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.
Plausible side chain atoms were detected with (near) zero occupancy
When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.
6 LYS ( 9-) A - CB 6 LYS ( 9-) A - CG 6 LYS ( 9-) A - CD 6 LYS ( 9-) A - CE 6 LYS ( 9-) A - NZ 11 GLU ( 14-) A - CG 11 GLU ( 14-) A - CD 11 GLU ( 14-) A - OE1 11 GLU ( 14-) A - OE2 42 LYS ( 45-) A - CD 42 LYS ( 45-) A - CE 42 LYS ( 45-) A - NZ 82 ASP ( 85-) A - CG 82 ASP ( 85-) A - OD1 82 ASP ( 85-) A - OD2 249 ASN ( 253-) A - CB 249 ASN ( 253-) A - CG 249 ASN ( 253-) A - OD1 249 ASN ( 253-) A - ND2
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'.
257 LYS ( 261-) A CB 257 LYS ( 261-) A CG 257 LYS ( 261-) A CD 257 LYS ( 261-) A CE 257 LYS ( 261-) A NZ
Obviously, the temperature at which the X-ray data was collected has some importance too:
Temperature cannot be read from the PDB file. This most likely means that
the temperature is listed as NULL (meaning unknown) in the PDB file.
Warning: More than 5 percent of buried atoms has low B-factor
For normal protein structures, no more than about 1 percent of the B factors
of buried atoms is below 5.0. The fact that this value is much higher in the
current structure could be a signal that the B-factors were restraints or
constraints to too-low values, misuse of B-factor field in the PDB file, or
a TLS/scaling problem. If the average B factor is low too, it is probably a
low temperature structure determination.
Percentage of buried atoms with B less than 5 : 7.04
Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
Chain identifier: A
Warning: Low bond length variability
Bond lengths were found to deviate less than normal from the mean Engh and
Huber [REF] and/or Parkinson et al [REF] standard bond lengths. 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 lengths: 0.636
RMS-deviation in bond distances: 0.015
Warning: Possible cell scaling problem
Comparison of bond distances with Engh and Huber [REF] standard values for
protein residues and Parkinson et al [REF] values for DNA/RNA shows a
significant systematic deviation. It could be that the unit cell used in
refinement was not accurate enough. The deformation matrix given below gives
the deviations found: the three numbers on the diagonal represent the
relative corrections needed along the A, B and C cell axis. These values are
1.000 in a normal case, but have significant deviations here (significant at
the 99.99 percent confidence level)
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
| 0.998171 0.000321 0.002863| | 0.000321 1.000148 -0.000826| | 0.002863 -0.000826 0.997391|Proposed new scale matrix
| 0.023445 -0.000003 0.006049| | -0.000008 0.023977 0.000020| | -0.000041 0.000012 0.014193|With corresponding cell
A = 42.622 B = 41.706 C = 72.710 Alpha= 90.101 Beta= 104.302 Gamma= 89.963
The CRYST1 cell dimensions
A = 42.700 B = 41.700 C = 73.000 Alpha= 90.000 Beta= 104.600 Gamma= 90.000
(Under-)estimated Z-score: 4.789
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.
14 HIS ( 17-) A CG ND1 CE1 109.61 4.0 61 HIS ( 64-) A CG ND1 CE1 109.82 4.2 204 THR ( 208-) A N CA C 99.91 -4.0
154 GLN ( 158-) A 4.53 203 VAL ( 207-) A 4.07 204 THR ( 208-) A 4.02
Tau angle RMS Z-score : 1.513
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.
77 LYS ( 80-) A -2.7 80 PRO ( 83-) A -2.4 57 LEU ( 60-) A -2.2 172 PHE ( 176-) A -2.2 163 ILE ( 167-) A -2.2 159 VAL ( 163-) A -2.1 47 SER ( 50-) A -2.1 19 ILE ( 22-) A -2.1 147 GLY ( 151-) A -2.0 89 GLN ( 92-) 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.
26 SER ( 29-) A PRO omega poor 72 ASP ( 75-) A Poor phi/psi 108 LYS ( 111-) A Poor phi/psi 174 ASN ( 178-) A Poor phi/psi 197 PRO ( 201-) A PRO omega poor 199 LEU ( 203-) A Poor phi/psi 239 ASP ( 243-) A Poor phi/psi 248 LYS ( 252-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -1.358
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!
4 TYR ( 7-) A 0 7 HIS ( 10-) A 0 16 ASP ( 19-) A 0 17 PHE ( 20-) A 0 21 LYS ( 24-) A 0 24 ARG ( 27-) A 0 25 GLN ( 28-) A 0 26 SER ( 29-) A 0 47 SER ( 50-) A 0 49 ASP ( 52-) A 0 51 ALA ( 54-) A 0 59 ASN ( 62-) A 0 61 HIS ( 64-) A 0 69 ASP ( 72-) A 0 70 SER ( 73-) A 0 72 ASP ( 75-) A 0 73 LYS ( 76-) A 0 74 ALA ( 77-) A 0 77 LYS ( 80-) A 0 80 PRO ( 83-) A 0 82 ASP ( 85-) A 0 89 GLN ( 92-) A 0 93 HIS ( 96-) A 0 100 GLN ( 103-) A 0 104 HIS ( 107-) A 0And so on for a total of 115 lines.
