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

Date : 2025-03-13
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/4xak/wctemp_0cyc/4xak_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                                                        4XAK
ATOM  *****  O   HOH A 802      -6.116  93.376  65.970  1.00 34.92       802 O
ATOM  *****  O   HOH A 803      20.124  99.586  42.932  1.00 55.12       803 O
ATOM  *****  O   HOH A 804      -0.702  87.575  61.231  1.00 64.61       804 O
ATOM  *****  O   HOH A 805      24.723  69.391  57.247  1.00 59.40       805 O
ATOM  *****  O   HOH A 806       0.706  90.814  71.915  1.00 45.91       806 O
ATOM  *****  O   HOH A 807      11.012  86.558  44.213  1.00 46.42       807 O
ATOM  *****  O   HOH A 808      17.840  93.185  38.081  1.00 57.64       808 O
ATOM  *****  O   HOH A 809      38.945  75.851  74.388  1.00 61.38       809 O
ATOM  *****  O   HOH A 810      12.985  84.298  42.828  1.00 39.84       810 O
ATOM  *****  O   HOH A 811      -0.898  99.778  73.974  1.00 45.27       811 O
ATOM  *****  O   HOH A 812      11.519  90.037  38.473  1.00 51.02       812 O
ATOM  *****  O   HOH A 813      22.994  73.899  66.843  1.00 52.12       813 O
ATOM  *****  O   HOH A 814      24.292  75.645  67.755  1.00 72.01       814 O
ATOM  *****  O   HOH A 815      34.987  73.019  65.393  1.00 49.94       815 O
ATOM  *****  O   HOH A 816      25.155  90.465  53.605  1.00 47.43       816 O
ATOM  *****  O   HOH A 817       5.048  87.415  56.241  1.00 47.08       817 O
ATOM  *****  O   HOH A 818       7.741  92.057  43.702  1.00 49.27       818 O
ATOM  *****  O   HOH A 819       1.746 103.576  63.228  1.00 37.75       819 O
ATOM  *****  O   HOH A 820      26.812  93.239  49.834  1.00 66.25       820 O
ATOM  *****  O   HOH A 821      12.681  88.324  67.170  1.00 47.92       821 O
ATOM  *****  O   HOH A 822       0.678 106.152  63.659  1.00 55.17       822 O
ATOM  *****  O   HOH A 823      29.076  87.902  56.513  1.00 45.67       823 O
ATOM  *****  O   HOH A 824      11.411 107.582  58.994  1.00 60.30       824 O
ATOM  *****  O   HOH A 825      30.464  77.728  66.943  1.00 48.19       825 O
ATOM  *****  O   HOH A 826      12.726  91.134  65.090  1.00 60.31       826 O
ATOM  *****  O   HOH A 827      25.842  92.627  46.194  1.00 45.67       827 O
ATOM  *****  O   HOH A 828       6.858  81.049  61.242  1.00 57.17       828 O
ATOM  *****  O   HOH A 829      31.447  83.159  47.360  1.00 38.50       829 O
ATOM  *****  O   HOH A 830      34.484  86.490  54.408  1.00 46.09       830 O
ATOM  *****  O   HOH A 831      10.558  89.703  49.994  1.00 40.48       831 O
ATOM  *****  O   HOH A 832      10.886 102.948  75.446  1.00 67.00       832 O
ATOM  *****  O   HOH A 833      30.134  76.862  69.350  1.00 56.51       833 O
ATOM  *****  O   HOH A 834      17.416  76.470  67.993  1.00 52.39       834 O
ATOM  *****  O   HOH A 835      33.014  87.777  56.367  1.00 52.20       835 O
ATOM  *****  O   HOH A 836      41.857  78.274  57.512  1.00 44.05       836 O
ATOM  *****  O   HOH A 837      40.881  77.602  55.507  1.00 48.93       837 O
ATOM  *****  O   HOH A 838      25.846  81.408  40.622  1.00 43.00       838 O
ATOM  *****  O   HOH A 839      25.540  67.509  55.349  1.00 69.20       839 O
ATOM  *****  O   HOH A 840      43.199  73.264  65.273  1.00 61.37       840 O
ATOM  *****  O   HOH A 841      43.899  76.122  52.495  1.00 60.52       841 O
ATOM  *****  O   HOH A 842      15.238  91.394  72.413  1.00 69.32       842 O
ATOM  *****  O   HOH A 843      13.398  89.056  71.833  1.00 54.00       843 O
ATOM  *****  O   HOH A 844       8.157  83.969  65.650  1.00 62.19       844 O
ATOM  *****  O   HOH A 845      11.449  83.323  62.193  1.00 53.30       845 O
ATOM  *****  O   HOH A 846      13.963  84.806  73.075  1.00 52.73       846 O
ATOM  *****  O   HOH A 847      13.008  82.895  72.036  1.00 61.47       847 O
ATOM  *****  O   HOH A 848      28.570  84.244  38.071  1.00 63.92       848 O
ATOM  *****  O   HOH H 302      63.554  38.500  26.707  1.00 45.41       302 O
ATOM  *****  O   HOH H 303      72.732  53.396  20.119  1.00 50.97       303 O
ATOM  *****  O   HOH H 304      25.672  67.270  24.713  1.00 56.81       304 O
ATOM  *****  O   HOH H 305      68.447  31.939  11.248  1.00 66.26       305 O
ATOM  *****  O   HOH H 306      25.041  75.999  35.353  1.00 55.90       306 O
ATOM  *****  O   HOH H 307      25.875  60.440  34.224  1.00 46.73       307 O
ATOM  *****  O   HOH H 308      26.144  67.727  22.434  1.00 52.91       308 O
ATOM  *****  O   HOH H 309      24.664  55.460  21.451  1.00 64.48       309 O
ATOM  *****  O   HOH H 310      41.376  67.550  26.595  1.00 31.47       310 O
ATOM  *****  O   HOH H 311      38.928  72.601  49.266  1.00 39.53       311 O
ATOM  *****  O   HOH H 312      51.377  52.315  24.360  1.00 46.99       312 O
ATOM  *****  O   HOH H 313      30.437  75.994  32.942  1.00 43.00       313 O
ATOM  *****  O   HOH H 314      48.753  60.393  33.816  1.00 52.02       314 O
ATOM  *****  O   HOH H 315      43.082  53.550  23.818  1.00 29.24       315 O
ATOM  *****  O   HOH H 316      49.970  64.894  43.515  1.00 38.15       316 O
ATOM  *****  O   HOH H 317      48.205  42.026  11.672  1.00 58.05       317 O
ATOM  *****  O   HOH H 318      50.433  69.196  50.185  1.00 58.03       318 O
ATOM  *****  O   HOH H 319      49.641  71.182  49.357  1.00 43.84       319 O
ATOM  *****  O   HOH H 320      35.281  49.455  23.061  1.00 47.78       320 O
ATOM  *****  O   HOH H 321      39.295  52.749  18.277  1.00 41.88       321 O
ATOM  *****  O   HOH H 322      27.447  62.249  47.002  1.00 34.60       322 O
ATOM  *****  O   HOH H 323      39.168  62.562  22.409  1.00 46.45       323 O
ATOM  *****  O   HOH H 324      51.152  54.941  22.706  1.00 46.76       324 O
ATOM  *****  O   HOH H 325      41.273  52.746  28.148  1.00 36.64       325 O
ATOM  *****  O   HOH H 326      30.605  49.242  26.739  1.00 51.62       326 O
ATOM  *****  O   HOH H 327      28.031  57.074  44.347  1.00 51.28       327 O
ATOM  *****  O   HOH H 328      38.507  56.343  20.634  1.00 55.43       328 O
ATOM  *****  O   HOH H 329      70.297  42.300   2.969  1.00 61.39       329 O
ATOM  *****  O   HOH H 330      36.157  48.614  30.967  1.00 52.93       330 O
ATOM  *****  O   HOH H 331      38.599  67.717  26.160  1.00 56.17       331 O
ATOM  *****  O   HOH H 332      48.859  73.279  52.675  1.00 59.68       332 O
ATOM  *****  O   HOH H 333      29.254  59.760  40.775  1.00 57.89       333 O
ATOM  *****  O   HOH H 334      27.626  57.916  49.277  1.00 49.25       334 O
ATOM  *****  O   HOH H 335      26.785  59.503  47.621  1.00 46.24       335 O
ATOM  *****  O   HOH H 336      76.563  40.323  22.734  1.00 59.32       336 O
ATOM  *****  O   HOH H 337      28.599  56.853  47.027  1.00 63.12       337 O
ATOM  *****  O   HOH H 338      30.510  67.508  25.535  1.00 45.33       338 O
ATOM  *****  O   HOH H 339      69.483  40.249   2.165  1.00 68.44       339 O
ATOM  *****  O   HOH H 340      34.403  72.418  24.182  1.00 64.27       340 O
ATOM  *****  O   HOH H 341      43.923  47.706  11.180  1.00 48.83       341 O
ATOM  *****  O   HOH H 342      32.212  65.657  24.618  1.00 76.07       342 O
ATOM  *****  O   HOH H 343      34.259  47.628  25.226  1.00 54.52       343 O
