 20 # Note: No C-alpha only residues
There are no residues that consist of only an alpha carbon atom.
 
# 21 # 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 (  104)   816 (  921) A Protein             /zata/tempdir/6we...
     2   817 ( 1003)   817 ( 1003) A Sugar               /zata/tempdir/6we...
     3   818 ( 1004)   818 ( 1004) A Sugar               /zata/tempdir/6we...
     4   819 ( 1005)   819 ( 1005) A Sugar               /zata/tempdir/6we...
     5   820 (  104)  1618 (  920) B Protein             /zata/tempdir/6we...
     6  1619 ( 1003)  1619 ( 1003) B Sugar               /zata/tempdir/6we...
     7  1620 ( 1004)  1620 ( 1004) B Sugar               /zata/tempdir/6we...
     8  1621 (    1)  1621 (    1) C Sugar               /zata/tempdir/6we...
     9  1622 (    2)  1622 (    2) C Sugar<-             /zata/tempdir/6we...
    10  1623 (    1)  1623 (    1) D Sugar               /zata/tempdir/6we...
    11  1624 (    2)  1624 (    2) D Sugar               /zata/tempdir/6we...
    12  1625 (    1)  1625 (    1) E Sugar               /zata/tempdir/6we...
    13  1626 (    2)  1626 (    2) E Sugar<-             /zata/tempdir/6we...
    14  1627 (    1)  1627 (    1) F Sugar               /zata/tempdir/6we...
    15  1628 (    2)  1628 (    2) F Sugar               /zata/tempdir/6we...
    16  1629 ( 1001)  1629 ( 1001) A  ZN                 /zata/tempdir/6we...
    17  1630 ( 1002)  1630 ( 1002) A  ZN                 /zata/tempdir/6we...
    18  1631 ( 1006)  1631 ( 1006) A SRA                 /zata/tempdir/6we...
    19  1632 ( 1007)  1632 ( 1007) A EDO                 /zata/tempdir/6we...
    20  1633 ( 1001)  1633 ( 1001) B  ZN                 /zata/tempdir/6we...
    21  1634 ( 1002)  1634 ( 1002) B  ZN                 /zata/tempdir/6we...
    22  1635 ( 1005)  1635 ( 1005) B SRA                 /zata/tempdir/6we...
    23  1636 (    3)  1636 (    3) C MAN  <-             /zata/tempdir/6we...
    24  1637 (    3)  1637 (    3) E BMA  <-             /zata/tempdir/6we...
    25  1638 ( HOH )  1638 ( HOH ) A water   (    1)     /zata/tempdir/6we...
    26  1639 ( HOH )  1639 ( HOH ) B water   (    1)     /zata/tempdir/6we...
MODELs skipped upon reading PDB file: 0
X-ray structure. No MODELs found
The total number of amino acids found is 1615
of which 358 have poor or (essentially) missing atoms
No nucleic acids observed in input file
Number of (recognized) sugars: 13
of which 9 have poor or (essentially) missing atoms
Number of water molecules: 2
Residue numbers increase monotonously OK
 
# 22 # Note: Chain identifiers seem OK
All ions seem to have a logical chain identifier, or there are no ions
present in the input file.
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
 
# 23 # Note: Ramachandran plot
In this Ramachandran plot x-signs represent glycines, squares represent
prolines, and plus-signs represent the other residues. If too many
plus-signs fall outside the contoured areas then the molecule is poorly
refined (or worse). Proline can only occur in the narrow region around
phi=-60 that also falls within the other contour islands.
 
