WHAT IF Check report

This file was created 2012-01-29 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 pdb5bca.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 : 0.540
CA-only RMS fit for the two chains : 0.331

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 : 0.511
CA-only RMS fit for the two chains : 0.320

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 : 0.539
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 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 C

All-atom RMS fit for the two chains : 0.492
CA-only RMS fit for the two chains : 0.275

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 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 : 0.595
CA-only RMS fit for the two chains : 0.366

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

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

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

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

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

Crystal temperature (K) :293.000

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

Geometric checks

Warning: Unusual bond lengths

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

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

 143 GLY   ( 143-)  A      CA   C     1.58    4.5

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

 |  0.997075  0.000644 -0.001401|
 |  0.000644  0.998140 -0.000471|
 | -0.001401 -0.000471  1.001347|
Proposed new scale matrix

 |  0.005640 -0.000003  0.001597|
 | -0.000006  0.008874  0.000004|
 |  0.000010  0.000003  0.007098|
With corresponding cell

    A    = 177.384  B   = 112.695  C    = 146.472
    Alpha=  90.072  Beta= 105.889  Gamma=  89.926

The CRYST1 cell dimensions

    A    = 177.900  B   = 112.900  C    = 146.200
    Alpha=  90.000  Beta= 105.800  Gamma=  90.000

Variance: 226.648
(Under-)estimated Z-score: 11.095

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.

   3 ASN   (   3-)  A      CA   CB   CG  108.16   -4.4
   7 MET   (   7-)  A     -C    N    CA  130.39    4.8
   8 ASN   (   8-)  A      CA   CB   CG  108.33   -4.3
  12 LYS   (  12-)  A      CA   C    O   113.69   -4.2
  19 LEU   (  19-)  A      N    CA   CB  118.83    4.9
  24 GLU   (  24-)  A      CB   CG   CD  120.07    4.4
  26 THR   (  26-)  A      CA   CB   OG1 103.13   -4.3
  31 PHE   (  31-)  A      CA   C    O   128.12    4.3
  31 PHE   (  31-)  A      CA   CB   CG  119.97    6.2
  37 TRP   (  37-)  A      CA   CB   CG  121.41    4.1
  41 ASN   (  41-)  A      CA   CB   CG  108.21   -4.4
  42 GLY   (  42-)  A      CA   C    O   112.24   -4.1
  43 PHE   (  43-)  A      CA   CB   CG  123.88   10.1
  47 THR   (  47-)  A      CA   CB   OG1 103.07   -4.4
  49 ASP   (  49-)  A     -O   -C    N   115.71   -4.6
  49 ASP   (  49-)  A      CA   CB   CG  116.65    4.1
  55 MET   (  55-)  A      N    CA   CB  103.37   -4.2
  58 ASN   (  58-)  A      CA   C    O   112.55   -4.9
  58 ASN   (  58-)  A      CA   CB   CG  107.96   -4.6
  58 ASN   (  58-)  A      ND2  CG   OD1 127.24    4.6
  60 ASP   (  60-)  A      N    CA   CB  100.79   -5.7
  60 ASP   (  60-)  A      CA   CB   CG  106.49   -6.1
  61 GLN   (  61-)  A      CG   CD   NE2 122.43    4.0
  61 GLN   (  61-)  A      NE2  CD   OE1 117.02   -5.6
  62 GLN   (  62-)  A     -O   -C    N   116.59   -4.0
And so on for a total of 579 lines.

