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 two or less which PRODRUG also cannot cope with), 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.
284 VO4 ( 501-) A - Atom types 285 PDV ( 502-) A - Atom types 286 GOL ( 503-) A - OK 287 GOL ( 504-) A - OK
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. The header of the PDB file states that TLS groups
were used. So, if WHAT IF complains about your B-factors, while 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:
Number of TLS groups mentione in PDB file header: 0
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
44 ARG ( 230-) A 86 ARG ( 272-) A 151 ARG ( 337-) A
3 TYR ( 189-) A 62 TYR ( 248-) A 75 TYR ( 261-) A 122 TYR ( 308-) A 197 TYR ( 383-) A
43 PHE ( 229-) A 85 PHE ( 271-) A 110 PHE ( 296-) A
45 ASP ( 231-) A 57 ASP ( 243-) A 114 ASP ( 300-) A 144 ASP ( 330-) A 207 ASP ( 393-) A 266 ASP ( 452-) A
38 GLU ( 224-) A 82 GLU ( 268-) A 90 GLU ( 276-) A 104 GLU ( 290-) A 177 GLU ( 363-) A 191 GLU ( 377-) A 263 GLU ( 449-) A 273 GLU ( 459-) 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.
172 THR ( 358-) A CB OG1 1.52 5.5
RMS Z-score for bond lengths: 0.384
RMS-deviation in bond distances: 0.009
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: 0.575
RMS-deviation in bond angles: 1.198
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.
38 GLU ( 224-) A 44 ARG ( 230-) A 45 ASP ( 231-) A 57 ASP ( 243-) A 82 GLU ( 268-) A 86 ARG ( 272-) A 90 GLU ( 276-) A 104 GLU ( 290-) A 114 ASP ( 300-) A 144 ASP ( 330-) A 151 ARG ( 337-) A 177 GLU ( 363-) A 191 GLU ( 377-) A 207 ASP ( 393-) A 263 GLU ( 449-) A 266 ASP ( 452-) A 273 GLU ( 459-) A
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.
259 VAL ( 445-) A -2.1
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.
35 CYS ( 221-) A omega poor 61 ASN ( 247-) A omega poor 114 ASP ( 300-) A Poor phi/psi, omega poor 132 THR ( 318-) A Poor phi/psi 139 ASP ( 325-) A Poor phi/psi 146 TYR ( 332-) A omega poor 169 PRO ( 355-) A omega poor 171 GLN ( 357-) A omega poor 211 LEU ( 397-) A Poor phi/psi 217 CYS ( 403-) A Poor phi/psi 240 GLN ( 426-) A Poor phi/psi 258 MET ( 444-) A omega poor 259 VAL ( 445-) A Poor phi/psi chi-1/chi-2 correlation Z-score : 0.812
It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.
13 SER ( 199-) A 0.37
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!
26 THR ( 212-) A 0 27 ASN ( 213-) A 0 31 TYR ( 217-) A 0 33 GLN ( 219-) A 0 34 ALA ( 220-) A 0 35 CYS ( 221-) A 0 36 GLY ( 222-) A 0 40 LEU ( 226-) A 0 41 ASN ( 227-) A 0 42 ARG ( 228-) A 0 43 PHE ( 229-) A 0 46 ILE ( 232-) A 0 50 ARG ( 236-) A 0 54 VAL ( 240-) A 0 55 ARG ( 241-) A 0 59 ASN ( 245-) A 0 60 ALA ( 246-) A 0 65 VAL ( 251-) A 0 67 ASN ( 253-) A 0 93 THR ( 279-) A 0 94 PRO ( 280-) A 0 99 LEU ( 285-) A 0 108 GLN ( 294-) A 0 115 TYR ( 301-) A 0 122 TYR ( 308-) A 0And so on for a total of 99 lines.
For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.
In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!
66 GLY ( 252-) A 1.53 12
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.