In a colour picture, the residues that are part of a helix are shown in blue,
strand residues in red. Preferred regions for helical residues are drawn in
blue, for strand residues in red, and for all other residues in green. A full
explanation of the Ramachandran plot together with a series of examples can
be found at the WHAT CHECK website [REF].
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 24 # 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 EVKSCKGRCFERTFGNCRCDAACVELGNCCLDYQETCIEPEHIWTCNKFRCGEKRLTRSL
( 104)-( 163)
                     70        80        90       100       110       120
                      |         |         |         |         |         |
   61 -  120 CACSDDCKDKGDCCINYSSVCQGEKSWVEEPCESINEPQCPAGFETPPTLLFSLDGFRAE
( 164)-( 223)
                    130       140       150       160       170       180
                      |         |         |         |         |         |
  121 -  180 YLHTWGGLLPVISKLKKCGTYTKNMRPVYPTKTFPNHYSIVTGLYPESHGIIDNKMYDPK
( 224)-( 283)
                    190       200       210       220       230       240
                      |         |         |         |         |         |
  181 -  240 MNASFSLKSKEKFNPEWYKGEPIWVTAKYQGLKSGTFFWPGSDVEINGIFPDIYKMYNGS
( 284)-( 343)
                    250       260       270       280       290       300
                      |         |         |         |         |         |
  241 -  300 VPFEERILAVLQWLQLPKDERPHFYTLYLEEPDSSGHSYGPVSSEVIKALQRVDGMVGML
( 344)-( 403)
                    310       320       330       340       350       360
                      |         |         |         |         |         |
  301 -  360 MDGLKELNLHRCLNLILISDHGMEQGSCKKYIYLNKYLGDVKNIKVIYGPAARLRPSDVP
( 404)-( 463)
                    370       380       390       400       410       420
                      |         |         |         |         |         |
  361 -  420 DKYYSFNYEGIARNLSCREPNQHFKPYLKHFLPKRLHFAKSDRIEPLTFYLDPQWQLALN
( 464)-( 523)
                    430       440       450       460       470       480
                      |         |         |         |         |         |
  421 -  480 PSERKYCGSGFHGSDNVFSNMQALFVGYGPGFKHGIEADTFENIEVYNLMCDLLNLTPAP
( 524)-( 583)
                    490       500       510       520       530       540
                      |         |         |         |         |         |
  481 -  540 NNGTHGSLNHLLKNPVYTPKHPKEVHPLVQCPFTRNPRDNLGCSCNPSILPIEDFQTQFN
( 584)-( 643)
                    550       560       570       580       590       600
                      |         |         |         |         |         |
  541 -  600 LTVAEEKIIKHETLPYGRPRVLQKENTICLLSQHQFMSGYSQDILMPLWTSYTVDRNDSF
( 644)-( 703)
                    610       620       630       640       650       660
                      |         |         |         |         |         |
  601 -  660 STEDFSNCLYQDFRIPLSPVHKCSFYKNNTKVSYGFLSPPQLNKNSSGIYSEALLTTNIV
( 704)-( 763)
                    670       680       690       700       710       720
                      |         |         |         |         |         |
  661 -  720 PMYQSFQVIWRYFHDTLLRKYAEERNGVNVVSGPVFDFDYDGRCDSLENLRQKRRVIRNQ
( 764)-( 823)
                    730       740       750       760       770       780
                      |         |         |         |         |         |
  721 -  780 EILIPTHFFIVLTSCKDTSQTPLHCENLDTLAFILPHRTDNSESCVHGDSSWVEELLMLH
( 824)-( 885)
                    790       800       810
                      |         |         |
  781 -  816 RARITDVEHITGLSFYQQRKEPVSDILKLKTHLPTF
( 886)-( 921)
           820       830       840       850       860       870
             |         |         |         |         |         |
  820 -  879 EVKSCKGRCFERTFGNCRCDAACVELGNCCLDYQETCIEPEHIWTCNKFRCGEKRLTRSL
( 104)-( 163)
           880       890       900       910       920       930
             |         |         |         |         |         |
  880 -  939 CACSDDCKDKGDCCINYSSVCQGEKSWVEEPCESINEPQCPAGFETPPTLLFSLDGFRAE
( 164)-( 223)
           940       950       960       970       980       990
             |         |         |         |         |         |
  940 -  999 YLHTWGGLLPVISKLKKCGTYTKNMRPVYPTKTFPNHYSIVTGLYPESHGIIDNKMYDPK
( 224)-( 283)
          1000      1010      1020      1030      1040      1050
             |         |         |         |         |         |
 1000 - 1059 MNASFSLKSKEKFNPEWYKGEPIWVTAKYQGLKSGTFFWPGSDVEINGIFPDIYKMYNGS
( 284)-( 343)
          1060      1070      1080      1090      1100      1110
             |         |         |         |         |         |
 1060 - 1119 VPFEERILAVLQWLQLPKDERPHFYTLYLEEPDSSGHSYGPVSSEVIKALQRVDGMVGML
( 344)-( 403)
          1120      1130      1140      1150      1160      1170
             |         |         |         |         |         |
 1120 - 1179 MDGLKELNLHRCLNLILISDHGMEQGSCKKYIYLNKYLGDVKNIKVIYGPAARLRPSDVP
( 404)-( 463)
          1180      1190      1200      1210      1220      1230
             |         |         |         |         |         |
 1180 - 1239 DKYYSFNYEGIARNLSCREPNQHFKPYLKHFLPKRLHFAKSDRIEPLTFYLDPQWQLALN
( 464)-( 523)
          1240      1250      1260      1270      1280      1290
             |         |         |         |         |         |
 1240 - 1299 PSERKYCGSGFHGSDNVFSNMQALFVGYGPGFKHGIEADTFENIEVYNLMCDLLNLTPAP
( 524)-( 583)
          1300      1310      1320      1330      1340      1350
             |         |         |         |         |         |
 1300 - 1359 NNGTHGSLNHLLKNPVYTPKHPKEVHPLVNPRDNLGCSCNPSILPIEDLTVAEEKIIKHE
( 584)-( 655)
          1360      1370      1380      1390      1400      1410
             |         |         |         |         |         |
 1360 - 1419 TLPYGRPRVLQKENTICLLSQHQFMSGYSQDILMPLWTSYTVDRNDSFSTEDFSNCLYQD
( 656)-( 715)
          1420      1430      1440      1450      1460      1470
             |         |         |         |         |         |
 1420 - 1479 FRIPLSPVHKCSFYKNNTKVSYGFLSPPQLNKNSSGIYSEALLTTNIVPMYQSFQVIWRY
( 716)-( 775)
          1480      1490      1500      1510      1520      1530
             |         |         |         |         |         |
 1480 - 1539 FHDTLLRKYAEERNGVNVVSGPVFDFDYDGRCDSLENLRQKRRVIRNILIPTHFFIVLTS
( 776)-( 837)
          1540      1550      1560      1570      1580      1590
             |         |         |         |         |         |
 1540 - 1599 CKDTSQTPLHCENLDTLAFILPHRTDNSESCVHSSWVEELLMLHRARITDVEHITGLSFY
( 838)-( 901)
          1600      1610
             |         |
 1600 - 1618 QQRKEPVSDILKLKTHLPT
( 902)-( 920)
 
 
 
 
# 25 # Note: No rounded coordinates detected
No significant rounding of atom coordinates has been detected.
 
# 26 # 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.
 
# 27 # Warning: Missing atoms
The atoms listed in the table below are missing from the entry. If many atoms
are missing, the other checks can become less sensitive. Be aware that it
often happens that groups at the termini of DNA or RNA are really missing,
so that the absence of these atoms normally is neither an error nor the
result of poor electron density. Some of the atoms listed here might also be
listed by other checks, most noticeably by the options in the previous
section that list missing atoms in several categories. The plausible atoms
with zero occupancy are not listed here, as they already got assigned a
non-zero occupancy, and thus are no longer 'missing'.
 
    1 GLU  ( 104-) A  -    CG
    1 GLU  ( 104-) A  -    CD
    1 GLU  ( 104-) A  -    OE1
    1 GLU  ( 104-) A  -    OE2
   14 PHE  ( 117-) A  -    CG
   14 PHE  ( 117-) A  -    CD1
   14 PHE  ( 117-) A  -    CD2
   14 PHE  ( 117-) A  -    CE1
   14 PHE  ( 117-) A  -    CE2
   14 PHE  ( 117-) A  -    CZ
   16 ASN  ( 119-) A  -    CG
   16 ASN  ( 119-) A  -    OD1
   16 ASN  ( 119-) A  -    ND2
   70 LYS  ( 173-) A  -    CG
   70 LYS  ( 173-) A  -    CD
And so on for a total of   345 lines.
 
# 28 # Warning: B-factors outside the range 0.0 - 100.0
In principle, B-factors can have a very wide range of values, but in
practice, B-factors should not be zero while B-factors above 100.0
are a good indicator that the location of that atom is meaningless. Be
aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms
with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with
a B-factor of zero were observed.
 
    1 GLU  ( 104-) A  -   High
    2 VAL  ( 105-) A  -   High
    3 LYS  ( 106-) A  -   High
   12 ARG  ( 115-) A  -   High
   13 THR  ( 116-) A  -   High
   14 PHE  ( 117-) A  -   High
   15 GLY  ( 118-) A  -   High
   16 ASN  ( 119-) A  -   High
   58 ARG  ( 161-) A  -   High
  180 LYS  ( 283-) A  -   High
  188 LYS  ( 291-) A  -   High
  329 LYS  ( 432-) A  -   High
  340 ASP  ( 443-) A  -   High
  361 ASP  ( 464-) A  -   High
  362 LYS  ( 465-) A  -   High
And so on for a total of   351 lines.
 
