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.
222 PHQ ( 1-) I -
For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.
217 LEU ( 2-) I - N bound to 222 PHQ ( 1-) I - C1
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: E
Coordinate problems, unexpected atoms, B-factor and occupancy checks
Warning: What type of B-factor?
WHAT IF does not yet know well how to cope with B-factors in case TLS has
been used. It simply assumes that the B-factor listed on the ATOM and HETATM
cards are the total B-factors. When TLS refinement is used that assumption
sometimes is not correct. TLS seems not mentioned in the header of the PDB
file. But anyway, if WHAT IF complains about your B-factors, and you think
that they are OK, then check for TLS related B-factor problems first.
Obviously, the temperature at which the X-ray data was collected has some importance too:
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: E
Warning: Unusual bond lengths
The bond lengths listed in the table below were found to deviate more than 4
sigma from standard bond lengths (both standard values and sigmas for amino
acid residues have been taken from Engh and Huber [REF], for DNA they were
taken from Parkinson et al [REF]). In the table below for each unusual bond
the bond length and the number of standard deviations it differs from the
normal value is given.
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.
5 VAL ( 5-) E CA CB 1.62 4.6
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
| 0.997793 0.000588 0.000352| | 0.000588 0.996314 -0.000792| | 0.000352 -0.000792 0.996529|Proposed new scale matrix
| 0.017962 0.010378 0.000002| | -0.000012 0.020778 0.000017| | -0.000006 0.000012 0.015575|With corresponding cell
A = 55.656 B = 55.566 C = 64.205 Alpha= 90.099 Beta= 89.960 Gamma= 119.984
The CRYST1 cell dimensions
A = 55.780 B = 55.780 C = 64.430 Alpha= 90.000 Beta= 90.000 Gamma= 120.000
(Under-)estimated Z-score: 6.138
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.
5 VAL ( 5-) E N CA CB 117.60 4.2 58 LEU ( 58-) E CA CB CG 102.25 -4.0 105 VAL ( 105-) E N CA C 98.72 -4.5 134 VAL ( 134-) E C CA CB 101.35 -4.6 151 GLY ( 151-) E N CA C 124.17 4.0 152 SER ( 152-) E -CA -C N 106.45 -4.7 152 SER ( 152-) E -C N CA 131.57 5.5 152 SER ( 152-) E N CA C 97.35 -4.9 195 ARG ( 195-) E N CA C 122.96 4.2 197 SER ( 197-) E N CA C 122.42 4.0 208 ARG ( 208-) E N CA C 122.93 4.2 208 ARG ( 208-) E CG CD NE 118.68 4.8 215 LYS ( 215-) E N CA C 99.61 -4.1
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.
103 PRO ( 103-) E N 8.5 25.30 -2.48 152 SER ( 152-) E C -6.3 -10.09 0.37 The average deviation= 1.712
56 CYS ( 56-) E 5.99 152 SER ( 152-) E 5.44 42 THR ( 42-) E 5.12 78 ASN ( 78-) E 4.88 215 LYS ( 215-) E 4.50 164 VAL ( 164-) E 4.38 141 PHE ( 141-) E 4.38 105 VAL ( 105-) E 4.37 195 ARG ( 195-) E 4.36 50 GLU ( 50-) E 4.36 208 ARG ( 208-) E 4.35 172 LYS ( 172-) E 4.14 197 SER ( 197-) E 4.13
Tau angle RMS Z-score : 1.932
Warning: Torsion angle evaluation shows unusual residues
The residues listed in the table below contain bad or abnormal
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.
86 TYR ( 86-) E -2.8 103 PRO ( 103-) E -2.7 2 PRO ( 2-) E -2.6 152 SER ( 152-) E -2.6 89 ILE ( 89-) E -2.5 197 SER ( 197-) E -2.4 102 GLY ( 102-) E -2.3 21 TYR ( 21-) E -2.3 93 GLN ( 93-) E -2.3 134 VAL ( 134-) E -2.3 45 LEU ( 45-) E -2.3 156 LYS ( 156-) E -2.2 128 GLN ( 128-) E -2.1 42 THR ( 42-) E -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.
