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.
261 4TR ( 270-) A - Fragmented
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.
37 LYS ( 39-) A - CE 37 LYS ( 39-) A - NZ 43 LYS ( 45-) A - CE 43 LYS ( 45-) A - NZ 51 GLN ( 53-) A - CG 51 GLN ( 53-) A - CD 51 GLN ( 53-) A - OE1 51 GLN ( 53-) A - NE2 78 LYS ( 80-) A - NZ 109 LYS ( 111-) A - CE 109 LYS ( 111-) A - NZ 124 LYS ( 127-) A - CE 124 LYS ( 127-) A - NZ 130 LYS ( 133-) A - CE 130 LYS ( 133-) A - NZ 156 LYS ( 159-) A - CE 156 LYS ( 159-) A - NZ 165 LYS ( 168-) A - CE 165 LYS ( 168-) A - NZ 210 LYS ( 213-) A - CE 210 LYS ( 213-) A - NZ 222 LYS ( 225-) A - CE 222 LYS ( 225-) A - NZ 225 LYS ( 228-) A - CD 225 LYS ( 228-) A - CE 225 LYS ( 228-) A - NZ 252 GLN ( 255-) A - CD 252 GLN ( 255-) A - OE1 252 GLN ( 255-) A - NE2
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: 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.
39 ASP ( 41-) A 240 ASP ( 243-) A
115 GLU ( 117-) A 235 GLU ( 238-) A 236 GLU ( 239-) A
RMS Z-score for bond lengths: 0.246
RMS-deviation in bond distances: 0.006
Warning: Low bond angle variability
Bond angles were found to deviate less than normal from the standard bond
angles (normal values for protein residues were taken from Engh and Huber
[REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below
is expected to be near 1.0 for a normally restrained data set. The fact that
it is lower than 0.667 in this structure might indicate that too-strong
restraints have been used in the refinement. This can only be a problem for
high resolution X-ray structures.
RMS Z-score for bond angles: 0.644
RMS-deviation in bond angles: 1.382
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.
39 ASP ( 41-) A 115 GLU ( 117-) A 235 GLU ( 238-) A 236 GLU ( 239-) A 240 ASP ( 243-) A
204 VAL ( 207-) A 4.02
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.
81 PRO ( 83-) A -2.6 173 PHE ( 176-) A -2.4 90 GLN ( 92-) A -2.3 160 VAL ( 163-) A -2.1 98 LEU ( 100-) A -2.1 148 GLY ( 151-) A -2.0 104 GLU ( 106-) 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.
2 HIS ( 4-) A Poor phi/psi 27 SER ( 29-) A PRO omega poor 63 ALA ( 65-) A Poor phi/psi 73 ASP ( 75-) A Poor phi/psi 74 LYS ( 76-) A Poor phi/psi 109 LYS ( 111-) A Poor phi/psi 175 ASN ( 178-) A Poor phi/psi 198 PRO ( 201-) A PRO omega poor 200 LEU ( 203-) A Poor phi/psi 240 ASP ( 243-) A Poor phi/psi 249 LYS ( 252-) A Poor phi/psi chi-1/chi-2 correlation Z-score : 0.081
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 TRP ( 5-) A 0 5 TYR ( 7-) A 0 8 HIS ( 10-) A 0 17 ASP ( 19-) A 0 18 PHE ( 20-) A 0 22 LYS ( 24-) A 0 25 ARG ( 27-) A 0 26 GLN ( 28-) A 0 27 SER ( 29-) A 0 48 SER ( 50-) A 0 52 ALA ( 54-) A 0 56 ARG ( 58-) A 0 60 ASN ( 62-) A 0 62 HIS ( 64-) A 0 63 ALA ( 65-) A 0 64 PHE ( 66-) A 0 70 ASP ( 72-) A 0 71 SER ( 73-) A 0 72 GLN ( 74-) A 0 73 ASP ( 75-) A 0 74 LYS ( 76-) A 0 75 ALA ( 77-) A 0 78 LYS ( 80-) A 0 81 PRO ( 83-) A 0 83 ASP ( 85-) A 0And so on for a total of 111 lines.
Standard deviation of omega values : 1.491
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.
