WHAT IF Check report

This file was created 2011-12-15 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 pdb3e3i.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 C

All-atom RMS fit for the two chains : 0.583
CA-only RMS fit for the two chains : 0.328

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: B and D

All-atom RMS fit for the two chains : 0.791
CA-only RMS fit for the two chains : 0.419

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 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 : 0.793
CA-only RMS fit for the two chains : 0.398

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: B and F

All-atom RMS fit for the two chains : 0.684
CA-only RMS fit for the two chains : 0.444

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 F

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 G

All-atom RMS fit for the two chains : 0.751
CA-only RMS fit for the two chains : 0.442

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 G

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.

2519 BCT   ( 233-)  B  -
2522 BCT   ( 232-)  C  -
2525 BCT   ( 232-)  D  -
2529 BCT   ( 233-)  E  -
2531 BCT   ( 231-)  F  -
2533 BCT   ( 231-)  G  -
2537 BCT   ( 233-)  H  -
2540 BCT   ( 232-)  I  -
2543 BCT   ( 232-)  J  -
2546 BCT   ( 232-)  K  -
2550 BCT   ( 232-)  L  -

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

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

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'.

1473 ASN   ( 219-)  G      CG
1473 ASN   ( 219-)  G      OD1
1473 ASN   ( 219-)  G      ND2
1893 ASN   ( 219-)  I      OD1
1893 ASN   ( 219-)  I      ND2
1894 ILE   ( 220-)  I      CG1
1894 ILE   ( 220-)  I      CG2
1894 ILE   ( 220-)  I      CD1

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: 12

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

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Nomenclature related problems

Warning: Tyrosine convention problem

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

  25 TYR   (  37-)  A
 220 TYR   (  12-)  B
 238 TYR   (  37-)  B
 382 TYR   ( 181-)  B
 445 TYR   (  37-)  C
 589 TYR   ( 181-)  C
 640 TYR   (  12-)  D
 658 TYR   (  37-)  D
 802 TYR   ( 181-)  D
 871 TYR   (  37-)  E
1065 TYR   (  12-)  F
1083 TYR   (  37-)  F
1227 TYR   ( 181-)  F
1291 TYR   (  37-)  G
1435 TYR   ( 181-)  G
1502 TYR   (  37-)  H
1646 TYR   ( 181-)  H
1696 TYR   (  12-)  I
1711 TYR   (  37-)  I
1906 TYR   (  12-)  J
1921 TYR   (  37-)  J
2065 TYR   ( 181-)  J
2111 TYR   (  12-)  K
2126 TYR   (  37-)  K
2335 TYR   (  37-)  L
2479 TYR   ( 181-)  L

Warning: Phenylalanine convention problem

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

  63 PHE   (  75-)  A
 175 PHE   ( 187-)  A
 276 PHE   (  75-)  B
 388 PHE   ( 187-)  B
 483 PHE   (  75-)  C
 595 PHE   ( 187-)  C
 696 PHE   (  75-)  D
 749 PHE   ( 128-)  D
 808 PHE   ( 187-)  D
 909 PHE   (  75-)  E
1021 PHE   ( 187-)  E
1121 PHE   (  75-)  F
1233 PHE   ( 187-)  F
1329 PHE   (  75-)  G
1441 PHE   ( 187-)  G
1540 PHE   (  75-)  H
1593 PHE   ( 128-)  H
1652 PHE   ( 187-)  H
1749 PHE   (  75-)  I
1802 PHE   ( 128-)  I
1861 PHE   ( 187-)  I
1959 PHE   (  75-)  J
2012 PHE   ( 128-)  J
2071 PHE   ( 187-)  J
2164 PHE   (  75-)  K
2276 PHE   ( 187-)  K
2373 PHE   (  75-)  L

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.

   2 ASP   (   2-)  A
  32 ASP   (  44-)  A
 132 ASP   ( 144-)  A
 210 ASP   (   2-)  B
 311 ASP   ( 110-)  B
 345 ASP   ( 144-)  B
 422 ASP   (   2-)  C
 452 ASP   (  44-)  C
 552 ASP   ( 144-)  C
 630 ASP   (   2-)  D
 731 ASP   ( 110-)  D
 765 ASP   ( 144-)  D
 843 ASP   (   2-)  E
 946 ASP   ( 112-)  E
 978 ASP   ( 144-)  E
1055 ASP   (   2-)  F
1263 ASP   (   2-)  G
1366 ASP   ( 112-)  G
1398 ASP   ( 144-)  G
1477 ASP   (   2-)  H
1575 ASP   ( 110-)  H
1609 ASP   ( 144-)  H
1686 ASP   (   2-)  I
1818 ASP   ( 144-)  I
1896 ASP   (   2-)  J
2028 ASP   ( 144-)  J
2101 ASP   (   2-)  K
2233 ASP   ( 144-)  K
2310 ASP   (   2-)  L
2408 ASP   ( 110-)  L
2442 ASP   ( 144-)  L

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.

