WHAT IF Check report

This file was created 2012-01-05 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb1o18.ent

Checks that need to be done early-on in validation

Warning: Class of space group could be incorrect

The space group symbol indicates a different class than the unit cell given on the CRYST1 card of the PDB file.

Possible cause: The unit cell may have pseudo-symmetry, or one of the cell dimensions or the space group might be given incorrectly.

Crystal class of the cell: CUBIC

Crystal class of the space group: TRICLINIC

Space group name: P 1

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.

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 7.434
CA-only RMS fit for the two chains : 7.427

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.

Chain identifiers of the two chains: A and D

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.

Chain identifiers of the two chains: A and G

All-atom RMS fit for the two chains : 12.375
CA-only RMS fit for the two chains : 12.406

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.

Chain identifiers of the two chains: A and G

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.

Chain identifiers of the two chains: A and J

All-atom RMS fit for the two chains : 17.297
CA-only RMS fit for the two chains : 17.346

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.

Chain identifiers of the two chains: A and J

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.

Chain identifiers of the two chains: A and M

All-atom RMS fit for the two chains : 12.322
CA-only RMS fit for the two chains : 12.353

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.

Chain identifiers of the two chains: A and M

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.

Chain identifiers of the two chains: A and P

All-atom RMS fit for the two chains : 13.997
CA-only RMS fit for the two chains : 14.036

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.

Chain identifiers of the two chains: A and P

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: 1277178.5
Volume of the Unit Cell V= 27008100.0
Space group multiplicity: 1
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 21.147
Vm by authors and this calculated Vm do not agree very well

Administrative problems that can generate validation failures

Warning: Overlapping residues or molecules

This molecule contains residues or molecules that overlap too much while not being (administrated as) alternate atom/residue pairs. The residues or molecules listed in the table below have been removed before the validation continued.

Overlapping residues or molecules (for short entities) are occasionally observed in the PDB. Often these are cases like, for example, two sugars that bind equally well in the same active site, are both seen overlapping in the density, and are both entered in the PDB file as separate entities. This can cause some false positive error messsages further down the validation path, and therefore the second of the overlapping entities has been deleted before the validation continued. If you want to validate both situations, make it two PDB files, one for each sugar. And fudge reality a bit by making the occupancy of the sugar atoms 1.0 in both cases, because many validation options are not executed on atoms with low occupancy. If you go for this two-file option, please make sure that any side chains that have alternate locations depending on the sugar bound are selected in each of the two cases in agreement with the sugar that you keep for validation in that particular file.

 212 GLN   ( 215-)  A  -
 405 VAL   ( 408-)  A  -
 406 GLY   ( 409-)  A  -
 408 GLU   ( 411-)  A  -
 534 GLU   ( 537-)  A  -
 540 PRO   ( 543-)  A  -
 553 ASP   ( 556-)  A  -
 626 GLU   ( 629-)  A  -
 629 GLY   ( 632-)  A  -
 630 GLY   ( 633-)  A  -
 634 LYS   ( 637-)  A  -
 639 LYS   ( 642-)  A  -
 644 GLN   ( 647-)  A  -
 729 ILE   ( 732-)  A  -
 733 GLN   ( 736-)  A  -
 758 GLY   ( 761-)  A  -
1176 ASP   ( 339-)  D  -
1245 VAL   ( 408-)  D  -
1248 GLU   ( 411-)  D  -
1374 GLU   ( 537-)  D  -
1375 GLU   ( 538-)  D  -
1393 ASP   ( 556-)  D  -
1474 LYS   ( 637-)  D  -
1479 LYS   ( 642-)  D  -
1481 SER   ( 644-)  D  -
And so on for a total of 162 lines.

Non-validating, descriptive output paragraph

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.

Chain identifier: A

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: Q

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: 1

Note: Ramachandran plot

Chain identifier: 2

Note: Ramachandran plot

Chain identifier: 3

Note: Ramachandran plot

Chain identifier: 4

Note: Ramachandran plot

Chain identifier: 5

Note: Ramachandran plot

Chain identifier: 6

Note: Ramachandran plot

Chain identifier: 7

Note: Ramachandran plot

Chain identifier: 8

Note: Ramachandran plot

Chain identifier: 9

Note: Ramachandran plot

Chain identifier: V

Note: Ramachandran plot

Chain identifier: W

Note: Ramachandran plot

Chain identifier: X

Note: Ramachandran plot

Chain identifier: Y

Note: Ramachandran plot

Chain identifier: Z

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

  16 MLY   (  19-)  A  -
  27 MLY   (  30-)  A  -
  32 MLY   (  35-)  A  -
  46 MLY   (  49-)  A  -
  52 MLY   (  55-)  A  -
  56 MLY   (  59-)  A  -
  60 MLY   (  63-)  A  -
  81 MLY   (  84-)  A  -
  84 MLY   (  87-)  A  -
 104 MLY   ( 107-)  A  -
 127 MLY   ( 130-)  A  -
 135 MLY   ( 138-)  A  -
 187 MLY   ( 190-)  A  -
 233 MLY   ( 236-)  A  -
 245 MLY   ( 248-)  A  -
 269 MLY   ( 272-)  A  -
 292 MLY   ( 295-)  A  -
 293 MLY   ( 296-)  A  -
 344 MLY   ( 348-)  A  -
 349 MLY   ( 353-)  A  -
 363 MLY   ( 367-)  A  -
 365 MLY   ( 369-)  A  -
 381 MLY   ( 385-)  A  -
 411 MLY   ( 415-)  A  -
 427 MLY   ( 431-)  A  -
And so on for a total of 266 lines.

Warning: What type of B-factor?

WHAT IF 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. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

Temperature not mentioned in PDB file. This most likely means that the temperature record is absent.
Room temperature assumed

Warning: Low M-factor

The B-factor flatness, the M-factor, is very low. This is very worrisome. I suggest you consult the WHAT CHECK website and/or a seasoned crystallographer.

The M-factor = 0.000

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: A

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: D

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: E

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: F

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: G

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: H

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: I

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: J

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: K

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: L

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: M

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: N

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: O

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: P

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: Q

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: R

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 1

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 2

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 3

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 4

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 5

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 6

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 7

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 8

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 9

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: V

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: W

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: X

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: Y

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: Z

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

1813 ARG   (  19-)  F  -
1829 ARG   (  35-)  F  -
1886 ARG   (  92-)  F  -
1902 ARG   ( 108-)  F  -
2927 ARG   (  19-)  I  -
2943 ARG   (  35-)  I  -
3000 ARG   (  92-)  I  -
3016 ARG   ( 108-)  I  -
4040 ARG   (  19-)  L  -
4056 ARG   (  35-)  L  -
4112 ARG   (  92-)  L  -
4128 ARG   ( 108-)  L  -
5153 ARG   (  19-)  O  -
5169 ARG   (  35-)  O  -
5226 ARG   (  92-)  O  -
5242 ARG   ( 108-)  O  -
6269 ARG   (  19-)  R  -
6285 ARG   (  35-)  R  -
6342 ARG   (  92-)  R  -
6358 ARG   ( 108-)  R  -

Warning: Tyrosine convention problem

The tyrosine residues listed in the table below have their chi-2 not between -90.0 and 90.0

1784 TYR   ( 150-)  E  -
1933 TYR   ( 139-)  F  -
2898 TYR   ( 150-)  H  -
3047 TYR   ( 139-)  I  -
4011 TYR   ( 150-)  K  -
4159 TYR   ( 139-)  L  -
5124 TYR   ( 150-)  N  -
5273 TYR   ( 139-)  O  -
6240 TYR   ( 150-)  Q  -
6389 TYR   ( 139-)  R  -

Warning: Phenylalanine convention problem

The phenylalanine residues listed in the table below have their chi-2 not between -90.0 and 90.0.

