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.
263 1SA ( 265-) A -
Plausible side chain atoms were detected with (near) zero occupancy
When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.
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 50 GLN ( 53-) A - CB 50 GLN ( 53-) A - CG 50 GLN ( 53-) A - CD 50 GLN ( 53-) A - OE1 50 GLN ( 53-) A - NE2 73 LYS ( 76-) A - CE 73 LYS ( 76-) A - NZ 82 ASP ( 85-) A - CG 82 ASP ( 85-) A - OD1 82 ASP ( 85-) A - OD2 129 LYS ( 133-) A - CG 129 LYS ( 133-) A - CD 129 LYS ( 133-) A - CE 129 LYS ( 133-) A - NZ 249 ASN ( 253-) A - CB 249 ASN ( 253-) A - CG 249 ASN ( 253-) A - OD1 249 ASN ( 253-) A - ND2 257 LYS ( 261-) A - CB 257 LYS ( 261-) A - CG 257 LYS ( 261-) A - CD 257 LYS ( 261-) A - CE 257 LYS ( 261-) A - NZ
Plausible backbone atoms were detected with (near) zero occupancy
When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. However, if a backbone atom is present in the PDB file, and its position seems 'logical' (i.e. normal bond lengths with all atoms it should be bound to, and those atoms exist normally) WHAT IF will set the occupancy to 1.0 if it believes that the full presence of this atom will be beneficial to the rest of the validation process. If you get weird errors at, or near, these atoms, please check by hand what is going on, and repair things intelligently before running this validation again.
73 LYS ( 76-) A - C
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
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
37 TYR ( 40-) A 48 TYR ( 51-) A 85 TYR ( 88-) A 124 TYR ( 128-) A 190 TYR ( 194-) A
227 PHE ( 231-) A
29 ASP ( 32-) A 31 ASP ( 34-) A 38 ASP ( 41-) A 69 ASP ( 72-) A 82 ASP ( 85-) A 98 ASP ( 101-) A 107 ASP ( 110-) A 135 ASP ( 139-) A 176 ASP ( 180-) A 186 ASP ( 190-) A 239 ASP ( 243-) A
11 GLU ( 14-) A 183 GLU ( 187-) A 210 GLU ( 214-) A 217 GLU ( 221-) A 230 GLU ( 234-) A 234 GLU ( 238-) 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.
202 CYS ( 206-) A N -C 1.53 10.3
RMS Z-score for bond lengths: 0.255
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.
203 VAL ( 207-) A -O -C N 132.06 5.7 203 VAL ( 207-) A -CA -C N 106.94 -4.6 203 VAL ( 207-) A -C N CA 111.21 -5.8
11 GLU ( 14-) A 29 ASP ( 32-) A 31 ASP ( 34-) A 38 ASP ( 41-) A 69 ASP ( 72-) A 82 ASP ( 85-) A 98 ASP ( 101-) A 107 ASP ( 110-) A 135 ASP ( 139-) A 176 ASP ( 180-) A 183 GLU ( 187-) A 186 ASP ( 190-) A 210 GLU ( 214-) A 217 GLU ( 221-) A 230 GLU ( 234-) A 234 GLU ( 238-) A 239 ASP ( 243-) A
203 VAL ( 207-) A 5.47 194 LEU ( 198-) A 4.25
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.
55 ARG ( 58-) A -2.7 172 PHE ( 176-) A -2.4 80 PRO ( 83-) A -2.2 147 GLY ( 151-) A -2.1 159 VAL ( 163-) 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 73 LYS ( 76-) A Poor phi/psi 107 ASP ( 110-) 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 chi-1/chi-2 correlation Z-score : -0.899
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 42 LYS ( 45-) 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 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 0And so on for a total of 116 lines.
Standard deviation of omega values : 1.668
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.
