WHAT IF Check report

This file was created 2011-12-16 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 pdb3kdn.ent

Checks that need to be done early-on in validation

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 B

All-atom RMS fit for the two chains : 0.486
CA-only RMS fit for the two chains : 0.289

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 B

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 C

All-atom RMS fit for the two chains : 0.471
CA-only RMS fit for the two chains : 0.290

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 C

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 : 0.453
CA-only RMS fit for the two chains : 0.290

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 E

All-atom RMS fit for the two chains : 0.496
CA-only RMS fit for the two chains : 0.283

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 E

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 F

All-atom RMS fit for the two chains : 0.395
CA-only RMS fit for the two chains : 0.231

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 F

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

4373 CAP   ( 600-)  A  -
4375 CAP   ( 600-)  B  -
4377 CAP   ( 600-)  C  -
4379 CAP   ( 600-)  D  -
4381 CAP   ( 600-)  E  -
4383 CAP   ( 600-)  F  -
4385 CAP   ( 600-)  G  -
4387 CAP   ( 600-)  H  -
4389 CAP   ( 600-)  I  -
4391 CAP   ( 600-)  J  -

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: B

Note: Ramachandran plot

Chain identifier: C

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

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

   1 ILE   (   8-)  A      CG1
   1 ILE   (   8-)  A      CG2
   1 ILE   (   8-)  A      CD1
   2 TYR   (   9-)  A      CG
   2 TYR   (   9-)  A      CD1
   2 TYR   (   9-)  A      CD2
   2 TYR   (   9-)  A      CE1
   2 TYR   (   9-)  A      CE2
   2 TYR   (   9-)  A      CZ
   2 TYR   (   9-)  A      OH
   3 ASP   (  10-)  A      CG
   3 ASP   (  10-)  A      OD1
   3 ASP   (  10-)  A      OD2
   4 TYR   (  11-)  A      CG
   4 TYR   (  11-)  A      CD1
   4 TYR   (  11-)  A      CD2
   4 TYR   (  11-)  A      CE1
   4 TYR   (  11-)  A      CE2
   4 TYR   (  11-)  A      CZ
   4 TYR   (  11-)  A      OH
   8 LYS   (  15-)  A      CG
   8 LYS   (  15-)  A      CD
   8 LYS   (  15-)  A      CE
   8 LYS   (  15-)  A      NZ
  10 TYR   (  17-)  A      CG
And so on for a total of 469 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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

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.

 115 ARG   ( 122-)  A
 402 ARG   ( 409-)  A
 496 ARG   (  66-)  B
 547 ARG   ( 117-)  B
 552 ARG   ( 122-)  B
 984 ARG   ( 117-)  C
1276 ARG   ( 409-)  C
1426 ARG   ( 122-)  D
1713 ARG   ( 409-)  D
1737 ARG   ( 433-)  D
1808 ARG   (  66-)  E
1859 ARG   ( 117-)  E
2007 ARG   ( 265-)  E
2080 ARG   ( 338-)  E
2151 ARG   ( 409-)  E
2175 ARG   ( 433-)  E
2296 ARG   ( 117-)  F
2588 ARG   ( 409-)  F
2682 ARG   (  66-)  G
2733 ARG   ( 117-)  G
2881 ARG   ( 265-)  G
3463 ARG   ( 409-)  H
3899 ARG   ( 409-)  I
3923 ARG   ( 433-)  I
3993 ARG   (  66-)  J
4049 ARG   ( 122-)  J
4192 ARG   ( 265-)  J
4265 ARG   ( 338-)  J
4336 ARG   ( 409-)  J

Warning: Tyrosine convention problem

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

   5 TYR   (  12-)  A
  55 TYR   (  62-)  A
  84 TYR   (  91-)  A
 161 TYR   ( 168-)  A
 442 TYR   (  12-)  B
 467 TYR   (  37-)  B
 489 TYR   (  59-)  B
 505 TYR   (  75-)  B
 521 TYR   (  91-)  B
 772 TYR   ( 342-)  B
 879 TYR   (  12-)  C
 929 TYR   (  62-)  C
 942 TYR   (  75-)  C
 958 TYR   (  91-)  C
1315 TYR   (  11-)  D
1316 TYR   (  12-)  D
1366 TYR   (  62-)  D
1379 TYR   (  75-)  D
1395 TYR   (  91-)  D
1728 TYR   ( 424-)  D
1754 TYR   (  12-)  E
1779 TYR   (  37-)  E
1804 TYR   (  62-)  E
1833 TYR   (  91-)  E
2084 TYR   ( 342-)  E
And so on for a total of 58 lines.

