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'.
1 THR ( 9-) A OG1 1 THR ( 9-) A CG2 2 LYS ( 10-) A CG 2 LYS ( 10-) A CD 2 LYS ( 10-) A CE 2 LYS ( 10-) A NZ 71 ARG ( 94-) A CG 71 ARG ( 94-) A CD 71 ARG ( 94-) A NE 71 ARG ( 94-) A CZ 71 ARG ( 94-) A NH1 71 ARG ( 94-) A NH2 102 ARG ( 125-) A CG 102 ARG ( 125-) A CD 102 ARG ( 125-) A NE 102 ARG ( 125-) A CZ 102 ARG ( 125-) A NH1 102 ARG ( 125-) A NH2 116 GLU ( 139-) A CG 116 GLU ( 139-) A CD 116 GLU ( 139-) A OE1 116 GLU ( 139-) A OE2 118 LYS ( 141-) A CG 118 LYS ( 141-) A CD 118 LYS ( 141-) A CEAnd so on for a total of 77 lines.
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.
272 GLU ( 295-) A 0.41
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) :180.000
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
4 TYR ( 12-) A 8 TYR ( 16-) A
337 PHE ( 360-) 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.
87 CYS ( 110-) A CA CB 1.63 5.1 87 CYS ( 110-) A CB SG 2.04 7.1
RMS Z-score for bond lengths: 0.428
RMS-deviation in bond distances: 0.010
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
| 0.997068 0.000197 -0.000070| | 0.000197 0.997529 -0.000280| | -0.000070 -0.000280 0.996892|Proposed new scale matrix
| 0.015590 -0.000003 0.000001| | -0.000003 0.014935 0.000004| | 0.000000 0.000003 0.011946|With corresponding cell
A = 64.145 B = 66.957 C = 83.709 Alpha= 90.032 Beta= 90.005 Gamma= 89.977
The CRYST1 cell dimensions
A = 64.333 B = 67.123 C = 83.969 Alpha= 90.000 Beta= 90.000 Gamma= 90.000
(Under-)estimated Z-score: 7.277
Warning: Low bond angle variability
Bond angles were found to deviate less than normal from the standard bond
angles (normal values for protein residues were taken from Engh and Huber
[REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below
is expected to be near 1.0 for a normally restrained data set. The fact that
it is lower than 0.667 in this structure might indicate that too-strong
restraints have been used in the refinement. This can only be a problem for
high resolution X-ray structures.
RMS Z-score for bond angles: 0.580
RMS-deviation in bond angles: 1.154
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.
336 THR ( 359-) A -2.5 217 LYS ( 240-) A -2.3 87 CYS ( 110-) A -2.3 277 PHE ( 300-) A -2.1 280 GLY ( 303-) A -2.0 52 THR ( 75-) A -2.0 160 LEU ( 183-) 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.
101 ASN ( 124-) A Poor phi/psi 211 HIS ( 234-) A Poor phi/psi 246 PHE ( 269-) A Poor phi/psi 251 GLY ( 274-) A omega poor 262 ASN ( 285-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -0.346
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!
24 SER ( 32-) A 0 25 ALA ( 33-) A 0 26 ASP ( 49-) A 0 27 ASP ( 50-) A 0 46 SER ( 69-) A 0 47 TYR ( 70-) A 0 51 GLU ( 74-) A 0 64 VAL ( 87-) A 0 65 TYR ( 88-) A 0 67 HIS ( 90-) A 0 68 ARG ( 91-) A 0 72 LYS ( 95-) A 0 75 MET ( 98-) A 0 85 TYR ( 108-) A 0 87 CYS ( 110-) A 0 95 SER ( 118-) A 0 97 GLN ( 120-) A 0 98 TYR ( 121-) A 0 99 PRO ( 122-) A 0 101 ASN ( 124-) A 0 102 ARG ( 125-) A 0 103 LEU ( 126-) A 0 124 SER ( 147-) A 0 140 PHE ( 163-) A 0 161 GLU ( 184-) A 0And so on for a total of 119 lines.
