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.
The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms, or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.
159 MOO ( 158-) A - Atom types
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) :298.000
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
119 TYR ( 119-) A 132 TYR ( 132-) A
82 PHE ( 82-) A
32 ASP ( 32-) A 129 ASP ( 129-) A
23 GLU ( 23-) A 139 GLU ( 139-) 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.
154 GLU ( 154-) A CD OE2 1.33 4.2
12 CYS ( 12-) A N CA CB 117.99 4.4 15 ASN ( 15-) A CA CB CG 118.36 5.8 16 ILE ( 16-) A N CA CB 118.79 4.9 20 PRO ( 20-) A N CA CB 107.41 4.0 26 PHE ( 26-) A CA CB CG 109.36 -4.4 27 ARG ( 27-) A C CA CB 101.69 -4.4 32 ASP ( 32-) A CA CB CG 120.24 7.6 36 SER ( 36-) A C CA CB 100.12 -5.3 38 ASN ( 38-) A CA CB CG 106.10 -6.5 45 ALA ( 45-) A C CA CB 102.45 -5.4 61 SER ( 61-) A CA CB OG 102.85 -4.1 66 HIS ( 66-) A CA CB CG 109.16 -4.6 69 ASN ( 69-) A CA CB CG 107.61 -5.0 81 ASP ( 81-) A CA CB CG 108.11 -4.5 83 VAL ( 83-) A -C N CA 113.45 -4.6 86 ASP ( 86-) A CA CB CG 108.04 -4.6 93 GLU ( 93-) A CB CG CD 119.97 4.3 108 ASN ( 108-) A CA CB CG 108.47 -4.1 126 ILE ( 126-) A N CA CB 117.75 4.3 140 THR ( 140-) A CA CB OG1 102.55 -4.7 147 ARG ( 147-) A CD NE CZ 132.45 6.0
23 GLU ( 23-) A 32 ASP ( 32-) A 129 ASP ( 129-) A 139 GLU ( 139-) A
Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.
Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.
Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.
12 CYS ( 12-) A CA -6.5 22.77 34.33 126 ILE ( 126-) A CA -9.6 18.75 33.24 The average deviation= 2.127
18 ARG ( 18-) A 6.15 11 VAL ( 11-) A 4.79 155 LYS ( 155-) A 4.01
Tau angle RMS Z-score : 1.517
Error: Side chain planarity problems
The side chains of the residues listed in the table below contain a planar
group that was found to deviate from planarity by more than 4.0 times the
expected value. For an amino acid residue that has a side chain with a
planar group, the RMS deviation of the atoms to a least squares plane was
determined. The number in the table is the number of standard deviations
this RMS value deviates from the expected value. Not knowing better yet, we
assume that planarity of the groups analyzed should be perfect.
135 ASP ( 135-) A 4.96 69 ASN ( 69-) A 4.62 15 ASN ( 15-) A 4.06
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.
130 PRO ( 130-) A -2.9 3 GLN ( 3-) A -2.2
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.
3 GLN ( 3-) A Poor phi/psi 34 ASN ( 34-) A Poor phi/psi 52 GLY ( 52-) A Poor phi/psi 123 LYS ( 123-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -1.580
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!
3 GLN ( 3-) A 0 12 CYS ( 12-) A 0 13 LEU ( 13-) A 0 16 ILE ( 16-) A 0 17 CYS ( 17-) A 0 18 ARG ( 18-) A 0 33 GLN ( 33-) A 0 34 ASN ( 34-) A 0 35 ILE ( 35-) A 0 42 ASP ( 42-) A 0 43 SER ( 43-) A 0 45 ALA ( 45-) A 0 46 VAL ( 46-) A 0 47 SER ( 47-) A 0 51 VAL ( 51-) A 0 74 ALA ( 74-) A 0 91 MET ( 91-) A 0 105 GLN ( 105-) A 0 109 CYS ( 109-) A 0 110 ARG ( 110-) A 0 122 GLN ( 122-) A 0 123 LYS ( 123-) A 0 125 LEU ( 125-) A 0 128 GLU ( 128-) A 0 132 TYR ( 132-) A 0And so on for a total of 52 lines.
Standard deviation of omega values : 3.076
Warning: Unusual PRO puckering amplitudes
The proline residues listed in the table below have a puckering amplitude
that is outside of normal ranges. Puckering parameters were calculated by
the method of Cremer and Pople [REF]. Normal PRO rings have a puckering
amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom
for a PRO residue, this could indicate disorder between the two different
normal ring forms (with C-gamma below and above the ring, respectively). If
Q is higher than 0.45 Angstrom something could have gone wrong during the
refinement. 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]
20 PRO ( 20-) A 0.11 LOW 57 PRO ( 57-) A 0.16 LOW 121 PRO ( 121-) A 0.12 LOW
55 PRO ( 55-) A 131.9 half-chair C-beta/C-alpha (126 degrees) 130 PRO ( 130-) A -34.0 envelop C-alpha (-36 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.
