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.
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.
60 ASN ( 84-) A - CB
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.
61 ASN ( 85-) A - CA
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 THR ( 25-) A OG1 1 THR ( 25-) A CG2 5 TYR ( 29-) A CG 5 TYR ( 29-) A CD1 5 TYR ( 29-) A CD2 5 TYR ( 29-) A CE1 5 TYR ( 29-) A CE2 5 TYR ( 29-) A CZ 5 TYR ( 29-) A OH 9 ASN ( 33-) A CG 9 ASN ( 33-) A OD1 9 ASN ( 33-) A ND2 15 SER ( 39-) A OG 44 LYS ( 68-) A CG 44 LYS ( 68-) A CD 44 LYS ( 68-) A CE 44 LYS ( 68-) A NZ 58 LYS ( 82-) A CG 58 LYS ( 82-) A CD 58 LYS ( 82-) A CE 58 LYS ( 82-) A NZ 59 VAL ( 83-) A CG1 59 VAL ( 83-) A CG2 60 ASN ( 84-) A CG 60 ASN ( 84-) A OD1And so on for a total of 53 lines.
55 GLY ( 79-) A High 56 GLU ( 80-) A High 57 TYR ( 81-) A High 58 LYS ( 82-) A High 59 VAL ( 83-) A High 60 ASN ( 84-) A High 61 ASN ( 85-) A High 62 LEU ( 86-) A High 63 PRO ( 87-) A High 64 VAL ( 88-) A High 86 ILE ( 110-) A High 87 ASN ( 111-) A High 88 HIS ( 112-) A High 89 ASN ( 113-) A High 91 SER ( 115-) A High 92 GLY ( 116-) A High 93 SER ( 117-) A High 94 LEU ( 118-) A High 95 SER ( 119-) A High 96 ILE ( 120-) A High 97 TYR ( 121-) A High 98 GLY ( 122-) A High 99 GLU ( 123-) A High 100 LYS ( 124-) A High 101 PHE ( 125-) A High 102 ASP ( 126-) A High 104 GLU ( 128-) A High 122 GLY ( 146-) A High 123 PRO ( 147-) A High 124 ASN ( 148-) A High
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: Arginine nomenclature problem
The arginine residues listed in the table below have their N-H-1 and N-H-2
73 ARG ( 97-) A
6 TYR ( 30-) A 172 TYR ( 196-) A
20 PHE ( 44-) A 35 PHE ( 59-) A 49 PHE ( 73-) A 131 PHE ( 155-) A
138 GLU ( 162-) A
169 PRO ( 193-) A N CA C 121.91 4.0
73 ARG ( 97-) A 138 GLU ( 162-) A
Ramachandran Z-score : -4.124
Warning: Torsion angle evaluation shows unusual residues
The residues listed in the table below contain bad or abnormal
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.
169 PRO ( 193-) A -3.1 69 THR ( 93-) A -2.4 149 ARG ( 173-) A -2.3 57 TYR ( 81-) A -2.3 79 MET ( 103-) A -2.3 78 PHE ( 102-) A -2.1 177 PRO ( 201-) 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.
60 ASN ( 84-) A Poor phi/psi 61 ASN ( 85-) A Poor phi/psi 77 GLU ( 101-) A Poor phi/psi 79 MET ( 103-) A Poor phi/psi 88 HIS ( 112-) A Poor phi/psi 90 GLY ( 114-) A Poor phi/psi 94 LEU ( 118-) A Poor phi/psi 100 LYS ( 124-) A Poor phi/psi 105 ASN ( 129-) A Poor phi/psi 110 HIS ( 134-) A Poor phi/psi 124 ASN ( 148-) A Poor phi/psi 169 PRO ( 193-) A Poor phi/psi 172 TYR ( 196-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -3.812
chi-1/chi-2 correlation Z-score : -3.812
Warning: Unusual backbone conformations
For the residues listed in the table below, the backbone formed by itself and
two neighbouring residues on either side is in a conformation that is not
seen very often in the database of solved protein structures. The number
given in the table is the number of similar backbone conformations in the
database with the same amino acid in the centre.
