WHAT IF Check report

This file was created 2011-12-21 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 pdb1aja.ent

Checks that need to be done early-on in validation

Warning: Unconventional cell on CRYST1

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

The CRYST1 cell dimensions

    A    = 195.020  B   = 166.930  C    =  76.440
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    =  76.440  B   = 133.923  C    = 133.923
    Alpha=  77.105  Beta= 106.582  Gamma= 106.582

Dimensions of the conventional cell

    A    =  76.440  B   = 166.930  C    = 195.020
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

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

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 3.643
CA-only RMS fit for the two chains : 1.987

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

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

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

 326 ALA   ( 332-)  A      CB
 397 GLU   ( 411-)  A      CG
 397 GLU   ( 411-)  A      CD
 397 GLU   ( 411-)  A      OE1
 397 GLU   ( 411-)  A      OE2
 486 ASP   (  51-)  B      CG
 486 ASP   (  51-)  B      OD1
 486 ASP   (  51-)  B      OD2
 687 GLN   ( 252-)  B      CG
 687 GLN   ( 252-)  B      CD
 687 GLN   ( 252-)  B      OE1
 687 GLN   ( 252-)  B      NE2
 831 GLU   ( 411-)  B      CG
 831 GLU   ( 411-)  B      CD
 831 GLU   ( 411-)  B      OE1
 831 GLU   ( 411-)  B      OE2
 832 HIS   ( 412-)  B      CG
 832 HIS   ( 412-)  B      ND1
 832 HIS   ( 412-)  B      CD2
 832 HIS   ( 412-)  B      CE1
 832 HIS   ( 412-)  B      NE2

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:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

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

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.

 109 TRP   ( 109-)  A      NE1  CE2   1.31   -5.3
 544 TRP   ( 109-)  B      CG   CD2   1.36   -4.0

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

 |  0.999302  0.000277 -0.000115|
 |  0.000277  1.002648 -0.000252|
 | -0.000115 -0.000252  1.002030|
Proposed new scale matrix

 |  0.005132 -0.000001  0.000000|
 | -0.000002  0.005975  0.000002|
 |  0.000002  0.000003  0.013056|
With corresponding cell

    A    = 194.872  B   = 167.359  C    =  76.596
    Alpha=  90.029  Beta=  90.008  Gamma=  89.968

The CRYST1 cell dimensions

    A    = 195.020  B   = 166.930  C    =  76.440
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 74.479
(Under-)estimated Z-score: 6.360

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.

   2 PRO   (   2-)  A     -CA  -C    N   126.28    6.3
   9 ASN   (   9-)  A      ND2  CG   OD1 118.56   -4.0
  39 ASP   (  39-)  A      CA   CB   CG  118.72    6.1
  51 ASP   (  51-)  A      CA   CB   CG  116.82    4.2
  63 ASN   (  63-)  A      CA   CB   CG  117.53    4.9
  71 PHE   (  71-)  A      CA   CB   CG  119.99    6.2
  76 ASP   (  76-)  A     -CA  -C    N   124.44    4.1
  84 TYR   (  84-)  A      CA   CB   CG  125.87    6.5
  96 PRO   (  96-)  A     -CA  -C    N   124.48    5.1
  97 ASP   (  97-)  A      N    CA   C    95.05   -5.8
 101 ASP   ( 101-)  A      CA   CB   CG  120.51    7.9
 111 THR   ( 111-)  A      N    CA   CB   99.71   -6.3
 111 THR   ( 111-)  A      C    CA   CB  118.22    4.3
 113 VAL   ( 113-)  A     -O   -C    N   115.94   -4.4
 117 ASN   ( 117-)  A      ND2  CG   OD1 118.40   -4.2
 123 ASP   ( 123-)  A      CA   CB   CG  121.11    8.5
 137 LYS   ( 137-)  A      CG   CD   CE   98.11   -5.7
 162 HIS   ( 162-)  A      CB   CG   ND1 128.93    4.9
 162 HIS   ( 162-)  A      CB   CG   CD2 123.67   -4.2
 168 CYS   ( 168-)  A      CA   CB   SG  104.89   -4.1
 181 ASN   ( 181-)  A      CB   CG   ND2 122.82    4.3
 181 ASN   ( 181-)  A      ND2  CG   OD1 116.00   -6.6
 184 GLU   ( 184-)  A      CB   CG   CD  120.28    4.5
 194 GLN   ( 194-)  A      NE2  CD   OE1 118.17   -4.4
 197 ASN   ( 197-)  A      ND2  CG   OD1 118.34   -4.3
And so on for a total of 161 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.