1668 PHE   (  31-)  E  -
1717 PHE   (  80-)  E  -
1738 PHE   ( 101-)  E  -
1752 PHE   ( 116-)  E  -
1775 PHE   ( 140-)  E  -
1808 PHE   (  14-)  F  -
1811 PHE   (  17-)  F  -
1859 PHE   (  65-)  F  -
1881 PHE   (  87-)  F  -
1888 PHE   (  94-)  F  -
2782 PHE   (  31-)  H  -
2831 PHE   (  80-)  H  -
2851 PHE   ( 101-)  H  -
2866 PHE   ( 116-)  H  -
2890 PHE   ( 140-)  H  -
2922 PHE   (  14-)  I  -
2925 PHE   (  17-)  I  -
2973 PHE   (  65-)  I  -
2995 PHE   (  87-)  I  -
3002 PHE   (  94-)  I  -
3894 PHE   (  31-)  K  -
3943 PHE   (  80-)  K  -
3964 PHE   ( 101-)  K  -
3979 PHE   ( 116-)  K  -
4002 PHE   ( 140-)  K  -
4035 PHE   (  14-)  L  -
4038 PHE   (  17-)  L  -
4085 PHE   (  65-)  L  -
4107 PHE   (  87-)  L  -
4114 PHE   (  94-)  L  -
5007 PHE   (  31-)  N  -
5056 PHE   (  80-)  N  -
5077 PHE   ( 101-)  N  -
5091 PHE   ( 116-)  N  -
5115 PHE   ( 140-)  N  -
5148 PHE   (  14-)  O  -
5151 PHE   (  17-)  O  -
5199 PHE   (  65-)  O  -
5221 PHE   (  87-)  O  -
5228 PHE   (  94-)  O  -
6123 PHE   (  31-)  Q  -
6172 PHE   (  80-)  Q  -
6193 PHE   ( 101-)  Q  -
6208 PHE   ( 116-)  Q  -
6231 PHE   ( 140-)  Q  -
6264 PHE   (  14-)  R  -
6267 PHE   (  17-)  R  -
6315 PHE   (  65-)  R  -
6337 PHE   (  87-)  R  -
6344 PHE   (  94-)  R  -

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

1657 ASP   (  20-)  E  -
1663 ASP   (  26-)  E  -
1682 ASP   (  45-)  E  -
1683 ASP   (  46-)  E  -
1732 ASP   (  95-)  E  -
1783 ASP   ( 149-)  E  -
1796 ASP   ( 162-)  E  -
1802 ASP   (   8-)  F  -
1826 ASP   (  32-)  F  -
1880 ASP   (  86-)  F  -
1889 ASP   (  95-)  F  -
2771 ASP   (  20-)  H  -
2777 ASP   (  26-)  H  -
2796 ASP   (  45-)  H  -
2797 ASP   (  46-)  H  -
2845 ASP   (  95-)  H  -
2897 ASP   ( 149-)  H  -
2910 ASP   ( 162-)  H  -
2916 ASP   (   8-)  I  -
2940 ASP   (  32-)  I  -
2994 ASP   (  86-)  I  -
3003 ASP   (  95-)  I  -
3883 ASP   (  20-)  K  -
3889 ASP   (  26-)  K  -
3908 ASP   (  45-)  K  -
And so on for a total of 55 lines.

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

1660 GLU   (  23-)  E  -
1662 GLU   (  25-)  E  -
1666 GLU   (  29-)  E  -
1686 GLU   (  49-)  E  -
1707 GLU   (  70-)  E  -
1723 GLU   (  86-)  E  -
1806 GLU   (  12-)  F  -
1861 GLU   (  67-)  F  -
1879 GLU   (  85-)  F  -
1883 GLU   (  89-)  F  -
1900 GLU   ( 106-)  F  -
1910 GLU   ( 116-)  F  -
1914 GLU   ( 120-)  F  -
1915 GLU   ( 121-)  F  -
1925 GLU   ( 131-)  F  -
2774 GLU   (  23-)  H  -
2776 GLU   (  25-)  H  -
2780 GLU   (  29-)  H  -
2800 GLU   (  49-)  H  -
2821 GLU   (  70-)  H  -
2837 GLU   (  86-)  H  -
2920 GLU   (  12-)  I  -
2975 GLU   (  67-)  I  -
2993 GLU   (  85-)  I  -
2997 GLU   (  89-)  I  -
And so on for a total of 75 lines.

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

   1 ASP   (   4-)  A  -   CG   OD1   1.33    4.4
  20 GLU   (  23-)  A  -   CD   OE1   1.33    4.3
  23 GLU   (  26-)  A  -   CD   OE1   1.33    4.1
  65 GLU   (  68-)  A  -   CD   OE2   1.33    4.2
  72 ASP   (  75-)  A  -   CG   OD1   1.34    4.8
  83 ASP   (  86-)  A  -   CG   OD1   1.34    4.6
  95 HIS   (  98-)  A  -   CB   CG    1.44   -4.3
 105 GLU   ( 108-)  A  -   CD   OE1   1.34    4.7
 199 SER   ( 202-)  A  -   CB   OG    1.52    5.1
 199 SER   ( 202-)  A  -   N   -C     1.24   -4.2
 214 THR   ( 217-)  A  -   CA   CB    1.61    4.0
 215 LEU   ( 218-)  A  -   CB   CG    1.69    7.8
 216 GLU   ( 219-)  A  -   N   -C     1.21   -5.8
 238 ASP   ( 241-)  A  -   CG   OD1   1.34    4.7
 285 PHE   ( 288-)  A  -   CA   C     1.44   -4.2
 298 ASP   ( 301-)  A  -   CG   OD1   1.33    4.0
 303 THR   ( 306-)  A  -   CB   OG1   1.36   -4.4
 324 ASP   ( 327-)  A  -   CG   OD1   1.33    4.5
 327 GLU   ( 330-)  A  -   CD   OE1   1.33    4.1
 342 ASP   ( 346-)  A  -   CG   OD2   1.33    4.5
 343 GLU   ( 347-)  A  -   CD   OE1   1.33    4.4
 372 GLU   ( 376-)  A  -   CD   OE1   1.33    4.2
 377 GLU   ( 381-)  A  -   CD   OE1   1.34    4.7
 407 GLU   ( 411-)  A  -   CD   OE1   1.34    5.0
 430 TYR   ( 434-)  A  -   CA   CB    1.44   -4.5
And so on for a total of 406 lines.

