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: Missing atoms
The atoms listed in the table below are missing from the entry. If many atoms
are missing, the other checks can become less sensitive. Be aware that it
often happens that groups at the termini of DNA or RNA are really missing,
so that the absence of these atoms normally is neither an error nor the
result of poor electron density. Some of the atoms listed here might also be
listed by other checks, most noticeably by the options in the previous
section that list missing atoms in several categories. The plausible atoms
with zero occupancy are not listed here, as they already got assigned a
non-zero occupancy, and thus are no longer 'missing'.
109 PRO ( 109-) A CG 109 PRO ( 109-) A CD
1 MET ( 1-) A High 2 GLU ( 2-) A High 3 VAL ( 3-) A High 4 LYS ( 4-) A High 8 ARG ( 8-) A High 9 ASP ( 9-) A High 10 LYS ( 10-) A High 11 ASN ( 11-) A High 12 ARG ( 12-) A High 22 GLU ( 22-) A High 23 GLU ( 23-) A High 26 GLN ( 26-) A High 30 LYS ( 30-) A High 33 ARG ( 33-) A High 36 ASN ( 36-) A High 37 GLN ( 37-) A High 38 ARG ( 38-) A High 39 VAL ( 39-) A High 40 GLU ( 40-) A High 41 ILE ( 41-) A High 42 PRO ( 42-) A High 43 GLY ( 43-) A High 44 PHE ( 44-) A High 45 ARG ( 45-) A High 46 LYS ( 46-) A HighAnd so on for a total of 59 lines.
Obviously, the temperature at which the X-ray data was collected has some importance too:
Number of TLS groups mentione in PDB file header: 4
Temperature cannot be read from the PDB file. This most likely means that
the temperature is listed as NULL (meaning unknown) in the PDB file.
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
17 TYR ( 17-) A 34 TYR ( 34-) A 65 TYR ( 65-) A
19 PHE ( 19-) A
9 ASP ( 9-) A 29 ASP ( 29-) A 72 ASP ( 72-) A
2 GLU ( 2-) A 5 GLU ( 5-) A 23 GLU ( 23-) A 40 GLU ( 40-) A 60 GLU ( 60-) A 93 GLU ( 93-) A 107 GLU ( 107-) A 108 GLU ( 108-) A
109 PRO ( 109-) A N CA CB 109.57 6.0
2 GLU ( 2-) A 5 GLU ( 5-) A 9 ASP ( 9-) A 23 GLU ( 23-) A 29 ASP ( 29-) A 40 GLU ( 40-) A 60 GLU ( 60-) A 72 ASP ( 72-) A 93 GLU ( 93-) A 107 GLU ( 107-) A 108 GLU ( 108-) A
22 GLU ( 22-) A 4.11
Ramachandran Z-score : -4.694
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.
58 LEU ( 58-) A -2.3 75 PRO ( 75-) A -2.3 98 THR ( 98-) A -2.3 91 GLU ( 91-) A -2.2 88 ILE ( 88-) A -2.1 83 LEU ( 83-) 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.
6 LEU ( 6-) A Poor phi/psi 10 LYS ( 10-) A Poor phi/psi 38 ARG ( 38-) A Poor phi/psi 58 LEU ( 58-) A Poor phi/psi 76 ASP ( 76-) A Poor phi/psi 92 ARG ( 92-) A Poor phi/psi 108 GLU ( 108-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -4.866
chi-1/chi-2 correlation Z-score : -4.866
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.
61 GLU ( 61-) 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 GLU ( 7-) A 0 9 ASP ( 9-) A 0 10 LYS ( 10-) A 0 11 ASN ( 11-) A 0 12 ARG ( 12-) A 0 38 ARG ( 38-) A 0 39 VAL ( 39-) A 0 42 PRO ( 42-) A 0 46 LYS ( 46-) A 0 48 ARG ( 48-) A 0 58 LEU ( 58-) A 0 60 GLU ( 60-) A 0 84 ILE ( 84-) A 0 85 LEU ( 85-) A 0 90 THR ( 90-) A 0 91 GLU ( 91-) A 0 92 ARG ( 92-) A 0 93 GLU ( 93-) A 0 97 VAL ( 97-) A 0 49 ILE ( 49-) A 1 6 LEU ( 6-) A 2 44 PHE ( 44-) A 2 57 LYS ( 57-) A 2 86 SER ( 86-) A 2 100 ARG ( 100-) A 2 107 GLU ( 107-) A 2
Standard deviation of omega values : 1.095
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]
109 PRO ( 109-) A 0.00 LOW
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.
