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.
214 SBA ( 300-) 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.
59 ARG ( 59-) A - CG 59 ARG ( 59-) A - CD 59 ARG ( 59-) A - NE 59 ARG ( 59-) A - CZ 59 ARG ( 59-) A - NH1 59 ARG ( 59-) A - NH2 73 GLN ( 73-) A - CD 73 GLN ( 73-) A - OE1 73 GLN ( 73-) A - NE2 77 GLN ( 77-) A - CG 77 GLN ( 77-) A - CD 77 GLN ( 77-) A - OE1 77 GLN ( 77-) A - NE2 98 ARG ( 98-) A - CD 98 ARG ( 98-) A - NE 98 ARG ( 98-) A - CZ 98 ARG ( 98-) A - NH1 98 ARG ( 98-) A - NH2 145 ARG ( 145-) A - CD 145 ARG ( 145-) A - NE 145 ARG ( 145-) A - CZ 145 ARG ( 145-) A - NH1 145 ARG ( 145-) A - NH2
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) :287.000
Warning: More than 5 percent of buried atoms has low B-factor
For normal protein structures, no more than about 1 percent of the B factors
of buried atoms is below 5.0. The fact that this value is much higher in the
current structure could be a signal that the B-factors were restraints or
constraints to too-low values, misuse of B-factor field in the PDB file, or
a TLS/scaling problem. If the average B factor is low too, it is probably a
low temperature structure determination.
Percentage of buried atoms with B less than 5 : 6.89
Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
Chain identifier: A
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.
93 ARG ( 93-) A -O -C N 130.04 4.4 93 ARG ( 93-) A -C N CA 130.24 4.7
56 CYS ( 56-) A 5.51 77 GLN ( 77-) A 5.02 73 GLN ( 73-) A 4.40
Tau angle RMS Z-score : 1.617
Error: Side chain planarity problems
The side chains of the residues listed in the table below contain a planar
group that was found to deviate from planarity by more than 4.0 times the
expected value. For an amino acid residue that has a side chain with a
planar group, the RMS deviation of the atoms to a least squares plane was
determined. The number in the table is the number of standard deviations
this RMS value deviates from the expected value. Not knowing better yet, we
assume that planarity of the groups analyzed should be perfect.
59 ARG ( 59-) A 7.00
Ramachandran Z-score : -3.861
Warning: Torsion angle evaluation shows unusual residues
The residues listed in the table below contain bad or abnormal
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.
78 TYR ( 78-) A -2.7 168 PRO ( 168-) A -2.6 166 TYR ( 166-) A -2.5 134 LEU ( 134-) A -2.5 116 TYR ( 116-) A -2.4 80 ILE ( 80-) A -2.4 86 TYR ( 86-) A -2.4 41 ARG ( 41-) A -2.3 156 LYS ( 156-) A -2.2 161 VAL ( 161-) A -2.2 128 GLN ( 128-) A -2.0 61 TYR ( 61-) A -2.0 25 CYS ( 25-) 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.
77 GLN ( 77-) A Poor phi/psi 78 TYR ( 78-) A Poor phi/psi 97 SER ( 97-) A Poor phi/psi 151 GLY ( 151-) A PRO omega poor 184 ASN ( 184-) A Poor phi/psi 194 GLY ( 194-) A Poor phi/psi 200 CYS ( 200-) A Poor phi/psi 202 LEU ( 202-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -4.249
chi-1/chi-2 correlation Z-score : -4.249
Warning: Unusual rotamers
The residues listed in the table below have a rotamer that is not seen very
often in the database of solved protein structures. This option determines
for every residue the position specific chi-1 rotamer distribution.
Thereafter it verified whether the actual residue in the molecule has the
most preferred rotamer or not. If the actual rotamer is the preferred one,
the score is 1.0. If the actual rotamer is unique, the score is 0.0. If
there are two preferred rotamers, with a population distribution of 3:2 and
your rotamer sits in the lesser populated rotamer, the score will be 0.667.
No value will be given if insufficient hits are found in the database.
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.
29 SER ( 29-) A 0.40
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!
12 ALA ( 12-) A 0 13 VAL ( 13-) A 0 22 CYS ( 22-) A 0 24 SER ( 24-) A 0 41 ARG ( 41-) A 0 42 THR ( 42-) A 0 46 ASN ( 46-) A 0 47 GLN ( 47-) A 0 48 TYR ( 48-) A 0 56 CYS ( 56-) A 0 58 ARG ( 58-) A 0 60 SER ( 60-) A 0 61 TYR ( 61-) A 0 63 CYS ( 63-) A 0 64 ASN ( 64-) A 0 67 TYR ( 67-) A 0 78 TYR ( 78-) A 0 82 TYR ( 82-) A 0 86 TYR ( 86-) A 0 89 GLU ( 89-) A 0 91 VAL ( 91-) A 0 93 ARG ( 93-) A 0 94 TYR ( 94-) A 0 95 CYS ( 95-) A 0 100 LYS ( 100-) A 0And so on for a total of 102 lines.