Warning: Phenylalanine convention problem

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

  70 PHE   (  77-)  A
 134 PHE   ( 141-)  A
 195 PHE   ( 202-)  A
 349 PHE   ( 356-)  A
 507 PHE   (  77-)  B
 566 PHE   ( 136-)  B
 571 PHE   ( 141-)  B
 632 PHE   ( 202-)  B
 944 PHE   (  77-)  C
1008 PHE   ( 141-)  C
1069 PHE   ( 202-)  C
1381 PHE   (  77-)  D
1445 PHE   ( 141-)  D
1506 PHE   ( 202-)  D
1660 PHE   ( 356-)  D
1819 PHE   (  77-)  E
1878 PHE   ( 136-)  E
1883 PHE   ( 141-)  E
1944 PHE   ( 202-)  E
2098 PHE   ( 356-)  E
2256 PHE   (  77-)  F
2320 PHE   ( 141-)  F
2381 PHE   ( 202-)  F
2693 PHE   (  77-)  G
2757 PHE   ( 141-)  G
2818 PHE   ( 202-)  G
2972 PHE   ( 356-)  G
3131 PHE   (  77-)  H
3195 PHE   ( 141-)  H
3256 PHE   ( 202-)  H
3410 PHE   ( 356-)  H
3567 PHE   (  77-)  I
3631 PHE   ( 141-)  I
3692 PHE   ( 202-)  I
3789 PHE   ( 299-)  I
3846 PHE   ( 356-)  I
4004 PHE   (  77-)  J
4068 PHE   ( 141-)  J
4129 PHE   ( 202-)  J
4283 PHE   ( 356-)  J

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.

 758 ASP   ( 328-)  B
1380 ASP   (  76-)  D
1632 ASP   ( 328-)  D
2164 ASP   ( 422-)  E
2692 ASP   (  76-)  G
2944 ASP   ( 328-)  G
3245 ASP   ( 191-)  H
3818 ASP   ( 328-)  I
4118 ASP   ( 191-)  J
4349 ASP   ( 422-)  J

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.

  56 GLU   (  63-)  A
 215 GLU   ( 222-)  A
 317 GLU   ( 324-)  A
 930 GLU   (  63-)  C
1071 GLU   ( 204-)  C
1402 GLU   (  98-)  D
1448 GLU   ( 144-)  D
2122 GLU   ( 380-)  E
2178 GLU   ( 436-)  E
2505 GLU   ( 326-)  F
2679 GLU   (  63-)  G
2714 GLU   (  98-)  G
2838 GLU   ( 222-)  G
3072 GLU   (  18-)  H
3198 GLU   ( 144-)  H
3539 GLU   (  49-)  I
3693 GLU   ( 203-)  I
3920 GLU   ( 430-)  I
4101 GLU   ( 174-)  J
4363 GLU   ( 436-)  J

Warning: Heavy atom naming convention problem

The atoms listed in the table below have nonstandard names in the input file. (Be aware that we sometimes consider an asterix and an apostrophe identical, and thus do not warn for the use of asterixes. Please be aware that the PDB wants us to deliberately make some nomenclature errors; especially in non-canonical amino acids.

