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.
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.
62 HIS ( 64-) A 0.90
Obviously, the temperature at which the X-ray data was collected has some importance too:
Crystal temperature (K) :293.000
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
5 TYR ( 7-) A
73 ASP ( 75-) A 172 ASP ( 175-) A
24 GLU ( 26-) A 67 GLU ( 69-) A 184 GLU ( 187-) 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.
62 HIS ( 64-) A C O 1.15 -4.1
24 GLU ( 26-) A 67 GLU ( 69-) A 73 ASP ( 75-) A 172 ASP ( 175-) A 184 GLU ( 187-) A
204 VAL ( 207-) A 4.33
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.
2 HIS ( 4-) A -3.0 81 PRO ( 83-) A -2.8 249 LYS ( 252-) A -2.5 173 PHE ( 176-) A -2.2 160 VAL ( 163-) A -2.2 190 THR ( 193-) A -2.2 90 GLN ( 92-) A -2.1 148 GLY ( 151-) 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.
27 SER ( 29-) A PRO omega poor 63 ALA ( 65-) A Poor phi/psi 109 LYS ( 111-) A Poor phi/psi 175 ASN ( 178-) A Poor phi/psi 198 PRO ( 201-) A PRO omega poor 240 ASP ( 243-) A Poor phi/psi 249 LYS ( 252-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -0.592
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 TRP ( 5-) A 0 5 TYR ( 7-) A 0 8 HIS ( 10-) A 0 17 ASP ( 19-) A 0 18 PHE ( 20-) A 0 22 LYS ( 24-) A 0 25 ARG ( 27-) A 0 26 GLN ( 28-) A 0 27 SER ( 29-) A 0 48 SER ( 50-) A 0 52 ALA ( 54-) A 0 60 ASN ( 62-) A 0 62 HIS ( 64-) A 0 63 ALA ( 65-) A 0 70 ASP ( 72-) A 0 71 SER ( 73-) A 0 73 ASP ( 75-) A 0 74 LYS ( 76-) A 0 78 LYS ( 80-) A 0 81 PRO ( 83-) A 0 83 ASP ( 85-) A 0 90 GLN ( 92-) A 0 94 HIS ( 96-) A 0 101 GLN ( 103-) A 0 105 HIS ( 107-) A 0And so on for a total of 116 lines.
Standard deviation of omega values : 2.034
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!
126 GLY ( 129-) A 1.62 10
81 PRO ( 83-) A -52.8 half-chair C-beta/C-alpha (-54 degrees) 192 PRO ( 195-) A -48.3 half-chair C-beta/C-alpha (-54 degrees) 212 PRO ( 215-) A -53.8 half-chair C-beta/C-alpha (-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.
43 LYS ( 45-) A CD <-> 260 DOD (1182 ) A O 0.21 2.59 INTRA BF 165 LYS ( 168-) A NZ <-> 260 DOD (1072 ) A O 0.15 2.55 INTRA BF 73 ASP ( 75-) A OD1 <-> 87 ARG ( 89-) A NE 0.11 2.59 INTRA 222 LYS ( 225-) A NZ <-> 260 DOD (1128 ) A O 0.10 2.60 INTRA BF 115 GLU ( 117-) A OE2 <-> 117 HIS ( 119-) A NE2 0.10 2.60 INTRA BL 105 HIS ( 107-) A NE2 <-> 191 TYR ( 194-) A OH 0.09 2.61 INTRA BL 130 LYS ( 133-) A NZ <-> 260 DOD (1144 ) A O 0.08 2.62 INTRA BF 39 ASP ( 41-) A OD1 <-> 41 SER ( 43-) A OG 0.07 2.33 INTRA 162 ASP ( 165-) A OD2 <-> 260 DOD (1170 ) A O 0.05 2.35 INTRA BF 13 HIS ( 15-) A ND1 <-> 16 LYS ( 18-) A NZ 0.05 2.95 INTRA 249 LYS ( 252-) A CB <-> 250 ASN ( 253-) A N 0.04 2.66 INTRA B3 49 TYR ( 51-) A OH <-> 120 HIS ( 122-) A NE2 0.04 2.66 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.
8 HIS ( 10-) A -6.44 2 HIS ( 4-) A -5.39 98 LEU ( 100-) A -5.21 133 GLN ( 136-) A -5.19
Chain identifier: A
Note: Second generation quality Z-score plot
The second generation quality Z-score smoothed over a 10 residue window
is plotted as function of the residue number. Low areas in the plot (below
-1.3) indicate unusual packing.
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.
260 DOD (1148 ) A O -5.04 19.84 21.37
1 HIS ( 3-) A 34 HIS ( 36-) A 134 GLN ( 137-) A 175 ASN ( 178-) A 252 GLN ( 255-) 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.
29 VAL ( 31-) A N 72 GLN ( 74-) A N 98 LEU ( 100-) A N 174 THR ( 177-) A OG1 179 ARG ( 182-) A NE 197 THR ( 200-) A N 201 LEU ( 204-) A N 227 ASN ( 230-) A ND2 241 ASN ( 244-) A ND2 242 TRP ( 245-) A N 257 PHE ( 260-) A N Only metal coordination for 94 HIS ( 96-) A NE2 Only metal coordination for 117 HIS ( 119-) A ND1
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.
260 DOD (1154 ) A O 0.90 K 4 ION-B 260 DOD (1193 ) A O 0.86 K 4 ION-B
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 : -0.455 2nd generation packing quality : 0.437 Ramachandran plot appearance : -1.628 chi-1/chi-2 rotamer normality : -0.592 Backbone conformation : -1.008
Bond lengths : 0.291 (tight) Bond angles : 0.667 Omega angle restraints : 0.370 (tight) Side chain planarity : 0.466 (tight) Improper dihedral distribution : 0.732 B-factor distribution : 0.491 Inside/Outside distribution : 0.944
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 : 2.00
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.1 2nd generation packing quality : 0.2 Ramachandran plot appearance : -1.0 chi-1/chi-2 rotamer normality : 0.2 Backbone conformation : -1.1
Bond lengths : 0.291 (tight) Bond angles : 0.667 Omega angle restraints : 0.370 (tight) Side chain planarity : 0.466 (tight) Improper dihedral distribution : 0.732 B-factor distribution : 0.491 Inside/Outside distribution : 0.944 ==============
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.