23 GLU ( 23-) E Poor phi/psi 65 ARG ( 65-) E Poor phi/psi 90 ALA ( 90-) E Poor phi/psi 101 GLY ( 101-) E Poor phi/psi 102 GLY ( 102-) E Poor phi/psi 103 PRO ( 103-) E Poor phi/psi 116 ASN ( 116-) E Poor phi/psi 128 GLN ( 128-) E Poor phi/psi 152 SER ( 152-) E Poor phi/psi 188 ASN ( 188-) E Poor phi/psi 196 ALA ( 196-) E Poor phi/psi 197 SER ( 197-) E Poor phi/psi 198 GLY ( 198-) E Poor phi/psi 204 CYS ( 204-) E Poor phi/psi chi-1/chi-2 correlation Z-score : -3.618
chi-1/chi-2 correlation Z-score : -3.618
Warning: Unusual rotamers
The residues listed in the table below have a rotamer that is not seen very
often in the database of solved protein structures. This option determines
for every residue the position specific chi-1 rotamer distribution.
Thereafter it verified whether the actual residue in the molecule has the
most preferred rotamer or not. If the actual rotamer is the preferred one,
the score is 1.0. If the actual rotamer is unique, the score is 0.0. If
there are two preferred rotamers, with a population distribution of 3:2 and
your rotamer sits in the lesser populated rotamer, the score will be 0.667.
No value will be given if insufficient hits are found in the database.
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.
69 SER ( 69-) E 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 GLU ( 3-) E 0 7 TRP ( 7-) E 0 10 LYS ( 10-) E 0 12 ALA ( 12-) E 0 18 HIS ( 18-) E 0 21 TYR ( 21-) E 0 22 CYS ( 22-) E 0 23 GLU ( 23-) E 0 24 SER ( 24-) E 0 41 LYS ( 41-) E 0 55 ASP ( 55-) E 0 56 CYS ( 56-) E 0 59 GLN ( 59-) E 0 60 SER ( 60-) E 0 61 TYR ( 61-) E 0 63 CYS ( 63-) E 0 64 ASN ( 64-) E 0 65 ARG ( 65-) E 0 78 ASN ( 78-) E 0 81 HIS ( 81-) E 0 86 TYR ( 86-) E 0 88 TYR ( 88-) E 0 89 ILE ( 89-) E 0 90 ALA ( 90-) E 0 93 GLN ( 93-) E 0And so on for a total of 96 lines.
Standard deviation of omega values : 2.195
Warning: Unusual peptide bond conformations
For the residues listed in the table below, the backbone formed by the
residue mentioned and the one C-terminal of it show systematic angular
deviations from normality that are consistent with a cis-peptide that
accidentally got refine in a trans conformation. This check follows the
recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not
yet fully matured...
195 ARG ( 195-) E 1.73
15 PRO ( 15-) E 101.0 envelop C-beta (108 degrees) 103 PRO ( 103-) E -175.2 envelop N (180 degrees) 201 PRO ( 201-) E -114.1 envelop C-gamma (-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.
The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.
It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.
Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.
25 CYS ( 25-) E SG <-> 221 0HQ ( 5-) I C1 1.55 1.85 INTRA BL 217 LEU ( 2-) I N <-> 222 PHQ ( 1-) I C1 1.38 1.32 INTRA B3 217 LEU ( 2-) I CA <-> 222 PHQ ( 1-) I C1 0.77 2.43 INTRA 25 CYS ( 25-) E SG <-> 219 GLY ( 4-) I C 0.60 2.80 INTRA BL 25 CYS ( 25-) E CB <-> 221 0HQ ( 5-) I C1 0.50 2.70 INTRA BL 112 ARG ( 112-) E NH1 <-> 223 HOH ( 229 ) E O 0.46 2.24 INTRA 81 HIS ( 81-) E NE2 <-> 101 GLY ( 101-) E C 0.25 2.85 INTRA 15 PRO ( 15-) E O <-> 17 LYS ( 17-) E NZ 0.23 2.47 INTRA BL 123 ASN ( 123-) E O <-> 127 HIS ( 127-) E CD2 0.22 2.58 INTRA 132 VAL ( 132-) E CG1 <-> 133 VAL ( 133-) E N 0.20 2.80 INTRA BL 39 LYS ( 39-) E O <-> 43 GLY ( 43-) E N 0.17 2.53 