WHAT IF Check report

This file was created 2012-08-30 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 pdb3zxw.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 : 0.234
CA-only RMS fit for the two chains : 0.150

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 E

All-atom RMS fit for the two chains : 0.256
CA-only RMS fit for the two chains : 0.150

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 G

All-atom RMS fit for the two chains : 0.229
CA-only RMS fit for the two chains : 0.135

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 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.

2234 CAP   ( 477-)  A  -
2239 CAP   ( 477-)  C  -
2245 CAP   ( 477-)  E  -
2251 CAP   ( 477-)  G  -

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

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

Warning: B-factors outside the range 0.0 - 100.0

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

 344 GLU   ( 355-)  A    High
 425 ASP   ( 436-)  A    High
 427 MET   ( 438-)  A    High
 428 ARG   ( 439-)  A    High
 429 GLU   ( 440-)  A    High
 439 ARG   ( 450-)  A    High
 440 TRP   ( 451-)  A    High
 449 GLU   ( 460-)  A    High
 453 GLU   ( 464-)  A    High
 464 ILE   ( 475-)  A    High
 477 ARG   (  26-)  B    High
 901 GLU   ( 355-)  C    High
 982 ASP   ( 436-)  C    High
 984 MET   ( 438-)  C    High
 985 ARG   ( 439-)  C    High
 986 GLU   ( 440-)  C    High
 996 ARG   ( 450-)  C    High
 997 TRP   ( 451-)  C    High
1006 GLU   ( 460-)  C    High
1010 GLU   ( 464-)  C    High
1021 ILE   ( 475-)  C    High
1034 ARG   (  26-)  D    High
1458 GLU   ( 355-)  E    High
1539 ASP   ( 436-)  E    High
1541 MET   ( 438-)  E    High
1542 ARG   ( 439-)  E    High
1543 GLU   ( 440-)  E    High
1553 ARG   ( 450-)  E    High
1554 TRP   ( 451-)  E    High
1563 GLU   ( 460-)  E    High
1567 GLU   ( 464-)  E    High
1578 ILE   ( 475-)  E    High
1591 ARG   (  26-)  F    High
2015 GLU   ( 355-)  G    High
2096 ASP   ( 436-)  G    High
2098 MET   ( 438-)  G    High
2099 ARG   ( 439-)  G    High
2100 GLU   ( 440-)  G    High
2110 ARG   ( 450-)  G    High
2111 TRP   ( 451-)  G    High
2120 GLU   ( 460-)  G    High
2124 GLU   ( 464-)  G    High
2135 ILE   ( 475-)  G    High
2148 ARG   (  26-)  H    High

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

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

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

RMS Z-score : 1.765 over 15674 bonds
Average difference in B over a bond : 4.33
RMS difference in B over a bond : 7.38

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

Nomenclature related problems

Warning: Heavy atom naming convention problem

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

 190 KCX   ( 201-)  A      CH     CX
 190 KCX   ( 201-)  A      OX1    OQ1
 190 KCX   ( 201-)  A      OX2    OQ2
 747 KCX   ( 201-)  C      CH     CX
 747 KCX   ( 201-)  C      OX1    OQ1
 747 KCX   ( 201-)  C      OX2    OQ2
1304 KCX   ( 201-)  E      CH     CX
1304 KCX   ( 201-)  E      OX1    OQ1
1304 KCX   ( 201-)  E      OX2    OQ2
1861 KCX   ( 201-)  G      CH     CX
1861 KCX   ( 201-)  G      OX1    OQ1
1861 KCX   ( 201-)  G      OX2    OQ2

Geometric checks

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.997049  0.000024  0.000116|
 |  0.000024  0.997126 -0.000115|
 |  0.000116 -0.000115  0.997494|
Proposed new scale matrix

 |  0.008996  0.000000 -0.000001|
 |  0.000000  0.008995  0.000001|
 |  0.000000  0.000000  0.002525|
With corresponding cell

    A    = 111.166  B   = 111.175  C    = 395.988
    Alpha=  90.009  Beta=  89.996  Gamma=  90.001

The CRYST1 cell dimensions

    A    = 111.500  B   = 111.500  C    = 397.000
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 577.742
(Under-)estimated Z-score: 17.715

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.