ATOM  *****  O   HOH H 344      27.543  75.059  41.503  1.00 43.29       344 O
ATOM  *****  O   HOH H 345      25.991  64.104  45.854  1.00 46.08       345 O
ATOM  *****  O   HOH H 346      71.989  49.051  27.759  1.00 71.41       346 O
ATOM  *****  O   HOH H 347      62.514  56.704  23.051  1.00 49.55       347 O
ATOM  *****  O   HOH H 348      49.539  57.695  20.611  1.00 50.59       348 O
ATOM  *****  O   HOH H 349      44.819  53.677   8.491  1.00 53.80       349 O
ATOM  *****  O   HOH H 350      47.401  56.374  34.047  1.00 56.15       350 O
ATOM  *****  O   HOH H 351      35.367  73.315  31.457  1.00 43.25       351 O
ATOM  *****  O   HOH H 352      34.497  74.523  29.769  1.00 48.54       352 O
ATOM  *****  O   HOH H 353      36.358  83.307  51.096  1.00 56.76       353 O
ATOM  *****  O   HOH H 354      27.776  75.811  37.076  1.00 53.82       354 O
ATOM  *****  O   HOH H 355      34.258  88.806  47.753  1.00 62.25       355 O
ATOM  *****  O   HOH H 356      46.818  72.659  52.287  1.00 58.07       356 O
ATOM  *****  O1  GOL L 500      54.413  54.038  16.397  1.00 53.43       O1  O
ATOM  *****  C2  GOL L 500      54.121  53.535  14.088  1.00 61.22       C2  C
ATOM  *****  O2  GOL L 500      53.354  52.416  13.706  1.00 68.44       O2  O
ATOM  *****  C3  GOL L 500      54.145  54.551  12.955  1.00 56.10       C3  C
ATOM  *****  O3  GOL L 500      54.876  54.018  11.876  1.00 55.72       O3  O
ATOM  *****  O1  GOL L 501      58.589  68.903  39.500  1.00 71.58       O1  O
ATOM  *****  C2  GOL L 501      60.166  70.623  39.016  1.00 67.11       C2  C
ATOM  *****  O2  GOL L 501      61.043  71.345  39.849  1.00 70.28       O2  O
ATOM  *****  C3  GOL L 501      60.776  70.516  37.626  1.00 59.49       C3  C
ATOM  *****  O3  GOL L 501      60.725  71.783  37.014  1.00 60.21       O3  O
ATOM  *****  O   HOH L 602      64.980  61.897  -2.751  1.00 70.15       602 O
ATOM  *****  O   HOH L 603      49.423  83.219  49.293  1.00 43.31       603 O
ATOM  *****  O   HOH L 604      66.212  80.276  42.617  1.00 30.98       604 O
ATOM  *****  O   HOH L 605      69.068  71.231  39.113  1.00 49.97       605 O
ATOM  *****  O   HOH L 606      58.770  87.328  38.417  1.00 60.62       606 O
ATOM  *****  O   HOH L 607      53.166  77.196  49.815  1.00 37.14       607 O
ATOM  *****  O   HOH L 608      50.985  89.124  42.077  1.00 62.24       608 O
ATOM  *****  O   HOH L 609      67.416  83.852  28.201  1.00 55.54       609 O
ATOM  *****  O   HOH L 610      58.860  75.204  49.740  1.00 44.82       610 O
ATOM  *****  O   HOH L 611      65.772  81.901  40.921  1.00 37.91       611 O
ATOM  *****  O   HOH L 612      63.141  83.210  40.446  1.00 34.64       612 O
ATOM  *****  O   HOH L 613      71.990  79.265  29.149  1.00 38.45       613 O
ATOM  *****  O   HOH L 614      59.820  76.316  47.979  1.00 43.81       614 O
ATOM  *****  O   HOH L 615      48.913  49.584  -4.841  1.00 72.46       615 O
ATOM  *****  O   HOH L 616      64.133  76.368  46.483  1.00 49.51       616 O
ATOM  *****  O   HOH L 617      73.089  66.102   4.086  1.00 58.75       617 O
ATOM  *****  O   HOH L 618      70.009  56.041  29.145  1.00 68.76       618 O
ATOM  *****  O   HOH L 619      74.111  63.659  19.423  1.00 55.89       619 O
ATOM  *****  O   HOH L 620      62.309  75.853  48.246  1.00 62.36       620 O
ATOM  *****  O   HOH L 621      53.422  90.616  42.329  1.00 58.89       621 O
ATOM  *****  O   HOH L 622      57.547  66.230  12.395  1.00 39.26       622 O
ATOM  *****  O   HOH L 623      44.010  73.398  28.338  1.00 34.75       623 O
ATOM  *****  O   HOH L 624      54.103  66.247  35.681  1.00 35.10       624 O
ATOM  *****  O   HOH L 625      50.458  63.624  30.724  1.00 45.67       625 O
ATOM  *****  O   HOH L 626      62.042  71.416  17.396  1.00 33.69       626 O
ATOM  *****  O   HOH L 627      56.204  65.169  10.565  1.00 56.02       627 O
ATOM  *****  O   HOH L 628      65.726  60.742  19.389  1.00 29.73       628 O
ATOM  *****  O   HOH L 629      50.340  63.599  28.506  1.00 56.40       629 O
ATOM  *****  O   HOH L 630      33.499  72.165  43.216  1.00 37.62       630 O
ATOM  *****  O   HOH L 631      48.850  42.565   9.479  1.00 51.66       631 O
ATOM  *****  O   HOH L 632      57.719  64.837  20.253  1.00 37.63       632 O
ATOM  *****  O   HOH L 633      62.211  83.554  37.858  1.00 44.17       633 O
ATOM  *****  O   HOH L 634      45.384  79.630  25.622  1.00 38.10       634 O
ATOM  *****  O   HOH L 635      49.083  85.656  26.578  1.00 39.10       635 O
ATOM  *****  O   HOH L 636      63.680  70.197   8.895  1.00 43.28       636 O
ATOM  *****  O   HOH L 637      59.726  69.197  26.373  1.00 55.82       637 O
ATOM  *****  O   HOH L 638      43.767  82.758  44.742  1.00 39.29       638 O
ATOM  *****  O   HOH L 639      46.527  93.095  35.057  1.00 65.28       639 O
ATOM  *****  O   HOH L 640      56.953  86.203  36.478  1.00 53.21       640 O
ATOM  *****  O   HOH L 641      41.974  75.126  27.182  1.00 58.29       641 O
ATOM  *****  O   HOH L 642      53.534  61.934  16.757  1.00 33.37       642 O
ATOM  *****  O   HOH L 643      73.844  66.664  10.895  1.00 42.77       643 O
ATOM  *****  O   HOH L 644      73.408  76.951  24.711  1.00 43.18       644 O
ATOM  *****  O   HOH L 645      54.820  67.864  27.311  1.00 46.77       645 O
ATOM  *****  O   HOH L 646      55.361  63.528   7.171  1.00 59.14       646 O
ATOM  *****  O   HOH L 647      59.091  73.228  17.745  1.00 64.15       647 O
ATOM  *****  O   HOH L 648      63.463  60.794  21.305  1.00 33.70       648 O
ATOM  *****  O   HOH L 649      66.730  71.376   3.437  1.00 55.99       649 O
ATOM  *****  O   HOH L 650      50.983  65.913  41.197  1.00 46.97       650 O
ATOM  *****  O   HOH L 651      64.438  60.870  27.130  1.00 55.02       651 O
ATOM  *****  O   HOH L 652      59.568  75.160  20.024  1.00 63.14       652 O
ATOM  *****  O   HOH L 653      35.739  87.698  42.167  1.00 54.45       653 O
ATOM  *****  O   HOH L 654      68.088  56.234  30.495  1.00 66.12       654 O
ATOM  *****  O   HOH L 655      40.812  91.823  39.225  1.00 49.35       655 O
ATOM  *****  O   HOH L 656      36.518  89.626  41.234  1.00 57.42       656 O
ATOM  *****  O   HOH L 657      51.241  84.340  38.005  1.00 37.34       657 O
ATOM  *****  O   HOH L 658      50.895  69.112  42.521  1.00 43.68       658 O
ATOM  *****  O   HOH L 659      53.273  70.290  43.510  1.00 39.30       659 O
ATOM  *****  O   HOH L 660      71.356  56.523  14.656  1.00 61.80       660 O
ATOM  *****  O   HOH L 661      55.096  63.288  20.370  1.00 55.79       661 O
ATOM  *****  O   HOH L 662      51.311  60.560  15.288  1.00 61.76       662 O
ATOM  *****  O   HOH L 663      52.283  50.915  12.403  1.00 49.39       663 O
ATOM  *****  O   HOH L 664      61.009  73.695  16.249  1.00 56.89       664 O
ATOM  *****  O   HOH L 665      60.714  83.696  26.462  1.00 48.26       665 O
ATOM  *****  O   HOH L 666      62.155  66.767  27.808  1.00 69.03       666 O
ATOM  *****  O   HOH L 667      50.496  68.332  28.286  1.00 47.33       667 O
ATOM  *****  O   HOH L 668      70.830  58.757   6.016  1.00 48.29       668 O
ATOM  *****  O   HOH L 669      73.550  68.811   9.682  1.00 48.30       669 O
ATOM  *****  O   HOH L 670      61.452  70.743   6.464  1.00 60.28       670 O