# 29 # 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.
 
  768 GLY  ( 871-) A  -        OK (2)
  816 PHE  ( 921-) A  -        OK
 1328 VAL  ( 612-) B  -        OK (6)
 1347 ASP  ( 637-) B  -        OK (6)
 1526 ASN  ( 822-) B  -        OK (2)
 1572 HIS  ( 870-) B  -        OK (4)
 1618 THR  ( 920-) B  -        OK
 
# 30 # Note: Weights administratively correct
All atomic occupancy factors ('weights') fall in the 0.0--1.0 range, which
makes them administratively correct.
 
# 31 # 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.
 
# 32 # 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.
 
# 33 # 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
 
# 34 # 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
 
# 35 # 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 :  0.635 over    9683 bonds
Average difference in B over a bond :    2.29
RMS difference in B over a bond :    3.18
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
 
# 36 # 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: B
 
# 37 # 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.
 
# 38 # Note: Valine nomenclature OK
No errors were detected in valine nomenclature.
 
# 39 # Note: Threonine nomenclature OK
No errors were detected in threonine nomenclature.
 
# 40 # Note: Isoleucine nomenclature OK
No errors were detected in isoleucine nomenclature.
 
# 41 # Note: Leucine nomenclature OK
No errors were detected in leucine nomenclature.
 
# 42 # Warning: Arginine nomenclature problem
The arginine residues listed in the table below have their NH1 and NH2
swapped.
 
   55 ARG  ( 158-) A  -
  292 ARG  ( 395-) A  -
  560 ARG  ( 663-) A  -
  679 ARG  ( 782-) A  -
  703 ARG  ( 806-) A  -
  837 ARG  ( 121-) B  -
  874 ARG  ( 158-) B  -
  965 ARG  ( 249-) B  -
 1080 ARG  ( 364-) B  -
 1111 ARG  ( 395-) B  -
 1192 ARG  ( 476-) B  -
 1522 ARG  ( 818-) B  -
 1602 ARG  ( 904-) B  -
 
# 43 # Note: Tyrosine torsion conventions OK
No errors were detected in tyrosine torsion angle conventions.
 
# 44 # Note: Phenylalanine torsion conventions OK
No errors were detected in phenylalanine torsion angle conventions.
 
# 45 # Note: Aspartic acid torsion conventions OK
No errors were detected in aspartic acid torsion angle conventions.
 
# 46 # Note: Glutamic acid torsion conventions OK
No errors were detected in glutamic acid torsion angle conventions.
 
# 47 # 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).
 
# 48 # Note: Heavy atom naming OK
No errors were detected in the atom names for non-hydrogen atoms. Please
be aware that the PDB wants us to deliberately make some nomenclature errors;
especially in non-canonical amino acids.
 
# 49 # Note: No decreasing residue numbers
All residue numbers are strictly increasing within each chain.
 
# 50 # Note: All bond lengths OK
All bond lengths are in agreement with standard bond lengths using a
tolerance of 4 sigma (both standard values and sigma for amino acids
have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson
et al [REF]).
 
# 51 # Warning: Low bond length variability
Bond lengths were found to deviate less than normal from the mean Engh and
Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS
Z-score given below is expected to be near 1.0 for a normally restrained
data set. The fact that it is lower than 0.667 in this structure might
indicate that too-strong restraints have been used in the refinement. This
can only be a problem  for high resolution X-ray structures.
 
 RMS Z-score for bond lengths: 0.661
 RMS-deviation in bond distances: 0.013
 
# 52 # 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
  0.012047  0.000000  0.000000
  0.000000  0.006244  0.000000
  0.000000  0.000000  0.004770
Unit Cell deformation matrix
  0.995625  0.000092 -0.000124
  0.000092  0.995178 -0.000081
 -0.000124 -0.000081  0.995026
Proposed new scale matrix
  0.012100 -0.000001  0.000002
  0.000000  0.006275  0.000000
  0.000000  0.000000  0.004794
With corresponding cell
    A    =  82.647  B   = 159.371  C    = 208.589
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000
 
The CRYST1 cell dimensions
    A    =  83.010  B   = 160.143  C    = 209.632
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000
 
 Variance: 1219.369
 (Under-)estimated Z-score: 25.736
 
# 53 # Warning: Unusual bond angles
The bond angles listed in the table below were found to deviate more than 4
sigma from standard bond angles (both standard values and sigma for protein
residues have been taken from Engh and Huber [REF], for DNA/RNA from
Parkinson et al [REF]). In the table below for each strange angle the bond
angle and the number of standard deviations it differs from the standard
values is given. Please note that disulphide bridges are neglected. Atoms
starting with "-" belong to the previous residue in the sequence.
 
  112 PHE  ( 215-) A  -    CA   CB   CG  118.35    4.5
  425 LYS  ( 528-) A  -    C    CA   CB  117.88    4.1
  812 HIS  ( 917-) A  -    CG   ND1  CE1 109.72    4.1
  831 ARG  ( 115-) B  -    CG   CD   NE  117.39    4.1
  931 PHE  ( 215-) B  -    CA   CB   CG  118.10    4.3
 
# 54 # Note: Normal bond angle variability
Bond angles were found to deviate normally from the mean standard bond angles
(normal values for protein residues were taken from Engh and Huber [REF], for
DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected
to be near 1.0 for a normally restrained data set, and this is indeed
observed for very high resolution X-ray structures.
 
 RMS Z-score for bond angles: 0.982
 RMS-deviation in bond angles: 1.807
 
# 55 # Error: Nomenclature error(s)
Checking for a hand-check. WHAT CHECK has over the course of this session
already corrected the handedness of atoms in several residues. These were
administrative corrections. These residues are listed here.
 
   55 ARG  ( 158-) A  -
  292 ARG  ( 395-) A  -
  560 ARG  ( 663-) A  -
  679 ARG  ( 782-) A  -
  703 ARG  ( 806-) A  -
  837 ARG  ( 121-) B  -
  874 ARG  ( 158-) B  -
  965 ARG  ( 249-) B  -
 1080 ARG  ( 364-) B  -
 1111 ARG  ( 395-) B  -
 1192 ARG  ( 476-) B  -
 1522 ARG  ( 818-) B  -
 1602 ARG  ( 904-) B  -
 
# 56 # Note: Chirality OK
All protein atoms have proper chirality. But, look at the previous table to
see a series of administrative chirality problems that were corrected
automatically upon reading-in the PDB file.
The average deviation= 0.791
 
# 57 # Note: Improper dihedral angle distribution OK
The RMS Z-score for all improper dihedrals in the structure is within normal
ranges.
 