 785 TYR   ( 239-)  C    -2.4
 253 ILE   ( 264-)  A    -2.4
 611 THR   (  65-)  C    -2.2
1544 GLY   ( 441-)  E    -2.2
1899 TYR   ( 239-)  G    -2.2
 326 GLY   ( 337-)  A    -2.1
1997 GLY   ( 337-)  G    -2.1
1725 THR   (  65-)  G    -2.1
1440 GLY   ( 337-)  E    -2.1
 228 TYR   ( 239-)  A    -2.1
 883 GLY   ( 337-)  C    -2.1
1735 THR   (  75-)  G    -2.1
1342 TYR   ( 239-)  E    -2.0
1178 THR   (  75-)  E    -2.0
 621 THR   (  75-)  C    -2.0
  64 THR   (  75-)  A    -2.0
  54 THR   (  65-)  A    -2.0
1168 THR   (  65-)  E    -2.0
1866 ILE   ( 206-)  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.

  12 THR   (  23-)  A  omega poor
  51 SER   (  62-)  A  Poor phi/psi
  52 THR   (  63-)  A  Poor phi/psi
 152 ASN   ( 163-)  A  Poor phi/psi
 164 LYS   ( 175-)  A  PRO omega poor
 188 PHE   ( 199-)  A  omega poor
 196 ASN   ( 207-)  A  Poor phi/psi
 250 GLU   ( 261-)  A  Poor phi/psi
 257 ASP   ( 268-)  A  omega poor
 286 MET   ( 297-)  A  Poor phi/psi
 290 MET   ( 301-)  A  omega poor
 320 VAL   ( 331-)  A  Poor phi/psi
 359 SER   ( 370-)  A  Poor phi/psi
 508 LYS   (  57-)  B  Poor phi/psi
 513 ASN   (  62-)  B  Poor phi/psi
 569 THR   (  23-)  C  omega poor
 608 SER   (  62-)  C  Poor phi/psi
 609 THR   (  63-)  C  Poor phi/psi
 641 ASN   (  95-)  C  Poor phi/psi
 709 ASN   ( 163-)  C  Poor phi/psi
 721 LYS   ( 175-)  C  PRO omega poor
 745 PHE   ( 199-)  C  omega poor
 753 ASN   ( 207-)  C  Poor phi/psi
 789 THR   ( 243-)  C  omega poor
 807 GLU   ( 261-)  C  Poor phi/psi
And so on for a total of 65 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.

1384 SER   ( 281-)  E    0.37
 827 SER   ( 281-)  C    0.38
1941 SER   ( 281-)  G    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!

   4 ALA   (  15-)  A      0
   7 LYS   (  18-)  A      0
  12 THR   (  23-)  A      0
  13 TYR   (  24-)  A      0
  14 TYR   (  25-)  A      0
  15 THR   (  26-)  A      0
  35 PRO   (  46-)  A      0
  50 SER   (  61-)  A      0
  51 SER   (  62-)  A      0
  52 THR   (  63-)  A      0
  55 TRP   (  66-)  A      0
  59 TRP   (  70-)  A      0
  63 LEU   (  74-)  A      0
  64 THR   (  75-)  A      0
  74 TYR   (  85-)  A      0
  75 ASP   (  86-)  A      0
  83 ASP   (  94-)  A      0
  84 ASN   (  95-)  A      0
  96 LEU   ( 107-)  A      0
  99 GLU   ( 110-)  A      0
 110 VAL   ( 121-)  A      0
 112 ASN   ( 123-)  A      0
 113 VAL   ( 124-)  A      0
 116 PHE   ( 127-)  A      0
 120 LYS   ( 131-)  A      0
And so on for a total of 797 lines.

Warning: Backbone oxygen evaluation

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

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

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

 318 GLY   ( 329-)  A   1.61   12
 951 GLY   ( 405-)  C   1.59   80
1508 GLY   ( 405-)  E   1.57   80

Warning: Unusual PRO puckering phases

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

  33 PRO   (  44-)  A   -64.4 envelop C-beta (-72 degrees)
  35 PRO   (  46-)  A   101.0 envelop C-beta (108 degrees)
 590 PRO   (  44-)  C     2.1 envelop N (0 degrees)
 956 PRO   ( 410-)  C    99.4 envelop C-beta (108 degrees)
 999 PRO   ( 453-)  C  -113.9 envelop C-gamma (-108 degrees)
1149 PRO   (  46-)  E   122.7 half-chair C-beta/C-alpha (126 degrees)
1704 PRO   (  44-)  G    44.3 envelop C-delta (36 degrees)
1870 PRO   ( 210-)  G    99.8 envelop C-beta (108 degrees)
1905 PRO   ( 245-)  G  -116.6 envelop C-gamma (-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.