  44 GLU   (  56-)  A
  79 GLU   (  91-)  A
 187 GLU   ( 199-)  A
 257 GLU   (  56-)  B
 292 GLU   (  91-)  B
 400 GLU   ( 199-)  B
 418 GLU   ( 217-)  B
 440 GLU   (  20-)  C
 441 GLU   (  21-)  C
 464 GLU   (  56-)  C
 467 GLU   (  59-)  C
 499 GLU   (  91-)  C
 607 GLU   ( 199-)  C
 625 GLU   ( 217-)  C
 677 GLU   (  56-)  D
 712 GLU   (  91-)  D
 790 GLU   ( 169-)  D
 838 GLU   ( 217-)  D
 890 GLU   (  56-)  E
 925 GLU   (  91-)  E
1033 GLU   ( 199-)  E
1051 GLU   ( 217-)  E
1102 GLU   (  56-)  F
1137 GLU   (  91-)  F
1282 GLU   (  21-)  G
1310 GLU   (  56-)  G
1345 GLU   (  91-)  G
1423 GLU   ( 169-)  G
1471 GLU   ( 217-)  G
1556 GLU   (  91-)  H
1682 GLU   ( 217-)  H
1730 GLU   (  56-)  I
1891 GLU   ( 217-)  I
1892 GLU   ( 218-)  I
1940 GLU   (  56-)  J
1975 GLU   (  91-)  J
2120 GLU   (  21-)  K
2145 GLU   (  56-)  K
2180 GLU   (  91-)  K
2288 GLU   ( 199-)  K
2354 GLU   (  56-)  L
2389 GLU   (  91-)  L
2497 GLU   ( 199-)  L

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

 |  0.998870 -0.000162  0.000183|
 | -0.000162  0.997978  0.000083|
 |  0.000183  0.000083  0.998333|
Proposed new scale matrix

 |  0.004361  0.000000  0.000337|
 |  0.000001  0.006937  0.000000|
 | -0.000002  0.000000  0.009578|
With corresponding cell

    A    = 229.309  B   = 144.154  C    = 104.716
    Alpha=  90.001  Beta=  94.405  Gamma=  90.011

The CRYST1 cell dimensions

    A    = 229.593  B   = 144.437  C    = 104.891
    Alpha=  90.000  Beta=  94.430  Gamma=  90.000

Variance: 229.824
(Under-)estimated Z-score: 11.173

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.

  40 LEU   (  52-)  A      CA   CB   CG  134.47    5.2
  93 HIS   ( 105-)  A      CG   ND1  CE1 109.65    4.0
 956 HIS   ( 122-)  E      CG   ND1  CE1 109.69    4.1
1376 HIS   ( 122-)  G      CG   ND1  CE1 109.69    4.1

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.

   2 ASP   (   2-)  A
  32 ASP   (  44-)  A
  44 GLU   (  56-)  A
  79 GLU   (  91-)  A
 132 ASP   ( 144-)  A
 187 GLU   ( 199-)  A
 210 ASP   (   2-)  B
 257 GLU   (  56-)  B
 292 GLU   (  91-)  B
 311 ASP   ( 110-)  B
 345 ASP   ( 144-)  B
 400 GLU   ( 199-)  B
 418 GLU   ( 217-)  B
 422 ASP   (   2-)  C
 440 GLU   (  20-)  C
 441 GLU   (  21-)  C
 452 ASP   (  44-)  C
 464 GLU   (  56-)  C
 467 GLU   (  59-)  C
 499 GLU   (  91-)  C
 552 ASP   ( 144-)  C
 607 GLU   ( 199-)  C
 625 GLU   ( 217-)  C
 630 ASP   (   2-)  D
 677 GLU   (  56-)  D
And so on for a total of 74 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.