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  1.001854  0.000044 -0.000191|
 |  0.000044  1.001717  0.000000|
 | -0.000191  0.000000  1.001695|
Proposed new scale matrix

 |  0.003327  0.000000  0.000000|
 |  0.000000  0.003327  0.000000|
 |  0.000000  0.000000  0.003327|
With corresponding cell

    A    = 300.586  B   = 300.545  C    = 300.539
    Alpha=  90.003  Beta=  90.003  Gamma=  90.003

The CRYST1 cell dimensions

    A    = 300.000  B   = 300.000  C    = 300.000
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 1133.884
(Under-)estimated Z-score: 24.817

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

  19 LYS   (  22-)  A  -   C    CA   CB  118.55    4.4
  35 VAL   (  38-)  A  -   N    CA   CB  102.73   -4.6
  44 PHE   (  47-)  A  -   C    CA   CB  100.97   -4.8
  68 THR   (  71-)  A  -   N    CA   CB  117.42    4.1
  72 ASP   (  75-)  A  -   N    CA   CB  122.88    7.3
  72 ASP   (  75-)  A  -   C    CA   CB  117.75    4.0
  79 PRO   (  82-)  A  -   N    CA   CB  109.39    5.8
  85 ILE   (  88-)  A  -   CB   CG1  CD1 101.55   -5.8
  95 HIS   (  98-)  A  -   C    CA   CB   87.27  -12.0
  95 HIS   (  98-)  A  -   CD2  CG   ND1 110.47    4.4
 101 TYR   ( 104-)  A  -   C    CA   CB  117.91    4.1
 115 TYR   ( 118-)  A  -   C    CA   CB  101.37   -4.6
 125 PRO   ( 128-)  A  -   N    CA   CB  108.17    4.7
 134 PRO   ( 137-)  A  -  -CA  -C    N   108.43   -5.6
 138 LEU   ( 141-)  A  -   C    CA   CB   97.90   -6.4
 150 PRO   ( 153-)  A  -   N    CA   CB  107.47    4.1
 158 ASN   ( 161-)  A  -   CA   CB   CG  107.55   -5.0
 158 ASN   ( 161-)  A  -   ND2  CG   OD1 127.33    4.7
 162 PHE   ( 165-)  A  -   N    CA   CB  100.35   -6.0
 162 PHE   ( 165-)  A  -   CA   CB   CG  108.79   -5.0
 169 ASN   ( 172-)  A  -   N    CA   CB  118.20    4.5
 170 GLN   ( 173-)  A  -   N    CA   CB  102.96   -4.4
 177 GLU   ( 180-)  A  -   N    CA   CB  118.52    4.7
 189 VAL   ( 192-)  A  -   CA   CB   CG1 102.02   -5.0
 193 PHE   ( 196-)  A  -   CA   CB   CG  108.15   -5.6
And so on for a total of 3063 lines.

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

1657 ASP   (  20-)  E  -
1660 GLU   (  23-)  E  -
1662 GLU   (  25-)  E  -
1663 ASP   (  26-)  E  -
1666 GLU   (  29-)  E  -
1682 ASP   (  45-)  E  -
1683 ASP   (  46-)  E  -
1686 GLU   (  49-)  E  -
1707 GLU   (  70-)  E  -
1723 GLU   (  86-)  E  -
1732 ASP   (  95-)  E  -
1783 ASP   ( 149-)  E  -
1796 ASP   ( 162-)  E  -
1802 ASP   (   8-)  F  -
1806 GLU   (  12-)  F  -
1813 ARG   (  19-)  F  -
1826 ASP   (  32-)  F  -
1829 ARG   (  35-)  F  -
1861 GLU   (  67-)  F  -
1879 GLU   (  85-)  F  -
1880 ASP   (  86-)  F  -
1883 GLU   (  89-)  F  -
1886 ARG   (  92-)  F  -
1889 ASP   (  95-)  F  -
1900 GLU   ( 106-)  F  -
And so on for a total of 150 lines.

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

  72 ASP   (  75-)  A  -   CA   -12.3     9.27    33.73
  95 HIS   (  98-)  A  -   CA     8.4    49.49    34.11
  95 HIS   (  98-)  A  -   C      8.5    12.92     0.15
 134 PRO   ( 137-)  A  -   N      6.1    17.57    -2.48
 261 ASP   ( 264-)  A  -   CA     7.8    49.31    33.73
 337 LEU   ( 341-)  A  -   CA    -8.5    21.15    34.19
 443 GLN   ( 447-)  A  -   CA   -12.3    10.24    33.96
 476 ILE   ( 480-)  A  -   CB     6.6    40.86    32.31
 617 THR   ( 625-)  A  -   CB     6.5    48.73    34.09
 620 GLY   ( 628-)  A  -   C     -6.2    -8.12     0.06
 637 THR   ( 648-)  A  -   CB   -13.7     3.46    34.09
 638 VAL   ( 649-)  A  -   C      7.9    11.04     0.15
 638 VAL   ( 649-)  A  -   CB   -35.1   -78.96   -32.96
 687 ASN   ( 698-)  A  -   CA     6.0    45.04    33.59
 743 THR   ( 756-)  A  -   CA     6.5    44.77    33.84
 749 HIS   ( 762-)  A  -   CA    -7.2    20.90    34.11
 819 MET   ( 832-)  A  -   CA    -7.6    20.57    34.17
 827 PRO   ( 840-)  A  -   N     -6.2   -22.84    -2.48
 902 ASP   (  75-)  D  -   CA   -12.3     9.31    33.73
 925 HIS   (  98-)  D  -   CA     8.3    49.44    34.11
 925 HIS   (  98-)  D  -   C      8.5    12.87     0.15
 964 PRO   ( 137-)  D  -   N      6.1    17.43    -2.48
1090 ASP   ( 264-)  D  -   CA     7.8    49.26    33.73
1167 LEU   ( 341-)  D  -   CA    -8.5    21.18    34.19
1272 GLN   ( 447-)  D  -   CA   -12.3    10.15    33.96
And so on for a total of 280 lines.

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

8207 ARG   ( 335-)  5  -   7.44
8579 ARG   ( 335-)  6  -   7.42
7835 ARG   ( 335-)  4  -   7.42
1040  ARG  ( 335-) W  -   7.41
1150  ARG  ( 335-) Z  -   7.41
7096 ARG   ( 335-)  2  -   7.41
8951 ARG   ( 335-)  7  -   7.40
9681 ARG   ( 335-)  9  -   7.39
1114  ARG  ( 335-) Y  -   7.39
1077  ARG  ( 335-) X  -   7.39
1004  ARG  ( 335-) V  -   7.37
7464 ARG   ( 335-)  3  -   7.35
4935 ALA   ( 784-)  M  -   6.67
6051 ALA   ( 784-)  P  -   6.64
3823 ALA   ( 784-)  J  -   6.64
1597 ALA   ( 784-)  D  -   6.63
 771 ALA   ( 784-)  A  -   6.54
2710 ALA   ( 784-)  G  -   6.51
4384 GLU   ( 219-)  M  -   6.31
5499 GLU   ( 219-)  P  -   6.30
2159 GLU   ( 219-)  G  -   6.27
3273 GLU   ( 219-)  J  -   6.27
 216 GLU   ( 219-)  A  -   6.24
1045 GLU   ( 219-)  D  -   6.21
7494 ALA   ( 365-)  3  -   6.11
And so on for a total of 300 lines.

