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 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. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.
173 ALA ( 173-) 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: 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.
173 ALA ( 173-) 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.
173 ALA (1001-) A 0.81 174 PRO (1002-) A 0.81
Obviously, the temperature at which the X-ray data was collected has some importance too:
Crystal temperature (K) :100.000
Error: The B-factors of bonded atoms show signs of over-refinement
For each of the bond types in a protein a distribution was derived for the
difference between the square roots of the B-factors of the two atoms. All
bonds in the current protein were scored against these distributions. The
number given below is the RMS Z-score over the structure. For a structure
with completely restrained B-factors within residues, this value will be
around 0.35, for extremely high resolution structures refined with free
isotropic B-factors this number is expected to be near 1.0. Any value over
1.5 is sign of severe over-refinement of B-factors.
RMS Z-score : 1.683 over 1162 bonds
Average difference in B over a bond : 4.72
RMS difference in B over a bond : 6.60
Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
Chain identifier: A
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.
70 GLN ( 70-) A CD OE1 1.32 4.4 70 GLN ( 70-) A CD NE2 1.23 -4.6
RMS Z-score for bond lengths: 0.398
RMS-deviation in bond distances: 0.008
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.
2 SER ( 2-) A -C N CA 133.29 6.4 8 PHE ( 8-) A CA CB CG 122.43 8.6 44 ASN ( 44-) A CA CB CG 108.02 -4.6 54 HIS ( 54-) A CG ND1 CE1 110.67 5.1 61 HIS ( 61-) A CA CB CG 109.08 -4.7 66 ASN ( 66-) A CA CB CG 106.99 -5.6 66 ASN ( 66-) A ND2 CG OD1 128.48 5.9 68 MET ( 68-) A -C N CA 113.84 -4.4 78 ASN ( 78-) A -C N CA 112.85 -4.9 88 GLU ( 88-) A CA C O 113.76 -4.1 90 PHE ( 90-) A CA CB CG 119.76 6.0 99 HIS ( 99-) A CA CB CG 118.17 4.4 99 HIS ( 99-) A CG ND1 CE1 110.23 4.6 109 ASN ( 109-) A CA CB CG 118.37 5.8 109 ASN ( 109-) A ND2 CG OD1 118.49 -4.1 133 HIS ( 133-) A CA CB CG 106.64 -7.2 133 HIS ( 133-) A CG ND1 CE1 110.00 4.4 172 LYS ( 172-) A CA C O 107.03 -8.1
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.
76 ARG ( 76-) A -2.5 67 PHE ( 67-) A -2.5 88 GLU ( 88-) A -2.3 51 LYS ( 51-) A -2.3 68 MET ( 68-) A -2.3 15 LYS ( 15-) A -2.2 116 GLY ( 116-) 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.
2 SER ( 2-) A Poor phi/psi 8 PHE ( 8-) A omega poor 44 ASN ( 44-) A omega poor 66 ASN ( 66-) A Poor phi/psi 67 PHE ( 67-) A Poor phi/psi 88 GLU ( 88-) A Poor phi/psi 132 LYS ( 132-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -1.495
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!
17 SER ( 17-) A 0 25 TYR ( 25-) A 0 26 ASP ( 26-) A 0 28 VAL ( 28-) A 0 29 VAL ( 29-) A 0 43 GLU ( 43-) A 0 44 ASN ( 44-) A 0 46 ILE ( 46-) A 0 49 SER ( 49-) A 0 53 LEU ( 53-) A 0 54 HIS ( 54-) A 0 55 PHE ( 55-) A 0 56 LYS ( 56-) A 0 58 SER ( 58-) A 0 60 PHE ( 60-) A 0 61 HIS ( 61-) A 0 62 ARG ( 62-) A 0 65 PRO ( 65-) A 0 66 ASN ( 66-) A 0 67 PHE ( 67-) A 0 68 MET ( 68-) A 0 74 PHE ( 74-) A 0 75 THR ( 75-) A 0 78 ASN ( 78-) A 0 80 THR ( 80-) A 0And so on for a total of 82 lines.
65 PRO ( 65-) A 0.06 LOW 174 PRO (1002-) A 0.49 HIGH
102 PRO ( 102-) A -115.0 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. 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.
