WHAT IF Check report

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

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

Verification log for pdb1pmo.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 : 0.612
CA-only RMS fit for the two chains : 0.241

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 : 0.606
CA-only RMS fit for the two chains : 0.239

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 : 0.596
CA-only RMS fit for the two chains : 0.243

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and E

All-atom RMS fit for the two chains : 0.657
CA-only RMS fit for the two chains : 0.294

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and E

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and F

All-atom RMS fit for the two chains : 0.613
CA-only RMS fit for the two chains : 0.247

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and F

Warning: Ligands for which a topology was generated automatically

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

2750 PLR   (1500-)  A  -
2751 TRS   (3236-)  A  -
2752 TRS   (3241-)  A  -
2753 TRS   (3251-)  A  -
2754 PLR   (1501-)  B  -
2755 TRS   (3237-)  B  -
2756 TRS   (3242-)  B  -
2757 PLR   (1502-)  C  -
2758 TRS   (3243-)  C  -
2759 TRS   (3250-)  C  -
2760 TRS   (3252-)  C  -
2761 PLR   (1503-)  D  -
2762 TRS   (3238-)  D  -
2763 TRS   (3244-)  D  -
2764 TRS   (3245-)  D  -
2765 PLR   (1504-)  E  -
2766 TRS   (3239-)  E  -
2767 TRS   (3246-)  E  -
2768 TRS   (3247-)  E  -
2769 TRS   (3253-)  E  -
2770 TRS   (3240-)  F  -
2771 TRS   (3248-)  F  -
2772 TRS   (3249-)  F  -
2773 PLR   (1505-)  F  -

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: Artificial side chains detected

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

 549 ASP   (  97-)  B
1806 LYS   ( 446-)  D

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) :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

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

 |  0.999048 -0.000020  0.000066|
 | -0.000020  0.999077 -0.000051|
 |  0.000066 -0.000051  0.998131|
Proposed new scale matrix

 |  0.008629  0.004982  0.000000|
 |  0.000000  0.009964  0.000000|
 |  0.000000  0.000000  0.004832|
With corresponding cell

    A    = 115.885  B   = 115.884  C    = 206.952
    Alpha=  90.001  Beta=  90.002  Gamma= 119.999

The CRYST1 cell dimensions

    A    = 115.995  B   = 115.995  C    = 207.350
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 147.616
(Under-)estimated Z-score: 8.954

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.

 207 GLU   ( 218-)  A      N    CA   C    97.12   -5.0
 670 GLU   ( 218-)  B      N    CA   C    96.78   -5.1
1124 GLU   ( 218-)  C      N    CA   C    96.70   -5.2
1578 GLU   ( 218-)  D      N    CA   C    96.49   -5.3
2041 GLU   ( 218-)  E      N    CA   C    96.86   -5.1
2495 GLU   ( 218-)  F      N    CA   C    96.53   -5.2

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.

1578 GLU   ( 218-)  D    5.10
2495 GLU   ( 218-)  F    5.09
1124 GLU   ( 218-)  C    5.03
 670 GLU   ( 218-)  B    5.00
2041 GLU   ( 218-)  E    4.98
 207 GLU   ( 218-)  A    4.89
2238 ALA   ( 415-)  E    4.71
 153 ILE   ( 164-)  A    4.25
1844 LYS   (  21-)  E    4.20
 616 ILE   ( 164-)  B    4.05

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.

1115 PHE   ( 209-)  C    -2.6
 991 ILE   (  85-)  C    -2.5
 769 PHE   ( 317-)  B    -2.4
2362 ILE   (  85-)  F    -2.4
 537 ILE   (  85-)  B    -2.4
  74 ILE   (  85-)  A    -2.4
1908 ILE   (  85-)  E    -2.4
1445 ILE   (  85-)  D    -2.4
1365 GLN   ( 459-)  C    -2.4
 294 TYR   ( 305-)  A    -2.4
1569 PHE   ( 209-)  D    -2.4
1844 LYS   (  21-)  E    -2.3
2486 PHE   ( 209-)  F    -2.3
 567 ASN   ( 115-)  B    -2.3
1854 ARG   (  31-)  E    -2.3
1819 GLN   ( 459-)  D    -2.3
 153 ILE   ( 164-)  A    -2.3
 198 PHE   ( 209-)  A    -2.3
 402 GLY   ( 413-)  A    -2.2
2652 ILE   ( 375-)  F    -2.2
1835 GLU   (  12-)  E    -2.2
1281 ILE   ( 375-)  C    -2.2
1845 SER   (  22-)  E    -2.2
 199 GLY   ( 210-)  A    -2.2
1570 GLY   ( 210-)  D    -2.2
And so on for a total of 53 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.