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.689

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

2898 TYR   ( 150-)  H  -  15.62
4011 TYR   ( 150-)  K  -  15.61
6240 TYR   ( 150-)  Q  -  15.58
1784 TYR   ( 150-)  E  -  15.50
5124 TYR   ( 150-)  N  -  15.36
4039 ASP   (  18-)  L  -   9.73
2926 ASP   (  18-)  I  -   9.73
5152 ASP   (  18-)  O  -   9.73
1812 ASP   (  18-)  F  -   9.70
6268 ASP   (  18-)  R  -   9.68
1744 ASP   ( 107-)  E  -   8.31
6199 ASP   ( 107-)  Q  -   8.19
3970 ASP   ( 107-)  K  -   8.17
2857 ASP   ( 107-)  H  -   8.16
5083 ASP   ( 107-)  N  -   8.13
6339 GLU   (  89-)  R  -   7.04
5223 GLU   (  89-)  O  -   7.04
4109 GLU   (  89-)  L  -   7.01
2997 GLU   (  89-)  I  -   6.89
1883 GLU   (  89-)  F  -   6.82
4022 GLU   ( 161-)  K  -   5.82
6251 GLU   ( 161-)  Q  -   5.80
1900 GLU   ( 106-)  F  -   5.78
5240 GLU   ( 106-)  O  -   5.76
5135 GLU   ( 161-)  N  -   5.73
And so on for a total of 96 lines.

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

4782 PHE   ( 623-)  M  -   CB   7.03
5898 PHE   ( 623-)  P  -   CB   7.02
3671 PHE   ( 623-)  J  -   CB   7.02
 615 PHE   ( 623-)  A  -   CB   7.02
1445 PHE   ( 623-)  D  -   CB   7.00
2558 PHE   ( 623-)  G  -   CB   6.99
1043  HIS  ( 371-) W  -    CB   5.62
8615 HIS   ( 371-)  6  -   CB   5.60
1117  HIS  ( 371-) Y  -    CB   5.60
9715 HIS   ( 371-)  9  -   CB   5.59
9350 HIS   ( 371-)  8  -   CB   5.59
8243 HIS   ( 371-)  5  -   CB   5.58
1007  HIS  ( 371-) V  -    CB   5.58
1154  HIS  ( 371-) Z  -    CB   5.57
7500 HIS   ( 371-)  3  -   CB   5.57
7132 HIS   ( 371-)  2  -   CB   5.57
8987 HIS   ( 371-)  7  -   CB   5.57
7871 HIS   ( 371-)  4  -   CB   5.57
6763 HIS   ( 371-)  1  -   CB   5.56
1080  HIS  ( 371-) X  -    CB   5.55
7674 HIS   ( 173-)  4  -   CB   4.20
1061  HIS  ( 173-) X  -    CB   4.18
1098  HIS  ( 173-) Y  -    CB   4.18
6571 HIS   ( 173-)  1  -   CB   4.18
8789 HIS   ( 173-)  7  -   CB   4.18
7304 HIS   ( 173-)  3  -   CB   4.18
9522 HIS   ( 173-)  9  -   CB   4.17
1134  HIS  ( 173-) Z  -    CB   4.17
1024  HIS  ( 173-) W  -    CB   4.17
9885 HIS   ( 173-)  V  -   CB   4.16
9156 HIS   ( 173-)  8  -   CB   4.15
8045 HIS   ( 173-)  5  -   CB   4.15
6934 HIS   ( 173-)  2  -   CB   4.15
8417 HIS   ( 173-)  6  -   CB   4.14
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -4.460

Torsion-related checks

Error: Ramachandran Z-score very low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is very low.

Ramachandran Z-score : -4.460

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 IF 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.

1776 PRO   ( 141-)  E  -   -2.9
2891 PRO   ( 141-)  H  -   -2.9
6232 PRO   ( 141-)  Q  -   -2.9
5116 PRO   ( 141-)  N  -   -2.9
4003 PRO   ( 141-)  K  -   -2.9
6097 PRO   ( 830-)  P  -   -2.9
2756 PRO   ( 830-)  G  -   -2.9
3868 PRO   ( 830-)  J  -   -2.9
4981 PRO   ( 830-)  M  -   -2.9
1642 PRO   ( 830-)  D  -   -2.9
 817 PRO   ( 830-)  A  -   -2.9
6054 ILE   ( 787-)  P  -   -2.8
 956 TYR   ( 129-)  D  -   -2.8
2069 TYR   ( 129-)  G  -   -2.8
4295 TYR   ( 129-)  M  -   -2.8
5409 TYR   ( 129-)  P  -   -2.8
3183 TYR   ( 129-)  J  -   -2.8
 126 TYR   ( 129-)  A  -   -2.8
1128  PRO  ( 109-) Z  -   -2.8
7240 PRO   ( 109-)  3  -   -2.8
6508 PRO   ( 109-)  1  -   -2.8
7610 PRO   ( 109-)  4  -   -2.8
6870 PRO   ( 109-)  2  -   -2.8
1091  PRO  ( 109-) Y  -   -2.8
9459 PRO   ( 109-)  9  -   -2.8
And so on for a total of 648 lines.

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.

   8 GLY   (  11-)  A  - Poor phi/psi
  18 GLU   (  21-)  A  - Poor phi/psi
  55 GLY   (  58-)  A  - Poor phi/psi
  70 LYS   (  73-)  A  - Poor phi/psi
 110 TRP   ( 113-)  A  - Poor phi/psi
 126 TYR   ( 129-)  A  - Poor phi/psi
 134 PRO   ( 137-)  A  - Poor phi/psi
 167 ARG   ( 170-)  A  - Poor phi/psi
 196 ILE   ( 199-)  A  - Poor phi/psi
 198 ALA   ( 201-)  A  - Poor phi/psi
 199 SER   ( 202-)  A  - Poor phi/psi
 201 GLU   ( 204-)  A  - Poor phi/psi
 208 SER   ( 211-)  A  - Poor phi/psi
 210 LYS   ( 213-)  A  - Poor phi/psi
 216 GLU   ( 219-)  A  - Poor phi/psi
 291 ASN   ( 294-)  A  - Poor phi/psi
 301 LEU   ( 304-)  A  - Poor phi/psi
 367 ARG   ( 371-)  A  - Poor phi/psi
 407 GLU   ( 411-)  A  - Poor phi/psi
 502 GLY   ( 507-)  A  - Poor phi/psi
 552 GLY   ( 560-)  A  - Poor phi/psi
 564 LYS   ( 572-)  A  - Poor phi/psi
 569 ALA   ( 577-)  A  - omega poor
 638 VAL   ( 649-)  A  - omega poor
 639 SER   ( 650-)  A  - Poor phi/psi
And so on for a total of 401 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -4.698

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.

 333 SER   ( 336-)  A  -   0.33
1162 SER   ( 336-)  D  -   0.33
2276 SER   ( 336-)  G  -   0.33
3390 SER   ( 336-)  J  -   0.33
4501 SER   ( 336-)  M  -   0.33
 156 SER   ( 159-)  A  -   0.36
 986 SER   ( 159-)  D  -   0.36
2099 SER   ( 159-)  G  -   0.36
3213 SER   ( 159-)  J  -   0.36
4325 SER   ( 159-)  M  -   0.36
5439 SER   ( 159-)  P  -   0.36
 416 SER   ( 420-)  A  -   0.37
1245 SER   ( 420-)  D  -   0.37
2357 SER   ( 420-)  G  -   0.37
3470 SER   ( 420-)  J  -   0.37
4583 SER   ( 420-)  M  -   0.37
5697 SER   ( 420-)  P  -   0.37
6677 SER   ( 281-)  1  -   0.40
7042 SER   ( 281-)  2  -   0.40
7412 SER   ( 281-)  3  -   0.40
7782 SER   ( 281-)  4  -   0.40
8153 SER   ( 281-)  5  -   0.40
8525 SER   ( 281-)  6  -   0.40
8897 SER   ( 281-)  7  -   0.40
9264 SER   ( 281-)  8  -   0.40
9628 SER   ( 281-)  9  -   0.40
9991 SER   ( 281-)  V  -   0.40
1035  SER  ( 281-) W  -   0.40
1071  SER  ( 281-) X  -   0.40
1108  SER  ( 281-) Y  -   0.40
1145  SER  ( 281-) Z  -   0.40
ERROR. Too many residues to use DSSP

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!