 182 KCX   ( 189-)  A      CH     CX
 182 KCX   ( 189-)  A      OX1    OQ1
 182 KCX   ( 189-)  A      OX2    OQ2
 619 KCX   ( 189-)  B      CH     CX
 619 KCX   ( 189-)  B      OX1    OQ1
 619 KCX   ( 189-)  B      OX2    OQ2
1056 KCX   ( 189-)  C      CH     CX
1056 KCX   ( 189-)  C      OX1    OQ1
1056 KCX   ( 189-)  C      OX2    OQ2
1493 KCX   ( 189-)  D      CH     CX
1493 KCX   ( 189-)  D      OX1    OQ1
1493 KCX   ( 189-)  D      OX2    OQ2
1931 KCX   ( 189-)  E      CH     CX
1931 KCX   ( 189-)  E      OX1    OQ1
1931 KCX   ( 189-)  E      OX2    OQ2
2368 KCX   ( 189-)  F      CH     CX
2368 KCX   ( 189-)  F      OX1    OQ1
2368 KCX   ( 189-)  F      OX2    OQ2
2805 KCX   ( 189-)  G      CH     CX
2805 KCX   ( 189-)  G      OX1    OQ1
2805 KCX   ( 189-)  G      OX2    OQ2
3243 KCX   ( 189-)  H      CH     CX
3243 KCX   ( 189-)  H      OX1    OQ1
3243 KCX   ( 189-)  H      OX2    OQ2
3679 KCX   ( 189-)  I      CH     CX
3679 KCX   ( 189-)  I      OX1    OQ1
3679 KCX   ( 189-)  I      OX2    OQ2
4116 KCX   ( 189-)  J      CH     CX
4116 KCX   ( 189-)  J      OX1    OQ1
4116 KCX   ( 189-)  J      OX2    OQ2

Geometric checks

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

 |  0.999215  0.000032 -0.000028|
 |  0.000032  0.999287 -0.000024|
 | -0.000028 -0.000024  0.999383|
Proposed new scale matrix

 |  0.010267  0.000000  0.002579|
 |  0.000000  0.004064  0.000000|
 |  0.000000  0.000000  0.007753|
With corresponding cell

    A    =  97.399  B   = 246.069  C    = 132.993
    Alpha=  90.002  Beta= 104.101  Gamma=  90.002

The CRYST1 cell dimensions

    A    =  97.474  B   = 246.241  C    = 133.080
    Alpha=  90.000  Beta= 104.100  Gamma=  90.000

Variance: 72.297
(Under-)estimated Z-score: 6.267

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.

  56 GLU   (  63-)  A
 115 ARG   ( 122-)  A
 215 GLU   ( 222-)  A
 317 GLU   ( 324-)  A
 402 ARG   ( 409-)  A
 496 ARG   (  66-)  B
 547 ARG   ( 117-)  B
 552 ARG   ( 122-)  B
 758 ASP   ( 328-)  B
 930 GLU   (  63-)  C
 984 ARG   ( 117-)  C
1071 GLU   ( 204-)  C
1276 ARG   ( 409-)  C
1380 ASP   (  76-)  D
1402 GLU   (  98-)  D
1426 ARG   ( 122-)  D
1448 GLU   ( 144-)  D
1632 ASP   ( 328-)  D
1713 ARG   ( 409-)  D
1737 ARG   ( 433-)  D
1808 ARG   (  66-)  E
1859 ARG   ( 117-)  E
2007 ARG   ( 265-)  E
2080 ARG   ( 338-)  E
2122 GLU   ( 380-)  E
And so on for a total of 59 lines.

Torsion-related checks

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.

2841 THR   ( 225-)  G    -2.9
3715 THR   ( 225-)  I    -2.7
 655 THR   ( 225-)  B    -2.7
1529 THR   ( 225-)  D    -2.7
4152 THR   ( 225-)  J    -2.7
2105 PHE   ( 363-)  E    -2.6
1967 THR   ( 225-)  E    -2.6
1092 THR   ( 225-)  C    -2.6
3279 THR   ( 225-)  H    -2.6
2979 PHE   ( 363-)  G    -2.6
3417 PHE   ( 363-)  H    -2.5
 921 THR   (  54-)  C    -2.5
3853 PHE   ( 363-)  I    -2.5
2542 PHE   ( 363-)  F    -2.5
4290 PHE   ( 363-)  J    -2.5
 218 THR   ( 225-)  A    -2.5
 420 THR   ( 427-)  A    -2.5
 793 PHE   ( 363-)  B    -2.5
3598 ILE   ( 108-)  I    -2.5
1230 PHE   ( 363-)  C    -2.5
2404 THR   ( 225-)  F    -2.5
1667 PHE   ( 363-)  D    -2.4
 484 THR   (  54-)  B    -2.4
 101 ILE   ( 108-)  A    -2.3
 538 ILE   ( 108-)  B    -2.3
And so on for a total of 75 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.

