WHAT IF Check report

This file was created 2012-01-19 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 pdb2b0d.ent

Administrative problems that can generate validation failures

Warning: Overlapping residues or molecules

This molecule contains residues or molecules that overlap too much while not being (administrated as) alternate atom/residue pairs. The residues or molecules listed in the table below have been removed before the validation continued.

Overlapping residues or molecules (for short entities) are occasionally observed in the PDB. Often these are cases like, for example, two sugars that bind equally well in the same active site, are both seen overlapping in the density, and are both entered in the PDB file as separate entities. This can cause some false positive error messsages further down the validation path, and therefore the second of the overlapping entities has been deleted before the validation continued. If you want to validate both situations, make it two PDB files, one for each sugar. And fudge reality a bit by making the occupancy of the sugar atoms 1.0 in both cases, because many validation options are not executed on atoms with low occupancy. If you go for this two-file option, please make sure that any side chains that have alternate locations depending on the sugar bound are selected in each of the two cases in agreement with the sugar that you keep for validation in that particular file.

 175 PRO   ( 162-)  A  -

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'.

  38 LYS   (  17-)  A      CG
  38 LYS   (  17-)  A      CD
  38 LYS   (  17-)  A      CE
  38 LYS   (  17-)  A      NZ
  56 SER   (  35-)  A      OG
  57 ASP   (  36-)  A      CG
  57 ASP   (  36-)  A      OD1
  57 ASP   (  36-)  A      OD2
  59 LYS   (  38-)  A      CG
  59 LYS   (  38-)  A      CD
  59 LYS   (  38-)  A      CE
  59 LYS   (  38-)  A      NZ
  78 GLU   (  57-)  A      CG
  78 GLU   (  57-)  A      CD
  78 GLU   (  57-)  A      OE1
  78 GLU   (  57-)  A      OE2
  79 LYS   (  58-)  A      CG
  79 LYS   (  58-)  A      CD
  79 LYS   (  58-)  A      CE
  79 LYS   (  58-)  A      NZ
  88 LYS   (  67-)  A      CG
  88 LYS   (  67-)  A      CD
  88 LYS   (  67-)  A      CE
  88 LYS   (  67-)  A      NZ
  89 GLN   (  68-)  A      CG
And so on for a total of 160 lines.

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

Nomenclature related problems

Warning: Tyrosine convention problem

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

  33 TYR   (  12-)  A
  93 TYR   (  72-)  A
 147 TYR   ( 128-)  A
 155 TYR   ( 136-)  A
 268 TYR   (  12-)  B
 382 TYR   ( 128-)  B

Warning: Phenylalanine convention problem

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

  96 PHE   (  75-)  A
 211 PHE   ( 199-)  A
 331 PHE   (  75-)  B
 359 PHE   ( 105-)  B
 367 PHE   ( 113-)  B
 450 PHE   ( 199-)  B

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

  95 ASP   (  74-)  A
 111 ASP   (  90-)  A
 184 ASP   ( 172-)  A
 222 ASP   ( 210-)  A
 226 ASP   ( 214-)  A
 269 ASP   (  13-)  B
 292 ASP   (  36-)  B
 461 ASP   ( 210-)  B

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

  48 GLU   (  27-)  A
 168 GLU   ( 155-)  A
 232 GLU   ( 220-)  A
 270 GLU   (  14-)  B
 301 GLU   (  45-)  B
 338 GLU   (  82-)  B
 452 GLU   ( 201-)  B
 471 GLU   ( 220-)  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.

 174 PRO   ( 162-)  A      CG   CD    1.35   -4.5
 256 ARG   ( 244-)  A      C    O     1.39    7.7
 257 LYS   ( 245-)  A      N   -C     1.64   15.5
 495 ARG   ( 244-)  B      C    O     1.33    5.1
 496 LYS   ( 245-)  B      N   -C     1.54   10.7

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

 |  1.000051 -0.000917  0.000668|
 | -0.000917  1.000795 -0.000487|
 |  0.000668 -0.000487  0.997007|
Proposed new scale matrix

 |  0.020832  0.006230  0.008949|
 |  0.000016  0.021546  0.005380|
 | -0.000011  0.000008  0.017185|
With corresponding cell

    A    =  48.003  B   =  48.459  C    =  63.422
    Alpha=  97.274  Beta= 108.956  Gamma= 106.686

The CRYST1 cell dimensions

    A    =  48.000  B   =  48.400  C    =  63.600
    Alpha=  97.200  Beta= 109.000  Gamma= 106.600

Variance: 46.482
(Under-)estimated Z-score: 5.025

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.