 747 KCX   ( 201-)  C      OX2 <-> 2239 CAP   ( 477-)  C      O3     0.35    2.05  INTRA
 684 LEU   ( 138-)  C      O   <->  862 LYS   ( 316-)  C      NZ     0.34    2.36  INTRA BL
1304 KCX   ( 201-)  E      OX2 <-> 2245 CAP   ( 477-)  E      O3     0.31    2.09  INTRA
1861 KCX   ( 201-)  G      OX2 <-> 2251 CAP   ( 477-)  G      O3     0.30    2.10  INTRA
1061 TRP   (  53-)  D      O   <-> 1290 ARG   ( 187-)  E      NH1    0.29    2.41  INTRA BF
 287 HIS   ( 298-)  A      ND1 <->  291 ASP   ( 302-)  A      OD2    0.29    2.41  INTRA
1818 GLU   ( 158-)  G      OE2 <-> 1985 HIS   ( 325-)  G      NE2    0.29    2.41  INTRA BL
 707 LYS   ( 161-)  C      NZ  <-> 2254 HOH   (2112 )  C      O      0.28    2.42  INTRA BL
 147 GLU   ( 158-)  A      OE2 <->  314 HIS   ( 325-)  A      NE2    0.27    2.43  INTRA BL
1821 LYS   ( 161-)  G      NZ  <-> 2252 HOH   (2131 )  A      O      0.26    2.44  INTRA
 704 GLU   ( 158-)  C      OE2 <->  871 HIS   ( 325-)  C      NE2    0.26    2.44  INTRA BL
 190 KCX   ( 201-)  A      OX2 <-> 2234 CAP   ( 477-)  A      O3     0.25    2.15  INTRA BL
1958 HIS   ( 298-)  G      ND1 <-> 1962 ASP   ( 302-)  G      OD2    0.24    2.46  INTRA
 150 LYS   ( 161-)  A      NZ  <-> 2252 HOH   (2101 )  A      O      0.22    2.48  INTRA BL
 215 HIS   ( 226-)  A    A NE2 <-> 2252 HOH   (2136 )  A      O      0.22    2.48  INTRA BL
1261 GLU   ( 158-)  E      OE2 <-> 1428 HIS   ( 325-)  E      NE2    0.21    2.49  INTRA BL
 844 HIS   ( 298-)  C      ND1 <->  848 ASP   ( 302-)  C      OD2    0.20    2.50  INTRA
1264 LYS   ( 161-)  E      NZ  <-> 2256 HOH   (2093 )  E      O      0.20    2.50  INTRA
1618 TRP   (  53-)  F      O   <-> 1847 ARG   ( 187-)  G      NH1    0.20    2.50  INTRA BF
1395 HIS   ( 292-)  E      NE2 <-> 1430 HIS   ( 327-)  E      NE2    0.19    2.81  INTRA BL
 838 HIS   ( 292-)  C      NE2 <->  873 HIS   ( 327-)  C      NE2    0.17    2.83  INTRA BL
 127 LEU   ( 138-)  A      O   <->  305 LYS   ( 316-)  A      NZ     0.17    2.53  INTRA BL
 281 HIS   ( 292-)  A      NE2 <->  316 HIS   ( 327-)  A      NE2    0.16    2.84  INTRA BL
1310 ASN   ( 207-)  E      ND2 <-> 2256 HOH   (2102 )  E      O      0.15    2.55  INTRA
1886 HIS   ( 226-)  G    A NE2 <-> 2258 HOH   (2117 )  G      O      0.14    2.56  INTRA
And so on for a total of 123 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

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.