 Improper dihedral RMS Z-score : 0.641
 
# 58 # Note: Tau angles OK
All of the tau angles (N-C-alpha-C) of amino acids fall within expected
RMS deviations.
 
# 59 # Note: Normal tau angle deviations
The RMS Z-score for the tau angles (N-C-alpha-C) in the structure falls
within the normal range that we guess to be 0.5 - 1.5. Be aware, we
determined the tau normal distributions from 500 high-resolution X-ray
structures, rather than from CSD data, so we cannot be 100 percent certain
about these numbers.
 
 Tau angle RMS Z-score : 0.816
 
# 60 # Note: Side chain planarity OK
All of the side chains of residues that have an intact planar group are
planar within expected RMS deviations.
 
# 61 # Note: Atoms connected to aromatic rings OK
All of the atoms that are connected to planar aromatic rings in side chains
of amino-acid residues are in the plane within expected RMS deviations.
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 
# 62 # Note: Ramachandran Z-score OK
The score expressing how well the backbone conformations of all residues
correspond to the known allowed areas in the Ramachandran plot is within
expected ranges for well-refined structures.
 
 Ramachandran Z-score : -2.761
 
# 63 # Note: Ramachandran check
The list contains per-residue Z-scores describing how well each residue
fits into the allowed areas of the Ramachandran plot will not be printed
because WHAT CHECK found no reason to cry.
 
# 64 # Warning: Torsion angle evaluation shows unusual residues
The residues listed in the table below contain bad or abnormal
torsion angles.
 
These scores give an impression of how `normal' the torsion angles in
protein residues are. All torsion angles except omega are used for
calculating a `normality' score. Average values and standard deviations were
obtained from the residues in the WHAT CHECK database. These are used to
calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a
score of less than -3.0 is worrying. For such residues more than one torsion
angle is in a highly unlikely position.
 
  272 PRO  ( 375-) A  -   -2.7
 1091 PRO  ( 375-) B  -   -2.6
 1326 PRO  ( 610-) B  -   -2.5
  360 PRO  ( 463-) A  -   -2.5
  991 ILE  ( 275-) B  -   -2.5
  172 ILE  ( 275-) A  -   -2.4
  829 PHE  ( 113-) B  -   -2.4
   10 PHE  ( 113-) A  -   -2.4
 1179 PRO  ( 463-) B  -   -2.4
 1036 PHE  ( 320-) B  -   -2.4
  217 PHE  ( 320-) A  -   -2.3
   13 THR  ( 116-) A  -   -2.3
  385 LYS  ( 488-) A  -   -2.3
 1086 LEU  ( 370-) B  -   -2.3
  267 LEU  ( 370-) A  -   -2.3
And so on for a total of    35 lines.
 
# 65 # Warning: Backbone evaluation reveals unusual conformations
The residues listed in the table below have abnormal backbone torsion
angles.
 
Residues with `forbidden' phi-psi combinations are listed, as well as
residues with unusual omega angles (deviating by more than 3 sigma from the
normal value). Please note that it is normal if about 5 percent of the
residues is listed here as having unusual phi-psi combinations.
 
    7 GLY  ( 110-) A  - Poor phi/psi
   10 PHE  ( 113-) A  - Poor phi/psi
   16 ASN  ( 119-) A  - Poor phi/psi, omega poor
   27 GLY  ( 130-) A  - Poor phi/psi
   36 THR  ( 139-) A  - omega poor
   39 GLU  ( 142-) A  - Omega to (next) Pro poor
   41 GLU  ( 144-) A  - omega poor
   45 THR  ( 148-) A  - omega poor
   52 GLY  ( 155-) A  - Poor phi/psi
   53 GLU  ( 156-) A  - omega poor
   71 GLY  ( 174-) A  - Poor phi/psi
   73 CYS  ( 176-) A  - omega poor
   83 GLY  ( 186-) A  - Poor phi/psi
   90 GLU  ( 193-) A  - Omega to (next) Pro poor
   97 GLU  ( 200-) A  - Omega to (next) Pro poor
And so on for a total of   222 lines.
 
# 66 # Error: Chi-1/chi-2 rotamer problems
List of residues with a poor chi-1/chi-2 combination. Be aware that for this
validation option the individual scores are far less important than the
overall score that is given below the table.
 
   31 LEU  ( 134-) A  -    -1.31
  110 LEU  ( 213-) A  -    -1.31
  267 LEU  ( 370-) A  -    -1.32
  313 LEU  ( 416-) A  -    -1.30
  411 LEU  ( 514-) A  -    -1.32
  508 LEU  ( 611-) A  -    -1.31
  570 LEU  ( 673-) A  -    -1.32
  707 LEU  ( 810-) A  -    -1.30
  777 LEU  ( 882-) A  -    -1.32
 1086 LEU  ( 370-) B  -    -1.32
 1132 LEU  ( 416-) B  -    -1.31
 1173 LEU  ( 457-) B  -    -1.32
 1230 LEU  ( 514-) B  -    -1.31
 1514 LEU  ( 810-) B  -    -1.32
 1580 LEU  ( 882-) B  -    -1.32
And so on for a total of   679 lines.
 
# 67 # 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 : -3.609
 
# 68 # Warning: Unusual rotamers
The residues listed in the table below have a rotamer that is not seen very
often in the database of solved protein structures. This option determines
for every residue the position specific chi-1 rotamer distribution.
Thereafter it verified whether the actual residue in the molecule has the
most preferred rotamer or not. If the actual rotamer is the preferred one,
the score is 1.0. If the actual rotamer is unique, the score is 0.0. If
there are two preferred rotamers, with a population distribution of 3:2 and
your rotamer sits in the lesser populated rotamer, the score will be 0.667.
No value will be given if insufficient hits are found in the database.
 
It is not necessarily an error if a few residues have rotamer values below
0.3, but careful inspection of all residues with these low values could be
worth it.
 
  390 HIS  ( 493-) A  -   0.34
  319 SER  ( 422-) A  -   0.35
 1138 SER  ( 422-) B  -   0.36
  591 SER  ( 694-) A  -   0.36
 1209 HIS  ( 493-) B  -   0.36
 1398 SER  ( 694-) B  -   0.36
 1235 GLN  ( 519-) B  -   0.37
   48 LYS  ( 151-) A  -   0.38
  168 SER  ( 271-) A  -   0.38
  987 SER  ( 271-) B  -   0.38
  867 LYS  ( 151-) B  -   0.39
  633 SER  ( 736-) A  -   0.39
 
# 69 # Warning: Unusual backbone conformations
For the residues listed in the table below, the backbone formed by itself and
two neighbouring residues on either side is in a conformation that is not
seen very often in the database of solved protein structures. The number
given in the table is the number of similar backbone conformations in the
database with the same amino acid in the centre.
 
