WHAT IF Check report

This file was created 2011-12-14 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 pdb1j8g.ent

Checks that need to be done early-on in validation

Error: Matthews Coefficient (Vm) too low

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

The fact that it is lower than 1.5 in this structure might be caused by a miscalculated value of Z on the CRYST1 card.

Molecular weight of all polymer chains: 9158.424
Volume of the Unit Cell V= 96905.234
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z low: Vm= 1.323
Vm by authors and this calculated Vm do not agree very well

Warning: Atoms on special positions with too high occupancy

Atoms detected at special positions with too high occupancy. These atoms will upon expansion by applying the symmetry matrices, result in multiple atoms at (nearly) the same position.

Atoms at special positions should have an occupancy that is smaller than 1/N where N is the multiplicity of the symmetry operator. So, an atom on a 2-fold axis should have occupancy less or equal 0.5, for a 3-fold axis this is 0.33, etc. If the occupancy is too high, application of the symmetry matrices will result in the presence of more than one atom at (nearly) the same position. WHAT IF will certainly report this as bumps, but other things will also go wrong. E.g. 3 waters at the same position will make three times more hydrogen bonds, they will be counted three times in packing analysis, etc. So, I suggest you first fix this problem and run WHAT IF again on the fixed PDB file. An atom is considered to be located at a special position if it is within 0.3 Angstrom from one of its own symmetry copies. See also the next check...

  28  NA   ( 512-)  A  - ANA

Warning: Ligands for which a topology was generated automatically

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

  38 SPM   (  62-)  B  -

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

  28  NA   ( 512-)  A  -

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

  28  NA   ( 512-)  A  -

Non-validating, descriptive output paragraph

Warning: Ions bound to the wrong chain

The ions listed in the table have a chain identifier that is the same as one of the protein, nucleic acid, or sugar chains. However, the ion seems bound to protein, nucleic acid, or sugar, with another chain identifier.

Obviously, this is not wrong, but it is confusing for users of this PDB file.

  31  CA   ( 510-)  A  -

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

Error: Weights outside the 0.0 -- 1.0 range

The atoms listed in the table below have their weight/occupancy outside the 0.0-1.0 range. This problem is not hampering proper WHAT IF functioning, but it is indicative of problems with the X-ray refinement.

  41 HOH   ( 127 )  C    B O   1.42

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

  24 OURA  (  36-)  D  -   0.85

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

Warning: Average B-factor problem

The average B-factor for all buried protein atoms normally lies between 10-30. Values around 3-10 are expected for X-ray studies performed at liquid nitrogen temperature.

Because of the extreme value for the average B-factor, no further analysis of the B-factors is performed.

Average B-factor for buried atoms : 0.000

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.

   6 OURA  (   6-)  A  -   C4   O4    1.20   -4.4
   7 OURA  (  11-)  B  -   C1'  N1    1.51    4.0
   7 OURA  (  11-)  B  -   N1   C2    1.34   -4.7
   7 OURA  (  11-)  B  -   C4   O4    1.29    7.3
  13 OURA  (  21-)  C  -   C6   C5    1.38    4.3
  21 OGUA  (  33-)  D  -   C8   N7    1.33    4.4

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 OGUA  (   4-)  A  -   P   -C3* -O3* 124.80    4.3
   7 OURA  (  11-)  B  -   N1   C6   C5  120.64   -4.1
   7 OURA  (  11-)  B  -   C5   C4   N3  117.39    4.6
   7 OURA  (  11-)  B  -   C4   N3   C2  123.22   -6.3
   7 OURA  (  11-)  B  -   N3   C2   O2  118.52   -5.3
   9 OGUA  (  13-)  B  -   N9   C8   N7  113.22    4.2
  11 OGUA  (  15-)  B  -   N9   C8   N7  113.32    4.4
  15 OGUA  (  23-)  C  -   N9   C8   N7  113.43    4.7
  18 OURA  (  26-)  C  -   C4   N3   C2  129.68    4.5
  22 OGUA  (  34-)  D  -   N9   C8   N7  113.80    5.4
  24 OURA  (  36-)  D  -   O5*  P   -O3* 118.14    7.4
  24 OURA  (  36-)  D  -   C3'  C4'  C5' 109.14   -4.2
  24 OURA  (  36-)  D  -   C3'  C2'  C1'  80.82  -23.0
  24 OURA  (  36-)  D  -   O3'  C3'  C4' 121.63    4.2
  24 OURA  (  36-)  D  -   O3'  C3'  C2' 138.56    9.8
  24 OURA  (  36-)  D  -   OP1  P    OP2 112.55   -4.7
  24 OURA  (  36-)  D  -   C5'  C4'  O4' 146.69   26.8
  24 OURA  (  36-)  D  -   C4'  O4'  C1'  84.22  -28.2
  24 OURA  (  36-)  D  -   O4'  C1'  C2' 131.37   17.8
  24 OURA  (  36-)  D  -   C5   C4   O4  135.90   16.7
  24 OURA  (  36-)  D  -   O4   C4   N3  110.83  -12.2
  24 OURA  (  36-)  D  -   O2'  C2'  C3'  92.45   -7.2

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.

  41 HOH   ( 127 )  C    A O   <->   41 HOH   ( 127 )  C    B O      1.15    1.05  INTRA
  24 OURA  (  36-)  D  -   C5  <->   42 HOH   (  82 )  D      O      1.15    1.65  INTRA BL
  24 OURA  (  36-)  D  -   N3  <->   42 HOH   (  95 )  D      O      0.41    2.29  INTRA BL
  41 HOH   ( 125 )  C      O   <->   41 HOH   ( 127 )  C    B O      0.34    1.86  INTRA

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.

  39 HOH   ( 146 )  A      O      4.97   34.20   16.53
  39 HOH   ( 156 )  A    B O      2.23   33.21   16.38
  39 HOH   ( 187 )  A      O      6.92   26.48   40.76
  39 HOH   ( 191 )  A    A O     -7.06   27.43   38.07
  39 HOH   ( 192 )  A      O     -6.14   26.39   41.25
  39 HOH   ( 202 )  A    B O     -5.48   27.23   34.23
  41 HOH   ( 125 )  C      O     10.89   23.32    9.81
  41 HOH   ( 127 )  C    A O     10.55   21.39   11.89
  41 HOH   ( 127 )  C    B O     10.47   22.20   11.23
  41 HOH   ( 200 )  C    A O      8.25   23.25    8.05
  41 HOH   ( 204 )  C    A O      6.95   30.06   14.15
  41 HOH   ( 204 )  C    B O      7.04   30.46   13.15
  41 HOH   ( 205 )  C    A O      3.61   32.95   14.62
  41 HOH   ( 205 )  C    B O      4.90   31.87   14.43

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+.

  27  CA   ( 511-)  A  -    0.47   0.64 Scores about as good as NA *1 and *2
  28  NA   ( 512-)  A  -  -.-  -.-  Part of ionic cluster *S
  28  NA   ( 512-)  A  -    1.23   0.99 Scores about as good as CA (Few ligands (4) ) *S ; *1 and *2
  31  CA   ( 510-)  A  -    0.47   0.66 Scores about as good as NA *1 and *2
  32  NA   ( 513-)  B  -  -.-  -.-  Part of ionic cluster *S
  35  CA   ( 509-)  C  -    0.69   0.84 Scores about as good as NA *1 and *2

Final summary