ATOM  *****  O   HOH L 671      68.659  52.555  -0.118  1.00 48.30       671 O
ATOM  *****  O   HOH L 672      53.075  64.250  15.324  1.00 46.00       672 O
ATOM  *****  O   HOH L 673      65.642  70.885   0.904  1.00 71.58       673 O
ATOM  *****  O   HOH L 674      71.421  56.180   6.594  1.00 59.93       674 O
ATOM  *****  O   HOH L 675      63.783  58.790  23.931  1.00 63.69       675 O
ATOM  *****  O   HOH L 676      72.878  62.819  17.205  1.00 52.34       676 O
ATOM  *****  O   HOH L 677      73.452  60.921   9.982  1.00 65.89       677 O
ATOM  *****  O   HOH L 678      32.431  84.392  33.924  1.00 61.20       678 O
ATOM  *****  O   HOH L 679      56.088  66.781  36.891  1.00 56.15       679 O
ATOM  *****  O   HOH B 802      58.521 -21.087  92.366  1.00 59.29       802 O
ATOM  *****  O   HOH B 803      76.903  -5.816 105.193  1.00 65.45       803 O
ATOM  *****  O   HOH B 804      77.598 -16.728 122.022  1.00 46.44       804 O
ATOM  *****  O   HOH B 805      73.547 -21.965 115.307  1.00 48.74       805 O
ATOM  *****  O   HOH B 806      69.244 -11.980 130.938  1.00 34.15       806 O
ATOM  *****  O   HOH B 807      71.799 -25.425 119.572  1.00 45.20       807 O
ATOM  *****  O   HOH B 808      69.939  -3.458 126.828  1.00 50.74       808 O
ATOM  *****  O   HOH B 809      70.567  -7.553 132.058  1.00 47.75       809 O
ATOM  *****  O   HOH B 810      65.815  -8.122 136.522  1.00 44.13       810 O
ATOM  *****  O   HOH B 811      56.944 -22.669  92.999  1.00 57.93       811 O
ATOM  *****  O   HOH B 812      66.379  -1.452  93.274  1.00 72.31       812 O
ATOM  *****  O   HOH B 813      64.713 -13.117 106.062  1.00 48.77       813 O
ATOM  *****  O   HOH B 814      71.953  -3.426 125.416  1.00 45.38       814 O
ATOM  *****  O   HOH B 815      66.902  -1.547 117.709  1.00 43.98       815 O
ATOM  *****  O   HOH B 816      56.008   1.094  94.492  1.00 61.57       816 O
ATOM  *****  O   HOH B 817      74.410   2.919 119.572  1.00 57.29       817 O
ATOM  *****  O   HOH B 818      67.134  -6.863 122.057  1.00 45.50       818 O
ATOM  *****  O   HOH B 819      59.697  -0.944 121.350  1.00 66.48       819 O
ATOM  *****  O   HOH B 820      61.619 -24.911 109.421  1.00 50.86       820 O
ATOM  *****  O   HOH B 821      57.473  -1.710 121.191  1.00 60.28       821 O
ATOM  *****  O   HOH B 822      62.166 -14.837  94.257  1.00 54.63       822 O
ATOM  *****  O   HOH B 823      45.840 -18.939 127.749  1.00 62.44       823 O
ATOM  *****  O   HOH B 824      51.744  -8.582 111.344  1.00 57.16       824 O
ATOM  *****  O   HOH B 825      46.479 -14.294 113.560  1.00 52.10       825 O
ATOM  *****  O   HOH B 826      58.496 -25.512 131.398  1.00 60.49       826 O
ATOM  *****  O   HOH B 827      63.004 -21.241 102.174  1.00 70.66       827 O
ATOM  *****  O   HOH B 828      55.545  -3.467 105.047  1.00 49.21       828 O
ATOM  *****  O   HOH B 829      49.533 -29.326 125.212  1.00 59.29       829 O
ATOM  *****  O   HOH B 830      47.495 -18.362 123.834  1.00 52.65       830 O
ATOM  *****  O   HOH B 831      62.022   1.679  93.914  1.00 60.49       831 O
ATOM  *****  O   HOH D 302      62.887  22.253  76.686  1.00 64.88       302 O
ATOM  *****  O   HOH D 303      73.807  31.789  70.983  1.00 47.28       303 O
ATOM  *****  O   HOH D 304      70.094  51.682  46.716  1.00 76.16       304 O
ATOM  *****  O   HOH D 305      73.595  32.424  80.729  1.00 55.81       305 O
ATOM  *****  O   HOH D 306      67.795  38.061  70.549  1.00 54.84       306 O
ATOM  *****  O   HOH D 307      70.216  39.111  71.277  1.00 57.56       307 O
ATOM  *****  O   HOH D 308      74.219  45.431  78.358  1.00 62.11       308 O
ATOM  *****  O   HOH D 309      73.615  12.795  73.010  1.00 54.53       309 O
ATOM  *****  O   HOH D 310      65.161  39.624  63.100  1.00 55.94       310 O
ATOM  *****  O   HOH D 311      69.457  33.783  81.354  1.00 58.58       311 O
ATOM  *****  O   HOH E 302      56.452  22.440  79.660  1.00 55.04       302 O
ATOM  *****  O   HOH E 303      58.980  34.375  56.641  1.00 55.66       303 O
ATOM  *****  O   HOH E 304      66.613  41.805  33.868  1.00 80.83       304 O
ATOM  *****  O   HOH E 305      62.274  29.604  54.528  1.00 69.15       305 O
ATOM  *****  O   HOH E 306      42.108  21.134  98.614  1.00 64.90       306 O
ATOM  *****  O   HOH E 307      57.890  46.235  72.659  1.00 71.33       307 O
ATOM  *****  O   HOH E 308      51.417  37.743  89.269  1.00 58.82       308 O
ATOM  *****  O   HOH E 309      53.271  37.138  90.730  1.00 56.56       309 O
ATOM  *****  O   HOH E 310      56.592  36.512  87.631  1.00 56.38       310 O
ATOM  *****  O   HOH E 311      59.057  37.531  87.979  1.00 57.63       311 O
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
Please check your SOUP carefully after this option finished.
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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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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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ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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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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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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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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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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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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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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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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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:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The 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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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:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The 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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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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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:
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:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The 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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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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ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The 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:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR reading coordinate file. WHAT IF is trying to recover.
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The line in the input file that created this problem is:
ERROR 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                                                        4XAK
 
