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.
121 RAP ( 225-) A -
Plausible side chain atoms were detected with (near) zero occupancy
When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.
1 GLU ( 106-) A - CD
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
Coordinate problems, unexpected atoms, B-factor and occupancy checks
Warning: B-factors outside the range 0.0 - 100.0
In principle, B-factors can have a very wide range of values, but in
practice, B-factors should not be zero while B-factors above 100.0
are a good indicator that the location of that atom is meaningless. Be
aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms
with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with
a B-factor of zero were observed.
47 SER ( 152-) A High 48 SER ( 153-) A High 49 LYS ( 154-) A High 50 LYS ( 155-) A High 51 LYS ( 156-) A High 52 LYS ( 157-) A High 53 ASN ( 158-) A High
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.
1 GLU ( 106-) A 0.94 2 GLY ( 107-) A 0.50
Obviously, the temperature at which the X-ray data was collected has some importance too:
Number of TLS groups mentione in PDB file header: 0
Crystal temperature (K) :100.000
Error: The B-factors of bonded atoms show signs of over-refinement
For each of the bond types in a protein a distribution was derived for the
difference between the square roots of the B-factors of the two atoms. All
bonds in the current protein were scored against these distributions. The
number given below is the RMS Z-score over the structure. For a structure
with completely restrained B-factors within residues, this value will be
around 0.35, for extremely high resolution structures refined with free
isotropic B-factors this number is expected to be near 1.0. Any value over
1.5 is sign of severe over-refinement of B-factors.
RMS Z-score : 1.563 over 793 bonds
Average difference in B over a bond : 4.11
RMS difference in B over a bond : 5.81
Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
Chain identifier: A
Nomenclature related problems
Warning: Arginine nomenclature problem
The arginine residues listed in the table below have their N-H-1 and N-H-2
68 ARG ( 173-) A
111 PHE ( 216-) A
117 ASP ( 222-) A 119 ASP ( 224-) A
1 GLU ( 106-) A
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.
37 GLY ( 142-) A C O 1.15 -4.1 58 SER ( 163-) A N CA 1.35 -5.5 107 THR ( 212-) A N CA 1.34 -5.9
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
| 1.013859 -0.000966 0.003668| | -0.000966 1.013880 -0.002382| | 0.003668 -0.002382 1.014382|Proposed new scale matrix
| 0.011517 0.000011 -0.000042| | 0.000011 0.011516 0.000027| | -0.000067 0.000044 0.018569|With corresponding cell
A = 86.833 B = 86.835 C = 53.854 Alpha= 90.269 Beta= 89.585 Gamma= 90.110
The CRYST1 cell dimensions
A = 85.649 B = 85.649 C = 53.090 Alpha= 90.000 Beta= 90.000 Gamma= 90.000
(Under-)estimated Z-score: 20.518
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.
58 SER ( 163-) A -C N CA 130.75 5.0
1 GLU ( 106-) A 68 ARG ( 173-) A 117 ASP ( 222-) A 119 ASP ( 224-) A
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.
88 GLU ( 193-) A C 6.6 9.50 -0.03 The average deviation= 1.354
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.
42 THR ( 147-) A -2.2 102 LYS ( 207-) A -2.1
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.
2 GLY ( 107-) A PRO omega poor 16 LYS ( 121-) A Poor phi/psi 48 SER ( 153-) A Poor phi/psi 92 ALA ( 197-) A Poor phi/psi 102 LYS ( 207-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -0.781
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!
4 PRO ( 109-) A 0 5 LYS ( 110-) A 0 15 ASP ( 120-) A 0 16 LYS ( 121-) A 0 17 THR ( 122-) A 0 18 ASN ( 123-) A 0 22 LYS ( 127-) A 0 34 LEU ( 139-) A 0 41 ASP ( 146-) A 0 46 THR ( 151-) A 0 47 SER ( 152-) A 0 48 SER ( 153-) A 0 50 LYS ( 155-) A 0 51 LYS ( 156-) A 0 52 LYS ( 157-) A 0 53 ASN ( 158-) A 0 58 SER ( 163-) A 0 61 VAL ( 166-) A 0 63 VAL ( 168-) A 0 65 LYS ( 170-) A 0 66 VAL ( 171-) A 0 79 LYS ( 184-) A 0 91 TRP ( 196-) A 0 92 ALA ( 197-) A 0 93 TYR ( 198-) A 0 96 LYS ( 201-) A 0 98 GLN ( 203-) A 0 102 LYS ( 207-) A 0 105 PRO ( 210-) A 0 117 ASP ( 222-) A 0 3 PRO ( 108-) A 1 6 TYR ( 111-) A 1 11 LEU ( 116-) A 1 21 LYS ( 126-) A 1 29 TRP ( 134-) A 1 40 PHE ( 145-) A 1 54 ALA ( 159-) A 1 67 ILE ( 172-) A 1 78 SER ( 183-) A 1 88 GLU ( 193-) A 1 95 LYS ( 200-) A 1 116 VAL ( 221-) A 1 12 LYS ( 117-) A 2 27 HIS ( 132-) A 2 36 ASP ( 141-) A 2 43 ASN ( 148-) A 2 45 GLN ( 150-) A 2 49 LYS ( 154-) A 2 59 PHE ( 164-) A 2 106 ASN ( 211-) A 2
4 PRO ( 109-) A 0.17 LOW 104 PRO ( 209-) A 0.14 LOW
3 PRO ( 108-) A 30.5 envelop C-delta (36 degrees) 56 PRO ( 161-) A 33.9 envelop C-delta (36 degrees) 89 PRO ( 194-) A 105.1 envelop C-beta (108 degrees)
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.
