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.
115 PTR ( 101-) A -
For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.
1 GLU ( 102-) A - N bound to 115 PTR ( 101-) A - C
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: B
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:
Temperature not mentioned in PDB file. This most likely means
that the temperature record is absent.
Room temperature assumed
Warning: Temperature factors given as "U", not as "B"
The average temperature factor found is very low. Probably they are given as
"U" values, and not as "B" values. Values will be multiplied by 8-pi-squared
for the analysis of B-factors.
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 : 3.224 over 579 bonds
Average difference in B over a bond : 9.44
RMS difference in B over a bond : 15.65
Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
Chain identifier: B
Warning: Directionality in bond lengths and no X-ray cell
Comparison of bond distances with Engh and Huber [REF] standard values for
protein residues and Parkinson et al [REF] standard values for DNA/RNA shows
a significant systematic deviation.
You have most probably seen symmetry problems earlier. Please correct these
and rerun this check to see the possible implications on the X-ray cell axes.
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.
15 PHE ( 150-) B CA CB CG 109.53 -4.3 37 PHE ( 172-) B CA CB CG 109.53 -4.3 56 PHE ( 191-) B CA CB CG 109.45 -4.3 66 HIS ( 201-) B CA CB CG 109.54 -4.3 77 PHE ( 212-) B CA CB CG 109.69 -4.1 85 PHE ( 220-) B CA CB CG 109.51 -4.3 98 HIS ( 233-) B CA CB CG 109.57 -4.2 104 HIS ( 239-) B CA CB CG 109.59 -4.2
70 ARG ( 205-) B 8.52 34 ARG ( 169-) B 8.11 40 ARG ( 175-) B 7.99 20 ARG ( 155-) B 7.40 82 ARG ( 217-) B 7.15 25 ARG ( 160-) B 6.16 105 ARG ( 240-) B 4.68
Ramachandran Z-score : -4.858
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.
45 THR ( 180-) B -2.6 38 LEU ( 173-) B -2.4 98 HIS ( 233-) B -2.4 15 PHE ( 150-) B -2.3 102 LEU ( 237-) B -2.2 75 GLY ( 210-) B -2.2 100 ASP ( 235-) B -2.1 40 ARG ( 175-) B -2.0 57 ASP ( 192-) B -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.
45 THR ( 180-) B Poor phi/psi 78 TYR ( 213-) B Poor phi/psi 100 ASP ( 235-) B Poor phi/psi 104 HIS ( 239-) B Poor phi/psi chi-1/chi-2 correlation Z-score : -6.749
chi-1/chi-2 correlation Z-score : -6.749
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.
23 SER ( 158-) B 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!
3 ILE ( 104-) A 0 4 GLU ( 105-) A 0 5 MET ( 140-) B 0 6 ASP ( 141-) B 0 10 ALA ( 145-) B 0 13 TRP ( 148-) B 0 15 PHE ( 150-) B 0 17 LYS ( 152-) B 0 28 LEU ( 163-) B 0 29 ASN ( 164-) B 0 34 ARG ( 169-) B 0 36 THR ( 171-) B 0 42 SER ( 177-) B 0 43 GLU ( 178-) B 0 46 LYS ( 181-) B 0 48 ALA ( 183-) B 0 58 ASN ( 193-) B 0 59 ALA ( 194-) B 0 60 LYS ( 195-) B 0 62 LEU ( 197-) B 0 74 SER ( 209-) B 0 79 ILE ( 214-) B 0 81 SER ( 216-) B 0 82 ARG ( 217-) B 0 83 THR ( 218-) B 0And so on for a total of 53 lines.
Standard deviation of omega values : 0.193
Warning: Backbone oxygen evaluation
The residues listed in the table below have an unusual backbone oxygen
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!