Standard deviation of omega values : 1.656
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]
68 PRO ( 68-) A 0.05 LOW 168 PRO ( 168-) A 0.46 HIGH
168 PRO ( 168-) A -119.1 half-chair C-delta/C-gamma (-126 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.
59 ARG ( 59-) A NH1 <-> 73 GLN ( 73-) A NE2 0.98 1.87 INTRA BL 77 GLN ( 77-) A CD <-> 78 TYR ( 78-) A CE1 0.60 2.60 INTRA 77 GLN ( 77-) A CG <-> 78 TYR ( 78-) A CE1 0.35 2.85 INTRA 93 ARG ( 93-) A CB <-> 96 ARG ( 96-) A NH2 0.35 2.75 INTRA 81 HIS ( 81-) A CE1 <-> 100 LYS ( 100-) A CB 0.33 2.87 INTRA 149 PHE ( 149-) A CE2 <-> 200 CYS ( 200-) A SG 0.33 3.07 INTRA BL 56 CYS ( 56-) A SG <-> 97 SER ( 97-) A OG 0.32 2.68 INTRA BF 67 TYR ( 67-) A CD2 <-> 69 TRP ( 69-) A CZ2 0.28 2.92 INTRA 55 ASP ( 55-) A CG <-> 93 ARG ( 93-) A O 0.27 2.53 INTRA 95 CYS ( 95-) A SG <-> 97 SER ( 97-) A OG 0.26 2.74 INTRA 201 GLY ( 201-) A O <-> 203 TYR ( 203-) A N 0.22 2.48 INTRA BL 128 GLN ( 128-) A NE2 <-> 208 TYR ( 208-) A CD2 0.21 2.89 INTRA BF 89 GLU ( 89-) A OE1 <-> 93 ARG ( 93-) A NH1 0.20 2.50 INTRA 37 ILE ( 37-) A CD1 <-> 41 ARG ( 41-) A NH1 0.19 2.91 INTRA 118 GLN ( 118-) A NE2 <-> 203 TYR ( 203-) A OH 0.16 2.54 INTRA BL 23 GLY ( 23-) A O <-> 26 TRP ( 26-) A NE1 0.13 2.57 INTRA BL 66 GLY ( 66-) A C <-> 67 TYR ( 67-) A CD1 0.11 2.99 INTRA 165 GLY ( 165-) A O <-> 172 LEU ( 172-) A N 0.11 2.59 INTRA BL 46 ASN ( 46-) A O <-> 48 TYR ( 48-) A CE2 0.11 2.69 INTRA 177 TRP ( 177-) A N <-> 215 HOH ( 453 ) A O 0.10 2.60 INTRA BL 38 ILE ( 38-) A O <-> 42 THR ( 42-) A N 0.09 2.61 INTRA 51 GLN ( 51-) A OE1 <-> 89 GLU ( 89-) A N 0.09 2.61 INTRA 77 GLN ( 77-) A CG <-> 78 TYR ( 78-) A CD1 0.09 3.11 INTRA 51 GLN ( 51-) A NE2 <-> 91 VAL ( 91-) A O 0.09 2.61 INTRA 59 ARG ( 59-) A NH1 <-> 73 GLN ( 73-) A CD 0.09 3.01 INTRA BLAnd so on for a total of 59 lines.
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.
145 ARG ( 145-) A -8.03 94 TYR ( 94-) A -6.39 78 TYR ( 78-) A -6.19 58 ARG ( 58-) A -5.46 77 GLN ( 77-) A -5.45 4 TYR ( 4-) A -5.43 9 GLN ( 9-) A -5.31 41 ARG ( 41-) A -5.18 64 ASN ( 64-) A -5.10
The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.
92 GLN ( 92-) A 94 - TYR 94- ( A) -5.11
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.
215 HOH ( 505 ) A O -17.34 25.21 -32.85
215 HOH ( 469 ) A O 215 HOH ( 487 ) A O
81 HIS ( 81-) A 169 ASN ( 169-) 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.
13 VAL ( 13-) A N 51 GLN ( 51-) A N 60 SER ( 60-) A N 69 TRP ( 69-) A N 73 GLN ( 73-) A NE2 79 GLY ( 79-) A N 140 ASP ( 140-) A N 146 GLY ( 146-) A N 153 CYS ( 153-) A N 154 GLY ( 154-) A N 160 ALA ( 160-) A N 169 ASN ( 169-) A N 175 ASN ( 175-) A ND2 177 TRP ( 177-) A NE1 181 TRP ( 181-) A N 191 ARG ( 191-) A NH1 192 GLY ( 192-) A 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.
159 HIS ( 159-) A ND1
55 ASP ( 55-) A H-bonding suggests Asn; but Alt-Rotamer 158 ASP ( 158-) 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 : -2.002 2nd generation packing quality : -1.895 Ramachandran plot appearance : -3.861 (poor) chi-1/chi-2 rotamer normality : -4.249 (bad) Backbone conformation : -0.341
Bond lengths : 0.502 (tight) Bond angles : 0.784 Omega angle restraints : 0.301 (tight) Side chain planarity : 0.940 Improper dihedral distribution : 1.050 Inside/Outside distribution : 1.049
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 : 2.50
Structure Z-scores, positive is better than average:
1st generation packing quality : -1.1 2nd generation packing quality : -0.6 Ramachandran plot appearance : -1.5 chi-1/chi-2 rotamer normality : -2.2 Backbone conformation : -0.0
Bond lengths : 0.502 (tight) Bond angles : 0.784 Omega angle restraints : 0.301 (tight) Side chain planarity : 0.940 Improper dihedral distribution : 1.050 Inside/Outside distribution : 1.049 ==============
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.