For this check, backbone conformations are compared with database structures
using C-alpha superpositions with some restraints on the backbone oxygen
positions.
 
A residue mentioned in the table can be part of a strange loop, or there
might be something wrong with it or its directly surrounding residues. There
are a few of these in every protein, but in any case it is worth looking at,
especially if a regular DSSP secondary structure (H or S for helix or strand,
respectively) is indicated!
 
    5 CYS  ( 108-) A  -       0
    9 CYS  ( 112-) A  -       0
   16 ASN  ( 119-) A  -       0
   17 CYS  ( 120-) A  -       0
   51 CYS  ( 154-) A  -       0
  151 THR  ( 254-) A  -       0
  218 PHE  ( 321-) A  -       0
  348 TYR  ( 451-) A  -       0
  359 VAL  ( 462-) A  -       0
  399 ALA  ( 502-) A  -       0
  400 LYS  ( 503-) A  -       0
  426 TYR  ( 529-) A  -       0
  432 HIS  ( 535-) A  -       0
  824 CYS  ( 108-) B  -       0
  828 CYS  ( 112-) B  -       0
And so on for a total of    54 lines.
 
# 70 # Note: Backbone conformation Z-score OK
The backbone conformation analysis gives a score that is normal for well
refined protein structures.
 
 Backbone conformation Z-score : -0.810
 
# 71 # Note: Omega angle restraint OK
The omega angles for trans-peptide bonds in a structure is expected to give a
gaussian distribution with the average around +178 degrees, and a standard
deviation around 5.5. In the current structure the standard deviation agrees
with this expectation.
 
Omega average and std. deviation= 179.610 6.762
 
# 72 # 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]
 
 1021 PRO  ( 305-) B  -   0.19 LOW
 
# 73 # Warning: Unusual PRO puckering phases
The proline residues listed in the table below have a puckering phase that is
not expected to occur in protein structures. Puckering parameters were
calculated by the method of Cremer and Pople [REF]. Normal PRO rings
approximately show a so-called envelope conformation with the C-gamma atom
above the plane of the ring (phi=+72 degrees), or a half-chair conformation
with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees).
If phi deviates strongly from these values, this is indicative of a very
strange conformation for a PRO residue, and definitely requires a manual
check of the data. Be aware that this is a warning with a low confidence
level. See: Who checks the checkers? Four validation tools applied to eight
atomic resolution structures [REF].
 
  360 PRO  ( 463-) A  -  -63.6 envelop C-beta (-72 degrees)
  380 PRO  ( 483-) A  -   47.5 half-chair C-delta/C-gamma (54 degrees)
 1179 PRO  ( 463-) B  -  -64.1 envelop C-beta (-72 degrees)
 1269 PRO  ( 553-) B  - -112.4 envelop C-gamma (-108 degrees)
 1326 PRO  ( 610-) B  -  101.2 envelop C-beta (108 degrees)
 1340 PRO  ( 630-) B  - -113.6 envelop C-gamma (-108 degrees)
 1426 PRO  ( 722-) B  - -124.6 half-chair C-delta/C-gamma (-126 degrees)
 1617 PRO  ( 919-) B  -   52.6 half-chair C-delta/C-gamma (54 degrees)
 
# 74 # 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!
 
 1455 GLY  ( 751-) B  -  1.54   47
 1337 SER  ( 627-) B  -  1.51   29
 
# 75 # Warning: Possible peptide flips
For the residues listed in the table below, the backbone formed by the
residue mentioned and the one N-terminal of it show systematic deviations
from normality that are consistent with a peptide flip. This can either
be a 180 degree flip of the entire peptide plane or a trans to cis flip.
(Cis to trans flips cannot be detected yet). The type can be TT+, TC-,
or TC+:
TT+ indicates a 180 degree flip of the entire peptide plane.
TC- indicates a trans to cis conversion that requires a flip of the N atom.
TC+ indicates a trans to cis conversion that requires a flip of the O atom.
Note that the method will only work correctly for PDB files with full
isotropic B-factors.
 
  260 GLU  ( 363-) A  - TT+   Likely
  901 GLN  ( 185-) B  - TT+   Likely
 1079 GLU  ( 363-) B  - TT+   Likely
 1233 GLN  ( 517-) B  - TT+   Likely
 1583 HIS  ( 885-) B  - TT+   Likely
 
# 76 # Error: Abnormally short interatomic distances
The pairs of atoms listed in the table below have an unusually short
distance; each bump is listed in only one direction,
 
The contact distances of all atom pairs have been checked. Two atoms are
said to `bump' if they are closer than the sum of their Van der Waals radii
minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom
is used. The first number in the table tells you how much shorter that
specific contact is than the acceptable limit. The second distance is the
distance between the centres of the two atoms.
 
The last text-item on each line represents the status of the atom pair. The
text `INTRA' means that the bump is between atoms that are explicitly listed
in the PDB file. `INTER' means it is an inter-symmetry bump. If the final
column contains the text 'HB', the bump criterion was relaxed because there
could be a hydrogen bond. Similarly relaxed criteria are used for 1--3 and
1--4 interactions (listed as 'B2' and 'B3', respectively). If the last column
is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes
the appearance of the bump somewhat less severe because the atoms probably
are not there anyway. BL, on the other hand, indicates that the bumping atoms
both have a low B-factor, and that makes the bumps more worrisome.
 
It seems likely that at least some of the reported bumps are caused by
administrative errors in the chain names. I.e. covalently bound atoms with
different non-blank chain-names are reported as bumps. In rare cases this is
not an error.
 
Bumps between atoms for which the sum of their occupancies is lower than one
are not reported. If the MODEL number does not exist (as is the case in most
X-ray files), a minus sign is printed instead.
 
