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 MAA ( 7-) C - 175 BMT ( 5-) C - 176 MVA ( 4-) C - 177 DAL ( 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 DAL ( 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 167 MLE ( 3-) 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 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 : 8.31
Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
Chain identifier: A
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
| 0.999198 0.000074 -0.001427| | 0.000074 1.005211 0.000356| | -0.001427 0.000356 0.992833|Proposed new scale matrix
| 0.027510 -0.000002 0.000040| | -0.000001 0.016290 -0.000006| | 0.000020 -0.000005 0.013947|With corresponding cell
A = 36.350 B = 61.387 C = 71.700 Alpha= 89.959 Beta= 90.164 Gamma= 89.992
The CRYST1 cell dimensions
A = 36.380 B = 61.070 C = 72.220 Alpha= 90.000 Beta= 90.000 Gamma= 90.000
(Under-)estimated Z-score: 5.605
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.
1 MET ( 1-) A CA CB CG 126.58 6.2 2 VAL ( 2-) A N CA C 98.91 -4.4 3 ASN ( 3-) A ND2 CG OD1 117.98 -4.6 8 PHE ( 8-) A CA CB CG 120.40 6.6 19 ARG ( 19-) A CB CG CD 98.16 -8.0 19 ARG ( 19-) A CG CD NE 117.87 4.3 19 ARG ( 19-) A NE CZ NH1 128.68 4.6 19 ARG ( 19-) A NE CZ NH2 108.64 -6.0 27 ASP ( 27-) A CA CB CG 118.73 6.1 28 LYS ( 28-) A CA CB CG 104.92 -4.6 53 PHE ( 53-) A CA CB CG 108.53 -5.3 54 HIS ( 54-) A CB CG ND1 129.03 5.0 67 PHE ( 67-) A CA CB CG 119.08 5.3 70 HIS ( 70-) A CA CB CG 109.74 -4.1 70 HIS ( 70-) A CB CG ND1 128.25 4.4 71 ASN ( 71-) A ND2 CG OD1 118.45 -4.1 81 GLU ( 81-) A CB CG CD 120.20 4.5 83 PHE ( 83-) A CA CB CG 120.27 6.5 84 GLU ( 84-) A CB CG CD 120.54 4.7 92 HIS ( 92-) A CB CG ND1 129.35 5.2 92 HIS ( 92-) A CB CG CD2 122.77 -4.9 102 ASN ( 102-) A CA CB CG 118.07 5.5 102 ASN ( 102-) A ND2 CG OD1 118.18 -4.4 106 ASN ( 106-) A ND2 CG OD1 118.02 -4.6 121 TRP ( 121-) A CG CD2 CE2 101.78 -4.5 143 GLU ( 143-) A C CA CB 102.09 -4.2 148 ARG ( 148-) A CG CD NE 118.12 4.5 149 ASN ( 149-) A ND2 CG OD1 118.32 -4.3
Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.
Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.
170 VAL ( 9-) C C -6.7 -9.03 0.15 The average deviation= 1.427
2 VAL ( 2-) A 4.30
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 -2.3 102 ASN ( 102-) A -2.1 109 GLY ( 109-) 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.
70 HIS ( 70-) A Poor phi/psi 106 ASN ( 106-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -1.397
It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.
40 SER ( 40-) A 0.36
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 29 VAL ( 29-) 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 51 SER ( 51-) 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 67 PHE ( 67-) A 0 68 THR ( 68-) 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 0And so on for a total of 86 lines.
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.
