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.
212 SO4 ( 215-) 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'.
1 VAL ( 5-) A CG1 1 VAL ( 5-) A CG2 9 GLU ( 13-) A CG 9 GLU ( 13-) A CD 9 GLU ( 13-) A OE1 9 GLU ( 13-) A OE2 18 GLU ( 22-) A CG 18 GLU ( 22-) A CD 18 GLU ( 22-) A OE1 18 GLU ( 22-) A OE2 83 ASN ( 87-) A CG 83 ASN ( 87-) A OD1 83 ASN ( 87-) A ND2 85 GLU ( 89-) A CG 85 GLU ( 89-) A CD 85 GLU ( 89-) A OE1 85 GLU ( 89-) A OE2 87 GLU ( 91-) A CG 87 GLU ( 91-) A CD 87 GLU ( 91-) A OE1 87 GLU ( 91-) A OE2
Obviously, the temperature at which the X-ray data was collected has some importance too:
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: Tyrosine convention problem
The tyrosine residues listed in the table below have their chi-2 not between
-90.0 and 90.0
101 TYR ( 105-) A 205 TYR ( 209-) A
4 PHE ( 8-) A 63 PHE ( 67-) A
57 ASP ( 61-) A 97 ASP ( 101-) A 125 ASP ( 129-) A 126 ASP ( 130-) A 159 ASP ( 163-) A
100 GLU ( 104-) A
RMS Z-score for bond lengths: 0.586
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
| 0.998083 -0.000745 0.000231| | -0.000745 0.997386 0.000962| | 0.000231 0.000962 0.997943|Proposed new scale matrix
| 0.012117 0.000009 -0.000003| | 0.000009 0.012126 -0.000012| | -0.000003 -0.000012 0.012119|With corresponding cell
A = 82.527 B = 82.470 C = 82.516 Alpha= 89.890 Beta= 89.973 Gamma= 90.086
The CRYST1 cell dimensions
A = 82.683 B = 82.683 C = 82.683 Alpha= 90.000 Beta= 90.000 Gamma= 90.000
(Under-)estimated Z-score: 4.211
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.
3 GLU ( 7-) A -C N CA 130.92 5.1 10 ASN ( 14-) A CA CB CG 117.85 5.3 14 PRO ( 18-) A N CA CB 107.82 4.4 16 ASN ( 20-) A CB CG ND2 123.54 4.8 16 ASN ( 20-) A ND2 CG OD1 116.61 -6.0 17 PRO ( 21-) A N CA CB 108.02 4.6 26 PRO ( 30-) A N CA CB 107.50 4.1 55 ARG ( 59-) A CG CD NE 119.84 5.5 60 MET ( 64-) A CA CB CG 126.08 6.0 77 HIS ( 81-) A CG ND1 CE1 109.85 4.3 84 GLU ( 88-) A CA C O 129.81 5.3 85 GLU ( 89-) A -CA -C N 108.13 -4.0 88 PRO ( 92-) A N CA CB 108.33 4.8 92 ASN ( 96-) A CA CB CG 108.14 -4.5 94 VAL ( 98-) A C CA CB 118.17 4.2 107 ASN ( 111-) A ND2 CG OD1 118.18 -4.4 113 HIS ( 117-) A CE1 NE2 CD2 114.22 5.6 118 HIS ( 122-) A CA CB CG 107.09 -6.7 128 PHE ( 132-) A CA CB CG 117.86 4.1 143 ASN ( 147-) A CA CB CG 107.38 -5.2 149 ARG ( 153-) A CG CD NE 99.35 -6.6 158 PRO ( 162-) A N CA CB 107.88 4.4 179 PRO ( 183-) A N CA CB 107.49 4.1 191 ASN ( 195-) A CA CB CG 107.29 -5.3 200 HIS ( 204-) A CA CB CG 109.18 -4.6
57 ASP ( 61-) A 97 ASP ( 101-) A 100 GLU ( 104-) A 125 ASP ( 129-) A 126 ASP ( 130-) A 159 ASP ( 163-) A
38 GLY ( 42-) A 4.06
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.
84 GLU ( 88-) A -2.4 61 PRO ( 65-) A -2.3 82 ILE ( 86-) A -2.3
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.
2 ASP ( 6-) A Poor phi/psi 45 ASN ( 49-) A Poor phi/psi 51 MET ( 55-) A Poor phi/psi 58 GLU ( 62-) A Poor phi/psi 60 MET ( 64-) A PRO omega poor 67 ARG ( 71-) A Poor phi/psi 83 ASN ( 87-) A Poor phi/psi 85 GLU ( 89-) A Poor phi/psi 114 GLN ( 118-) A Poor phi/psi 119 GLY ( 123-) A PRO omega poor 126 ASP ( 130-) A Poor phi/psi 132 GLN ( 136-) A Poor phi/psi 137 LYS ( 141-) A Poor phi/psi 149 ARG ( 153-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -2.533
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!
