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.
353 WBT (1355-) 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: B-factors outside the range 0.0 - 100.0
In principle, B-factors can have a very wide range of values, but in
practice, B-factors should not be zero while B-factors above 100.0
are a good indicator that the location of that atom is meaningless. Be
aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms
with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with
a B-factor of zero were observed.
117 GLN ( 120-) A High 169 ALA ( 172-) A High 170 ARG ( 173-) A High 171 HIS ( 174-) A High 250 GLU ( 253-) A High 350 LEU ( 353-) A High 351 ASP ( 354-) A High 352 GLN ( 355-) A High
In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. In many cases the N- or C-terminal residues are too disordered to see. In case of the N-terminus, you can see from the residue numbers if there are missing residues, but at the C-terminus this is impossible. Therefore, often the position of the backbone nitrogen of the first residue missing at the C-terminal end is calculated and added to indicate that there are missing residues. As a single N causes validation trouble, we remove these single-N-residues before doing the validation. But, if you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or removed N is the cause.
352 GLN ( 355-) A
Obviously, the temperature at which the X-ray data was collected has some importance too:
Number of TLS groups mentione in PDB file header: 0
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: 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
| 0.998117 -0.000534 0.000821| | -0.000534 0.998596 -0.000865| | 0.000821 -0.000865 0.995313|Proposed new scale matrix
| 0.022010 0.000012 -0.000018| | 0.000006 0.011698 0.000010| | -0.000007 0.000007 0.007937|With corresponding cell
A = 45.433 B = 85.482 C = 125.989 Alpha= 90.099 Beta= 89.906 Gamma= 90.061
The CRYST1 cell dimensions
A = 45.519 B = 85.602 C = 126.577 Alpha= 90.000 Beta= 90.000 Gamma= 90.000
(Under-)estimated Z-score: 7.327
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.
293 ARG ( 296-) A CG CD NE 103.04 -4.4 327 ARG ( 330-) A CG CD NE 117.31 4.0
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.
164 LEU ( 167-) A -2.7 159 CYS ( 162-) A -2.6 166 PHE ( 169-) A -2.6 349 PRO ( 352-) A -2.5 286 LEU ( 289-) A -2.3 193 ASN ( 196-) A -2.3 103 THR ( 106-) A -2.3 71 LEU ( 74-) A -2.2 221 PRO ( 224-) A -2.2 16 GLU ( 19-) A -2.1 83 LEU ( 86-) 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.
12 LYS ( 15-) A Poor phi/psi 23 ASN ( 26-) A Poor phi/psi 36 CYS ( 39-) A omega poor 97 ASN ( 100-) A Poor phi/psi 106 MET ( 109-) A Poor phi/psi, omega poor 142 ASP ( 145-) A Poor phi/psi 146 ARG ( 149-) A Poor phi/psi 159 CYS ( 162-) A Poor phi/psi 194 TRP ( 197-) A omega poor 195 MET ( 198-) A Poor phi/psi 200 THR ( 203-) A omega poor 221 PRO ( 224-) A Poor phi/psi 263 PRO ( 266-) A omega poor 326 SER ( 329-) A omega poor 350 LEU ( 353-) A omega poor chi-1/chi-2 correlation Z-score : -2.593
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.
251 SER ( 254-) A 0.38
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!
10 LEU ( 13-) A 0 12 LYS ( 15-) A 0 21 TYR ( 24-) A 0 22 GLN ( 25-) A 0 23 ASN ( 26-) A 0 26 PRO ( 29-) A 0 29 SER ( 32-) A 0 32 TYR ( 35-) A 0 53 SER ( 56-) A 0 54 ARG ( 57-) A 0 56 PHE ( 59-) A 0 57 GLN ( 60-) A 0 74 HIS ( 77-) A 0 75 MET ( 78-) A 0 76 LYS ( 79-) A 0 85 ASP ( 88-) A 0 89 PRO ( 92-) A 0 95 GLU ( 98-) A 0 96 PHE ( 99-) A 0 97 ASN ( 100-) A 0 98 ASP ( 101-) A 0 103 THR ( 106-) A 0 106 MET ( 109-) A 0 116 CYS ( 119-) A 0 117 GLN ( 120-) A 0And so on for a total of 112 lines.
26 PRO ( 29-) A 103.7 envelop C-beta (108 degrees) 347 PRO ( 350-) A 48.6 half-chair C-delta/C-gamma (54 degrees) 349 PRO ( 352-) A 138.9 envelop C-alpha (144 degrees)
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.