49 LYS ( 154-) A CG <-> 53 ASN ( 158-) A ND2 0.93 2.17 INTRA BF 121 RAP ( 225-) A C51 <-> 122 HOH ( 31 ) A O 0.90 1.90 INTRA 49 LYS ( 154-) A CD <-> 53 ASN ( 158-) A ND2 0.80 2.30 INTRA BF 48 SER ( 153-) A O <-> 52 LYS ( 157-) A CD 0.32 2.48 INTRA BF 65 LYS ( 170-) A NZ <-> 122 HOH ( 31 ) A O 0.25 2.45 INTRA BF 52 LYS ( 157-) A CG <-> 53 ASN ( 158-) A N 0.23 2.77 INTRA BF 72 GLU ( 177-) A OE1 <-> 122 HOH ( 65 ) A O 0.21 2.19 INTRA BL 52 LYS ( 157-) A NZ <-> 53 ASN ( 158-) A ND2 0.20 2.65 INTRA BF 49 LYS ( 154-) A CA <-> 52 LYS ( 157-) A CG 0.15 3.05 INTRA BF 112 GLU ( 217-) A CG <-> 122 HOH ( 291 ) A O 0.11 2.69 INTRA BF 49 LYS ( 154-) A CE <-> 53 ASN ( 158-) A ND2 0.08 3.02 INTRA BF 27 HIS ( 132-) A ND1 <-> 58 SER ( 163-) A A OG 0.07 2.63 INTRA BF 49 LYS ( 154-) A N <-> 50 LYS ( 155-) A N 0.06 2.54 INTRA BF 18 ASN ( 123-) A ND2 <-> 122 HOH ( 52 ) A O 0.02 2.68 INTRA 119 ASP ( 224-) A O <-> 122 HOH ( 267 ) A O 0.02 2.38 INTRA BF 49 LYS ( 154-) A NZ <-> 122 HOH ( 277 ) A O 0.01 2.69 INTRA BF 43 ASN ( 148-) A N <-> 44 ILE ( 149-) A N 0.01 2.59 INTRA BL 1 GLU ( 106-) A N <-> 122 HOH ( 279 ) A O 0.01 2.69 INTRA BF 49 LYS ( 154-) A C <-> 50 LYS ( 155-) A C 0.01 2.79 INTRA BF
Chain identifier: A
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.
93 TYR ( 198-) A -6.49 96 LYS ( 201-) A -5.85 65 LYS ( 170-) A -5.71 95 LYS ( 200-) A -5.12
Chain identifier: A
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.
101 ALA ( 206-) A -3.25 102 LYS ( 207-) A -3.08
The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.
100 ASP ( 205-) A - 103 ILE ( 208-) A -2.50
Chain identifier: A
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.
122 HOH ( 64 ) A O 22.39 11.45 20.76 122 HOH ( 92 ) A O 3.50 40.67 33.66 122 HOH ( 98 ) A O 1.27 41.88 3.37 122 HOH ( 101 ) A O 17.94 14.27 17.36 122 HOH ( 257 ) A O 17.24 42.68 14.56 122 HOH ( 286 ) A O 8.02 33.17 -1.11
122 HOH ( 239 ) A O
18 ASN ( 123-) A 53 ASN ( 158-) A
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.
5 LYS ( 110-) A N 49 LYS ( 154-) A N 50 LYS ( 155-) A N 66 VAL ( 171-) A N 67 ILE ( 172-) A N 70 TRP ( 175-) A NE1 90 GLU ( 195-) A N 93 TYR ( 198-) A OH
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.
122 HOH ( 6 ) A O 1.09 K 4 122 HOH ( 13 ) A O 1.09 K 4 122 HOH ( 39 ) A O 0.98 K 4 Ion-B H2O-B 122 HOH ( 96 ) A O 0.98 K 5 Ion-B 122 HOH ( 258 ) A O 0.95 K 4 Ion-B
71 ASP ( 176-) A H-bonding suggests Asn; but Alt-Rotamer
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 : -1.247 2nd generation packing quality : -2.245 Ramachandran plot appearance : 1.823 chi-1/chi-2 rotamer normality : -0.781 Backbone conformation : 0.050
Bond lengths : 1.383 Bond angles : 0.859 Omega angle restraints : 0.937 Side chain planarity : 0.650 (tight) Improper dihedral distribution : 1.139 B-factor distribution : 1.563 (loose) Inside/Outside distribution : 0.941
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 : 1.95
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.3 2nd generation packing quality : -1.9 Ramachandran plot appearance : 2.0 chi-1/chi-2 rotamer normality : -0.3 Backbone conformation : -0.7
Bond lengths : 1.383 Bond angles : 0.859 Omega angle restraints : 0.937 Side chain planarity : 0.650 (tight) Improper dihedral distribution : 1.139 B-factor distribution : 1.563 (loose) Inside/Outside distribution : 0.941 ==============
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.