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.
163 0DY ( 1-) A - Atom types
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.
131 MET ( 215-) A - CE 138 ARG ( 222-) A - CD 138 ARG ( 222-) A - NE 138 ARG ( 222-) A - CZ 138 ARG ( 222-) A - NH1 138 ARG ( 222-) A - NH2
In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.
158 GLY ( 242-) A -
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: Missing atoms
The atoms listed in the table below are missing from the entry. If many atoms
are missing, the other checks can become less sensitive. Be aware that it
often happens that groups at the termini of DNA or RNA are really missing,
so that the absence of these atoms normally is neither an error nor the
result of poor electron density. Some of the atoms listed here might also be
listed by other checks, most noticeably by the options in the previous
section that list missing atoms in several categories. The plausible atoms
with zero occupancy are not listed here, as they already got assigned a
non-zero occupancy, and thus are no longer 'missing'.
158 GLY ( 242-) A O
Obviously, the temperature at which the X-ray data was collected has some importance too:
Crystal temperature (K) :283.000
Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
Chain identifier: A
Warning: Unusual bond lengths
The bond lengths listed in the table below were found to deviate more than 4
sigma from standard bond lengths (both standard values and sigmas for amino
acid residues have been taken from Engh and Huber [REF], for DNA they were
taken from Parkinson et al [REF]). In the table below for each unusual bond
the bond length and the number of standard deviations it differs from the
normal value is given.
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.
56 ILE ( 140-) A CA CB 1.61 4.1
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
| 0.995688 0.001418 -0.001221| | 0.001418 0.994537 0.000807| | -0.001221 0.000807 0.999466|Proposed new scale matrix
| 0.030306 -0.000043 0.000037| | -0.000021 0.014482 -0.000012| | 0.000017 -0.000011 0.013777|With corresponding cell
A = 32.997 B = 69.051 C = 72.583 Alpha= 89.907 Beta= 90.140 Gamma= 89.837
The CRYST1 cell dimensions
A = 33.140 B = 69.430 C = 72.620 Alpha= 90.000 Beta= 90.000 Gamma= 90.000
(Under-)estimated Z-score: 6.532
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.
64 GLY ( 148-) A N CA C 124.77 4.2 105 TYR ( 189-) A -C N CA 128.95 4.0 154 GLN ( 238-) A CA CB CG 105.03 -4.5
64 GLY ( 148-) A 4.02
Tau angle RMS Z-score : 1.508
Warning: Torsion angle evaluation shows unusual residues
The residues listed in the table below contain bad or abnormal
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.
41 PRO ( 125-) A -2.7 49 GLN ( 133-) A -2.2 3 LYS ( 87-) 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.
61 ARG ( 145-) A Poor phi/psi 66 ASN ( 150-) A Poor phi/psi 73 ASN ( 157-) A Poor phi/psi 77 ALA ( 161-) A Poor phi/psi 101 THR ( 185-) A Poor phi/psi 104 ASN ( 188-) A omega poor 142 ASN ( 226-) A Poor phi/psi 157 TYR ( 241-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -1.324
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.
118 SER ( 202-) A 0.36
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 TRP ( 88-) A 0 5 GLU ( 89-) A 0 6 ARG ( 90-) A 0 8 ASN ( 92-) A 0 15 ASN ( 99-) A 0 19 GLN ( 103-) A 0 39 ALA ( 123-) A 0 48 SER ( 132-) A 0 49 GLN ( 133-) A 0 60 GLN ( 144-) A 0 61 ARG ( 145-) A 0 63 HIS ( 147-) A 0 66 ASN ( 150-) A 0 70 ASP ( 154-) A 0 72 PRO ( 156-) A 0 73 ASN ( 157-) A 0 77 ALA ( 161-) A 0 81 GLN ( 165-) A 0 82 PRO ( 166-) A 0 84 GLN ( 168-) A 0 86 ILE ( 170-) A 0 100 ASN ( 184-) A 0 102 SER ( 186-) A 0 103 ALA ( 187-) A 0 104 ASN ( 188-) A 0And so on for a total of 69 lines.
Standard deviation of omega values : 2.372
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]
146 PRO ( 230-) A 0.49 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.
6 ARG ( 90-) A NH2 <-> 53 ASP ( 137-) A CG 0.31 2.79 INTRA 6 ARG ( 90-) A NH2 <-> 53 ASP ( 137-) A OD1 0.22 2.48 INTRA 6 ARG ( 90-) A NH2 <-> 53 ASP ( 137-) A OD2 0.16 2.54 INTRA 93 ASP ( 177-) A O <-> 98 TRP ( 182-) A NE1 0.11 2.59 INTRA BL 100 ASN ( 184-) A N <-> 101 THR ( 185-) A N 0.11 2.49 INTRA BL 19 GLN ( 103-) A NE2 <-> 96 GLU ( 180-) A O 0.05 2.65 INTRA 12 ARG ( 96-) A O <-> 56 ILE ( 140-) A N 0.02 2.68 INTRA BL 157 TYR ( 241-) A CB <-> 158 GLY ( 242-) A N 0.01 2.69 INTRA B3
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.
84 GLN ( 168-) A -7.08 49 GLN ( 133-) A -6.98 14 ARG ( 98-) A -6.57 81 GLN ( 165-) A -6.39 51 GLU ( 135-) A -5.07
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.
134 ASN ( 218-) 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.
6 ARG ( 90-) A N 17 THR ( 101-) A N 49 GLN ( 133-) A N 52 ALA ( 136-) A N 61 ARG ( 145-) A N 62 ASP ( 146-) A N 65 ASP ( 149-) A N 71 GLY ( 155-) A N 76 LEU ( 160-) A N 77 ALA ( 161-) A N 98 TRP ( 182-) A N 104 ASN ( 188-) A N 134 ASN ( 218-) A N 135 TYR ( 219-) A N 135 TYR ( 219-) A OH 136 ALA ( 220-) A N 138 ARG ( 222-) A N 143 TYR ( 227-) A OH Only metal coordination for 63 HIS ( 147-) A NE2 Only metal coordination for 65 ASP ( 149-) A OD2 Only metal coordination for 78 HIS ( 162-) A NE2 Only metal coordination for 91 HIS ( 175-) A ND1 Only metal coordination for 96 GLU ( 180-) A OE2 Only metal coordination for 113 HIS ( 197-) A NE2 Only metal coordination for 123 HIS ( 207-) A NE2
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.
114 GLU ( 198-) A OE1 114 GLU ( 198-) A OE2
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 : -1.644 2nd generation packing quality : -0.472 Ramachandran plot appearance : -0.272 chi-1/chi-2 rotamer normality : -1.324 Backbone conformation : 0.040
Bond lengths : 0.959 Bond angles : 0.974 Omega angle restraints : 0.431 (tight) Side chain planarity : 1.001 Improper dihedral distribution : 1.425 B-factor distribution : 0.406 Inside/Outside distribution : 0.947
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 : 2.00
Structure Z-scores, positive is better than average:
1st generation packing quality : -1.5 2nd generation packing quality : -0.3 Ramachandran plot appearance : 0.3 chi-1/chi-2 rotamer normality : -0.5 Backbone conformation : -0.1
Bond lengths : 0.959 Bond angles : 0.974 Omega angle restraints : 0.431 (tight) Side chain planarity : 1.001 Improper dihedral distribution : 1.425 B-factor distribution : 0.406 Inside/Outside distribution : 0.947 ==============
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.