32 TYR ( 35-) A N <-> 168 LEU ( 171-) A O 0.25 2.45 INTRA BF 50 LYS ( 53-) A NZ <-> 68 GLU ( 71-) A OE2 0.21 2.49 INTRA BL 58 SER ( 61-) A OG <-> 61 HIS ( 64-) A ND1 0.20 2.50 INTRA BF 320 TYR ( 323-) A CE2 <-> 322 GLN ( 325-) A CG 0.18 3.02 INTRA BL 74 HIS ( 77-) A ND1 <-> 353 HOH (2056 ) A O 0.18 2.52 INTRA 246 LYS ( 249-) A NZ <-> 289 ASP ( 292-) A OD2 0.17 2.53 INTRA 106 MET ( 109-) A N <-> 352 WBT (1355-) A N23 0.13 2.87 INTRA 246 LYS ( 249-) A NZ <-> 291 ASP ( 294-) A OD2 0.12 2.58 INTRA 280 ASP ( 283-) A OD2 <-> 284 LYS ( 287-) A NZ 0.08 2.62 INTRA BL 146 ARG ( 149-) A NH2 <-> 353 HOH (2122 ) A O 0.06 2.64 INTRA BF 73 LYS ( 76-) A NZ <-> 353 HOH (2054 ) A O 0.06 2.64 INTRA BL 268 ALA ( 271-) A O <-> 353 HOH (2177 ) A O 0.05 2.35 INTRA BL 73 LYS ( 76-) A NZ <-> 341 GLU ( 344-) A OE1 0.05 2.65 INTRA BL 144 ILE ( 147-) A O <-> 146 ARG ( 149-) A NH1 0.04 2.66 INTRA 176 MET ( 179-) A SD <-> 182 THR ( 185-) A CG2 0.04 3.36 INTRA BF 139 HIS ( 142-) A ND1 <-> 353 HOH (2119 ) A O 0.03 2.67 INTRA BL 212 GLU ( 215-) A O <-> 216 GLY ( 219-) A N 0.03 2.67 INTRA BL 283 GLU ( 286-) A O <-> 353 HOH (2186 ) A O 0.03 2.37 INTRA 165 ASP ( 168-) A OD2 <-> 353 HOH (2126 ) A O 0.03 2.37 INTRA BL 137 TYR ( 140-) A O <-> 140 SER ( 143-) A OG 0.02 2.38 INTRA BL 247 ILE ( 250-) A CD1 <-> 256 ILE ( 259-) A CD1 0.02 3.18 INTRA 207 GLY ( 210-) A CA <-> 285 MET ( 288-) A CE 0.02 3.18 INTRA BL 171 HIS ( 174-) A NE2 <-> 176 MET ( 179-) A SD 0.01 3.29 INTRA BF 230 LYS ( 233-) A NZ <-> 353 HOH (2156 ) A O 0.01 2.69 INTRA BF 82 GLY ( 85-) A N <-> 353 HOH (2068 ) A O 0.01 2.69 INTRA BF 206 VAL ( 209-) A O <-> 210 MET ( 213-) A N 0.01 2.69 INTRA BL 264 LYS ( 267-) A NZ <-> 283 GLU ( 286-) A OE2 0.01 2.69 INTRA BL 121 ASP ( 124-) A OD2 <-> 275 ASN ( 278-) A ND2 0.01 2.69 INTRA 140 SER ( 143-) A OG <-> 317 ALA ( 320-) A N 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.
91 ARG ( 94-) A -7.66 179 TYR ( 182-) A -7.08 350 LEU ( 353-) A -6.69 261 GLN ( 264-) A -6.18 2 ARG ( 5-) A -6.17 74 HIS ( 77-) A -5.76 76 LYS ( 79-) A -5.59 57 GLN ( 60-) A -5.23 196 HIS ( 199-) A -5.16 346 VAL ( 349-) A -5.02 42 LYS ( 45-) A -5.00
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.
81 ILE ( 84-) A -2.53
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.
353 HOH (2028 ) A O -23.94 21.94 53.67 353 HOH (2098 ) A O -25.99 19.90 53.28
353 HOH (2106 ) A O Marked this atom as acceptor 352 WBT (1355-) A F1
309 HIS ( 312-) 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.
13 THR ( 16-) A N 22 GLN ( 25-) A NE2 58 SER ( 61-) A N 60 ILE ( 63-) A N 64 ARG ( 67-) A NE 79 ASN ( 82-) A N 92 SER ( 95-) A N 99 VAL ( 102-) A N 106 MET ( 109-) A N 149 LYS ( 152-) A N 165 ASP ( 168-) A N 178 GLY ( 181-) A N 186 ARG ( 189-) A NE 195 MET ( 198-) A N 203 ILE ( 206-) A N 224 ASP ( 227-) A N 228 GLN ( 231-) A NE2
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.
353 HOH (2232 ) A O 1.11 K 4 Ion-B
175 GLU ( 178-) A H-bonding suggests Gln 340 ASP ( 343-) 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 : -0.878 2nd generation packing quality : -1.434 Ramachandran plot appearance : -1.669 chi-1/chi-2 rotamer normality : -2.593 Backbone conformation : -0.160
Bond lengths : 0.600 (tight) Bond angles : 0.751 Omega angle restraints : 1.063 Side chain planarity : 0.669 Improper dihedral distribution : 0.758 B-factor distribution : 0.703 Inside/Outside distribution : 1.033
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 : 2.00
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.6 2nd generation packing quality : -1.0 Ramachandran plot appearance : -1.0 chi-1/chi-2 rotamer normality : -1.6 Backbone conformation : -0.3
Bond lengths : 0.600 (tight) Bond angles : 0.751 Omega angle restraints : 1.063 Side chain planarity : 0.669 Improper dihedral distribution : 0.758 B-factor distribution : 0.703 Inside/Outside distribution : 1.033 ==============
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.