  17 GLU   (  28-)  A  Poor phi/psi
  45 ALA   (  56-)  A  Poor phi/psi
  98 HIS   ( 109-)  A  Poor phi/psi
 150 PRO   ( 161-)  A  Poor phi/psi
 203 THR   ( 214-)  A  Poor phi/psi
 249 TRP   ( 260-)  A  Poor phi/psi
 250 ASP   ( 261-)  A  Poor phi/psi
 265 LYS   ( 276-)  A  Poor phi/psi
 268 LEU   ( 279-)  A  Poor phi/psi
 272 GLY   ( 283-)  A  Poor phi/psi
 306 PHE   ( 317-)  A  Poor phi/psi
 375 GLU   ( 386-)  A  Poor phi/psi
 376 ASP   ( 387-)  A  Poor phi/psi
 402 GLY   ( 413-)  A  Poor phi/psi
 480 GLU   (  28-)  B  Poor phi/psi
 508 ALA   (  56-)  B  Poor phi/psi
 561 HIS   ( 109-)  B  Poor phi/psi
 568 GLY   ( 116-)  B  Poor phi/psi
 613 PRO   ( 161-)  B  Poor phi/psi
 666 THR   ( 214-)  B  Poor phi/psi
 686 THR   ( 234-)  B  Poor phi/psi
 713 ASP   ( 261-)  B  Poor phi/psi
 728 LYS   ( 276-)  B  Poor phi/psi
 731 LEU   ( 279-)  B  Poor phi/psi
 769 PHE   ( 317-)  B  Poor phi/psi
And so on for a total of 77 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.

 901 SER   ( 449-)  B    0.36
1809 SER   ( 449-)  D    0.36
2272 SER   ( 449-)  E    0.36
2726 SER   ( 449-)  F    0.36
 848 SER   ( 396-)  B    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!

   9 ALA   (  20-)  A      0
  15 ILE   (  26-)  A      0
  16 ALA   (  27-)  A      0
  17 GLU   (  28-)  A      0
  18 SER   (  29-)  A      0
  19 LYS   (  30-)  A      0
  22 PRO   (  33-)  A      0
  23 LEU   (  34-)  A      0
  24 HIS   (  35-)  A      0
  26 MET   (  37-)  A      0
  40 TYR   (  51-)  A      0
  47 GLN   (  58-)  A      0
  49 LEU   (  60-)  A      0
  51 THR   (  62-)  A      0
  52 PHE   (  63-)  A      0
  53 CYS   (  64-)  A      0
  55 THR   (  66-)  A      0
  73 TRP   (  84-)  A      0
  74 ILE   (  85-)  A      0
  97 TRP   ( 108-)  A      0
  98 HIS   ( 109-)  A      0
 108 VAL   ( 119-)  A      0
 113 ILE   ( 124-)  A      0
 141 THR   ( 152-)  A      0
 142 ASP   ( 153-)  A      0
And so on for a total of 1031 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.331

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

2131 GLY   ( 308-)  E   2.40   10
 374 GLY   ( 385-)  A   2.18   80
1097 PRO   ( 191-)  C   1.77   12
 643 PRO   ( 191-)  B   1.77   12
1551 PRO   ( 191-)  D   1.77   12
2014 PRO   ( 191-)  E   1.76   12
2468 PRO   ( 191-)  F   1.76   12
 180 PRO   ( 191-)  A   1.76   12

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

1844 LYS   (  21-)  E   1.98

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.

