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.
109 RAP ( 501-) A -
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'.
3 GLN ( 3-) A CG 3 GLN ( 3-) A CD 3 GLN ( 3-) A OE1 3 GLN ( 3-) A NE2 13 ARG ( 13-) A CD 13 ARG ( 13-) A NE 13 ARG ( 13-) A CZ 13 ARG ( 13-) A NH1 13 ARG ( 13-) A NH2 17 LYS ( 17-) A CG 17 LYS ( 17-) A CD 17 LYS ( 17-) A CE 17 LYS ( 17-) A NZ 18 ARG ( 18-) A CG 18 ARG ( 18-) A CD 18 ARG ( 18-) A NE 18 ARG ( 18-) A CZ 18 ARG ( 18-) A NH1 18 ARG ( 18-) A NH2 32 ASP ( 32-) A CG 32 ASP ( 32-) A OD1 32 ASP ( 32-) A OD2 44 LYS ( 44-) A CD 44 LYS ( 44-) A CE 44 LYS ( 44-) A NZ 50 LEU ( 50-) A CD1 50 LEU ( 50-) A CD2 52 LYS ( 52-) A CD 52 LYS ( 52-) A CE 52 LYS ( 52-) A NZ
Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.
WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.
54 GLU ( 54-) A 0.50
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: Aspartic acid convention problem
The aspartic acid residues listed in the table below have their chi-2 not
between -90.0 and 90.0, or their proton on OD1 instead of OD2.
37 ASP ( 37-) A 79 ASP ( 79-) A
5 GLU ( 5-) A 60 GLU ( 60-) A 102 GLU ( 102-) A
RMS Z-score for bond lengths: 0.341
RMS-deviation in bond distances: 0.007
Warning: Low bond angle variability
Bond angles were found to deviate less than normal from the standard bond
angles (normal values for protein residues were taken from Engh and Huber
[REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below
is expected to be near 1.0 for a normally restrained data set. The fact that
it is lower than 0.667 in this structure might indicate that too-strong
restraints have been used in the refinement. This can only be a problem for
high resolution X-ray structures.
RMS Z-score for bond angles: 0.522
RMS-deviation in bond angles: 1.032
Error: Nomenclature error(s)
Checking for a hand-check. WHAT IF has over the course of this session
already corrected the handedness of atoms in several residues. These were
administrative corrections. These residues are listed here.
5 GLU ( 5-) A 37 ASP ( 37-) A 60 GLU ( 60-) A 79 ASP ( 79-) A 102 GLU ( 102-) 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.
94 HIS ( 94-) A -2.3 14 THR ( 14-) A -2.2
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.
24 VAL ( 24-) A omega poor 81 ALA ( 81-) A Poor phi/psi 94 HIS ( 94-) A Poor phi/psi chi-1/chi-2 correlation Z-score : 0.489
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 GLU ( 5-) A 0 11 ASP ( 11-) A 0 13 ARG ( 13-) A 0 14 THR ( 14-) A 0 18 ARG ( 18-) A 0 29 MET ( 29-) A 0 31 GLU ( 31-) A 0 32 ASP ( 32-) A 0 34 LYS ( 34-) A 0 37 ASP ( 37-) A 0 50 LEU ( 50-) A 0 53 GLN ( 53-) A 0 54 GLU ( 54-) A 0 65 GLN ( 65-) A 0 68 VAL ( 68-) A 0 80 TYR ( 80-) A 0 81 ALA ( 81-) A 0 82 TYR ( 82-) A 0 85 THR ( 85-) A 0 87 HIS ( 87-) A 0 88 PRO ( 88-) A 0 90 ILE ( 90-) A 0 93 PRO ( 93-) A 0 94 HIS ( 94-) A 0 6 THR ( 6-) A 1 7 ILE ( 7-) A 1 25 HIS ( 25-) A 1 36 PHE ( 36-) A 1 42 ARG ( 42-) A 1 52 LYS ( 52-) A 1 84 ALA ( 84-) A 1 91 ILE ( 91-) A 1 100 ASP ( 100-) A 1 8 SER ( 8-) A 2 15 PHE ( 15-) A 2 22 CYS ( 22-) A 2 38 SER ( 38-) A 2 49 MET ( 49-) A 2 56 ILE ( 56-) A 2 67 SER ( 67-) A 2 70 GLN ( 70-) A 2 105 LYS ( 105-) A 2
93 PRO ( 93-) A 99.4 envelop C-beta (108 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.
51 GLY ( 51-) A N <-> 60 GLU ( 60-) A OE2 0.04 2.66 INTRA 26 TYR ( 26-) A N <-> 39 SER ( 39-) A OG 0.03 2.67 INTRA 74 LEU ( 74-) A N <-> 99 PHE ( 99-) A O 0.02 2.68 INTRA
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.
42 ARG ( 42-) A -5.69 49 MET ( 49-) A -5.36 82 TYR ( 82-) A -5.28 94 HIS ( 94-) A -5.16
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.
52 LYS ( 52-) A -3.47 53 GLN ( 53-) A -2.90 13 ARG ( 13-) A -2.61 17 LYS ( 17-) A -2.60 54 GLU ( 54-) A -2.55
The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.
51 GLY ( 51-) A - 54 GLU ( 54-) A -2.50
Chain identifier: A
Water, ion, and hydrogenbond related checks
Warning: Water molecules need moving
The water molecules listed in the table below were found to be significantly
closer to a symmetry related non-water molecule than to the ones given in the
coordinate file. For optimal viewing convenience revised coordinates for
these water molecules should be given.
The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.
110 HOH (1125 ) A O 10.49 15.36 12.22 110 HOH (1133 ) A O 13.75 -9.67 17.52
94 HIS ( 94-) 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.
40 ARG ( 40-) A N 40 ARG ( 40-) A NH2 41 ASP ( 41-) A N 55 VAL ( 55-) A N 56 ILE ( 56-) A N 82 TYR ( 82-) A OH
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 : -0.439 2nd generation packing quality : -1.734 Ramachandran plot appearance : 0.852 chi-1/chi-2 rotamer normality : 0.489 Backbone conformation : 0.129
Bond lengths : 0.341 (tight) Bond angles : 0.522 (tight) Omega angle restraints : 1.016 Side chain planarity : 0.215 (tight) Improper dihedral distribution : 0.458 B-factor distribution : 0.336 Inside/Outside distribution : 0.911
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 : 1.70
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.3 2nd generation packing quality : -1.4 Ramachandran plot appearance : 0.5 chi-1/chi-2 rotamer normality : 0.5 Backbone conformation : -0.3
Bond lengths : 0.341 (tight) Bond angles : 0.522 (tight) Omega angle restraints : 1.016 Side chain planarity : 0.215 (tight) Improper dihedral distribution : 0.458 B-factor distribution : 0.336 Inside/Outside distribution : 0.911 ==============
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.