99 PRO ( 122-) A -124.2 half-chair C-delta/C-gamma (-126 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.
31 PRO ( 54-) A O <-> 80 ARG ( 103-) A NH1 0.13 2.57 INTRA 55 ASN ( 78-) A ND2 <-> 355 HOH ( 472 ) A O 0.06 2.64 INTRA BL 223 LYS ( 246-) A NZ <-> 260 ASP ( 283-) A OD2 0.05 2.65 INTRA BL 41 ASP ( 64-) A N <-> 56 ASN ( 79-) A OD1 0.04 2.66 INTRA BL 150 ARG ( 173-) A NH2 <-> 287 GLU ( 310-) A O 0.03 2.67 INTRA 60 LYS ( 83-) A NZ <-> 352 GLY ( 375-) A O 0.03 2.67 INTRA BL 302 HIS ( 325-) A ND1 <-> 311 MET ( 334-) A N 0.02 2.98 INTRA BL 115 ASN ( 138-) A O <-> 119 ASN ( 142-) A N 0.01 2.69 INTRA BF 51 GLU ( 74-) A OE1 <-> 312 HIS ( 335-) A ND1 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.
190 ARG ( 213-) A -7.89 47 TYR ( 70-) A -7.86 350 LYS ( 373-) A -6.49 44 ARG ( 67-) A -6.21 38 ARG ( 61-) A -6.04 98 TYR ( 121-) A -5.81 123 ARG ( 146-) A -5.77 97 GLN ( 120-) A -5.70 305 ASN ( 328-) A -5.60 179 ASN ( 202-) A -5.54 186 ASN ( 209-) A -5.41 207 ASN ( 230-) A -5.37 94 ASN ( 117-) A -5.13 261 ARG ( 284-) A -5.13 63 GLN ( 86-) A -5.04 68 ARG ( 91-) A -5.01
The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.
268 THR ( 291-) A 270 - PRO 293- ( A) -4.42
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.
71 ARG ( 94-) A -3.59 102 ARG ( 125-) A -3.58 121 ARG ( 144-) A -3.11 348 LYS ( 371-) A -2.95 324 GLY ( 347-) A -2.93 239 LYS ( 262-) A -2.63 206 ARG ( 229-) A -2.59 2 LYS ( 10-) A -2.59 64 VAL ( 87-) A -2.52
Chain identifier: A
Water, ion, and hydrogenbond related checks
Error: HIS, ASN, GLN side chain flips
Listed here are Histidine, Asparagine or Glutamine residues for
which the orientation determined from hydrogen bonding analysis are
different from the assignment given in the input. Either they could
form energetically more favourable hydrogen bonds if the terminal
group was rotated by 180 degrees, or there is no assignment in the
input file (atom type 'A') but an assignment could be made. Be aware,
though, that if the topology could not be determined for one or more
ligands, then this option will make errors.
55 ASN ( 78-) A 162 ASN ( 185-) A 186 ASN ( 209-) 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.
13 ASP ( 21-) A N 39 MET ( 62-) A N 43 TYR ( 66-) A OH 55 ASN ( 78-) A N 80 ARG ( 103-) A NH1 90 VAL ( 113-) A N 228 GLY ( 251-) A N 261 ARG ( 284-) A NE 269 SER ( 292-) A N 276 ASN ( 299-) A ND2 285 GLN ( 308-) A N 298 GLY ( 321-) A N 343 ASN ( 366-) A ND2
Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.
Waters are not listed by this option.
176 GLU ( 199-) A OE1 291 ASP ( 314-) A OD1
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.
355 HOH ( 412 ) A O 0.92 K 4
171 ASP ( 194-) A H-bonding suggests Asn 176 GLU ( 199-) A H-bonding suggests Gln; but Alt-Rotamer 212 ASP ( 235-) 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 : -1.301 2nd generation packing quality : -1.723 Ramachandran plot appearance : 0.944 chi-1/chi-2 rotamer normality : -0.346 Backbone conformation : -0.158
Bond lengths : 0.428 (tight) Bond angles : 0.580 (tight) Omega angle restraints : 0.932 Side chain planarity : 0.351 (tight) Improper dihedral distribution : 0.573 B-factor distribution : 0.364 Inside/Outside distribution : 0.991
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 : 1.90
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.9 2nd generation packing quality : -1.3 Ramachandran plot appearance : 1.5 chi-1/chi-2 rotamer normality : 0.2 Backbone conformation : -0.5
Bond lengths : 0.428 (tight) Bond angles : 0.580 (tight) Omega angle restraints : 0.932 Side chain planarity : 0.351 (tight) Improper dihedral distribution : 0.573 B-factor distribution : 0.364 Inside/Outside distribution : 0.991 ==============
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.