WHAT IF Check report

This file was created 2013-12-09 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 pdb2yev.ent

Checks that need to be done early-on in validation

Warning: Nonstandard space group setting

The space group name given represents a non-standard setting.

Space group name: I 1 2 1

Conventional space group : C 1 2 1

Warning: Unconventional cell on CRYST1

The derived `conventional cell' is different from the cell given on the CRYST1 card.

The CRYST1 cell dimensions

    A    = 127.250  B   =  76.030  C    = 300.267
    Alpha=  90.000  Beta=  92.210  Gamma=  90.000

Dimensions of a reduced cell

    A    =  76.030  B   = 127.250  C    = 165.217
    Alpha=  69.509  Beta= 103.302  Gamma=  90.000

Dimensions of the conventional cell

    A    = 321.568  B   =  76.030  C    = 127.250
    Alpha=  90.000  Beta= 111.082  Gamma=  90.000

Transformation to conventional cell

 | -1.000000  0.000000 -1.000000|
 |  0.000000  1.000000  0.000000|
 |  1.000000  0.000000  0.000000|

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 : 0.426
CA-only RMS fit for the two chains : 0.141

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: B and E

All-atom RMS fit for the two chains : 0.522
CA-only RMS fit for the two chains : 0.162

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: B 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: C and F

All-atom RMS fit for the two chains : 0.384
CA-only RMS fit for the two chains : 0.021

Warning: Topology could not be determined for some ligands

Some ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

2326 FME   (   1-)  C  -         OK
2329 5PL   ( 900-)  A  -
2330 HAS   (1015-)  A  -         Atom types
2331 HAS   (1016-)  A  -         Atom types
2333 7E8   (1300-)  A  -         OK
2335 CUA   ( 585-)  B  -         Atom types
2336 HEC   ( 587-)  B  -         Atom types
2338 5PL   ( 900-)  D  -
2339 HAS   (1015-)  D  -         Atom types
2340 HAS   (1016-)  D  -         Atom types
2344 CUA   ( 585-)  E  -         Atom types
2345 HEC   ( 587-)  E  -         Atom types
2347 7E9   ( 701-)  D  -         OK
2348 7E8   (1301-)  A  -         OK
2349 4AG   (1200-)  A  -         OK
2350 FME   (   1-)  F  -         OK

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

1100 VAL   (   2-)  C  -   N   bound to 2326 FME   (   1-)  C  -   C
2262 VAL   (   2-)  F  -   N   bound to 2350 FME   (   1-)  F  -   C

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

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

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 TRP   (  12-)  A    High
   2 ALA   (  13-)  A    High
   3 VAL   (  14-)  A    High
   4 LEU   (  15-)  A    High
  48 GLN   (  59-)  A    High
  92 ASP   ( 103-)  A    High
 139 GLU   ( 150-)  A    High
 173 GLN   ( 184-)  A    High
 179 LYS   ( 190-)  A    High
 269 ARG   ( 280-)  A    High
 270 GLN   ( 281-)  A    High
 273 TRP   ( 284-)  A    High
 290 MET   ( 301-)  A    High
 329 LYS   ( 340-)  A    High
 332 MET   ( 343-)  A    High
 406 ARG   ( 417-)  A    High
 474 TRP   ( 485-)  A    High
 478 ARG   ( 489-)  A    High
 482 LYS   ( 493-)  A    High
 502 LYS   ( 513-)  A    High
 507 ASP   ( 518-)  A    High
 509 LYS   ( 520-)  A    High
 513 GLU   ( 524-)  A    High
 524 LYS   ( 535-)  A    High
 525 LYS   ( 536-)  A    High
And so on for a total of 279 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: 20

Crystal temperature (K) :100.000

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 2.350 over 15693 bonds
Average difference in B over a bond : 8.24
RMS difference in B over a bond : 10.50

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

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

 |  0.999220  0.000019  0.000013|
 |  0.000019  0.999393 -0.000148|
 |  0.000013 -0.000148  0.999216|
Proposed new scale matrix

 |  0.007865  0.000000  0.000303|
 |  0.000000  0.013161  0.000002|
 |  0.000000  0.000000  0.003336|
With corresponding cell

    A    = 127.144  B   =  75.982  C    = 300.018
    Alpha=  90.010  Beta=  92.209  Gamma=  90.001

The CRYST1 cell dimensions

    A    = 127.250  B   =  76.030  C    = 300.267
    Alpha=  90.000  Beta=  92.210  Gamma=  90.000

Variance: 42.417
(Under-)estimated Z-score: 4.800

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.

