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 MS5 (1263-) 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.
56 ARG ( 58-) A 0.50 67 GLU ( 69-) 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) :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
56 ARG ( 58-) A
123 ASP ( 130-) A 168 ASP ( 175-) A
180 GLU ( 187-) A 227 GLU ( 234-) 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.
120 LYS ( 127-) A N -C 1.64 15.7
RMS Z-score for bond lengths: 0.397
RMS-deviation in bond distances: 0.009
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
| 0.998111 -0.000755 -0.000147| | -0.000755 0.997258 0.000070| | -0.000147 0.000070 0.998215|Proposed new scale matrix
| 0.023817 0.000018 0.000004| | 0.000011 0.013983 0.000000| | 0.000002 0.000000 0.013513|With corresponding cell
A = 41.987 B = 71.514 C = 74.002 Alpha= 90.001 Beta= 90.017 Gamma= 90.087
The CRYST1 cell dimensions
A = 42.067 B = 71.708 C = 74.136 Alpha= 90.000 Beta= 90.000 Gamma= 90.000
(Under-)estimated Z-score: 4.795
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.
62 HIS ( 64-) A CG ND1 CE1 109.62 4.0
RMS Z-score for bond angles: 0.642
RMS-deviation in bond angles: 1.282
Error: Nomenclature error(s)
Checking for a hand-check. WHAT IF has over the course of this session
already corrected the handedness of atoms in several residues. These were
administrative corrections. These residues are listed here.
56 ARG ( 58-) A 123 ASP ( 130-) A 168 ASP ( 175-) A 180 GLU ( 187-) A 227 GLU ( 234-) 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.
94 LEU ( 100-) A -2.5 169 PHE ( 176-) A -2.5 77 PRO ( 83-) A -2.2 86 GLN ( 92-) A -2.2 56 ARG ( 58-) 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.
27 SER ( 29-) A PRO omega poor 78 LEU ( 84-) A omega poor 80 GLY ( 86-) A omega poor 86 GLN ( 92-) A omega poor 105 LYS ( 111-) A Poor phi/psi 171 ASN ( 178-) A Poor phi/psi 184 TYR ( 191-) A omega poor 190 SER ( 197-) A omega poor 194 PRO ( 201-) A PRO omega poor 196 LEU ( 203-) A Poor phi/psi 200 VAL ( 207-) A omega poor 208 PRO ( 215-) A omega poor 236 ASP ( 243-) A Poor phi/psi 245 LYS ( 252-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -0.666
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 17 ASP ( 19-) 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 52 ALA ( 54-) A 0 56 ARG ( 58-) A 0 60 ASN ( 62-) A 0 62 HIS ( 64-) A 0 63 ALA ( 65-) A 0 64 PHE ( 66-) A 0 69 ASP ( 71-) A 0 70 ASP ( 72-) A 0 71 ALA ( 77-) A 0 72 VAL ( 78-) A 0 74 LYS ( 80-) A 0 77 PRO ( 83-) A 0 79 ASP ( 85-) A 0 85 ILE ( 91-) A 0And so on for a total of 117 lines.
230 PRO ( 237-) A -117.0 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.
86 GLN ( 92-) A NE2 <-> 88 HIS ( 94-) A ND1 0.26 2.74 INTRA BL 56 ARG ( 58-) A NH1 <-> 261 HOH (2070 ) A O 0.25 2.45 INTRA 39 ASP ( 41-) A OD2 <-> 250 LYS ( 257-) A CE 0.22 2.58 INTRA 13 HIS ( 15-) A ND1 <-> 16 LYS ( 18-) A NZ 0.22 2.78 INTRA BL 56 ARG ( 58-) A NH1 <-> 261 HOH (2071 ) A O 0.11 2.59 INTRA 218 LYS ( 225-) A NZ <-> 261 HOH (2216 ) A O 0.10 2.60 INTRA 101 HIS ( 107-) A NE2 <-> 187 TYR ( 194-) A OH 0.07 2.63 INTRA BL 225 ASN ( 232-) A OD1 <-> 232 GLU ( 239-) A N 0.06 2.64 INTRA 261 HOH (2152 ) A O <-> 261 HOH (2208 ) A O 0.06 2.14 INTRA 173 ASP ( 180-) A OD2 <-> 175 ARG ( 182-) A NH2 0.04 2.66 INTRA 16 LYS ( 18-) A O <-> 258 FMT (1266-) A C 0.04 2.76 INTRA 49 TYR ( 51-) A OH <-> 116 HIS ( 122-) A NE2 0.03 2.67 INTRA BL 20 ILE ( 22-) A O <-> 23 GLY ( 25-) A N 0.02 2.68 INTRA BL 111 GLU ( 117-) A OE2 <-> 113 HIS ( 119-) A NE2 0.01 2.69 INTRA BL 192 THR ( 199-) A OG1 <-> 260 MS5 (1263-) A NAC 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.
8 HIS ( 10-) A -6.01 2 HIS ( 4-) A -5.55 94 LEU ( 100-) A -5.10
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.
16 LYS ( 18-) A -2.54
The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.
243 PRO ( 250-) A - 246 ASN ( 253-) A -1.97
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.
261 HOH (2074 ) A O 261 HOH (2205 ) A O Metal-coordinating Histidine residue 88 fixed to 1 Metal-coordinating Histidine residue 90 fixed to 1 Metal-coordinating Histidine residue 113 fixed to 1 Metal-coordinating Histidine residue 2 fixed to 1 Metal-coordinating Histidine residue 62 fixed to 1 Metal-coordinating Histidine residue 34 fixed to 1
86 GLN ( 92-) 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.
29 VAL ( 31-) A N 81 THR ( 87-) A OG1 94 LEU ( 100-) A N 193 THR ( 200-) A N 197 LEU ( 204-) A N 225 ASN ( 232-) A N 237 ASN ( 244-) A ND2 238 TRP ( 245-) A N 253 PHE ( 260-) A N Only metal coordination for 62 HIS ( 64-) A NE2 Only metal coordination for 88 HIS ( 94-) A NE2 Only metal coordination for 90 HIS ( 96-) A NE2 Only metal coordination for 113 HIS ( 119-) A ND1
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.
65 ASN ( 67-) A OD1
The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.
255 ZN (1262-) A -.- -.- Too few ligands (1) 256 ZN (1264-) A -.- -.- Low probability ion. Occ=0.50
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.
261 HOH (2110 ) A O 1.07 K 4 261 HOH (2211 ) A O 0.95 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 : -0.083 2nd generation packing quality : 0.256 Ramachandran plot appearance : -0.880 chi-1/chi-2 rotamer normality : -0.666 Backbone conformation : -0.845
Bond lengths : 0.397 (tight) Bond angles : 0.642 (tight) Omega angle restraints : 1.084 Side chain planarity : 0.567 (tight) Improper dihedral distribution : 0.594 B-factor distribution : 0.391 Inside/Outside distribution : 0.942
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 : 1.49
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.2 2nd generation packing quality : -0.4 Ramachandran plot appearance : -1.3 chi-1/chi-2 rotamer normality : -1.2 Backbone conformation : -1.4
Bond lengths : 0.397 (tight) Bond angles : 0.642 (tight) Omega angle restraints : 1.084 Side chain planarity : 0.567 (tight) Improper dihedral distribution : 0.594 B-factor distribution : 0.391 Inside/Outside distribution : 0.942 ==============
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.