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.
260 0CR ( 263-) A - Size
The left-hand residue has been removed, and the right hand residue has been kept for validation. Be aware that WHAT IF calls everything a residue. Two residues are defined as overlapping if the two smallest ellipsoids encompassing the two residues interpenetrate by 33% of the longest axis. Many artefacts can actually cause this problem. The most often observed reason is alternative residue conformations expressed by two residues that accidentally both got 1.0 occupancy for all atoms.
261 XE ( 265-) A - 260 0CR ( 263-) A - 0.8
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: Occupancies atoms do not add up to 1.0.
In principle, the occupancy of all alternates of one atom should add up till
1.0. A valid exception is the missing atom (i.e. an atom not seen in the
electron density) that is allowed to have a 0.0 occupancy. Sometimes this
even happens when there are no alternate atoms given...
Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.
WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.
11 GLU ( 14-) A 0.50 132 GLN ( 136-) A 0.40
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
55 ARG ( 58-) A
37 TYR ( 40-) A 48 TYR ( 51-) A 85 TYR ( 88-) A 124 TYR ( 128-) A 190 TYR ( 194-) A
127 PHE ( 131-) A
16 ASP ( 19-) A 29 ASP ( 32-) A 31 ASP ( 34-) A 38 ASP ( 41-) A 69 ASP ( 72-) A 82 ASP ( 85-) A 126 ASP ( 130-) A
11 GLU ( 14-) A 66 GLU ( 69-) A 183 GLU ( 187-) A 201 GLU ( 205-) A 217 GLU ( 221-) A 235 GLU ( 239-) 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.
50 GLN ( 53-) A CD OE1 1.33 4.8 50 GLN ( 53-) A CD NE2 1.22 -5.0
RMS Z-score for bond lengths: 0.311
RMS-deviation in bond distances: 0.007
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.
11 GLU ( 14-) A 16 ASP ( 19-) A 29 ASP ( 32-) A 31 ASP ( 34-) A 38 ASP ( 41-) A 55 ARG ( 58-) A 66 GLU ( 69-) A 69 ASP ( 72-) A 82 ASP ( 85-) A 126 ASP ( 130-) A 183 GLU ( 187-) A 201 GLU ( 205-) A 217 GLU ( 221-) A 235 GLU ( 239-) A
203 VAL ( 207-) A 4.94 194 LEU ( 198-) A 4.30
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 -2.6 172 PHE ( 176-) A -2.4 89 GLN ( 92-) A -2.0 80 PRO ( 83-) A -2.0 147 GLY ( 151-) 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 72 ASP ( 75-) 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 199 LEU ( 203-) A Poor phi/psi 239 ASP ( 243-) A Poor phi/psi 248 LYS ( 252-) A Poor phi/psi chi-1/chi-2 correlation Z-score : 0.187
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 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 34 THR ( 37-) A 0 35 ALA ( 38-) A 0 47 SER ( 50-) A 0 50 GLN ( 53-) 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 74 ALA ( 77-) A 0 77 LYS ( 80-) A 0 80 PRO ( 83-) A 0 82 ASP ( 85-) A 0 88 ILE ( 91-) A 0And so on for a total of 118 lines.
Standard deviation of omega values : 1.475
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]
198 PRO ( 202-) A 0.46 HIGH
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.
7 HIS ( 10-) A ND1 <-> 263 HOH (1060 ) A O 0.27 2.43 INTRA BF 12 HIS ( 15-) A ND1 <-> 15 LYS ( 18-) A NZ 0.15 2.85 INTRA BL 124 TYR ( 128-) A CZ <-> 133 GLN ( 137-) A CG 0.14 3.06 INTRA BF 126 ASP ( 130-) A CG <-> 129 LYS ( 133-) A CE 0.12 3.08 INTRA BF 104 HIS ( 107-) A NE2 <-> 190 TYR ( 194-) A OH 0.10 2.60 INTRA BL 72 ASP ( 75-) A OD1 <-> 86 ARG ( 89-) A NH2 0.09 2.61 INTRA BF 114 GLU ( 117-) A OE2 <-> 116 HIS ( 119-) A NE2 0.08 2.62 INTRA BL 192 GLY ( 196-) A N <-> 203 VAL ( 207-) A O 0.06 2.64 INTRA BL 50 GLN ( 53-) A N <-> 263 HOH (1046 ) A O 0.06 2.64 INTRA BF 24 ARG ( 27-) A NE <-> 263 HOH (1007 ) A O 0.05 2.65 INTRA 1 HIS ( 4-) A CB <-> 2 TRP ( 5-) A N 0.05 2.65 INTRA BF 248 LYS ( 252-) A CB <-> 249 ASN ( 253-) A N 0.05 2.65 INTRA B3 124 TYR ( 128-) A OH <-> 133 GLN ( 137-) A CG 0.04 2.76 INTRA BF 19 ILE ( 22-) A O <-> 22 GLY ( 25-) A N 0.03 2.67 INTRA BL 228 ASN ( 232-) A OD1 <-> 235 GLU ( 239-) A N 0.03 2.67 INTRA BF 5 GLY ( 8-) A O <-> 9 GLY ( 12-) A N 0.03 2.67 INTRA 96 SER ( 99-) A N <-> 97 LEU ( 100-) A N 0.02 2.58 INTRA B3 222 PHE ( 226-) A CD2 <-> 262 XE ( 266-) A XE 0.01 3.19 INTRA 30 ILE ( 33-) A N <-> 105 THR ( 108-) A O 0.01 2.69 INTRA BL 42 LYS ( 45-) A O <-> 263 HOH (1151 ) A O 0.01 2.39 INTRA 121 ASN ( 124-) A N <-> 136 GLY ( 140-) A O 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 -6.40 97 LEU ( 100-) A -5.32 132 GLN ( 136-) A -5.15
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.
132 GLN ( 136-) A -2.66 15 LYS ( 18-) A -2.55
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.
50 GLN ( 53-) A 226 ASN ( 230-) 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 71 GLN ( 74-) A N 97 LEU ( 100-) A N 126 ASP ( 130-) A N 133 GLN ( 137-) A NE2 196 THR ( 200-) A N 200 LEU ( 204-) A N 226 ASN ( 230-) 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 (1159 ) A O 0.95 K 4
29 ASP ( 32-) 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 : -0.198 2nd generation packing quality : 0.535 Ramachandran plot appearance : -1.598 chi-1/chi-2 rotamer normality : 0.187 Backbone conformation : -0.750
Bond lengths : 0.311 (tight) Bond angles : 0.679 Omega angle restraints : 0.268 (tight) Side chain planarity : 0.200 (tight) Improper dihedral distribution : 0.594 B-factor distribution : 0.463 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 : 1.70
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.1 2nd generation packing quality : -0.2 Ramachandran plot appearance : -2.0 chi-1/chi-2 rotamer normality : 0.1 Backbone conformation : -1.0
Bond lengths : 0.311 (tight) Bond angles : 0.679 Omega angle restraints : 0.268 (tight) Side chain planarity : 0.200 (tight) Improper dihedral distribution : 0.594 B-factor distribution : 0.463 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.