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.
294 ACT ( 601-) A -
Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.
41 ASN (1716-) A - 202 GLN (1882-) A -
In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.
41 ASN (1716-) A - 123 GLN (1803-) A - 202 GLN (1882-) A - 239 ARG (1919-) 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.
33 GLU (1708-) A 0.66 169 CYS (1849-) A 0.66 195 GLU (1875-) A 0.66
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
Temperature cannot be read from the PDB file. This most likely means that
the temperature is listed as NULL (meaning unknown) in the PDB file.
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
53 ARG (1728-) A 89 ARG (1769-) A
92 TYR (1772-) A 145 TYR (1825-) A 210 TYR (1890-) A 253 TYR (1933-) A
166 PHE (1846-) A 183 PHE (1863-) A
133 ASP (1813-) A 209 ASP (1889-) A
91 GLU (1771-) A 195 GLU (1875-) 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.
11 ASN (1686-) A CB CG 1.63 4.6
RMS Z-score for bond lengths: 0.431
RMS-deviation in bond distances: 0.010
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.
16 HIS (1691-) A CG ND1 CE1 109.70 4.1
53 ARG (1728-) A 89 ARG (1769-) A 91 GLU (1771-) A 133 ASP (1813-) A 195 GLU (1875-) A 209 ASP (1889-) 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.
216 GLY (1896-) A -2.1 24 SER (1699-) 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.
23 ASP (1698-) A Poor phi/psi 25 ASN (1700-) A Poor phi/psi 35 LEU (1710-) A omega poor 51 GLU (1726-) A omega poor 61 ILE (1736-) A omega poor 73 GLY (1748-) A omega poor 75 SER (1755-) A omega poor 77 TYR (1757-) A omega poor 89 ARG (1769-) A omega poor 90 ARG (1770-) A Poor phi/psi 92 TYR (1772-) A omega poor 114 ASN (1794-) A Poor phi/psi 122 THR (1802-) A omega poor 134 HIS (1814-) A omega poor 144 TYR (1824-) A omega poor 166 PHE (1846-) A omega poor 173 GLN (1853-) A Poor phi/psi 185 TYR (1865-) A omega poor 191 HIS (1871-) A omega poor 216 GLY (1896-) A omega poor 223 HIS (1903-) A omega poor 224 CYS (1904-) A Poor phi/psi 228 VAL (1908-) A Poor phi/psi 248 ASP (1928-) A omega poor 265 HIS (1945-) A Poor phi/psi 266 MET (1946-) A omega poor 267 VAL (1947-) A Poor phi/psi, omega poor chi-1/chi-2 correlation Z-score : 0.940
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 LYS (1678-) A 0 5 SER (1680-) A 0 6 CYS (1681-) A 0 23 ASP (1698-) A 0 24 SER (1699-) A 0 25 ASN (1700-) A 0 38 VAL (1713-) A 0 44 CYS (1719-) A 0 49 LEU (1724-) A 0 57 ARG (1732-) A 0 58 TYR (1733-) A 0 61 ILE (1736-) A 0 67 THR (1742-) A 0 72 SER (1747-) A 0 75 SER (1755-) A 0 78 ILE (1758-) A 0 79 ASN (1759-) A 0 87 ASN (1767-) A 0 88 PHE (1768-) A 0 89 ARG (1769-) A 0 90 ARG (1770-) A 0 92 TYR (1772-) A 0 102 THR (1782-) A 0 113 GLN (1793-) A 0 114 ASN (1794-) A 0And so on for a total of 114 lines.
Standard deviation of omega values : 7.357
Warning: Backbone oxygen evaluation
The residues listed in the table below have an unusual backbone oxygen
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!
227 GLY (1907-) A 1.50 62
7 PRO (1682-) A 40.7 envelop C-delta (36 degrees) 50 PRO (1725-) A 52.1 half-chair C-delta/C-gamma (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.
