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.
283 UA1 ( 401-) A -
In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.
277 ARG (1967-) 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'.
277 ARG (1967-) A O
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: Arginine nomenclature problem
The arginine residues listed in the table below have their N-H-1 and N-H-2
203 ARG (1893-) A
89 TYR (1772-) A 142 TYR (1825-) A 200 TYR (1890-) A
11 PHE (1688-) A 163 PHE (1846-) A
21 ASP (1698-) A 130 ASP (1813-) A 136 ASP (1819-) A 180 ASP (1870-) A 199 ASP (1889-) A 238 ASP (1928-) A
31 GLU (1708-) A 88 GLU (1771-) A 185 GLU (1875-) A 260 GLU (1950-) 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
| 0.996462 -0.000274 -0.000654| | -0.000274 0.997706 -0.000279| | -0.000654 -0.000279 0.996503|Proposed new scale matrix
| 0.008858 0.000003 0.002369| | 0.000007 0.025836 0.000007| | 0.000010 0.000004 0.015505|With corresponding cell
A = 112.914 B = 38.705 C = 66.773 Alpha= 90.023 Beta= 105.011 Gamma= 90.031
The CRYST1 cell dimensions
A = 113.313 B = 38.795 C = 66.983 Alpha= 90.000 Beta= 104.940 Gamma= 90.000
(Under-)estimated Z-score: 7.300
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.
14 HIS (1691-) A CG ND1 CE1 109.70 4.1 42 CYS (1719-) A -C N CA 129.18 4.2 144 ASP (1827-) A -C N CA 129.53 4.3 147 LEU (1830-) A CA CB CG 102.04 -4.1 165 ILE (1848-) A C CA CB 99.48 -5.6 213 HIS (1903-) A CG ND1 CE1 109.71 4.1 229 ARG (1919-) A CG CD NE 120.29 5.8
21 ASP (1698-) A 31 GLU (1708-) A 88 GLU (1771-) A 130 ASP (1813-) A 136 ASP (1819-) A 180 ASP (1870-) A 185 GLU (1875-) A 199 ASP (1889-) A 203 ARG (1893-) A 238 ASP (1928-) A 260 GLU (1950-) A
Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.
Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.
Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.
165 ILE (1848-) A CB -7.2 22.89 32.31 254 VAL (1944-) A CB 6.8 -23.99 -32.96 The average deviation= 1.069
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.
124 LYS (1807-) A -2.4 257 VAL (1947-) A -2.4 165 ILE (1848-) A -2.3 204 SER (1894-) A -2.2 92 THR (1775-) 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.
22 SER (1699-) A Poor phi/psi 23 ASN (1700-) A Poor phi/psi 41 SER (1718-) A omega poor 59 ILE (1736-) A omega poor 74 TYR (1757-) A omega poor 89 TYR (1772-) A omega poor 111 ASN (1794-) A Poor phi/psi 119 THR (1802-) A omega poor 130 ASP (1813-) A omega poor 136 ASP (1819-) A Poor phi/psi, omega poor 139 SER (1822-) A omega poor 163 PHE (1846-) A omega poor 175 TYR (1865-) A omega poor 181 HIS (1871-) A Poor phi/psi 182 GLY (1872-) A omega poor 204 SER (1894-) A PRO omega poor 206 GLY (1896-) A omega poor 207 ALA (1897-) A omega poor 208 GLY (1898-) A Poor phi/psi 214 CYS (1904-) A Poor phi/psi 255 HIS (1945-) A Poor phi/psi 257 VAL (1947-) A Poor phi/psi, omega poor chi-1/chi-2 correlation Z-score : -1.709
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.
189 SER (1879-) A 0.37
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 SER (1680-) A 0 21 ASP (1698-) A 0 22 SER (1699-) A 0 23 ASN (1700-) A 0 36 VAL (1713-) A 0 38 ARG (1715-) A 0 39 ASN (1716-) A 0 42 CYS (1719-) A 0 43 ASP (1720-) A 0 56 TYR (1733-) A 0 69 LEU (1746-) A 0 70 SER (1747-) A 0 71 CYS (1754-) A 0 72 SER (1755-) A 0 76 ASN (1759-) A 0 77 ALA (1760-) A 0 84 ASN (1767-) A 0 85 PHE (1768-) A 0 86 ARG (1769-) A 0 87 ARG (1770-) A 0 89 TYR (1772-) A 0 99 THR (1782-) A 0 110 GLN (1793-) A 0 111 ASN (1794-) A 0 112 VAL (1795-) A 0And so on for a total of 110 lines.
Standard deviation of omega values : 7.827
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]
209 PRO (1899-) A 0.07 LOW
48 PRO (1725-) A 131.4 half-chair C-beta/C-alpha (126 degrees) 205 PRO (1895-) A 22.6 half-chair N/C-delta (18 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.