   4 MET   (   7-)  A  -     0
   7 PHE   (  10-)  A  -     0
  14 LEU   (  17-)  A  -     0
  15 ARG   (  18-)  A  -     0
  16 MLY   (  19-)  A  -     0
  27 MLY   (  30-)  A  -     0
  28 PRO   (  31-)  A  -     0
  32 MLY   (  35-)  A  -     0
  33 SER   (  36-)  A  -     0
  34 SER   (  37-)  A  -     0
  42 GLN   (  45-)  A  -     0
  43 SER   (  46-)  A  -     0
  44 PHE   (  47-)  A  -     0
  46 MLY   (  49-)  A  -     0
  52 MLY   (  55-)  A  -     0
  53 GLU   (  56-)  A  -     0
  56 MLY   (  59-)  A  -     0
  60 MLY   (  63-)  A  -     0
  62 GLU   (  65-)  A  -     0
  65 GLU   (  68-)  A  -     0
  72 ASP   (  75-)  A  -     0
  73 GLN   (  76-)  A  -     0
  81 MLY   (  84-)  A  -     0
  83 ASP   (  86-)  A  -     0
  84 MLY   (  87-)  A  -     0
And so on for a total of 4527 lines.

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 IF database with superposable C-alpha coordinates, and some restraining 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!

 894 GLY   (  67-)  D  -  2.50   80
2007 GLY   (  67-)  G  -  2.50   80
5347 GLY   (  67-)  P  -  2.50   80
4233 GLY   (  67-)  M  -  2.50   80
3121 GLY   (  67-)  J  -  2.50   80
  64 GLY   (  67-)  A  -  2.50   80
2466 PRO   ( 529-)  G  -  2.40   10
4692 PRO   ( 529-)  M  -  2.40   10
5806 PRO   ( 529-)  P  -  2.29   11
3579 PRO   ( 529-)  J  -  2.29   11
 524 PRO   ( 529-)  A  -  2.29   11
4445 PRO   ( 280-)  M  -  2.20   10
5560 PRO   ( 280-)  P  -  2.20   10
3334 PRO   ( 280-)  J  -  2.20   10
1106 PRO   ( 280-)  D  -  2.20   10
2220 PRO   ( 280-)  G  -  2.20   10
 277 PRO   ( 280-)  A  -  2.20   10
 403 GLY   ( 407-)  A  -  2.03   16
3682 GLY   ( 635-)  J  -  1.94   10
8390 GLY   ( 146-)  6  -  1.59   80
7277 GLY   ( 146-)  3  -  1.59   80
6907 GLY   ( 146-)  2  -  1.59   80
1058  GLY  ( 146-) X  -  1.59   80
1132  GLY  ( 146-) Z  -  1.59   80
1095  GLY  ( 146-) Y  -  1.58   80
7647 GLY   ( 146-)  4  -  1.58   80
8018 GLY   ( 146-)  5  -  1.58   80
8762 GLY   ( 146-)  7  -  1.58   80

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

  12 PRO   (  15-)  A  -   0.04 LOW
  28 PRO   (  31-)  A  -   0.09 LOW
  40 PRO   (  43-)  A  -   0.10 LOW
  79 PRO   (  82-)  A  -   0.15 LOW
  80 PRO   (  83-)  A  -   0.13 LOW
 125 PRO   ( 128-)  A  -   0.07 LOW
 130 PRO   ( 133-)  A  -   0.15 LOW
 134 PRO   ( 137-)  A  -   0.18 LOW
 149 PRO   ( 152-)  A  -   0.20 LOW
 224 PRO   ( 227-)  A  -   0.04 LOW
 277 PRO   ( 280-)  A  -   0.11 LOW
 294 PRO   ( 297-)  A  -   0.08 LOW
 306 PRO   ( 309-)  A  -   0.20 LOW
 320 PRO   ( 323-)  A  -   0.14 LOW
 373 PRO   ( 377-)  A  -   0.08 LOW
 400 PRO   ( 404-)  A  -   0.15 LOW
 450 PRO   ( 454-)  A  -   0.02 LOW
 524 PRO   ( 529-)  A  -   0.13 LOW
 537 PRO   ( 543-)  A  -   0.06 LOW
 560 PRO   ( 568-)  A  -   0.02 LOW
 562 PRO   ( 570-)  A  -   0.07 LOW
 594 PRO   ( 602-)  A  -   0.03 LOW
 658 PRO   ( 669-)  A  -   0.13 LOW
 666 PRO   ( 677-)  A  -   0.02 LOW
 672 PRO   ( 683-)  A  -   0.10 LOW
And so on for a total of 275 lines.

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].

 150 PRO   ( 153-)  A  -  171.6 envelop N (180 degrees)
 817 PRO   ( 830-)  A  -  156.3 half-chair C-alpha/N (162 degrees)
 980 PRO   ( 153-)  D  -  171.3 envelop N (180 degrees)
1642 PRO   ( 830-)  D  -  156.5 half-chair C-alpha/N (162 degrees)
1776 PRO   ( 141-)  E  - -160.4 half-chair N/C-delta (-162 degrees)
1835 PRO   (  41-)  F  -  -10.8 half-chair C-alpha/N (-18 degrees)
2093 PRO   ( 153-)  G  -  171.7 envelop N (180 degrees)
2756 PRO   ( 830-)  G  -  156.7 half-chair C-alpha/N (162 degrees)
2891 PRO   ( 141-)  H  - -159.8 half-chair N/C-delta (-162 degrees)
2949 PRO   (  41-)  I  -  -10.7 half-chair C-alpha/N (-18 degrees)
3207 PRO   ( 153-)  J  -  171.5 envelop N (180 degrees)
3868 PRO   ( 830-)  J  -  156.8 half-chair C-alpha/N (162 degrees)
4003 PRO   ( 141-)  K  - -160.5 half-chair N/C-delta (-162 degrees)
4062 PRO   (  41-)  L  -  -10.4 half-chair C-alpha/N (-18 degrees)
4319 PRO   ( 153-)  M  -  171.5 envelop N (180 degrees)
4981 PRO   ( 830-)  M  -  156.7 half-chair C-alpha/N (162 degrees)
5116 PRO   ( 141-)  N  - -160.3 half-chair N/C-delta (-162 degrees)
5175 PRO   (  41-)  O  -  -10.7 half-chair C-alpha/N (-18 degrees)
5433 PRO   ( 153-)  P  -  171.5 envelop N (180 degrees)
6097 PRO   ( 830-)  P  -  156.6 half-chair C-alpha/N (162 degrees)
6232 PRO   ( 141-)  Q  - -160.5 half-chair N/C-delta (-162 degrees)
6291 PRO   (  41-)  R  -  -10.5 half-chair C-alpha/N (-18 degrees)
6508 PRO   ( 109-)  1  -  112.3 envelop C-beta (108 degrees)
6870 PRO   ( 109-)  2  -  112.3 envelop C-beta (108 degrees)
7240 PRO   ( 109-)  3  -  112.4 envelop C-beta (108 degrees)
7610 PRO   ( 109-)  4  -  112.3 envelop C-beta (108 degrees)
7981 PRO   ( 109-)  5  -  112.3 envelop C-beta (108 degrees)
8353 PRO   ( 109-)  6  -  112.3 envelop C-beta (108 degrees)
8725 PRO   ( 109-)  7  -  112.4 envelop C-beta (108 degrees)
9094 PRO   ( 109-)  8  -  112.3 envelop C-beta (108 degrees)
9459 PRO   ( 109-)  9  -  112.3 envelop C-beta (108 degrees)
9822 PRO   ( 109-)  V  -  112.4 envelop C-beta (108 degrees)
1018  PRO  ( 109-) W  -  112.3 envelop C-beta (108 degrees)
1054  PRO  ( 109-) X  -  112.3 envelop C-beta (108 degrees)
1091  PRO  ( 109-) Y  -  112.3 envelop C-beta (108 degrees)
1128  PRO  ( 109-) Z  -  112.4 envelop C-beta (108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short distance; each bump is listed in only one direction,

