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.
326 SCN (1322-) 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: 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:
Crystal temperature (K) :283.000
Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
Chain identifier: A
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.
131 ILE ( 131-) A N CA C 98.54 -4.5
133 LEU ( 133-) A 5.43 68 ALA ( 68-) A 4.80 273 GLN ( 273-) A 4.38 115 TRP ( 115-) A 4.12 77 ALA ( 77-) A 4.08 295 LEU ( 295-) A 4.02
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.
132 PRO ( 132-) A -2.8 6 THR ( 6-) A -2.7 107 SER ( 107-) A -2.3 92 SER ( 92-) A -2.2 119 GLU ( 119-) A -2.1 25 SER ( 25-) 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.
26 THR ( 26-) A Poor phi/psi 46 TYR ( 46-) A Poor phi/psi 50 LEU ( 50-) A PRO omega poor 60 ASN ( 60-) A Poor phi/psi 89 ASN ( 89-) A Poor phi/psi 92 SER ( 92-) A Poor phi/psi 105 HIS ( 105-) A Poor phi/psi 107 SER ( 107-) A Poor phi/psi 118 SER ( 118-) A Poor phi/psi 152 THR ( 152-) A Poor phi/psi 157 TYR ( 157-) A Poor phi/psi 159 ASN ( 159-) A Poor phi/psi 194 THR ( 194-) A Poor phi/psi 251 TYR ( 251-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -0.103
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.
282 SER ( 282-) A 0.36
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!
5 SER ( 5-) A 0 14 LEU ( 14-) A 0 24 TYR ( 24-) A 0 25 SER ( 25-) A 0 26 THR ( 26-) A 0 27 TYR ( 27-) A 0 30 LEU ( 30-) A 0 34 THR ( 34-) A 0 35 ARG ( 35-) A 0 37 ASP ( 37-) A 0 45 LYS ( 45-) A 0 46 TYR ( 46-) A 0 49 THR ( 49-) A 0 51 PRO ( 51-) A 0 53 SER ( 53-) A 0 55 TRP ( 55-) A 0 58 ALA ( 58-) A 0 60 ASN ( 60-) A 0 61 GLN ( 61-) A 0 62 PHE ( 62-) A 0 63 PHE ( 63-) A 0 91 LEU ( 91-) A 0 92 SER ( 92-) A 0 93 TYR ( 93-) A 0 96 ASN ( 96-) A 0And so on for a total of 118 lines.
Standard deviation of omega values : 1.479
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!
277 PRO ( 277-) A 1.90 10
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.
231 HIS ( 231-) A NE2 <-> 326 SCN (1322-) A S 0.92 2.38 INTRA 166 GLU ( 166-) A OE2 <-> 326 SCN (1322-) A S 0.42 2.58 INTRA 111 ASN ( 111-) A O <-> 318 LYS ( 323-) A NZ 0.28 2.42 INTRA 226 ASP ( 226-) A OD1 <-> 231 HIS ( 231-) A ND1 0.22 2.48 INTRA 1 ILE ( 1-) A N <-> 327 HOH (2002 ) A O 0.19 2.51 INTRA 206 SER ( 206-) A O <-> 239 LYS ( 239-) A NZ 0.17 2.53 INTRA BL 231 HIS ( 231-) A CE1 <-> 326 SCN (1322-) A S 0.17 3.23 INTRA 166 GLU ( 166-) A CD <-> 326 SCN (1322-) A S 0.16 3.24 INTRA 190 GLU ( 190-) A CD <-> 320 CA (1317-) A CA 0.15 3.05 INTRA BL 243 LEU ( 243-) A O <-> 247 GLY ( 247-) A N 0.14 2.56 INTRA BL 28 TYR ( 28-) A N <-> 57 ASP ( 57-) A O 0.11 2.59 INTRA BL 215 ASP ( 215-) A N <-> 216 HIS ( 216-) A N 0.08 2.52 INTRA BL 42 TYR ( 42-) A N <-> 102 SER ( 102-) A O 0.08 2.62 INTRA BL 63 PHE ( 63-) A N <-> 327 HOH (2045 ) A O 0.08 2.62 INTRA 183 ASN ( 183-) A N <-> 184 PRO ( 184-) A CD 0.07 2.93 INTRA 32 ASP ( 32-) A OD2 <-> 35 ARG ( 35-) A NH1 0.07 2.63 INTRA BL 126 ASP ( 126-) A OD1 <-> 128 GLN ( 128-) A N 0.07 2.63 INTRA 47 ARG ( 47-) A NE <-> 327 HOH (2030 ) A O 0.07 2.63 INTRA 1 ILE ( 1-) A N <-> 327 HOH (2001 ) A O 0.06 2.64 INTRA 129 THR ( 129-) A O <-> 194 THR ( 194-) A N 0.06 2.64 INTRA 274 TYR ( 274-) A OH <-> 294 ASP ( 294-) A OD2 0.06 2.34 INTRA 196 GLY ( 196-) A N <-> 327 HOH (2111 ) A O 0.04 2.66 INTRA 222 THR ( 222-) A N <-> 327 HOH (2130 ) A O 0.04 2.66 INTRA 254 SER ( 254-) A O <-> 308 GLN ( 308-) A NE2 0.04 2.66 INTRA 114 