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.
163 EPE (1002-) A - 164 ACT (1001-) A -
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: 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
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 : 1.605 over 1137 bonds
Average difference in B over a bond : 3.59
RMS difference in B over a bond : 4.91
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: Tyrosine convention problem
The tyrosine residues listed in the table below have their chi-2 not between
-90.0 and 90.0
44 TYR ( 61-) A 105 TYR ( 122-) A
66 PHE ( 83-) A 130 PHE ( 147-) A 142 PHE ( 159-) A
46 ASP ( 63-) A 67 ASP ( 84-) A
138 GLU ( 155-) A
38 GLU ( 55-) A N CA C 122.86 4.2 42 THR ( 59-) A N CA C 97.70 -4.8
46 ASP ( 63-) A 67 ASP ( 84-) A 138 GLU ( 155-) A
42 THR ( 59-) A 4.52 105 TYR ( 122-) A 4.47
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.
46 ASP ( 63-) A Poor phi/psi 61 ARG ( 78-) A Poor phi/psi 80 GLN ( 97-) A Poor phi/psi 87 CYS ( 104-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -0.947
It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.
119 SER ( 136-) A 0.36
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!
7 THR ( 24-) A 0 8 LYS ( 25-) A 0 9 SER ( 26-) A 0 35 VAL ( 52-) A 0 36 SER ( 53-) A 0 37 VAL ( 54-) A 0 44 TYR ( 61-) A 0 45 GLU ( 62-) A 0 53 PRO ( 70-) A 0 56 ASP ( 73-) A 0 61 ARG ( 78-) A 0 79 LYS ( 96-) A 0 80 GLN ( 97-) A 0 86 HIS ( 103-) A 0 87 CYS ( 104-) A 0 88 ALA ( 105-) A 0 89 ALA ( 106-) A 0 91 VAL ( 108-) A 0 93 ARG ( 110-) A 0 106 HIS ( 123-) A 0 120 CYS ( 137-) A 0 123 ILE ( 140-) A 0 124 ILE ( 141-) A 0 126 PRO ( 143-) A 0 127 ASN ( 144-) A 0And so on for a total of 53 lines.
Standard deviation of omega values : 1.630
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.
79 LYS ( 96-) A NZ <-> 165 HOH (1124 ) A O 0.20 2.50 INTRA BF 118 LYS ( 135-) A NZ <-> 165 HOH (1073 ) A O 0.19 2.51 INTRA BF 1 SER ( 18-) A CA <-> 165 HOH (1144 ) A O 0.15 2.65 INTRA 31 MET ( 48-) A SD <-> 72 HIS ( 89-) A CE1 0.11 3.29 INTRA BL 87 CYS ( 104-) A SG <-> 90 GLY ( 107-) A N 0.09 3.21 INTRA BL 1 SER ( 18-) A N <-> 165 HOH (1144 ) A O 0.09 2.61 INTRA BF 118 LYS ( 135-) A NZ <-> 165 HOH (1094 ) A O 0.07 2.63 INTRA BF 36 SER ( 53-) A O <-> 51 GLN ( 68-) A NE2 0.07 2.63 INTRA 56 ASP ( 73-) A N <-> 165 HOH (1018 ) A O 0.07 2.63 INTRA 8 LYS ( 25-) A N <-> 164 ACT (1001-) A O 0.06 2.64 INTRA 139 PHE ( 156-) A O <-> 143 GLY ( 160-) A N 0.05 2.65 INTRA 148 HIS ( 165-) A O <-> 159 ASP ( 176-) A N 0.04 2.66 INTRA BL 19 ASN ( 36-) A ND2 <-> 42 THR ( 59-) A N 0.03 2.82 INTRA BL 90 GLY ( 107-) A O <-> 121 ARG ( 138-) A NE 0.03 2.67 INTRA BL 31 MET ( 48-) A SD <-> 48 GLN ( 65-) A CD 0.02 3.38 INTRA BL 67 ASP ( 84-) A N <-> 68 PRO ( 85-) A CD 0.02 2.98 INTRA BL 87 CYS ( 104-) A SG <-> 163 EPE (1002-) A S 0.02 3.58 INTRA 131 TRP ( 148-) A CG <-> 158 PRO ( 175-) A CG 0.01 3.19 INTRA 27 ASN ( 44-) A N <-> 28 GLN ( 45-) A N 0.01 2.59 INTRA BL
Chain identifier: A
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: A
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: 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.
165 HOH (1085 ) A O 28.00 48.40 1.15 165 HOH (1089 ) A O 39.40 25.68 -12.37 165 HOH (1141 ) A O 48.98 32.16 1.25 165 HOH (1146 ) A O 34.47 19.31 3.40
19 ASN ( 36-) A 72 HIS ( 89-) 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.
8 LYS ( 25-) A N 88 ALA ( 105-) A N 89 ALA ( 106-) A N 91 VAL ( 108-) A N 92 SER ( 109-) A N 93 ARG ( 110-) A N 93 ARG ( 110-) A NE 94 SER ( 111-) A OG 127 ASN ( 144-) A ND2 144 LYS ( 161-) A N 147 VAL ( 164-) A N 148 HIS ( 165-) A N
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.
165 HOH (1047 ) A O 1.14 K 4
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 : 0.360 2nd generation packing quality : -0.482 Ramachandran plot appearance : -0.364 chi-1/chi-2 rotamer normality : -0.947 Backbone conformation : -0.733
Bond lengths : 0.328 (tight) Bond angles : 0.698 Omega angle restraints : 0.296 (tight) Side chain planarity : 0.284 (tight) Improper dihedral distribution : 0.637 B-factor distribution : 1.605 (loose) Inside/Outside distribution : 1.042
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 : 2.00
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.8 2nd generation packing quality : -0.4 Ramachandran plot appearance : 0.2 chi-1/chi-2 rotamer normality : -0.2 Backbone conformation : -0.9
Bond lengths : 0.328 (tight) Bond angles : 0.698 Omega angle restraints : 0.296 (tight) Side chain planarity : 0.284 (tight) Improper dihedral distribution : 0.637 B-factor distribution : 1.605 (loose) Inside/Outside distribution : 1.042 ==============
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.