Warning: Chirality deviations detected

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

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

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

  35 LEU   (  35-)  A      C     -6.6   -10.30     0.20
  50 PHE   (  50-)  A      C     -6.0    -9.62     0.23
  72 ALA   (  72-)  A      C     -7.5   -11.38     0.08
 174 ARG   ( 174-)  A      C      6.1     9.37     0.13
 196 THR   ( 196-)  A      C      6.5    10.10     0.30
 216 GLU   ( 216-)  A      C      6.0     8.73    -0.03
 238 GLU   ( 238-)  A      C      6.4     9.28    -0.03
 502 TRP   ( 502-)  A      C     -6.6    -9.44     0.23
 570 ASP   (  54-)  B      C     -6.1    -9.34    -0.01
 605 HIS   (  89-)  B      C      6.6    10.04     0.15
 650 ALA   ( 134-)  B      C     -7.8   -11.88     0.08
 654 ILE   ( 138-)  B      CA     6.3    42.68    33.24
 684 GLY   ( 168-)  B      C      7.0     9.33     0.06
 784 ILE   ( 268-)  B      C     -8.7   -11.33     0.03
 792 PHE   ( 276-)  B      C     -7.6   -12.16     0.23
 816 ILE   ( 300-)  B      C     -8.2   -10.73     0.03
 868 ASN   ( 352-)  B      CA     6.8    46.47    33.59
1079 THR   (  47-)  C      C     -7.7   -11.21     0.30
1139 VAL   ( 107-)  C      C     -7.1    -9.63     0.15
1163 ASN   ( 131-)  C      C      6.1     9.91     0.27
1233 SER   ( 201-)  C      C     -6.5   -10.34     0.37
1252 ALA   ( 220-)  C      C     -8.9   -13.57     0.08
1430 TYR   ( 398-)  C      C     -6.2    -9.28     0.33
1565 ALA   (  17-)  D      C      6.5    10.10     0.08
1566 PRO   (  18-)  D      C      6.6    10.81     0.42
1598 PHE   (  50-)  D      C     -7.0   -11.23     0.23
1610 GLN   (  62-)  D      C     -6.1    -9.31     0.15
1686 ILE   ( 138-)  D      C     -9.2   -12.04     0.03
1694 TYR   ( 146-)  D      C    -10.6   -16.24     0.33
1910 ILE   ( 362-)  D      C      6.0     7.95     0.03
The average deviation= 1.987

Error: Tau angle problems

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

 276 PHE   ( 276-)  A    5.88
2002 TYR   ( 454-)  D    5.67
1689 GLU   ( 141-)  D    5.04
1824 PHE   ( 276-)  D    4.94
 733 VAL   ( 217-)  B    4.76
1307 ALA   ( 275-)  C    4.74
1762 LEU   ( 214-)  D    4.67
2005 GLN   ( 457-)  D    4.65
 141 GLU   ( 141-)  A    4.58
1806 GLN   ( 258-)  D    4.41
1270 GLU   ( 238-)  C    4.38
 398 TYR   ( 398-)  A    4.30
1189 LYS   ( 157-)  C    4.30
 151 ALA   ( 151-)  A    4.28
 603 SER   (  87-)  B    4.25
   4 GLY   (   4-)  A    4.24
  96 GLY   (  96-)  A    4.23
1619 PHE   (  71-)  D    4.18
 154 LYS   ( 154-)  A    4.08
1415 GLU   ( 383-)  C    4.07
  25 VAL   (  25-)  A    4.05
 926 LYS   ( 410-)  B    4.01

Warning: High tau angle deviations

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

Tau angle RMS Z-score : 1.531

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.

 647 ASN   ( 131-)  B    4.48
1121 HIS   (  89-)  C    4.23

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.

1058 THR   (  26-)  C    -3.6
 542 THR   (  26-)  B    -3.4
  26 THR   (  26-)  A    -3.3
1542 THR   ( 510-)  C    -3.2
 510 THR   ( 510-)  A    -3.2
2058 THR   ( 510-)  D    -3.1
1219 PRO   ( 187-)  C    -3.1
 187 PRO   ( 187-)  A    -3.1
 703 PRO   ( 187-)  B    -3.1
1020 PRO   ( 504-)  B    -3.0
2052 PRO   ( 504-)  D    -3.0
1735 PRO   ( 187-)  D    -3.0
1889 PRO   ( 341-)  D    -3.0
 504 PRO   ( 504-)  A    -3.0
1536 PRO   ( 504-)  C    -2.9
1945 ARG   ( 397-)  D    -2.8
1026 THR   ( 510-)  B    -2.7
 857 PRO   ( 341-)  B    -2.7
1772 LYS   ( 224-)  D    -2.6
   5 LYS   (   5-)  A    -2.6
 997 PHE   ( 481-)  B    -2.6
1480 SER   ( 448-)  C    -2.6
 398 TYR   ( 398-)  A    -2.5
 300 ILE   ( 300-)  A    -2.5
 341 PRO   ( 341-)  A    -2.5
And so on for a total of 86 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.

