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: 32685.301
Volume of the Unit Cell V= 837460.250
Space group multiplicity: 6
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 4.270
Vm by authors and this calculated Vm agree reasonably well
Matthews coefficient read from REMARK 280 Vm= 3.920
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.
287 PO4 ( 436-) 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'.
3 ARG ( 47-) A NE 3 ARG ( 47-) A CZ 3 ARG ( 47-) A NH1 3 ARG ( 47-) A NH2 4 GLU ( 48-) A CD 4 GLU ( 48-) A OE1 4 GLU ( 48-) A OE2 25 GLN ( 69-) A CG 25 GLN ( 69-) A CD 25 GLN ( 69-) A OE1 25 GLN ( 69-) A NE2 47 GLU ( 91-) A CD 47 GLU ( 91-) A OE1 47 GLU ( 91-) A OE2 61 LYS ( 105-) A CG 61 LYS ( 105-) A CD 61 LYS ( 105-) A CE 61 LYS ( 105-) A NZ 79 GLN ( 123-) A CG 79 GLN ( 123-) A CD 79 GLN ( 123-) A OE1 79 GLN ( 123-) A NE2 80 GLU ( 124-) A CD 80 GLU ( 124-) A OE1 80 GLU ( 124-) A OE2And so on for a total of 78 lines.
Obviously, the temperature at which the X-ray data was collected has some importance too:
Number of TLS groups mentione in PDB file header: 1
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
100 TYR ( 144-) A 146 TYR ( 194-) A
9 PHE ( 53-) A 183 PHE ( 231-) A
RMS Z-score for bond lengths: 0.556
RMS-deviation in bond distances: 0.014
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
| 0.996887 0.000258 0.000104| | 0.000258 0.998117 0.000327| | 0.000104 0.000327 0.994134|Proposed new scale matrix
| 0.007891 0.004549 -0.000002| | -0.000002 0.009102 -0.000003| | -0.000002 -0.000006 0.016804|With corresponding cell
A = 126.701 B = 126.789 C = 59.511 Alpha= 89.973 Beta= 89.988 Gamma= 119.944
The CRYST1 cell dimensions
A = 127.101 B = 127.101 C = 59.863 Alpha= 90.000 Beta= 90.000 Gamma= 120.000
(Under-)estimated Z-score: 8.626
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.
258 ARG ( 306-) A CA CB CG 105.97 -4.1
134 GLU ( 178-) A 4.13
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.
130 THR ( 174-) A -2.5 196 GLY ( 244-) A -2.0 140 PRO ( 188-) 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.
42 ASN ( 86-) A Poor phi/psi 75 ARG ( 119-) A Poor phi/psi 80 GLU ( 124-) A omega poor 83 ASP ( 127-) A omega poor 84 TYR ( 128-) A omega poor 94 ASP ( 138-) A Poor phi/psi 98 LYS ( 142-) A Poor phi/psi 100 TYR ( 144-) A omega poor 122 GLU ( 166-) A Poor phi/psi 167 LEU ( 215-) A omega poor 172 GLN ( 220-) A Poor phi/psi 185 ALA ( 233-) A Poor phi/psi 189 HIS ( 237-) A Poor phi/psi 196 GLY ( 244-) A Poor phi/psi 265 ILE ( 313-) A Poor phi/psi chi-1/chi-2 correlation Z-score : 0.574
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.
112 SER ( 156-) A 0.40
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!
13 ALA ( 57-) A 0 24 ARG ( 68-) A 0 25 GLN ( 69-) A 0 26 PRO ( 70-) A 0 43 PHE ( 87-) A 0 50 ASP ( 94-) A 0 52 PRO ( 96-) A 0 54 HIS ( 98-) A 0 60 TYR ( 104-) A 0 66 ASN ( 110-) A 0 69 SER ( 113-) A 0 72 CYS ( 116-) A 0 75 ARG ( 119-) A 0 77 GLN ( 121-) A 0 78 SER ( 122-) A 0 81 ASP ( 125-) A 0 83 ASP ( 127-) A 0 84 TYR ( 128-) A 0 85 ILE ( 129-) A 0 86 ASN ( 130-) A 0 93 TYR ( 137-) A 0 94 ASP ( 138-) A 0 96 LYS ( 140-) A 0 97 GLU ( 141-) A 0 98 LYS ( 142-) A 0And so on for a total of 106 lines.
106 PRO ( 150-) A 0.07 LOW 217 PRO ( 265-) A 0.13 LOW
67 PRO ( 111-) A -112.1 envelop C-gamma (-108 degrees) 160 PRO ( 208-) A 101.0 envelop C-beta (108 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.
