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'.
60 LYS ( 85-) A CG 60 LYS ( 85-) A CD 60 LYS ( 85-) A CE 60 LYS ( 85-) A NZ 64 ILE ( 90-) A CG1 64 ILE ( 90-) A CG2 64 ILE ( 90-) A CD1
Obviously, the temperature at which the X-ray data was collected has some importance too:
Number of TLS groups mentione in PDB file header: 0
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: A
Nomenclature related problems
Warning: Arginine nomenclature problem
The arginine residues listed in the table below have their N-H-1 and N-H-2
6 ARG ( 24-) A 10 ARG ( 28-) A
90 TYR ( 116-) A
54 PHE ( 72-) A 84 PHE ( 110-) A
51 ASP ( 69-) A 63 ASP ( 89-) A
5 GLU ( 23-) A 70 GLU ( 96-) A 110 GLU ( 136-) A
5 GLU ( 23-) A 6 ARG ( 24-) A 10 ARG ( 28-) A 51 ASP ( 69-) A 63 ASP ( 89-) A 70 GLU ( 96-) A 110 GLU ( 136-) A
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.
10 ARG ( 28-) A -2.7 99 PRO ( 125-) A -2.5 113 LEU ( 139-) A -2.3 18 ARG ( 36-) A -2.2 21 LEU ( 39-) 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.
10 ARG ( 28-) A Poor phi/psi 18 ARG ( 36-) A Poor phi/psi 41 VAL ( 59-) A omega poor 64 ILE ( 90-) A omega poor 91 ALA ( 117-) A Poor phi/psi 98 PRO ( 124-) A PRO omega poor 104 ASN ( 130-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -3.694
chi-1/chi-2 correlation Z-score : -3.694
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!
9 GLN ( 27-) A 0 10 ARG ( 28-) A 0 14 ILE ( 32-) A 0 15 SER ( 33-) A 0 18 ARG ( 36-) A 0 22 LYS ( 40-) A 0 25 ILE ( 43-) A 0 26 ARG ( 44-) A 0 29 ALA ( 47-) A 0 31 ASP ( 49-) A 0 36 ASP ( 54-) A 0 49 HIS ( 67-) A 0 51 ASP ( 69-) A 0 54 PHE ( 72-) A 0 55 ASP ( 73-) A 0 56 SER ( 74-) A 0 57 ASN ( 75-) A 0 58 LEU ( 83-) A 0 59 MET ( 84-) A 0 60 LYS ( 85-) A 0 61 LEU ( 86-) A 0 62 GLU ( 88-) A 0 63 ASP ( 89-) A 0 67 TRP ( 93-) A 0 78 ARG ( 104-) A 0And so on for a total of 51 lines.
For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.
In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!
28 GLY ( 46-) A 1.78 32
53 PRO ( 71-) A -124.7 half-chair C-delta/C-gamma (-126 degrees) 99 PRO ( 125-) A -40.1 envelop C-alpha (-36 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.
1 GLN ( 19-) A N <-> 5 GLU ( 23-) A OE1 0.25 2.45 INTRA BF 83 ARG ( 109-) A NH1 <-> 118 HOH ( 166 ) A O 0.22 2.48 INTRA BF 23 ASP ( 41-) A OD2 <-> 118 HOH ( 166 ) A O 0.17 2.23 INTRA BL 30 GLY ( 48-) A O <-> 77 ARG ( 103-) A NE 0.14 2.56 INTRA BF 49 HIS ( 67-) A NE2 <-> 118 HOH ( 187 ) A O 0.05 2.65 INTRA BF 87 LYS ( 113-) A NZ <-> 118 HOH ( 153 ) A O 0.05 2.65 INTRA BF 84 PHE ( 110-) A N <-> 109 PHE ( 135-) A O 0.04 2.66 INTRA BL 6 ARG ( 24-) A NH2 <-> 9 GLN ( 27-) A CD 0.03 3.07 INTRA BF 12 LEU ( 30-) A O <-> 22 LYS ( 40-) A N 0.02 2.68 INTRA BL 22 LYS ( 40-) A NZ <-> 80 GLU ( 106-) A OE2 0.01 2.69 INTRA BL 96 GLY ( 122-) A C <-> 97 CYS ( 123-) A SG 0.01 3.29 INTRA BF 45 GLY ( 63-) A N <-> 55 ASP ( 73-) A O 0.01 2.69 INTRA BF
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.
95 LEU ( 121-) A -5.92 49 HIS ( 67-) A -5.58 92 TYR ( 118-) A -5.04
Chain identifier: A
Warning: Low packing Z-score for some residues
The residues listed in the table below have an unusual packing
environment according to the 2nd generation packing check. The score
listed in the table is a packing normality Z-score: positive means
better than average, negative means worse than average. Only residues
scoring less than -2.50 are listed here. These are the unusual
residues in the structure, so it will be interesting to take a
special look at them.
100 LEU ( 126-) A -2.79 64 ILE ( 90-) A -2.58
Chain identifier: A
Water, ion, and hydrogenbond related checks
Error: Water molecules without hydrogen bonds
The water molecules listed in the table below do not form any hydrogen bonds,
neither with the protein or DNA/RNA, nor with other water molecules. This is
a strong indication of a refinement problem. The last number on each line is
the identifier of the water molecule in the input file.
118 HOH ( 186 ) A O
1 GLN ( 19-) A 9 GLN ( 27-) 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 ( 20-) A N 34 ALA ( 52-) A N 47 LEU ( 65-) A N
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 : -0.550 2nd generation packing quality : -0.231 Ramachandran plot appearance : -0.290 chi-1/chi-2 rotamer normality : -3.694 (poor) Backbone conformation : 0.177
Bond lengths : 0.470 (tight) Bond angles : 0.686 Omega angle restraints : 1.224 Side chain planarity : 0.426 (tight) Improper dihedral distribution : 0.766 B-factor distribution : 0.360 Inside/Outside distribution : 1.095
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 : 2.10
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.1 2nd generation packing quality : -0.0 Ramachandran plot appearance : 0.5 chi-1/chi-2 rotamer normality : -2.3 Backbone conformation : 0.2
Bond lengths : 0.470 (tight) Bond angles : 0.686 Omega angle restraints : 1.224 Side chain planarity : 0.426 (tight) Improper dihedral distribution : 0.766 B-factor distribution : 0.360 Inside/Outside distribution : 1.095 ==============
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.