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.
148 4GE (1165-) A - 149 12P (1164-) 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'.
6 GLU ( 12-) A CG 6 GLU ( 12-) A CD 6 GLU ( 12-) A OE1 6 GLU ( 12-) A OE2
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.
37 ARG ( 54-) A 0.50
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) :277.000
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
17 TYR ( 23-) A 75 TYR ( 92-) A
86 PHE ( 103-) A 93 PHE ( 110-) A 117 PHE ( 134-) A
85 ASP ( 102-) A 95 ASP ( 112-) A
34 GLU ( 51-) A 59 GLU ( 76-) A 67 GLU ( 84-) A 70 GLU ( 87-) A 84 GLU ( 101-) A
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.
29 GLU ( 35-) A CD OE2 1.36 5.8
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
| 0.995711 -0.001039 0.000808| | -0.001039 0.998062 0.001291| | 0.000808 0.001291 0.993335|Proposed new scale matrix
| 0.014635 0.008440 -0.000023| | 0.000018 0.016849 -0.000022| | -0.000010 -0.000016 0.012666|With corresponding cell
A = 68.373 B = 68.555 C = 78.949 Alpha= 89.918 Beta= 89.907 Gamma= 120.031
The CRYST1 cell dimensions
A = 68.668 B = 68.668 C = 79.477 Alpha= 90.000 Beta= 90.000 Gamma= 120.000
(Under-)estimated Z-score: 7.301
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.
140 HIS ( 157-) A CG ND1 CE1 109.61 4.0
34 GLU ( 51-) A 59 GLU ( 76-) A 67 GLU ( 84-) A 70 GLU ( 87-) A 84 GLU ( 101-) A 85 ASP ( 102-) A 95 ASP ( 112-) A
115 LYS ( 132-) A 4.01
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.
31 PRO ( 37-) A -2.7 42 HIS ( 59-) A -2.4 125 ARG ( 142-) 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.
24 ASN ( 30-) A Poor phi/psi 30 ARG ( 36-) A PRO omega poor 32 SER ( 38-) A omega poor 40 CYS ( 57-) A omega poor 53 PRO ( 70-) A Poor phi/psi 92 GLN ( 109-) A omega poor 102 ARG ( 119-) A Poor phi/psi 114 GLN ( 131-) A omega poor 130 SER ( 147-) A omega poor 140 HIS ( 157-) A omega poor chi-1/chi-2 correlation Z-score : -1.710
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.
91 SER ( 108-) 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!
3 PRO ( 9-) A 0 5 TRP ( 11-) A 0 6 GLU ( 12-) A 0 11 ARG ( 17-) A 0 13 SER ( 19-) A 0 21 HIS ( 27-) A 0 24 ASN ( 30-) A 0 25 ALA ( 31-) A 0 31 PRO ( 37-) A 0 32 SER ( 38-) A 0 33 GLY ( 39-) A 0 34 GLU ( 51-) A 0 35 PRO ( 52-) A 0 36 ALA ( 53-) A 0 47 HIS ( 64-) A 0 51 ARG ( 68-) A 0 52 ARG ( 69-) A 0 53 PRO ( 70-) A 0 54 SER ( 71-) A 0 57 ARG ( 74-) A 0 58 GLN ( 75-) A 0 62 THR ( 79-) A 0 81 SER ( 98-) A 0 84 GLU ( 101-) A 0 96 CYS ( 113-) A 0And so on for a total of 63 lines.
Standard deviation of omega values : 7.449
Warning: Unusual PRO puckering phases
The proline residues listed in the table below have a puckering phase that is
not expected to occur in protein structures. Puckering parameters were
calculated by the method of Cremer and Pople [REF]. Normal PRO rings
approximately show a so-called envelope conformation with the C-gamma atom
above the plane of the ring (phi=+72 degrees), or a half-chair conformation
with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees).
If phi deviates strongly from these values, this is indicative of a very
strange conformation for a PRO residue, and definitely requires a manual
check of the data. 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].
2 PRO ( 8-) A 45.8 half-chair C-delta/C-gamma (54 degrees) 31 PRO ( 37-) A -31.0 envelop C-alpha (-36 degrees) 53 PRO ( 70-) A 20.4 half-chair N/C-delta (18 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.