  22 PHE   (  29-)  A  omega poor
  44 SER   (  51-)  A  Poor phi/psi
  67 ALA   (  74-)  A  omega poor
 144 GLU   ( 151-)  A  Poor phi/psi
 156 LYS   ( 163-)  A  PRO omega poor
 188 THR   ( 195-)  A  Poor phi/psi
 225 ALA   ( 232-)  A  Poor phi/psi
 277 MET   ( 284-)  A  Poor phi/psi
 281 PHE   ( 288-)  A  Poor phi/psi
 302 GLY   ( 309-)  A  Poor phi/psi
 311 ALA   ( 318-)  A  Poor phi/psi
 350 TYR   ( 357-)  A  Poor phi/psi
 411 GLY   ( 418-)  A  Poor phi/psi
 419 LYS   ( 426-)  A  Poor phi/psi
 420 THR   ( 427-)  A  Poor phi/psi
 454 ASP   (  24-)  B  omega poor
 481 SER   (  51-)  B  Poor phi/psi
 581 GLU   ( 151-)  B  Poor phi/psi
 593 LYS   ( 163-)  B  PRO omega poor
 625 THR   ( 195-)  B  Poor phi/psi
 662 ALA   ( 232-)  B  Poor phi/psi
 679 LEU   ( 249-)  B  omega poor
 714 MET   ( 284-)  B  Poor phi/psi
 739 GLY   ( 309-)  B  Poor phi/psi
 787 TYR   ( 357-)  B  Poor phi/psi
And so on for a total of 104 lines.

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!

   3 ASP   (  10-)  A      0
   4 TYR   (  11-)  A      0
   7 ASP   (  14-)  A      0
  16 ARG   (  23-)  A      0
  30 TYR   (  37-)  A      0
  32 ILE   (  39-)  A      0
  43 SER   (  50-)  A      0
  44 SER   (  51-)  A      0
  45 THR   (  52-)  A      0
  48 TRP   (  55-)  A      0
  53 PRO   (  60-)  A      0
  54 TRP   (  61-)  A      0
  55 TYR   (  62-)  A      0
  68 TYR   (  75-)  A      0
  69 ASP   (  76-)  A      0
  73 MET   (  80-)  A      0
  75 ASP   (  82-)  A      0
  77 SER   (  84-)  A      0
  87 HIS   (  94-)  A      0
  91 GLU   (  98-)  A      0
  92 ALA   (  99-)  A      0
 101 ILE   ( 108-)  A      0
 102 ALA   ( 109-)  A      0
 104 ASN   ( 111-)  A      0
 112 LYS   ( 119-)  A      0
And so on for a total of 1521 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!

1912 PRO   ( 170-)  E   1.80   11
 411 GLY   ( 418-)  A   1.56   80
1260 GLY   ( 393-)  C   1.51   80

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

  12 PRO   (  19-)  A   -64.8 envelop C-beta (-72 degrees)
  95 PRO   ( 102-)  A   101.8 envelop C-beta (108 degrees)
 370 PRO   ( 377-)  A  -116.0 envelop C-gamma (-108 degrees)
 436 PRO   ( 443-)  A   106.2 envelop C-beta (108 degrees)
 807 PRO   ( 377-)  B  -112.4 envelop C-gamma (-108 degrees)
1898 PRO   ( 156-)  E  -125.9 half-chair C-delta/C-gamma (-126 degrees)
2162 PRO   ( 420-)  E   121.8 half-chair C-beta/C-alpha (126 degrees)
2335 PRO   ( 156-)  F  -132.4 half-chair C-delta/C-gamma (-126 degrees)
2577 PRO   ( 398-)  F   109.3 envelop C-beta (108 degrees)
2580 PRO   ( 401-)  F  -115.9 envelop C-gamma (-108 degrees)
2772 PRO   ( 156-)  G  -115.3 envelop C-gamma (-108 degrees)
3059 PRO   ( 443-)  G    50.5 half-chair C-delta/C-gamma (54 degrees)
3073 PRO   (  19-)  H    46.1 half-chair C-delta/C-gamma (54 degrees)
3497 PRO   ( 443-)  H    99.8 envelop C-beta (108 degrees)
3646 PRO   ( 156-)  I  -123.9 half-chair C-delta/C-gamma (-126 degrees)
3946 PRO   (  19-)  J    42.3 envelop C-delta (36 degrees)

Bump checks

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.

