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.
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) :293.000
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
78 TYR ( 78-) A 105 TYR ( 105-) A 141 TYR ( 141-) A
8 ASP ( 8-) A 151 ASP ( 151-) A
19 GLU ( 19-) A 26 GLU ( 26-) A 72 GLU ( 72-) A 132 GLU ( 132-) A
149 ILE ( 149-) A N CA C 96.40 -5.3
8 ASP ( 8-) A 19 GLU ( 19-) A 26 GLU ( 26-) A 72 GLU ( 72-) A 132 GLU ( 132-) A 151 ASP ( 151-) A
149 ILE ( 149-) A 5.46 42 PHE ( 42-) A 4.28
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.
53 THR ( 53-) A -3.1 158 PRO ( 158-) A -3.1 50 MET ( 50-) A -2.3 159 PHE ( 159-) A -2.2 66 ILE ( 66-) A -2.1 98 GLY ( 98-) A -2.1 17 PHE ( 17-) A -2.0
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.
35 ASN ( 35-) A Poor phi/psi 50 MET ( 50-) A Poor phi/psi 95 ASN ( 95-) A Poor phi/psi 99 SER ( 99-) A Poor phi/psi 113 MET ( 113-) A Poor phi/psi 141 TYR ( 141-) A Poor phi/psi 158 PRO ( 158-) A Poor phi/psi 159 PHE ( 159-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -1.123
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!
9 VAL ( 9-) A 0 17 PHE ( 17-) A 0 18 CYS ( 18-) A 0 20 ARG ( 20-) A 0 34 SER ( 34-) A 0 38 ASN ( 38-) A 0 42 PHE ( 42-) A 0 43 HIS ( 43-) A 0 47 LYS ( 47-) A 0 49 PHE ( 49-) A 0 50 MET ( 50-) A 0 53 THR ( 53-) A 0 59 THR ( 59-) A 0 64 ASN ( 64-) A 0 67 TRP ( 67-) A 0 78 TYR ( 78-) A 0 80 LYS ( 80-) A 0 81 HIS ( 81-) A 0 82 ASN ( 82-) A 0 84 ARG ( 84-) A 0 89 MET ( 89-) A 0 90 ALA ( 90-) A 0 92 ASN ( 92-) A 0 95 ASN ( 95-) A 0 96 THR ( 96-) A 0And so on for a total of 71 lines.
Standard deviation of omega values : 1.191
Warning: Unusual PRO puckering phases
The proline residues listed in the table below have a puckering phase that is
not expected to occur in protein structures. Puckering parameters were
calculated by the method of Cremer and Pople [REF]. Normal PRO rings
approximately show a so-called envelope conformation with the C-gamma atom
above the plane of the ring (phi=+72 degrees), or a half-chair conformation
with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees).
If phi deviates strongly from these values, this is indicative of a very
strange conformation for a PRO residue, and definitely requires a manual
check of the data. 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].
