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.
260 AL8 ( 555-) A -
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.
257 LYS ( 261-) 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: Missing atoms
The atoms listed in the table below are missing from the entry. If many atoms
are missing, the other checks can become less sensitive. Be aware that it
often happens that groups at the termini of DNA or RNA are really missing,
so that the absence of these atoms normally is neither an error nor the
result of poor electron density. Some of the atoms listed here might also be
listed by other checks, most noticeably by the options in the previous
section that list missing atoms in several categories. The plausible atoms
with zero occupancy are not listed here, as they already got assigned a
non-zero occupancy, and thus are no longer 'missing'.
1 HIS ( 4-) A CB 1 HIS ( 4-) A CG 1 HIS ( 4-) A ND1 1 HIS ( 4-) A CD2 1 HIS ( 4-) A CE1 1 HIS ( 4-) A NE2 257 LYS ( 261-) A O
Obviously, the temperature at which the X-ray data was collected has some importance too:
Crystal temperature (K) :298.000
Warning: More than 2 percent of buried atoms has low B-factor
For protein structures determined at room temperature, no more than
about 1 percent of the B factors of buried atoms is below 5.0.
Percentage of buried atoms with B less than 5 : 3.11
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.
7 HIS ( 10-) A CG CD2 1.42 6.2 14 HIS ( 17-) A CG CD2 1.43 6.4 33 HIS ( 36-) A CG CD2 1.42 6.1 61 HIS ( 64-) A CG CD2 1.43 6.7 61 HIS ( 64-) A ND1 CE1 1.37 4.2 91 HIS ( 94-) A CG CD2 1.40 4.1 93 HIS ( 96-) A CG CD2 1.42 5.6 116 HIS ( 119-) A CG CD2 1.42 5.9
7 HIS ( 10-) A CG ND1 CE1 110.69 5.1 14 HIS ( 17-) A CG ND1 CE1 110.68 5.1 14 HIS ( 17-) A CB CG CD2 135.36 4.8 33 HIS ( 36-) A CG ND1 CE1 110.66 5.1 33 HIS ( 36-) A CB CG CD2 135.09 4.6 61 HIS ( 64-) A CG ND1 CE1 110.55 5.0 61 HIS ( 64-) A CB CG CD2 134.82 4.4 91 HIS ( 94-) A CG ND1 CE1 110.84 5.2 91 HIS ( 94-) A CB CG CD2 134.71 4.3 93 HIS ( 96-) A CG ND1 CE1 110.40 4.8 93 HIS ( 96-) A CB CG CD2 134.84 4.4 116 HIS ( 119-) A CG ND1 CE1 110.75 5.2 116 HIS ( 119-) A CB CG CD2 136.86 6.0 204 THR ( 208-) A N CA C 98.04 -4.7
204 THR ( 208-) A 4.82 203 VAL ( 207-) A 4.58 93 HIS ( 96-) A 4.15
For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.
7 HIS ( 10-) A CB 6.41 Since there is no DNA and no protein with hydrogens, no uncalibrated planarity check was performed. Ramachandran Z-score : -2.761
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.
57 LEU ( 60-) A -2.4 235 GLU ( 239-) A -2.2 80 PRO ( 83-) A -2.2 204 THR ( 208-) A -2.1 41 LEU ( 44-) A -2.1 89 GLN ( 92-) A -2.1 189 THR ( 193-) A -2.0 76 LEU ( 79-) A -2.0 19 ILE ( 22-) 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.
26 SER ( 29-) A PRO omega poor 62 ALA ( 65-) A Poor phi/psi 72 ASP ( 75-) A Poor phi/psi 108 LYS ( 111-) A Poor phi/psi 197 PRO ( 201-) A PRO omega poor 199 LEU ( 203-) A Poor phi/psi 239 ASP ( 243-) A Poor phi/psi 248 LYS ( 252-) A Poor phi/psi 249 ASN ( 253-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -2.364
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!
4 TYR ( 7-) A 0 16 ASP ( 19-) A 0 17 PHE ( 20-) A 0 21 LYS ( 24-) A 0 24 ARG ( 27-) A 0 25 GLN ( 28-) A 0 26 SER ( 29-) A 0 47 SER ( 50-) A 0 49 ASP ( 52-) A 0 51 ALA ( 54-) A 0 55 ARG ( 58-) A 0 59 ASN ( 62-) A 0 61 HIS ( 64-) A 0 62 ALA ( 65-) A 0 69 ASP ( 72-) A 0 70 SER ( 73-) A 0 72 ASP ( 75-) A 0 73 LYS ( 76-) A 0 77 LYS ( 80-) A 0 80 PRO ( 83-) A 0 82 ASP ( 85-) A 0 88 ILE ( 91-) A 0 89 GLN ( 92-) A 0 93 HIS ( 96-) A 0 100 GLN ( 103-) A 0And so on for a total of 119 lines.