35 LEU ( 35-) A O <-> 38 ARG ( 38-) A N 0.29 2.41 INTRA BF 53 VAL ( 53-) A O <-> 57 LYS ( 57-) A N 0.16 2.54 INTRA BF 71 MET ( 71-) A O <-> 74 ILE ( 74-) A N 0.14 2.56 INTRA BL 31 ALA ( 31-) A CA <-> 69 PHE ( 69-) A CE2 0.14 3.06 INTRA BL 24 ILE ( 24-) A O <-> 28 GLU ( 28-) A N 0.12 2.58 INTRA BL 54 LEU ( 54-) A O <-> 58 LEU ( 58-) A N 0.11 2.59 INTRA BF 78 LEU ( 78-) A CD1 <-> 87 PRO ( 87-) A CG 0.10 3.10 INTRA BL 25 ALA ( 25-) A O <-> 29 ASP ( 29-) A N 0.06 2.64 INTRA BL 74 ILE ( 74-) A N <-> 75 PRO ( 75-) A CD 0.06 2.94 INTRA BL 75 PRO ( 75-) A C <-> 77 THR ( 77-) A N 0.05 2.85 INTRA BL 28 GLU ( 28-) A O <-> 31 ALA ( 31-) A CB 0.05 2.75 INTRA BL 26 GLN ( 26-) A O <-> 30 LYS ( 30-) A N 0.02 2.68 INTRA BL 22 GLU ( 22-) A O <-> 25 ALA ( 25-) A N 0.01 2.69 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.
48 ARG ( 48-) A -6.73 100 ARG ( 100-) A -6.54 108 GLU ( 108-) A -6.42 92 ARG ( 92-) A -6.39 85 LEU ( 85-) A -6.34 107 GLU ( 107-) A -5.80 106 HIS ( 106-) A -5.61 45 ARG ( 45-) A -5.56 82 LYS ( 82-) A -5.39 91 GLU ( 91-) A -5.25 97 VAL ( 97-) A -5.13
The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.
82 LYS ( 82-) A 85 - LEU 85- ( A) -5.26 90 THR ( 90-) A 92 - ARG 92- ( A) -5.24 106 HIS ( 106-) A 108 - GLU 108- ( A) -5.94
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 - 109 : -1.924
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
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.
63 GLN ( 63-) 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.
7 GLU ( 7-) A N 79 LYS ( 79-) A N 85 LEU ( 85-) A N 89 VAL ( 89-) A N 106 HIS ( 106-) A N
68 ASP ( 68-) 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 : -3.559 2nd generation packing quality : -0.623 Ramachandran plot appearance : -4.694 (bad) chi-1/chi-2 rotamer normality : -4.866 (bad) Backbone conformation : 1.158
Bond lengths : 0.459 (tight) Bond angles : 0.636 (tight) Omega angle restraints : 0.199 (tight) Side chain planarity : 0.304 (tight) Improper dihedral distribution : 0.644 B-factor distribution : 0.516 Inside/Outside distribution : 1.104
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 : 3.20
Structure Z-scores, positive is better than average:
1st generation packing quality : -2.2 2nd generation packing quality : 1.3 Ramachandran plot appearance : -1.7 chi-1/chi-2 rotamer normality : -2.4 Backbone conformation : 2.0
Bond lengths : 0.459 (tight) Bond angles : 0.636 (tight) Omega angle restraints : 0.199 (tight) Side chain planarity : 0.304 (tight) Improper dihedral distribution : 0.644 B-factor distribution : 0.516 Inside/Outside distribution : 1.104 ==============
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.