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.
260 STB ( 555-) A -
Plausible backbone atoms were detected with (near) zero occupancy
When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. However, if a backbone atom is present in the PDB file, and its position seems 'logical' (i.e. normal bond lengths with all atoms it should be bound to, and those atoms exist normally) WHAT IF will set the occupancy to 1.0 if it believes that the full presence of this atom will be beneficial to the rest of the validation process. If you get weird errors at, or near, these atoms, please check by hand what is going on, and repair things intelligently before running this validation again.
256 LYS ( 261-) A - C 256 LYS ( 261-) A - O
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.
10 GLU ( 14-) A 0.30
Obviously, the temperature at which the X-ray data was collected has some importance too:
Crystal temperature (K) : 93.000
Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
Chain identifier: A
Warning: Unusual bond lengths
The bond lengths listed in the table below were found to deviate more than 4
sigma from standard bond lengths (both standard values and sigmas for amino
acid residues have been taken from Engh and Huber [REF], for DNA they were
taken from Parkinson et al [REF]). In the table below for each unusual bond
the bond length and the number of standard deviations it differs from the
normal value is given.
Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.
90 HIS ( 94-) A CG CD2 1.41 5.1 92 HIS ( 96-) A CG CD2 1.42 6.1 92 HIS ( 96-) A ND1 CE1 1.37 4.1 115 HIS ( 119-) A CG CD2 1.41 5.1
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
| 0.998160 0.000258 0.000082| | 0.000258 0.999027 0.000203| | 0.000082 0.000203 0.997194|Proposed new scale matrix
| 0.023462 -0.000007 0.006115| | -0.000006 0.024004 -0.000005| | -0.000001 -0.000003 0.014196|With corresponding cell
A = 42.622 B = 41.659 C = 72.795 Alpha= 89.985 Beta= 104.604 Gamma= 89.970
The CRYST1 cell dimensions
A = 42.700 B = 41.700 C = 73.000 Alpha= 90.000 Beta= 104.600 Gamma= 90.000
(Under-)estimated Z-score: 4.196
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.
90 HIS ( 94-) A CG ND1 CE1 110.84 5.2 90 HIS ( 94-) A CB CG CD2 135.73 5.1 92 HIS ( 96-) A N CA C 99.65 -4.1 92 HIS ( 96-) A CG ND1 CE1 110.42 4.8 92 HIS ( 96-) A CB CG CD2 134.65 4.3 115 HIS ( 119-) A CG ND1 CE1 110.49 4.9 115 HIS ( 119-) A CB CG CD2 135.38 4.8
202 VAL ( 207-) A 4.66 92 HIS ( 96-) A 4.31 153 GLN ( 158-) A 4.10 73 ALA ( 77-) A 4.02
Tau angle RMS Z-score : 1.510
Warning: Torsion angle evaluation shows unusual residues
The residues listed in the table below contain bad or abnormal
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.
171 PHE ( 176-) A -2.4 88 GLN ( 92-) A -2.2 201 CYS ( 206-) A -2.1 146 GLY ( 151-) A -2.1 158 VAL ( 163-) 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.
25 SER ( 29-) A PRO omega poor 61 ALA ( 65-) A Poor phi/psi 107 LYS ( 111-) A Poor phi/psi 124 GLY ( 129-) A Poor phi/psi 173 ASN ( 178-) A Poor phi/psi 196 PRO ( 201-) A PRO omega poor 238 ASP ( 243-) A Poor phi/psi 247 LYS ( 252-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -1.162
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 TYR ( 7-) A 0 6 HIS ( 10-) A 0 16 PHE ( 20-) A 0 20 LYS ( 24-) A 0 23 ARG ( 27-) A 0 24 GLN ( 28-) A 0 25 SER ( 29-) A 0 46 SER ( 50-) A 0 49 GLN ( 53-) A 0 50 ALA ( 54-) A 0 58 ASN ( 62-) A 0 60 HIS ( 64-) A 0 61 ALA ( 65-) A 0 68 ASP ( 72-) A 0 69 SER ( 73-) A 0 76 LYS ( 80-) A 0 79 PRO ( 83-) A 0 81 ASP ( 85-) A 0 88 GLN ( 92-) A 0 92 HIS ( 96-) A 0 99 GLN ( 103-) A 0 102 GLU ( 106-) A 0 103 HIS ( 107-) A 0 105 VAL ( 109-) A 0 107 LYS ( 111-) A 0And so on for a total of 117 lines.