1135 LYS   (  89-)  F    -2.5
1119 THR   (  73-)  F    -2.3
2414 ILE   ( 116-)  L    -2.3
1370 ILE   ( 116-)  G    -2.3
 923 LYS   (  89-)  E    -2.2
 379 GLY   ( 178-)  B    -2.2
1742 ASN   (  68-)  I    -2.2
2134 SER   (  45-)  K    -2.2
1012 GLY   ( 178-)  E    -2.2
1790 ILE   ( 116-)  I    -2.2
 317 ILE   ( 116-)  B    -2.2
1432 GLY   ( 178-)  G    -2.1
 950 ILE   ( 116-)  E    -2.1
 586 GLY   ( 178-)  C    -2.1
2267 GLY   ( 178-)  K    -2.1
1643 GLY   ( 178-)  H    -2.1
2062 GLY   ( 178-)  J    -2.1
 799 GLY   ( 178-)  D    -2.1
  34 ARG   (  46-)  A    -2.1
 737 ILE   ( 116-)  D    -2.1
1224 GLY   ( 178-)  F    -2.1
 166 GLY   ( 178-)  A    -2.1
 104 ILE   ( 116-)  A    -2.1
 666 SER   (  45-)  D    -2.1
1852 GLY   ( 178-)  I    -2.1
  56 ASN   (  68-)  A    -2.1
2157 ASN   (  68-)  K    -2.1
2476 GLY   ( 178-)  L    -2.1
 524 ILE   ( 116-)  C    -2.1
1929 SER   (  45-)  J    -2.1
1719 SER   (  45-)  I    -2.1
2418 LEU   ( 120-)  L    -2.1
1299 SER   (  45-)  G    -2.1
1114 ASN   (  68-)  F    -2.1
1581 ILE   ( 116-)  H    -2.0
1585 LEU   ( 120-)  H    -2.0
1510 SER   (  45-)  H    -2.0
1390 LYS   ( 136-)  G    -2.0
2343 SER   (  45-)  L    -2.0
 274 THR   (  73-)  B    -2.0
 741 LEU   ( 120-)  D    -2.0
1322 ASN   (  68-)  G    -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.

  25 TYR   (  37-)  A  omega poor
  55 ALA   (  67-)  A  Poor phi/psi
  57 GLN   (  69-)  A  omega poor
 205 GLU   ( 217-)  A  Poor phi/psi
 262 PHE   (  61-)  B  omega poor
 268 ALA   (  67-)  B  Poor phi/psi
 290 LYS   (  89-)  B  Poor phi/psi
 301 ASN   ( 100-)  B  Poor phi/psi
 386 ASP   ( 185-)  B  Poor phi/psi
 418 GLU   ( 217-)  B  Poor phi/psi, omega poor
 445 TYR   (  37-)  C  omega poor
 469 PHE   (  61-)  C  omega poor
 475 ALA   (  67-)  C  Poor phi/psi
 477 GLN   (  69-)  C  omega poor
 497 LYS   (  89-)  C  Poor phi/psi
 625 GLU   ( 217-)  C  Poor phi/psi
 681 LEU   (  60-)  D  omega poor
 688 ALA   (  67-)  D  Poor phi/psi
 710 LYS   (  89-)  D  Poor phi/psi
 806 ASP   ( 185-)  D  Poor phi/psi
 894 LEU   (  60-)  E  omega poor
 901 ALA   (  67-)  E  Poor phi/psi
 923 LYS   (  89-)  E  Poor phi/psi
1019 ASP   ( 185-)  E  Poor phi/psi
1083 TYR   (  37-)  F  omega poor
And so on for a total of 63 lines.

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.

1000 SER   ( 166-)  E    0.35
 221 SER   (  13-)  B    0.36
 641 SER   (  13-)  D    0.36
2321 SER   (  13-)  L    0.36
 854 SER   (  13-)  E    0.36
1066 SER   (  13-)  F    0.36
1697 SER   (  13-)  I    0.36
1488 SER   (  13-)  H    0.37
2502 SER   ( 204-)  L    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!

  20 GLU   (  20-)  A      0
  21 GLU   (  21-)  A      0
  22 THR   (  34-)  A      0
  23 PRO   (  35-)  A      0
  29 ALA   (  41-)  A      0
  34 ARG   (  46-)  A      0
  35 VAL   (  47-)  A      0
  45 PRO   (  57-)  A      0
  47 GLU   (  59-)  A      0
  53 ASN   (  65-)  A      0
  54 VAL   (  66-)  A      0
  55 ALA   (  67-)  A      0
  56 ASN   (  68-)  A      0
  57 GLN   (  69-)  A      0
  61 THR   (  73-)  A      0
  74 ASP   (  86-)  A      0
  79 GLU   (  91-)  A      0
  87 THR   (  99-)  A      0
  89 CYS   ( 101-)  A      0
 101 LEU   ( 113-)  A      0
 103 LEU   ( 115-)  A      0
 161 LYS   ( 173-)  A      0
 179 GLN   ( 191-)  A      0
 181 VAL   ( 193-)  A      0
 183 ALA   ( 195-)  A      0
And so on for a total of 831 lines.