 266 VAL   ( 266-)  A      CB    -6.2   -41.08   -32.96
The average deviation= 1.388

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.

  97 ASP   (  97-)  A    5.22
 500 ALA   (  65-)  B    5.08
 589 ALA   ( 154-)  B    4.85
 154 ALA   ( 154-)  A    4.80
  65 ALA   (  65-)  A    4.61
 249 ALA   ( 249-)  A    4.55
 728 ASN   ( 293-)  B    4.33
 376 LYS   ( 382-)  A    4.29
 801 ALA   ( 373-)  B    4.14
 684 ALA   ( 249-)  B    4.07
 467 ALA   (  32-)  B    4.05

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 : 1.563

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.

 361 THR   ( 367-)  A    -3.1
 115 THR   ( 115-)  A    -3.0
 795 THR   ( 367-)  B    -3.0
 550 THR   ( 115-)  B    -2.9
 171 PRO   ( 171-)  A    -2.7
 403 LEU   ( 417-)  A    -2.7
 837 LEU   ( 417-)  B    -2.6
 429 LYS   ( 443-)  A    -2.6
 606 PRO   ( 171-)  B    -2.4
 711 HIS   ( 276-)  B    -2.3
 685 ASN   ( 250-)  B    -2.3
 439 MET   (   4-)  B    -2.2
 248 GLU   ( 248-)  A    -2.2
 279 ILE   ( 279-)  A    -2.2
 623 LYS   ( 188-)  B    -2.2
 798 HIS   ( 370-)  B    -2.1
 274 THR   ( 274-)  A    -2.1
 868 LEU   ( 448-)  B    -2.1
 172 SER   ( 172-)  A    -2.1
 866 LEU   ( 446-)  B    -2.1
 432 LEU   ( 446-)  A    -2.1
 583 THR   ( 148-)  B    -2.1
 682 THR   ( 247-)  B    -2.1
 378 PRO   ( 384-)  A    -2.1
 132 ILE   ( 132-)  A    -2.1
 567 ILE   ( 132-)  B    -2.1
 683 GLU   ( 248-)  B    -2.0
   7 LEU   (   7-)  A    -2.0
 673 SER   ( 238-)  B    -2.0
 223 LYS   ( 223-)  A    -2.0
 269 LEU   ( 269-)  A    -2.0
 482 LEU   (  47-)  B    -2.0
  19 PRO   (  19-)  A    -2.0
 127 LYS   ( 127-)  A    -2.0
 293 ASN   ( 293-)  A    -2.0
 519 TYR   (  84-)  B    -2.0
 644 LYS   ( 209-)  B    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

 123 ASP   ( 123-)  A  Poor phi/psi
 222 GLY   ( 222-)  A  Poor phi/psi
 276 HIS   ( 276-)  A  Poor phi/psi
 284 VAL   ( 284-)  A  omega poor
 293 ASN   ( 293-)  A  Poor phi/psi
 327 ALA   ( 333-)  A  Poor phi/psi
 411 HIS   ( 425-)  A  Poor phi/psi
 437 PRO   (   2-)  B  Poor phi/psi
 439 MET   (   4-)  B  Poor phi/psi
 550 THR   ( 115-)  B  Poor phi/psi
 603 CYS   ( 168-)  B  Poor phi/psi
 657 GLY   ( 222-)  B  Poor phi/psi
 711 HIS   ( 276-)  B  Poor phi/psi
 728 ASN   ( 293-)  B  Poor phi/psi
 759 ALA   ( 324-)  B  Poor phi/psi
 845 HIS   ( 425-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.545

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 : -3.545

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.

 677 SER   ( 242-)  B    0.35

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!

   7 LEU   (   7-)  A      0
   9 ASN   (   9-)  A      0
  10 ARG   (  10-)  A      0
  12 ALA   (  12-)  A      0
  13 GLN   (  13-)  A      0
  15 ASP   (  15-)  A      0
  18 ALA   (  18-)  A      0
  19 PRO   (  19-)  A      0
  23 ARG   (  23-)  A      0
  26 THR   (  26-)  A      0
  28 ASP   (  28-)  A      0
  38 SER   (  38-)  A      0
  39 ASP   (  39-)  A      0
  43 LYS   (  43-)  A      0
  44 ASN   (  44-)  A      0
  51 ASP   (  51-)  A      0
  53 MET   (  53-)  A      0
  77 ALA   (  77-)  A      0
  86 HIS   (  86-)  A      0
 116 TYR   ( 116-)  A      0
 117 ASN   ( 117-)  A      0
 120 LEU   ( 120-)  A      0
 124 ILE   ( 124-)  A      0
 149 ALA   ( 149-)  A      0
 150 GLU   ( 150-)  A      0
And so on for a total of 334 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!