   4 DGUA  (   4-)  C      N9   C8   N7  113.14    4.1
   5 DADE  (   5-)  C      C2'  C1'  N9  104.58   -6.0
   6 DADE  (   6-)  C      C2'  C1'  N9  104.43   -6.1
  12 DADE  (   1-)  D      C2'  C1'  N9  120.67    4.0
  15 DGUA  (   4-)  D      O4'  C1'  N9  111.04    4.1
  19 DTHY  (   8-)  D      C2'  C1'  N1  122.35    5.1
  83 ILE   (  62-)  A      CB   CG1  CD1  99.44   -6.8
 125 THR   ( 106-)  A      N    CA   C    99.31   -4.2
 150 HIS   ( 131-)  A      CG   ND1  CE1 109.62    4.0
 171 GLU   ( 158-)  A     -O   -C    N   116.21   -4.2
 172 ILE   ( 159-)  A     -C    N    CA  111.26   -5.8
 174 PRO   ( 162-)  A      CB   CG   CD   89.56   -5.2
 174 PRO   ( 162-)  A      CG   CD   N   122.98   13.2
 174 PRO   ( 162-)  A      CD   N    CA   96.03  -11.4
 256 ARG   ( 244-)  A      CA   C    O   109.95   -6.4
 257 LYS   ( 245-)  A     -O   -C    N   138.59    9.7
 327 HIS   (  71-)  B      CG   ND1  CE1 109.62    4.0
 360 THR   ( 106-)  B      N    CA   C    99.26   -4.3
 385 HIS   ( 131-)  B      CG   ND1  CE1 109.83    4.2
 388 ILE   ( 134-)  B      N    CA   C    99.88   -4.0
 495 ARG   ( 244-)  B      CA   C    O   113.13   -4.5
 496 LYS   ( 245-)  B     -O   -C    N   132.33    5.8
 496 LYS   ( 245-)  B     -CA  -C    N   104.84   -5.7

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  48 GLU   (  27-)  A
  95 ASP   (  74-)  A
 111 ASP   (  90-)  A
 168 GLU   ( 155-)  A
 184 ASP   ( 172-)  A
 222 ASP   ( 210-)  A
 226 ASP   ( 214-)  A
 232 GLU   ( 220-)  A
 269 ASP   (  13-)  B
 270 GLU   (  14-)  B
 292 ASP   (  36-)  B
 301 GLU   (  45-)  B
 338 GLU   (  82-)  B
 452 GLU   ( 201-)  B
 461 ASP   ( 210-)  B
 471 GLU   ( 220-)  B

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.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 256 ARG   ( 244-)  A      C     -6.9   -10.40     0.13
 495 ARG   ( 244-)  B      C    -12.7   -19.25     0.13
The average deviation= 1.276

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.

 305 ARG   (  49-)  B    5.69
  38 LYS   (  17-)  A    5.31
 259 LEU   (   3-)  B    4.55
 182 LEU   ( 170-)  A    4.49
 325 GLN   (  69-)  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 : 1.560

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.

 329 PRO   (  73-)  B    -2.9
  94 PRO   (  73-)  A    -2.9
 404 ILE   ( 153-)  B    -2.7
 350 THR   (  94-)  B    -2.7
 115 THR   (  94-)  A    -2.6
 148 ILE   ( 129-)  A    -2.4
 383 ILE   ( 129-)  B    -2.3
 372 THR   ( 118-)  B    -2.3
 137 THR   ( 118-)  A    -2.1
 117 THR   (  96-)  A    -2.0
 291 SER   (  35-)  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.

  91 ASN   (  70-)  A  Poor phi/psi
  93 TYR   (  72-)  A  PRO omega poor
  99 TYR   (  78-)  A  Poor phi/psi
 131 SER   ( 112-)  A  Poor phi/psi
 139 ASN   ( 120-)  A  Poor phi/psi
 241 LYS   ( 229-)  A  Poor phi/psi
 255 GLY   ( 243-)  A  Poor phi/psi
 256 ARG   ( 244-)  A  Poor phi/psi
 328 TYR   (  72-)  B  PRO omega poor
 366 SER   ( 112-)  B  Poor phi/psi
 374 ASN   ( 120-)  B  Poor phi/psi
 396 ALA   ( 142-)  B  omega poor
 438 THR   ( 187-)  B  Poor phi/psi
 480 LYS   ( 229-)  B  Poor phi/psi
 495 ARG   ( 244-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.721

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.