# 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
  0.020923  0.000000  0.000000
  0.000000  0.006808  0.000000
  0.000000  0.000000  0.004987
 
# 5 # Note: Non crystallographic symmetry RMS plot
The plot shows the RMS differences between two similar chains on a residue-
by-residue basis. Individual "spikes" can be indicative of interesting or
wrong residues. If all residues show a high RMS value, the structure could
be incorrectly refined.
 
In the TeX file, a plot has been inserted here
 
Chain identifiers of the two chains: A and B
 
 All-atom RMS fit for the two chains : 0.950
 CA-only RMS fit for the two chains : 0.604
 
# 6 # Note: Non crystallographic symmetry backbone difference plot
The plot shows the differences in backbone torsion angles between two
similar chains on a residue-by-residue basis. Individual "spikes" can be
indicative of interesting or wrong residues. If all residues show high
differences, the structure could be incorrectly refined.
 
In the TeX file, a plot has been inserted here
 
Chain identifiers of the two chains: A and B
 
# 7 # Warning: Problem detected upon counting molecules and matrices
The parameter Z as given on the CRYST card represents the molecular
multiplicity in the crystallographic cell. Normally, Z equals the number of
matrices of the space group multiplied by the number of NCS relations. The
value of Z is multiplied by the integrated molecular weight of the molecules
in the file to determine the Matthews coefficient. This relation is being
validated in this option. Be aware that the validation can get confused if
both multiple copies of the molecule are present in the ATOM records and
MTRIX records are present in the header of the PDB file.
 
 Space group as read from CRYST card: P 21 21 21
 Number of matrices in space group: 4
 Highest polymer chain multiplicity in structure: 2
 Highest polymer chain multiplicity according to SEQRES: 2
 No explicit MTRIX NCS matrices found in the input file
 Value of Z as found on the CRYST1 card: 0
 Z, symmetry, and molecular multiplicity disagree
 Could it be that Z must be: 8
 
# 8 # Error: Matthews Coefficient (Vm) very high
 
The Matthews coefficient [REF] is defined as the density of the protein
structure in cubic Angstroms per Dalton. Normal values are between 1.5
(tightly packed, little room for solvent) and 4.0 (loosely packed, much
space for solvent). Some very loosely packed structures can get values a bit
higher than that.
 
Numbers this high are almost always caused by giving the wrong value for Z
on the CRYST1 card (or not giving this number at all).
 
 Molecular weight of all polymer chains: 138512.500
 Volume of the Unit Cell V= 1407582.4
 Space group multiplicity: 4
 No NCS symmetry matrices (MTRIX records) found in PDB file
 Matthews coefficient for observed atoms and Z is high: Vm= 20.324
 No Matthews coefficient given in REMARK 280
 Or should we use the previously suggested Z = 8
 which would result in Vm= 2.541
 And remember, a matrix counting problem has been reported earlier already
 
# 9 # Note: Z missing on CRYST1 card
The messages above seem likely caused by the fact that Z is missing from the
CRYST1 card.
 
# 10 # Note: All atoms are sufficiently far away from symmetry axes
None of the atoms in the structure is closer than 0.77 Angstrom to a proper
symmetry axis.
 
# 11 # Note: Chain identifiers OK
WHAT CHECK has not detected any serious chain identifier problems. But be
aware that WHAT CHECK doesn't care about the chain identifiers of waters.
 
# 12 # 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 # Note: No attached groups interfere with hydrogen bond calculations
It seems there are no sugars, lipids, etc., bound (or very close) to atoms
that otherwise could form hydrogen bonds.
 
# 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 (  381)   211 (  591) A Protein             To check
     2   212 (  701)   212 (  701) A Sugar               To check
     3   213 (  702)   213 (  702) A Sugar               To check
     4   214 (    1)   440 (  215) H Protein             To check
     5   441 (    1)   652 (  212) L Protein             To check
     6   653 (  381)   863 (  591) B Protein             To check
     7   864 (  701)   864 (  701) B Sugar               To check
     8   865 (  702)   865 (  702) B Sugar               To check
     9   866 (    1)  1003 (  126) D Protein             To check
    10  1004 (  135)  1083 (  214) D Protein             To check
    11  1084 (    1)  1233 (  150) E Protein             To check
    12  1234 (  155)  1290 (  211) E Protein             To check
    13  1291 (  500)  1291 (  500) L GOL                 To check
    14  1292 (  501)  1292 (  501) L GOL                 To check
    15  1293 ( HOH )  1293 ( HOH ) A water   (    1)     To check
    16  1294 ( HOH )  1294 ( HOH ) H water   (    1)     To check
    17  1295 ( HOH )  1295 ( HOH ) L water   (    1)     To check
    18  1296 ( HOH )  1296 ( HOH ) B water   (    1)     To check
    19  1297 ( HOH )  1297 ( HOH ) D water   (    1)     To check
    20  1298 ( HOH )  1298 ( HOH ) E water   (    1)     To check
MODELs skipped upon reading PDB file: 0
X-ray structure. No MODELs found
The total number of amino acids found is 1286
of which 244 have poor or (essentially) missing atoms
No nucleic acids observed in input file
Number of (recognized) sugars: 4
Number of water molecules: 6
Residue numbers increase monotonously OK
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
 
# 22 # Note: Ramachandran plot
In this Ramachandran plot x-signs represent glycines, squares represent
prolines, and plus-signs represent the other residues. If too many
plus-signs fall outside the contoured areas then the molecule is poorly
refined (or worse). Proline can only occur in the narrow region around
phi=-60 that also falls within the other contour islands.
 
In a colour picture, the residues that are part of a helix are shown in blue,
strand residues in red. Preferred regions for helical residues are drawn in
blue, for strand residues in red, and for all other residues in green. A full
explanation of the Ramachandran plot together with a series of examples can
be found at the WHAT CHECK website [REF].
 