 239 HIS   ( 250-)  A      N    CA   CB  117.32    4.0
 924 HIS   ( 162-)  B      CG   ND1  CE1 109.60    4.0
1401 HIS   ( 250-)  D      N    CA   CB  117.40    4.1
1538 HIS   ( 387-)  D      CG   ND1  CE1 109.67    4.1

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.

 239 HIS   ( 250-)  A    6.83
1401 HIS   ( 250-)  D    6.64

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.

2080 THR   ( 156-)  E    -2.7
 918 THR   ( 156-)  B    -2.7
 310 ILE   ( 321-)  A    -2.5
 133 PRO   ( 144-)  A    -2.5
1472 ILE   ( 321-)  D    -2.5
1295 PRO   ( 144-)  D    -2.5
1602 THR   ( 451-)  D    -2.4
 440 THR   ( 451-)  A    -2.4
1292 PHE   ( 141-)  D    -2.4
 130 PHE   ( 141-)  A    -2.4
 262 ARG   ( 273-)  A    -2.4
1424 ARG   ( 273-)  D    -2.4
1119 ILE   (  21-)  C    -2.3
2281 ILE   (  21-)  F    -2.3
2109 PHE   ( 185-)  E    -2.2
2204 VAL   ( 280-)  E    -2.2
1042 VAL   ( 280-)  B    -2.2
 567 PRO   ( 578-)  A    -2.2
1600 TYR   ( 449-)  D    -2.2
 438 TYR   ( 449-)  A    -2.2
  70 PHE   (  81-)  A    -2.2
1037 LEU   ( 275-)  B    -2.2
2199 LEU   ( 275-)  E    -2.2
1729 PRO   ( 578-)  D    -2.1
1232 PHE   (  81-)  D    -2.1
1529 ASP   ( 378-)  D    -2.1
 367 ASP   ( 378-)  A    -2.1
2128 SER   ( 204-)  E    -2.1
 789 PRO   (  27-)  B    -2.1
 947 PHE   ( 185-)  B    -2.1
 966 SER   ( 204-)  B    -2.1
 293 VAL   ( 304-)  A    -2.1
1455 VAL   ( 304-)  D    -2.0
1344 ILE   ( 193-)  D    -2.0
  52 GLY   (  63-)  A    -2.0
 921 ASP   ( 159-)  B    -2.0
 830 PRO   (  68-)  B    -2.0

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.

  46 ASN   (  57-)  A  Poor phi/psi
  70 PHE   (  81-)  A  Poor phi/psi, omega poor
 130 PHE   ( 141-)  A  Poor phi/psi
 132 TYR   ( 143-)  A  PRO omega poor
 141 GLY   ( 152-)  A  Poor phi/psi
 218 TRP   ( 229-)  A  omega poor
 237 TYR   ( 248-)  A  omega poor
 238 SER   ( 249-)  A  omega poor
 262 ARG   ( 273-)  A  Poor phi/psi
 332 MET   ( 343-)  A  Poor phi/psi
 367 ASP   ( 378-)  A  Poor phi/psi
 422 THR   ( 433-)  A  omega poor
 437 ARG   ( 448-)  A  Poor phi/psi
 499 SER   ( 510-)  A  PRO omega poor
 505 ASN   ( 516-)  A  Poor phi/psi
 566 VAL   ( 577-)  A  PRO omega poor
 789 PRO   (  27-)  B  Poor phi/psi
 887 GLN   ( 125-)  B  omega poor
 903 ASN   ( 141-)  B  Poor phi/psi
 916 GLU   ( 154-)  B  omega poor
 921 ASP   ( 159-)  B  Poor phi/psi
 958 PHE   ( 196-)  B  omega poor
 973 ARG   ( 211-)  B  omega poor
1008 ASN   ( 246-)  B  Poor phi/psi
1017 ARG   ( 255-)  B  Poor phi/psi
1039 ALA   ( 277-)  B  Poor phi/psi
1208 ASN   (  57-)  D  Poor phi/psi
1232 PHE   (  81-)  D  Poor phi/psi, omega poor
1292 PHE   ( 141-)  D  Poor phi/psi
1294 TYR   ( 143-)  D  PRO omega poor
1303 GLY   ( 152-)  D  Poor phi/psi
1380 TRP   ( 229-)  D  omega poor
1400 SER   ( 249-)  D  omega poor
1424 ARG   ( 273-)  D  Poor phi/psi
1494 MET   ( 343-)  D  Poor phi/psi
1529 ASP   ( 378-)  D  Poor phi/psi
1584 THR   ( 433-)  D  omega poor
1599 ARG   ( 448-)  D  Poor phi/psi
1661 SER   ( 510-)  D  PRO omega poor
1667 ASN   ( 516-)  D  Poor phi/psi
1728 VAL   ( 577-)  D  PRO omega poor
1951 PRO   (  27-)  E  Poor phi/psi
2049 GLN   ( 125-)  E  omega poor
2065 ASN   ( 141-)  E  Poor phi/psi
2078 GLU   ( 154-)  E  omega poor
2083 ASP   ( 159-)  E  Poor phi/psi
2120 PHE   ( 196-)  E  omega poor
2135 ARG   ( 211-)  E  omega poor
2179 ARG   ( 255-)  E  Poor phi/psi
2201 ALA   ( 277-)  E  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.747