1995 LEU   ( 335-)  G      -6.96
 881 LEU   ( 335-)  C      -6.84
 324 LEU   ( 335-)  A      -6.78
1438 LEU   ( 335-)  E      -6.75
1117 GLN   (  14-)  E      -6.38
 428 ARG   ( 439-)  A      -6.29
 985 ARG   ( 439-)  C      -6.29
   3 GLN   (  14-)  A      -6.22
 560 GLN   (  14-)  C      -6.20
1674 GLN   (  14-)  G      -6.14
 997 TRP   ( 451-)  C      -5.94
 138 GLN   ( 149-)  A      -5.94
1670 LYS   ( 105-)  F      -5.92
 440 TRP   ( 451-)  A      -5.92
1113 LYS   ( 105-)  D      -5.89
1023 TYR   (  15-)  D      -5.88
2227 LYS   ( 105-)  H      -5.87
 556 LYS   ( 105-)  B      -5.87
 695 GLN   ( 149-)  C      -5.83
2179 LYS   (  57-)  H      -5.78
1809 GLN   ( 149-)  G      -5.78
1065 LYS   (  57-)  D      -5.76
1622 LYS   (  57-)  F      -5.75
2099 ARG   ( 439-)  G      -5.74
 508 LYS   (  57-)  B      -5.73
And so on for a total of 56 lines.

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.

 323 LYS   ( 334-)  A       325 - GLU    336- ( A)         -5.37
 880 LYS   ( 334-)  C       882 - GLU    336- ( C)         -5.37
1437 LYS   ( 334-)  E      1439 - GLU    336- ( E)         -5.29
1571 GLU   ( 468-)  E      1573 - GLU    470- ( E)         -4.10
1994 LYS   ( 334-)  G      1996 - GLU    336- ( G)         -5.43

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

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.

 845 ALA   ( 299-)  C   -2.75
1765 LEU   ( 105-)  G   -2.70
 651 LEU   ( 105-)  C   -2.69
1208 LEU   ( 105-)  E   -2.69
  94 LEU   ( 105-)  A   -2.66

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

Water, ion, and hydrogenbond related checks

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.

2254 HOH   (2143 )  C      O
2256 HOH   (2163 )  E      O
2258 HOH   (2009 )  G      O
2258 HOH   (2167 )  G      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.

 104 ASN   ( 115-)  A
 138 GLN   ( 149-)  A
 142 HIS   ( 153-)  A
 316 HIS   ( 327-)  A
 461 GLN   ( 472-)  A
 513 ASN   (  62-)  B
 526 GLN   (  75-)  B
 661 ASN   ( 115-)  C
 699 HIS   ( 153-)  C
 753 ASN   ( 207-)  C
 873 HIS   ( 327-)  C
1018 GLN   ( 472-)  C
1083 GLN   (  75-)  D
1218 ASN   ( 115-)  E
1256 HIS   ( 153-)  E
1430 HIS   ( 327-)  E
1575 GLN   ( 472-)  E
1627 ASN   (  62-)  F
1640 GLN   (  75-)  F
1775 ASN   ( 115-)  G
1813 HIS   ( 153-)  G
2016 GLN   ( 356-)  G
2132 GLN   ( 472-)  G
2184 ASN   (  62-)  H
2197 GLN   (  75-)  H

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.

  17 ASP   (  28-)  A      N
  54 THR   (  65-)  A      OG1
  56 THR   (  67-)  A      N
  95 ASP   ( 106-)  A      N
 101 SER   ( 112-)  A      OG
 112 ASN   ( 123-)  A      ND2
 156 ARG   ( 167-)  A      N
 162 THR   ( 173-)  A      N
 162 THR   ( 173-)  A      OG1
 164 LYS   ( 175-)  A      N
 164 LYS   ( 175-)  A      NZ
 167 LEU   ( 178-)  A      N
 168 GLY   ( 179-)  A      N
 200 PHE   ( 211-)  A      N
 201 GLN   ( 212-)  A      NE2
 228 TYR   ( 239-)  A      OH
 235 THR   ( 246-)  A      N
 253 ILE   ( 264-)  A      N
 284 ARG   ( 295-)  A      NE
 284 ARG   ( 295-)  A      NH1
 292 ARG   ( 303-)  A      N
 312 GLY   ( 323-)  A      N
 321 VAL   ( 332-)  A      N
 327 ASP   ( 338-)  A      N
 368 SER   ( 379-)  A      N
And so on for a total of 133 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.