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). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 417 TYR   ( 424-)  A      CE2 <->  421 HIS   ( 428-)  A      CE1    0.74    2.46  INTRA BF
4255 ASP   ( 328-)  J      OD1 <-> 4256 ILE   ( 329-)  J      CD1    0.72    2.08  INTRA
 142 MET   ( 149-)  A      CE  <->  243 LYS   ( 250-)  A      CD     0.66    2.54  INTRA
 171 TYR   ( 178-)  A      CE1 <->  208 LYS   ( 215-)  A      NZ     0.65    2.45  INTRA BF
 417 TYR   ( 424-)  A      CZ  <->  421 HIS   ( 428-)  A      CE1    0.65    2.55  INTRA BF
2277 GLU   (  98-)  F      CD  <-> 4397 HOH   (2195 )  F      O      0.59    2.21  INTRA
 142 MET   ( 149-)  A      CE  <->  243 LYS   ( 250-)  A      CE     0.58    2.62  INTRA
2118 GLN   ( 376-)  E      CB  <-> 4396 HOH   (2871 )  E      O      0.55    2.25  INTRA BF
 758 ASP   ( 328-)  B      OD1 <->  759 ILE   ( 329-)  B      CD1    0.52    2.28  INTRA
 389 GLY   ( 396-)  A      O   <->  430 LYS   ( 437-)  A      NZ     0.50    2.20  INTRA BF
4255 ASP   ( 328-)  J      CG  <-> 4256 ILE   ( 329-)  J      CD1    0.50    2.70  INTRA
3371 THR   ( 317-)  H      CG2 <-> 4399 HOH   (2909 )  H      O      0.50    2.30  INTRA
 645 LYS   ( 215-)  B      NZ  <->  649 GLU   ( 219-)  B      OE2    0.49    2.21  INTRA
4101 GLU   ( 174-)  J      OE2 <-> 4138 LYS   ( 211-)  J      NZ     0.48    2.22  INTRA
2555 GLN   ( 376-)  F      CG  <-> 4397 HOH   (2817 )  F      O      0.48    2.32  INTRA
 325 GLN   ( 332-)  A      OE1 <->  344 HIS   ( 351-)  A      CE1    0.48    2.32  INTRA BF
  31 THR   (  38-)  A      CG2 <->   34 GLN   (  41-)  A      OE1    0.48    2.32  INTRA BF
 171 TYR   ( 178-)  A      CZ  <->  208 LYS   ( 215-)  A      NZ     0.45    2.65  INTRA BF
 417 TYR   ( 424-)  A      CD2 <->  421 HIS   ( 428-)  A      ND1    0.45    2.65  INTRA BF
3450 GLY   ( 396-)  H      O   <-> 3491 LYS   ( 437-)  H      NZ     0.45    2.25  INTRA BF
3371 THR   ( 317-)  H      N   <-> 4399 HOH   (1011 )  H      O      0.45    2.25  INTRA
 142 MET   ( 149-)  A      CE  <->  243 LYS   ( 250-)  A      CB     0.45    2.75  INTRA
 369 GLN   ( 376-)  A      CB  <-> 4392 HOH   (2304 )  A      O      0.45    2.35  INTRA BF
 317 GLU   ( 324-)  A      OE1 <->  318 GLY   ( 325-)  A      N      0.44    2.16  INTRA BF
2170 HIS   ( 428-)  E      NE2 <-> 4396 HOH   (2782 )  E      O      0.44    2.26  INTRA BF
And so on for a total of 987 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: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

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

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.

