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.
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
38 SPM ( 62-) B -
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 -
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 -
Obviously, this is not wrong, but it is confusing for users of this PDB file.
31 CA ( 510-) A -
41 HOH ( 127 ) C B O 1.42
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
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
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
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
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
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
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