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!
11 LEU ( 35-) A 0 25 LEU ( 49-) A 0 27 ASN ( 51-) A 0 29 PHE ( 53-) A 0 38 PHE ( 62-) A 0 39 GLN ( 63-) A 0 54 THR ( 78-) A 0 56 GLU ( 80-) A 0 57 TYR ( 81-) A 0 59 VAL ( 83-) A 0 60 ASN ( 84-) A 0 61 ASN ( 85-) A 0 66 TYR ( 90-) A 0 70 ILE ( 94-) A 0 71 PHE ( 95-) A 0 72 HIS ( 96-) A 0 76 LYS ( 100-) A 0 77 GLU ( 101-) A 0 78 PHE ( 102-) A 0 79 MET ( 103-) A 0 81 GLN ( 105-) A 0 86 ILE ( 110-) A 0 87 ASN ( 111-) A 0 88 HIS ( 112-) A 0 89 ASN ( 113-) A 0And so on for a total of 102 lines.
Standard deviation of omega values : 1.080
Warning: Unusual PRO puckering phases
The proline residues listed in the table below have a puckering phase that is
not expected to occur in protein structures. Puckering parameters were
calculated by the method of Cremer and Pople [REF]. Normal PRO rings
approximately show a so-called envelope conformation with the C-gamma atom
above the plane of the ring (phi=+72 degrees), or a half-chair conformation
with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees).
If phi deviates strongly from these values, this is indicative of a very
strange conformation for a PRO residue, and definitely requires a manual
check of the data. Be aware that this is a warning with a low confidence
level. See: Who checks the checkers? Four validation tools applied to eight
atomic resolution structures [REF].
169 PRO ( 193-) A 104.5 envelop C-beta (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.
145 VAL ( 169-) A N <-> 187 HOH ( 213 ) A O 0.36 2.34 INTRA BF 24 ASN ( 48-) A ND2 <-> 181 VAL ( 205-) A CG2 0.33 2.77 INTRA BF 73 ARG ( 97-) A NH2 <-> 187 HOH ( 222 ) A O 0.28 2.42 INTRA BF 178 ILE ( 202-) A N <-> 187 HOH ( 212 ) A O 0.25 2.45 INTRA BF 86 ILE ( 110-) A CG2 <-> 87 ASN ( 111-) A ND2 0.24 2.86 INTRA BF 105 ASN ( 129-) A CG <-> 107 ASP ( 131-) A OD2 0.22 2.58 INTRA BF 94 LEU ( 118-) A CD2 <-> 95 SER ( 119-) A N 0.21 2.79 INTRA BF 138 GLU ( 162-) A O <-> 140 LEU ( 164-) A N 0.19 2.51 INTRA BL 86 ILE ( 110-) A CD1 <-> 93 SER ( 117-) A N 0.19 2.91 INTRA BF 24 ASN ( 48-) A OD1 <-> 29 PHE ( 53-) A CA 0.17 2.63 INTRA BL 137 CYS ( 161-) A SG <-> 140 LEU ( 164-) A CD1 0.17 3.23 INTRA BL 84 ASP ( 108-) A OD1 <-> 88 HIS ( 112-) A N 0.16 2.54 INTRA BF 58 LYS ( 82-) A CA <-> 62 LEU ( 86-) A O 0.16 2.64 INTRA BF 86 ILE ( 110-) A CD1 <-> 93 SER ( 117-) A C 0.13 3.07 INTRA BF 38 PHE ( 62-) A CD2 <-> 148 GLY ( 172-) A N 0.13 2.97 INTRA BF 102 ASP ( 126-) A CA <-> 124 ASN ( 148-) A ND2 0.12 2.98 INTRA BF 69 THR ( 93-) A CG2 <-> 70 ILE ( 94-) A N 0.12 2.88 INTRA BF 47 GLU ( 71-) A OE1 <-> 51 GLN ( 75-) A NE2 0.11 2.59 INTRA BF 68 ASN ( 92-) A N <-> 180 VAL ( 204-) A O 0.11 2.59 INTRA BF 42 VAL ( 66-) A CA <-> 104 GLU ( 128-) A OE2 0.10 2.70 INTRA BF 138 GLU ( 162-) A O <-> 141 ASP ( 165-) A N 0.10 2.60 INTRA BL 26 GLY ( 50-) A N <-> 177 PRO ( 201-) A O 0.09 2.61 INTRA BF 47 GLU ( 71-) A O <-> 51 GLN ( 75-) A CG 0.08 2.72 INTRA BF 87 ASN ( 111-) A CB <-> 89 ASN ( 113-) A OD1 0.08 2.72 INTRA BF 86 ILE ( 110-) A C <-> 87 ASN ( 111-) A ND2 0.08 2.92 INTRA BFAnd so on for a total of 52 lines.