   3 ASN   (   3-)  A  Poor phi/psi
  26 THR   (  26-)  A  Poor phi/psi
  61 GLN   (  61-)  A  Poor phi/psi
 170 ALA   ( 170-)  A  Poor phi/psi
 176 PRO   ( 176-)  A  Poor phi/psi
 186 TYR   ( 186-)  A  PRO omega poor
 243 ASN   ( 243-)  A  Poor phi/psi
 281 GLN   ( 281-)  A  Poor phi/psi
 291 VAL   ( 291-)  A  omega poor
 331 CYS   ( 331-)  A  Poor phi/psi
 340 TYR   ( 340-)  A  PRO omega poor
 389 ASN   ( 389-)  A  Poor phi/psi
 396 LEU   ( 396-)  A  omega poor
 398 TYR   ( 398-)  A  Poor phi/psi
 428 ASN   ( 428-)  A  Poor phi/psi
 449 TRP   ( 449-)  A  Poor phi/psi
 476 GLU   ( 476-)  A  Poor phi/psi
 494 SER   ( 494-)  A  Poor phi/psi
 503 ASN   ( 503-)  A  PRO omega poor
 519 ASN   (   3-)  B  Poor phi/psi
 542 THR   (  26-)  B  Poor phi/psi
 577 GLN   (  61-)  B  Poor phi/psi
 608 GLY   (  92-)  B  Poor phi/psi
 629 ASP   ( 113-)  B  Poor phi/psi
 650 ALA   ( 134-)  B  Poor phi/psi
And so on for a total of 92 lines.

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.223

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.

 717 SER   ( 201-)  B    0.36
1729 SER   ( 181-)  D    0.38

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 ASN   (   3-)  A      0
   7 MET   (   7-)  A      0
   8 ASN   (   8-)  A      0
  20 LYS   (  20-)  A      0
  25 VAL   (  25-)  A      0
  26 THR   (  26-)  A      0
  51 TRP   (  51-)  A      0
  52 TRP   (  52-)  A      0
  58 ASN   (  58-)  A      0
  60 ASP   (  60-)  A      0
  61 GLN   (  61-)  A      0
  62 GLN   (  62-)  A      0
  63 PHE   (  63-)  A      0
  65 PHE   (  65-)  A      0
  66 SER   (  66-)  A      0
  87 SER   (  87-)  A      0
  89 HIS   (  89-)  A      0
  91 CYS   (  91-)  A      0
  95 VAL   (  95-)  A      0
  99 CYS   (  99-)  A      0
 100 ASN   ( 100-)  A      0
 101 VAL   ( 101-)  A      0
 103 ILE   ( 103-)  A      0
 106 TRP   ( 106-)  A      0
 110 GLN   ( 110-)  A      0
And so on for a total of 826 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]