 489 TYR   (  59-)  B      -6.58
 336 LYS   ( 343-)  A      -6.21
1801 TYR   (  59-)  E      -6.14
1363 TYR   (  59-)  D      -6.08
3549 TYR   (  59-)  I      -6.04
3344 ARG   ( 290-)  H      -5.98
3113 TYR   (  59-)  H      -5.94
  52 TYR   (  59-)  A      -5.91
2469 ARG   ( 290-)  F      -5.78
1157 ARG   ( 290-)  C      -5.76
2675 TYR   (  59-)  G      -5.73
 720 ARG   ( 290-)  B      -5.71
2906 ARG   ( 290-)  G      -5.70
3780 ARG   ( 290-)  I      -5.70
4217 ARG   ( 290-)  J      -5.64
3033 GLN   ( 417-)  G      -5.61
 283 ARG   ( 290-)  A      -5.60
1721 GLN   ( 417-)  D      -5.59
 847 GLN   ( 417-)  B      -5.57
3907 GLN   ( 417-)  I      -5.55
2032 ARG   ( 290-)  E      -5.48
3377 LEU   ( 323-)  H      -5.46
1594 ARG   ( 290-)  D      -5.43
3986 TYR   (  59-)  J      -5.42
3494 HIS   ( 440-)  H      -5.40
1362 LEU   (  58-)  D      -5.37
 926 TYR   (  59-)  C      -5.35
3217 LYS   ( 163-)  H      -5.27
2633 TYR   (  17-)  G      -5.26
1905 LYS   ( 163-)  E      -5.26
1321 TYR   (  17-)  D      -5.24
1030 LYS   ( 163-)  C      -5.23
3392 ARG   ( 338-)  H      -5.19
 768 ARG   ( 338-)  B      -5.18
2080 ARG   ( 338-)  E      -5.18
2779 LYS   ( 163-)  G      -5.17
2954 ARG   ( 338-)  G      -5.13
4265 ARG   ( 338-)  J      -5.11
  48 TRP   (  55-)  A      -5.10
1205 ARG   ( 338-)  C      -5.10
3653 LYS   ( 163-)  I      -5.09
3828 ARG   ( 338-)  I      -5.09
1642 ARG   ( 338-)  D      -5.08
3492 TRP   ( 438-)  H      -5.08
2517 ARG   ( 338-)  F      -5.08
 447 TYR   (  17-)  B      -5.05
 286 TYR   ( 293-)  A      -5.05
 331 ARG   ( 338-)  A      -5.05
 431 TRP   ( 438-)  A      -5.04

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.

1740 GLU   ( 436-)  D      1742 - TRP    438- ( D)         -4.21
2178 GLU   ( 436-)  E      2180 - TRP    438- ( E)         -4.40
3111 THR   (  57-)  H      3113 - TYR     59- ( H)         -4.82
3926 GLU   ( 436-)  I      3928 - TRP    438- ( I)         -4.24

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: B

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: C

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

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.

2238 TYR   (  59-)  F   -3.41
 110 ARG   ( 117-)  A   -3.06
1325 LYS   (  21-)  D   -3.03
1403 ALA   (  99-)  D   -3.02
 966 ALA   (  99-)  C   -2.98
  51 LEU   (  58-)  A   -2.95
  14 LYS   (  21-)  A   -2.86
2465 ALA   ( 286-)  F   -2.85
2902 ALA   ( 286-)  G   -2.85
4213 ALA   ( 286-)  J   -2.83
 716 ALA   ( 286-)  B   -2.83
   2 TYR   (   9-)  A   -2.82
1153 ALA   ( 286-)  C   -2.82
3548 LEU   (  58-)  I   -2.82
   4 TYR   (  11-)  A   -2.81
 279 ALA   ( 286-)  A   -2.80
3776 ALA   ( 286-)  I   -2.75
1800 LEU   (  58-)  E   -2.69
2237 LEU   (  58-)  F   -2.63
  10 TYR   (  17-)  A   -2.61
3062 ILE   (   8-)  H   -2.57

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: B

Note: Second generation quality Z-score plot

Chain identifier: C

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

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

4395 HOH   (1756 )  D      O     -9.69   11.48  -33.68
4395 HOH   (1757 )  D      O    -10.21   13.49  -34.99
4400 HOH   (1786 )  I      O    -22.79   -8.84  -28.54

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

4393 HOH   ( 687 )  B      O
4395 HOH   (2652 )  D      O

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.

