WHAT IF Check report

This file was created 2012-06-08 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 pdb3izf.ent

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'.

 114 DGUA  ( 120-)  A  -   O4'
 114 DGUA  ( 120-)  A  -   C1'
 114 DGUA  ( 120-)  A  -   C2'
 114 DGUA  ( 120-)  A  -   N9
 114 DGUA  ( 120-)  A  -   C8
 114 DGUA  ( 120-)  A  -   N7
 114 DGUA  ( 120-)  A  -   C5
 114 DGUA  ( 120-)  A  -   C6
 114 DGUA  ( 120-)  A  -   O6
 114 DGUA  ( 120-)  A  -   N1
 114 DGUA  ( 120-)  A  -   C2
 114 DGUA  ( 120-)  A  -   N2
 114 DGUA  ( 120-)  A  -   N3
 114 DGUA  ( 120-)  A  -   C4
 115 DADE  ( 121-)  A  -   O4'
 115 DADE  ( 121-)  A  -   C1'
 115 DADE  ( 121-)  A  -   C2'
 115 DADE  ( 121-)  A  -   N9
 115 DADE  ( 121-)  A  -   C8
 115 DADE  ( 121-)  A  -   N7
 115 DADE  ( 121-)  A  -   C5
 115 DADE  ( 121-)  A  -   C6
 115 DADE  ( 121-)  A  -   N6
 115 DADE  ( 121-)  A  -   N1
 115 DADE  ( 121-)  A  -   C2
And so on for a total of 1505 lines.

Warning: C-terminal nitrogen atoms detected.

It is becoming habit to indicate that a residue is not the true C-terminus by including only the backbone N of the next residue. This has been observed in this PDB file.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. In many cases the N- or C-terminal residues are too disordered to see. In case of the N-terminus, you can see from the residue numbers if there are missing residues, but at the C-terminus this is impossible. Therefore, often the position of the backbone nitrogen of the first residue missing at the C-terminal end is calculated and added to indicate that there are missing residues. As a single N causes validation trouble, we remove these single-N-residues before doing the validation. But, if you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or removed N is the cause.

3245 DTHY  (3280-)  A  -
3244 DADE  (3279-)  A  -
3243 DCYT  (3278-)  A  -
3242 DTHY  (3277-)  A  -
3241 DGUA  (3276-)  A  -
3240 DTHY  (3275-)  A  -
3239 DADE  (3274-)  A  -
3238 DADE  (3273-)  A  -
3237 DCYT  (3272-)  A  -
3236 DGUA  (3271-)  A  -
3235 DTHY  (3270-)  A  -
3234 DTHY  (3269-)  A  -
3233 DADE  (3268-)  A  -
3232 DADE  (3267-)  A  -
3231 DGUA  (3266-)  A  -
3230 DCYT  (3265-)  A  -
3229 DGUA  (3264-)  A  -
3228 DGUA  (3263-)  A  -
3227 DTHY  (3262-)  A  -
3226 DCYT  (3261-)  A  -
3225 DGUA  (3260-)  A  -
3224 DTHY  (3259-)  A  -
3175 DADE  (3210-)  A  -
3174 DADE  (3209-)  A  -
3173 DGUA  (3208-)  A  -
And so on for a total of 75 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:

Temperature not mentioned in PDB file. This most likely means that the temperature record is absent.
Room temperature assumed

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.

   1 OGUA  (   1-)  A  -   P    OP2   1.60    6.8
   1 OGUA  (   1-)  A  -   O4'  C1'   1.32   -7.5
   1 OGUA  (   1-)  A  -   C1'  C2'   1.66   13.4
   2 OURA  (   2-)  A  -   C1'  C2'   1.62    9.6
   3 OURA  (   3-)  A  -   O4'  C1'   1.46    4.1
   4 OURA  (   4-)  A  -   O4'  C1'   1.47    4.5
   5 OGUA  (   5-)  A  -   O4'  C1'   1.51    7.8
   5 OGUA  (   5-)  A  -   C1'  C2'   1.42  -10.4
   6 OADE  (   6-)  A  -   O4'  C1'   1.48    5.7
   7 OCYT  (   7-)  A  -   O4'  C1'   1.70   23.6
   7 OCYT  (   7-)  A  -   C1'  C2'   1.45   -7.9
   8 OCYT  (   8-)  A  -   O4'  C1'   1.55   11.2
   8 OCYT  (   8-)  A  -   C1'  C2'   1.41  -11.9
   9 OURA  (   9-)  A  -   O4'  C1'   1.61   16.3
   9 OURA  (   9-)  A  -   C1'  C2'   1.30  -22.8
  10 OCYT  (  10-)  A  -   O4'  C1'   1.51    7.9
  10 OCYT  (  10-)  A  -   C1'  C2'   1.47   -5.7
  11 OADE  (  11-)  A  -   O4'  C1'   1.53    9.5
  11 OADE  (  11-)  A  -   C1'  C2'   1.47   -5.5
  13 OADE  (  13-)  A  -   O4'  C1'   1.55   11.4
  13 OADE  (  13-)  A  -   C1'  C2'   1.45   -7.6
  14 OURA  (  14-)  A  -   O4'  C1'   1.46    4.1
  15 OCYT  (  15-)  A  -   O4'  C1'   1.58   14.2
  15 OCYT  (  15-)  A  -   C1'  C2'   1.40  -13.0
  16 OADE  (  16-)  A  -   O4'  C1'   1.52    8.9
And so on for a total of 5332 lines.