172 THR ( 358-) A CG2 <-> 173 ALA ( 359-) A N 0.27 2.73 INTRA 172 THR ( 358-) A CG2 <-> 288 HOH ( 157 ) A O 0.25 2.55 INTRA 234 ASN ( 420-) A ND2 <-> 288 HOH ( 88 ) A O 0.24 2.46 INTRA 168 PHE ( 354-) A CE1 <-> 223 ARG ( 409-) A CD 0.08 3.12 INTRA 39 LYS ( 225-) A NZ <-> 288 HOH ( 610 ) A O 0.08 2.62 INTRA BF 223 ARG ( 409-) A CG <-> 285 PDV ( 502-) A O5 0.07 2.73 INTRA 69 ARG ( 255-) A NE <-> 208 ASP ( 394-) A OD1 0.06 2.64 INTRA 115 TYR ( 301-) A OH <-> 216 HIS ( 402-) A NE2 0.05 2.65 INTRA BL 223 ARG ( 409-) A N <-> 285 PDV ( 502-) A O3 0.05 2.65 INTRA 35 CYS ( 221-) A N <-> 36 GLY ( 222-) A CA 0.04 2.86 INTRA 1 SER ( 187-) A N <-> 2 PRO ( 188-) A CD 0.03 2.97 INTRA 108 GLN ( 294-) A NE2 <-> 288 HOH ( 617 ) A O 0.02 2.68 INTRA 35 CYS ( 221-) A SG <-> 288 HOH ( 539 ) A O 0.02 2.98 INTRA 232 CYS ( 418-) A SG <-> 246 MET ( 432-) A SD 0.01 3.44 INTRA 194 ARG ( 380-) A NH2 <-> 211 LEU ( 397-) A O 0.01 2.69 INTRA 114 ASP ( 300-) A OD1 <-> 288 HOH ( 575 ) A O 0.01 2.39 INTRA
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.
171 GLN ( 357-) A -7.01 3 TYR ( 189-) A -5.92 35 CYS ( 221-) A -5.83 109 ARG ( 295-) A -5.80 275 GLN ( 461-) A -5.50 118 GLN ( 304-) A -5.37 234 ASN ( 420-) A -5.10
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.
205 VAL ( 391-) A -2.64 51 GLN ( 237-) A -2.60
The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.
203 SER ( 389-) A - 206 ALA ( 392-) A -1.98
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.
164 HIS ( 350-) 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.
95 VAL ( 281-) A N 100 ALA ( 286-) A N 118 GLN ( 304-) A N 188 GLN ( 374-) A NE2 202 SER ( 388-) A OG 218 ARG ( 404-) A NE 219 ALA ( 405-) A N 221 VAL ( 407-) A N 222 GLY ( 408-) A N 223 ARG ( 409-) A N 223 ARG ( 409-) A NE 255 ASN ( 441-) A N 255 ASN ( 441-) A ND2
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.
288 HOH ( 110 ) A O 0.88 K 4 ION-B 288 HOH ( 121 ) A O 0.89 K 4 288 HOH ( 144 ) A O 1.04 K 4 ION-B
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 : 0.149 2nd generation packing quality : -0.372 Ramachandran plot appearance : 1.014 chi-1/chi-2 rotamer normality : 0.812 Backbone conformation : 0.284
Bond lengths : 0.384 (tight) Bond angles : 0.575 (tight) Omega angle restraints : 1.030 Side chain planarity : 0.491 (tight) Improper dihedral distribution : 0.554 B-factor distribution : 0.367 Inside/Outside distribution : 0.939
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 : 1.42
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.3 2nd generation packing quality : -0.8 Ramachandran plot appearance : 0.4 chi-1/chi-2 rotamer normality : 0.3 Backbone conformation : -0.2
Bond lengths : 0.384 (tight) Bond angles : 0.575 (tight) Omega angle restraints : 1.030 Side chain planarity : 0.491 (tight) Improper dihedral distribution : 0.554 B-factor distribution : 0.367 Inside/Outside distribution : 0.939 ==============
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.