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.

 258 SER   ( 269-)  A    0.34
1420 SER   ( 269-)  D    0.35
1617 SER   ( 466-)  D    0.35
 191 SER   ( 202-)  A    0.36
 186 SER   ( 197-)  A    0.36
1348 SER   ( 197-)  D    0.36
1712 SER   ( 561-)  D    0.36
1859 SER   ( 708-)  D    0.36
 455 SER   ( 466-)  A    0.37
 155 SER   ( 166-)  A    0.37
 818 SER   (  56-)  B    0.38
1638 SER   ( 487-)  D    0.38
1980 SER   (  56-)  E    0.38
1317 SER   ( 166-)  D    0.38
 156 SER   ( 167-)  A    0.38
1318 SER   ( 167-)  D    0.38
 550 SER   ( 561-)  A    0.39

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!

  10 THR   (  21-)  A      0
  11 VAL   (  22-)  A      0
  13 HIS   (  24-)  A      0
  45 PRO   (  56-)  A      0
  46 ASN   (  57-)  A      0
  48 GLN   (  59-)  A      0
  49 PHE   (  60-)  A      0
  50 LEU   (  61-)  A      0
  51 THR   (  62-)  A      0
  53 GLU   (  64-)  A      0
  68 PHE   (  79-)  A      0
  69 PHE   (  80-)  A      0
  70 PHE   (  81-)  A      0
  71 ILE   (  82-)  A      0
  77 THR   (  88-)  A      0
  82 PHE   (  93-)  A      0
  93 VAL   ( 104-)  A      0
  95 LEU   ( 106-)  A      0
 115 MET   ( 126-)  A      0
 120 PRO   ( 131-)  A      0
 124 PRO   ( 135-)  A      0
 125 SER   ( 136-)  A      0
 126 VAL   ( 137-)  A      0
 131 TYR   ( 142-)  A      0
 132 TYR   ( 143-)  A      0
And so on for a total of 588 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].

 240 PRO   ( 251-)  A   100.8 envelop C-beta (108 degrees)
 519 PRO   ( 530-)  A  -117.3 half-chair C-delta/C-gamma (-126 degrees)
 830 PRO   (  68-)  B   100.4 envelop C-beta (108 degrees)
1026 PRO   ( 264-)  B  -125.6 half-chair C-delta/C-gamma (-126 degrees)
1681 PRO   ( 530-)  D  -117.3 half-chair C-delta/C-gamma (-126 degrees)
2188 PRO   ( 264-)  E  -120.8 half-chair C-delta/C-gamma (-126 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.