In the TeX file, a plot has been inserted here
 
Chain identifier: H
 
# 23 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: L
 
# 24 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 25 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: E
 
# 26 # 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 VECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSLFSVNDFTCSQISPAAIASNCYSS
( 381)-( 440)
                     70        80        90       100       110       120
                      |         |         |         |         |         |
   61 -  120 LILDYFSYPLSMKSDLSVSSAGPISQFNYKQSFSNPTCLILATVPHNLTTITKPLKYSYI
( 441)-( 500)
                    130       140       150       160       170       180
                      |         |         |         |         |         |
  121 -  180 NKCSRFLSDDRTEVPQLVNANQYSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGST
( 501)-( 560)
                    190       200       210
                      |         |         |
  181 -  211 VAMTEQLQMGFGITVQYGTDTNSVCPKLEFA
( 561)-( 591)
                 220       230       240       250       260       270
                   |         |         |         |         |         |
  214 -  273 QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAPGQGLEWMGGIIPIFGTASY
(   1)-(  59)
                 280       290       300       310       320       330
                   |         |         |         |         |         |
  274 -  333 AQKFQGRVTITADKSTSTAYMELSSLRSEDTAVYYCARVGYCSSTSCNRGAFDIWGQGTM
(  60)-( 108)
                 340       350       360       370       380       390
                   |         |         |         |         |         |
  334 -  393 VTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
( 109)-( 168)
                 400       410       420       430       440
                   |         |         |         |         |
  394 -  440 VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS
( 169)-( 215)
                    450       460       470       480       490       500
                      |         |         |         |         |         |
  441 -  500 DIQLTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPS
(   1)-(  60)
                    510       520       530       540       550       560
                      |         |         |         |         |         |
  501 -  560 RFSGSGSGTDFTLTISSLQPEDFATYYCQQLNSYPLTFGGGTKVEIKRTVAAPSVFIFPP
(  61)-( 120)
                    570       580       590       600       610       620
                      |         |         |         |         |         |
  561 -  620 SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
( 121)-( 180)
                    630       640       650
                      |         |         |
  621 -  652 LSKADYEKHKVYACEVTHQGLSSPVTKSFNRG
( 181)-( 212)
                  660       670       680       690       700       710
                    |         |         |         |         |         |
  653 -  712 VECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSLFSVNDFTCSQISPAAIASNCYSS
( 381)-( 440)
                  720       730       740       750       760       770
                    |         |         |         |         |         |
  713 -  772 LILDYFSYPLSMKSDLSVSSAGPISQFNYKQSFSNPTCLILATVPHNLTTITKPLKYSYI
( 441)-( 500)
                  780       790       800       810       820       830
                    |         |         |         |         |         |
  773 -  832 NKCSRFLSDDRTEVPQLVNANQYSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGST
( 501)-( 560)
                  840       850       860
                    |         |         |
  833 -  863 VAMTEQLQMGFGITVQYGTDTNSVCPKLEFA
( 561)-( 591)
               870       880       890       900       910       920
                 |         |         |         |         |         |
  866 -  925 QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAPGQGLEWMGGIIPIFGTASY
(   1)-(  59)
               930       940       950       960       970       980
                 |         |         |         |         |         |
  926 -  985 AQKFQGRVTITADKSTSTAYMELSSLRSEDTAVYYCARVGYCSSTSCNRGAFDIWGQGTM
(  60)-( 108)
               990      1000
                 |         |
  986 - 1003 VTVSSASTKGPSVFPLAP
( 109)-( 126)
                1010      1020      1030      1040      1050      1060
                   |         |         |         |         |         |
 1004 - 1063 TAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTY
( 135)-( 194)
                1070      1080
                   |         |
 1064 - 1083 ICNVNHKPSNTKVDKKVEPK
( 195)-( 214)
                1090      1100      1110      1120      1130      1140
                   |         |         |         |         |         |
 1084 - 1143 DIQLTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPS
(   1)-(  60)
                1150      1160      1170      1180      1190      1200
                   |         |         |         |         |         |
 1144 - 1203 RFSGSGSGTDFTLTISSLQPEDFATYYCQQLNSYPLTFGGGTKVEIKRTVAAPSVFIFPP
(  61)-( 120)
                1210      1220      1230
                   |         |         |
 1204 - 1233 SDEQLKSGTASVVCLLNNFYPREAKVQWKV
( 121)-( 150)
                1240      1250      1260      1270      1280      1290
                   |         |         |         |         |         |
 1234 - 1290 QSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR
( 155)-( 211)
 
 
 
 
# 27 # Note: No rounded coordinates detected
No significant rounding of atom coordinates has been detected.
 
# 28 # 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.
 
# 29 # Note: No missing atoms detected in residues
All expected atoms are present in residues. This validation option has not
looked at 'things' that can or should be attached to the elementary building
blocks (amino acids, nucleotides). Even the C-terminal oxygens are treated
separately.
 
# 30 # 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.
 
   78 VAL  ( 458-) A  -   High
   79 SER  ( 459-) A  -   High
   80 SER  ( 460-) A  -   High
  107 ASN  ( 487-) A  -   High
  131 ARG  ( 511-) A  -   High
  199 THR  ( 579-) A  -   High
  200 ASP  ( 580-) A  -   High
  201 THR  ( 581-) A  -   High
  209 GLU  ( 589-) A  -   High
  214 GLN  (   1-) H  -   High
  354 LYS  ( 129-) H  -   High
  357 SER  ( 132-) H  -   High
  358 GLY  ( 133-) H  -   High
  415 GLY  ( 190-) H  -   High
  416 THR  ( 191-) H  -   High
And so on for a total of   243 lines.
 
# 31 # 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.
 
  211 ALA  ( 591-) A  -        OK
  440 SER  ( 215-) H  -        OK
  652 GLY  ( 212-) L  -        OK
  863 ALA  ( 591-) B  -        OK
 1003 PRO  ( 126-) D  -        OK (8)
 1083 LYS  ( 214-) D  -        OK
 1233 VAL  ( 150-) E  -        OK (4)
 1290 ARG  ( 211-) E  -        -OXT
 
# 32 # Note: Weights administratively correct
All atomic occupancy factors ('weights') fall in the 0.0--1.0 range, which
makes them administratively correct.
 
# 33 # 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.
 
# 34 # 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.
 
# 35 # 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
 
# 36 # 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
 
# 37 # 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 :  0.872 over    7475 bonds
Average difference in B over a bond :    3.19
RMS difference in B over a bond :    4.32
 
# 38 # Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
number.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: H
 
# 39 # Note: B-factor plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: L
 
# 40 # Note: B-factor plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 41 # Note: B-factor plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: E
 
# 42 # 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.
 
# 43 # Note: Valine nomenclature OK
No errors were detected in valine nomenclature.
 
# 44 # Note: Threonine nomenclature OK
No errors were detected in threonine nomenclature.
 
# 45 # Note: Isoleucine nomenclature OK
No errors were detected in isoleucine nomenclature.
 
# 46 # Note: Leucine nomenclature OK
No errors were detected in leucine nomenclature.
 
# 47 # Note: Arginine nomenclature OK
No errors were detected in arginine nomenclature.
 
# 48 # Warning: Tyrosine convention problem
The tyrosine residues listed in the table below have their chi-2 not between
-90.0 and 90.0
 
  119 TYR  ( 499-) A  -
 
# 49 # Warning: Phenylalanine convention problem
The phenylalanine residues listed in the table below have their chi-2 not
between -90.0 and 90.0.
 
  745 PHE  ( 473-) B  -
 
# 50 # Note: Aspartic acid torsion conventions OK
No errors were detected in aspartic acid torsion angle conventions.
 
# 51 # Note: Glutamic acid torsion conventions OK
No errors were detected in glutamic acid torsion angle conventions.
 
# 52 # 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).
 
# 53 # 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.
 
# 54 # Note: No decreasing residue numbers
All residue numbers are strictly increasing within each chain.
 
# 55 # 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]).
 
# 56 # 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: 0.164
 RMS-deviation in bond distances: 0.004
 
# 57 # Note: No bond length directionality
Comparison of bond distances with Engh and Huber [REF] standard values for
protein residues and Parkinson et al [REF] values for DNA/RNA does not show
significant systematic deviations.
 
# 58 # Note: All bond angles OK
All bond angles are in agreement with standard bond angles using a tolerance
of 4 sigma (both standard values and sigma for protein residues have been
taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al. [REF]).
Please note that disulphide bridges are neglected.
 
# 59 # Warning: Low bond angle variability
Bond angles were found to deviate less than normal from the standard bond
angles (normal values for protein residues were taken from Engh and Huber
[REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below
is expected to be near 1.0 for a normally restrained data set. The fact that
it is lower than 0.667 in this structure might indicate that too-strong
restraints have been used in the refinement. This can only be a problem for
high resolution X-ray structures.
 
 RMS Z-score for bond angles: 0.337
 RMS-deviation in bond angles: 0.733
 
# 60 # Note: Residue hand check OK
No atoms are observed that have the wrong handedness. Be aware, though, that
WHAT CHECK might have corrected the handedness of some atoms already. The
handedness has not been corrected for any case where the problem is worse
than just an administrative discomfort.
 