 297 SER   (  41-)  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!

   3 DADE  (   3-)  C      0
   4 DGUA  (   4-)  C      0
   5 DADE  (   5-)  C      0
   6 DADE  (   6-)  C      0
   7 DTHY  (   7-)  C      0
   8 DTHY  (   8-)  C      0
   9 DCYT  (   9-)  C      0
  10 DTHY  (  10-)  C      0
  11 DTHY  (  11-)  C      0
  12 DADE  (   1-)  D      0
  13 DADE  (   2-)  D      0
  14 DADE  (   3-)  D      0
  15 DGUA  (   4-)  D      0
  16 DADE  (   5-)  D      0
  17 DADE  (   6-)  D      0
  18 DTHY  (   7-)  D      0
  19 DTHY  (   8-)  D      0
  20 DCYT  (   9-)  D      0
  21 DTHY  (  10-)  D      0
  22 DTHY  (  11-)  D      0
  23 SER   (   2-)  A      0
  24 LEU   (   3-)  A      0
  38 LYS   (  17-)  A      0
  42 CYS   (  21-)  A      0
  44 ILE   (  23-)  A      0
And so on for a total of 202 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 : 2.356

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!

 455 GLY   ( 204-)  B   1.61   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]

 104 PRO   (  83-)  A    0.46 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].

 329 PRO   (  73-)  B   -62.2 half-chair C-beta/C-alpha (-54 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 395 VAL   ( 141-)  B      CB  <->  397 THR   ( 143-)  B      O      0.55    2.25  INTRA BF
  11 DTHY  (  11-)  C      N3  <->   13 DADE  (   2-)  D      N1     0.53    2.47  INTRA BF
   2 DADE  (   2-)  C      N1  <->   22 DTHY  (  11-)  D      N3     0.50    2.50  INTRA
  10 DTHY  (  10-)  C      C2' <->   11 DTHY  (  11-)  C      C7     0.48    2.72  INTRA BF
   7 DTHY  (   7-)  C      N3  <->   17 DADE  (   6-)  D      N1     0.46    2.54  INTRA
   3 DADE  (   3-)  C      N1  <->   21 DTHY  (  10-)  D      N3     0.44    2.56  INTRA
  12 DADE  (   1-)  D      C2' <->   13 DADE  (   2-)  D      C5'    0.35    2.85  INTRA
 326 ASN   (  70-)  B      ND2 <->  504 HOH   ( 312 )  B      O      0.35    2.35  INTRA BF
   6 DADE  (   6-)  C      N1  <->   18 DTHY  (   7-)  D      N3     0.31    2.69  INTRA
  39 TYR   (  18-)  A      CZ  <->  285 LYS   (  29-)  B      NZ     0.29    2.81  INTRA
 480 LYS   ( 229-)  B      NZ  <->  504 HOH   ( 282 )  B      O      0.28    2.42  INTRA
  13 DADE  (   2-)  D      C6  <->   14 DADE  (   3-)  D      N1     0.27    2.83  INTRA
  12 DADE  (   1-)  D      C2' <->   13 DADE  (   2-)  D      O4'    0.25    2.55  INTRA
  13 DADE  (   2-)  D      C6  <->   14 DADE  (   3-)  D      C2     0.25    2.95  INTRA
  70 ARG   (  49-)  A      NH1 <->  503 HOH   ( 511 )  A      O      0.23    2.47  INTRA
 168 GLU   ( 155-)  A      O   <->  171 GLU   ( 158-)  A      N      0.22    2.48  INTRA BF
 495 ARG   ( 244-)  B      N   <->  496 LYS   ( 245-)  B      N      0.22    2.38  INTRA B3
   9 DCYT  (   9-)  C      N3  <->   15 DGUA  (   4-)  D      N1     0.21    2.79  INTRA
  10 DTHY  (  10-)  C      C2' <->   11 DTHY  (  11-)  C      C5     0.21    2.99  INTRA BF
 483 ASN   ( 232-)  B      ND2 <->  504 HOH   ( 272 )  B      O      0.20    2.50  INTRA
   2 DADE  (   2-)  C      C3' <->  474 SER   ( 223-)  B      OG     0.20    2.60  INTRA BF
 465 ASP   ( 214-)  B      O   <->  469 ASN   ( 218-)  B      ND2    0.19    2.51  INTRA BL
 494 GLY   ( 243-)  B      C   <->  496 LYS   ( 245-)  B      N      0.19    2.71  INTRA
   4 DGUA  (   4-)  C      N1  <->   20 DCYT  (   9-)  D      N3     0.18    2.82  INTRA
   5 DADE  (   5-)  C      N7  <->  436 ASN   ( 185-)  B      ND2    0.17    2.83  INTRA BL
And so on for a total of 93 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

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.

