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.
455 PG4 (2697-) A - 456 DAN (2692-) 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.
91 GLN (1333-) A - 441 MET (1683-) 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.
91 GLN (1333-) A - 441 MET (1683-) A -
Plausible side chain atoms were detected with (near) zero occupancy
When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.
71 GLU (1313-) A - CD 71 GLU (1313-) A - OE1 71 GLU (1313-) A - OE2 153 LYS (1395-) A - CD 153 LYS (1395-) A - CE 153 LYS (1395-) A - NZ 230 LYS (1472-) A - CD 230 LYS (1472-) A - CE 230 LYS (1472-) A - NZ 276 LYS (1518-) A - CE 276 LYS (1518-) A - NZ
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: C-terminal nitrogen atoms detected.
It is becoming habit to indicate that a residue is not the true C-terminus
by including only the backbone N of the next residue. This has been
observed in this PDB file.
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. In many cases the N- or C-terminal residues are too disordered to see. In case of the N-terminus, you can see from the residue numbers if there are missing residues, but at the C-terminus this is impossible. Therefore, often the position of the backbone nitrogen of the first residue missing at the C-terminal end is calculated and added to indicate that there are missing residues. As a single N causes validation trouble, we remove these single-N-residues before doing the validation. But, if you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or removed N is the cause.
449 GLY (1691-) A
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.
2 GLU (1244-) A 0.50 8 GLU (1250-) A 0.80 32 LYS (1274-) A 0.30 45 HIS (1287-) A 0.90 54 ASP (1296-) A 0.80 63 GLU (1305-) A 0.50 81 LYS (1323-) A 0.80 93 ASP (1335-) A 0.60 94 GLU (1336-) A 0.40 108 LYS (1350-) A 0.90 124 ASP (1366-) A 0.50 137 LYS (1379-) A 0.50 138 GLU (1380-) A 0.70 143 GLU (1385-) A 0.50 149 LYS (1391-) A 0.80 152 ASN (1394-) A 0.90 155 GLU (1397-) A 0.50 166 LYS (1408-) A 0.80 184 LYS (1426-) A 0.70 196 ASP (1438-) A 0.90 197 ASP (1439-) A 0.80 203 GLU (1445-) A 0.50 205 GLN (1447-) A 0.30 213 LYS (1455-) A 0.90 217 LYS (1459-) A 0.80 233 GLU (1475-) A 0.80 247 GLU (1489-) A 0.40 263 LYS (1505-) A 0.20 269 GLU (1511-) A 0.90 278 GLU (1520-) A 0.50 290 ASP (1532-) A 0.60 291 ASP (1533-) A 0.90 302 GLU (1544-) A 0.80 343 GLU (1585-) A 0.80 355 GLN (1597-) A 0.30 361 ASP (1603-) A 0.90 371 ARG (1613-) A 0.50 390 GLU (1632-) A 0.40 393 GLU (1635-) A 0.90 397 GLU (1639-) A 0.50 448 SER (1690-) A 0.80
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
23 TYR (1265-) A 128 TYR (1370-) A 188 TYR (1430-) A 243 TYR (1485-) A 318 TYR (1560-) A 396 TYR (1638-) A 402 TYR (1644-) A 413 TYR (1655-) A 428 TYR (1670-) A
13 PHE (1255-) A 99 PHE (1341-) A 105 PHE (1347-) A 165 PHE (1407-) A 209 PHE (1451-) A 325 PHE (1567-) A 365 PHE (1607-) A 398 PHE (1640-) A
336 GLU (1578-) 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
| 0.995421 -0.001036 -0.000374| | -0.001036 0.993214 0.000025| | -0.000374 0.000025 0.995487|Proposed new scale matrix
| 0.014481 0.000015 0.000005| | 0.000015 0.014171 0.000000| | 0.000004 0.000000 0.010157|With corresponding cell
A = 69.055 B = 70.566 C = 98.456 Alpha= 90.001 Beta= 90.043 Gamma= 90.119
The CRYST1 cell dimensions
A = 69.370 B = 71.046 C = 98.900 Alpha= 90.000 Beta= 90.000 Gamma= 90.000
(Under-)estimated Z-score: 15.124
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.
336 GLU (1578-) A
352 ASN (1594-) A 4.43
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.
345 TYR (1587-) A -3.1 186 THR (1428-) A -2.8 40 ILE (1282-) A -2.7 90 ILE (1332-) A -2.7 51 PRO (1293-) A -2.6 25 ILE (1267-) A -2.6 348 LEU (1590-) A -2.4 225 ARG (1467-) A -2.4 296 THR (1538-) A -2.2 224 GLY (1466-) A -2.2 102 VAL (1344-) A -2.1 293 PRO (1535-) A -2.1 343 GLU (1585-) A -2.1 417 THR (1659-) A -2.0 314 ASN (1556-) 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.
5 VAL (1247-) A omega poor 19 ASN (1261-) A Poor phi/psi 24 ARG (1266-) A omega poor 25 ILE (1267-) A Poor phi/psi 43 ARG (1285-) A omega poor 50 ALA (1292-) A PRO omega poor 59 VAL (1301-) A omega poor 79 PRO (1321-) A omega poor 80 ASP (1322-) A Poor phi/psi 81 LYS (1323-) A Poor phi/psi, omega poor 83 SER (1325-) A omega poor 86 ASP (1328-) A Poor phi/psi 108 LYS (1350-) A Poor phi/psi 116 LEU (1358-) A omega poor 144 ASN (1386-) A Poor phi/psi 151 SER (1393-) A Poor phi/psi 158 THR (1400-) A omega poor 172 ASP (1414-) A Poor phi/psi 197 ASP (1439-) A Poor phi/psi 255 VAL (1497-) A omega poor 261 SER (1503-) A Poor phi/psi 274 ASN (1516-) A Poor phi/psi 296 THR (1538-) A Poor phi/psi 312 MET (1554-) A omega poor 345 TYR (1587-) A Poor phi/psi 375 ASN (1617-) A Poor phi/psi 384 ASN (1626-) A omega poor 409 GLY (1651-) A omega poor 412 ALA (1654-) A Poor phi/psi 416 LEU (1658-) A omega poor 434 GLU (1676-) A Poor phi/psi chi-1/chi-2 correlation Z-score : 0.126
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!
