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: 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) :100.000
Warning: More than 5 percent of buried atoms has low B-factor
For normal protein structures, no more than about 1 percent of the B factors
of buried atoms is below 5.0. The fact that this value is much higher in the
current structure could be a signal that the B-factors were restraints or
constraints to too-low values, misuse of B-factor field in the PDB file, or
a TLS/scaling problem. If the average B factor is low too, it is probably a
low temperature structure determination.
Percentage of buried atoms with B less than 5 : 27.59
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: Aspartic acid convention problem
The aspartic acid residues listed in the table below have their chi-2 not
between -90.0 and 90.0, or their proton on OD1 instead of OD2.
31 ASP ( 34-) A
183 GLU ( 187-) A
RMS Z-score for bond lengths: 0.254
RMS-deviation in bond distances: 0.006
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.
204 THR ( 208-) A N CA C 98.78 -4.4
RMS Z-score for bond angles: 0.655
RMS-deviation in bond angles: 1.441
Error: Nomenclature error(s)
Checking for a hand-check. WHAT IF has over the course of this session
already corrected the handedness of atoms in several residues. These were
administrative corrections. These residues are listed here.
31 ASP ( 34-) A 183 GLU ( 187-) A
203 VAL ( 207-) A 5.34 204 THR ( 208-) A 4.50 194 LEU ( 198-) A 4.42
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.
172 PHE ( 176-) A -2.3 88 ILE ( 91-) A -2.1 80 PRO ( 83-) A -2.1 159 VAL ( 163-) A -2.1 147 GLY ( 151-) A -2.1 19 ILE ( 22-) A -2.0 89 GLN ( 92-) 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 61 HIS ( 64-) A Poor phi/psi 108 LYS ( 111-) A Poor phi/psi 174 ASN ( 178-) A Poor phi/psi 197 PRO ( 201-) A PRO omega poor 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 : -0.752
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 7 HIS ( 10-) 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 35 ALA ( 38-) A 0 47 SER ( 50-) A 0 51 ALA ( 54-) A 0 55 ARG ( 58-) A 0 59 ASN ( 62-) A 0 61 HIS ( 64-) A 0 69 ASP ( 72-) A 0 70 SER ( 73-) A 0 72 ASP ( 75-) A 0 73 LYS ( 76-) A 0 74 ALA ( 77-) A 0 77 LYS ( 80-) A 0 80 PRO ( 83-) A 0 82 ASP ( 85-) A 0 89 GLN ( 92-) A 0 93 HIS ( 96-) A 0 96 SER ( 99-) A 0 100 GLN ( 103-) A 0And so on for a total of 117 lines.
Standard deviation of omega values : 1.575
Error: Abnormally short interatomic distances
The pairs of atoms listed in the table below have an unusually short
interactomic distance; each bump is listed in only one direction.
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.
258 PHE ( 300-) A CD1 <-> 262 PHE ( 300-) A O'' 0.59 2.21 INTRA 12 HIS ( 15-) A ND1 <-> 15 LYS ( 18-) A NZ 0.26 2.74 INTRA BL 64 ASN ( 67-) A ND2 <-> 263 HOH ( 431 ) A O 0.19 2.51 INTRA 176 ASP ( 180-) A OD2 <-> 178 ARG ( 182-) A NH2 0.17 2.53 INTRA BL 44 LEU ( 47-) A CD2 <-> 45 SER ( 48-) A N 0.17 2.83 INTRA BL 72 ASP ( 75-) A OD1 <-> 86 ARG ( 89-) A NE 0.16 2.54 INTRA 258 PHE ( 300-) A CG <-> 262 PHE ( 300-) A O'' 0.12 2.68 INTRA 38 ASP ( 41-) A OD1 <-> 40 SER ( 43-) A N 0.11 2.59 INTRA 114 GLU ( 117-) A OE2 <-> 116 HIS ( 119-) A NE2 0.10 2.60 INTRA BL 56 ILE ( 59-) A CD1 <-> 163 ILE ( 167-) A CD1 0.09 3.11 INTRA BL 56 ILE ( 59-) A CD1 <-> 57 LEU ( 60-) A N 0.09 2.91 INTRA BL 60 GLY ( 63-) A CA <-> 166 LYS ( 170-) A NZ 0.09 3.01 INTRA 104 HIS ( 107-) A NE2 <-> 190 TYR ( 194-) A OH 0.09 2.61 INTRA BL 192 GLY ( 196-) A N <-> 203 VAL ( 207-) A O 0.08 2.62 INTRA BL 59 ASN ( 62-) A CG <-> 61 HIS ( 64-) A NE2 0.08 3.02 INTRA 48 TYR ( 51-) A OH <-> 119 HIS ( 122-) A NE2 0.08 2.62 INTRA BL 174 ASN ( 178-) A N <-> 263 HOH ( 301 ) A O 0.07 2.63 INTRA BL 132 GLN ( 136-) A N <-> 133 GLN ( 137-) A N 0.07 2.53 INTRA BL 152 GLY ( 156-) A N <-> 263 HOH ( 323 ) A O 0.06 2.64 INTRA BL 141 GLY ( 145-) A C <-> 142 ILE ( 146-) A CD1 0.06 3.04 INTRA BL 59 ASN ( 62-) A ND2 <-> 61 HIS ( 64-) A CE1 0.06 3.04 INTRA 24 ARG ( 27-) A CG <-> 201 GLU ( 205-) A CD 0.05 3.15 INTRA BL 15 LYS ( 18-) A NZ <-> 263 HOH ( 342 ) A O 0.04 2.66 INTRA BL 247 LEU ( 251-) A CD1 <-> 252 ILE ( 256-) A CD1 0.03 3.17 INTRA BL 247 LEU ( 251-) A CD2 <-> 252 ILE ( 256-) A CD1 0.03 3.17 INTRA BL 61 HIS ( 64-) A ND1 <-> 263 HOH ( 349 ) A O 0.03 2.67 INTRA 227 PHE ( 231-) A N <-> 228 ASN ( 232-) A N 0.03 2.57 INTRA BL 55 ARG ( 58-) A CG <-> 56 ILE ( 59-) A N 0.03 2.97 INTRA BL 29 ASP ( 32-) A OD2 <-> 108 LYS ( 111-) A NZ 0.03 2.67 INTRA 96 SER ( 99-) A N <-> 97 LEU ( 100-) A N 0.02 2.58 INTRA BL 255 SER ( 259-) A N <-> 256 PHE ( 260-) A N 0.02 2.58 INTRA BL 126 ASP ( 130-) A OD1 <-> 129 LYS ( 133-) A N 0.02 2.68 INTRA BL 248 LYS ( 252-) A CB <-> 249 ASN ( 253-) A N 0.01 2.69 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.
7 HIS ( 10-) A -5.93 97 LEU ( 100-) A -5.29
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
Error: Water clusters without contacts with non-water atoms
The water molecules listed in the table below are part of water molecule
clusters that do not make contacts with non-waters. These water molecules are
part of clusters that have a distance at least 1 Angstrom larger than the
sum of the Van der Waals radii to the nearest non-solvent atom. Because
these kinds of water clusters usually are not observed with X-ray diffraction
their presence could indicate a refinement artifact. The number in brackets
is the identifier of the water molecule in the input file.
263 HOH ( 336 ) A O ERROR. No atoms within 50 A?
263 HOH ( 336 ) A O 263 HOH ( 447 ) 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
50 GLN ( 53-) A 133 GLN ( 137-) A 174 ASN ( 178-) 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.
28 VAL ( 31-) A N 31 ASP ( 34-) A N 64 ASN ( 67-) A ND2 71 GLN ( 74-) A N 97 LEU ( 100-) A N 161 ASP ( 165-) A N 196 THR ( 200-) A N 200 LEU ( 204-) A N 217 GLU ( 221-) A N 226 ASN ( 230-) A ND2 229 GLY ( 233-) A N 240 ASN ( 244-) A ND2 241 TRP ( 245-) A N 256 PHE ( 260-) A N Only metal coordination for 93 HIS ( 96-) A NE2 Only metal coordination for 116 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.
263 HOH ( 312 ) A O 1.06 K 4 H2O-B
29 ASP ( 32-) A H-bonding suggests Asn; but Alt-Rotamer 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 : 0.095 2nd generation packing quality : 0.875 Ramachandran plot appearance : -1.519 chi-1/chi-2 rotamer normality : -0.752 Backbone conformation : -0.786
Bond lengths : 0.254 (tight) Bond angles : 0.655 (tight) Omega angle restraints : 0.286 (tight) Side chain planarity : 0.214 (tight) Improper dihedral distribution : 0.580 Inside/Outside distribution : 0.960
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 : 1.60
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.4 2nd generation packing quality : -0.3 Ramachandran plot appearance : -2.0 chi-1/chi-2 rotamer normality : -1.1 Backbone conformation : -1.2
Bond lengths : 0.254 (tight) Bond angles : 0.655 (tight) Omega angle restraints : 0.286 (tight) Side chain planarity : 0.214 (tight) Improper dihedral distribution : 0.580 Inside/Outside distribution : 0.960 ==============
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.