Warning: Unusual PRO puckering amplitudes

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

  23 PRO   (  35-)  A    0.15 LOW
1919 PRO   (  35-)  J    0.07 LOW

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].

2023 PRO   ( 139-)  J   103.5 envelop C-beta (108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short 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.

 421 MET   (   1-)  C      C   <-> 2553 HOH   ( 273 )  C      O      0.53    2.27  INTRA BF
   1 MET   (   1-)  A      N   <-> 2551 HOH   ( 271 )  A      O      0.53    2.17  INTRA BF
 606 ARG   ( 198-)  C      NH2 <->  610 GLU   ( 202-)  C      OE2    0.52    2.18  INTRA BF
 204 ASP   ( 216-)  A      O   <->  206 GLU   ( 218-)  A      N      0.50    2.20  INTRA BF
 842 MET   (   1-)  E      SD  <-> 1427 LYS   ( 173-)  G      NZ     0.49    2.81  INTRA
 374 LYS   ( 173-)  B      NZ  <->  629 MET   (   1-)  D      SD     0.40    2.90  INTRA
  74 ASP   (  86-)  A      O   <->   77 LYS   (  89-)  A      NZ     0.39    2.31  INTRA
  24 HIS   (  36-)  A      CD2 <->  423 LYS   (   3-)  C      NZ     0.38    2.72  INTRA
1752 LEU   (  78-)  I      CD1 <-> 1837 ILE   ( 163-)  I      CD1    0.37    2.83  INTRA
 421 MET   (   1-)  C      O   <-> 2553 HOH   ( 273 )  C      O      0.37    2.03  INTRA BF
 325 ARG   ( 124-)  B      NE  <-> 2521 SO4   ( 232-)  B      O4     0.37    2.33  INTRA BF
 486 LEU   (  78-)  C      CD1 <->  571 ILE   ( 163-)  C      CD1    0.31    2.89  INTRA
 920 ASP   (  86-)  E      O   <->  923 LYS   (  89-)  E      NZ     0.30    2.40  INTRA
2202 LEU   ( 113-)  K      N   <-> 2206 ASN   ( 117-)  K      OD1    0.30    2.40  INTRA
   3 LYS   (   3-)  A      NZ  <->  444 HIS   (  36-)  C      CD2    0.29    2.81  INTRA BF
  52 ARG   (  64-)  A      NH1 <-> 2522 BCT   ( 232-)  C      C      0.29    2.81  INTRA BL
  38 GLU   (  50-)  A      OE2 <->  472 ARG   (  64-)  C      NH2    0.29    2.41  INTRA BF
1551 ASP   (  86-)  H      O   <-> 1554 LYS   (  89-)  H      NZ     0.27    2.43  INTRA
2007 ILE   ( 123-)  J      CD1 <-> 2034 ASN   ( 150-)  J      OD1    0.27    2.53  INTRA
 214 GLN   (   6-)  B      NE2 <->  218 ASN   (  10-)  B      OD1    0.27    2.43  INTRA
1543 LEU   (  78-)  H      CD1 <-> 1628 ILE   ( 163-)  H      CD1    0.27    2.93  INTRA
 624 ASP   ( 216-)  C      O   <->  626 GLU   ( 218-)  C      N      0.25    2.45  INTRA BF
1078 HIS   (  32-)  F      ND1 <-> 1105 GLU   (  59-)  F      OE2    0.25    2.45  INTRA BF
  52 ARG   (  64-)  A      NH1 <-> 2522 BCT   ( 232-)  C      O3     0.24    2.46  INTRA BL
1997 LEU   ( 113-)  J      N   <-> 2001 ASN   ( 117-)  J      OD1    0.22    2.48  INTRA
And so on for a total of 266 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

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.