2004 PRO   ( 181-)  E      O   <-> 2016 ARG   ( 193-)  E      NH2    0.38    2.32  INTRA
 170 PRO   ( 181-)  A      O   <->  182 ARG   ( 193-)  A      NH2    0.34    2.36  INTRA
1836 LEU   (  13-)  E      O   <-> 1845 SER   (  22-)  E      N      0.33    2.37  INTRA BF
 596 ARG   ( 144-)  B      NH1 <->  689 ASP   ( 237-)  B      O      0.33    2.37  INTRA BF
1373 LEU   (  13-)  D      N   <-> 2777 HOH   (3293 )  D      O      0.29    2.41  INTRA
 230 HIS   ( 241-)  A      ND1 <->  258 SER   ( 269-)  A      OG     0.28    2.42  INTRA BL
2742 HIS   ( 465-)  F      ND1 <-> 2779 HOH   (3308 )  F      O      0.27    2.43  INTRA
2288 HIS   ( 465-)  E      ND1 <-> 2778 HOH   (3307 )  E      O      0.27    2.43  INTRA
 111 ASN   ( 122-)  A      N   <-> 2753 TRS   (3251-)  A      O1     0.27    2.43  INTRA
1105 ASP   ( 199-)  C      OD1 <-> 1107 ASN   ( 201-)  C      N      0.27    2.43  INTRA
1994 ARG   ( 171-)  E      NH1 <-> 2575 GLU   ( 298-)  F      O      0.26    2.44  INTRA
1541 PRO   ( 181-)  D      O   <-> 1553 ARG   ( 193-)  D      NH2    0.25    2.45  INTRA
1087 PRO   ( 181-)  C      O   <-> 1099 ARG   ( 193-)  C      NH2    0.25    2.45  INTRA
1601 HIS   ( 241-)  D      ND1 <-> 1629 SER   ( 269-)  D      OG     0.25    2.45  INTRA BL
 635 ARG   ( 183-)  B      NE  <->  866 GLU   ( 414-)  B      OE2    0.24    2.46  INTRA BF
2087 LEU   ( 264-)  E      O   <-> 2113 ARG   ( 290-)  E      NH2    0.24    2.46  INTRA
 378 GLY   ( 389-)  A      C   <->  444 GLN   ( 455-)  A      NE2    0.24    2.86  INTRA
 633 PRO   ( 181-)  B      O   <->  645 ARG   ( 193-)  B      NH2    0.23    2.47  INTRA
1599 ASP   ( 239-)  D      OD2 <-> 1628 LYS   ( 268-)  D      NZ     0.23    2.47  INTRA
1845 SER   (  22-)  E      OG  <-> 1846 ILE   (  23-)  E      N      0.23    2.37  INTRA BF
2552 HIS   ( 275-)  F      NE2 <-> 2773 PLR   (1505-)  F      O1P    0.22    2.48  INTRA BL
 917 HIS   ( 465-)  B      ND1 <-> 2775 HOH   (3339 )  B      O      0.22    2.48  INTRA BF
2008 GLY   ( 185-)  E      N   <-> 2769 TRS   (3253-)  E      O1     0.21    2.49  INTRA BF
 330 LYS   ( 341-)  A      NZ  <->  488 GLU   (  36-)  B      OE2    0.20    2.50  INTRA
 919 LEU   (  13-)  C      N   <-> 2776 HOH   (3318 )  C      O      0.20    2.50  INTRA
And so on for a total of 349 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

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.

 566 LYS   ( 114-)  B      -6.98
2391 LYS   ( 114-)  F      -6.44
1020 LYS   ( 114-)  C      -6.32
 457 GLN   (   5-)  B      -6.26
1937 LYS   ( 114-)  E      -6.16
 103 LYS   ( 114-)  A      -6.00
1474 LYS   ( 114-)  D      -5.88
1196 ARG   ( 290-)  C      -5.65
1212 LEU   ( 306-)  C      -5.42
1391 ARG   (  31-)  D      -5.24
 295 LEU   ( 306-)  A      -5.17
1573 TYR   ( 213-)  D      -5.13
 742 ARG   ( 290-)  B      -5.11
2490 TYR   ( 213-)  F      -5.09
2308 ARG   (  31-)  F      -5.09
2583 LEU   ( 306-)  F      -5.07
 665 TYR   ( 213-)  B      -5.06
2567 ARG   ( 290-)  F      -5.05
  20 ARG   (  31-)  A      -5.04
1158 PRO   ( 252-)  C      -5.03
1333 ARG   ( 427-)  C      -5.01
 879 ARG   ( 427-)  B      -5.00
1666 LEU   ( 306-)  D      -5.00
1650 ARG   ( 290-)  D      -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

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.

 532 ILE   (  80-)  B   -2.88
1903 ILE   (  80-)  E   -2.87
2357 ILE   (  80-)  F   -2.82
  69 ILE   (  80-)  A   -2.80
1440 ILE   (  80-)  D   -2.79
 986 ILE   (  80-)  C   -2.77
1540 ILE   ( 180-)  D   -2.67
1857 LEU   (  34-)  E   -2.61
1938 ASN   ( 115-)  E   -2.60
1086 ILE   ( 180-)  C   -2.60
 504 LEU   (  52-)  B   -2.59
 169 ILE   ( 180-)  A   -2.57
1817 ILE   ( 457-)  D   -2.56
 632 ILE   ( 180-)  B   -2.56
2457 ILE   ( 180-)  F   -2.55
 446 ILE   ( 457-)  A   -2.55
2003 ILE   ( 180-)  E   -2.53
2734 ILE   ( 457-)  F   -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

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.

2774 HOH   (3295 )  A      O     38.22  -24.08  -12.49
2776 HOH   (3370 )  C      O    106.34   23.65  -31.12
2779 HOH   (3405 )  F      O     30.81   -1.10   31.13

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.