111 ASN (1794-) A ND2 <-> 284 HOH ( 141 ) A O 0.49 2.21 INTRA BL 164 LYS (1847-) A CE <-> 167 HIS (1857-) A CD2 0.33 2.87 INTRA BF 167 HIS (1857-) A CD2 <-> 284 HOH ( 124 ) A O 0.21 2.59 INTRA BF 284 HOH ( 93 ) A O <-> 284 HOH ( 193 ) A O 0.16 2.04 INTRA 24 TYR (1701-) A OH <-> 28 LYS (1705-) A NZ 0.16 2.54 INTRA 132 TYR (1815-) A OH <-> 213 HIS (1903-) A NE2 0.16 2.54 INTRA BL 161 ARG (1844-) A NH2 <-> 284 HOH ( 47 ) A O 0.15 2.55 INTRA 188 GLN (1878-) A CG <-> 284 HOH ( 37 ) A O 0.12 2.68 INTRA 121 CYS (1804-) A O <-> 128 LYS (1811-) A N 0.11 2.59 INTRA BL 161 ARG (1844-) A NH1 <-> 284 HOH ( 11 ) A O 0.10 2.60 INTRA BL 108 TRP (1791-) A O <-> 168 ARG (1858-) A A NH1 0.07 2.63 INTRA BL 128 LYS (1811-) A NZ <-> 180 ASP (1870-) A OD2 0.07 2.63 INTRA 167 HIS (1857-) A NE2 <-> 284 HOH ( 124 ) A O 0.06 2.64 INTRA BF 162 GLU (1845-) A OE1 <-> 171 ARG (1861-) A NH1 0.06 2.64 INTRA 114 ASN (1797-) A ND2 <-> 284 HOH ( 51 ) A O 0.06 2.64 INTRA 167 HIS (1857-) A CE1 <-> 284 HOH ( 134 ) A O 0.06 2.74 INTRA BF 260 GLU (1950-) A OE1 <-> 284 HOH ( 162 ) A O 0.06 2.34 INTRA 214 CYS (1904-) A SG <-> 217 GLY (1907-) A N 0.05 3.25 INTRA BL 214 CYS (1904-) A SG <-> 283 UA1 ( 401-) A S14 0.05 3.55 INTRA 284 HOH ( 29 ) A O <-> 284 HOH ( 77 ) A O 0.05 2.15 INTRA 116 VAL (1799-) A N <-> 211 VAL (1901-) A O 0.05 2.65 INTRA BL 67 VAL (1744-) A O <-> 284 HOH ( 56 ) A O 0.05 2.35 INTRA BL 37 GLY (1714-) A O <-> 40 GLN (1717-) A NE2 0.04 2.66 INTRA BL 102 ASP (1785-) A OD1 <-> 284 HOH ( 151 ) A O 0.04 2.36 INTRA 123 GLU (1806-) A OE2 <-> 220 ARG (1910-) A NH1 0.03 2.67 INTRA BL 218 VAL (1908-) A CG2 <-> 219 GLY (1909-) A N 0.03 2.97 INTRA BL 284 HOH ( 92 ) A O <-> 284 HOH ( 196 ) A O 0.03 2.17 INTRA 153 SER (1836-) A N <-> 160 ILE (1843-) A O 0.02 2.68 INTRA BL 171 ARG (1861-) A CD <-> 284 HOH ( 51 ) A O 0.02 2.78 INTRA 279 LEU (1969-) A N <-> 280 ARG (1970-) A N 0.02 2.58 INTRA BL 214 CYS (1904-) A SG <-> 217 GLY (1907-) A CA 0.02 3.38 INTRA BL 142 TYR (1825-) A OH <-> 284 HOH ( 31 ) A O 0.01 2.39 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.
86 ARG (1769-) A -7.13 279 LEU (1969-) A -6.02 203 ARG (1893-) A -5.75 185 GLU (1875-) A -5.53 181 HIS (1871-) A -5.39 85 PHE (1768-) A -5.31 84 ASN (1767-) A -5.23 177 VAL (1867-) 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.
83 ASN (1766-) A 87 - ARG 1770- ( A) -5.34
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.
58 ASN (1735-) A -2.71 143 GLY (1826-) 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.
284 HOH ( 78 ) A O 284 HOH ( 81 ) A O 284 HOH ( 86 ) A O Marked this atom as acceptor 282 CL ( 203-) A CL
114 ASN (1797-) A 167 HIS (1857-) 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.
57 ASN (1734-) A N 102 ASP (1785-) A N 119 THR (1802-) A N 133 TRP (1816-) A N 136 ASP (1819-) A N 158 TRP (1841-) A N 168 ARG (1858-) A A NE 171 ARG (1861-) A NE 171 ARG (1861-) A NH2 186 THR (1876-) A N 216 ALA (1906-) A N 218 VAL (1908-) A N 219 GLY (1909-) A N 220 ARG (1910-) A N 220 ARG (1910-) A NE 220 ARG (1910-) A NH2 239 SER (1929-) A N 256 MET (1946-) A N 280 ARG (1970-) 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.
284 HOH ( 136 ) A O 1.04 K 4
248 ASP (1938-) 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 : -0.239 2nd generation packing quality : -0.839 Ramachandran plot appearance : -0.783 chi-1/chi-2 rotamer normality : -1.709 Backbone conformation : 0.727
Bond lengths : 0.556 (tight) Bond angles : 0.939 Omega angle restraints : 1.423 (loose) Side chain planarity : 0.502 (tight) Improper dihedral distribution : 0.997 B-factor distribution : 1.127 Inside/Outside distribution : 1.052
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 : 2.15
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.3 2nd generation packing quality : -0.2 Ramachandran plot appearance : 0.2 chi-1/chi-2 rotamer normality : -0.9 Backbone conformation : 0.7
Bond lengths : 0.556 (tight) Bond angles : 0.939 Omega angle restraints : 1.423 (loose) Side chain planarity : 0.502 (tight) Improper dihedral distribution : 0.997 B-factor distribution : 1.127 Inside/Outside distribution : 1.052 ==============
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.