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.
258 MMC ( 263-) A - Atom types 259 PTS ( 264-) 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. 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:
Temperature cannot be read from the PDB file. This most likely means that
the temperature is listed as NULL (meaning unknown) in the PDB file.
Warning: More than 5 percent of buried atoms has low B-factor
For normal protein structures, no more than about 1 percent of the B factors
of buried atoms is below 5.0. The fact that this value is much higher in the
current structure could be a signal that the B-factors were restraints or
constraints to too-low values, misuse of B-factor field in the PDB file, or
a TLS/scaling problem. If the average B factor is low too, it is probably a
low temperature structure determination.
Percentage of buried atoms with B less than 5 : 6.53
Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
Chain identifier: A
Warning: Possible cell scaling problem
Comparison of bond distances with Engh and Huber [REF] standard values for
protein residues and Parkinson et al [REF] values for DNA/RNA shows a
significant systematic deviation. It could be that the unit cell used in
refinement was not accurate enough. The deformation matrix given below gives
the deviations found: the three numbers on the diagonal represent the
relative corrections needed along the A, B and C cell axis. These values are
1.000 in a normal case, but have significant deviations here (significant at
the 99.99 percent confidence level)
There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.
Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.
If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.
Unit Cell deformation matrix
| 1.003873 0.000262 0.000225| | 0.000262 1.002863 0.000074| | 0.000225 0.000074 0.999774|Proposed new scale matrix
| 0.023316 -0.000007 0.006168| | -0.000006 0.023781 -0.000002| | -0.000003 -0.000001 0.014230|With corresponding cell
A = 42.886 B = 42.051 C = 72.686 Alpha= 90.000 Beta= 104.805 Gamma= 89.970
The CRYST1 cell dimensions
A = 42.720 B = 41.930 C = 72.690 Alpha= 90.000 Beta= 104.770 Gamma= 90.000
(Under-)estimated Z-score: 5.366
Warning: Unusual bond angles
The bond angles listed in the table below were found to deviate more than 4
sigma from standard bond angles (both standard values and sigma for protein
residues have been taken from Engh and Huber [REF], for DNA/RNA from
Parkinson et al [REF]). In the table below for each strange angle the bond
angle and the number of standard deviations it differs from the standard
values is given. Please note that disulphide bridges are neglected. Atoms
starting with "-" belong to the previous residue in the sequence.
1 HIS ( 4-) A CA CB CG 104.78 -9.0 2 TRP ( 5-) A CD1 CG CD2 112.80 4.1 2 TRP ( 5-) A CG CD1 NE1 104.27 -4.6 2 TRP ( 5-) A CG CD2 CE2 101.92 -4.4 7 HIS ( 10-) A CA CB CG 108.20 -5.6 7 HIS ( 10-) A CB CG CD2 123.80 -4.1 12 HIS ( 15-) A NE2 CD2 CG 102.32 -4.2 12 HIS ( 15-) A CD2 CG ND1 113.45 7.3 13 TRP ( 16-) A CG CD2 CE2 101.81 -4.5 14 HIS ( 17-) A CD2 CG ND1 113.08 7.0 21 LYS ( 24-) A CA CB CG 124.53 5.2 27 PRO ( 30-) A -CA -C N 123.92 4.7 31 ASP ( 34-) A CA CB CG 117.65 5.0 33 HIS ( 36-) A CA CB CG 109.24 -4.6 49 ASP ( 52-) A CA CB CG 118.20 5.6 59 ASN ( 62-) A ND2 CG OD1 118.33 -4.3 63 PHE ( 66-) A CA CB CG 118.57 4.8 64 ASN ( 67-) A CB CG ND2 122.98 4.4 72 ASP ( 75-) A CA CB CG 116.73 4.1 77 LYS ( 80-) A CB CG CD 99.85 -5.0 86 ARG ( 89-) A CB CG CD 106.05 -4.0 90 PHE ( 93-) A CA CB CG 122.27 8.5 93 HIS ( 96-) A CB CG ND1 128.34 4.5 94 TRP ( 97-) A CG CD2 CE2 101.79 -4.5 100 GLN ( 103-) A NE2 CD OE1 116.13 -6.5And so on for a total of 63 lines.
156 VAL ( 160-) A 4.08
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.