75 GLY ( 210-) B 1.59 80
33 PRO ( 168-) B -61.8 half-chair C-beta/C-alpha (-54 degrees) 111 PRO ( 246-) B -63.0 half-chair C-beta/C-alpha (-54 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 GLU ( 102-) A N <-> 115 PTR ( 101-) A C 1.40 1.30 INTRA BF 112 ACE ( 100-) A C <-> 115 PTR ( 101-) A N 1.39 1.31 INTRA BF 1 GLU ( 102-) A CA <-> 115 PTR ( 101-) A C 0.78 2.42 INTRA BF 112 ACE ( 100-) A CH3 <-> 115 PTR ( 101-) A N 0.67 2.43 INTRA BF 112 ACE ( 100-) A O <-> 115 PTR ( 101-) A N 0.50 2.20 INTRA BF 28 LEU ( 163-) B CD2 <-> 64 VAL ( 199-) B CG2 0.35 2.85 INTRA BL 76 GLY ( 211-) B C <-> 77 PHE ( 212-) B CD1 0.25 2.85 INTRA BF 38 LEU ( 173-) B CD2 <-> 110 CYS ( 245-) B SG 0.21 3.19 INTRA BF 26 LEU ( 161-) B O <-> 32 ASN ( 167-) B ND2 0.21 2.49 INTRA BL 11 GLU ( 146-) B OE2 <-> 13 TRP ( 148-) B CZ2 0.19 2.61 INTRA BF 28 LEU ( 163-) B CG <-> 64 VAL ( 199-) B CG2 0.19 3.01 INTRA BL 76 GLY ( 211-) B C <-> 77 PHE ( 212-) B CG 0.18 2.92 INTRA BL 37 PHE ( 172-) B CD1 <-> 108 THR ( 243-) B O 0.18 2.62 INTRA BF 56 PHE ( 191-) B CD1 <-> 57 ASP ( 192-) B N 0.16 2.84 INTRA BF 5 MET ( 140-) B CG <-> 6 ASP ( 141-) B N 0.16 2.84 INTRA BF 3 ILE ( 104-) A CD1 <-> 67 TYR ( 202-) B CE2 0.14 3.06 INTRA BF 92 VAL ( 227-) B O <-> 96 SER ( 231-) B CB 0.14 2.66 INTRA BL 52 SER ( 187-) B C <-> 53 VAL ( 188-) B CG2 0.11 2.99 INTRA BL 1 GLU ( 102-) A CA <-> 115 PTR ( 101-) A O 0.11 2.69 INTRA BF 112 ACE ( 100-) A O <-> 115 PTR ( 101-) A CA 0.11 2.69 INTRA BF 87 SER ( 222-) B C <-> 89 GLN ( 224-) B N 0.10 2.80 INTRA BL 27 LEU ( 162-) B CD1 <-> 64 VAL ( 199-) B CG1 0.10 3.10 INTRA BL 72 LEU ( 207-) B C <-> 74 SER ( 209-) B N 0.06 2.84 INTRA BL 5 MET ( 140-) B O <-> 7 SER ( 142-) B N 0.06 2.64 INTRA BF 68 LYS ( 203-) B N <-> 115 PTR ( 101-) A CD1 0.06 3.04 INTRA BF 87 SER ( 222-) B O <-> 89 GLN ( 224-) B N 0.05 2.65 INTRA BL 13 TRP ( 148-) B CE3 <-> 39 VAL ( 174-) B CG2 0.05 3.15 INTRA BL 37 PHE ( 172-) B CE1 <-> 108 THR ( 243-) B O 0.04 2.76 INTRA BF 92 VAL ( 227-) B O <-> 96 SER ( 231-) B OG 0.04 2.36 INTRA BL 42 SER ( 177-) B OG <-> 48 ALA ( 183-) B O 0.03 2.37 INTRA BF 48 ALA ( 183-) B C <-> 49 TYR ( 184-) B CD1 0.03 3.07 INTRA BF 49 TYR ( 184-) B C <-> 50 CYS ( 185-) B SG 0.02 3.28 INTRA BF
Chain identifier: B
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.
60 LYS ( 195-) B -6.62 34 ARG ( 169-) B -5.81 82 ARG ( 217-) B -5.41 17 LYS ( 152-) B -5.22
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 - 111 : -1.594
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: B
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: B
Water, ion, and hydrogenbond related checks
Warning: Buried unsatisfied hydrogen bond donors
The buried hydrogen bond donors listed in the table below have a hydrogen
atom that is not involved in a hydrogen bond in the optimized hydrogen bond
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.
11 GLU ( 146-) B N 13 TRP ( 148-) B N 16 GLY ( 151-) B N 18 ILE ( 153-) B N 23 SER ( 158-) B OG 31 GLU ( 166-) B N 40 ARG ( 175-) B NH1 40 ARG ( 175-) B NH2 45 THR ( 180-) B N 60 LYS ( 195-) B N 68 LYS ( 203-) B N 79 ILE ( 214-) B N 80 THR ( 215-) B N 83 THR ( 218-) B N 87 SER ( 222-) B N 95 TYR ( 230-) B OH
43 GLU ( 178-) B H-bonding suggests Gln 55 ASP ( 190-) B 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 : -2.735 2nd generation packing quality : -2.216 Ramachandran plot appearance : -4.858 (bad) chi-1/chi-2 rotamer normality : -6.749 (bad) Backbone conformation : -1.109
Bond lengths : 0.957 Bond angles : 1.007 Omega angle restraints : 0.035 (tight) Side chain planarity : 2.805 (loose) Improper dihedral distribution : 0.734 B-factor distribution : 3.224 (loose) Inside/Outside distribution : 0.919 ==============
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.