  482 ASN  ( 585-) A  -    ND2  <-->   1621 NAG  (   1-) C  -    C1   1.67    1.43  INTRA BL
 1301 ASN  ( 585-) B  -    ND2  <-->   1625 NAG  (   1-) E  -    C1   1.67    1.43  INTRA BL
 1057 ASN  ( 341-) B  -    ND2  <-->   1627 NAG  (   1-) F  -    C1   1.66    1.44  INTRA BF
  182 ASN  ( 285-) A  -    ND2  <-->    818 NAG  (1004-) A  -    C1   1.65    1.45  INTRA BF
 1001 ASN  ( 285-) B  -    ND2  <-->   1620 NAG  (1004-) B  -    C1   1.64    1.46  INTRA BF
  628 ASN  ( 731-) A  -    ND2  <-->    819 NAG  (1005-) A  -    C1   1.64    1.46  INTRA BF
 1193 ASN  ( 477-) B  -    ND2  <-->   1619 NAG  (1003-) B  -    C1   1.64    1.46  INTRA BF
  374 ASN  ( 477-) A  -    ND2  <-->    817 NAG  (1003-) A  -    C1   1.64    1.46  INTRA BF
  238 ASN  ( 341-) A  -    ND2  <-->   1623 NAG  (   1-) D  -    C1   1.63    1.47  INTRA BF
 1621 NAG  (   1-) C  -    O4   <-->   1622 NAG  (   2-) C  -    C1   1.17    1.43  INTRA BL
 1625 NAG  (   1-) E  -    O4   <-->   1626 NAG  (   2-) E  -    C1   1.16    1.44  INTRA BF
 1627 NAG  (   1-) F  -    O4   <-->   1628 NAG  (   2-) F  -    C1   1.15    1.45  INTRA BF
 1623 NAG  (   1-) D  -    O4   <-->   1624 NAG  (   2-) D  -    C1   1.14    1.46  INTRA BF
  482 ASN  ( 585-) A  -    CG   <-->   1621 NAG  (   1-) C  -    C1   0.73    2.47  INTRA BL
 1301 ASN  ( 585-) B  -    CG   <-->   1625 NAG  (   1-) E  -    C1   0.73    2.47  INTRA BL
And so on for a total of   131 lines.
 
# 77 # Note: Some notes regarding these bumps
The bumps have been binned in 5 categories ranging from 'please look at'
till 'must fix'. Additionally, the integrated sum of all bumps, the squared
sum of all bumps, and these latter two values normalized by the number of
contacts are listed too for comparison purposes between, for example, small
and large proteins.
 
Total bump value: 44.158
Total bump value per residue: 0.080
Total number of bumps: 131
Total squared bump value: 40.588
Total number of bumps in the mildest bin: 79
Total number of bumps in the second bin: 18
Total number of bumps in the middle bin: 21
Total number of bumps in the fourth bin: 0
Total number of bumps in the worst bin: 13
 
# 78 # Note: Inside/outside distribution check
The following list contains per-residue Z-scores describing how well the
residue's observed accessibility fits the expected one. A positive Z-score
indicates "more exposure than usual", whereas a negative Z-score means
"more buried than usual". The absolute value of the Z-score must be used to
judge the quality. Today WHAT CHECK saw no reason to complain.
 
# 79 # Note: Inside/Outside residue distribution normal
The distribution of residue types over the inside and the outside of the
protein is normal.
 
inside/outside RMS Z-score : 1.055
 
# 80 # Note: Inside/Outside RMS Z-score plot
The Inside/Outside distribution normality RMS Z-score over a 15 residue
window is plotted as function of the residue number. High areas in the plot
(above 1.5) indicate unusual inside/outside patterns.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 81 # Warning: Abnormal packing environment for some residues
The residues listed in the table below have an unusual packing environment.
 
The packing environment of the residues is compared with the average packing
environment for all residues of the same type in good PDB files. A low
packing score can indicate one of several things: Poor packing, misthreading
of the sequence through the density, crystal contacts, contacts with a
co-factor, or the residue is part of the active site. It is not uncommon to
see a few of these, but in any case this requires further inspection of the
residue.
 
 1417 TYR  ( 713-) B  -  -9.27
 1525 ARG  ( 821-) B  -  -8.20
  831 ARG  ( 115-) B  -  -8.17
   12 ARG  ( 115-) A  -  -7.87
 1245 TYR  ( 529-) B  -  -7.38
 1519 GLN  ( 815-) B  -  -6.99
 1316 TYR  ( 600-) B  -  -6.95
  497 TYR  ( 600-) A  -  -6.91
 1522 ARG  ( 818-) B  -  -6.77
  426 TYR  ( 529-) A  -  -6.66
  767 HIS  ( 870-) A  -  -6.52
  510 GLN  ( 613-) A  -  -6.37
 1327 LEU  ( 611-) B  -  -6.36
  188 LYS  ( 291-) A  -  -6.29
 1007 LYS  ( 291-) B  -  -6.20
And so on for a total of    56 lines.
 
# 82 # Warning: Abnormal packing environment for sequential residues
A stretch of at least three sequential residues with a questionable packing
environment was found. This could indicate that these residues are part
of a strange loop. It might also be an indication of misthreading in the
density. However, it can also indicate that one or more residues in this
stretch have other problems such as, for example, missing atoms, very
weird angles or bond lengths, etc.
 
The table below lists the first and last residue in each stretch found,
as well as the average residue score of the series.
 
  766 VAL  ( 869-) A  -      768 --- GLY   871- (A ) -       -5.11
 
# 83 # Note: Structural average packing environment OK
The structural average packing score is within normal ranges.
 
 
Average for range     1 - 1628 :  -0.977
 
# 84 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as function
of the residue number. Low areas in the plot (below -2.0) indicate unusual
packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 85 # Warning: Low packing Z-score for some residues
The residues listed in the table below have an unusual packing
environment according to the 2nd generation packing check. The score
listed in the table is a packing normality Z-score: positive means
better than average, negative means worse than average. Only residues
scoring less than -2.50 are listed here. These are the unusual
residues in the structure, so it will be interesting to take a
special look at them.
 
 1457 TYR  ( 753-) B  -  -3.37
 1438 LYS  ( 734-) B  -  -3.26
 1244 LYS  ( 528-) B  -  -3.11
 1410 GLU  ( 706-) B  -  -3.08
 1373 ASN  ( 669-) B  -  -3.07
 1339 ASN  ( 629-) B  -  -3.06
 1528 LEU  ( 826-) B  -  -3.01
 1521 ARG  ( 817-) B  -  -2.92
 1416 LEU  ( 712-) B  -  -2.89
 1382 GLN  ( 678-) B  -  -2.85
  947 LEU  ( 231-) B  -  -2.83
  832 THR  ( 116-) B  -  -2.82
 1449 LEU  ( 745-) B  -  -2.77
 1524 ILE  ( 820-) B  -  -2.74
 1334 LEU  ( 624-) B  -  -2.74
And so on for a total of    32 lines.
 
# 86 # Warning: Abnormal packing Z-score for sequential residues
A stretch of at least four sequential residues with a 2nd generation packing
Z-score below -1.75 was found. This could indicate that these residues are
part of a strange loop or that the residues in this range are incomplete,
but it might also be an indication of misthreading.
 
The table below lists the first and last residue in each stretch found,
as well as the average residue Z-score of the series.
 