 234 PRO   ( 234-)  A    0.01 LOW
 283 PRO   ( 283-)  A    0.47 HIGH
 301 PRO   ( 301-)  A    0.14 LOW
 419 PRO   ( 419-)  A    0.16 LOW
 534 PRO   (  18-)  B    0.48 HIGH
 648 PRO   ( 132-)  B    0.19 LOW
 685 PRO   ( 169-)  B    0.17 LOW
 692 PRO   ( 176-)  B    0.51 HIGH
 703 PRO   ( 187-)  B    0.48 HIGH
 749 PRO   ( 233-)  B    0.17 LOW
 799 PRO   ( 283-)  B    0.12 LOW
 814 PRO   ( 298-)  B    0.46 HIGH
 823 PRO   ( 307-)  B    0.14 LOW
 935 PRO   ( 419-)  B    0.10 LOW
1134 PRO   ( 102-)  C    0.15 LOW
1164 PRO   ( 132-)  C    0.51 HIGH
1265 PRO   ( 233-)  C    0.19 LOW
1378 PRO   ( 346-)  C    0.13 LOW
1462 PRO   ( 430-)  C    0.47 HIGH
1571 PRO   (  23-)  D    0.18 LOW
1632 PRO   (  84-)  D    0.07 LOW
1650 PRO   ( 102-)  D    0.16 LOW
1680 PRO   ( 132-)  D    0.17 LOW
1782 PRO   ( 234-)  D    0.13 LOW
1855 PRO   ( 307-)  D    0.20 LOW
1967 PRO   ( 419-)  D    0.11 LOW
2054 PRO   ( 506-)  D    0.18 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].

  84 PRO   (  84-)  A    -7.6 envelop N (0 degrees)
 187 PRO   ( 187-)  A   -50.4 half-chair C-beta/C-alpha (-54 degrees)
 233 PRO   ( 233-)  A   -62.0 half-chair C-beta/C-alpha (-54 degrees)
 341 PRO   ( 341-)  A   -45.4 half-chair C-beta/C-alpha (-54 degrees)
 504 PRO   ( 504-)  A   -32.9 envelop C-alpha (-36 degrees)
 506 PRO   ( 506-)  A    22.7 half-chair N/C-delta (18 degrees)
 539 PRO   (  23-)  B    38.6 envelop C-delta (36 degrees)
 703 PRO   ( 187-)  B   -57.8 half-chair C-beta/C-alpha (-54 degrees)
 862 PRO   ( 346-)  B  -117.4 half-chair C-delta/C-gamma (-126 degrees)
1020 PRO   ( 504-)  B   -44.5 envelop C-alpha (-36 degrees)
1219 PRO   ( 187-)  C   -47.2 half-chair C-beta/C-alpha (-54 degrees)
1373 PRO   ( 341-)  C   -54.8 half-chair C-beta/C-alpha (-54 degrees)
1536 PRO   ( 504-)  C   -36.0 envelop C-alpha (-36 degrees)
1538 PRO   ( 506-)  C    50.9 half-chair C-delta/C-gamma (54 degrees)
1735 PRO   ( 187-)  D   -61.5 half-chair C-beta/C-alpha (-54 degrees)
1846 PRO   ( 298-)  D  -113.5 envelop C-gamma (-108 degrees)
1889 PRO   ( 341-)  D   -53.7 half-chair C-beta/C-alpha (-54 degrees)
2052 PRO   ( 504-)  D   -49.3 half-chair C-beta/C-alpha (-54 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.

