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.
The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.
Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).
Molecular weight of all polymer chains: 32678.051
Volume of the Unit Cell V= 839476.438
Space group multiplicity: 6
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 4.282
Vm by authors and this calculated Vm agree reasonably well
Matthews coefficient read from REMARK 280 Vm= 3.960
Warning: Ligands for which a topology was generated automatically
The topology for the ligands in the table below were determined
automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG
server to automatically generate topology information for ligands. For this
PDB file that seems to have gone fine, but be aware that automatic topology
generation is a complicated task. So, if you get messages that you fail to
understand or that you believe are wrong, and one of these ligands is
involved, then check the ligand topology first.
286 PO4 ( 340-) A - 287 PO4 ( 341-) A - 288 GOL ( 401-) 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'.
5 GLU ( 48-) A CD 5 GLU ( 48-) A OE1 5 GLU ( 48-) A OE2 48 GLU ( 91-) A CD 48 GLU ( 91-) A OE1 48 GLU ( 91-) A OE2 62 LYS ( 105-) A CG 62 LYS ( 105-) A CD 62 LYS ( 105-) A CE 62 LYS ( 105-) A NZ 80 GLN ( 123-) A CG 80 GLN ( 123-) A CD 80 GLN ( 123-) A OE1 80 GLN ( 123-) A NE2 134 CYS ( 183-) A SG 141 GLU ( 190-) A CD 141 GLU ( 190-) A OE1 141 GLU ( 190-) A OE2 153 GLN ( 202-) A CD 153 GLN ( 202-) A OE1 153 GLN ( 202-) A NE2 206 GLU ( 255-) A CG 206 GLU ( 255-) A CD 206 GLU ( 255-) A OE1 206 GLU ( 255-) A OE2 209 GLU ( 258-) A CG 209 GLU ( 258-) A CD 209 GLU ( 258-) A OE1 209 GLU ( 258-) A OE2 210 THR ( 259-) A OG1 210 THR ( 259-) A CG2 213 HIS ( 262-) A CG 213 HIS ( 262-) A ND1 213 HIS ( 262-) A CD2 213 HIS ( 262-) A CE1 213 HIS ( 262-) A NE2
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 ASN ( 44-) A 0.50 82 ASP ( 125-) A 0.50 117 GLU ( 160-) A 0.50 157 GLU ( 206-) A 0.50 192 GLU ( 241-) 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: Tyrosine convention problem
The tyrosine residues listed in the table below have their chi-2 not between
-90.0 and 90.0
101 TYR ( 144-) A 137 TYR ( 186-) A
10 PHE ( 53-) A 182 PHE ( 231-) A
187 ASP ( 236-) 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
| 0.995843 0.000816 -0.000130| | 0.000816 0.997366 0.000390| | -0.000130 0.000390 0.996601|Proposed new scale matrix
| 0.007896 0.004548 0.000000| | -0.000007 0.009109 -0.000004| | 0.000002 -0.000007 0.016724|With corresponding cell
A = 126.585 B = 126.627 C = 59.795 Alpha= 89.951 Beta= 90.021 Gamma= 119.892
The CRYST1 cell dimensions
A = 127.106 B = 127.106 C = 59.999 Alpha= 90.000 Beta= 90.000 Gamma= 120.000
(Under-)estimated Z-score: 7.969
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.
55 HIS ( 98-) A CG ND1 CE1 109.64 4.0
187 ASP ( 236-) A
13 THR ( 56-) A 4.06
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.
131 THR ( 174-) A -2.5 147 PRO ( 196-) A -2.3
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.
43 ASN ( 86-) A Poor phi/psi 76 ARG ( 119-) A Poor phi/psi 81 GLU ( 124-) A omega poor 84 ASP ( 127-) A omega poor 85 TYR ( 128-) A omega poor 95 ASP ( 138-) A Poor phi/psi 99 LYS ( 142-) A Poor phi/psi 101 TYR ( 144-) A omega poor 123 GLU ( 166-) A Poor phi/psi 145 TYR ( 194-) A omega poor 171 GLN ( 220-) A Poor phi/psi 184 ALA ( 233-) A Poor phi/psi 188 HIS ( 237-) A Poor phi/psi 264 ILE ( 313-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -0.307
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.
113 SER ( 156-) 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!
14 ALA ( 57-) A 0 25 ARG ( 68-) A 0 26 GLN ( 69-) A 0 27 PRO ( 70-) A 0 40 ILE ( 83-) A 0 42 SER ( 85-) A 0 43 ASN ( 86-) A 0 44 PHE ( 87-) A 0 51 ASP ( 94-) A 0 53 PRO ( 96-) A 0 55 HIS ( 98-) A 0 60 ARG ( 103-) A 0 61 TYR ( 104-) A 0 67 ASN ( 110-) A 0 70 SER ( 113-) A 0 73 CYS ( 116-) A 0 76 ARG ( 119-) A 0 78 GLN ( 121-) A 0 80 GLN ( 123-) A 0 81 GLU ( 124-) A 0 82 ASP ( 125-) A 0 84 ASP ( 127-) A 0 85 TYR ( 128-) A 0 86 ILE ( 129-) A 0 87 ASN ( 130-) A 0And so on for a total of 110 lines.