 196 ASN   ( 207-)  A      OD1
 257 ASP   ( 268-)  A      OD1
 281 HIS   ( 292-)  A      NE2
 390 GLN   ( 401-)  A      OE1
 814 ASP   ( 268-)  C      OD1
 814 ASP   ( 268-)  C      OD2
 838 HIS   ( 292-)  C      NE2
 947 GLN   ( 401-)  C      OE1
1310 ASN   ( 207-)  E      OD1
1371 ASP   ( 268-)  E      OD1
1395 HIS   ( 292-)  E      NE2
1504 GLN   ( 401-)  E      OE1
1867 ASN   ( 207-)  G      OD1
1928 ASP   ( 268-)  G      OD1
2061 GLN   ( 401-)  G      OE1

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+.

2233  MG   ( 476-)  A     0.73   1.29 Scores about as good as CA
2238  MG   ( 476-)  C     0.73   1.27 Scores about as good as CA
2244  MG   ( 476-)  E     0.69   1.17 Scores about as good as CA
2248  MG   ( 476-)  G     0.70   1.19 Scores about as good as CA

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.

2252 HOH   (2088 )  A      O  0.94  K  4 NCS 3/3
2252 HOH   (2109 )  A      O  0.88  K  4 Ion-B NCS 3/3
2252 HOH   (2133 )  A      O  1.12  K  4 NCS 3/3
2254 HOH   (2072 )  C      O  0.94  K  4 NCS 3/3
2254 HOH   (2109 )  C      O  0.92  K  4 Ion-B NCS 3/3
2254 HOH   (2183 )  C      O  0.85  K  4 Ion-B NCS 3/3
2256 HOH   (2080 )  E      O  1.02  K  4 NCS 3/3
2256 HOH   (2085 )  E      O  0.89  K  4 ION-B NCS 3/3
2256 HOH   (2092 )  E      O  0.89  K  4 Ion-B NCS 3/3
2258 HOH   (2128 )  G      O  1.12  K  4 NCS 3/3

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.

 248 GLU   ( 259-)  A   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
 257 ASP   ( 268-)  A   H-bonding suggests Asn; but Alt-Rotamer
 291 ASP   ( 302-)  A   H-bonding suggests Asn; Ligand-contact
 462 ASP   ( 473-)  A   H-bonding suggests Asn; Ligand-contact
 632 ASP   (  86-)  C   H-bonding suggests Asn; Ligand-contact
 814 ASP   ( 268-)  C   H-bonding suggests Asn; but Alt-Rotamer
1019 ASP   ( 473-)  C   H-bonding suggests Asn; Ligand-contact
1263 ASP   ( 160-)  E   H-bonding suggests Asn; but Alt-Rotamer
1371 ASP   ( 268-)  E   H-bonding suggests Asn; but Alt-Rotamer
1405 ASP   ( 302-)  E   H-bonding suggests Asn; Ligand-contact
1499 ASP   ( 396-)  E   H-bonding suggests Asn
1576 ASP   ( 473-)  E   H-bonding suggests Asn; Ligand-contact
1928 ASP   ( 268-)  G   H-bonding suggests Asn; but Alt-Rotamer
1946 ASP   ( 286-)  G   H-bonding suggests Asn
1962 ASP   ( 302-)  G   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 :  -0.599
  2nd generation packing quality :   0.329
  Ramachandran plot appearance   :  -0.389
  chi-1/chi-2 rotamer normality  :  -1.192
  Backbone conformation          :  -0.326

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.361 (tight)
  Bond angles                    :   0.548 (tight)
  Omega angle restraints         :   0.953
  Side chain planarity           :   0.292 (tight)
  Improper dihedral distribution :   0.501
  B-factor distribution          :   1.765 (loose)
  Inside/Outside distribution    :   1.074

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 : 2.10


Structure Z-scores, positive is better than average:

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

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.361 (tight)
  Bond angles                    :   0.548 (tight)
  Omega angle restraints         :   0.953
  Side chain planarity           :   0.292 (tight)
  Improper dihedral distribution :   0.501
  B-factor distribution          :   1.765 (loose)
  Inside/Outside distribution    :   1.074
==============

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.