1498 GLN   (  33-)  H      -7.35
 454 ARG   (  46-)  C      -7.33
2331 GLN   (  33-)  L      -7.20
1707 GLN   (  33-)  I      -7.17
  34 ARG   (  46-)  A      -7.16
2122 GLN   (  33-)  K      -7.15
1917 GLN   (  33-)  J      -7.08
 867 GLN   (  33-)  E      -6.46
2135 ARG   (  46-)  K      -6.38
2344 ARG   (  46-)  L      -6.33
1720 ARG   (  46-)  I      -6.29
1092 ARG   (  46-)  F      -6.28
 654 GLN   (  33-)  D      -6.23
1930 ARG   (  46-)  J      -6.18
1079 GLN   (  33-)  F      -6.14
 234 GLN   (  33-)  B      -5.95
1891 GLU   ( 217-)  I      -5.93
1287 GLN   (  33-)  G      -5.90
1300 ARG   (  46-)  G      -5.68
1511 ARG   (  46-)  H      -5.57
1892 GLU   ( 218-)  I      -5.54
 247 ARG   (  46-)  B      -5.54
 880 ARG   (  46-)  E      -5.53
2054 ARG   ( 170-)  J      -5.50
 667 ARG   (  46-)  D      -5.50
  88 ASN   ( 100-)  A      -5.38
 508 ASN   ( 100-)  C      -5.18
1844 ARG   ( 170-)  I      -5.14
1565 ASN   ( 100-)  H      -5.08
1354 ASN   ( 100-)  G      -5.06
 440 GLU   (  20-)  C      -5.03
 861 GLU   (  20-)  E      -5.02
2328 GLU   (  20-)  L      -5.01
1914 GLU   (  20-)  J      -5.00
1073 GLU   (  20-)  F      -5.00
1495 GLU   (  20-)  H      -5.00

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

Note: Quality value plot

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

Chain identifier: K

Note: Quality value plot

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

Chain identifier: L

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.

  87 THR   (  99-)  A   -2.54
  34 ARG   (  46-)  A   -2.52

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

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

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.

 513 HIS   ( 105-)  C
1707 GLN   (  33-)  I

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.

  80 HIS   (  92-)  A      N
  99 LYS   ( 111-)  A      N
 101 LEU   ( 113-)  A      N
 151 ILE   ( 163-)  A      N
 186 ARG   ( 198-)  A      NH1
 207 ASN   ( 219-)  A      N
 240 TRP   (  39-)  B      NE1
 265 ARG   (  64-)  B      NH1
 270 GLN   (  69-)  B      NE2
 274 THR   (  73-)  B      N
 293 HIS   (  92-)  B      N
 477 GLN   (  69-)  C      NE2
 481 THR   (  73-)  C      N
 485 CYS   (  77-)  C      N
 500 HIS   (  92-)  C      N
 509 CYS   ( 101-)  C      N
 519 LYS   ( 111-)  C      N
 521 LEU   ( 113-)  C      N
 606 ARG   ( 198-)  C      NE
 630 ASP   (   2-)  D      N
 652 ASP   (  31-)  D      N
 660 TRP   (  39-)  D      NE1
 666 SER   (  45-)  D      OG
 685 ARG   (  64-)  D      NH1
 694 THR   (  73-)  D      N
And so on for a total of 96 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.

 207 ASN   ( 219-)  A      OD1
 610 GLU   ( 202-)  C      OE2
 823 GLU   ( 202-)  D      OE1
1158 ASP   ( 112-)  F      OD2
1186 GLU   ( 140-)  F      OE2
1541 ASN   (  76-)  H      OD1
1577 ASP   ( 112-)  H      OD2
1750 ASN   (  76-)  I      OD1

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.

2553 HOH   ( 258 )  C      O  0.91  K  4 Ion-B
2558 HOH   ( 244 )  H      O  0.90  K  6
2559 HOH   ( 253 )  I      O  0.91  K  4
2561 HOH   ( 245 )  K      O  0.97  K  5
2562 HOH   ( 242 )  L      O  1.13  K  5

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.

 178 ASP   ( 190-)  A   H-bonding suggests Asn; but Alt-Rotamer
 419 GLU   ( 218-)  B   H-bonding suggests Gln
 625 GLU   ( 217-)  C   H-bonding suggests Gln
 811 ASP   ( 190-)  D   H-bonding suggests Asn; but Alt-Rotamer
2119 GLU   (  20-)  K   H-bonding suggests Gln
2279 ASP   ( 190-)  K   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 :   0.842
  2nd generation packing quality :  -0.737
  Ramachandran plot appearance   :   0.531
  chi-1/chi-2 rotamer normality  :  -2.183
  Backbone conformation          :   0.387

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.484 (tight)
  Bond angles                    :   0.675
  Omega angle restraints         :   0.995
  Side chain planarity           :   0.617 (tight)
  Improper dihedral distribution :   0.614
  B-factor distribution          :   0.374
  Inside/Outside distribution    :   0.985

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 : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.3
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :   1.0
  chi-1/chi-2 rotamer normality  :  -1.2
  Backbone conformation          :   0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.484 (tight)
  Bond angles                    :   0.675
  Omega angle restraints         :   0.995
  Side chain planarity           :   0.617 (tight)
  Improper dihedral distribution :   0.614
  B-factor distribution          :   0.374
  Inside/Outside distribution    :   0.985
==============

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.