 431 LEU   ( 180-)  B      -6.32
 192 LEU   ( 180-)  A      -6.24
 256 ARG   ( 244-)  A      -6.23
 233 ARG   ( 221-)  A      -6.17
 495 ARG   ( 244-)  B      -6.11
 472 ARG   ( 221-)  B      -5.74
 176 LYS   ( 164-)  A      -5.18
  92 HIS   (  71-)  A      -5.15
 452 GLU   ( 201-)  B      -5.11
 121 LYS   ( 102-)  A      -5.04
 118 ASN   (  97-)  A      -5.03

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.

  91 ASN   (  70-)  A   -4.02
  90 GLN   (  69-)  A   -3.46
 325 GLN   (  69-)  B   -3.43
 215 LYS   ( 203-)  A   -3.22
  89 GLN   (  68-)  A   -3.02
 496 LYS   ( 245-)  B   -2.98
 324 GLN   (  68-)  B   -2.97
 356 LYS   ( 102-)  B   -2.76
 409 GLU   ( 158-)  B   -2.76
 326 ASN   (  70-)  B   -2.73
 123 LYS   ( 104-)  A   -2.65
 358 LYS   ( 104-)  B   -2.64
 167 ASN   ( 154-)  A   -2.62
 411 PRO   ( 160-)  B   -2.57
 454 LYS   ( 203-)  B   -2.56

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

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

  87 PRO   (  66-)  A     -   91 ASN   (  70-)  A        -2.87
 322 PRO   (  66-)  B     -  326 ASN   (  70-)  B        -2.44

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

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.

 503 HOH   ( 547 )  A      O    -14.68   -2.97  -21.07
 503 HOH   ( 551 )  A      O    -15.45    0.30  -20.92
 503 HOH   ( 603 )  A      O    -27.31   -9.78   29.95
 503 HOH   ( 604 )  A      O    -25.63   -8.12   27.64

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.

 504 HOH   ( 287 )  B      O
 504 HOH   ( 307 )  B      O
 504 HOH   ( 331 )  B      O

Error: HIS, ASN, GLN side chain flips

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

  36 ASN   (  15-)  A
 139 ASN   ( 120-)  A
 271 ASN   (  15-)  B
 309 ASN   (  53-)  B
 327 HIS   (  71-)  B
 444 HIS   ( 193-)  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.

  48 GLU   (  27-)  A      N
  55 GLY   (  34-)  A      N
 100 LYS   (  79-)  A      N
 175 TYR   ( 163-)  A      N
 187 VAL   ( 175-)  A      N
 200 ASN   ( 188-)  A      ND2
 217 ILE   ( 205-)  A      N
 220 SER   ( 208-)  A      N
 234 THR   ( 222-)  A      N
 236 GLN   ( 224-)  A      N
 244 ASN   ( 232-)  A      N
 290 GLY   (  34-)  B      N
 326 ASN   (  70-)  B      N
 326 ASN   (  70-)  B      ND2
 340 ASN   (  84-)  B      N
 375 ILE   ( 121-)  B      N
 397 THR   ( 143-)  B      N
 405 ASN   ( 154-)  B      N
 414 TYR   ( 163-)  B      N
 416 GLY   ( 165-)  B      N
 426 VAL   ( 175-)  B      N
 446 HIS   ( 195-)  B      N
 459 SER   ( 208-)  B      N
 473 THR   ( 222-)  B      N
 496 LYS   ( 245-)  B      N
Only metal coordination for   66 GLU  (  45-) A      OE2

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+.

 500  CA   ( 502-)  A   -.-  -.-  Low probability ion. B= 81.1

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.

 503 HOH   ( 557 )  A      O  0.98  K  4 Ion-B H2O-B
 503 HOH   ( 614 )  A      O  0.86 NA  4 *2

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 :  -0.479
  2nd generation packing quality :  -1.748
  Ramachandran plot appearance   :  -1.605
  chi-1/chi-2 rotamer normality  :  -1.721
  Backbone conformation          :   0.135

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.551 (tight)
  Bond angles                    :   0.816
  Omega angle restraints         :   0.428 (tight)
  Side chain planarity           :   0.550 (tight)
  Improper dihedral distribution :   1.131
  B-factor distribution          :   0.867
  Inside/Outside distribution    :   0.990

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -1.2
  Ramachandran plot appearance   :  -1.0
  chi-1/chi-2 rotamer normality  :  -0.8
  Backbone conformation          :  -0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.551 (tight)
  Bond angles                    :   0.816
  Omega angle restraints         :   0.428 (tight)
  Side chain planarity           :   0.550 (tight)
  Improper dihedral distribution :   1.131
  B-factor distribution          :   0.867
  Inside/Outside distribution    :   0.990
==============

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.