  74 GLY   (  74-)  A   1.74   13
  50 GLY   (  50-)  A   1.53   11

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]

   2 PRO   (   2-)  A    0.49 HIGH
 130 PRO   ( 130-)  A    0.03 LOW
 171 PRO   ( 171-)  A    0.47 HIGH
 297 PRO   ( 297-)  A    0.03 LOW
 440 PRO   (   5-)  B    0.05 LOW
 531 PRO   (  96-)  B    0.48 HIGH
 614 PRO   ( 179-)  B    0.46 HIGH
 763 PRO   ( 335-)  B    0.45 HIGH

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].

  19 PRO   (  19-)  A  -115.5 envelop C-gamma (-108 degrees)
 288 PRO   ( 288-)  A    99.7 envelop C-beta (108 degrees)
 700 PRO   ( 265-)  B    46.3 half-chair C-delta/C-gamma (54 degrees)
 807 PRO   ( 379-)  B  -113.3 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.

 293 ASN   ( 293-)  A      CB  <->  296 VAL   ( 296-)  A      CG2    0.17    3.03  INTRA
 294 ASP   ( 294-)  A      N   <->  295 SER   ( 295-)  A      N      0.17    2.43  INTRA B3
 634 ARG   ( 199-)  B      NH2 <->  667 ARG   ( 232-)  B      O      0.17    2.53  INTRA
  75 ILE   (  75-)  A      O   <->  404 ARG   ( 418-)  A      NH2    0.13    2.57  INTRA BL
 766 GLN   ( 338-)  B      NE2 <->  830 TYR   ( 402-)  B      OH     0.12    2.58  INTRA
 663 GLN   ( 228-)  B      OE1 <->  667 ARG   ( 232-)  B      NH1    0.11    2.59  INTRA
 235 GLN   ( 235-)  A      NE2 <->  248 GLU   ( 248-)  A      O      0.10    2.60  INTRA
 683 GLU   ( 248-)  B      CG  <->  688 LYS   ( 253-)  B      NZ     0.09    3.01  INTRA BF
  86 HIS   (  86-)  A      NE2 <->  401 SER   ( 415-)  A      O      0.08    2.62  INTRA BL
 459 ARG   (  24-)  B      NH2 <->  503 ALA   (  68-)  B      O      0.07    2.63  INTRA BL
 439 MET   (   4-)  B      CE  <->  473 SER   (  38-)  B      CB     0.07    3.13  INTRA BF
 110 SER   ( 110-)  A      O   <->  132 ILE   ( 132-)  A      N      0.07    2.63  INTRA BL
 506 PHE   (  71-)  B      O   <->  508 LYS   (  73-)  B      NZ     0.06    2.64  INTRA
 521 HIS   (  86-)  B      NE2 <->  835 SER   ( 415-)  B      O      0.06    2.64  INTRA BL
 603 CYS   ( 168-)  B      SG  <->  613 CYS   ( 178-)  B      N      0.06    3.24  INTRA
 439 MET   (   4-)  B      CA  <->  440 PRO   (   5-)  B      CD     0.06    2.74  INTRA BF
 326 ALA   ( 332-)  A      N   <->  327 ALA   ( 333-)  A      N      0.04    2.56  INTRA B3
 332 GLN   ( 338-)  A      NE2 <->  396 TYR   ( 402-)  A      OH     0.04    2.66  INTRA
 293 ASN   ( 293-)  A      CG  <->  295 SER   ( 295-)  A      OG     0.04    2.76  INTRA
 148 THR   ( 148-)  A      N   <->  149 ALA   ( 149-)  A      N      0.03    2.57  INTRA BL
  62 ARG   (  62-)  A      O   <->   66 GLU   (  66-)  A      N      0.03    2.67  INTRA BL
 608 ALA   ( 173-)  B      O   <->  612 LYS   ( 177-)  B      N      0.03    2.67  INTRA
 118 GLY   ( 118-)  A      O   <->  166 ARG   ( 166-)  A      N      0.03    2.67  INTRA BL
 748 ASN   ( 313-)  B      OD1 <->  750 LYS   ( 315-)  B      N      0.03    2.67  INTRA BF
 459 ARG   (  24-)  B      NH1 <->  505 GLY   (  70-)  B      O      0.02    2.68  INTRA BL
 675 ALA   ( 240-)  B      N   <->  730 SER   ( 295-)  B      O      0.02    2.68  INTRA BF
 436 THR   (   1-)  B      O   <->  438 GLU   (   3-)  B      N      0.02    2.68  INTRA BF
 474 ASP   (  39-)  B      O   <->  845 HIS   ( 425-)  B      NE2    0.01    2.69  INTRA
 560 HIS   ( 125-)  B      N   <->  561 GLU   ( 126-)  B      N      0.01    2.59  INTRA BL
  90 ASN   (  90-)  A      N   <->   95 LYS   (  95-)  A      O      0.01    2.69  INTRA BL
 125 HIS   ( 125-)  A      N   <->  126 GLU   ( 126-)  A      N      0.01    2.59  INTRA BL

