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.
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'.
79 ARG ( 85-) A CZ 79 ARG ( 85-) A NH1 79 ARG ( 85-) A NH2 164 ARG ( 170-) A CZ 164 ARG ( 170-) A NH1 164 ARG ( 170-) A NH2
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
Nomenclature related problems
Warning: Arginine nomenclature problem
The arginine residues listed in the table below have their N-H-1 and N-H-2
146 ARG ( 152-) A
59 PHE ( 65-) A 89 PHE ( 95-) A 119 PHE ( 125-) A 135 PHE ( 141-) A
162 GLU ( 168-) 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
| 0.996278 0.000998 -0.000414| | 0.000998 0.994759 0.000198| | -0.000414 0.000198 0.995932|Proposed new scale matrix
| 0.026810 -0.000027 0.000011| | -0.000015 0.015350 -0.000003| | 0.000006 -0.000003 0.014479|With corresponding cell
A = 37.300 B = 65.145 C = 69.066 Alpha= 89.977 Beta= 90.048 Gamma= 89.885
The CRYST1 cell dimensions
A = 37.432 B = 65.504 C = 69.341 Alpha= 90.000 Beta= 90.000 Gamma= 90.000
(Under-)estimated Z-score: 7.674
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.
132 HIS ( 138-) A CG ND1 CE1 109.82 4.2
146 ARG ( 152-) A 162 GLU ( 168-) A
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.
67 MET ( 73-) A -2.2 66 PHE ( 72-) A -2.1 115 GLY ( 121-) 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.
5 PHE ( 11-) A omega poor 6 PHE ( 12-) A omega poor 8 ILE ( 14-) A omega poor 12 ASN ( 18-) A Poor phi/psi 23 PHE ( 29-) A Poor phi/psi 49 GLN ( 55-) A Poor phi/psi 56 SER ( 62-) A Poor phi/psi 58 LEU ( 64-) A omega poor 65 ASP ( 71-) A Poor phi/psi 79 ARG ( 85-) A omega poor 98 HIS ( 104-) A Poor phi/psi 100 ALA ( 106-) A omega poor 102 PHE ( 108-) A Poor phi/psi 112 ASP ( 118-) A Poor phi/psi 157 SER ( 163-) A Poor phi/psi 163 VAL ( 169-) A omega poor chi-1/chi-2 correlation Z-score : -1.788
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 CYS ( 10-) A 0 12 ASN ( 18-) A 0 14 PRO ( 20-) A 0 15 ALA ( 21-) A 0 23 PHE ( 29-) A 0 26 VAL ( 32-) A 0 27 CYS ( 33-) A 0 41 GLU ( 47-) A 0 42 LYS ( 48-) A 0 44 THR ( 50-) A 0 49 GLN ( 55-) A 0 52 LEU ( 58-) A 0 53 HIS ( 59-) A 0 54 TYR ( 60-) A 0 55 LYS ( 61-) A 0 56 SER ( 62-) A 0 59 PHE ( 65-) A 0 60 HIS ( 66-) A 0 64 LYS ( 70-) A 0 66 PHE ( 72-) A 0 67 MET ( 73-) A 0 74 SER ( 80-) A 0 75 GLU ( 81-) A 0 77 ASN ( 83-) A 0 79 ARG ( 85-) A 0And so on for a total of 91 lines.
Standard deviation of omega values : 7.435
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]
173 PRO ( 179-) A 0.17 LOW
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.
109 ARG ( 115-) A NH1 <-> 179 HOH ( 286 ) A O 0.26 2.44 INTRA 127 HIS ( 133-) A ND1 <-> 179 HOH ( 297 ) A O 0.22 2.48 INTRA 60 HIS ( 66-) A ND1 <-> 179 HOH ( 229 ) A O 0.17 2.53 INTRA 76 GLY ( 82-) A O <-> 158 LYS ( 164-) A NZ 0.11 2.59 INTRA 72 ASP ( 78-) A OD2 <-> 78 GLY ( 84-) A N 0.09 2.61 INTRA BL 56 SER ( 62-) A N <-> 165 ILE ( 171-) A O 0.07 2.63 INTRA 98 HIS ( 104-) A N <-> 129 ASP ( 135-) A OD1 0.07 2.63 INTRA BL 45 GLY ( 51-) A N <-> 50 LYS ( 56-) A O 0.05 2.65 INTRA 36 CYS ( 42-) A O <-> 40 GLY ( 46-) A N 0.04 2.66 INTRA BL 98 HIS ( 104-) A CE1 <-> 134 VAL ( 140-) A CG2 0.03 3.17 INTRA BL 57 CYS ( 63-) A SG <-> 71 GLY ( 77-) A C 0.03 3.37 INTRA BL 65 ASP ( 71-) A N <-> 149 GLU ( 155-) A OE2 0.02 2.68 INTRA BL 8 ILE ( 14-) A O <-> 15 ALA ( 21-) 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.
109 ARG ( 115-) A -7.49 172 ILE ( 178-) A -6.01
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.
127 HIS ( 133-) A -2.65
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.
179 HOH ( 288 ) A O
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.
55 LYS ( 61-) A N 94 PHE ( 100-) A N 100 ALA ( 106-) A N 123 LYS ( 129-) A N
92 GLU ( 98-) A H-bonding suggests Gln 154 ASP ( 160-) A H-bonding suggests Asn; but Alt-Rotamer
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 : -0.470 2nd generation packing quality : -0.992 Ramachandran plot appearance : -0.361 chi-1/chi-2 rotamer normality : -1.788 Backbone conformation : -1.070
Bond lengths : 0.735 Bond angles : 0.779 Omega angle restraints : 1.352 (loose) Side chain planarity : 0.873 Improper dihedral distribution : 0.819 B-factor distribution : 1.147 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 : 1.80
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.1 2nd generation packing quality : -1.0 Ramachandran plot appearance : -0.3 chi-1/chi-2 rotamer normality : -1.4 Backbone conformation : -1.4
Bond lengths : 0.735 Bond angles : 0.779 Omega angle restraints : 1.352 (loose) Side chain planarity : 0.873 Improper dihedral distribution : 0.819 B-factor distribution : 1.147 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.