176 HOH (2132 ) A O <-> 176 HOH (2133 ) A O 0.21 1.99 INTRA BF 128 TRP ( 128-) A NE1 <-> 176 HOH (2180 ) A O 0.21 2.49 INTRA 48 LYS ( 48-) A NZ <-> 176 HOH (2088 ) A O 0.20 2.50 INTRA 75 THR ( 75-) A OG1 <-> 76 ARG ( 76-) A NH2 0.20 2.50 INTRA BF 125 LYS ( 125-) A NZ <-> 176 HOH (2174 ) A O 0.20 2.50 INTRA BF 5 LYS ( 5-) A NZ <-> 176 HOH (2013 ) A O 0.20 2.50 INTRA BF 155 GLN ( 155-) A N <-> 176 HOH (2205 ) A O 0.18 2.52 INTRA BL 176 HOH (2030 ) A O <-> 176 HOH (2031 ) A O 0.15 2.05 INTRA BF 31 LYS ( 31-) A NZ <-> 176 HOH (2063 ) A O 0.14 2.56 INTRA 176 HOH (2117 ) A O <-> 176 HOH (2215 ) A O 0.13 2.07 INTRA 96 LYS ( 96-) A NZ <-> 97 GLU ( 97-) A OE2 0.13 2.57 INTRA BF 113 ASN ( 113-) A ND2 <-> 176 HOH (2163 ) A O 0.11 2.59 INTRA 109 ASN ( 109-) A ND2 <-> 176 HOH (2157 ) A O 0.11 2.59 INTRA 123 THR ( 123-) A O <-> 176 HOH (2170 ) A O 0.10 2.30 INTRA 100 THR ( 100-) A CA <-> 125 LYS ( 125-) A NZ 0.10 3.00 INTRA BF 99 HIS ( 99-) A O <-> 125 LYS ( 125-) A NZ 0.10 2.60 INTRA BF 73 ASP ( 73-) A CG <-> 77 GLY ( 77-) A N 0.10 3.00 INTRA BL 158 LYS ( 158-) A NZ <-> 176 HOH (2207 ) A O 0.10 2.60 INTRA BF 73 ASP ( 73-) A OD1 <-> 76 ARG ( 76-) A N 0.10 2.60 INTRA 123 THR ( 123-) A N <-> 124 VAL ( 124-) A N 0.10 2.50 INTRA B3 109 ASN ( 109-) A N <-> 173 ALA (1001-) A O 0.10 2.60 INTRA BL 66 ASN ( 66-) A ND2 <-> 176 HOH (2122 ) A O 0.09 2.61 INTRA 62 ARG ( 62-) A A NH2 <-> 176 HOH (2113 ) A O 0.07 2.63 INTRA 62 ARG ( 62-) A A NH2 <-> 175 PRO (1002-) A O'' 0.06 2.64 INTRA 103 GLY ( 103-) A N <-> 122 CYS ( 122-) A O 0.06 2.64 INTRA 142 GLY ( 142-) A O <-> 145 VAL ( 145-) A N 0.06 2.64 INTRA BL 73 ASP ( 73-) A OD2 <-> 81 GLY ( 81-) A N 0.06 2.64 INTRA 9 ASP ( 9-) A OD1 <-> 19 ARG ( 19-) A NE 0.05 2.65 INTRA BL 35 ASN ( 35-) A OD1 <-> 85 ILE ( 85-) A N 0.04 2.66 INTRA BL 114 THR ( 114-) A O <-> 176 HOH (2166 ) A O 0.04 2.36 INTRA 47 GLY ( 47-) A O <-> 50 GLY ( 50-) A N 0.04 2.66 INTRA BL 125 LYS ( 125-) A N <-> 176 HOH (2173 ) A O 0.04 2.66 INTRA 9 ASP ( 9-) A O <-> 166 ALA ( 166-) A N 0.03 2.67 INTRA BL 95 PHE ( 95-) A N <-> 96 LYS ( 96-) A N 0.03 2.57 INTRA BL 152 ASN ( 152-) A O <-> 160 VAL ( 160-) A N 0.02 2.68 INTRA BL 114 THR ( 114-) A N <-> 176 HOH (2141 ) A O 0.02 2.68 INTRA BL 95 PHE ( 95-) A N <-> 176 HOH (2146 ) A O 0.02 2.68 INTRA 21 VAL ( 21-) A O <-> 140 VAL ( 140-) A N 0.02 2.68 INTRA BL 81 GLY ( 81-) A O <-> 118 GLN ( 118-) A NE2 0.01 2.69 INTRA 76 ARG ( 76-) A CG <-> 80 THR ( 80-) A OG1 0.01 2.79 INTRA BF
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.
155 GLN ( 155-) A -6.25 48 LYS ( 48-) A -5.69 76 ARG ( 76-) A -5.21
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.
176 HOH (2015 ) A O 62.61 36.51 5.24 176 HOH (2016 ) A O 63.87 29.86 -0.61 176 HOH (2075 ) A O 48.18 40.88 29.08
176 HOH (2127 ) A O
109 ASN ( 109-) A 155 GLN ( 155-) 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 LYS ( 5-) A N 49 SER ( 49-) A OG 56 LYS ( 56-) A N 84 SER ( 84-) A OG 94 ASN ( 94-) A N 123 THR ( 123-) A OG1 124 VAL ( 124-) A N 128 TRP ( 128-) A N 161 LYS ( 161-) A N
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.
176 HOH (2081 ) A O 0.97 K 5 176 HOH (2143 ) A O 1.02 K 4 176 HOH (2151 ) A O 1.02 K 4 176 HOH (2185 ) A O 0.95 K 4 Ion-B 176 HOH (2200 ) A O 0.88 K 5 Ion-B 176 HOH (2211 ) A O 0.90 K 4
26 ASP ( 26-) A 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 : -0.705 2nd generation packing quality : -1.385 Ramachandran plot appearance : -0.427 chi-1/chi-2 rotamer normality : -1.495 Backbone conformation : 0.150
Bond lengths : 0.398 (tight) Bond angles : 1.225 Omega angle restraints : 1.039 Side chain planarity : 0.482 (tight) Improper dihedral distribution : 0.640 B-factor distribution : 1.683 (loose) Inside/Outside distribution : 0.907
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 : 1.90
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.2 2nd generation packing quality : -1.1 Ramachandran plot appearance : -0.1 chi-1/chi-2 rotamer normality : -0.8 Backbone conformation : -0.1
Bond lengths : 0.398 (tight) Bond angles : 1.225 Omega angle restraints : 1.039 Side chain planarity : 0.482 (tight) Improper dihedral distribution : 0.640 B-factor distribution : 1.683 (loose) Inside/Outside distribution : 0.907 ==============
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.