Standard deviation of omega values : 1.407
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!
125 GLY ( 129-) A 1.71 14
80 PRO ( 83-) A 0.45 HIGH 151 PRO ( 155-) A 0.45 HIGH
191 PRO ( 195-) A 49.4 half-chair C-delta/C-gamma (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.
93 HIS ( 96-) A CD2 <-> 116 HIS ( 119-) A CE1 0.13 3.07 INTRA BL 100 GLN ( 103-) A NE2 <-> 239 ASP ( 243-) A OD1 0.13 2.57 INTRA 68 ASP ( 71-) A OD2 <-> 73 LYS ( 76-) A NZ 0.10 2.60 INTRA 63 PHE ( 66-) A C <-> 64 ASN ( 67-) A ND2 0.10 2.90 INTRA 69 ASP ( 72-) A OD2 <-> 120 TRP ( 123-) A NE1 0.08 2.62 INTRA 71 GLN ( 74-) A O <-> 73 LYS ( 76-) A N 0.08 2.62 INTRA 200 LEU ( 204-) A CB <-> 202 CYS ( 206-) A SG 0.08 3.32 INTRA 48 TYR ( 51-) A OH <-> 119 HIS ( 122-) A NE2 0.06 2.64 INTRA 147 GLY ( 151-) A N <-> 214 VAL ( 218-) A O 0.06 2.64 INTRA 104 HIS ( 107-) A NE2 <-> 190 TYR ( 194-) A OH 0.05 2.65 INTRA BL 243 PRO ( 247-) A O <-> 245 GLN ( 249-) A NE2 0.04 2.66 INTRA BL 12 HIS ( 15-) A ND1 <-> 15 LYS ( 18-) A NZ 0.04 2.96 INTRA 77 LYS ( 80-) A NZ <-> 84 THR ( 87-) A OG1 0.04 2.66 INTRA 18 PRO ( 21-) A C <-> 20 ALA ( 23-) A N 0.04 2.86 INTRA 5 GLY ( 8-) A O <-> 9 GLY ( 12-) A N 0.04 2.66 INTRA 132 GLN ( 136-) A N <-> 133 GLN ( 137-) A N 0.03 2.57 INTRA B3 164 LYS ( 168-) A O <-> 226 ASN ( 230-) A N 0.03 2.67 INTRA BL 92 PHE ( 95-) A N <-> 261 HOH ( 295 ) A O 0.02 2.68 INTRA BL 91 HIS ( 94-) A NE2 <-> 260 AL8 ( 555-) A N21 0.02 2.98 INTRA BL 255 SER ( 259-) A N <-> 256 PHE ( 260-) A N 0.01 2.59 INTRA B3
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.
7 HIS ( 10-) A -6.08 97 LEU ( 100-) A -5.37 132 GLN ( 136-) A -5.10
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.
261 HOH ( 304 ) A O -18.47 -20.13 8.16
261 HOH ( 480 ) A O 261 HOH ( 481 ) A O Metal-coordinating Histidine residue 91 fixed to 1 Metal-coordinating Histidine residue 93 fixed to 1 Metal-coordinating Histidine residue 116 fixed to 1
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.
28 VAL ( 31-) A N 42 LYS ( 45-) A N 63 PHE ( 66-) A N 71 GLN ( 74-) A N 97 LEU ( 100-) A N 121 ASN ( 124-) A ND2 196 THR ( 200-) A N 200 LEU ( 204-) A N 218 GLN ( 222-) A NE2 226 ASN ( 230-) A ND2 240 ASN ( 244-) A ND2 241 TRP ( 245-) A N 252 ILE ( 256-) A N 256 PHE ( 260-) A N Only metal coordination for 91 HIS ( 94-) A NE2 Only metal coordination for 93 HIS ( 96-) A NE2 Only metal coordination for 116 HIS ( 119-) A ND1
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.
11 GLU ( 14-) A OE2
158 ASP ( 162-) 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 : -0.124 2nd generation packing quality : 0.410 Ramachandran plot appearance : -2.761 chi-1/chi-2 rotamer normality : -2.364 Backbone conformation : -1.154
Bond lengths : 0.558 (tight) Bond angles : 0.759 Omega angle restraints : 0.256 (tight) Side chain planarity : 0.454 (tight) Improper dihedral distribution : 0.891 B-factor distribution : 1.398 Inside/Outside distribution : 0.955
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 : 2.60
Structure Z-scores, positive is better than average:
1st generation packing quality : 1.0 2nd generation packing quality : 1.8 Ramachandran plot appearance : -0.3 chi-1/chi-2 rotamer normality : -0.2 Backbone conformation : -0.4
Bond lengths : 0.558 (tight) Bond angles : 0.759 Omega angle restraints : 0.256 (tight) Side chain planarity : 0.454 (tight) Improper dihedral distribution : 0.891 B-factor distribution : 1.398 Inside/Outside distribution : 0.955 ==============
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.