19 LYS (1694-) A A NZ <-> 295 HOH ( 531 ) A O 0.59 2.11 INTRA 53 ARG (1728-) A A CD <-> 295 HOH ( 430 ) A O 0.51 2.29 INTRA 243 GLN (1923-) A NE2 <-> 295 HOH ( 151 ) A O 0.47 2.23 INTRA 295 HOH ( 462 ) A O <-> 295 HOH ( 585 ) A O 0.46 1.74 INTRA 16 HIS (1691-) A CE1 <-> 295 HOH ( 538 ) A O 0.41 2.39 INTRA 19 LYS (1694-) A A CE <-> 295 HOH ( 531 ) A O 0.37 2.43 INTRA 16 HIS (1691-) A NE2 <-> 295 HOH ( 538 ) A O 0.29 2.41 INTRA 295 HOH ( 385 ) A O <-> 295 HOH ( 426 ) A O 0.27 1.93 INTRA 258 ASP (1938-) A A OD2 <-> 295 HOH ( 441 ) A O 0.26 2.14 INTRA 127 LYS (1807-) A CG <-> 190 ASP (1870-) A OD2 0.20 2.60 INTRA 92 TYR (1772-) A A CE2 <-> 239 ARG (1919-) A B NE 0.19 2.91 INTRA BL 144 TYR (1824-) A CE1 <-> 149 ILE (1829-) A A CG1 0.18 3.02 INTRA BL 288 LYS (1968-) A A CD <-> 295 HOH ( 383 ) A O 0.17 2.63 INTRA 190 ASP (1870-) A O <-> 191 HIS (1871-) A A CG 0.17 2.53 INTRA 55 LYS (1730-) A NZ <-> 295 HOH ( 41 ) A O 0.16 2.54 INTRA 12 GLN (1687-) A A NE2 <-> 295 HOH ( 147 ) A O 0.15 2.55 INTRA 268 GLN (1948-) A NE2 <-> 295 HOH ( 186 ) A O 0.14 2.56 INTRA 148 LEU (1828-) A CD2 <-> 170 GLY (1850-) A CA 0.13 3.07 INTRA 249 SER (1929-) A B OG <-> 295 HOH ( 414 ) A O 0.11 2.29 INTRA 213 ARG (1893-) A CG <-> 295 HOH ( 374 ) A O 0.11 2.69 INTRA 37 ASP (1712-) A OD1 <-> 295 HOH ( 225 ) A O 0.10 2.30 INTRA 14 GLU (1689-) A OE2 <-> 18 MET (1693-) A A CE 0.09 2.71 INTRA 181 ARG (1861-) A A NH2 <-> 213 ARG (1893-) A NH2 0.09 2.76 INTRA 295 HOH ( 463 ) A O <-> 295 HOH ( 477 ) A O 0.09 2.11 INTRA 196 THR (1876-) A OG1 <-> 198 GLN (1878-) A CG 0.09 2.71 INTRA 16 HIS (1691-) A ND1 <-> 295 HOH ( 531 ) A O 0.09 2.61 INTRA 295 HOH ( 76 ) A O <-> 295 HOH ( 226 ) A O 0.08 2.12 INTRA 295 HOH ( 268 ) A O <-> 295 HOH ( 529 ) A O 0.07 2.13 INTRA 181 ARG (1861-) A A NH2 <-> 295 HOH ( 550 ) A O 0.07 2.63 INTRA 284 LEU (1964-) A O <-> 288 LYS (1968-) A A CG 0.06 2.74 INTRA 173 GLN (1853-) A NE2 <-> 295 HOH ( 497 ) A O 0.06 2.64 INTRA 54 GLY (1729-) A N <-> 295 HOH ( 140 ) A O 0.06 2.64 INTRA 103 LYS (1783-) A A NZ <-> 295 HOH ( 468 ) A O 0.05 2.65 INTRA 70 LYS (1745-) A NZ <-> 295 HOH ( 439 ) A O 0.02 2.68 INTRA 92 TYR (1772-) A A CE2 <-> 239 ARG (1919-) A B NH2 0.02 3.08 INTRA BL 196 THR (1876-) A CB <-> 198 GLN (1878-) A CG 0.02 3.18 INTRA 36 LYS (1711-) A NZ <-> 295 HOH ( 532 ) A O 0.01 2.69 INTRA 208 ARG (1888-) A NH2 <-> 295 HOH ( 44 ) A O 0.01 2.69 INTRA 224 CYS (1904-) A SG <-> 227 GLY (1907-) A N 0.01 3.29 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.
