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.
128 GDP ( 1-) B -
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.
18 GLN (1353-) B - CG 26 ASP (1375-) B - CB 26 ASP (1375-) B - CG 26 ASP (1375-) B - OD1 26 ASP (1375-) B - OD2 38 ARG (1398-) B - CG 38 ARG (1398-) B - CD 38 ARG (1398-) B - NE 39 GLU (1399-) B - CG 39 GLU (1399-) B - CD 39 GLU (1399-) B - OE1 39 GLU (1399-) B - OE2 51 GLN (1411-) B - CB 51 GLN (1411-) B - CG 52 ARG (1412-) B - CD 63 LYS (1423-) B - CG 63 LYS (1423-) B - CD 63 LYS (1423-) B - CE 63 LYS (1423-) B - NZ 65 GLN (1425-) B - CB 65 GLN (1425-) B - CG 65 GLN (1425-) B - CD 65 GLN (1425-) B - OE1 65 GLN (1425-) B - NE2 67 GLU (1427-) B - CG 67 GLU (1427-) B - CD 67 GLU (1427-) B - OE1 67 GLU (1427-) B - OE2 69 ASP (1429-) B - OD1 69 ASP (1429-) B - OD2 84 SER (1444-) B - CB 84 SER (1444-) B - OG 108 ARG (1483-) B - CB 108 ARG (1483-) B - CG 118 GLU (1493-) B - CB 118 GLU (1493-) B - CG
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: B
Coordinate problems, unexpected atoms, B-factor and occupancy checks
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. The header of the PDB file states that TLS groups
were used. So, if WHAT IF complains about your B-factors, while 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:
Number of TLS groups mentione in PDB file header: 13
Crystal temperature (K) :100.000
Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
Chain identifier: B
Nomenclature related problems
Warning: Arginine nomenclature problem
The arginine residues listed in the table below have their N-H-1 and N-H-2
38 ARG (1398-) B 121 ARG (1501-) B
55 TYR (1415-) B
76 PHE (1436-) B
23 ASP (1372-) B 26 ASP (1375-) B 109 ASP (1484-) B
117 GLU (1492-) B
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.
90 VAL (1450-) B CA CB 1.63 5.2 113 VAL (1488-) B CA CB 1.62 4.7
45 HIS (1405-) B C CA CB 119.93 5.2 74 TRP (1434-) B C CA CB 100.38 -5.1 93 HIS (1453-) B CG ND1 CE1 109.87 4.3 114 ASN (1489-) B N CA C 99.07 -4.3 124 ILE (1504-) B C CA CB 118.05 4.2
23 ASP (1372-) B 26 ASP (1375-) B 38 ARG (1398-) B 109 ASP (1484-) B 117 GLU (1492-) B 121 ARG (1501-) B
114 ASN (1489-) B 4.14
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.
68 VAL (1428-) B -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.
16 LEU (1350-) B omega poor 50 THR (1410-) B omega poor 55 TYR (1415-) B omega poor 60 ASP (1420-) B omega poor 67 GLU (1427-) B omega poor 84 SER (1444-) B omega poor 93 HIS (1453-) B Poor phi/psi 113 VAL (1488-) B omega poor 114 ASN (1489-) B omega poor chi-1/chi-2 correlation Z-score : -3.680
chi-1/chi-2 correlation Z-score : -3.680
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!
4 MSE (1338-) B 0 6 VAL (1340-) B 0 8 ASN (1342-) B 0 9 THR (1343-) B 0 11 SER (1345-) B 0 16 LEU (1350-) B 0 17 LEU (1351-) B 0 18 GLN (1353-) B 0 19 LEU (1354-) B 0 20 MSE (1355-) B 0 21 GLY (1370-) B 0 22 ILE (1371-) B 0 27 TRP (1376-) B 0 28 PRO (1377-) B 0 29 LEU (1388-) B 0 30 VAL (1389-) B 0 31 LEU (1390-) B 0 32 VAL (1392-) B 0 33 TRP (1393-) B 0 36 ALA (1396-) B 0 49 MSE (1409-) B 0 50 THR (1410-) B 0 52 ARG (1412-) B 0 61 LEU (1421-) B 0 63 LYS (1423-) B 0And so on for a total of 60 lines.