# 61 # Note: Chirality OK
All protein atoms have proper chirality, or there is no intact protein
present in the PDB file.
The average deviation= 0.378
 
# 62 # 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 : 0.310
 
# 63 # Note: Tau angles OK
All of the tau angles (N-C-alpha-C) of amino acids fall within expected
RMS deviations.
 
# 64 # Note: Low tau angle deviations
The RMS Z-score for the tau angles (N-C-alpha-C) in the structure is rather
low. For well refined structures this number is expected to be near 1.0. The
fact that it is lower than 0.5 probably means that the tau angles were
strongly restrained during refinement. Whether this is a problem or not
depends on the quality and quantity of experimental data. 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 : 0.490
 
# 65 # Note: Side chain planarity OK
All of the side chains of residues that have an intact planar group are
planar within expected RMS deviations.
 
# 66 # 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.
 
# 67 # Warning: Ramachandran Z-score low
The score expressing how well the backbone conformations of all residues
correspond to the known allowed areas in the Ramachandran plot is a bit low.
 
 Ramachandran Z-score : -3.402
 
# 68 # 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.
 
# 69 # 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.
 
 1018 PRO  ( 149-) D  -   -3.1
  372 PRO  ( 147-) H  -   -3.0
 1016 PRO  ( 147-) D  -   -3.0
  374 PRO  ( 149-) H  -   -2.9
  695 PHE  ( 423-) B  -   -2.7
  363 LEU  ( 138-) H  -   -2.7
   43 PHE  ( 423-) A  -   -2.6
 1007 LEU  ( 138-) D  -   -2.6
  451 LEU  (  11-) L  -   -2.4
  403 LEU  ( 178-) H  -   -2.4
 1260 LEU  ( 181-) E  -   -2.2
  783 ARG  ( 511-) B  -   -2.1
  217 LEU  (   4-) H  -   -2.1
  916 ILE  (  51-) D  -   -2.1
  241 THR  (  28-) H  -   -2.1
  381 SER  ( 156-) H  -   -2.1
  243 SER  (  30-) H  -   -2.1
   76 LEU  ( 456-) A  -   -2.1
  689 LEU  ( 417-) B  -   -2.0
  942 SER  (  76-) D  -   -2.0
  545 GLU  ( 105-) L  -   -2.0
 1152 THR  (  69-) E  -   -2.0
  895 SER  (  30-) D  -   -2.0
 
# 70 # Warning: Backbone evaluation reveals unusual conformations
The residues listed in the table below have abnormal backbone torsion
angles.
 
Residues with `forbidden' phi-psi combinations are listed, as well as
residues with unusual omega angles (deviating by more than 3 sigma from the
normal value). Please note that it is normal if about 5 percent of the
residues is listed here as having unusual phi-psi combinations.
 
    6 SER  ( 386-) A  - Omega to (next) Pro poor
   11 GLY  ( 391-) A  - Poor phi/psi
   12 THR  ( 392-) A  - Omega to (next) Pro poor
   13 PRO  ( 393-) A  - Omega to (next) Pro poor
   47 GLN  ( 427-) A  - Poor phi/psi
   49 SER  ( 429-) A  - Omega to (next) Pro poor
   68 TYR  ( 448-) A  - Omega to (next) Pro poor
   82 GLY  ( 462-) A  - Omega to (next) Pro poor
   95 ASN  ( 475-) A  - Omega to (next) Pro poor
  104 VAL  ( 484-) A  - Omega to (next) Pro poor
  113 LYS  ( 493-) A  - Omega to (next) Pro poor
  130 ASP  ( 510-) A  - Poor phi/psi
  134 VAL  ( 514-) A  - Omega to (next) Pro poor
  141 ASN  ( 521-) A  - Poor phi/psi
  144 SER  ( 524-) A  - Omega to (next) Pro poor
And so on for a total of   164 lines.
 
# 71 # 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  ( 411-) A  -    -1.32
   61 LEU  ( 441-) A  -    -1.31
   76 LEU  ( 456-) A  -    -1.30
  168 LEU  ( 548-) A  -    -1.32
  217 LEU  (   4-) H  -    -1.32
  363 LEU  ( 138-) H  -    -1.32
  403 LEU  ( 178-) H  -    -1.31
  451 LEU  (  11-) L  -    -1.31
  473 LEU  (  33-) L  -    -1.31
  494 LEU  (  54-) L  -    -1.30
  518 LEU  (  78-) L  -    -1.30
  531 LEU  (  91-) L  -    -1.32
  615 LEU  ( 175-) L  -    -1.31
  641 LEU  ( 201-) L  -    -1.32
  660 LEU  ( 388-) B  -    -1.32
And so on for a total of   478 lines.
 
# 72 # Note: chi-1/chi-2 angle correlation Z-score OK
The score expressing how well the chi-1/chi-2 angles of all residues
correspond to the populated areas in the database is
within expected ranges for well-refined structures.
 
 chi-1/chi-2 correlation Z-score : -2.762
 
# 73 # 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.
 
  148 SER  ( 528-) A  -   0.34
  800 SER  ( 528-) B  -   0.34
 1049 SER  ( 180-) D  -   0.35
  758 HIS  ( 486-) B  -   0.35
  600 GLN  ( 160-) L  -   0.36
   98 CYS  ( 478-) A  -   0.36
  750 CYS  ( 478-) B  -   0.36
 1255 SER  ( 176-) E  -   0.36
  403 LEU  ( 178-) H  -   0.37
  768 LYS  ( 496-) B  -   0.38
  405 SER  ( 180-) H  -   0.39
  770 SER  ( 498-) B  -   0.39
  916 ILE  (  51-) D  -   0.39
  697 CYS  ( 425-) B  -   0.39
 
# 74 # 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!
 
   88 ASN  ( 468-) A  -       0
  130 ASP  ( 510-) A  -       0
  199 THR  ( 579-) A  -       0
  242 PHE  (  29-) H  -       0
  740 ASN  ( 468-) B  -       0
  894 PHE  (  29-) D  -       0
   47 GLN  ( 427-) A  -       1
  173 TRP  ( 553-) A  -       1
  970 THR  ( 100A) D  -       1
 1113 ARG  (  30-) E  -       1
 1134 ALA  (  51-) E  -       1
 1176 SER  (  93-) E  -       1
  200 ASP  ( 580-) A  -       2
  322 ARG  ( 100E) H  -       2
  371 PHE  ( 146-) H  -       2
  372 PRO  ( 147-) H  -       2
  373 GLU  ( 148-) H  -       2
  470 ARG  (  30-) L  -       2
  523 PHE  (  83-) L  -       2
  582 ARG  ( 142-) L  -       2
  699 GLN  ( 427-) B  -       2
  782 ASP  ( 510-) B  -       2
  974 ARG  ( 100E) D  -       2
 1015 PHE  ( 146-) D  -       2
 1016 PRO  ( 147-) D  -       2
 1017 GLU  ( 148-) D  -       2
 1175 ASN  (  92-) E  -       2
 1177 TYR  (  94-) E  -       2
 1225 ARG  ( 142-) E  -       2
 
# 75 # 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 : -0.279
 
# 76 # Warning: Omega angles too tightly restrained
The omega angles for trans-peptide bonds in a structure are expected to give
a gaussian distribution with the average around +178 degrees and a standard
deviation around 5.5 degrees. These expected values were obtained from very
accurately determined structures. Many protein structures are too tightly
restrained. This seems to be the case with the current structure too, as the
observed standard deviation is below 4.0 degrees.
 