89 ARG (1769-) A -7.10 191 HIS (1871-) A -6.83 174 LEU (1854-) A -6.55 213 ARG (1893-) A -5.59 87 ASN (1767-) A -5.30 88 PHE (1768-) A -5.18 2 ARG (1677-) A -5.02
The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.
86 ASN (1766-) A 90 - ARG 1770- ( A) -5.37
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.
173 GLN (1853-) A -2.83
Chain identifier: A
Water, ion, and hydrogenbond related checks
Error: Water clusters without contacts with non-water atoms
The water molecules listed in the table below are part of water molecule
clusters that do not make contacts with non-waters. These water molecules are
part of clusters that have a distance at least 1 Angstrom larger than the
sum of the Van der Waals radii to the nearest non-solvent atom. Because
these kinds of water clusters usually are not observed with X-ray diffraction
their presence could indicate a refinement artifact. The number in brackets
is the identifier of the water molecule in the input file.
295 HOH ( 436 ) A O 295 HOH ( 523 ) A O ERROR. No atoms within 50 A? ERROR. No atoms within 50 A?
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.
295 HOH ( 2 ) A O -14.98 33.18 28.11 295 HOH ( 505 ) A O -15.13 18.92 31.17 295 HOH ( 516 ) A O -7.86 25.16 1.36 295 HOH ( 517 ) A O -14.99 27.53 14.60 295 HOH ( 518 ) A O -15.39 31.35 15.02 295 HOH ( 519 ) A O -14.20 28.68 16.94 295 HOH ( 521 ) A O -14.27 30.21 18.70 295 HOH ( 594 ) A O 6.96 36.77 -10.43
295 HOH ( 436 ) A O 295 HOH ( 523 ) A O 295 HOH ( 587 ) A O Marked this atom as acceptor 292 CL ( 602-) A CL Marked this atom as acceptor 293 CL ( 603-) A CL
25 ASN (1700-) A 86 ASN (1766-) A 117 ASN (1797-) A 242 GLN (1922-) 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.
5 SER (1680-) A N 11 ASN (1686-) A N 53 ARG (1728-) A N 122 THR (1802-) A N 136 TRP (1816-) A N 139 ASP (1819-) A N 170 GLY (1850-) A N 187 VAL (1867-) A N 249 SER (1929-) A N 266 MET (1946-) A N 287 ARG (1967-) A NE 287 ARG (1967-) A NH2
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.
295 HOH ( 5 ) A O 0.96 K 4 295 HOH ( 29 ) A O 1.02 K 4 295 HOH ( 130 ) A O 1.14 K 4 295 HOH ( 402 ) A O 0.98 K 4 Ion-B 295 HOH ( 475 ) A O 0.90 K 5
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 : -0.290 2nd generation packing quality : -1.232 Ramachandran plot appearance : 0.220 chi-1/chi-2 rotamer normality : 0.940 Backbone conformation : -0.026
Bond lengths : 0.431 (tight) Bond angles : 0.681 Omega angle restraints : 1.338 (loose) Side chain planarity : 0.631 (tight) Improper dihedral distribution : 0.731 B-factor distribution : 0.771 Inside/Outside distribution : 1.036
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 : 1.30
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.0 2nd generation packing quality : -1.3 Ramachandran plot appearance : -0.3 chi-1/chi-2 rotamer normality : 0.4 Backbone conformation : -0.3
Bond lengths : 0.431 (tight) Bond angles : 0.681 Omega angle restraints : 1.338 (loose) Side chain planarity : 0.631 (tight) Improper dihedral distribution : 0.731 B-factor distribution : 0.771 Inside/Outside distribution : 1.036 ==============
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.