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 INV ( 555-) A - 262 INV ( 666-) 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.
1 HIS ( 3-) A 0.50 2 HIS ( 4-) A 0.50 12 GLU ( 14-) A 0.50 62 HIS ( 64-) A 0.70 133 GLN ( 136-) A 0.40
Obviously, the temperature at which the X-ray data was collected has some importance too:
Crystal temperature (K) :298.000
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
5 TYR ( 7-) A 112 TYR ( 114-) A 188 TYR ( 191-) A
64 PHE ( 66-) A
32 ASP ( 34-) A
24 GLU ( 26-) A 233 GLU ( 236-) A
RMS Z-score for bond lengths: 0.544
RMS-deviation in bond distances: 0.013
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
| 0.996678 -0.000024 0.000317| | -0.000024 0.996354 0.000190| | 0.000317 0.000190 0.994302|Proposed new scale matrix
| 0.023275 0.000000 0.006206| | 0.000000 0.023833 -0.000005| | -0.000004 -0.000003 0.014086|With corresponding cell
A = 42.960 B = 41.959 C = 73.465 Alpha= 89.978 Beta= 104.911 Gamma= 90.003
The CRYST1 cell dimensions
A = 43.103 B = 42.113 C = 73.885 Alpha= 90.000 Beta= 104.910 Gamma= 90.000
(Under-)estimated Z-score: 9.403
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.
2 HIS ( 4-) A CG ND1 CE1 109.60 4.0 94 HIS ( 96-) A N CA C 98.41 -4.6
24 GLU ( 26-) A 32 ASP ( 34-) A 233 GLU ( 236-) A
204 VAL ( 207-) A 6.13 94 HIS ( 96-) A 4.87
Tau angle RMS Z-score : 1.581
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.
81 PRO ( 83-) A -2.7 173 PHE ( 176-) A -2.5 28 PRO ( 30-) A -2.4 48 SER ( 50-) A -2.1 192 PRO ( 195-) A -2.1 148 GLY ( 151-) A -2.0 51 GLN ( 53-) A -2.0 58 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.
2 HIS ( 4-) A Poor phi/psi 27 SER ( 29-) A PRO omega poor 62 HIS ( 64-) A Poor phi/psi 63 ALA ( 65-) A Poor phi/psi 73 ASP ( 75-) A Poor phi/psi 108 ASP ( 110-) A Poor phi/psi 109 LYS ( 111-) A Poor phi/psi 175 ASN ( 178-) A Poor phi/psi 198 PRO ( 201-) A PRO omega poor 240 ASP ( 243-) A Poor phi/psi 249 LYS ( 252-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -1.664
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.
128 VAL ( 131-) 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!
3 TRP ( 5-) A 0 5 TYR ( 7-) A 0 8 HIS ( 10-) A 0 18 PHE ( 20-) A 0 22 LYS ( 24-) A 0 25 ARG ( 27-) A 0 26 GLN ( 28-) A 0 27 SER ( 29-) A 0 48 SER ( 50-) A 0 50 ASP ( 52-) A 0 51 GLN ( 53-) A 0 52 ALA ( 54-) A 0 60 ASN ( 62-) A 0 62 HIS ( 64-) A 0 70 ASP ( 72-) A 0 71 SER ( 73-) A 0 73 ASP ( 75-) A 0 74 LYS ( 76-) A 0 75 ALA ( 77-) A 0 78 LYS ( 80-) A 0 81 PRO ( 83-) A 0 83 ASP ( 85-) A 0 90 GLN ( 92-) A 0 94 HIS ( 96-) A 0 97 SER ( 99-) A 0And so on for a total of 117 lines.
Standard deviation of omega values : 1.813
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]
11 PRO ( 13-) A 0.47 HIGH
44 PRO ( 46-) A -112.2 envelop C-gamma (-108 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.
94 HIS ( 96-) A NE2 <-> 117 HIS ( 119-) A ND1 0.37 2.63 INTRA BL 94 HIS ( 96-) A NE2 <-> 117 HIS ( 119-) A CE1 0.28 2.82 INTRA BL 94 HIS ( 96-) A CD2 <-> 117 HIS ( 119-) A CE1 0.24 2.96 INTRA BL 92 HIS ( 94-) A NE2 <-> 261 INV ( 555-) A NP2 0.10 2.90 INTRA BL 94 HIS ( 96-) A NE2 <-> 261 INV ( 555-) A NP2 0.10 2.90 INTRA BL 28 PRO ( 30-) A O <-> 246 GLN ( 249-) A N 0.08 2.62 INTRA BL 73 ASP ( 75-) A OD1 <-> 87 ARG ( 89-) A NE 0.08 2.62 INTRA 27 SER ( 29-) A O <-> 243 ARG ( 246-) A NH1 0.07 2.63 INTRA BL 72 GLN ( 74-) A O <-> 74 LYS ( 76-) A N 0.06 2.64 INTRA 94 HIS ( 96-) A CD2 <-> 117 HIS ( 119-) A ND1 0.05 3.05 INTRA BL 13 HIS ( 15-) A ND1 <-> 16 LYS ( 18-) A NZ 0.05 2.95 INTRA BL 62 HIS ( 64-) A CB <-> 263 HOH ( 265 ) A O 0.05 2.75 INTRA 134 GLN ( 137-) A C <-> 260 HG ( 263-) A HG 0.03 3.17 INTRA BL 249 LYS ( 252-) A CB <-> 250 ASN ( 253-) A N 0.01 2.69 INTRA B3
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.
8 HIS ( 10-) A -6.00 2 HIS ( 4-) A -5.72 133 GLN ( 136-) A -5.06 98 LEU ( 100-) A -5.05
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.
263 HOH ( 278 ) A O 263 HOH ( 354 ) A O Marked this atom as acceptor 261 INV ( 555-) A F21 Marked this atom as acceptor 262 INV ( 666-) A F21 Metal-coordinating Histidine residue 92 fixed to 1 Metal-coordinating Histidine residue 94 fixed to 1 Metal-coordinating Histidine residue 117 fixed to 1
51 GLN ( 53-) A 175 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.
2 HIS ( 4-) A N 29 VAL ( 31-) A N 50 ASP ( 52-) A N 72 GLN ( 74-) A N 98 LEU ( 100-) A N 122 ASN ( 124-) A ND2 127 ASP ( 130-) A N 128 VAL ( 131-) A N 174 THR ( 177-) A OG1 197 THR ( 200-) A N 201 LEU ( 204-) A N 230 GLY ( 233-) A N 241 ASN ( 244-) A ND2 257 PHE ( 260-) A N Only metal coordination for 94 HIS ( 96-) A NE2 Only metal coordination for 117 HIS ( 119-) A ND1
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 : -0.809 2nd generation packing quality : 0.159 Ramachandran plot appearance : -1.619 chi-1/chi-2 rotamer normality : -1.664 Backbone conformation : -0.928
Bond lengths : 0.544 (tight) Bond angles : 0.776 Omega angle restraints : 0.330 (tight) Side chain planarity : 0.642 (tight) Improper dihedral distribution : 0.961 B-factor distribution : 0.623 Inside/Outside distribution : 0.954
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 : 1.93
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.2 2nd generation packing quality : -0.3 Ramachandran plot appearance : -1.4 chi-1/chi-2 rotamer normality : -1.0 Backbone conformation : -1.4
Bond lengths : 0.544 (tight) Bond angles : 0.776 Omega angle restraints : 0.330 (tight) Side chain planarity : 0.642 (tight) Improper dihedral distribution : 0.961 B-factor distribution : 0.623 Inside/Outside distribution : 0.954 ==============
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.