109 PRO ( 109-) A -113.8 envelop C-gamma (-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.
84 ARG ( 84-) A NE <-> 161 HOH ( 223 ) A O 0.20 2.50 INTRA 55 ASP ( 55-) A OD2 <-> 60 GLY ( 60-) A N 0.12 2.58 INTRA BL 4 THR ( 4-) A OG1 <-> 155 HIS ( 155-) A NE2 0.11 2.59 INTRA 48 GLY ( 48-) A N <-> 132 GLU ( 132-) A OE2 0.10 2.60 INTRA BL 91 ASN ( 91-) A ND2 <-> 161 HOH ( 202 ) A O 0.10 2.60 INTRA 3 VAL ( 3-) A O <-> 14 ILE ( 14-) A N 0.10 2.60 INTRA BL 64 ASN ( 64-) A ND2 <-> 65 SER ( 65-) A N 0.09 2.66 INTRA 35 ASN ( 35-) A CB <-> 38 ASN ( 38-) A ND2 0.09 3.01 INTRA 18 CYS ( 18-) A N <-> 25 CYS ( 25-) A SG 0.09 3.21 INTRA 142 ARG ( 142-) A NH1 <-> 161 HOH ( 217 ) A O 0.08 2.62 INTRA 113 MET ( 113-) A N <-> 161 HOH ( 216 ) A O 0.07 2.63 INTRA 108 GLN ( 108-) A N <-> 109 PRO ( 109-) A CD 0.07 2.93 INTRA 65 SER ( 65-) A C <-> 67 TRP ( 67-) A N 0.07 2.83 INTRA 159 PHE ( 159-) A CD2 <-> 160 ALA ( 160-) A N 0.06 2.94 INTRA BF 6 HIS ( 6-) A O <-> 150 LYS ( 150-) A N 0.06 2.64 INTRA 47 LYS ( 47-) A C <-> 49 PHE ( 49-) A N 0.05 2.85 INTRA BL 137 ASN ( 137-) A O <-> 141 TYR ( 141-) A N 0.04 2.66 INTRA 105 TYR ( 105-) A N <-> 106 GLY ( 106-) A N 0.03 2.57 INTRA BL 134 LEU ( 134-) A CD1 <-> 147 VAL ( 147-) A CG2 0.02 3.18 INTRA 108 GLN ( 108-) A O <-> 110 HIS ( 110-) A N 0.02 2.68 INTRA 84 ARG ( 84-) A NH1 <-> 105 TYR ( 105-) A O 0.02 2.68 INTRA BL 18 CYS ( 18-) A CA <-> 25 CYS ( 25-) A SG 0.02 2.98 INTRA B3 81 HIS ( 81-) A ND1 <-> 112 ASP ( 112-) A OD1 0.01 2.69 INTRA 45 ASN ( 45-) A ND2 <-> 131 LEU ( 131-) A O 0.01 2.69 INTRA 3 VAL ( 3-) A CG1 <-> 4 THR ( 4-) A N 0.01 2.99 INTRA BL
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.
61 ARG ( 61-) A -7.96 159 PHE ( 159-) A -6.79 78 TYR ( 78-) A -5.53 84 ARG ( 84-) A -5.41 144 LEU ( 144-) A -5.39 107 LYS ( 107-) A -5.36 20 ARG ( 20-) A -5.31 92 ASN ( 92-) A -5.21 75 TYR ( 75-) A -5.19
The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.
157 ASN ( 157-) A 160 - ALA 160- ( A) -4.94
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
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.
64 ASN ( 64-) 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.
2 SER ( 2-) A N 18 CYS ( 18-) A N 72 GLU ( 72-) A N 83 VAL ( 83-) A N 96 THR ( 96-) A N 106 GLY ( 106-) A N 126 GLU ( 126-) A N 159 PHE ( 159-) A N
129 ASP ( 129-) A H-bonding suggests Asn
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 : -1.203 2nd generation packing quality : -1.076 Ramachandran plot appearance : -2.250 chi-1/chi-2 rotamer normality : -1.123 Backbone conformation : -0.123
Bond lengths : 0.281 (tight) Bond angles : 0.627 (tight) Omega angle restraints : 0.216 (tight) Side chain planarity : 0.208 (tight) Improper dihedral distribution : 0.636 B-factor distribution : 0.510 Inside/Outside distribution : 1.006
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 : 2.60
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.5 2nd generation packing quality : 0.3 Ramachandran plot appearance : 0.1 chi-1/chi-2 rotamer normality : 0.9 Backbone conformation : 0.7
Bond lengths : 0.281 (tight) Bond angles : 0.627 (tight) Omega angle restraints : 0.216 (tight) Side chain planarity : 0.208 (tight) Improper dihedral distribution : 0.636 B-factor distribution : 0.510 Inside/Outside distribution : 1.006 ==============
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.