PHE ( 114-) A O <-> 121 VAL ( 121-) A N 0.04 2.66 INTRA BL 66 TYR ( 66-) A O <-> 105 HIS ( 105-) A NE2 0.04 2.66 INTRA BL 209 ALA ( 209-) A C <-> 211 TYR ( 211-) A N 0.03 2.87 INTRA 280 ASN ( 280-) A N <-> 283 GLN ( 283-) A OE1 0.03 2.67 INTRA 28 TYR ( 28-) A O <-> 57 ASP ( 57-) A N 0.03 2.67 INTRA BL 108 GLN ( 108-) A NE2 <-> 327 HOH (2077 ) A O 0.03 2.67 INTRA BL 308 GLN ( 308-) A O <-> 312 ALA ( 312-) A N 0.02 2.68 INTRA BL 131 ILE ( 131-) A O <-> 132 PRO ( 132-) A C 0.02 2.58 INTRA BL 221 TYR ( 221-) A N <-> 233 ASN ( 233-) A OD1 0.01 2.69 INTRA BL 46 TYR ( 46-) A N <-> 105 HIS ( 105-) A O 0.01 2.69 INTRA BL 310 PHE ( 310-) A O <-> 315 VAL ( 315-) A N 0.01 2.69 INTRA BL 215 ASP ( 215-) A O <-> 250 HIS ( 250-) A NE2 0.01 2.69 INTRA BL 112 ASN ( 112-) A OD1 <-> 317 VAL ( 322-) A N 0.01 2.69 INTRA 234 SER ( 234-) A N <-> 235 GLY ( 235-) A N 0.01 2.59 INTRA BL 226 ASP ( 226-) A N <-> 327 HOH (2132 ) 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.
221 TYR ( 221-) A -5.89 88 HIS ( 88-) A -5.76 108 GLN ( 108-) A -5.66 246 GLN ( 246-) A -5.52 182 LYS ( 182-) A -5.36 273 GLN ( 273-) A -5.18 225 GLN ( 225-) A -5.14
The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.
225 GLN ( 225-) A 228 - GLY 228- ( A) -4.43
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.
44 ALA ( 44-) A -2.76
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.
301 GLN ( 301-) 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.
35 ARG ( 35-) A N 49 THR ( 49-) A N 97 ASN ( 97-) A ND2 112 ASN ( 112-) A N 155 LEU ( 155-) A N 209 ALA ( 209-) A N 216 HIS ( 216-) A N 261 ASP ( 261-) A N Only metal coordination for 142 HIS ( 142-) A NE2 Only metal coordination for 146 HIS ( 146-) A NE2 Only metal coordination for 166 GLU ( 166-) A OE1 Only metal coordination for 190 GLU ( 190-) A OE2
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.
166 GLU ( 166-) A OE2 231 HIS ( 231-) A NE2 238 ASN ( 238-) 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+.
320 CA (1317-) A -.- -.- Part of ionic cluster 320 CA (1317-) A 0.48 1.41 Scores about as good as K 321 CA (1318-) A -.- -.- Part of ionic cluster 321 CA (1318-) A 0.63 0.86 Scores about as good as NA 322 CA (1319-) A 0.52 0.73 Scores about as good as NA 323 CA (1320-) A 0.58 0.81 Scores about as good as NA
37 ASP ( 37-) A H-bonding suggests Asn 119 GLU ( 119-) A H-bonding suggests Gln 143 GLU ( 143-) A H-bonding suggests Gln 294 ASP ( 294-) A H-bonding suggests Asn; but Alt-Rotamer 311 ASP ( 311-) 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 : -0.747 2nd generation packing quality : -1.175 Ramachandran plot appearance : -0.279 chi-1/chi-2 rotamer normality : -0.103 Backbone conformation : -0.270
Bond lengths : 0.327 (tight) Bond angles : 0.628 (tight) Omega angle restraints : 0.269 (tight) Side chain planarity : 0.261 (tight) Improper dihedral distribution : 0.594 B-factor distribution : 0.790 Inside/Outside distribution : 1.018
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 : 2.18
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.1 2nd generation packing quality : -0.5 Ramachandran plot appearance : 0.8 chi-1/chi-2 rotamer normality : 1.0 Backbone conformation : -0.2
Bond lengths : 0.327 (tight) Bond angles : 0.628 (tight) Omega angle restraints : 0.269 (tight) Side chain planarity : 0.261 (tight) Improper dihedral distribution : 0.594 B-factor distribution : 0.790 Inside/Outside distribution : 1.018 ==============
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.