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.
193 PEG ( 115-) A - 194 FK5 ( 114-) 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'.
33 LYS ( -44-) A CG 33 LYS ( -44-) A CD 33 LYS ( -44-) A CE 33 LYS ( -44-) A NZ 38 GLU ( -39-) A CG 38 GLU ( -39-) A CD 38 GLU ( -39-) A OE1 38 GLU ( -39-) A OE2 40 ASP ( -37-) A CG 40 ASP ( -37-) A OD1 40 ASP ( -37-) A OD2 74 GLN ( -3-) A CG 74 GLN ( -3-) A CD 74 GLN ( -3-) A OE1 74 GLN ( -3-) A NE2 101 ARG ( 24-) A CG 101 ARG ( 24-) A CD 101 ARG ( 24-) A NE 101 ARG ( 24-) A CZ 101 ARG ( 24-) A NH1 101 ARG ( 24-) A NH2 124 LYS ( 47-) A CG 124 LYS ( 47-) A CD 124 LYS ( 47-) A CE 124 LYS ( 47-) A NZ 131 GLU ( 54-) A CG 131 GLU ( 54-) A CD 131 GLU ( 54-) A OE1 131 GLU ( 54-) A OE2 169 ARG ( 92-) A CG 169 ARG ( 92-) A CD 169 ARG ( 92-) A NE 169 ARG ( 92-) A CZ 169 ARG ( 92-) A NH1 169 ARG ( 92-) A NH2
Obviously, the temperature at which the X-ray data was collected has some importance too:
Number of TLS groups mentione in PDB file header: 2
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
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: 0.602
RMS-deviation in bond distances: 0.012
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
| 0.997245 -0.000714 -0.000704| | -0.000714 0.997930 0.000691| | -0.000704 0.000691 0.996737|Proposed new scale matrix
| 0.010416 0.000003 0.006409| | 0.000023 0.032035 -0.000022| | 0.000011 -0.000011 0.015845|With corresponding cell
A = 96.046 B = 31.216 C = 74.135 Alpha= 89.889 Beta= 121.645 Gamma= 90.082
The CRYST1 cell dimensions
A = 96.310 B = 31.280 C = 74.320 Alpha= 90.000 Beta= 121.570 Gamma= 90.000
(Under-)estimated Z-score: 5.003
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.
109 HIS ( 32-) A CG ND1 CE1 109.61 4.0
146 GLY ( 69-) A 4.11
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.
61 ASP ( -16-) A Poor phi/psi 65 ASN ( -12-) A Poor phi/psi 108 VAL ( 31-) A omega poor 171 ALA ( 94-) A omega poor 178 ASN ( 101-) A Poor phi/psi 179 ALA ( 102-) A omega poor 183 PHE ( 106-) A omega poor chi-1/chi-2 correlation Z-score : 0.625
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!
9 ASP ( -68-) A 0 11 SER ( -66-) A 0 35 GLN ( -42-) A 0 42 LEU ( -35-) A 0 62 MET ( -15-) A 0 64 ASP ( -13-) A 0 65 ASN ( -12-) A 0 72 ARG ( -5-) A 0 75 ILE ( -2-) A 0 85 SER ( 8-) A 0 92 LEU ( 15-) A 0 98 ALA ( 21-) A 0 100 ALA ( 23-) A 0 102 ALA ( 25-) A 0 120 PHE ( 43-) A 0 121 ASP ( 44-) A 0 128 ASP ( 51-) A 0 134 LEU ( 57-) A 0 138 MET ( 61-) A 0 139 VAL ( 62-) A 0 148 GLN ( 71-) A 0 150 MET ( 73-) A 0 152 VAL ( 75-) A 0 164 LEU ( 87-) A 0 166 TYR ( 89-) A 0And so on for a total of 59 lines.
176 PRO ( 99-) A 0.06 LOW
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.
6 LYS ( -71-) A NZ <-> 13 GLU ( -64-) A CD 0.45 2.65 INTRA 6 LYS ( -71-) A NZ <-> 13 GLU ( -64-) A OE1 0.32 2.38 INTRA BF 6 LYS ( -71-) A NZ <-> 13 GLU ( -64-) A CB 0.20 2.90 INTRA 88 LYS ( 11-) A NZ <-> 195 HOH ( 125 ) A O 0.16 2.54 INTRA 25 ARG ( -52-) A NH2 <-> 195 HOH ( 120 ) A O 0.15 2.55 INTRA 6 LYS ( -71-) A NZ <-> 13 GLU ( -64-) A CG 0.13 2.97 INTRA 109 HIS ( 32-) A ND1 <-> 123 SER ( 46-) A OG 0.13 2.57 INTRA 6 LYS ( -71-) A CE <-> 13 GLU ( -64-) A CD 0.12 3.08 INTRA 4 ASN ( -73-) A O <-> 65 ASN ( -12-) A N 0.10 2.60 INTRA 78 SER ( 1-) A N <-> 195 HOH ( 263 ) A O 0.06 2.64 INTRA 19 LYS ( -58-) A NZ <-> 195 HOH ( 155 ) A O 0.05 2.65 INTRA 104 GLN ( 27-) A NE2 <-> 195 HOH ( 136 ) A O 0.02 2.68 INTRA BF 119 LYS ( 42-) A NZ <-> 125 ASP ( 48-) A OD2 0.02 2.68 INTRA 116 ASP ( 39-) A OD1 <-> 118 GLN ( 41-) A N 0.01 2.69 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.
166 TYR ( 89-) A -6.39 75 ILE ( -2-) A -6.34 138 MET ( 61-) A -6.04 72 ARG ( -5-) A -5.78 126 ARG ( 49-) A -5.73 34 ARG ( -43-) A -5.71 163 GLN ( 86-) A -5.68 84 GLU ( 7-) A -5.55 35 GLN ( -42-) A -5.51
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.
74 GLN ( -3-) A -3.18 138 MET ( 61-) A -2.78 174 VAL ( 97-) A -2.76 169 ARG ( 92-) A -2.66 40 ASP ( -37-) A -2.54 124 LYS ( 47-) A -2.51
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.
195 HOH ( 132 ) A O 6.09 -21.05 34.01 195 HOH ( 150 ) A O 1.23 -20.99 39.12
118 GLN ( 41-) 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.
105 THR ( 28-) A N 140 ILE ( 63-) A N 143 TRP ( 66-) A NE1 166 TYR ( 89-) A OH
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.
195 HOH ( 141 ) A O 0.91 K 4 195 HOH ( 144 ) A O 0.88 K 4 ION-B 195 HOH ( 183 ) A O 1.07 K 5
189 ASP ( 112-) A H-bonding suggests Asn
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 : -0.289 2nd generation packing quality : -1.039 Ramachandran plot appearance : 0.627 chi-1/chi-2 rotamer normality : 0.625 Backbone conformation : 0.652
Bond lengths : 0.602 (tight) Bond angles : 0.746 Omega angle restraints : 1.067 Side chain planarity : 0.877 Improper dihedral distribution : 0.862 B-factor distribution : 0.440 Inside/Outside distribution : 0.979
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 : 1.55
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.0 2nd generation packing quality : -1.2 Ramachandran plot appearance : 0.2 chi-1/chi-2 rotamer normality : 0.3 Backbone conformation : 0.4
Bond lengths : 0.602 (tight) Bond angles : 0.746 Omega angle restraints : 1.067 Side chain planarity : 0.877 Improper dihedral distribution : 0.862 B-factor distribution : 0.440 Inside/Outside distribution : 0.979 ==============
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.