 1370 GLN  ( 666-) B  -   ---  1373 ASN  ( 669-) B  -      -2.25
 1388 SER  ( 684-) B  -   ---  1393 MET  ( 689-) B  -      -1.98
 1417 TYR  ( 713-) B  -   ---  1422 ILE  ( 718-) B  -      -2.23
 1426 PRO  ( 722-) B  -   ---  1429 LYS  ( 725-) B  -      -2.01
 1456 ILE  ( 752-) B  -   ---  1459 GLU  ( 755-) B  -      -2.02
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
 
# 87 # Note: Second generation quality Z-score plot
The second generation quality Z-score smoothed over a 10 residue window
is plotted as function of the residue number. Low areas in the plot (below
-1.3) indicate unusual packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 88 # Warning: No crystallisation information
No, or very inadequate, crystallisation information was observed upon
reading the PDB file header records. This information should be available
in the form of a series of REMARK 280 lines. Without this information a
few things, such as checking ions in the structure, cannot be performed
optimally.
 
# 89 # Note: Water contacts OK
All water clusters make at least one contact with a non-water atom.
 
# 90 # Note: No waters need moving
All water molecules are sufficiently close to the asymmetric unit given in
the input file.
 
# 91 # Note: Water hydrogen bonds OK
All water molecules can form hydrogen bonds.
 
# 92 # Error: His, Asn, Gln side chain flips
Listed here are Histidine, Asparagine or Glutamine residues for
which the orientation determined from hydrogen bonding analysis are
different from the assignment given in the input. Either they could
form energetically more favourable hydrogen bonds if the terminal
group was rotated by 180 degrees, or there is no assignment in the
input file (atom type 'A') but an assignment could be made. Be aware,
though, that if the topology could not be determined for one or more
ligands, then this option will make errors.
 
  607 ASN  ( 710-) A  -
  628 ASN  ( 731-) A  -
  835 ASN  ( 119-) B  -
 1046 ASN  ( 330-) B  -
 1202 HIS  ( 486-) B  -
 1380 GLN  ( 676-) B  -
 
# 93 # Note: Histidine type assignments
For all complete HIS residues in the structure a tentative assignment to
HIS-D (protonated on ND1), HIS-E (protonated on NE2), or HIS-H (protonated
on both ND1 and NE2, positively charged) is made based on the hydrogen bond
network. A second assignment is made based on which of the Engh and Huber
[REF] histidine geometries fits best to the structure.
 
In the table below all normal histidine residues are listed. The assignment
based on the geometry of the residue is listed first, together with the RMS
Z-score for the fit to the Engh and Huber parameters. For all residues where
the H-bond assignment is different, the assignment is listed in the last
columns, together with its RMS Z-score to the Engh and Huber parameters.
 
As always, the RMS Z-scores should be close to 1.0 if the residues were
restrained to the Engh and Huber parameters during refinement, and if
enough (high resolution) data is available.
 
Please note that because the differences between the geometries of the
different types are small it is possible that the geometric assignment given
here does not correspond to the type used in refinement. This is especially
true if the RMS Z-scores are much higher than 1.0.
 
If the two assignments differ, or the `geometry' RMS Z-score is high, it is
advisable to verify the hydrogen bond assignment, check the HIS type used
during the refinement and possibly adjust it.
 
   42 HIS  ( 145-) A  -   HIS-E   0.28
  123 HIS  ( 226-) A  -   HIS-E   0.31
  157 HIS  ( 260-) A  -   HIS-E   0.31 HIS-D   0.93
  169 HIS  ( 272-) A  -   HIS-E   0.38
  263 HIS  ( 366-) A  -   HIS-E   0.48
  277 HIS  ( 380-) A  -   HIS-E   0.30 HIS-D   1.14
  310 HIS  ( 413-) A  -   HIS-E   0.49
  321 HIS  ( 424-) A  -   HIS-E   0.44 HIS-D   0.94
  383 HIS  ( 486-) A  -   HIS-E   0.38 HIS-D   1.10
  390 HIS  ( 493-) A  -   HIS-E   0.41
  397 HIS  ( 500-) A  -   HIS-E   0.34
  432 HIS  ( 535-) A  -   HIS-E   0.46 HIS-D   1.01
  454 HIS  ( 557-) A  -   HIS-E   0.48 HIS-D   0.95
  485 HIS  ( 588-) A  -   HIS-E   0.48
  490 HIS  ( 593-) A  -   HIS-E   0.45
And so on for a total of    53 lines.
 
# 94 # Warning: Buried unsatisfied hydrogen bond donors
The buried hydrogen bond donors listed in the table below have a hydrogen
atom that is not involved in a hydrogen bond in the optimized hydrogen bond
network.
 
Hydrogen bond donors that are buried inside the protein normally use all of
their hydrogens to form hydrogen bonds within the protein. If there are any
non hydrogen bonded buried hydrogen bond donors in the structure they will
be listed here. In very good structures the number of listed atoms will tend
to zero.
 
Waters are not listed by this option.
 
    3 LYS  ( 106-) A  -    N
    8 ARG  ( 111-) A  -    NH1
   19 CYS  ( 122-) A  -    N
   20 ASP  ( 123-) A  -    N
   32 ASP  ( 135-) A  -    N
   50 ARG  ( 153-) A  -    NH1
   55 ARG  ( 158-) A  -    NH1
   58 ARG  ( 161-) A  -    N
   61 CYS  ( 164-) A  -    N
   68 LYS  ( 171-) A  -    N
   83 GLY  ( 186-) A  -    N
  109 THR  ( 212-) A  -    OG1
  121 TYR  ( 224-) A  -    OH
  146 ARG  ( 249-) A  -    NE
  153 THR  ( 256-) A  -    N
And so on for a total of   144 lines.
 
# 95 # Warning: Buried unsatisfied hydrogen bond acceptors
The buried side-chain hydrogen bond acceptors listed in the table below are
not involved in a hydrogen bond in the optimized hydrogen bond network.
 
Side-chain hydrogen bond acceptors buried inside the protein normally form
hydrogen bonds within the protein. If there are any not hydrogen bonded in
the optimized hydrogen bond network they will be listed here.
 
Waters are not listed by this option.
 
  465 GLU  ( 568-) A  -    OE2
 1592 HIS  ( 894-) B  -    ND1
 
# 96 # Note: Some notes regarding these donors and acceptors
The donors and acceptors have been counted, also as function of their
accessibility. The buried donors and acceptors have been binned in five
categories ranging from not forming any hydrogen bond till forming a poor
till perfect hydrogen bond. Obviously, the buried donors and acceptors
with no or just a poor hydrogen bond should be a topic of concern. As every
protein contains more acceptors than donors, unsatisfied donors are more in
need of attention than unsatisfied acceptors.
 
