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.
328 SAR (2001-) E - 329 SAR (2002-) E - 330 DMS (2011-) E - 331 DMS (2012-) E - 332 SAR (2003-) E -
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: E
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'.
316 LYS ( 316-) E CG 316 LYS ( 316-) E CD 316 LYS ( 316-) E CE 316 LYS ( 316-) E NZ
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: E
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
27 TYR ( 27-) E 151 TYR ( 151-) E
226 ASP ( 226-) E
187 GLU ( 187-) E
Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.
256 VAL ( 256-) E CB CG2 1.66 4.1
There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.
Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.
If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.
Unit Cell deformation matrix
| 0.994685 -0.000092 0.000269| | -0.000092 0.993354 -0.000296| | 0.000269 -0.000296 0.994600|Proposed new scale matrix
| 0.010434 0.000000 -0.000003| | 0.000000 0.010448 0.000003| | -0.000003 0.000003 0.009496|With corresponding cell
A = 95.836 B = 95.708 C = 105.304 Alpha= 90.034 Beta= 89.969 Gamma= 90.001
The CRYST1 cell dimensions
A = 96.346 B = 96.346 C = 105.875 Alpha= 90.000 Beta= 90.000 Gamma= 90.000
(Under-)estimated Z-score: 13.659
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.
161 SER ( 161-) E CA CB OG 102.79 -4.2 203 ARG ( 203-) E CG CD NE 102.12 -4.9 216 HIS ( 216-) E CG ND1 CE1 109.85 4.3 250 HIS ( 250-) E CG ND1 CE1 110.16 4.6
187 GLU ( 187-) E 226 ASP ( 226-) E
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.
26 THR ( 26-) E -3.0 131 ILE ( 131-) E -2.3 92 SER ( 92-) E -2.3 157 TYR ( 157-) E -2.2 20 ILE ( 20-) E -2.2 51 PRO ( 51-) E -2.1 119 GLU ( 119-) E -2.1 107 SER ( 107-) E -2.1 185 ASP ( 185-) E -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.
26 THR ( 26-) E Poor phi/psi 45 LYS ( 45-) E Poor phi/psi 46 TYR ( 46-) E Poor phi/psi 50 LEU ( 50-) E PRO omega poor 60 ASN ( 60-) E Poor phi/psi 61 GLN ( 61-) E omega poor 92 SER ( 92-) E Poor phi/psi 97 ASN ( 97-) E Poor phi/psi 107 SER ( 107-) E Poor phi/psi 114 PHE ( 114-) E omega poor 130 PHE ( 130-) E omega poor 132 PRO ( 132-) E omega poor 152 THR ( 152-) E Poor phi/psi 157 TYR ( 157-) E Poor phi/psi 159 ASN ( 159-) E Poor phi/psi 181 ASN ( 181-) E Poor phi/psi chi-1/chi-2 correlation Z-score : 0.014
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.
161 SER ( 161-) E 0.37
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!
5 SER ( 5-) E 0 14 LEU ( 14-) E 0 17 GLN ( 17-) E 0 24 TYR ( 24-) E 0 25 SER ( 25-) E 0 26 THR ( 26-) E 0 30 LEU ( 30-) E 0 34 THR ( 34-) E 0 35 ARG ( 35-) E 0 37 ASP ( 37-) E 0 44 ALA ( 44-) E 0 45 LYS ( 45-) E 0 46 TYR ( 46-) E 0 51 PRO ( 51-) E 0 53 SER ( 53-) E 0 55 TRP ( 55-) E 0 58 ALA ( 58-) E 0 60 ASN ( 60-) E 0 61 GLN ( 61-) E 0 62 PHE ( 62-) E 0 63 PHE ( 63-) E 0 91 LEU ( 91-) E 0 92 SER ( 92-) E 0 93 TYR ( 93-) E 0 96 ASN ( 96-) E 0And so on for a total of 124 lines.
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.