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

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.

 275 TYR   ( 275-)  A      -7.17
 710 TYR   ( 275-)  B      -7.13
 376 LYS   ( 382-)  A      -6.25
 252 GLN   ( 252-)  A      -6.03
 810 LYS   ( 382-)  B      -5.86
  92 LYS   (  92-)  A      -5.84
 438 GLU   (   3-)  B      -5.75
 527 LYS   (  92-)  B      -5.70
   4 MET   (   4-)  A      -5.41
 727 ARG   ( 292-)  B      -5.36
   3 GLU   (   3-)  A      -5.34
 749 GLU   ( 314-)  B      -5.25
 787 GLU   ( 359-)  B      -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

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.

 811 ALA   ( 383-)  B   -2.68

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

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

 670 GLN   ( 235-)  B
 762 ASN   ( 334-)  B

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.

  10 ARG   (  10-)  A      N
  23 ARG   (  23-)  A      NE
  30 THR   (  30-)  A      OG1
  62 ARG   (  62-)  A      NH1
  78 LEU   (  78-)  A      N
  81 THR   (  81-)  A      N
  83 GLN   (  83-)  A      NE2
 100 THR   ( 100-)  A      N
 103 ALA   ( 103-)  A      N
 113 VAL   ( 113-)  A      N
 122 VAL   ( 122-)  A      N
 143 THR   ( 143-)  A      OG1
 145 ASN   ( 145-)  A      ND2
 217 ALA   ( 217-)  A      N
 267 ARG   ( 267-)  A      NE
 268 TRP   ( 268-)  A      N
 296 VAL   ( 296-)  A      N
 330 CYS   ( 336-)  A      N
 356 THR   ( 362-)  A      N
 365 ALA   ( 371-)  A      N
 393 VAL   ( 399-)  A      N
 396 TYR   ( 402-)  A      OH
 401 SER   ( 415-)  A      N
 404 ARG   ( 418-)  A      N
 404 ARG   ( 418-)  A      NH2
And so on for a total of 61 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.

  57 GLU   (  57-)  A      OE2
 382 GLN   ( 388-)  A      OE1
 521 HIS   (  86-)  B      ND1
 816 GLN   ( 388-)  B      OE1

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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.

   3 GLU   (   3-)  A   H-bonding suggests Gln
  57 GLU   (  57-)  A   H-bonding suggests Gln
 248 GLU   ( 248-)  A   H-bonding suggests Gln
 338 ASP   ( 344-)  A   H-bonding suggests Asn
 438 GLU   (   3-)  B   H-bonding suggests Gln
 470 ASP   (  35-)  B   H-bonding suggests Asn
 492 GLU   (  57-)  B   H-bonding suggests Gln
 769 GLU   ( 341-)  B   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.680
  2nd generation packing quality :  -1.076
  Ramachandran plot appearance   :  -1.553
  chi-1/chi-2 rotamer normality  :  -3.545 (poor)
  Backbone conformation          :  -0.178

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.628 (tight)
  Bond angles                    :   1.421
  Omega angle restraints         :   0.782
  Side chain planarity           :   0.767
  Improper dihedral distribution :   1.134
  B-factor distribution          :   0.824
  Inside/Outside distribution    :   0.925

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 : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :   0.0
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :  -1.6
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.628 (tight)
  Bond angles                    :   1.421
  Omega angle restraints         :   0.782
  Side chain planarity           :   0.767
  Improper dihedral distribution :   1.134
  B-factor distribution          :   0.824
  Inside/Outside distribution    :   0.925
==============

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
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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.