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.
174 SAR ( 7-) C - 175 BMT ( 5-) C - 176 MVA ( 4-) C - 177 VAD ( 1-) C -
For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.
166 MLE ( 2-) C - N bound to 177 VAD ( 1-) C - C
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: Artificial side chains detected
At least two residues (listed in the table below) were detected with chi-1
equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally,
the listed residues have probably not been refined.
166 MLE ( 2-) C 169 MLE ( 8-) C 171 MLE ( 10-) C
Obviously, the temperature at which the X-ray data was collected has some importance too:
Crystal temperature (K) :293.000
Warning: More than 2 percent of buried atoms has low B-factor
For protein structures determined at room temperature, no more than
about 1 percent of the B factors of buried atoms is below 5.0.
Percentage of buried atoms with B less than 5 : 4.02
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: 0.424
RMS-deviation in bond distances: 0.011
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.
126 HIS ( 126-) A CG ND1 CE1 109.67 4.1
53 PHE ( 53-) A 4.00
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.
61 MET ( 61-) A -2.4 2 VAL ( 2-) A -2.3 76 LYS ( 76-) A -2.2 109 GLY ( 109-) A -2.1 17 LEU ( 17-) A -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.
60 PHE ( 60-) A Poor phi/psi 70 HIS ( 70-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -0.406
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!
12 VAL ( 12-) A 0 16 PRO ( 16-) A 0 25 PHE ( 25-) A 0 26 ALA ( 26-) A 0 28 LYS ( 28-) A 0 43 GLU ( 43-) A 0 44 LYS ( 44-) A 0 46 PHE ( 46-) A 0 48 TYR ( 48-) A 0 49 LYS ( 49-) A 0 53 PHE ( 53-) A 0 54 HIS ( 54-) A 0 58 PRO ( 58-) A 0 60 PHE ( 60-) A 0 61 MET ( 61-) A 0 68 THR ( 68-) A 0 69 ARG ( 69-) A 0 70 HIS ( 70-) A 0 71 ASN ( 71-) A 0 73 THR ( 73-) A 0 79 TYR ( 79-) A 0 81 GLU ( 81-) A 0 83 PHE ( 83-) A 0 86 GLU ( 86-) A 0 87 ASN ( 87-) A 0And so on for a total of 84 lines.
Standard deviation of omega values : 1.822
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.
168 THR ( 6-) C N <-> 175 BMT ( 5-) C C 1.37 1.33 INTRA B3 166 MLE ( 2-) C N <-> 177 VAD ( 1-) C C 1.37 1.33 INTRA B3 168 THR ( 6-) C C <-> 174 SAR ( 7-) C N 1.37 1.33 INTRA B3 169 MLE ( 8-) C N <-> 174 SAR ( 7-) C C 1.37 1.33 INTRA B3 167 LEU ( 3-) C C <-> 176 MVA ( 4-) C N 1.37 1.33 INTRA B3 175 BMT ( 5-) C N <-> 176 MVA ( 4-) C C 1.36 1.34 INTRA B3 175 BMT ( 5-) C CA <-> 176 MVA ( 4-) C C 0.80 2.40 INTRA 169 MLE ( 8-) C CN <-> 174 SAR ( 7-) C C 0.78 2.42 INTRA 166 MLE ( 2-) C CN <-> 177 VAD ( 1-) C C 0.78 2.42 INTRA 166 MLE ( 2-) C CA <-> 177 VAD ( 1-) C C 0.76 2.44 INTRA 169 MLE ( 8-) C CA <-> 174 SAR ( 7-) C C 0.76 2.44 INTRA 168 THR ( 6-) C CA <-> 175 BMT ( 5-) C C 0.76 2.44 INTRA 175 BMT ( 5-) C CN <-> 176 MVA ( 4-) C C 0.74 2.46 INTRA 167 LEU ( 3-) C CA <-> 176 MVA ( 4-) C N 0.66 2.44 INTRA 168 THR ( 6-) C CA <-> 174 SAR ( 7-) C N 0.65 2.45 INTRA 168 THR ( 6-) C O <-> 174 SAR ( 7-) C N 0.45 2.25 INTRA 167 LEU ( 3-) C O <-> 176 MVA ( 4-) C N 0.45 2.25 INTRA 166 MLE ( 2-) C CN <-> 177 VAD ( 1-) C CA 0.43 2.77 INTRA 169 MLE ( 8-) C CN <-> 174 SAR ( 7-) C CA 0.43 2.77 INTRA 175 BMT ( 5-) C CN <-> 176 MVA ( 4-) C CA 0.34 2.86 INTRA 