64 ARG ( 64-) A NE <-> 69 ASN ( 69-) A OD1 0.51 2.19 INTRA BF 33 GLN ( 33-) A OE1 <-> 157 ARG ( 157-) A NH2 0.49 2.21 INTRA BF 52 GLY ( 52-) A O <-> 73 LYS ( 73-) A NZ 0.49 2.21 INTRA 93 GLU ( 93-) A OE2 <-> 97 ARG ( 97-) A NH2 0.45 2.25 INTRA BF 3 GLN ( 3-) A OE1 <-> 38 ASN ( 38-) A ND2 0.43 2.27 INTRA BF 12 CYS ( 12-) A SG <-> 15 ASN ( 15-) A N 0.41 2.89 INTRA BL 64 ARG ( 64-) A NH2 <-> 69 ASN ( 69-) A CB 0.41 2.69 INTRA 64 ARG ( 64-) A NH2 <-> 69 ASN ( 69-) A CA 0.37 2.73 INTRA 56 ASP ( 56-) A OD1 <-> 58 ARG ( 58-) A N 0.26 2.44 INTRA BL 64 ARG ( 64-) A CZ <-> 69 ASN ( 69-) A CA 0.25 2.95 INTRA BF 64 ARG ( 64-) A NH2 <-> 70 THR ( 70-) A N 0.25 2.60 INTRA 3 GLN ( 3-) A CD <-> 38 ASN ( 38-) A ND2 0.24 2.86 INTRA BF 33 GLN ( 33-) A CD <-> 157 ARG ( 157-) A NH2 0.24 2.86 INTRA BF 3 GLN ( 3-) A CG <-> 38 ASN ( 38-) A CG 0.21 2.99 INTRA BF 19 SER ( 19-) A N <-> 20 PRO ( 20-) A CD 0.19 2.81 INTRA BL 4 VAL ( 4-) A CG2 <-> 5 THR ( 5-) A N 0.19 2.81 INTRA BF 93 GLU ( 93-) A CG <-> 97 ARG ( 97-) A NH2 0.18 2.92 INTRA BF 129 ASP ( 129-) A OD1 <-> 131 TYR ( 131-) A N 0.17 2.53 INTRA 30 VAL ( 30-) A CG1 <-> 36 SER ( 36-) A N 0.16 2.94 INTRA BL 120 ASP ( 120-) A OD2 <-> 147 ARG ( 147-) A NH1 0.14 2.56 INTRA 30 VAL ( 30-) A CG1 <-> 36 SER ( 36-) A CA 0.14 3.06 INTRA BL 12 CYS ( 12-) A SG <-> 15 ASN ( 15-) A CA 0.13 3.27 INTRA BL 12 CYS ( 12-) A SG <-> 159 MOO ( 158-) A O2 0.12 2.88 INTRA 126 ILE ( 126-) A CG1 <-> 127 ILE ( 127-) A N 0.10 2.90 INTRA BL 52 GLY ( 52-) A N <-> 74 ALA ( 74-) A O 0.09 2.61 INTRA BLAnd so on for a total of 56 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.
132 TYR ( 132-) A -7.85 131 TYR ( 131-) A -7.20 2 GLU ( 2-) A -5.90 3 GLN ( 3-) A -5.68 65 ASN ( 65-) A -5.31
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: 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.
66 HIS ( 66-) 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.
13 LEU ( 13-) A N 16 ILE ( 16-) A N 17 CYS ( 17-) A N 18 ARG ( 18-) A N 18 ARG ( 18-) A NE 37 ASP ( 37-) A N 50 ASN ( 50-) A N 64 ARG ( 64-) A NH1 70 THR ( 70-) A N 93 GLU ( 93-) A N 108 ASN ( 108-) A N 110 ARG ( 110-) A NE 117 GLY ( 117-) A N 128 GLU ( 128-) A N 147 ARG ( 147-) A NH1
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.
144 GLN ( 144-) A OE1
154 GLU ( 154-) A H-bonding suggests Gln
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 : -0.273 2nd generation packing quality : -1.552 Ramachandran plot appearance : -0.541 chi-1/chi-2 rotamer normality : -1.580 Backbone conformation : -0.481
Bond lengths : 0.768 Bond angles : 1.397 Omega angle restraints : 0.559 (tight) Side chain planarity : 1.882 Improper dihedral distribution : 1.722 (loose) B-factor distribution : 1.216 Inside/Outside distribution : 1.010
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 : 2.20
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.3 2nd generation packing quality : -0.7 Ramachandran plot appearance : 0.6 chi-1/chi-2 rotamer normality : -0.3 Backbone conformation : -0.4
Bond lengths : 0.768 Bond angles : 1.397 Omega angle restraints : 0.559 (tight) Side chain planarity : 1.882 Improper dihedral distribution : 1.722 (loose) B-factor distribution : 1.216 Inside/Outside distribution : 1.010 ==============
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.