189 THR ( 193-) A -2.3 57 LEU ( 60-) A -2.3 55 ARG ( 58-) A -2.3 198 PRO ( 202-) A -2.1 47 SER ( 50-) A -2.1 249 ASN ( 253-) A -2.1 172 PHE ( 176-) A -2.1 89 GLN ( 92-) 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 108 LYS ( 111-) 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 249 ASN ( 253-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -1.489
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 12 HIS ( 15-) A 0 13 TRP ( 16-) A 0 17 PHE ( 20-) A 0 23 GLU ( 26-) A 0 24 ARG ( 27-) A 0 26 SER ( 29-) A 0 47 SER ( 50-) A 0 49 ASP ( 52-) A 0 59 ASN ( 62-) A 0 61 HIS ( 64-) A 0 69 ASP ( 72-) A 0 70 SER ( 73-) A 0 72 ASP ( 75-) A 0 73 LYS ( 76-) A 0 77 LYS ( 80-) A 0 80 PRO ( 83-) A 0 82 ASP ( 85-) A 0 88 ILE ( 91-) A 0 89 GLN ( 92-) A 0 100 GLN ( 103-) A 0 103 GLU ( 106-) A 0 104 HIS ( 107-) A 0 108 LYS ( 111-) A 0And so on for a total of 120 lines.
27 PRO ( 30-) A 0.45 HIGH 80 PRO ( 83-) A 0.45 HIGH 197 PRO ( 201-) A 0.48 HIGH 246 PRO ( 250-) A 0.46 HIGH
18 PRO ( 21-) A -115.0 envelop C-gamma (-108 degrees) 177 PRO ( 181-) A 50.8 half-chair C-delta/C-gamma (54 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.
12 HIS ( 15-) A ND1 <-> 15 LYS ( 18-) A NZ 0.14 2.86 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 -6.08 97 LEU ( 100-) A -5.57 33 HIS ( 36-) A -5.14
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.
15 LYS ( 18-) A -2.62
Chain identifier: A
Water, ion, and hydrogenbond related checks
Warning: Water molecules need moving
The water molecules listed in the table below were found to be significantly
closer to a symmetry related non-water molecule than to the ones given in the
coordinate file. For optimal viewing convenience revised coordinates for
these water molecules should be given.
The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.
260 HOH ( 345 ) A O -7.77 1.59 35.92 260 HOH ( 353 ) A O -13.65 -18.44 15.58 260 HOH ( 382 ) A O -2.73 -17.42 5.46 260 HOH ( 405 ) A O -21.42 -6.30 -1.87 260 HOH ( 414 ) A O -18.36 -3.42 -2.59
260 HOH ( 316 ) A O 260 HOH ( 321 ) A O 260 HOH ( 409 ) A O 260 HOH ( 436 ) A O Metal-coordinating Histidine residue 91 fixed to 1 Metal-coordinating Histidine residue 93 fixed to 1 Metal-coordinating Histidine residue 116 fixed to 1
174 ASN ( 178-) A 251 GLN ( 255-) 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 31 ASP ( 34-) A N 71 GLN ( 74-) A N 97 LEU ( 100-) A N 196 THR ( 200-) A N 200 LEU ( 204-) A N 223 ARG ( 227-) A NH1 Only metal coordination for 93 HIS ( 96-) A NE2 Only metal coordination for 116 HIS ( 119-) A ND1
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.
11 GLU ( 14-) A OE2
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.
260 HOH ( 363 ) A O 0.95 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 : -0.320 2nd generation packing quality : 0.218 Ramachandran plot appearance : -1.583 chi-1/chi-2 rotamer normality : -1.489 Backbone conformation : -1.286
Bond lengths : 0.753 Bond angles : 1.491 Omega angle restraints : 0.906 Side chain planarity : 0.522 (tight) Improper dihedral distribution : 1.070 Inside/Outside distribution : 0.950
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 : 2.10
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.1 2nd generation packing quality : 0.3 Ramachandran plot appearance : -0.7 chi-1/chi-2 rotamer normality : -0.4 Backbone conformation : -1.2
Bond lengths : 0.753 Bond angles : 1.491 Omega angle restraints : 0.906 Side chain planarity : 0.522 (tight) Improper dihedral distribution : 1.070 Inside/Outside distribution : 0.950 ==============
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.