3 GLU ( 7-) A 0 7 ILE ( 11-) A 0 8 ARG ( 12-) A 0 9 GLU ( 13-) A 0 12 VAL ( 16-) A 0 15 TRP ( 19-) A 0 34 ALA ( 38-) A 0 37 ILE ( 41-) A 0 39 GLU ( 43-) A 0 44 ALA ( 48-) A 0 45 ASN ( 49-) A 0 49 SER ( 53-) A 0 50 PRO ( 54-) A 0 51 MET ( 55-) A 0 56 SER ( 60-) A 0 57 ASP ( 61-) A 0 60 MET ( 64-) A 0 61 PRO ( 65-) A 0 67 ARG ( 71-) A 0 71 GLN ( 75-) A 0 72 ASP ( 76-) A 0 77 HIS ( 81-) A 0 84 GLU ( 88-) A 0 85 GLU ( 89-) A 0 87 GLU ( 91-) A 0And so on for a total of 91 lines.
17 PRO ( 21-) A 0.17 LOW 32 PRO ( 36-) A 0.18 LOW 158 PRO ( 162-) A 0.12 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.
170 THR ( 174-) A N <-> 174 GLU ( 178-) A OE2 0.34 2.36 INTRA 83 ASN ( 87-) A N <-> 87 GLU ( 91-) A O 0.32 2.38 INTRA BF 85 GLU ( 89-) A N <-> 86 GLY ( 90-) A N 0.26 2.34 INTRA BF 108 ASN ( 112-) A O <-> 191 ASN ( 195-) A ND2 0.16 2.54 INTRA BL 72 ASP ( 76-) A OD1 <-> 113 HIS ( 117-) A ND1 0.14 2.56 INTRA BL 13 THR ( 17-) A CB <-> 14 PRO ( 18-) A CD 0.08 3.02 INTRA 67 ARG ( 71-) A NE <-> 108 ASN ( 112-) A ND2 0.07 2.78 INTRA BL 18 GLU ( 22-) A CA <-> 19 PRO ( 23-) A CD 0.07 2.73 INTRA BF 55 ARG ( 59-) A NH1 <-> 57 ASP ( 61-) A OD2 0.06 2.64 INTRA BL 80 GLU ( 84-) A OE2 <-> 82 ILE ( 86-) A O 0.06 2.34 INTRA BF 130 GLY ( 134-) A N <-> 146 LEU ( 150-) A O 0.04 2.66 INTRA BL 110 SER ( 114-) A O <-> 129 ILE ( 133-) A N 0.03 2.67 INTRA BL 202 ALA ( 206-) A O <-> 206 LYS ( 210-) A N 0.02 2.68 INTRA BL 132 GLN ( 136-) A OE1 <-> 149 ARG ( 153-) A NE 0.01 2.69 INTRA 161 ARG ( 165-) A NH1 <-> 178 LEU ( 182-) A O 0.01 2.69 INTRA 49 SER ( 53-) A CB <-> 50 PRO ( 54-) A CD 0.01 3.09 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.
84 GLU ( 88-) A -6.66 3 GLU ( 7-) A -5.47 4 PHE ( 8-) A -5.31
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.
85 GLU ( 89-) A -2.65 18 GLU ( 22-) A -2.55
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.
213 HOH ( 231 ) A O 2.93 67.62 42.88
108 ASN ( 112-) A 142 ASN ( 146-) 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.
3 GLU ( 7-) A N 13 THR ( 17-) A OG1 46 VAL ( 50-) A N 71 GLN ( 75-) A NE2 87 GLU ( 91-) A N 127 THR ( 131-) A N 180 GLU ( 184-) A N 182 THR ( 186-) A N 187 TYR ( 191-) A N Only metal coordination for 77 HIS ( 81-) A ND1 Only metal coordination for 113 HIS ( 117-) A NE2 Only metal coordination for 118 HIS ( 122-) A NE2
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.
2 ASP ( 6-) A OD2 90 GLU ( 94-) A OE1 95 GLU ( 99-) A OE1 116 GLN ( 120-) A OE1
80 GLU ( 84-) 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 : 0.473 2nd generation packing quality : -1.347 Ramachandran plot appearance : 0.018 chi-1/chi-2 rotamer normality : -2.533 Backbone conformation : 0.051
Bond lengths : 0.586 (tight) Bond angles : 1.353 Omega angle restraints : 0.754 Side chain planarity : 0.810 Improper dihedral distribution : 1.359 B-factor distribution : 0.517 Inside/Outside distribution : 1.001
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 : 1.95
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.8 2nd generation packing quality : -1.3 Ramachandran plot appearance : 0.1 chi-1/chi-2 rotamer normality : -1.7 Backbone conformation : -0.6
Bond lengths : 0.586 (tight) Bond angles : 1.353 Omega angle restraints : 0.754 Side chain planarity : 0.810 Improper dihedral distribution : 1.359 B-factor distribution : 0.517 Inside/Outside distribution : 1.001 ==============
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.