325 CL ( 324-) E CL <-> 333 HOH ( 499 ) E O 1.10 1.70 INTRA 322 ZN ( 321-) E ZN <-> 325 CL ( 324-) E CL 1.05 2.15 INTRA 231 HIS ( 231-) E NE2 <-> 333 HOH ( 499 ) E O 0.53 2.17 INTRA 273 GLN ( 273-) E CG <-> 333 HOH ( 584 ) E O 0.40 2.40 INTRA BF 333 HOH ( 587 ) E O <-> 333 HOH ( 588 ) E O 0.36 1.84 INTRA 45 LYS ( 45-) E NZ <-> 333 HOH ( 586 ) E O 0.22 2.48 INTRA BL 269 ARG ( 269-) E NH1 <-> 333 HOH ( 584 ) E O 0.16 2.54 INTRA BF 330 DMS (2011-) E C1 <-> 333 HOH ( 578 ) E O 0.15 2.65 INTRA 226 ASP ( 226-) E OD1 <-> 231 HIS ( 231-) E ND1 0.14 2.56 INTRA BL 196 GLY ( 196-) E N <-> 333 HOH ( 461 ) E O 0.13 2.57 INTRA 1 ILE ( 1-) E N <-> 31 GLN ( 31-) E NE2 0.10 2.75 INTRA 146 HIS ( 146-) E ND1 <-> 165 ASN ( 165-) E OD1 0.09 2.61 INTRA BL 129 THR ( 129-) E O <-> 194 THR ( 194-) E N 0.09 2.61 INTRA 206 SER ( 206-) E O <-> 239 LYS ( 239-) E NZ 0.08 2.62 INTRA BL 32 ASP ( 32-) E N <-> 39 ILE ( 39-) E O 0.07 2.63 INTRA BL 81 TYR ( 81-) E OH <-> 97 ASN ( 97-) E ND2 0.05 2.65 INTRA BL 262 LYS ( 262-) E NZ <-> 333 HOH ( 573 ) E O 0.05 2.65 INTRA 273 GLN ( 273-) E CD <-> 333 HOH ( 584 ) E O 0.05 2.75 INTRA BF 307 LYS ( 307-) E NZ <-> 333 HOH ( 560 ) E O 0.05 2.65 INTRA 301 GLN ( 301-) E N <-> 333 HOH ( 549 ) E O 0.04 2.66 INTRA 68 ALA ( 68-) E N <-> 69 PRO ( 69-) E CD 0.03 2.97 INTRA BL 115 TRP ( 115-) E NE1 <-> 333 HOH ( 508 ) E O 0.03 2.67 INTRA BL 142 HIS ( 142-) E ND1 <-> 170 ASP ( 170-) E OD1 0.03 2.67 INTRA BL 126 ASP ( 126-) E OD1 <-> 128 GLN ( 128-) E N 0.03 2.67 INTRA 222 THR ( 222-) E N <-> 333 HOH ( 433 ) E O 0.02 2.68 INTRA 167 ALA ( 167-) E O <-> 171 ILE ( 171-) E N 0.02 2.68 INTRA BL 274 TYR ( 274-) E OH <-> 294 ASP ( 294-) E OD2 0.02 2.38 INTRA BL 21 ASN ( 21-) E N <-> 333 HOH ( 419 ) E O 0.02 2.68 INTRA 207 ASP ( 207-) E OD1 <-> 333 HOH ( 427 ) E O 0.01 2.39 INTRA 66 TYR ( 66-) E O <-> 105 HIS ( 105-) E NE2 0.01 2.69 INTRA BL 101 ARG ( 101-) E N <-> 333 HOH ( 438 ) E O 0.01 2.69 INTRA BL 316 LYS ( 316-) E N <-> 333 HOH ( 478 ) E O 0.01 2.69 INTRA
Chain identifier: E
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.
182 LYS ( 182-) E -5.90 88 HIS ( 88-) E -5.82 221 TYR ( 221-) E -5.60 246 GLN ( 246-) E -5.55 108 GLN ( 108-) E -5.45 273 GLN ( 273-) E -5.27
The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.
225 GLN ( 225-) E 228 - GLY 228- ( E) -4.36
Chain identifier: E
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.
44 ALA ( 44-) E -2.73
Chain identifier: E
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.
31 GLN ( 31-) E 33 ASN ( 33-) E 183 ASN ( 183-) E 308 GLN ( 308-) E
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.
35 ARG ( 35-) E N 49 THR ( 49-) E N 97 ASN ( 97-) E ND2 155 LEU ( 155-) E N 216 HIS ( 216-) E N Only metal coordination for 142 HIS ( 142-) E NE2 Only metal coordination for 177 GLU ( 177-) E OE1 Only metal coordination for 190 GLU ( 190-) E OE2 Only metal coordination for 250 HIS ( 250-) E ND1
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.
238 ASN ( 238-) E OD1
The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.
317 CA ( 317-) E -.- -.- Part of ionic cluster 317 CA ( 317-) E 0.77 1.01 Scores about as good as NA *1 and *2 318 CA ( 318-) E -.- -.- Part of ionic cluster 318 CA ( 318-) E 1.81 1.00 Is perhaps ZN *1 and *2 322 ZN ( 321-) E -.- -.- Too few ligands (1) 323 ZN ( 322-) E -.- -.- Too few ligands (3)
The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.
333 HOH ( 468 ) E O 1.10 K 4
37 ASP ( 37-) E H-bonding suggests Asn 119 GLU ( 119-) E H-bonding suggests Gln 294 ASP ( 294-) E 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 : -0.702 2nd generation packing quality : -1.327 Ramachandran plot appearance : -0.621 chi-1/chi-2 rotamer normality : 0.014 Backbone conformation : -0.289
Bond lengths : 0.942 Bond angles : 0.875 Omega angle restraints : 1.071 Side chain planarity : 1.060 Improper dihedral distribution : 0.939 B-factor distribution : 0.688 Inside/Outside distribution : 1.019
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 : -0.3 2nd generation packing quality : -0.9 Ramachandran plot appearance : 0.2 chi-1/chi-2 rotamer normality : 0.8 Backbone conformation : -0.3
Bond lengths : 0.942 Bond angles : 0.875 Omega angle restraints : 1.071 Side chain planarity : 1.060 Improper dihedral distribution : 0.939 B-factor distribution : 0.688 Inside/Outside distribution : 1.019 ==============
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.