  34 GLN   (  41-)  A
 347 GLN   ( 354-)  A
 784 GLN   ( 354-)  B
1199 GLN   ( 332-)  C
1221 GLN   ( 354-)  C
1307 HIS   ( 440-)  C
1636 GLN   ( 332-)  D
1658 GLN   ( 354-)  D
1744 HIS   ( 440-)  D
2096 GLN   ( 354-)  E
2493 HIS   ( 314-)  F
2533 GLN   ( 354-)  F
2948 GLN   ( 332-)  G
2970 GLN   ( 354-)  G
3056 HIS   ( 440-)  G
3408 GLN   ( 354-)  H
3844 GLN   ( 354-)  I
3866 GLN   ( 376-)  I
3907 GLN   ( 417-)  I
4259 GLN   ( 332-)  J
4281 GLN   ( 354-)  J

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.

  44 SER   (  51-)  A      OG
  52 TYR   (  59-)  A      N
  55 TYR   (  62-)  A      N
  75 ASP   (  82-)  A      N
 104 ASN   ( 111-)  A      ND2
 156 LYS   ( 163-)  A      N
 156 LYS   ( 163-)  A      NZ
 158 LYS   ( 165-)  A      NZ
 159 VAL   ( 166-)  A      N
 192 TYR   ( 199-)  A      N
 193 ASN   ( 200-)  A      ND2
 198 ARG   ( 205-)  A      NE
 222 ASN   ( 229-)  A      ND2
 225 ALA   ( 232-)  A      N
 275 ARG   ( 282-)  A      NE
 315 LYS   ( 322-)  A      NZ
 360 SER   ( 367-)  A      OG
 362 GLY   ( 369-)  A      N
 368 ILE   ( 375-)  A      N
 369 GLN   ( 376-)  A      N
 382 GLN   ( 389-)  A      NE2
 384 GLY   ( 391-)  A      N
 385 GLY   ( 392-)  A      N
 415 ASP   ( 422-)  A      N
 484 THR   (  54-)  B      OG1
And so on for a total of 203 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.

  71 HIS   (  78-)  A      ND1
 248 ASP   ( 255-)  A      OD1
 248 ASP   ( 255-)  A      OD2
 307 HIS   ( 314-)  A      ND1
 332 GLU   ( 339-)  A      OE1
 685 ASP   ( 255-)  B      OD1
 685 ASP   ( 255-)  B      OD2
 744 HIS   ( 314-)  B      ND1
1122 ASP   ( 255-)  C      OD1
1181 HIS   ( 314-)  C      ND1
1208 HIS   ( 341-)  C      NE2
1559 ASP   ( 255-)  D      OD1
1559 ASP   ( 255-)  D      OD2
1618 HIS   ( 314-)  D      ND1
1997 ASP   ( 255-)  E      OD1
1997 ASP   ( 255-)  E      OD2
2056 HIS   ( 314-)  E      ND1
2434 ASP   ( 255-)  F      OD1
2434 ASP   ( 255-)  F      OD2
2458 HIS   ( 279-)  F      NE2
2871 ASP   ( 255-)  G      OD1
2871 ASP   ( 255-)  G      OD2
2930 HIS   ( 314-)  G      ND1
3309 ASP   ( 255-)  H      OD1
3368 HIS   ( 314-)  H      ND1
3745 ASP   ( 255-)  I      OD1
3804 HIS   ( 314-)  I      ND1
4182 ASP   ( 255-)  J      OD1
4182 ASP   ( 255-)  J      OD2
4241 HIS   ( 314-)  J      ND1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

4386  MG   ( 500-)  H     0.66   1.14 Is perhaps CA *2

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

4392 HOH   ( 951 )  A      O  1.13  K  4 NCS 8/8
4392 HOH   (1568 )  A      O  0.96  K  4 Ion-B H2O-B NCS 1/1
4393 HOH   (2937 )  B      O  1.00 NA  4 NCS 1/1
4395 HOH   ( 478 )  D      O  0.95  K  4 NCS 9/9
4395 HOH   (2063 )  D      O  0.88  K  6 NCS 2/2
4395 HOH   (2153 )  D      O  0.96  K  4 Ion-B H2O-B NCS 4/4
4396 HOH   ( 720 )  E      O  0.86  K  5 Ion-B
4396 HOH   (1564 )  E      O  0.98  K  5 NCS 3/3
4396 HOH   (2293 )  E      O  0.88  K  5 Ion-B
4398 HOH   ( 470 )  G      O  0.92  K  4 Ion-B NCS 5/5
4398 HOH   ( 492 )  G      O  0.91  K  4 NCS 6/6
4398 HOH   (1870 )  G      O  0.86  K  4 NCS 5/5
4398 HOH   (2923 )  G      O  0.88 NA  4 NCS 1/1
4399 HOH   (2740 )  H      O  1.03  K  4 ION-B NCS 1/1
4400 HOH   (1032 )  I      O  0.86  K  4 Ion-B NCS 4/4
4400 HOH   (1956 )  I      O  0.88  K  4 NCS 7/7
4401 HOH   ( 969 )  J      O  0.96  K  4 NCS 4/4

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.