1401 HIS   ( 250-)  D      NE2 <-> 1405 TYR   ( 254-)  D      CE2    1.78    1.32  INTRA BL
 239 HIS   ( 250-)  A      NE2 <->  243 TYR   ( 254-)  A      CE2    1.77    1.33  INTRA BL
2262 VAL   (   2-)  F      N   <-> 2350 FME   (   1-)  F      C      1.37    1.33  INTRA BF
1401 HIS   ( 250-)  D      CE1 <-> 1405 TYR   ( 254-)  D      CE2    0.86    2.34  INTRA BL
 239 HIS   ( 250-)  A      CE1 <->  243 TYR   ( 254-)  A      CE2    0.86    2.34  INTRA BF
1401 HIS   ( 250-)  D      CD2 <-> 1405 TYR   ( 254-)  D      CE2    0.82    2.38  INTRA BL
 239 HIS   ( 250-)  A      CD2 <->  243 TYR   ( 254-)  A      CE2    0.80    2.40  INTRA BL
1401 HIS   ( 250-)  D      NE2 <-> 1405 TYR   ( 254-)  D      CD2    0.78    2.32  INTRA BL
 239 HIS   ( 250-)  A      NE2 <->  243 TYR   ( 254-)  A      CD2    0.77    2.33  INTRA BL
2262 VAL   (   2-)  F      CA  <-> 2350 FME   (   1-)  F      C      0.76    2.44  INTRA BF
1401 HIS   ( 250-)  D      NE2 <-> 1405 TYR   ( 254-)  D      CZ     0.73    2.37  INTRA BL
 239 HIS   ( 250-)  A      NE2 <->  243 TYR   ( 254-)  A      CZ     0.73    2.37  INTRA BL
1401 HIS   ( 250-)  D      CD2 <-> 1405 TYR   ( 254-)  D      CD2    0.43    2.77  INTRA BL
 239 HIS   ( 250-)  A      CD2 <->  243 TYR   ( 254-)  A      CD2    0.41    2.79  INTRA BL
2227 MET   ( 303-)  E      SD  <-> 2345 HEC   ( 587-)  E      NA     0.40    2.90  INTRA BF
1538 HIS   ( 387-)  D      NE2 <-> 2339 HAS   (1015-)  D      ND     0.35    2.65  INTRA BL
1401 HIS   ( 250-)  D      CE1 <-> 1405 TYR   ( 254-)  D      CZ     0.34    2.86  INTRA BL
 239 HIS   ( 250-)  A      CE1 <->  243 TYR   ( 254-)  A      CZ     0.34    2.86  INTRA BF
1680 ARG   ( 529-)  D      NH2 <-> 2000 GLN   (  76-)  E      OE1    0.34    2.36  INTRA BF
  66 MET   (  77-)  A      CB  <-> 2330 HAS   (1015-)  A      CAC    0.33    2.87  INTRA BL
 376 HIS   ( 387-)  A      NE2 <-> 2330 HAS   (1015-)  A      ND     0.31    2.69  INTRA BL
1065 MET   ( 303-)  B      SD  <-> 2336 HEC   ( 587-)  B      NA     0.29    3.01  INTRA BL
1228 MET   (  77-)  D      CB  <-> 2339 HAS   (1015-)  D      CAC    0.29    2.91  INTRA BF
2175 HIS   ( 251-)  E      NE2 <-> 2345 HEC   ( 587-)  E      ND     0.27    2.73  INTRA BF
1013 HIS   ( 251-)  B      NE2 <-> 2336 HEC   ( 587-)  B      ND     0.27    2.73  INTRA BL
And so on for a total of 185 lines.

Packing, accessibility and threading

Warning: Inside/Outside residue distribution unusual

The distribution of residue types over the inside and the outside of the protein is unusual. Normal values for the RMS Z-score below are between 0.84 and 1.16. The fact that it is higher in this structure could be caused by transmembrane helices, by the fact that it is part of a multimeric active unit, or by mistraced segments in the density.

inside/outside RMS Z-score : 1.166

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

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.

1065 MET   ( 303-)  B      -6.74
2227 MET   ( 303-)  E      -6.17
2181 MET   ( 257-)  E      -6.03
 598 HIS   ( 609-)  A      -5.99
2290 GLU   (  30-)  F      -5.98
1128 GLU   (  30-)  C      -5.95
1064 LYS   ( 302-)  B      -5.85
1644 LYS   ( 493-)  D      -5.82
1253 ARG   ( 102-)  D      -5.80
 139 GLU   ( 150-)  A      -5.78
  91 ARG   ( 102-)  A      -5.77
 537 HIS   ( 548-)  A      -5.76
1161 HIS   (  63-)  C      -5.75
 478 ARG   ( 489-)  A      -5.74
1640 ARG   ( 489-)  D      -5.67
1699 HIS   ( 548-)  D      -5.65
1019 MET   ( 257-)  B      -5.62
 137 GLN   ( 148-)  A      -5.58
 745 ARG   ( 756-)  A      -5.55
1760 HIS   ( 609-)  D      -5.53
2002 HIS   (  78-)  E      -5.52
 672 ARG   ( 683-)  A      -5.50
 482 LYS   ( 493-)  A      -5.50
1997 GLU   (  73-)  E      -5.41
2169 GLN   ( 245-)  E      -5.41
And so on for a total of 51 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.

 596 GLU   ( 607-)  A       598 - HIS    609- ( A)         -4.95

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

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

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.