For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.
In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!
3 PRO ( 46-) A 1.58 15
139 PRO ( 188-) A -65.1 envelop C-beta (-72 degrees) 147 PRO ( 196-) A -61.7 half-chair C-beta/C-alpha (-54 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.
134 CYS ( 183-) A N <-> 289 HOH ( 603 ) A O 0.11 2.59 INTRA BF 140 THR ( 189-) A N <-> 289 HOH ( 536 ) A O 0.10 2.60 INTRA BF 120 TRP ( 163-) A O <-> 175 ARG ( 224-) A NH1 0.09 2.61 INTRA BL 227 ARG ( 276-) A NH1 <-> 287 PO4 ( 341-) A O1 0.09 2.61 INTRA BL 43 ASN ( 86-) A ND2 <-> 257 ARG ( 306-) A O 0.08 2.62 INTRA BL 16 HIS ( 59-) A N <-> 248 ASP ( 297-) A OD1 0.07 2.63 INTRA BL 42 SER ( 85-) A O <-> 262 GLY ( 311-) A N 0.05 2.65 INTRA BL 272 PHE ( 321-) A O <-> 276 THR ( 325-) A N 0.05 2.65 INTRA BL 131 THR ( 174-) A OG1 <-> 287 PO4 ( 341-) A O2 0.04 2.36 INTRA BL 284 LEU ( 333-) A CA <-> 285 PRO ( 334-) A CD 0.03 2.77 INTRA BF 158 CYS ( 207-) A CB <-> 159 PRO ( 208-) A CD 0.02 3.08 INTRA BF 227 ARG ( 276-) A NH2 <-> 286 PO4 ( 340-) A O2 0.02 2.68 INTRA BL 76 ARG ( 119-) A NE <-> 83 GLY ( 126-) A O 0.01 2.69 INTRA BF 164 ARG ( 213-) A N <-> 179 HIS ( 228-) 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.
60 ARG ( 103-) A -6.80 189 GLN ( 238-) A -5.79 192 GLU ( 241-) A -5.73 69 GLN ( 112-) A -5.70 244 ARG ( 293-) A -5.70 132 GLN ( 175-) A -5.67 25 ARG ( 68-) A -5.60 188 HIS ( 237-) A -5.09 26 GLN ( 69-) A -5.06 78 GLN ( 121-) A -5.05
The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.
24 GLN ( 67-) A 26 - GLN 69- ( A) -5.20 94 TYR ( 137-) A 96 - GLY 139- ( A) -4.15
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.
213 HIS ( 262-) A -3.36 106 GLY ( 149-) A -2.57
Chain identifier: A
Water, ion, and hydrogenbond related checks
Warning: Water molecules need moving
The water molecules listed in the table below were found to be significantly
closer to a symmetry related non-water molecule than to the ones given in the
coordinate file. For optimal viewing convenience revised coordinates for
these water molecules should be given.
The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.
289 HOH ( 617 ) A O 42.81 32.63 18.60
289 HOH ( 502 ) A O 289 HOH ( 539 ) A O
9 HIS ( 52-) A 188 HIS ( 237-) 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.
25 ARG ( 68-) A NE 79 SER ( 122-) A OG 82 ASP ( 125-) A N 101 TYR ( 144-) A OH 132 GLN ( 175-) A N 138 TRP ( 187-) A N 160 GLU ( 209-) A N 164 ARG ( 213-) A NH1 193 SER ( 242-) A N 197 LEU ( 246-) A N 221 SER ( 270-) A OG 223 ALA ( 272-) A N 225 ILE ( 274-) A N 226 GLY ( 275-) A N 227 ARG ( 276-) A N 227 ARG ( 276-) A NE 227 ARG ( 276-) A NH1 227 ARG ( 276-) A NH2 235 ARG ( 284-) A NE 246 GLU ( 295-) 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.
289 HOH ( 420 ) A O 0.86 K 4 *2 289 HOH ( 467 ) A O 0.80 K 5 *2
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 : -0.595 2nd generation packing quality : -1.099 Ramachandran plot appearance : -0.741 chi-1/chi-2 rotamer normality : -0.307 Backbone conformation : -0.161
Bond lengths : 0.573 (tight) Bond angles : 0.674 Omega angle restraints : 1.121 Side chain planarity : 0.505 (tight) Improper dihedral distribution : 0.680 B-factor distribution : 0.548 Inside/Outside distribution : 0.998
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 : 2.40
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.2 2nd generation packing quality : -0.0 Ramachandran plot appearance : 0.8 chi-1/chi-2 rotamer normality : 1.3 Backbone conformation : 0.2
Bond lengths : 0.573 (tight) Bond angles : 0.674 Omega angle restraints : 1.121 Side chain planarity : 0.505 (tight) Improper dihedral distribution : 0.680 B-factor distribution : 0.548 Inside/Outside distribution : 0.998 ==============
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.