  60 ASN   (  71-)  A
1527 HIS   ( 167-)  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.

  57 ASP   (  68-)  A      N
  72 ASN   (  83-)  A      N
 103 LYS   ( 114-)  A      N
 106 GLN   ( 117-)  A      N
 109 GLY   ( 120-)  A      N
 111 ASN   ( 122-)  A      N
 115 SER   ( 126-)  A      N
 116 SER   ( 127-)  A      N
 152 GLN   ( 163-)  A      NE2
 157 LYS   ( 168-)  A      NZ
 189 GLU   ( 200-)  A      N
 193 GLY   ( 204-)  A      N
 201 THR   ( 212-)  A      OG1
 202 TYR   ( 213-)  A      N
 203 THR   ( 214-)  A      OG1
 246 ASP   ( 257-)  A      N
 249 TRP   ( 260-)  A      N
 250 ASP   ( 261-)  A      N
 264 HIS   ( 275-)  A      NE2
 280 ASP   ( 291-)  A      N
 281 GLU   ( 292-)  A      N
 287 GLU   ( 298-)  A      N
 302 PHE   ( 313-)  A      N
 307 SER   ( 318-)  A      N
 311 GLY   ( 322-)  A      N
And so on for a total of 192 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.

  86 ASP   (  97-)  A      OD1
 549 ASP   (  97-)  B      OD1
1003 ASP   (  97-)  C      OD1
1250 ASN   ( 344-)  C      OD1
1457 ASP   (  97-)  D      OD1
1920 ASP   (  97-)  E      OD1
2374 ASP   (  97-)  F      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.

2774 HOH   (3289 )  A      O  1.08  K  4 Ion-B
2775 HOH   (3267 )  B      O  0.89  K  4
2775 HOH   (3283 )  B      O  0.87  K  5
2775 HOH   (3284 )  B      O  1.05  K  4
2776 HOH   (3376 )  C      O  1.02  K  4
2776 HOH   (3378 )  C      O  0.87  K  4
2777 HOH   (3399 )  D      O  1.12  K  4 Ion-B
2778 HOH   (3290 )  E      O  0.97  K  4
2779 HOH   (3361 )  F      O  0.98  K  4

Warning: Possible wrong residue type

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

 168 GLU   ( 179-)  A   H-bonding suggests Gln; but Alt-Rotamer
 222 ASP   ( 233-)  A   H-bonding suggests Asn
 375 GLU   ( 386-)  A   H-bonding suggests Gln
 383 ASP   ( 394-)  A   H-bonding suggests Asn; but Alt-Rotamer
 429 ASP   ( 440-)  A   H-bonding suggests Asn; but Alt-Rotamer
 685 ASP   ( 233-)  B   H-bonding suggests Asn
 807 ASP   ( 355-)  B   H-bonding suggests Asn
 902 ASP   ( 450-)  B   H-bonding suggests Asn
1052 GLU   ( 146-)  C   H-bonding suggests Gln
1210 ASP   ( 304-)  C   H-bonding suggests Asn
1356 ASP   ( 450-)  C   H-bonding suggests Asn
1715 ASP   ( 355-)  D   H-bonding suggests Asn
1754 ASP   ( 394-)  D   H-bonding suggests Asn; but Alt-Rotamer
1810 ASP   ( 450-)  D   H-bonding suggests Asn
1835 GLU   (  12-)  E   H-bonding suggests Gln
1851 GLU   (  28-)  E   H-bonding suggests Gln; but Alt-Rotamer
2273 ASP   ( 450-)  E   H-bonding suggests Asn
2510 ASP   ( 233-)  F   H-bonding suggests Asn
2632 ASP   ( 355-)  F   H-bonding suggests Asn
2663 GLU   ( 386-)  F   H-bonding suggests Gln; 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 :  -0.249
  2nd generation packing quality :  -1.126
  Ramachandran plot appearance   :  -0.872
  chi-1/chi-2 rotamer normality  :  -1.728
  Backbone conformation          :  -0.391

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.297 (tight)
  Bond angles                    :   0.606 (tight)
  Omega angle restraints         :   0.242 (tight)
  Side chain planarity           :   0.276 (tight)
  Improper dihedral distribution :   0.591
  B-factor distribution          :   0.354
  Inside/Outside distribution    :   0.993

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 : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.4
  2nd generation packing quality :  -0.3
  Ramachandran plot appearance   :   0.5
  chi-1/chi-2 rotamer normality  :  -0.3
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.297 (tight)
  Bond angles                    :   0.606 (tight)
  Omega angle restraints         :   0.242 (tight)
  Side chain planarity           :   0.276 (tight)
  Improper dihedral distribution :   0.591
  B-factor distribution          :   0.354
  Inside/Outside distribution    :   0.993
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    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,
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      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.