Standard deviation of omega values : 1.565
Warning: Unusual PRO puckering amplitudes
The proline residues listed in the table below have a puckering amplitude
that is outside of normal ranges. Puckering parameters were calculated by
the method of Cremer and Pople [REF]. Normal PRO rings have a puckering
amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom
for a PRO residue, this could indicate disorder between the two different
normal ring forms (with C-gamma below and above the ring, respectively). If
Q is higher than 0.45 Angstrom something could have gone wrong during the
refinement. Be aware that this is a warning with a low confidence level. See:
Who checks the checkers? Four validation tools applied to eight atomic
resolution structures [REF]
133 PRO ( 138-) A 0.45 HIGH
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.
63 ASN ( 67-) A ND2 <-> 90 HIS ( 94-) A CB 0.20 2.90 INTRA 11 HIS ( 15-) A ND1 <-> 14 LYS ( 18-) A NZ 0.16 2.84 INTRA BL 242 PRO ( 247-) A O <-> 244 GLN ( 249-) A NE2 0.15 2.55 INTRA BL 4 GLY ( 8-) A O <-> 8 GLY ( 12-) A N 0.12 2.58 INTRA 131 GLN ( 136-) A N <-> 132 GLN ( 137-) A N 0.10 2.50 INTRA BL 68 ASP ( 72-) A OD2 <-> 119 TRP ( 123-) A NE1 0.05 2.65 INTRA 99 GLN ( 103-) A NE2 <-> 238 ASP ( 243-) A OD1 0.04 2.66 INTRA 199 LEU ( 204-) A CB <-> 201 CYS ( 206-) A SG 0.03 3.37 INTRA 92 HIS ( 96-) A NE2 <-> 115 HIS ( 119-) A ND1 0.03 2.97 INTRA BL 18 ILE ( 22-) A O <-> 21 GLY ( 25-) A N 0.03 2.67 INTRA 76 LYS ( 80-) A NZ <-> 261 HOH ( 661 ) A O 0.03 2.67 INTRA 44 SER ( 48-) A N <-> 76 LYS ( 80-) A O 0.03 2.67 INTRA 47 TYR ( 51-) A OH <-> 118 HIS ( 122-) A NE2 0.02 2.68 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.
6 HIS ( 10-) A -5.72 96 LEU ( 100-) A -5.49 131 GLN ( 136-) A -5.08 23 ARG ( 27-) A -5.01
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
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.
261 HOH ( 614 ) A O -13.62 -16.88 -0.21 261 HOH ( 641 ) A O -1.55 9.57 28.83 261 HOH ( 649 ) A O -13.47 -18.83 15.04 261 HOH ( 682 ) A O -27.70 -10.84 23.19 261 HOH ( 692 ) A O -5.65 -19.82 23.38
261 HOH ( 609 ) A O 261 HOH ( 647 ) A O 261 HOH ( 656 ) A O 261 HOH ( 686 ) A O Metal-coordinating Histidine residue 90 fixed to 1 Metal-coordinating Histidine residue 92 fixed to 1 Metal-coordinating Histidine residue 115 fixed to 1
32 HIS ( 36-) A 173 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.
27 VAL ( 31-) A N 70 GLN ( 74-) A N 96 LEU ( 100-) A N 195 THR ( 200-) A N 199 LEU ( 204-) A N 255 PHE ( 260-) A N Only metal coordination for 92 HIS ( 96-) A NE2 Only metal coordination for 115 HIS ( 119-) A ND1
157 ASP ( 162-) A H-bonding suggests Asn; but Alt-Rotamer 160 ASP ( 165-) A H-bonding suggests Asn 231 GLU ( 236-) 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 : -0.497 2nd generation packing quality : 0.426 Ramachandran plot appearance : -2.575 chi-1/chi-2 rotamer normality : -1.162 Backbone conformation : -1.015
Bond lengths : 0.463 (tight) Bond angles : 0.731 Omega angle restraints : 0.285 (tight) Side chain planarity : 0.434 (tight) Improper dihedral distribution : 0.801 B-factor distribution : 0.993 Inside/Outside distribution : 0.953
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 : 2.40
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.4 2nd generation packing quality : 1.2 Ramachandran plot appearance : -0.6 chi-1/chi-2 rotamer normality : 0.5 Backbone conformation : -0.7
Bond lengths : 0.463 (tight) Bond angles : 0.731 Omega angle restraints : 0.285 (tight) Side chain planarity : 0.434 (tight) Improper dihedral distribution : 0.801 B-factor distribution : 0.993 Inside/Outside distribution : 0.953 ==============
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.