13 HIS ( 15-) A ND1 <-> 16 LYS ( 18-) A NZ 0.19 2.81 INTRA BL 65 ASN ( 67-) A ND2 <-> 262 HOH ( 441 ) A O 0.18 2.52 INTRA 76 VAL ( 78-) A CG2 <-> 78 LYS ( 80-) A NZ 0.10 3.00 INTRA 196 THR ( 199-) A OG1 <-> 261 4TR ( 270-) A N1 0.09 2.61 INTRA BL 1 HIS ( 3-) A N <-> 262 HOH ( 310 ) A O 0.09 2.61 INTRA BF 249 LYS ( 252-) A NZ <-> 262 HOH ( 389 ) A O 0.08 2.62 INTRA 105 HIS ( 107-) A NE2 <-> 191 TYR ( 194-) A OH 0.07 2.63 INTRA BL 177 ASP ( 180-) A OD2 <-> 179 ARG ( 182-) A NH2 0.07 2.63 INTRA 92 HIS ( 94-) A ND1 <-> 262 HOH ( 441 ) A O 0.06 2.64 INTRA 165 LYS ( 168-) A NZ <-> 225 LYS ( 228-) A O 0.06 2.64 INTRA BL 74 LYS ( 76-) A CB <-> 75 ALA ( 77-) A N 0.06 2.64 INTRA BF 195 LEU ( 198-) A CD2 <-> 261 4TR ( 270-) A BR 0.04 3.16 INTRA 26 GLN ( 28-) A NE2 <-> 243 ARG ( 246-) A NH1 0.04 2.81 INTRA BL 25 ARG ( 27-) A C <-> 251 ARG ( 254-) A NH1 0.04 3.06 INTRA BL 165 LYS ( 168-) A CE <-> 227 ASN ( 230-) A ND2 0.04 3.06 INTRA 249 LYS ( 252-) A CB <-> 250 ASN ( 253-) A N 0.03 2.67 INTRA B3 72 GLN ( 74-) A C <-> 74 LYS ( 76-) A N 0.02 2.88 INTRA BF 49 TYR ( 51-) A OH <-> 120 HIS ( 122-) A NE2 0.02 2.68 INTRA BL 72 GLN ( 74-) A O <-> 74 LYS ( 76-) A N 0.02 2.68 INTRA BF 65 ASN ( 67-) A ND2 <-> 262 HOH ( 298 ) A O 0.02 2.68 INTRA 2 HIS ( 4-) A CD2 <-> 3 TRP ( 5-) A N 0.02 2.98 INTRA BF 63 ALA ( 65-) A CA <-> 238 MET ( 241-) A SD 0.01 3.39 INTRA BL 115 GLU ( 117-) A OE2 <-> 117 HIS ( 119-) A NE2 0.01 2.69 INTRA BL 1 HIS ( 3-) A N <-> 2 HIS ( 4-) A N 0.01 2.59 INTRA BF
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.
8 HIS ( 10-) A -5.95 2 HIS ( 4-) A -5.43 133 GLN ( 136-) A -5.02
Chain identifier: A
Warning: Abnormal packing Z-score for sequential residues
A stretch of at least four sequential residues with a 2nd generation packing
Z-score below -1.75 was found. This could indicate that these residues are
part of a strange loop or that the residues in this range are incomplete,
but it might also be an indication of misthreading.
The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.
247 PRO ( 250-) A - 250 ASN ( 253-) A -1.85
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.
1 HIS ( 3-) A 2 HIS ( 4-) A 26 GLN ( 28-) A 65 ASN ( 67-) A 72 GLN ( 74-) 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.
29 VAL ( 31-) A N 98 LEU ( 100-) A N 127 ASP ( 130-) A N 162 ASP ( 165-) A N 165 LYS ( 168-) A N 197 THR ( 200-) A N 201 LEU ( 204-) A N 230 GLY ( 233-) A N 242 TRP ( 245-) A N 257 PHE ( 260-) A N Only metal coordination for 62 HIS ( 64-) A NE2 Only metal coordination for 92 HIS ( 94-) A NE2 Only metal coordination for 94 HIS ( 96-) A NE2 Only metal coordination for 117 HIS ( 119-) A ND1
The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.
259 ZN ( 262-) A -.- -.- Too few ligands (1) 260 ZN ( 263-) A -.- -.- Too few ligands (2)
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.
262 HOH ( 275 ) A O 0.99 K 4
159 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 : -0.491 2nd generation packing quality : 0.016 Ramachandran plot appearance : -1.486 chi-1/chi-2 rotamer normality : 0.081 Backbone conformation : -0.911
Bond lengths : 0.246 (tight) Bond angles : 0.644 (tight) Omega angle restraints : 0.271 (tight) Side chain planarity : 0.219 (tight) Improper dihedral distribution : 0.580 B-factor distribution : 0.760 Inside/Outside distribution : 0.957
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 : 1.76
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.2 2nd generation packing quality : -0.5 Ramachandran plot appearance : -1.5 chi-1/chi-2 rotamer normality : 0.3 Backbone conformation : -1.3
Bond lengths : 0.246 (tight) Bond angles : 0.644 (tight) Omega angle restraints : 0.271 (tight) Side chain planarity : 0.219 (tight) Improper dihedral distribution : 0.580 B-factor distribution : 0.760 Inside/Outside distribution : 0.957 ==============
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.