 537 LYS   (  21-)  B      NZ  <->  570 ASP   (  54-)  B      OD2    0.74    1.96  INTRA
  51 TRP   (  51-)  A      CZ2 <->   91 CYS   (  91-)  A      SG     0.61    2.79  INTRA
1564 MET   (  16-)  D      CG  <-> 1945 ARG   ( 397-)  D      NH1    0.59    2.51  INTRA
1316 ILE   ( 284-)  C      N   <-> 2075 HOH   ( 639 )  C      O      0.57    2.13  INTRA
1005 ASP   ( 489-)  B      OD1 <-> 1007 THR   ( 491-)  B      OG1    0.56    1.84  INTRA BF
 216 GLU   ( 216-)  A      OE2 <->  219 LYS   ( 219-)  A      NZ     0.56    2.14  INTRA
1730 ASP   ( 182-)  D      O   <-> 1739 LYS   ( 191-)  D      NZ     0.53    2.17  INTRA
1406 ASN   ( 374-)  C      OD1 <-> 1408 GLU   ( 376-)  C      N      0.52    2.18  INTRA BF
1232 LYS   ( 200-)  C      NZ  <-> 2075 HOH   ( 773 )  C      O      0.52    2.18  INTRA
 489 ASP   ( 489-)  A      OD1 <->  491 THR   ( 491-)  A      CG2    0.50    2.30  INTRA BF
 216 GLU   ( 216-)  A      CD  <->  219 LYS   ( 219-)  A      NZ     0.50    2.60  INTRA
 678 LYS   ( 162-)  B      NZ  <-> 2074 HOH   ( 679 )  B      O      0.48    2.22  INTRA
1306 ASN   ( 274-)  C      ND2 <-> 2075 HOH   ( 701 )  C      O      0.47    2.23  INTRA
 938 GLN   ( 422-)  B      NE2 <-> 1026 THR   ( 510-)  B      N      0.47    2.38  INTRA
1144 SER   ( 112-)  C      N   <-> 2075 HOH   ( 731 )  C      O      0.45    2.25  INTRA
1234 LYS   ( 202-)  C      NZ  <-> 2075 HOH   ( 727 )  C      O      0.44    2.26  INTRA
 226 ILE   ( 226-)  A      N   <-> 2073 HOH   ( 784 )  A      O      0.44    2.26  INTRA
 549 ASN   (  33-)  B      OD1 <->  552 ARG   (  36-)  B      NH1    0.44    2.26  INTRA
 943 LYS   ( 427-)  B      N   <-> 1030 SER   ( 514-)  B      O      0.44    2.26  INTRA
 462 SER   ( 462-)  A      O   <->  465 ASN   ( 465-)  A      N      0.43    2.27  INTRA BF
 454 TYR   ( 454-)  A      N   <->  455 PRO   ( 455-)  A      CD     0.42    2.58  INTRA
1196 TYR   ( 164-)  C      OH  <-> 1360 THR   ( 328-)  C      OG1    0.41    1.99  INTRA
 461 ASP   ( 461-)  A      O   <->  465 ASN   ( 465-)  A      N      0.40    2.30  INTRA BF
1121 HIS   (  89-)  C      ND1 <-> 1198 SER   ( 166-)  C      OG     0.39    2.31  INTRA BL
 306 LYS   ( 306-)  A      NZ  <-> 2073 HOH   ( 615 )  A      O      0.39    2.31  INTRA BL
And so on for a total of 515 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

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.

1372 TYR   ( 340-)  C      -8.29
 856 TYR   ( 340-)  B      -8.17
1888 TYR   ( 340-)  D      -8.04
 340 TYR   ( 340-)  A      -7.97
1218 TYR   ( 186-)  C      -6.42
1734 TYR   ( 186-)  D      -6.40
 702 TYR   ( 186-)  B      -6.19
2036 LYS   ( 488-)  D      -6.14
 186 TYR   ( 186-)  A      -6.11
1520 LYS   ( 488-)  C      -6.05
1210 TYR   ( 178-)  C      -5.98
1004 LYS   ( 488-)  B      -5.96
 694 TYR   ( 178-)  B      -5.95
 488 LYS   ( 488-)  A      -5.91
 433 ILE   ( 433-)  A      -5.87
 949 ILE   ( 433-)  B      -5.87
1829 GLN   ( 281-)  D      -5.87
1726 TYR   ( 178-)  D      -5.75
1981 ILE   ( 433-)  D      -5.67
1465 ILE   ( 433-)  C      -5.65
1951 TYR   ( 403-)  D      -5.65
 178 TYR   ( 178-)  A      -5.63
1142 GLN   ( 110-)  C      -5.57
1313 GLN   ( 281-)  C      -5.57
 403 TYR   ( 403-)  A      -5.57
And so on for a total of 66 lines.

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

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.