Warning: High bond length deviations

Bond lengths were found to deviate more than normal from the mean standard bond lengths (standard values for protein residues were taken from Engh and Huber [REF], for DNA/RNA these values were taken from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is higher than 1.5 in this structure might indicate that the restraints used in the refinement were not strong enough. This will also occur if a different bond length dictionary is used.

RMS Z-score for bond lengths: 1.795
RMS-deviation in bond distances: 0.020

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.

   1 OGUA  (   1-)  A  -   OP1  P    OP2 106.13   -9.0
   1 OGUA  (   1-)  A  -   C4'  O4'  C1' 116.00    7.1
   1 OGUA  (   1-)  A  -   O4'  C1'  N9  124.52   16.3
   1 OGUA  (   1-)  A  -   C2'  C1'  N9   99.86   -8.5
   2 OURA  (   2-)  A  -   P   -C3* -O3* 137.82   15.1
   2 OURA  (   2-)  A  -   C3'  C4'  O4'  99.61   -4.2
   2 OURA  (   2-)  A  -   C4'  O4'  C1' 114.48    5.4
   2 OURA  (   2-)  A  -   O4'  C1'  C2'  99.95   -4.6
   2 OURA  (   2-)  A  -   O4'  C1'  N1  119.81   11.6
   2 OURA  (   2-)  A  -   C2'  C1'  N1  103.44   -6.2
   3 OURA  (   3-)  A  -   P   -C3* -O3* 112.51   -6.0
   3 OURA  (   3-)  A  -   O4'  C1'  N1  115.23    7.0
   4 OURA  (   4-)  A  -   O4'  C1'  N1  115.21    7.0
   5 OGUA  (   5-)  A  -   N9   C8   N7  113.12    4.0
   7 OCYT  (   7-)  A  -   P   -C3* -O3* 127.47    6.5
   7 OCYT  (   7-)  A  -   C3'  C2'  C1' 109.29    8.7
   7 OCYT  (   7-)  A  -   O4'  C1'  C2'  98.22   -5.8
   7 OCYT  (   7-)  A  -   C2'  C1'  N1  125.62    7.6
   8 OCYT  (   8-)  A  -   P   -C3* -O3* 141.66   18.3
   8 OCYT  (   8-)  A  -   C2'  C1'  N1  120.56    4.5
   9 OURA  (   9-)  A  -   P   -C3* -O3* 147.35   23.0
   9 OURA  (   9-)  A  -   C3'  C4'  C5' 126.51    7.3
   9 OURA  (   9-)  A  -   C3'  C4'  O4'  98.55   -5.0
   9 OURA  (   9-)  A  -   C4'  O4'  C1' 104.64   -5.5
   9 OURA  (   9-)  A  -   C2'  C1'  N1  124.16    6.7
And so on for a total of 9962 lines.

Warning: Uncalibrated side chain planarity problems

The residues listed in the table below contain a planar group that was found to deviate from planarity by more than 0.10 Angstrom RMS. Please be aware that this check cannot be callibrated and that the cutoff of 0.10 Angstrom thus is a wild guess.

1730 OGUA  (1766-)  A  -   0.12
1732 OURA  (1768-)  A  -   0.12
 721 OURA  ( 731-)  A  -   0.11
2511 OADE  (2562-)  A  -   0.11
 723 OGUA  ( 733-)  A  -   0.10
Since there is no protein, no ramachandran check was performed.
Since there is no protein, no torsion angle evaluation was performed.
Since there is no protein, no ramachandran check was performed.
Since there is no protein, no rotamer check was performed.
Since there is no protein, no backbone conformation check was performed.
Since there is no protein, no ramachandran check was performed.
Since there is no protein, no backbone oxygen evaluation was performed.