167 LEU ( 3-) C CA <-> 176 MVA ( 4-) C CN 0.33 2.87 INTRA 52 CYS ( 52-) A SG <-> 155 LYS ( 155-) A NZ 0.32 2.98 INTRA 168 THR ( 6-) C CA <-> 174 SAR ( 7-) C CN 0.27 2.93 INTRA 1 MET ( 1-) A SD <-> 2 VAL ( 2-) A N 0.24 2.96 INTRA BF 52 CYS ( 52-) A SG <-> 157 THR ( 157-) A CG2 0.12 3.28 INTRA 44 LYS ( 44-) A O <-> 178 HOH (2071 ) A O 0.11 2.29 INTRA BF 70 HIS ( 70-) A CD2 <-> 178 HOH (2096 ) A O 0.11 2.69 INTRA 175 BMT ( 5-) C CA <-> 176 MVA ( 4-) C O 0.10 2.70 INTRA 167 LEU ( 3-) C O <-> 176 MVA ( 4-) C CA 0.08 2.72 INTRA 65 GLY ( 65-) A N <-> 178 HOH (2095 ) A O 0.06 2.64 INTRA 168 THR ( 6-) C O <-> 174 SAR ( 7-) C CA 0.06 2.74 INTRA 166 MLE ( 2-) C CA <-> 177 VAD ( 1-) C O 0.04 2.76 INTRA 44 LYS ( 44-) A C <-> 178 HOH (2071 ) A O 0.04 2.76 INTRA BF 102 ASN ( 102-) A ND2 <-> 178 HOH (2132 ) A O 0.04 2.66 INTRA BL 170 LEU ( 9-) C CA <-> 171 MLE ( 10-) C CN 0.04 2.76 INTRA BF 169 MLE ( 8-) C CA <-> 174 SAR ( 7-) C O 0.04 2.76 INTRA 171 MLE ( 10-) C CD2 <-> 172 ALA ( 11-) C N 0.03 2.97 INTRA BF 52 CYS ( 52-) A CB <-> 178 HOH (2098 ) A O 0.03 2.77 INTRA 6 VAL ( 6-) A CG1 <-> 7 PHE ( 7-) A N 0.02 2.98 INTRA 154 LYS ( 154-) A NZ <-> 178 HOH (2194 ) A O 0.02 2.68 INTRA 169 MLE ( 8-) C CN <-> 174 SAR ( 7-) C N 0.02 3.08 INTRA 116 THR ( 116-) A N <-> 117 ALA ( 117-) A N 0.01 2.59 INTRA BL 168 THR ( 6-) C CA <-> 175 BMT ( 5-) C O 0.01 2.79 INTRA 59 GLY ( 59-) A N <-> 143 GLU ( 143-) A OE2 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.
148 ARG ( 148-) A -7.88 170 LEU ( 9-) C -7.17 144 ARG ( 144-) A -5.27
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.
120 GLU ( 120-) A -2.82
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.
178 HOH (2008 ) A O 2.86 52.57 47.52 178 HOH (2035 ) A O -2.00 70.42 75.32 178 HOH (2036 ) A O 15.55 38.16 66.14
178 HOH (2111 ) A O 178 HOH (2177 ) A O 179 HOH (2003 ) C O Unrecognized bound group for 167 Bound atom= 176 MVA ( 4-) C N
102 ASN ( 102-) 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.
1 MET ( 1-) A N 35 ASN ( 35-) A ND2 46 PHE ( 46-) A N 87 ASN ( 87-) A N 94 GLY ( 94-) A N 102 ASN ( 102-) A N 117 ALA ( 117-) A N 121 TRP ( 121-) A N 154 LYS ( 154-) A N
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.
178 HOH (2160 ) A O 1.10 K 4 178 HOH (2182 ) A O 0.96 K 4
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 : -1.237 2nd generation packing quality : -2.241 Ramachandran plot appearance : -0.659 chi-1/chi-2 rotamer normality : -0.406 Backbone conformation : -0.441
Bond lengths : 0.424 (tight) Bond angles : 0.701 Omega angle restraints : 0.331 (tight) Side chain planarity : 0.526 (tight) Improper dihedral distribution : 0.923 B-factor distribution : 0.986 Inside/Outside distribution : 0.938
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 : 1.86
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.7 2nd generation packing quality : -1.6 Ramachandran plot appearance : -0.4 chi-1/chi-2 rotamer normality : 0.1 Backbone conformation : -0.7
Bond lengths : 0.424 (tight) Bond angles : 0.701 Omega angle restraints : 0.331 (tight) Side chain planarity : 0.526 (tight) Improper dihedral distribution : 0.923 B-factor distribution : 0.986 Inside/Outside distribution : 0.938 ==============
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.