1264 LEU   ( 232-)  C   -2.86
1649 VAL   ( 101-)  D   -2.71
1871 ALA   ( 323-)  D   -2.51

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

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.

2073 HOH   ( 787 )  A      O     82.39    5.98   48.58

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.

2073 HOH   ( 719 )  A      O
2074 HOH   ( 725 )  B      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.

 215 ASN   ( 215-)  A
 311 ASN   ( 311-)  A
 725 ASN   ( 209-)  B
 755 GLN   ( 239-)  B
 759 ASN   ( 243-)  B
 867 GLN   ( 351-)  B
 994 ASN   ( 478-)  B
1306 ASN   ( 274-)  C
1343 ASN   ( 311-)  C
1787 GLN   ( 239-)  D
2018 ASN   ( 470-)  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.

   7 MET   (   7-)  A      N
  20 LYS   (  20-)  A      N
  27 ASN   (  27-)  A      N
  41 ASN   (  41-)  A      ND2
  47 THR   (  47-)  A      OG1
  58 ASN   (  58-)  A      N
  59 GLY   (  59-)  A      N
  81 LYS   (  81-)  A      N
  89 HIS   (  89-)  A      N
  99 CYS   (  99-)  A      N
 106 TRP   ( 106-)  A      N
 117 TYR   ( 117-)  A      N
 167 GLY   ( 167-)  A      N
 183 GLY   ( 183-)  A      N
 194 ALA   ( 194-)  A      N
 213 SER   ( 213-)  A      N
 227 SER   ( 227-)  A      N
 228 GLU   ( 228-)  A      N
 253 TYR   ( 253-)  A      OH
 293 TRP   ( 293-)  A      N
 297 ASN   ( 297-)  A      N
 330 THR   ( 330-)  A      N
 342 GLU   ( 342-)  A      N
 369 ALA   ( 369-)  A      N
 397 ARG   ( 397-)  A      NH1
And so on for a total of 115 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.

 698 ASP   ( 182-)  B      OD2
 903 ASN   ( 387-)  B      OD1
 938 GLN   ( 422-)  B      OE1
1229 GLU   ( 197-)  C      OE2
1419 ASN   ( 387-)  C      OD1

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+.

2070  CA   ( 602-)  B     0.85   1.10 Scores about as good as NA

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.

2074 HOH   ( 682 )  B      O  1.06  K  4 Ion-B NCS 1/1

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.

  97 ASP   (  97-)  A   H-bonding suggests Asn
 318 ASP   ( 318-)  A   H-bonding suggests Asn; but Alt-Rotamer
1005 ASP   ( 489-)  B   H-bonding suggests Asn; but Alt-Rotamer
1129 ASP   (  97-)  C   H-bonding suggests Asn
1409 GLU   ( 377-)  C   H-bonding suggests Gln; but Alt-Rotamer
1810 GLU   ( 262-)  D   H-bonding suggests Gln; but Alt-Rotamer
1884 ASP   ( 336-)  D   H-bonding suggests Asn

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 :  -0.780
  2nd generation packing quality :  -1.546
  Ramachandran plot appearance   :  -2.046
  chi-1/chi-2 rotamer normality  :  -3.223 (poor)
  Backbone conformation          :  -0.952

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.680
  Bond angles                    :   1.658
  Omega angle restraints         :   0.812
  Side chain planarity           :   1.070
  Improper dihedral distribution :   1.713 (loose)
  B-factor distribution          :   0.660
  Inside/Outside distribution    :   0.999

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 : 2.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -0.7
  Ramachandran plot appearance   :  -0.7
  chi-1/chi-2 rotamer normality  :  -1.8
  Backbone conformation          :  -0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.680
  Bond angles                    :   1.658
  Omega angle restraints         :   0.812
  Side chain planarity           :   1.070
  Improper dihedral distribution :   1.713 (loose)
  B-factor distribution          :   0.660
  Inside/Outside distribution    :   0.999
==============

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.