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short 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.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

2561 OURA  (2612-)  A  -   C1'  <->  2751 OADE  (2803-)  A  -   C2   1.08    2.12  INTRA BL
2182 OADE  (2220-)  A  -   N6   <->  2183 OGUA  (2221-)  A  -   C2   0.98    2.12  INTRA BF
 338 OGUA  ( 345-)  A  -   O2'  <->  3303 OGUA  (  25-)  B  -   N2   0.93    1.77  INTRA BL
2941 OADE  (2994-)  A  -   N1   <->  3087 OADE  (3142-)  A  -   N6   0.88    2.12  INTRA BL
1612 OADE  (1647-)  A  -   N6   <->  1772 OGUA  (1808-)  A  -   O2'  0.81    1.89  INTRA BF
2581 OGUA  (2632-)  A  -   N1   <->  2595 OCYT  (2646-)  A  -   N3   0.72    2.28  INTRA BL
1888 OURA  (1925-)  A  -   N3   <->  2150 OADE  (2188-)  A  -   N1   0.69    2.31  INTRA BL
1610 OURA  (1645-)  A  -   N3   <->  1774 OADE  (1810-)  A  -   N1   0.68    2.32  INTRA BF
 653 OADE  ( 660-)  A  -   N7   <->  1399 OCYT  (1432-)  A  -   N4   0.67    2.33  INTRA BL
3466 OGUA  (  30-)  C  -   N2   <->  3483 OCYT  (  47-)  C  -   N3   0.67    2.33  INTRA BL
1247 OGUA  (1268-)  A  -   N2   <->  1252 OADE  (1273-)  A  -   N7   0.66    2.34  INTRA BL
2561 OURA  (2612-)  A  -   O4'  <->  2751 OADE  (2803-)  A  -   N1   0.65    1.90  INTRA BL
2241 OADE  (2279-)  A  -   N1   <->  2248 OURA  (2286-)  A  -   N3   0.64    2.36  INTRA BL
1591 OADE  (1625-)  A  -   N6   <->  1783 OURA  (1819-)  A  -   O4   0.64    2.06  INTRA BF
2965 OURA  (3019-)  A  -   N3   <->  2981 OADE  (3035-)  A  -   N1   0.63    2.37  INTRA BL
 365 OADE  ( 372-)  A  -   N6   <->   366 OADE  ( 373-)  A  -   N1   0.63    2.37  INTRA BL
1648 OADE  (1683-)  A  -   N7   <->  1649 OURA  (1684-)  A  -   C4   0.63    2.47  INTRA BF
2182 OADE  (2220-)  A  -   N6   <->  2183 OGUA  (2221-)  A  -   N2   0.62    2.23  INTRA BF
1648 OADE  (1683-)  A  -   C8   <->  1649 OURA  (1684-)  A  -   C5   0.61    2.59  INTRA BF
2561 OURA  (2612-)  A  -   O4'  <->  2751 OADE  (2803-)  A  -   C2   0.60    2.20  INTRA BL
2412 OGUA  (2450-)  A  -   N2   <->  2458 OCYT  (2496-)  A  -   O2   0.60    2.10  INTRA BL
2817 OURA  (2869-)  A  -   O2   <->  2821 OURA  (2873-)  A  -   C5   0.59    2.21  INTRA BL
1833 OCYT  (1870-)  A  -   C3'  <->  1834 OURA  (1871-)  A  -   C5   0.59    2.51  INTRA BL
1320 OURA  (1341-)  A  -   N3   <->  1333 OADE  (1363-)  A  -   N1   0.58    2.42  INTRA BF
3225 OCYT  (3338-)  A  -   O2   <->  3253 OGUA  (3366-)  A  -   N2   0.58    2.12  INTRA BF
And so on for a total of 2149 lines.

Water, ion, and hydrogenbond related checks

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.

  19 OURA  (  19-)  A  -   N3
  21 OGUA  (  21-)  A  -   N1
  24 OGUA  (  24-)  A  -   N1
  25 OURA  (  25-)  A  -   N3
  26 OADE  (  26-)  A  -   N6
  40 OGUA  (  41-)  A  -   N1
  42 OADE  (  43-)  A  -   N6
  54 OGUA  (  55-)  A  -   N1
  63 OGUA  (  64-)  A  -   N2
  68 OCYT  (  69-)  A  -   N4
  76 OADE  (  77-)  A  -   N6
  77 OURA  (  78-)  A  -   N3
  94 OADE  (  95-)  A  -   N6
 103 OGUA  ( 104-)  A  -   N1
 113 OADE  ( 114-)  A  -   N6
 120 OURA  ( 126-)  A  -   N3
 123 OURA  ( 129-)  A  -   N3
 133 OGUA  ( 139-)  A  -   N1
 156 OGUA  ( 162-)  A  -   N1
 170 OURA  ( 177-)  A  -   N3
 171 OURA  ( 178-)  A  -   N3
 175 OURA  ( 182-)  A  -   N3
 181 OURA  ( 188-)  A  -   N3
 189 OGUA  ( 196-)  A  -   N2
 199 OGUA  ( 206-)  A  -   N2
And so on for a total of 396 lines.

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.

Final summary