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

1757 LEU   ( 121-)  E  -   CD1  <->  1763 PHE   ( 128-)  E  -   CD2  2.62    0.58  INTRA
5096 LEU   ( 121-)  N  -   CD1  <->  5103 PHE   ( 128-)  N  -   CD2  2.62    0.58  INTRA
2871 LEU   ( 121-)  H  -   CD1  <->  2878 PHE   ( 128-)  H  -   CD2  2.62    0.58  INTRA
3984 LEU   ( 121-)  K  -   CD1  <->  3991 PHE   ( 128-)  K  -   CD2  2.61    0.59  INTRA
6213 LEU   ( 121-)  Q  -   CD1  <->  6220 PHE   ( 128-)  Q  -   CD2  2.61    0.59  INTRA
1459 LYS   ( 642-)  D  -   CE   <->  9690 SER   ( 344-)  9  -   CB   2.45    0.75  INTRA
 632 LYS   ( 642-)  A  -   CE   <->  9325 SER   ( 344-)  8  -   CB   2.45    0.75  INTRA
6600 THR   ( 202-)  1  -   N    <->  1109  ILE  ( 287-) Y  -    CD1  2.35    0.75  INTRA
5112 TRP   ( 137-)  N  -   CH2  <->  5120 GLY   ( 146-)  N  -   N    2.29    0.81  INTRA
1772 TRP   ( 137-)  E  -   CH2  <->  1780 GLY   ( 146-)  E  -   N    2.29    0.81  INTRA
2887 TRP   ( 137-)  H  -   CH2  <->  2895 GLY   ( 146-)  H  -   N    2.29    0.81  INTRA
5910 LYS   ( 637-)  P  -   C    <->  6740 ILE   ( 345-)  1  -   CD1  2.21    0.99  INTRA
1455 LYS   ( 637-)  D  -   C    <->  9691 ILE   ( 345-)  9  -   CD1  2.21    0.99  INTRA
3684 LYS   ( 637-)  J  -   C    <->  1041  ILE  ( 345-) W  -    CD1  2.21    0.99  INTRA
 628 LYS   ( 637-)  A  -   C    <->  9326 ILE   ( 345-)  8  -   CD1  2.21    0.99  INTRA
1072  LYS  ( 291-) X  -    CB   <->  1141  ASP  ( 244-) Z  -    CB   2.19    1.01  INTRA
5831 ASP   ( 556-)  P  -   OD2  <->  7174 GLN   (  41-)  3  -   NE2  2.18    0.52  INTRA
 548 ASP   ( 556-)  A  -   C    <->  9762 GLN   (  49-)  V  -   N    2.14    0.96  INTRA
1378 ASP   ( 556-)  D  -   C    <->  1012  GLN  (  49-) W  -    N    2.14    0.96  INTRA
5495 GLN   ( 215-)  P  -   CD   <->  5619 ILE   ( 340-)  P  -   N    2.12    0.98  INTRA
3269 GLN   ( 215-)  J  -   CD   <->  3393 ILE   ( 340-)  J  -   N    2.12    0.98  INTRA
2155 GLN   ( 215-)  G  -   CD   <->  2279 ILE   ( 340-)  G  -   N    2.11    0.99  INTRA
 212 GLN   ( 215-)  A  -   CD   <->   336 ILE   ( 340-)  A  -   N    2.11    0.99  INTRA
4733 LYS   ( 574-)  M  -   NZ   <->  4748 ASP   ( 589-)  M  -   OD2  2.06    0.64  INTRA
5849 LYS   ( 574-)  P  -   NZ   <->  5864 ASP   ( 589-)  P  -   OD2  2.06    0.64  INTRA
And so on for a total of 8075 lines.

Packing, accessibility and threading

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.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

Note: Inside/Outside RMS Z-score plot

Chain identifier: Q

Note: Inside/Outside RMS Z-score plot

Chain identifier: R

Note: Inside/Outside RMS Z-score plot

Chain identifier: 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: 4

Note: Inside/Outside RMS Z-score plot

Chain identifier: 5

Note: Inside/Outside RMS Z-score plot

Chain identifier: 6

Note: Inside/Outside RMS Z-score plot

Chain identifier: 7

Note: Inside/Outside RMS Z-score plot

Chain identifier: 8

Note: Inside/Outside RMS Z-score plot

Chain identifier: 9

Note: Inside/Outside RMS Z-score plot

Chain identifier: V

Note: Inside/Outside RMS Z-score plot

Chain identifier: W

Note: Inside/Outside RMS Z-score plot

Chain identifier: X

Note: Inside/Outside RMS Z-score plot

Chain identifier: Y

Note: Inside/Outside RMS Z-score plot

Chain identifier: Z

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.

4040 ARG   (  19-)  L  -     -7.72
2927 ARG   (  19-)  I  -     -7.72
6269 ARG   (  19-)  R  -     -7.70
5153 ARG   (  19-)  O  -     -7.70
9391 GLN   (  41-)  9  -     -7.52
6440 GLN   (  41-)  1  -     -7.52
9755 GLN   (  41-)  V  -     -7.52
1048  GLN  (  41-) X  -     -7.52
1011  GLN  (  41-) W  -     -7.52
9026 GLN   (  41-)  8  -     -7.52
7913 GLN   (  41-)  5  -     -7.52
8285 GLN   (  41-)  6  -     -7.52
8657 GLN   (  41-)  7  -     -7.52
1084  GLN  (  41-) Y  -     -7.51
7542 GLN   (  41-)  4  -     -7.51
1121  GLN  (  41-) Z  -     -7.51
1813 ARG   (  19-)  F  -     -7.47
4295 TYR   ( 129-)  M  -     -7.41
 126 TYR   ( 129-)  A  -     -7.41
5409 TYR   ( 129-)  P  -     -7.41
3183 TYR   ( 129-)  J  -     -7.41
2069 TYR   ( 129-)  G  -     -7.41
 956 TYR   ( 129-)  D  -     -7.40
7174 GLN   (  41-)  3  -     -7.31
6805 GLN   (  41-)  2  -     -7.23
And so on for a total of 327 lines.

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.