Standard deviation of omega values : 8.519
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]
86 PRO (1446-) B 0.17 LOW
105 PRO (1480-) B -65.4 envelop C-beta (-72 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.
109 ASP (1484-) B CG <-> 110 TYR (1485-) B N 0.34 2.66 INTRA BF 72 LYS (1432-) B CG <-> 104 PHE (1479-) B CZ 0.22 2.98 INTRA 95 ASP (1455-) B OD2 <-> 128 GDP ( 1-) B N2 0.21 2.49 INTRA 72 LYS (1432-) B N <-> 73 PRO (1433-) B CD 0.21 2.79 INTRA 1 MSE (1335-) B CE <-> 31 LEU (1390-) B CD2 0.21 2.99 INTRA 8 ASN (1342-) B O <-> 11 SER (1345-) B OG 0.20 2.20 INTRA BL 45 HIS (1405-) B ND1 <-> 47 HIS (1407-) B N 0.18 2.82 INTRA BL 110 TYR (1485-) B CE2 <-> 112 PHE (1487-) B CE2 0.14 3.06 INTRA BF 66 ALA (1426-) B N <-> 67 GLU (1427-) B N 0.13 2.47 INTRA B3 72 LYS (1432-) B CD <-> 104 PHE (1479-) B CZ 0.13 3.07 INTRA 123 THR (1503-) B O <-> 125 ILE (1505-) B N 0.11 2.59 INTRA BF 23 ASP (1372-) B OD2 <-> 25 LYS (1374-) B NZ 0.11 2.59 INTRA BF 115 ALA (1490-) B N <-> 128 GDP ( 1-) B O6 0.11 2.59 INTRA 44 THR (1404-) B C <-> 45 HIS (1405-) B C 0.05 2.75 INTRA BL 3 LEU (1337-) B O <-> 33 TRP (1393-) B N 0.03 2.67 INTRA BL 61 LEU (1421-) B N <-> 62 SER (1422-) B N 0.03 2.57 INTRA BL 13 LYS (1347-) B NZ <-> 36 ALA (1396-) B O 0.02 2.68 INTRA BL 13 LYS (1347-) B CE <-> 35 PHE (1395-) B O 0.02 2.78 INTRA BL 69 ASP (1429-) B C <-> 71 MSE (1431-) B N 0.01 2.89 INTRA BL
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.
2 LYS (1336-) B -6.52 108 ARG (1483-) B -5.99 118 GLU (1493-) B -5.98 81 ARG (1441-) B -5.79 121 ARG (1501-) B -5.62 65 GLN (1425-) B -5.26
The protein is probably threaded correctly, but either poorly refined, or it is just a protein with an unusual (but correct) structure. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].
Average for range 1 - 125 : -1.523
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
Chain identifier: B
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: B
Water, ion, and hydrogenbond related checks
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.
114 ASN (1489-) B
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.
3 LEU (1337-) B N 7 GLY (1341-) B N 10 GLY (1344-) B N 12 GLY (1346-) B N 13 LYS (1347-) B N 13 LYS (1347-) B NZ 15 THR (1349-) B N 27 TRP (1376-) B N 30 VAL (1389-) B N 59 TYR (1419-) B OH 60 ASP (1420-) B N 64 GLY (1424-) B N 68 VAL (1428-) B N 69 ASP (1429-) B N 71 MSE (1431-) B N 81 ARG (1441-) B NH1 93 HIS (1453-) B N 102 LEU (1474-) B N 104 PHE (1479-) B N 109 ASP (1484-) B N 110 TYR (1485-) B N 111 HIS (1486-) B ND1 115 ALA (1490-) B N
Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.
Waters are not listed by this option.
34 ASP (1394-) B OD1
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+.
127 MG ( 2-) B -.- -.- Too few ligands (3)
95 ASP (1455-) B H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
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 : -2.558 2nd generation packing quality : -1.969 Ramachandran plot appearance : -2.698 chi-1/chi-2 rotamer normality : -3.680 (poor) Backbone conformation : 1.224
Bond lengths : 0.960 Bond angles : 1.011 Omega angle restraints : 1.549 (loose) Side chain planarity : 0.724 Improper dihedral distribution : 1.088 B-factor distribution : 1.256 Inside/Outside distribution : 1.093
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 : 2.43
Structure Z-scores, positive is better than average:
1st generation packing quality : -2.0 2nd generation packing quality : -0.7 Ramachandran plot appearance : -0.7 chi-1/chi-2 rotamer normality : -1.8 Backbone conformation : 1.7
Bond lengths : 0.960 Bond angles : 1.011 Omega angle restraints : 1.549 (loose) Side chain planarity : 0.724 Improper dihedral distribution : 1.088 B-factor distribution : 1.256 Inside/Outside distribution : 1.093 ==============
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.