 226 ASP   ( 233-)  A   H-bonding suggests Asn
 248 ASP   ( 255-)  A   H-bonding suggests Asn; but Alt-Rotamer
 266 ASP   ( 273-)  A   H-bonding suggests Asn
 406 ASP   ( 413-)  A   H-bonding suggests Asn; but Alt-Rotamer
 663 ASP   ( 233-)  B   H-bonding suggests Asn
 685 ASP   ( 255-)  B   H-bonding suggests Asn; but Alt-Rotamer
1021 ASP   ( 154-)  C   H-bonding suggests Asn; but Alt-Rotamer
1100 ASP   ( 233-)  C   H-bonding suggests Asn
1122 ASP   ( 255-)  C   H-bonding suggests Asn; but Alt-Rotamer
1280 ASP   ( 413-)  C   H-bonding suggests Asn
1537 ASP   ( 233-)  D   H-bonding suggests Asn
1559 ASP   ( 255-)  D   H-bonding suggests Asn; but Alt-Rotamer
1975 ASP   ( 233-)  E   H-bonding suggests Asn
1997 ASP   ( 255-)  E   H-bonding suggests Asn
2155 ASP   ( 413-)  E   H-bonding suggests Asn; but Alt-Rotamer
2412 ASP   ( 233-)  F   H-bonding suggests Asn
2434 ASP   ( 255-)  F   H-bonding suggests Asn; but Alt-Rotamer
2849 ASP   ( 233-)  G   H-bonding suggests Asn
2871 ASP   ( 255-)  G   H-bonding suggests Asn; but Alt-Rotamer
3029 ASP   ( 413-)  G   H-bonding suggests Asn
3271 GLU   ( 217-)  H   H-bonding suggests Gln; but Alt-Rotamer
3287 ASP   ( 233-)  H   H-bonding suggests Asn
3309 ASP   ( 255-)  H   H-bonding suggests Asn; but Alt-Rotamer
3327 ASP   ( 273-)  H   H-bonding suggests Asn; but Alt-Rotamer
3644 ASP   ( 154-)  I   H-bonding suggests Asn; but Alt-Rotamer
3723 ASP   ( 233-)  I   H-bonding suggests Asn
3745 ASP   ( 255-)  I   H-bonding suggests Asn; but Alt-Rotamer
4081 ASP   ( 154-)  J   H-bonding suggests Asn; but Alt-Rotamer
4160 ASP   ( 233-)  J   H-bonding suggests Asn
4182 ASP   ( 255-)  J   H-bonding suggests Asn; but Alt-Rotamer
4340 ASP   ( 413-)  J   H-bonding suggests Asn; but Alt-Rotamer

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 :  -0.217
  2nd generation packing quality :  -0.980
  Ramachandran plot appearance   :  -1.107
  chi-1/chi-2 rotamer normality  :  -0.495
  Backbone conformation          :  -0.228

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.212 (tight)
  Bond angles                    :   0.466 (tight)
  Omega angle restraints         :   0.852
  Side chain planarity           :   0.195 (tight)
  Improper dihedral distribution :   0.418
  B-factor distribution          :   0.330
  Inside/Outside distribution    :   1.036

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 : 2.09


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.2
  2nd generation packing quality :  -0.6
  Ramachandran plot appearance   :  -0.3
  chi-1/chi-2 rotamer normality  :   0.4
  Backbone conformation          :  -0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.212 (tight)
  Bond angles                    :   0.466 (tight)
  Omega angle restraints         :   0.852
  Side chain planarity           :   0.195 (tight)
  Improper dihedral distribution :   0.418
  B-factor distribution          :   0.330
  Inside/Outside distribution    :   1.036
==============

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.