55 ARG ( 58-) A CD <-> 66 GLU ( 69-) A OE1 0.28 2.52 INTRA 72 ASP ( 75-) A CG <-> 86 ARG ( 89-) A NH2 0.16 2.94 INTRA 12 HIS ( 15-) A ND1 <-> 15 LYS ( 18-) A NZ 0.14 2.86 INTRA BL 164 LYS ( 168-) A NZ <-> 264 HOH ( 426 ) A O 0.13 2.57 INTRA 202 CYS ( 206-) A N <-> 203 VAL ( 207-) A N 0.12 2.48 INTRA BL 44 LEU ( 47-) A CD2 <-> 45 SER ( 48-) A N 0.12 2.88 INTRA BL 132 GLN ( 136-) A N <-> 133 GLN ( 137-) A N 0.09 2.51 INTRA BL 126 ASP ( 130-) A OD1 <-> 129 LYS ( 133-) A N 0.09 2.61 INTRA 114 GLU ( 117-) A OE2 <-> 116 HIS ( 119-) A NE2 0.08 2.62 INTRA BL 104 HIS ( 107-) A NE2 <-> 190 TYR ( 194-) A OH 0.07 2.63 INTRA BL 22 GLY ( 25-) A O <-> 248 LYS ( 252-) A NZ 0.07 2.63 INTRA 168 LYS ( 172-) A NZ <-> 264 HOH ( 544 ) A O 0.05 2.65 INTRA 137 LEU ( 141-) A N <-> 202 CYS ( 206-) A O 0.05 2.65 INTRA BL 126 ASP ( 130-) A OD1 <-> 128 GLY ( 132-) A N 0.05 2.65 INTRA 55 ARG ( 58-) A CD <-> 66 GLU ( 69-) A CD 0.04 3.16 INTRA 157 VAL ( 161-) A CG1 <-> 221 LYS ( 225-) A CD 0.03 3.17 INTRA 18 PRO ( 21-) A C <-> 20 ALA ( 23-) A N 0.03 2.87 INTRA BL 48 TYR ( 51-) A OH <-> 119 HIS ( 122-) A NE2 0.02 2.68 INTRA BL 174 ASN ( 178-) A N <-> 264 HOH ( 458 ) A O 0.02 2.68 INTRA BL 24 ARG ( 27-) A CG <-> 201 GLU ( 205-) A CD 0.01 3.19 INTRA BL 227 PHE ( 231-) A N <-> 228 ASN ( 232-) A N 0.01 2.59 INTRA BL 64 ASN ( 67-) A ND2 <-> 261 GOL ( 700-) A O2 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 -5.98 97 LEU ( 100-) A -5.03
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.
243 PRO ( 247-) A -2.68
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.
7 HIS ( 10-) A 64 ASN ( 67-) 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 49 ASP ( 52-) A N 50 GLN ( 53-) A N 71 GLN ( 74-) A N 97 LEU ( 100-) A N 165 THR ( 169-) A N 178 ARG ( 182-) A NH1 196 THR ( 200-) A N 200 LEU ( 204-) A N 226 ASN ( 230-) A ND2 240 ASN ( 244-) A ND2 241 TRP ( 245-) 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.
66 GLU ( 69-) A OE1
82 ASP ( 85-) A H-bonding suggests Asn 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 : -0.049 2nd generation packing quality : 0.720 Ramachandran plot appearance : -1.407 chi-1/chi-2 rotamer normality : -0.899 Backbone conformation : -0.827
Bond lengths : 0.255 (tight) Bond angles : 0.688 Omega angle restraints : 0.303 (tight) Side chain planarity : 0.215 (tight) Improper dihedral distribution : 0.588 B-factor distribution : 0.669 Inside/Outside distribution : 0.953
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 : 1.55
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.3 2nd generation packing quality : -0.3 Ramachandran plot appearance : -1.9 chi-1/chi-2 rotamer normality : -1.4 Backbone conformation : -1.3
Bond lengths : 0.255 (tight) Bond angles : 0.688 Omega angle restraints : 0.303 (tight) Side chain planarity : 0.215 (tight) Improper dihedral distribution : 0.588 B-factor distribution : 0.669 Inside/Outside distribution : 0.953 ==============
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.