Standard deviation of omega values : 2.410
Warning: Unusual PRO puckering amplitudes
The proline residues listed in the table below have a puckering amplitude
that is outside of normal ranges. Puckering parameters were calculated by
the method of Cremer and Pople [REF]. Normal PRO rings have a puckering
amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom
for a PRO residue, this could indicate disorder between the two different
normal ring forms (with C-gamma below and above the ring, respectively). If
Q is higher than 0.45 Angstrom something could have gone wrong during the
refinement. Be aware that this is a warning with a low confidence level. See:
Who checks the checkers? Four validation tools applied to eight atomic
resolution structures [REF]
27 PRO ( 30-) A 0.48 HIGH 151 PRO ( 155-) A 0.45 HIGH 197 PRO ( 201-) A 0.47 HIGH
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.
114 GLN ( 117-) A NE2 <-> 116 HIS ( 119-) A NE2 0.50 2.50 INTRA BL 104 HIS ( 107-) A ND1 <-> 114 GLN ( 117-) A NE2 0.19 2.81 INTRA BL 145 LYS ( 149-) A NZ <-> 213 SER ( 217-) A CB 0.12 2.98 INTRA 48 TYR ( 51-) A OH <-> 119 HIS ( 122-) A NE2 0.10 2.60 INTRA BL 12 HIS ( 15-) A ND1 <-> 15 LYS ( 18-) A NZ 0.09 2.91 INTRA BL 72 ASP ( 75-) A OD1 <-> 86 ARG ( 89-) A NE 0.09 2.61 INTRA 19 ILE ( 22-) A O <-> 22 GLY ( 25-) A N 0.08 2.62 INTRA BL 243 PRO ( 247-) A O <-> 245 GLN ( 249-) A NE2 0.05 2.65 INTRA BL 196 THR ( 200-) A C <-> 197 PRO ( 201-) A C 0.04 2.76 INTRA BL 37 TYR ( 40-) A CD1 <-> 256 PHE ( 260-) A C 0.02 3.18 INTRA 18 PRO ( 21-) A C <-> 20 ALA ( 23-) A N 0.02 2.88 INTRA BL 69 ASP ( 72-) A OD2 <-> 120 TRP ( 123-) A NE1 0.02 2.68 INTRA BL 52 THR ( 55-) A N <-> 73 LYS ( 76-) A NZ 0.01 2.84 INTRA 104 HIS ( 107-) A NE2 <-> 190 TYR ( 194-) A OH 0.01 2.69 INTRA BL 217 GLU ( 221-) A O <-> 221 LYS ( 225-) A CE 0.01 2.79 INTRA 174 ASN ( 178-) A N <-> 259 HOH ( 303 ) A O 0.01 2.69 INTRA BL 93 HIS ( 96-) A ND1 <-> 240 ASN ( 244-) A O 0.01 2.69 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.
7 HIS ( 10-) A -6.10 97 LEU ( 100-) A -5.05
Chain identifier: A
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: 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.
259 HOH ( 368 ) A O 11.45 -7.04 22.75 259 HOH ( 427 ) A O -13.24 -18.15 15.67
259 HOH ( 415 ) A O Metal-coordinating Histidine residue 91 fixed to 1 Metal-coordinating Histidine residue 93 fixed to 1 Metal-coordinating Histidine residue 116 fixed to 1
33 HIS ( 36-) A 50 GLN ( 53-) A 133 GLN ( 137-) A 174 ASN ( 178-) 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 TRP ( 5-) A N 26 SER ( 29-) A OG 28 VAL ( 31-) A N 42 LYS ( 45-) A N 52 THR ( 55-) A N 71 GLN ( 74-) A N 73 LYS ( 76-) A NZ 97 LEU ( 100-) A N 114 GLN ( 117-) A NE2 116 HIS ( 119-) A NE2 178 ARG ( 182-) A NH1 196 THR ( 200-) A N 200 LEU ( 204-) A N 240 ASN ( 244-) A ND2 241 TRP ( 245-) A N 249 ASN ( 253-) A N 256 PHE ( 260-) A N Only metal coordination for 93 HIS ( 96-) A NE2 Only metal coordination for 116 HIS ( 119-) A ND1
235 GLU ( 239-) A H-bonding suggests Gln
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 : -0.216 2nd generation packing quality : 0.419 Ramachandran plot appearance : -1.333 chi-1/chi-2 rotamer normality : -1.358 Backbone conformation : -0.790
Bond lengths : 0.636 (tight) Bond angles : 0.837 Omega angle restraints : 0.438 (tight) Side chain planarity : 0.628 (tight) Improper dihedral distribution : 1.198 Inside/Outside distribution : 0.949
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 : 1.80
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.2 2nd generation packing quality : -0.2 Ramachandran plot appearance : -1.3 chi-1/chi-2 rotamer normality : -1.0 Backbone conformation : -1.1
Bond lengths : 0.636 (tight) Bond angles : 0.837 Omega angle restraints : 0.438 (tight) Side chain planarity : 0.628 (tight) Improper dihedral distribution : 1.198 Inside/Outside distribution : 0.949 ==============
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.