Omega average and std. deviation= 179.620 3.985
 
# 77 # Note: PRO puckering amplitude OK
Puckering amplitudes for all PRO residues are within normal ranges.
 
# 78 # 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].
 
  374 PRO  ( 149-) H  -  -54.5 half-chair C-beta/C-alpha (-54 degrees)
  520 PRO  (  80-) L  -  155.3 half-chair C-alpha/N (162 degrees)
 1016 PRO  ( 147-) D  -  -65.0 envelop C-beta (-72 degrees)
 1018 PRO  ( 149-) D  -  -19.2 half-chair C-alpha/N (-18 degrees)
 1178 PRO  (  95-) E  -   22.2 half-chair N/C-delta (18 degrees)
 
# 79 # 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!
 
  358 GLY  ( 133-) H  -  3.47   80
 1151 GLY  (  68-) E  -  1.84   28
  198 GLY  ( 578-) A  -  1.74   80
  508 GLY  (  68-) L  -  1.54   18
   76 LEU  ( 456-) A  -  1.50   38
 
# 80 # 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.
 
  108 LEU  ( 488-) A  - TT+   Highly likely
  141 ASN  ( 521-) A  - TT+   Highly likely
  244 SER  (  31-) H  - TT+   Highly likely
  517 SER  (  77-) L  - TT+   Highly likely
  591 ASP  ( 151-) L  - TT+   Highly likely
  728 LEU  ( 456-) B  - TT+   Highly likely
  782 ASP  ( 510-) B  - TT+   Highly likely
  793 ASN  ( 521-) B  - TT+   Highly likely
  950 SER  (  82B) D  - TT+   Highly likely
 1133 ALA  (  50-) E  - TT+   Highly likely
 1250 SER  ( 171-) E  - TT+   Highly likely
   26 ASN  ( 406-) A  - TT+   Likely
   81 ALA  ( 461-) A  - TT+   Likely
   82 GLY  ( 462-) A  - TT+   Likely
  107 ASN  ( 487-) A  - TT+   Likely
And so on for a total of    73 lines.
 
# 81 # Error: Abnormally short interatomic distances
The pairs of atoms listed in the table below have an unusually short
interactomic distance; each bump is listed in only one direction.
 
The contact distances of all atom pairs have been checked. Two atoms are
said to `bump' if they are closer than the sum of their Van der Waals radii
minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom
is used. The first number in the table tells you how much shorter that
specific contact is than the acceptable limit. The second distance is the
distance between the centres of the two atoms. Although we believe that two
water atoms at 2.4 A distance are too close, we only report water pairs that
are closer than this rather short distance.
 
INTRA and INTER indicate whether the clashes are between atoms in the same
asymmetric unit, or atoms in symmetry related asymmetric units, respectively.
The last text-item on each line represents the status of the atom pair. If
the final column contains the text 'HB', the bump criterion was relaxed
because there could be a hydrogen bond. Similarly relaxed criteria are used
for 1--3 and 1--4 interactions (listed as 'B2' and 'B3', respectively).
If the last column is 'BF', the sum of the B-factors of the atoms is higher
than 80, which makes the appearance of the bump somewhat less severe because
the atoms probably are not there anyway. BL, on the other hand, indicates
that the bumping atoms both have a low B-factor, and that makes the bumps
more worrisome.
 
Bumps between atoms for which the sum of their occupancies is lower than one
are not reported. If the MODEL number does not exist (as is the case in most
X-ray files), a minus sign is printed instead.
 
  759 ASN  ( 487-) B  -    ND2 <-->   865 NAG  ( 702-) B  -    C1     1.67    1.43  INTRA BF
  682 ASN  ( 410-) B  -    ND2 <-->   864 NAG  ( 701-) B  -    C1     1.66    1.44  INTRA BF
  107 ASN  ( 487-) A  -    ND2 <-->   213 NAG  ( 702-) A  -    C1     1.66    1.44  INTRA BF
   30 ASN  ( 410-) A  -    ND2 <-->   212 NAG  ( 701-) A  -    C1     1.66    1.44  INTRA BF
   30 ASN  ( 410-) A  -    CG  <-->   212 NAG  ( 701-) A  -    C1     0.80    2.40  INTRA BF
  682 ASN  ( 410-) B  -    CG  <-->   864 NAG  ( 701-) B  -    C1     0.79    2.41  INTRA BF
  107 ASN  ( 487-) A  -    CG  <-->   213 NAG  ( 702-) A  -    C1     0.76    2.44  INTRA BF
  759 ASN  ( 487-) B  -    CG  <-->   865 NAG  ( 702-) B  -    C1     0.76    2.44  INTRA BF
  759 ASN  ( 487-) B  -    ND2 <-->   865 NAG  ( 702-) B  -    C2     0.72    2.38  INTRA BF
  682 ASN  ( 410-) B  -    ND2 <-->   864 NAG  ( 701-) B  -    C2     0.65    2.45  INTRA BF
  107 ASN  ( 487-) A  -    ND2 <-->   213 NAG  ( 702-) A  -    C2     0.64    2.46  INTRA BF
   30 ASN  ( 410-) A  -    ND2 <-->   212 NAG  ( 701-) A  -    C2     0.61    2.49  INTRA BF
 1009 CYS  ( 140-) D  -    SG  <-->  1065 CYS  ( 196-) D  -    CB     0.46    2.04  INTRA BF
  365 CYS  ( 140-) H  -    SG  <-->   421 CYS  ( 196-) H  -    CB     0.40    2.10  INTRA BL
 1268 HIS  ( 189-) E  -    O   <-->  1290 ARG  ( 211-) E  -    NH1    0.40    2.30  INTRA BF
And so on for a total of   135 lines.
 
# 82 # 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: 25.230
Total bump value per residue: 0.105
Total number of bumps: 135
Total squared bump value: 17.720
Total number of bumps in the mildest bin: 112
Total number of bumps in the second bin: 11
Total number of bumps in the middle bin: 4
Total number of bumps in the fourth bin: 4
Total number of bumps in the worst bin: 4
 
# 83 # 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.
 
# 84 # Note: Inside/Outside residue distribution normal
The distribution of residue types over the inside and the outside of the
protein is normal.
 
inside/outside RMS Z-score : 0.956
 
# 85 # 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: H
 
# 86 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: L
 
# 87 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 88 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: E
 
# 89 # 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.
 
  651 ARG  ( 211-) L  -  -7.28
  862 PHE  ( 590-) B  -  -7.05
  210 PHE  ( 590-) A  -  -6.96
  767 LEU  ( 495-) B  -  -6.62
  115 LEU  ( 495-) A  -  -6.61
 1177 TYR  (  94-) E  -  -6.48
  439 LYS  ( 214-) H  -  -6.26
   47 GLN  ( 427-) A  -  -6.24
  534 TYR  (  94-) L  -  -6.03
  699 GLN  ( 427-) B  -  -6.01
  256 GLN  (  43-) H  -  -6.01
  820 LEU  ( 548-) B  -  -5.98
 1101 ARG  (  18-) E  -  -5.98
  168 LEU  ( 548-) A  -  -5.90
 1017 GLU  ( 148-) D  -  -5.67
  330 GLN  ( 105-) H  -  -5.65
 1225 ARG  ( 142-) E  -  -5.60
  908 GLN  (  43-) D  -  -5.58
  373 GLU  ( 148-) H  -  -5.49
  982 GLN  ( 105-) D  -  -5.46
  783 ARG  ( 511-) B  -  -5.35
  745 PHE  ( 473-) B  -  -5.15
  197 TYR  ( 577-) A  -  -5.07
  482 LYS  (  42-) L  -  -5.07
 1248 LYS  ( 169-) E  -  -5.04
 
# 90 # 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.
 
  209 GLU  ( 589-) A  -      211 --- ALA   591- (A ) -       -5.28
 
# 91 # Note: Structural average packing environment OK
The structural average packing score is within normal ranges.
 
 
Average for range     1 - 1290 :  -0.569
 
# 92 # 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: H
 
# 93 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as function
of the residue number. Low areas in the plot (below -2.0) indicate unusual
packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: L
 
# 94 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as function
of the residue number. Low areas in the plot (below -2.0) indicate unusual
packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 95 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as function
of the residue number. Low areas in the plot (below -2.0) indicate unusual
packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: E
 
# 96 # Warning: Low packing Z-score for some residues
The residues listed in the table below have an unusual packing
environment according to the 2nd generation packing check. The score
listed in the table is a packing normality Z-score: positive means
better than average, negative means worse than average. Only residues
scoring less than -2.50 are listed here. These are the unusual
residues in the structure, so it will be interesting to take a
special look at them.
 
  759 ASN  ( 487-) B  -  -2.75
  440 SER  ( 215-) H  -  -2.60
 1189 ILE  ( 106-) E  -  -2.55
 
# 97 # Note: No series of residues with abnormal new packing environment
There are no stretches of four or more residues each having a packing
Z-score worse than -1.75.
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
 
# 98 # Note: Second generation quality Z-score plot
The second generation quality Z-score smoothed over a 10 residue window
is plotted as function of the residue number. Low areas in the plot (below
-1.3) indicate unusual packing.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: H
 
# 99 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: L
 
# 100 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 101 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: E
 
# 102 # 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.
 
# 103 # Note: Water contacts OK
All water clusters make at least one contact with a non-water atom.
 
# 104 # Note: No waters need moving
All water molecules are sufficiently close to the asymmetric unit given in
the input file.
 