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.
170 TYR ( 194-) A -7.00 6 TYR ( 30-) A -6.63 2 ILE ( 26-) A -6.25 3 ILE ( 27-) A -6.11 97 TYR ( 121-) A -5.84 175 LYS ( 199-) A -5.38 57 TYR ( 81-) A -5.31
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.
100 LYS ( 124-) A -2.75 62 LEU ( 86-) A -2.74 143 LYS ( 167-) A -2.50
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.
110 HIS ( 134-) 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.
7 LEU ( 31-) A N 41 ILE ( 65-) A N 62 LEU ( 86-) A N 67 LYS ( 91-) A N 69 THR ( 93-) A OG1 85 PHE ( 109-) A N 86 ILE ( 110-) A N 90 GLY ( 114-) A N 91 SER ( 115-) A N 92 GLY ( 116-) A N 94 LEU ( 118-) A N 95 SER ( 119-) A OG 103 ASP ( 127-) A N 105 ASN ( 129-) A N 112 LYS ( 136-) A N 120 ASN ( 144-) A N 121 SER ( 145-) A N 125 THR ( 149-) A N 126 ASN ( 150-) A N 129 GLN ( 153-) A NE2 134 THR ( 158-) A OG1 135 LYS ( 159-) A N 139 TRP ( 163-) A N 148 GLY ( 172-) A N 152 ASP ( 176-) A N 170 TYR ( 194-) A N 171 ILE ( 195-) A N 173 LYS ( 197-) A N 176 ILE ( 200-) A N
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.
152 ASP ( 176-) A OD2
84 ASP ( 108-) A H-bonding suggests Asn 104 GLU ( 128-) A H-bonding suggests Gln; but Alt-Rotamer 111 ASP ( 135-) A H-bonding suggests Asn 141 ASP ( 165-) 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 : -1.429 2nd generation packing quality : -1.775 Ramachandran plot appearance : -4.124 (bad) chi-1/chi-2 rotamer normality : -3.812 (poor) Backbone conformation : -1.365
Bond lengths : 0.318 (tight) Bond angles : 0.594 (tight) Omega angle restraints : 0.196 (tight) Side chain planarity : 0.207 (tight) Improper dihedral distribution : 0.622 B-factor distribution : 0.435 Inside/Outside distribution : 1.098
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 : 2.80
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.5 2nd generation packing quality : -0.2 Ramachandran plot appearance : -1.6 chi-1/chi-2 rotamer normality : -1.6 Backbone conformation : -0.7
Bond lengths : 0.318 (tight) Bond angles : 0.594 (tight) Omega angle restraints : 0.196 (tight) Side chain planarity : 0.207 (tight) Improper dihedral distribution : 0.622 B-factor distribution : 0.435 Inside/Outside distribution : 1.098 ==============
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.