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.
261 SU0 ( 263-) A -
Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.
168 LYS ( 172-) A -
In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.
168 LYS ( 172-) 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: Occupancies atoms do not add up to 1.0.
In principle, the occupancy of all alternates of one atom should add up till
1.0. A valid exception is the missing atom (i.e. an atom not seen in the
electron density) that is allowed to have a 0.0 occupancy. Sometimes this
even happens when there are no alternate atoms given...
Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.
WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.
61 HIS ( 64-) A 0.96
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
Error: The B-factors of bonded atoms show signs of over-refinement
For each of the bond types in a protein a distribution was derived for the
difference between the square roots of the B-factors of the two atoms. All
bonds in the current protein were scored against these distributions. The
number given below is the RMS Z-score over the structure. For a structure
with completely restrained B-factors within residues, this value will be
around 0.35, for extremely high resolution structures refined with free
isotropic B-factors this number is expected to be near 1.0. Any value over
1.5 is sign of severe over-refinement of B-factors.
RMS Z-score : 1.601 over 1853 bonds
Average difference in B over a bond : 3.96
RMS difference in B over a bond : 5.14
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: Arginine nomenclature problem
The arginine residues listed in the table below have their N-H-1 and N-H-2
55 ARG ( 58-) A
4 TYR ( 7-) A
72 ASP ( 75-) A 171 ASP ( 175-) A
23 GLU ( 26-) A 66 GLU ( 69-) A 235 GLU ( 239-) A
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
| 0.997222 -0.000449 0.000213| | -0.000449 0.992365 -0.000824| | 0.000213 -0.000824 1.000744|Proposed new scale matrix
| 0.023795 0.000016 0.005964| | 0.000011 0.024459 0.000020| | -0.000003 0.000012 0.014395|With corresponding cell
A = 42.024 B = 40.885 C = 71.612 Alpha= 90.079 Beta= 104.060 Gamma= 90.052
The CRYST1 cell dimensions
A = 42.140 B = 41.200 C = 71.580 Alpha= 90.000 Beta= 104.130 Gamma= 90.000
(Under-)estimated Z-score: 8.697
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.
104 HIS ( 107-) A CG ND1 CE1 109.65 4.1
23 GLU ( 26-) A 55 ARG ( 58-) A 66 GLU ( 69-) A 72 ASP ( 75-) A 171 ASP ( 175-) A 235 GLU ( 239-) A
93 HIS ( 96-) A 4.97
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.
159 VAL ( 163-) A -2.2 163 ILE ( 167-) A -2.1 147 GLY ( 151-) A -2.1 89 GLN ( 92-) A -2.1 57 LEU ( 60-) 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.
26 SER ( 29-) A PRO omega poor 54 LEU ( 57-) A omega poor 57 LEU ( 60-) A omega poor 61 HIS ( 64-) A Poor phi/psi 80 PRO ( 83-) A omega poor 89 GLN ( 92-) A omega poor 108 LYS ( 111-) A Poor phi/psi 117 LEU ( 120-) A omega poor 174 ASN ( 178-) A Poor phi/psi 187 TYR ( 191-) A omega poor 193 SER ( 197-) A omega poor 197 PRO ( 201-) A PRO omega poor 199 LEU ( 203-) A Poor phi/psi 201 GLU ( 205-) A omega poor 248 LYS ( 252-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -0.684
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!
4 TYR ( 7-) A 0 7 HIS ( 10-) A 0 16 ASP ( 19-) A 0 17 PHE ( 20-) A 0 21 LYS ( 24-) A 0 23 GLU ( 26-) A 0 24 ARG ( 27-) A 0 25 GLN ( 28-) A 0 26 SER ( 29-) A 0 47 SER ( 50-) A 0 59 ASN ( 62-) A 0 61 HIS ( 64-) A 0 69 ASP ( 72-) A 0 70 SER ( 73-) A 0 72 ASP ( 75-) A 0 73 LYS ( 76-) A 0 77 LYS ( 80-) A 0 80 PRO ( 83-) A 0 82 ASP ( 85-) A 0 89 GLN ( 92-) A 0 100 GLN ( 103-) A 0 104 HIS ( 107-) A 0 108 LYS ( 111-) A 0 112 ALA ( 115-) A 0 113 ALA ( 116-) A 0And so on for a total of 121 lines.