12 LEU (1254-) A 0 13 PHE (1255-) A 0 15 PRO (1257-) A 0 17 PHE (1259-) A 0 18 LEU (1260-) A 0 19 ASN (1261-) A 0 21 SER (1263-) A 0 22 ASN (1264-) A 0 24 ARG (1266-) A 0 25 ILE (1267-) A 0 26 PRO (1268-) A 0 33 GLU (1275-) A 0 45 HIS (1287-) A 0 49 ASP (1291-) A 0 50 ALA (1292-) A 0 52 ASN (1294-) A 0 53 ASN (1295-) A 0 64 ASP (1306-) A 0 67 LYS (1309-) A 0 68 THR (1310-) A 0 71 GLU (1313-) A 0 76 MET (1318-) A 0 79 PRO (1321-) A 0 80 ASP (1322-) A 0 81 LYS (1323-) A 0And so on for a total of 199 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!
224 GLY (1466-) A 1.60 11 185 GLY (1427-) A 1.59 14
9 PRO (1251-) A 0.17 LOW 204 PRO (1446-) A 0.13 LOW
368 PRO (1610-) A 37.2 envelop C-delta (36 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.
203 GLU (1445-) A OE2 <-> 456 HOH (2187 ) A O 0.31 2.09 INTRA 456 HOH (2197 ) A O <-> 456 HOH (2198 ) A O 0.16 2.04 INTRA 413 TYR (1655-) A OH <-> 455 DAN (2692-) A C2 0.16 2.64 INTRA 52 ASN (1294-) A OD1 <-> 456 HOH (2067 ) A O 0.15 2.25 INTRA 395 LYS (1637-) A NZ <-> 397 GLU (1639-) A OE2 0.11 2.59 INTRA 32 LYS (1274-) A N <-> 91 GLN (1333-) A A OE1 0.11 2.59 INTRA BL 292 ALA (1534-) A N <-> 293 PRO (1535-) A CD 0.09 2.91 INTRA BL 367 ASN (1609-) A CB <-> 368 PRO (1610-) A CD 0.07 3.03 INTRA BL 359 GLY (1601-) A N <-> 456 HOH (2315 ) A O 0.01 2.69 INTRA BL 170 LYS (1412-) A NZ <-> 456 HOH (2160 ) 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.
371 ARG (1613-) A -7.30 108 LYS (1350-) A -5.67 390 GLU (1632-) A -5.51 278 GLU (1520-) A -5.43 32 LYS (1274-) A -5.18 210 GLN (1452-) A -5.16 71 GLU (1313-) A -5.07
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.
355 GLN (1597-) A -3.05
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.
456 HOH (2063 ) A O -6.07 3.72 24.94
456 HOH (2033 ) A O
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.
14 HIS (1256-) A N 24 ARG (1266-) A NH2 43 ARG (1285-) A NH2 50 ALA (1292-) A N 91 GLN (1333-) A N 181 LEU (1423-) A N 206 ASN (1448-) A ND2 209 PHE (1451-) A N 253 SER (1495-) A N 290 ASP (1532-) A N 313 ARG (1555-) A NE 355 GLN (1597-) A N 372 SER (1614-) A N 374 SER (1616-) A OG 431 THR (1673-) A N Only metal coordination for 54 ASP (1296-) A OD1
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.
86 ASP (1328-) 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+.
449 CA (2691-) A 0.79 1.03 Scores about as good as NA 450 MG (2693-) A -.- -.- Too few ligands (3) 451 MG (2694-) A 0.51 1.03 Is perhaps NA 452 MG (2695-) A -.- -.- Too few ligands (3) 453 MG (2696-) A 0.31 1.09 Could be K (Few ligands (4) )
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.
456 HOH (2292 ) A O 0.94 K 4
64 ASP (1306-) A H-bonding suggests Asn 196 ASP (1438-) A H-bonding suggests Asn; but Alt-Rotamer 260 ASP (1502-) A H-bonding suggests Asn 326 ASP (1568-) A H-bonding suggests Asn; but Alt-Rotamer 343 GLU (1585-) A H-bonding suggests Gln; but Alt-Rotamer 434 GLU (1676-) A H-bonding suggests Gln
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 : 0.408 2nd generation packing quality : -0.670 Ramachandran plot appearance : 0.290 chi-1/chi-2 rotamer normality : 0.126 Backbone conformation : 0.223
Bond lengths : 0.799 Bond angles : 0.843 Omega angle restraints : 1.252 Side chain planarity : 1.217 Improper dihedral distribution : 1.100 B-factor distribution : 0.666 Inside/Outside distribution : 0.981
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 : 1.50
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.7 2nd generation packing quality : -1.0 Ramachandran plot appearance : -0.3 chi-1/chi-2 rotamer normality : -0.4 Backbone conformation : -0.2
Bond lengths : 0.799 Bond angles : 0.843 Omega angle restraints : 1.252 Side chain planarity : 1.217 Improper dihedral distribution : 1.100 B-factor distribution : 0.666 Inside/Outside distribution : 0.981 ==============
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.