 593 HIS   ( 604-)  A   -3.03
1451 HIS   ( 300-)  D   -2.56
 289 HIS   ( 300-)  A   -2.55
 836 PRO   (  74-)  B   -2.55
1998 PRO   (  74-)  E   -2.54

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

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.

 664 HIS   ( 675-)  A
 710 GLN   ( 721-)  A
 833 GLN   (  71-)  B
1003 GLN   ( 241-)  B
1161 HIS   (  63-)  C
1208 ASN   (  57-)  D
1216 GLN   (  65-)  D
1299 GLN   ( 148-)  D
1539 ASN   ( 388-)  D
1760 HIS   ( 609-)  D

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 LEU   (  15-)  A      N
  39 ARG   (  50-)  A      NH1
  44 VAL   (  55-)  A      N
  52 GLY   (  63-)  A      N
  72 ILE   (  83-)  A      N
  93 VAL   ( 104-)  A      N
  97 ARG   ( 108-)  A      NH2
  99 ASN   ( 110-)  A      ND2
 116 SER   ( 127-)  A      N
 126 VAL   ( 137-)  A      N
 128 TRP   ( 139-)  A      N
 128 TRP   ( 139-)  A      NE1
 160 ASN   ( 171-)  A      ND2
 171 ARG   ( 182-)  A      N
 194 ASN   ( 205-)  A      ND2
 239 HIS   ( 250-)  A      NE2
 287 ALA   ( 298-)  A      N
 317 LYS   ( 328-)  A      NZ
 327 GLY   ( 338-)  A      N
 338 TRP   ( 349-)  A      NE1
 369 TYR   ( 380-)  A      OH
 382 GLY   ( 393-)  A      N
 411 HIS   ( 422-)  A      NE2
 426 GLN   ( 437-)  A      NE2
 431 TYR   ( 442-)  A      OH
And so on for a total of 141 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.

 320 ASN   ( 331-)  A      OD1
 362 ASP   ( 373-)  A      OD1
 377 ASN   ( 388-)  A      OD1
 426 GLN   ( 437-)  A      OE1
 652 ASN   ( 663-)  A      OD1
 767 ASP   ( 778-)  A      OD1
1044 ASN   ( 282-)  B      OD1
1243 ASN   (  92-)  D      OD1
1482 ASN   ( 331-)  D      OD1
1524 ASP   ( 373-)  D      OD1
1588 GLN   ( 437-)  D      OE1
1814 ASN   ( 663-)  D      OD1
1858 GLN   ( 707-)  D      OE1
1929 ASP   ( 778-)  D      OD1
2008 GLU   (  84-)  E      OE2
2206 ASN   ( 282-)  E      OD1
2246 GLU   ( 322-)  E      OE2

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+.

2334  MG   (1801-)  A     0.51   1.03 Is perhaps NA *2
2343  MG   (1801-)  D     0.58   1.16 Is perhaps NA *2

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.

 669 ASP   ( 680-)  A   H-bonding suggests Asn; but Alt-Rotamer
 948 GLU   ( 186-)  B   H-bonding suggests Gln; but Alt-Rotamer
 999 GLU   ( 237-)  B   H-bonding suggests Gln; but Alt-Rotamer
1027 GLU   ( 265-)  B   H-bonding suggests Gln
1831 ASP   ( 680-)  D   H-bonding suggests Asn
2110 GLU   ( 186-)  E   H-bonding suggests Gln; but Alt-Rotamer
2189 GLU   ( 265-)  E   H-bonding suggests Gln

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 :   0.003
  2nd generation packing quality :  -0.211
  Ramachandran plot appearance   :  -0.281
  chi-1/chi-2 rotamer normality  :  -0.747
  Backbone conformation          :   0.542

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.250 (tight)
  Bond angles                    :   0.490 (tight)
  Omega angle restraints         :   0.814
  Side chain planarity           :   0.426 (tight)
  Improper dihedral distribution :   0.491
  B-factor distribution          :   2.350 (loose)
  Inside/Outside distribution    :   1.166 (unusual)

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 : 2.36


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.9
  2nd generation packing quality :   0.6
  Ramachandran plot appearance   :   1.1
  chi-1/chi-2 rotamer normality  :   0.8
  Backbone conformation          :   0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.250 (tight)
  Bond angles                    :   0.490 (tight)
  Omega angle restraints         :   0.814
  Side chain planarity           :   0.426 (tight)
  Improper dihedral distribution :   0.491
  B-factor distribution          :   2.350 (loose)
  Inside/Outside distribution    :   1.166 (unusual)
==============

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.