172 ALA ( 11-) C C <-> 177 DAL ( 1-) C N 1.38 1.32 INTRA B3 166 MLE ( 2-) C N <-> 177 DAL ( 1-) C C 1.37 1.33 INTRA B3 168 VAL ( 6-) C N <-> 175 BMT ( 5-) C C 1.36 1.34 INTRA B3 169 MLE ( 8-) C N <-> 174 MAA ( 7-) C C 1.36 1.34 INTRA B3 168 VAL ( 6-) C C <-> 174 MAA ( 7-) C N 1.36 1.34 INTRA B3 175 BMT ( 5-) C N <-> 176 MVA ( 4-) C C 1.36 1.34 INTRA B3 167 MLE ( 3-) C C <-> 176 MVA ( 4-) C N 1.35 1.35 INTRA B3 166 MLE ( 2-) C CA <-> 177 DAL ( 1-) C C 0.85 2.35 INTRA 175 BMT ( 5-) C CA <-> 176 MVA ( 4-) C C 0.81 2.39 INTRA 169 MLE ( 8-) C CA <-> 174 MAA ( 7-) C C 0.77 2.43 INTRA 168 VAL ( 6-) C CA <-> 175 BMT ( 5-) C C 0.76 2.44 INTRA 169 MLE ( 8-) C CN <-> 174 MAA ( 7-) C C 0.73 2.47 INTRA 172 ALA ( 11-) C CA <-> 177 DAL ( 1-) C N 0.72 2.38 INTRA 175 BMT ( 5-) C CN <-> 176 MVA ( 4-) C C 0.70 2.50 INTRA 166 MLE ( 2-) C CN <-> 177 DAL ( 1-) C C 0.64 2.56 INTRA 168 VAL ( 6-) C CA <-> 174 MAA ( 7-) C N 0.61 2.49 INTRA 167 MLE ( 3-) C CA <-> 176 MVA ( 4-) C N 0.60 2.50 INTRA 167 MLE ( 3-) C O <-> 176 MVA ( 4-) C N 0.48 2.22 INTRA 172 ALA ( 11-) C O <-> 177 DAL ( 1-) C N 0.45 2.25 INTRA 168 VAL ( 6-) C O <-> 174 MAA ( 7-) C N 0.45 2.25 INTRA 52 CYS ( 52-) A SG <-> 155 LYS ( 155-) A NZ 0.40 2.90 INTRA 169 MLE ( 8-) C CN <-> 174 MAA ( 7-) C CA 0.35 2.85 INTRA 175 BMT ( 5-) C CN <-> 176 MVA ( 4-) C CA 0.28 2.92 INTRA 168 VAL ( 6-) C CA <-> 174 MAA ( 7-) C CM 0.28 2.92 INTRA 166 MLE ( 2-) C CN <-> 177 DAL ( 1-) C CA 0.19 3.01 INTRA 167 MLE ( 3-) C CA <-> 176 MVA ( 4-) C CN 0.18 3.02 INTRA 1 MET ( 1-) A N <-> 178 HOH (2001 ) A O 0.17 2.53 INTRA 167 MLE ( 3-) C O <-> 176 MVA ( 4-) C CA 0.17 2.63 INTRA 175 BMT ( 5-) C CA <-> 176 MVA ( 4-) C O 0.15 2.65 INTRA 166 MLE ( 2-) C CA <-> 177 DAL ( 1-) C O 0.14 2.66 INTRA 172 ALA ( 11-) C O <-> 177 DAL ( 1-) C CA 0.10 2.70 INTRA 168 VAL ( 6-) C O <-> 174 MAA ( 7-) C CA 0.09 2.71 INTRA 169 MLE ( 8-) C CA <-> 174 MAA ( 7-) C O 0.07 2.73 INTRA 168 VAL ( 6-) C CA <-> 175 BMT ( 5-) C O 0.03 2.77 INTRA 9 ASP ( 9-) A OD1 <-> 19 ARG ( 19-) A CD 0.01 2.79 INTRA BL 52 CYS ( 52-) A CB <-> 155 LYS ( 155-) A NZ 0.01 3.09 INTRA 68 THR ( 68-) A OG1 <-> 75 GLY ( 75-) 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.
148 ARG ( 148-) A -7.76 69 ARG ( 69-) A -5.63 144 ARG ( 144-) A -5.47
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 (2038 ) A O -68.22 31.40 118.75 178 HOH (2064 ) A O -60.33 39.76 121.40
178 HOH (2141 ) A O 179 HOH (2004 ) C O Unrecognized bound group for 167 Bound atom= 176 MVA ( 4-) C N
3 ASN ( 3-) A 70 HIS ( 70-) A 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.
19 ARG ( 19-) A NE 70 HIS ( 70-) 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
Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.
Waters are not listed by this option.
9 ASP ( 9-) A OD1
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 (2090 ) A O 1.08 K 4 178 HOH (2138 ) A O 0.95 K 4 ION-B
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 : -1.151 2nd generation packing quality : -2.055 Ramachandran plot appearance : -0.459 chi-1/chi-2 rotamer normality : -1.397 Backbone conformation : -0.376
Bond lengths : 0.769 Bond angles : 1.408 Omega angle restraints : 0.760 Side chain planarity : 0.642 (tight) Improper dihedral distribution : 1.192 Inside/Outside distribution : 0.932
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 : 1.90
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.7 2nd generation packing quality : -1.5 Ramachandran plot appearance : -0.1 chi-1/chi-2 rotamer normality : -0.7 Backbone conformation : -0.7
Bond lengths : 0.769 Bond angles : 1.408 Omega angle restraints : 0.760 Side chain planarity : 0.642 (tight) Improper dihedral distribution : 1.192 Inside/Outside distribution : 0.932 ==============
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.