 568 GLU   ( 576-)  A  -    570 - HIS    578- ( A)  -      -4.28
 975 ARG   ( 148-)  D  -    977 - GLU    150- ( D)  -      -4.73
1398 GLU   ( 576-)  D  -   1400 - HIS    578- ( D)  -      -4.28
2088 ARG   ( 148-)  G  -   2090 - GLU    150- ( G)  -      -4.79
2511 GLU   ( 576-)  G  -   2513 - HIS    578- ( G)  -      -4.27
2639 ARG   ( 708-)  G  -   2641 - GLY    710- ( G)  -      -4.61
3202 ARG   ( 148-)  J  -   3204 - GLU    150- ( J)  -      -4.67
3624 GLU   ( 576-)  J  -   3626 - HIS    578- ( J)  -      -4.26
4314 ARG   ( 148-)  M  -   4316 - GLU    150- ( M)  -      -4.73
4735 GLU   ( 576-)  M  -   4737 - HIS    578- ( M)  -      -4.27
4862 ARG   ( 708-)  M  -   4864 - GLY    710- ( M)  -      -4.53
5428 ARG   ( 148-)  P  -   5430 - GLU    150- ( P)  -      -4.73
5851 GLU   ( 576-)  P  -   5853 - HIS    578- ( P)  -      -4.27
5978 ARG   ( 708-)  P  -   5980 - GLY    710- ( P)  -      -4.57
6438 ARG   (  39-)  1  -   6440 - GLN     41- ( 1)  -      -6.73
6803 ARG   (  39-)  2  -   6806 - GLY     42- ( 2)  -      -6.02
7172 ARG   (  39-)  3  -   7174 - GLN     41- ( 3)  -      -6.67
7540 ARG   (  39-)  4  -   7542 - GLN     41- ( 4)  -      -6.73
7911 ARG   (  39-)  5  -   7913 - GLN     41- ( 5)  -      -6.73
8283 ARG   (  39-)  6  -   8285 - GLN     41- ( 6)  -      -6.73
8655 ARG   (  39-)  7  -   8657 - GLN     41- ( 7)  -      -6.73
9024 ARG   (  39-)  8  -   9026 - GLN     41- ( 8)  -      -6.72
9389 ARG   (  39-)  9  -   9391 - GLN     41- ( 9)  -      -6.72
9753 ARG   (  39-)  V  -   9755 - GLN     41- ( V)  -      -6.72
1011  ARG  (  39-) W  -    1011 -  GLN    41- (W ) -       -6.72
1047  ARG  (  39-) X  -    1048 -  GLN    41- (X ) -       -6.75
1084  ARG  (  39-) Y  -    1084 -  GLN    41- (Y ) -       -6.73
1121  ARG  (  39-) Z  -    1121 -  GLN    41- (Z ) -       -6.70

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.

Chain identifier: A

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.

Chain identifier: D

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.

Chain identifier: E

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.

Chain identifier: F

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.

Chain identifier: G

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.

Chain identifier: H

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.

Chain identifier: I

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.

Chain identifier: J

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.

Chain identifier: K

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.

Chain identifier: L

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.

Chain identifier: M

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.

Chain identifier: N

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.

Chain identifier: O

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.

Chain identifier: P

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.

Chain identifier: Q

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.

Chain identifier: R

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.

Chain identifier: 1

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.

Chain identifier: 2

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.

Chain identifier: 3

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.

Chain identifier: 4

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.

Chain identifier: 5

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.

Chain identifier: 6

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.

Chain identifier: 7

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.

Chain identifier: 8

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.

Chain identifier: 9

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.

Chain identifier: V

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.

Chain identifier: W

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.

Chain identifier: X

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.

Chain identifier: Y

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.

Chain identifier: Z

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.

5140 ALA   (   6-)  O  -  -3.14
 109 ALA   ( 112-)  A  -  -2.88
3166 ALA   ( 112-)  J  -  -2.88
 939 ALA   ( 112-)  D  -  -2.88
4278 ALA   ( 112-)  M  -  -2.88
5392 ALA   ( 112-)  P  -  -2.88
2052 ALA   ( 112-)  G  -  -2.88
6870 PRO   ( 109-)  2  -  -2.85
1018  PRO  ( 109-) W  -  -2.85
1091  PRO  ( 109-) Y  -  -2.85
1128  PRO  ( 109-) Z  -  -2.85
9822 PRO   ( 109-)  V  -  -2.85
6508 PRO   ( 109-)  1  -  -2.85
1054  PRO  ( 109-) X  -  -2.85
8284 HIS   (  40-)  6  -  -2.82
9414 ILE   (  64-)  9  -  -2.71
8680 ILE   (  64-)  7  -  -2.69
5124 TYR   ( 150-)  N  -  -2.69
1784 TYR   ( 150-)  E  -  -2.68
2690 HIS   ( 762-)  G  -  -2.67
7912 HIS   (  40-)  5  -  -2.62
3442 LEU   ( 389-)  J  -  -2.62
4554 LEU   ( 389-)  M  -  -2.62
 385 LEU   ( 389-)  A  -  -2.62
2401 ILE   ( 464-)  G  -  -2.62
2328 LEU   ( 389-)  G  -  -2.62
5668 LEU   ( 389-)  P  -  -2.62
 460 ILE   ( 464-)  A  -  -2.62
5741 ILE   ( 464-)  P  -  -2.62
1215 LEU   ( 389-)  D  -  -2.62
3514 ILE   ( 464-)  J  -  -2.62
4627 ILE   ( 464-)  M  -  -2.62
1289 ILE   ( 464-)  D  -  -2.61
9777 ILE   (  64-)  V  -  -2.57
3625 ALA   ( 577-)  J  -  -2.55
9049 ILE   (  64-)  8  -  -2.53
1526 GLY   ( 710-)  D  -  -2.52

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

 587 TRP   ( 595-)  A  -  -  590 MLY   ( 598-)  A  -   -251.21
1417 TRP   ( 595-)  D  -  - 1420 MLY   ( 598-)  D  -   -251.21
1456 GLY   ( 639-)  D  -  - 1460 GLY   ( 643-)  D  -     -1.70
2530 TRP   ( 595-)  G  -  - 2533 MLY   ( 598-)  G  -   -251.22
2766 PRO   ( 840-)  G  -  - 2769 LYS   ( 843-)  G  -     -1.91
3643 TRP   ( 595-)  J  -  - 3646 MLY   ( 598-)  J  -   -251.21
3878 PRO   ( 840-)  J  -  - 3881 LYS   ( 843-)  J  -     -1.95
4754 TRP   ( 595-)  M  -  - 4757 MLY   ( 598-)  M  -   -251.21
5870 TRP   ( 595-)  P  -  - 5873 MLY   ( 598-)  P  -   -251.22
1154  ILE  ( 369-) Z  -   - 1154  ARG  ( 372-) Z  -      -1.72
ERROR. Too many residues to use DSSP

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.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: Q

Note: Second generation quality Z-score plot

Chain identifier: R

Note: Second generation quality Z-score plot

Chain identifier: 1

Note: Second generation quality Z-score plot

Chain identifier: 2

Note: Second generation quality Z-score plot

Chain identifier: 3

Note: Second generation quality Z-score plot

Chain identifier: 4

Note: Second generation quality Z-score plot

Chain identifier: 5

Note: Second generation quality Z-score plot

Chain identifier: 6

Note: Second generation quality Z-score plot

Chain identifier: 7

Note: Second generation quality Z-score plot

Chain identifier: 8

Note: Second generation quality Z-score plot

Chain identifier: 9

Note: Second generation quality Z-score plot

Chain identifier: V

Note: Second generation quality Z-score plot

Chain identifier: W

Note: Second generation quality Z-score plot

Chain identifier: X

Note: Second generation quality Z-score plot

Chain identifier: Y

Note: Second generation quality Z-score plot

Chain identifier: Z

Water, ion, and hydrogenbond related checks

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.