33 GLY ( 39-) A C <-> 125 ARG ( 142-) A NH1 0.55 2.55 INTRA BF 15 ARG ( 21-) A NH2 <-> 150 HOH (2009 ) A O 0.47 2.23 INTRA BF 52 ARG ( 69-) A NH2 <-> 148 4GE (1165-) A O14 0.39 2.31 INTRA 149 12P (1164-) A C36 <-> 150 HOH (2006 ) A O 0.33 2.37 INTRA 102 ARG ( 119-) A NE <-> 150 HOH (2075 ) A O 0.29 2.41 INTRA 84 GLU ( 101-) A OE1 <-> 150 HOH (2063 ) A O 0.26 2.14 INTRA 42 HIS ( 59-) A ND1 <-> 140 HIS ( 157-) A ND1 0.19 2.81 INTRA BL 15 ARG ( 21-) A NH2 <-> 150 HOH (2007 ) A O 0.17 2.53 INTRA 29 GLU ( 35-) A OE2 <-> 150 HOH (2019 ) A O 0.17 2.23 INTRA 29 GLU ( 35-) A CD <-> 150 HOH (2019 ) A O 0.16 2.64 INTRA 110 ARG ( 127-) A N <-> 150 HOH (2078 ) A O 0.15 2.55 INTRA 114 GLN ( 131-) A NE2 <-> 150 HOH (2083 ) A O 0.14 2.56 INTRA 125 ARG ( 142-) A N <-> 128 GLU ( 145-) A OE1 0.11 2.59 INTRA 113 MET ( 130-) A N <-> 150 HOH (2080 ) A O 0.09 2.61 INTRA 60 LYS ( 77-) A N <-> 150 HOH (2040 ) A O 0.09 2.61 INTRA 83 GLU ( 100-) A OE1 <-> 150 HOH (2062 ) A O 0.09 2.31 INTRA BF 115 LYS ( 132-) A NZ <-> 119 ASP ( 136-) A OD1 0.08 2.62 INTRA 52 ARG ( 69-) A O <-> 54 SER ( 71-) A N 0.07 2.63 INTRA 109 SER ( 126-) A N <-> 112 GLN ( 129-) A OE1 0.07 2.63 INTRA 20 ASN ( 26-) A O <-> 24 ASN ( 30-) A N 0.05 2.65 INTRA BL 59 GLU ( 76-) A N <-> 150 HOH (2038 ) A O 0.04 2.66 INTRA 39 ARG ( 56-) A O <-> 145 THR ( 162-) A N 0.03 2.67 INTRA BL 98 SER ( 115-) A O <-> 103 GLY ( 120-) A N 0.03 2.67 INTRA BL 14 GLY ( 20-) A N <-> 15 ARG ( 21-) A N 0.03 2.57 INTRA B3 96 CYS ( 113-) A SG <-> 148 4GE (1165-) A N11 0.02 3.28 INTRA BL 115 LYS ( 132-) A N <-> 116 PRO ( 133-) A CD 0.02 2.98 INTRA 49 GLN ( 66-) A OE1 <-> 150 HOH (2026 ) A O 0.01 2.39 INTRA BF 10 SER ( 16-) A N <-> 15 ARG ( 21-) A O 0.01 2.69 INTRA
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.
51 ARG ( 68-) A -7.23 30 ARG ( 36-) A -6.30 57 ARG ( 74-) A -5.81 52 ARG ( 69-) A -5.53 92 GLN ( 109-) A -5.17 110 ARG ( 127-) A -5.03
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.
150 HOH (2047 ) A O 150 HOH (2049 ) A O 150 HOH (2056 ) A O Marked this atom as acceptor 148 4GE (1165-) A CL1
24 ASN ( 30-) 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.
46 LYS ( 63-) A NZ 112 GLN ( 129-) A N 115 LYS ( 132-) A N
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.
150 HOH (2016 ) A O 0.97 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 : -1.225 2nd generation packing quality : 0.094 Ramachandran plot appearance : 0.195 chi-1/chi-2 rotamer normality : -1.710 Backbone conformation : -0.494
Bond lengths : 0.942 Bond angles : 0.902 Omega angle restraints : 1.354 (loose) Side chain planarity : 0.848 Improper dihedral distribution : 0.984 B-factor distribution : 0.592 Inside/Outside distribution : 0.989
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 : -1.0 2nd generation packing quality : 0.0 Ramachandran plot appearance : 0.7 chi-1/chi-2 rotamer normality : -0.8 Backbone conformation : -0.6
Bond lengths : 0.942 Bond angles : 0.902 Omega angle restraints : 1.354 (loose) Side chain planarity : 0.848 Improper dihedral distribution : 0.984 B-factor distribution : 0.592 Inside/Outside distribution : 0.989 ==============
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.