Total number of donors: 2302
- of which buried: 1135
Total number of acceptors: 2570
- of which buried: 931
Total number of donor+acceptors: 315
  (e.g. the Ser Ogamma that can donate and accept)
- of which buried: 81
Buried donors: 1135
- without H-bond: 131
- essentially without H-bond: 0
- with only a very poor H-bond: 18
- with a poor H-bond: 26
- with a H-bond: 960
Buried acceptors: 931
- without H-bond: 194
- essentially without H-bond: 1
- with only a very poor H-bond: 9
- with a poor H-bond: 20
- with a H-bond: 707
 
# 97 # Note: Content of the PDB file as interpreted by WHAT CHECK
Content of the PDB file as interpreted by WHAT CHECK.
WHAT CHECK has read your PDB file, and stored it internally in what is called
'the soup'. The content of this soup is listed here. An extensive explanation
of all frequently used WHAT CHECK output formats can be found at
swift.cmbi.ru.nl. Look under output formats. A course on reading this
'Molecules' table is part of the WHAT CHECK website.
 
     1     1 (  104)   768 (  871) A Protein             /zata/tempdir/6we...
     2   769 (  874)   816 (  921) A Protein             /zata/tempdir/6we...
     3   817 ( 1003)   817 ( 1003) A Sugar               /zata/tempdir/6we...
     4   818 ( 1004)   818 ( 1004) A Sugar               /zata/tempdir/6we...
     5   819 ( 1005)   819 ( 1005) A Sugar               /zata/tempdir/6we...
     6   820 (  104)  1328 (  612) B Protein             /zata/tempdir/6we...
     7  1329 (  619)  1347 (  637) B Protein             /zata/tempdir/6we...
     8  1348 (  644)  1526 (  822) B Protein             /zata/tempdir/6we...
     9  1527 (  825)  1572 (  870) B Protein             /zata/tempdir/6we...
    10  1573 (  875)  1618 (  920) B Protein             /zata/tempdir/6we...
    11  1619 ( 1003)  1619 ( 1003) B Sugar               /zata/tempdir/6we...
    12  1620 ( 1004)  1620 ( 1004) B Sugar               /zata/tempdir/6we...
    13  1621 (    1)  1621 (    1) C Sugar               /zata/tempdir/6we...
    14  1622 (    2)  1622 (    2) C Sugar<-             /zata/tempdir/6we...
    15  1623 (    1)  1623 (    1) D Sugar               /zata/tempdir/6we...
And so on for a total of    31 lines.
 
# 98 # Note: Summary report
This is an overall summary of the quality of the structure as compared with
current reliable structures. Numbers in brackets are the average and standard
deviation observed for a large number of files determined with a similar
resolution.
 
The second table mostly gives an impression of how well the model conforms
to common refinement restraint values. These numbers are less than 1.0 if the
spread in data is too little, and larger than 1.0 when the spread is too
large. The former does not need to be a problem, the latter always is bad.
 
 Structure Z-scores, positive is better than average:
  Resolution read from PDB file  :   2.650
  1st generation packing quality :  -1.193 (          (  -0.8,  2.5))
  2nd generation packing quality :  -3.134 (poor      (  -1.6,  1.2))
  Ramachandran plot appearance   :  -2.761 (          (  -2.9,  1.6))
  chi-1/chi-2 rotamer normality  :  -3.609 (poor      (  -4.7,  1.8))
  Backbone conformation          :  -0.810 (          (  -0.9,  3.7))
  Inside/Outside distribution    :   1.055
 
 RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.661 (tight)
  Bond angles                    :   0.982
  Omega angle restraints         :   1.229
  Side chain planarity           :   0.460 (tight)
  Improper dihedral distribution :   0.641
  B-factor distribution          :   0.635
 
# 99 # Note: Introduction to refinement recommendations
First, be aware that the recommendations for crystallographers listed below
are produced by a computer program that was written by a guy who got his
PhD in NMR...
 
We have tried to convert the messages written in this report into a small
set of things you can do with your refinement software to get a better
structure. The things you should do first are listed first. And in some
cases you should first fix that problem, then refine a bit further, and
then run WHAT CHECK again before looking at other problems. If, for example,
WHAT CHECK has found a problem with the SCALE and CRYST cards, then you must
first fix that problem, refine the structure a bit further, and run WHAT
CHECK again because errors in the SCALE and or CRYST card can lead to many
problems elsewhere in the validation process.
 
It is also important to keep in mind that WHAT CHECK is software and that it
occasionally totally misunderstands what is the cause of a problem. But, if
WHAT CHECK lists a problem there normally is a problem albeit that it not
always is the actual problem that gets listed.
 
# 100 # Note: Matthews coefficient problem
WHAT CHECK detected a Matthews coefficient problem. Most times this is an
administrative problem caused by typing the wrong cell multiplicity number
on the CRYST card (or not typing it at all). Occasionally it is caused by
typing the wrong space group on the CRYST card. You better fix this problem,
but normally this problem does not cause WHAT CHECK to give any erroneous
error messages further down in the report.
 
# 101 # 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.
 
# 102 # Error: Bumps in your structure
Upon analysing the bumps in your structure, WHAT CHECK got very, very
worried. Sometimes this means that you have forgotten to lower the
occupancy of overlapping ligands, residues, or water molecules. But,
whatever is the origin of this problem, you have to analyse it and
fix it.
 
# 103 # Note: Bond angle variabilty Z-score high
With a resolution of 2.5-3.0 Angstrom, you dont have enough data to warrant
the bond angle variability that we observed (almost 1.0). So, you better
tighten
the screws on the bond angle target values a bit.
 
# 104 # 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.
 
# 105 # 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.
 
 1621 NAG  (   1-) C  -     83.94
  482 ASN  ( 585-) A  -     54.47
 1625 NAG  (   1-) E  -     49.45
 1301 ASN  ( 585-) B  -     45.74
 1622 NAG  (   2-) C  -     27.45
  831 ARG  ( 115-) B  -     19.39
 1417 TYR  ( 713-) B  -     18.53
 1525 ARG  ( 821-) B  -     16.49
   12 ARG  ( 115-) A  -     15.75
 1316 TYR  ( 600-) B  -     14.91
  497 TYR  ( 600-) A  -     14.82
 1245 TYR  ( 529-) B  -     14.75
 1519 GLN  ( 815-) B  -     13.97
 1522 ARG  ( 818-) B  -     13.61
  816 PHE  ( 921-) A  -     13.61
And so on for a total of   146 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.