 124 ASN   ( 127-)  A  -
 477 ASN   ( 481-)  A  -
 583 ASN   ( 591-)  A  -
 647 ASN   ( 658-)  A  -
 677 HIS   ( 688-)  A  -
 954 ASN   ( 127-)  D  -
1306 ASN   ( 481-)  D  -
1413 ASN   ( 591-)  D  -
1474 ASN   ( 658-)  D  -
2067 ASN   ( 127-)  G  -
2418 ASN   ( 481-)  G  -
2526 ASN   ( 591-)  G  -
2589 ASN   ( 658-)  G  -
2690 HIS   ( 762-)  G  -
3181 ASN   ( 127-)  J  -
3531 ASN   ( 481-)  J  -
3639 ASN   ( 591-)  J  -
3702 ASN   ( 658-)  J  -
4293 ASN   ( 127-)  M  -
4644 ASN   ( 481-)  M  -
4750 ASN   ( 591-)  M  -
4812 ASN   ( 658-)  M  -
4842 HIS   ( 688-)  M  -
5407 ASN   ( 127-)  P  -
5758 ASN   ( 481-)  P  -
And so on for a total of 59 lines.

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.

   4 MET   (   7-)  A  -   N
   5 ALA   (   8-)  A  -   N
   7 PHE   (  10-)  A  -   N
   8 GLY   (  11-)  A  -   N
  22 ILE   (  25-)  A  -   N
  42 GLN   (  45-)  A  -   N
  44 PHE   (  47-)  A  -   N
  46 MLY   (  49-)  A  -   N
  56 MLY   (  59-)  A  -   N
  58 THR   (  61-)  A  -   N
  82 TYR   (  85-)  A  -   OH
  98 ALA   ( 101-)  A  -   N
 106 ARG   ( 109-)  A  -   NH1
 109 ALA   ( 112-)  A  -   N
 110 TRP   ( 113-)  A  -   NE1
 112 ILE   ( 115-)  A  -   N
 115 TYR   ( 118-)  A  -   OH
 119 PHE   ( 122-)  A  -   N
 120 CYS   ( 123-)  A  -   N
 122 THR   ( 125-)  A  -   OG1
 131 VAL   ( 134-)  A  -   N
 132 TYR   ( 135-)  A  -   N
 133 ASN   ( 136-)  A  -   N
 135 MLY   ( 138-)  A  -   N
 138 LEU   ( 141-)  A  -   N
And so on for a total of 1691 lines.

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.

  93 HIS   (  96-)  A  -   ND1
  95 HIS   (  98-)  A  -   ND1
 105 GLU   ( 108-)  A  -   OE2
 151 HIS   ( 154-)  A  -   ND1
 227 GLU   ( 230-)  A  -   OE2
 238 ASP   ( 241-)  A  -   OD1
 356 HIS   ( 360-)  A  -   ND1
 407 GLU   ( 411-)  A  -   OE1
 472 GLU   ( 476-)  A  -   OE2
 501 GLU   ( 506-)  A  -   OE1
 581 ASP   ( 589-)  A  -   OD2
 591 ASN   ( 599-)  A  -   OD1
 644 GLU   ( 655-)  A  -   OE2
 687 ASN   ( 698-)  A  -   OD1
 708 ASP   ( 719-)  A  -   OD1
 913 ASP   (  86-)  D  -   OD2
 923 HIS   (  96-)  D  -   ND1
 925 HIS   (  98-)  D  -   ND1
 935 GLU   ( 108-)  D  -   OE2
 981 HIS   ( 154-)  D  -   ND1
1056 GLU   ( 230-)  D  -   OE2
1067 ASP   ( 241-)  D  -   OD1
1161 ASP   ( 335-)  D  -   OD1
1186 HIS   ( 360-)  D  -   ND1
1301 GLU   ( 476-)  D  -   OE2
And so on for a total of 314 lines.

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.

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

 216 GLU   ( 219-)  A  -  H-bonding suggests Gln
 217 ASP   ( 220-)  A  -  H-bonding suggests Asn
 238 ASP   ( 241-)  A  -  H-bonding suggests Asn; but Alt-Rotamer
 314 GLU   ( 317-)  A  -  H-bonding suggests Gln
 380 ASP   ( 384-)  A  -  H-bonding suggests Asn
 533 GLU   ( 539-)  A  -  H-bonding suggests Gln
 597 GLU   ( 605-)  A  -  H-bonding suggests Gln
 708 ASP   ( 719-)  A  -  H-bonding suggests Asn
 795 GLU   ( 808-)  A  -  H-bonding suggests Gln
1045 GLU   ( 219-)  D  -  H-bonding suggests Gln
1046 ASP   ( 220-)  D  -  H-bonding suggests Asn
1067 ASP   ( 241-)  D  -  H-bonding suggests Asn; but Alt-Rotamer
1143 GLU   ( 317-)  D  -  H-bonding suggests Gln
1165 ASP   ( 339-)  D  -  H-bonding suggests Asn; but Alt-Rotamer
1210 ASP   ( 384-)  D  -  H-bonding suggests Asn
1364 GLU   ( 539-)  D  -  H-bonding suggests Gln
1427 GLU   ( 605-)  D  -  H-bonding suggests Gln
1598 GLU   ( 785-)  D  -  H-bonding suggests Gln
1620 GLU   ( 808-)  D  -  H-bonding suggests Gln
1662 GLU   (  25-)  E  -  H-bonding suggests Gln; but Alt-Rotamer
1663 ASP   (  26-)  E  -  H-bonding suggests Asn; but Alt-Rotamer
1666 GLU   (  29-)  E  -  H-bonding suggests Gln
1672 ASP   (  35-)  E  -  H-bonding suggests Asn; but Alt-Rotamer
1686 GLU   (  49-)  E  -  H-bonding suggests Gln
1702 ASP   (  65-)  E  -  H-bonding suggests Asn
And so on for a total of 214 lines.

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.890
  2nd generation packing quality :  -1.961
  Ramachandran plot appearance   :  -4.460 (bad)
  chi-1/chi-2 rotamer normality  :  -4.698 (bad)
  Backbone conformation          :  -0.987

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.963
  Bond angles                    :   1.547
  Omega angle restraints         :   0.752
  Side chain planarity           :   1.422
  Improper dihedral distribution :   1.846 (loose)
  B-factor distribution          :   0.362
  Inside/Outside distribution    :   1.012

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 70.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.9
  2nd generation packing quality :  -1.0
  Ramachandran plot appearance   :  -2.2
  chi-1/chi-2 rotamer normality  :  -2.3
  Backbone conformation          :  -0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.963
  Bond angles                    :   1.547
  Omega angle restraints         :   0.752
  Side chain planarity           :   1.422
  Improper dihedral distribution :   1.846 (loose)
  B-factor distribution          :   0.362
  Inside/Outside distribution    :   1.012
==============

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 inform

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).

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).

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).

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).

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.