27 PRO ( 30-) A 0.46 HIGH
134 PRO ( 138-) A 46.0 half-chair C-delta/C-gamma (54 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.
154 GLN ( 158-) A NE2 <-> 157 VAL ( 161-) A CG2 0.27 2.83 INTRA 143 PHE ( 147-) A N <-> 262 HOH ( 270 ) A O 0.20 2.50 INTRA BL 154 GLN ( 158-) A CD <-> 157 VAL ( 161-) A CG2 0.18 3.02 INTRA 46 VAL ( 49-) A O <-> 262 HOH ( 423 ) A O 0.17 2.23 INTRA 109 LYS ( 112-) A NZ <-> 262 HOH ( 362 ) A O 0.15 2.55 INTRA 262 HOH ( 353 ) A O <-> 262 HOH ( 419 ) A O 0.14 2.06 INTRA BF 262 HOH ( 437 ) A O <-> 262 HOH ( 438 ) A O 0.13 2.07 INTRA 150 LYS ( 154-) A NZ <-> 262 HOH ( 374 ) A O 0.11 2.59 INTRA 12 HIS ( 15-) A ND1 <-> 15 LYS ( 18-) A NZ 0.09 2.91 INTRA 171 ASP ( 175-) A OD2 <-> 262 HOH ( 410 ) A O 0.09 2.31 INTRA BF 243 PRO ( 247-) A O <-> 245 GLN ( 249-) A NE2 0.07 2.63 INTRA BL 114 GLU ( 117-) A OE2 <-> 116 HIS ( 119-) A NE2 0.07 2.63 INTRA BL 248 LYS ( 252-) A N <-> 262 HOH ( 399 ) A O 0.06 2.64 INTRA 104 HIS ( 107-) A NE2 <-> 190 TYR ( 194-) A OH 0.04 2.66 INTRA BL 48 TYR ( 51-) A OH <-> 119 HIS ( 122-) A NE2 0.04 2.66 INTRA BL 24 ARG ( 27-) A CG <-> 201 GLU ( 205-) A CD 0.03 3.17 INTRA 109 LYS ( 112-) A NZ <-> 262 HOH ( 403 ) A O 0.03 2.67 INTRA 93 HIS ( 96-) A ND1 <-> 240 ASN ( 244-) A O 0.03 2.67 INTRA BL 63 PHE ( 66-) A N <-> 262 HOH ( 307 ) A O 0.02 2.68 INTRA BL 123 LYS ( 127-) A NZ <-> 262 HOH ( 389 ) A O 0.01 2.69 INTRA BF 29 ASP ( 32-) A OD1 <-> 108 LYS ( 111-) A N 0.01 2.69 INTRA BL 96 SER ( 99-) A N <-> 97 LEU ( 100-) A N 0.01 2.59 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.
7 HIS ( 10-) A -6.36 97 LEU ( 100-) A -5.17 132 GLN ( 136-) A -5.17
Chain identifier: A
Note: Second generation quality Z-score plot
The second generation quality Z-score smoothed over a 10 residue window
is plotted as function of the residue number. Low areas in the plot (below
-1.3) indicate unusual packing.
Chain identifier: A
Water, ion, and hydrogenbond related checks
Error: Water molecules without hydrogen bonds
The water molecules listed in the table below do not form any hydrogen bonds,
neither with the protein or DNA/RNA, nor with other water molecules. This is
a strong indication of a refinement problem. The last number on each line is
the identifier of the water molecule in the input file.
262 HOH ( 421 ) A O Metal-coordinating Histidine residue 91 fixed to 1 Metal-coordinating Histidine residue 93 fixed to 1 Metal-coordinating Histidine residue 116 fixed to 1
174 ASN ( 178-) 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.
28 VAL ( 31-) A N 33 HIS ( 36-) A N 49 ASP ( 52-) A N 50 GLN ( 53-) A N 71 GLN ( 74-) A N 97 LEU ( 100-) A N 126 ASP ( 130-) A N 161 ASP ( 165-) A N 196 THR ( 200-) A N 200 LEU ( 204-) A N 226 ASN ( 230-) A ND2 240 ASN ( 244-) A ND2 241 TRP ( 245-) A N 256 PHE ( 260-) A N Only metal coordination for 91 HIS ( 94-) A NE2 Only metal coordination for 93 HIS ( 96-) A NE2 Only metal coordination for 116 HIS ( 119-) A ND1
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.
262 HOH ( 336 ) A O 0.88 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 : 0.075 2nd generation packing quality : 0.695 Ramachandran plot appearance : -1.393 chi-1/chi-2 rotamer normality : -0.684 Backbone conformation : -1.034
Bond lengths : 0.741 Bond angles : 0.844 Omega angle restraints : 1.236 Side chain planarity : 1.027 Improper dihedral distribution : 0.949 B-factor distribution : 1.601 (loose) Inside/Outside distribution : 0.946
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 : 1.80
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.4 2nd generation packing quality : -0.1 Ramachandran plot appearance : -1.3 chi-1/chi-2 rotamer normality : -0.4 Backbone conformation : -1.3
Bond lengths : 0.741 Bond angles : 0.844 Omega angle restraints : 1.236 Side chain planarity : 1.027 Improper dihedral distribution : 0.949 B-factor distribution : 1.601 (loose) Inside/Outside distribution : 0.946 ==============
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.