INTRA 25 CYS ( 25-) E N <-> 221 0HQ ( 5-) I C1 0.17 2.93 INTRA BL 200 SER ( 200-) E N <-> 201 PRO ( 201-) E CD 0.17 2.83 INTRA 27 ALA ( 27-) E CA <-> 223 HOH ( 331 ) E O 0.16 2.64 INTRA 196 ALA ( 196-) E N <-> 207 TYR ( 207-) E OH 0.16 2.54 INTRA 108 ASN ( 108-) E ND2 <-> 216 ASN ( 216-) E OD1 0.16 2.54 INTRA 81 HIS ( 81-) E NE2 <-> 102 GLY ( 102-) E N 0.15 2.85 INTRA 52 GLU ( 52-) E O <-> 56 CYS ( 56-) E N 0.15 2.55 INTRA BL 112 ARG ( 112-) E NH2 <-> 208 ARG ( 208-) E O 0.15 2.55 INTRA 89 ILE ( 89-) E CG2 <-> 91 LYS ( 91-) E CG 0.15 3.05 INTRA 71 SER ( 71-) E CB <-> 223 HOH ( 331 ) E O 0.15 2.65 INTRA 30 THR ( 30-) E CG2 <-> 223 HOH ( 247 ) E O 0.15 2.65 INTRA BL 150 GLU ( 150-) E CD <-> 172 LYS ( 172-) E NZ 0.13 2.97 INTRA 106 LYS ( 106-) E NZ <-> 223 HOH ( 248 ) E O 0.13 2.57 INTRA 68 GLN ( 68-) E NE2 <-> 209 SER ( 209-) E O 0.11 2.59 INTRA BLAnd so on for a total of 61 lines.
Chain identifier: E
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.
21 TYR ( 21-) E -8.93 145 LYS ( 145-) E -5.75 99 GLN ( 99-) E -5.67 77 GLN ( 77-) E -5.64 78 ASN ( 78-) E -5.28 195 ARG ( 195-) E -5.09 18 HIS ( 18-) E -5.04
Chain identifier: E
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.
151 GLY ( 151-) E -2.65
Chain identifier: E
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.
223 HOH ( 283 ) E O 11.63 46.69 23.14
223 HOH ( 237 ) E O 223 HOH ( 323 ) E O 223 HOH ( 325 ) E O Unrecognized bound group for 219 Bound atom= 221 0HQ ( 5-) I C1
18 HIS ( 18-) E 51 GLN ( 51-) E 78 ASN ( 78-) E 99 GLN ( 99-) E 128 GLN ( 128-) E
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.
26 TRP ( 26-) E N 44 ASN ( 44-) E N 46 VAL ( 46-) E N 60 SER ( 60-) E N 70 THR ( 70-) E N 82 LEU ( 82-) E N 90 ALA ( 90-) E N 91 LYS ( 91-) E N 108 ASN ( 108-) E ND2 112 ARG ( 112-) E NH2 115 SER ( 115-) E N 140 ASP ( 140-) E N 179 ASN ( 179-) E ND2 194 ARG ( 194-) E NE 195 ARG ( 195-) E NE 195 ARG ( 195-) E NH2 197 SER ( 197-) E OG 202 GLY ( 202-) E N 207 TYR ( 207-) E OH
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.
81 HIS ( 81-) E NE2 150 GLU ( 150-) E OE2
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.
223 HOH ( 232 ) E O 1.05 K 4 223 HOH ( 241 ) E O 0.92 K 4
57 ASP ( 57-) E H-bonding suggests Asn; but Alt-Rotamer 158 ASP ( 158-) E H-bonding suggests Asn
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 : -1.381 2nd generation packing quality : -2.046 Ramachandran plot appearance : -2.784 chi-1/chi-2 rotamer normality : -3.618 (poor) Backbone conformation : -0.011
Bond lengths : 0.819 Bond angles : 1.016 Omega angle restraints : 0.399 (tight) Side chain planarity : 0.908 Improper dihedral distribution : 1.515 (loose) B-factor distribution : 1.007 Inside/Outside distribution : 1.004
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 : 2.10
Structure Z-scores, positive is better than average:
1st generation packing quality : -1.0 2nd generation packing quality : -1.4 Ramachandran plot appearance : -1.7 chi-1/chi-2 rotamer normality : -2.2 Backbone conformation : 0.0
Bond lengths : 0.819 Bond angles : 1.016 Omega angle restraints : 0.399 (tight) Side chain planarity : 0.908 Improper dihedral distribution : 1.515 (loose) B-factor distribution : 1.007 Inside/Outside distribution : 1.004 ==============
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.