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'.
1 GLU ( 22-) A CG 1 GLU ( 22-) A CD 1 GLU ( 22-) A OE1 1 GLU ( 22-) A OE2 60 GLN ( 81-) A CG 60 GLN ( 81-) A CD 60 GLN ( 81-) A OE1 60 GLN ( 81-) A NE2 149 ASN ( 170-) A CG 149 ASN ( 170-) A OD1 149 ASN ( 170-) A ND2 150 SER ( 171-) A OG
Obviously, the temperature at which the X-ray data was collected has some importance too:
Crystal temperature (K) :293.000
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 : 1.536 over 1131 bonds
Average difference in B over a bond : 4.00
RMS difference in B over a bond : 5.15
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
50 TYR ( 71-) A
27 PHE ( 48-) A
11 ASP ( 32-) A 52 ASP ( 73-) A 73 ASP ( 94-) A 138 ASP ( 159-) A
17 GLU ( 38-) A 144 GLU ( 165-) A
11 ASP ( 32-) A 17 GLU ( 38-) A 52 ASP ( 73-) A 73 ASP ( 94-) A 138 ASP ( 159-) A 144 GLU ( 165-) 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.
16 SER ( 37-) A -2.5 63 MET ( 84-) A -2.4 110 GLY ( 131-) A -2.1 62 PHE ( 83-) 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.
14 ILE ( 35-) A Poor phi/psi 15 ASP ( 36-) A Poor phi/psi 16 SER ( 37-) A Poor phi/psi 52 ASP ( 73-) A Poor phi/psi 61 ASN ( 82-) A Poor phi/psi 63 MET ( 84-) A Poor phi/psi 74 GLY ( 95-) A Poor phi/psi 107 ASN ( 128-) A Poor phi/psi 149 ASN ( 170-) A Poor phi/psi 151 HIS ( 172-) A Poor phi/psi 152 ASP ( 173-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -2.014
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!
13 MET ( 34-) A 0 14 ILE ( 35-) A 0 15 ASP ( 36-) A 0 16 SER ( 37-) A 0 19 LEU ( 40-) A 0 21 ARG ( 42-) A 0 27 PHE ( 48-) A 0 30 ASP ( 51-) A 0 45 GLU ( 66-) A 0 48 PHE ( 69-) A 0 50 TYR ( 71-) A 0 51 LYS ( 72-) A 0 53 SER ( 74-) A 0 54 ILE ( 75-) A 0 55 PHE ( 76-) A 0 56 HIS ( 77-) A 0 60 GLN ( 81-) A 0 61 ASN ( 82-) A 0 62 PHE ( 83-) A 0 63 MET ( 84-) A 0 70 THR ( 91-) A 0 71 ASN ( 92-) A 0 72 PHE ( 93-) A 0 73 ASP ( 94-) A 0 75 THR ( 96-) A 0And so on for a total of 91 lines.
Standard deviation of omega values : 1.479
Error: Abnormally short interatomic distances
The pairs of atoms listed in the table below have an unusually short
interactomic distance; each bump is listed in only one direction.
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 ( 22-) A N <-> 168 HOH ( 188 ) A O 0.49 2.21 INTRA 70 THR ( 91-) A C <-> 71 ASN ( 92-) A ND2 0.31 2.69 INTRA 70 THR ( 91-) A OG1 <-> 77 GLY ( 98-) A N 0.13 2.57 INTRA 1 GLU ( 22-) A CA <-> 168 HOH ( 188 ) A O 0.12 2.68 INTRA 40 GLN ( 61-) A OE1 <-> 46 HIS ( 67-) A NE2 0.12 2.58 INTRA 12 VAL ( 33-) A CG1 <-> 13 MET ( 34-) A N 0.05 2.95 INTRA 52 ASP ( 73-) A N <-> 160 ILE ( 181-) A O 0.05 2.65 INTRA 149 ASN ( 170-) A CB <-> 150 SER ( 171-) A N 0.05 2.65 INTRA BF 150 SER ( 171-) A O <-> 153 ARG ( 174-) A NE 0.04 2.66 INTRA BF 56 HIS ( 77-) A ND1 <-> 168 HOH ( 193 ) A O 0.03 2.67 INTRA 149 ASN ( 170-) A N <-> 153 ARG ( 174-) A O 0.03 2.67 INTRA BF 67 GLY ( 88-) A N <-> 168 HOH ( 192 ) A O 0.02 2.68 INTRA BL 94 HIS ( 115-) A ND1 <-> 124 ASP ( 145-) A OD1 0.02 2.68 INTRA 11 ASP ( 32-) A N <-> 162 ALA ( 183-) A O 0.02 2.68 INTRA 88 GLU ( 109-) A N <-> 168 HOH ( 191 ) A O 0.01 2.69 INTRA BL 111 SER ( 132-) A N <-> 112 GLN ( 133-) A N 0.01 2.59 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.
151 HIS ( 172-) A -6.29 83 GLU ( 104-) A -5.06
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.
46 HIS ( 67-) A -2.86
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.
71 ASN ( 92-) A 91 ASN ( 112-) A 103 ASN ( 124-) 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.
17 GLU ( 38-) A N 48 PHE ( 69-) A N 54 ILE ( 75-) A N 56 HIS ( 77-) A N 89 ASN ( 110-) A N 95 PHE ( 116-) A N 118 ALA ( 139-) A N 122 TRP ( 143-) A NE1
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 : -1.051 2nd generation packing quality : -1.371 Ramachandran plot appearance : -2.216 chi-1/chi-2 rotamer normality : -2.014 Backbone conformation : -1.531
Bond lengths : 0.355 (tight) Bond angles : 0.646 (tight) Omega angle restraints : 0.269 (tight) Side chain planarity : 0.221 (tight) Improper dihedral distribution : 0.664 B-factor distribution : 1.536 (loose) Inside/Outside distribution : 0.977
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 : 2.70
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.0 2nd generation packing quality : 0.2 Ramachandran plot appearance : 0.4 chi-1/chi-2 rotamer normality : 0.2 Backbone conformation : -0.8
Bond lengths : 0.355 (tight) Bond angles : 0.646 (tight) Omega angle restraints : 0.269 (tight) Side chain planarity : 0.221 (tight) Improper dihedral distribution : 0.664 B-factor distribution : 1.536 (loose) Inside/Outside distribution : 0.977 ==============
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.