# 105 # Note: Water hydrogen bonds OK
All water molecules can form hydrogen bonds.
 
# 106 # 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.
 
   95 ASN  ( 475-) A  -
  136 GLN  ( 516-) A  -
  389 HIS  ( 164-) H  -
  471 ASN  (  31-) L  -
  519 GLN  (  79-) L  -
  578 ASN  ( 138-) L  -
  595 GLN  ( 155-) L  -
  738 GLN  ( 466-) B  -
  747 ASN  ( 475-) B  -
  788 GLN  ( 516-) B  -
  930 GLN  (  64-) D  -
 1138 GLN  (  55-) E  -
 1175 ASN  (  92-) E  -
 
# 107 # 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.
 
  106 HIS  ( 486-) A  -   HIS-H   0.06 HIS-E   0.58
  389 HIS  ( 164-) H  -   HIS-H   0.06 HIS-D   0.56
  425 HIS  ( 200-) H  -   HIS-H   0.07
  629 HIS  ( 189-) L  -   HIS-H   0.08 HIS-D   0.58
  638 HIS  ( 198-) L  -   HIS-H   0.03 HIS-E   0.58
  758 HIS  ( 486-) B  -   HIS-H   0.04 HIS-E   0.58
 1033 HIS  ( 164-) D  -   HIS-H   0.04 HIS-E   0.58
 1069 HIS  ( 200-) D  -   HIS-H   0.10
 1268 HIS  ( 189-) E  -   HIS-H   0.05 HIS-D   0.54
 1277 HIS  ( 198-) E  -   HIS-H   0.07 HIS-E   0.57
 
# 108 # 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.
 
   16 VAL  ( 396-) A  -    N
   17 TYR  ( 397-) A  -    N
   30 ASN  ( 410-) A  -    ND2
   82 GLY  ( 462-) A  -    N
   84 ILE  ( 464-) A  -    N
   92 SER  ( 472-) A  -    N
   95 ASN  ( 475-) A  -    N
  116 LYS  ( 496-) A  -    N
  123 CYS  ( 503-) A  -    N
  139 ASN  ( 519-) A  -    N
  144 SER  ( 524-) A  -    N
  161 TYR  ( 541-) A  -    OH
  162 ARG  ( 542-) A  -    NH2
  220 SER  (   7-) H  -    OG
  244 SER  (  31-) H  -    OG
And so on for a total of    84 lines.
 
# 109 # 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.
 
   75 ASP  ( 455-) A  -    OD1
  457 ASP  (  17-) L  -    OD1
 1115 ASP  (  32-) E  -    OD2
 1234 GLN  ( 155-) E  -    OE1
 
# 110 # 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: 1894
- of which buried: 860
Total number of acceptors: 2013
- of which buried: 718
Total number of donor+acceptors: 370
  (e.g. the Ser Ogamma that can donate and accept)
- of which buried: 67
Buried donors: 860
- without H-bond: 76
- essentially without H-bond: 0
- with only a very poor H-bond: 14
- with a poor H-bond: 14
- with a H-bond: 756
Buried acceptors: 718
- without H-bond: 116
- essentially without H-bond: 0
- with only a very poor H-bond: 11
- with a poor H-bond: 24
- with a H-bond: 567
 
# 111 # 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 (  381)   211 (  591) A Protein             To check
     2   212 (  701)   212 (  701) A Sugar               To check
     3   213 (  702)   213 (  702) A Sugar               To check
     4   214 (    1)   440 (  215) H Protein             To check
     5   441 (    1)   652 (  212) L Protein             To check
     6   653 (  381)   863 (  591) B Protein             To check
     7   864 (  701)   864 (  701) B Sugar               To check
     8   865 (  702)   865 (  702) B Sugar               To check
     9   866 (    1)  1003 (  126) D Protein             To check
    10  1004 (  135)  1083 (  214) D Protein             To check
    11  1084 (    1)  1233 (  150) E Protein             To check
    12  1234 (  155)  1290 (  211) E Protein             To check
    13  1291 (  500)  1291 (  500) L GOL                 To check
    14  1292 (  501)  1292 (  501) L GOL                 To check
    15  1293 ( HOH )  1293 ( HOH ) A water   (    1)     To check
    16  1294 ( HOH )  1294 ( HOH ) H water   (    1)     To check
    17  1295 ( HOH )  1295 ( HOH ) L water   (    1)     To check
    18  1296 ( HOH )  1296 ( HOH ) B water   (    1)     To check
    19  1297 ( HOH )  1297 ( HOH ) D water   (    1)     To check
    20  1298 ( HOH )  1298 ( HOH ) E water   (    1)     To check
 
# 112 # 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  :   2.450
  1st generation packing quality :  -0.174 (          (  -0.3,  2.5))
  2nd generation packing quality :  -0.513 (          (  -1.4,  1.2))
  Ramachandran plot appearance   :  -3.402 (poor      (  -2.4,  1.5))
  chi-1/chi-2 rotamer normality  :  -2.762 (          (  -4.2,  1.7))
  Backbone conformation          :  -0.279 (          (  -0.7,  3.6))
  Inside/Outside distribution    :   0.956
 
 RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.164 (tight)
  Bond angles                    :   0.337 (tight)
  Omega angle restraints         :   0.725 (tight)
  Side chain planarity           :   0.138 (tight)
  Improper dihedral distribution :   0.310
  B-factor distribution          :   0.872
 
# 113 # 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.
 
# 114 # 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.
 
# 115 # 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.
 
# 116 # Note: Bond length variabilty Z-score low
With a resolution of 1.5-2.5 Angstrom, you might have enough data to warrant
more bond length variability that we observed (less than 0.25). If your
resolution is close to 1.5 Angstrom, you should allow the refinement
software more freedom when it comes to applying the bond length target
restraints. If your resolution is close to 2.5 Angstrom, you should do
this too, but you might want to be a bit careful with it.
 
# 117 # Note: Bond angle variabilty Z-score low
With a resolution of 1.5-2.5 Angstrom, you might have enough data to warrant
more bond angle variability that we observed (less than 0.5). If your
resolution is close to 1.5 Angstrom, you can consider allowing the
refinement software more freedom when it comes to applying the bond angle
target restraints. If your resolution is close to 2.5 Angstrom, you can do
this too, but you might want to be a bit careful.
 
# 118 # Note: His, Asn, Gln side chain flips.
His, Asn, and Gln have an asymmetry in their side chain that is hard to
detect unless you have data at much better than 1.0 Angstrom resolution.
WHAT CHECK thinks that your structure contains His, Asn, or Gln residues that
will make better hydrogen bonds when flipped around their chi-2, chi-2, or
chi-3 side chain torsion angle, respectively. You better
check these Asn, His, and Gln residues, and if you use a refinement program
that includes molecular dynamics, then you must (after the
flips were made) refine a bit further before running WHAT CHECK again.
 
# 119 # 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.
 
 1290 ARG  ( 211-) E  -     14.74
  651 ARG  ( 211-) L  -     14.56
  862 PHE  ( 590-) B  -     14.10
  210 PHE  ( 590-) A  -     13.93
  767 LEU  ( 495-) B  -     13.24
  115 LEU  ( 495-) A  -     13.21
 1177 TYR  (  94-) E  -     13.00
 1083 LYS  ( 214-) D  -     12.83
  439 LYS  ( 214-) H  -     12.52
   47 GLN  ( 427-) A  -     12.52
 1017 GLU  ( 148-) D  -     12.38
 1225 ARG  ( 142-) E  -     12.20
  534 TYR  (  94-) L  -     12.10
  699 GLN  ( 427-) B  -     12.05
  373 GLU  ( 148-) H  -     12.03
And so on for a total of   110 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.