135 CYS ( 183-) A CB <-> 288 HOH ( 718 ) A O 0.54 2.26 INTRA BF 222 CYS ( 270-) A SG <-> 229 THR ( 277-) A A CG2 0.34 3.06 INTRA BL 135 CYS ( 183-) A N <-> 288 HOH ( 714 ) A O 0.32 2.38 INTRA BF 75 ARG ( 119-) A NE <-> 82 GLY ( 126-) A O 0.25 2.45 INTRA BF 24 ARG ( 68-) A NE <-> 288 HOH ( 542 ) A O 0.20 2.50 INTRA BF 188 ASP ( 236-) A OD2 <-> 288 HOH ( 578 ) A O 0.10 2.30 INTRA BF 1 THR ( 45-) A N <-> 2 PRO ( 46-) A CD 0.09 2.91 INTRA BF 138 TYR ( 186-) A OH <-> 221 HIS ( 269-) A NE2 0.08 2.62 INTRA 227 GLY ( 275-) A N <-> 287 PO4 ( 436-) A O4 0.08 2.62 INTRA BL 24 ARG ( 68-) A NH1 <-> 288 HOH ( 599 ) A O 0.07 2.63 INTRA BF 24 ARG ( 68-) A NH2 <-> 288 HOH ( 604 ) A O 0.06 2.64 INTRA BF 137 HIS ( 185-) A A CE1 <-> 139 TRP ( 187-) A O 0.06 2.74 INTRA BF 142 GLU ( 190-) A N <-> 288 HOH ( 507 ) A O 0.05 2.65 INTRA BF 243 LYS ( 291-) A NZ <-> 288 HOH ( 630 ) A O 0.05 2.65 INTRA BF 44 VAL ( 88-) A A CG2 <-> 48 ASP ( 92-) A CB 0.04 3.16 INTRA BF 134 GLU ( 178-) A A OE1 <-> 288 HOH ( 718 ) A O 0.04 2.36 INTRA BF 265 ILE ( 313-) A CD1 <-> 274 LEU ( 322-) A A CD1 0.03 3.17 INTRA 59 ARG ( 103-) A NH2 <-> 288 HOH ( 590 ) A O 0.02 2.68 INTRA BF 154 GLN ( 202-) A N <-> 166 GLN ( 214-) A O 0.02 2.68 INTRA 138 TYR ( 186-) A OH <-> 180 HIS ( 228-) A NE2 0.02 2.68 INTRA 276 HIS ( 324-) A ND1 <-> 288 HOH ( 535 ) A O 0.01 2.69 INTRA 77 GLN ( 121-) A OE1 <-> 288 HOH ( 588 ) A O 0.01 2.39 INTRA BF 184 SER ( 232-) A N <-> 288 HOH ( 667 ) A O 0.01 2.69 INTRA BF
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.
59 ARG ( 103-) A -6.70 190 GLN ( 238-) A -5.92 245 ARG ( 293-) A -5.79 24 ARG ( 68-) A -5.65 284 GLN ( 332-) A -5.60 23 GLN ( 67-) A -5.38 189 HIS ( 237-) A -5.22
The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.
284 GLN ( 332-) A 286 - PRO 334- ( A) -4.70
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.
214 HIS ( 262-) A -3.35 133 ARG ( 177-) A -2.54 105 GLY ( 149-) A -2.52
The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.
206 GLU ( 254-) A - 210 GLU ( 258-) A -1.71
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.
54 HIS ( 98-) 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.
47 GLU ( 91-) A N 132 LEU ( 176-) A N 139 TRP ( 187-) A N 194 SER ( 242-) A N 224 ALA ( 272-) A N 226 ILE ( 274-) A N 227 GLY ( 275-) A N 228 ARG ( 276-) A N 228 ARG ( 276-) A NE 228 ARG ( 276-) A NH2 229 THR ( 277-) A A OG1 236 ARG ( 284-) A NE 247 GLU ( 295-) A N 277 THR ( 325-) A OG1
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.
189 HIS ( 237-) A A ND1
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.
288 HOH ( 462 ) A O 1.01 K 4 *2 288 HOH ( 470 ) A O 0.98 K 4 *2 288 HOH ( 478 ) A O 0.99 K 4 *2 288 HOH ( 505 ) A O 1.09 K 4 *2 288 HOH ( 578 ) A O 1.13 K 6 *2 288 HOH ( 690 ) A O 0.85 K 5 *2 ION-B
188 ASP ( 236-) A H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
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 : -0.603 2nd generation packing quality : -1.213 Ramachandran plot appearance : 0.456 chi-1/chi-2 rotamer normality : 0.574 Backbone conformation : -0.047
Bond lengths : 0.556 (tight) Bond angles : 0.672 Omega angle restraints : 1.012 Side chain planarity : 0.620 (tight) Improper dihedral distribution : 0.667 B-factor distribution : 0.669 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 : 1.85
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.0 2nd generation packing quality : -1.0 Ramachandran plot appearance : 1.3 chi-1/chi-2 rotamer normality : 0.7 Backbone conformation : -0.0
Bond lengths : 0.556 (tight) Bond angles : 0.672 Omega angle restraints : 1.012 Side chain planarity : 0.620 (tight) Improper dihedral distribution : 0.667 B-factor distribution : 0.669 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.