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.
260 HGB ( 263-) A - Atom types 261 URE ( 264-) A - OK
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.
62 ALA ( 65-) 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'.
11 GLU ( 14-) A CB 11 GLU ( 14-) A CG 11 GLU ( 14-) A CD 11 GLU ( 14-) A OE1 11 GLU ( 14-) A OE2 62 ALA ( 65-) A N
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.
61 HIS ( 64-) A 0.70
Obviously, the temperature at which the X-ray data was collected has some importance too:
Crystal temperature (K) :295.000
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 : 46.81
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.
120 TRP ( 123-) A N -C 1.42 4.5 123 LYS ( 127-) A N -C 1.45 6.1 201 GLU ( 205-) A C O 1.34 5.5
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
| 1.000831 0.000783 0.004913| | 0.000783 0.988658 0.000233| | 0.004913 0.000233 0.997776|Proposed new scale matrix
| 0.023305 -0.000020 0.005833| | -0.000019 0.024071 -0.000006| | -0.000070 -0.000003 0.014160|With corresponding cell
A = 42.857 B = 41.544 C = 72.712 Alpha= 89.996 Beta= 103.772 Gamma= 89.910
The CRYST1 cell dimensions
A = 42.820 B = 42.020 C = 73.030 Alpha= 90.000 Beta= 104.260 Gamma= 90.000
(Under-)estimated Z-score: 13.078
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 N CA CB 120.09 5.6 1 HIS ( 4-) A CA CB CG 105.27 -8.5 1 HIS ( 4-) A CG ND1 CE1 110.11 4.5 7 HIS ( 10-) A CA CB CG 105.96 -7.8 8 ASN ( 11-) A ND2 CG OD1 117.97 -4.6 14 HIS ( 17-) A CG ND1 CE1 111.27 5.7 18 PRO ( 21-) A N CA CB 109.14 5.6 23 GLU ( 26-) A -C N CA 129.17 4.1 23 GLU ( 26-) A C CA CB 102.42 -4.0 24 ARG ( 27-) A CA CB CG 126.55 6.2 25 GLN ( 28-) A NE2 CD OE1 117.18 -5.4 26 SER ( 29-) A -C N CA 131.76 5.6 26 SER ( 29-) A CA C O 113.48 -4.3 27 PRO ( 30-) A -O -C N 129.54 5.4 29 ASP ( 32-) A -C N CA 110.06 -6.5 33 HIS ( 36-) A CA CB CG 105.07 -8.7 34 THR ( 37-) A CA CB OG1 101.19 -5.6 36 LYS ( 39-) A CA CB CG 129.06 7.5 55 ARG ( 58-) A N CA CB 101.53 -5.3 57 LEU ( 60-) A N CA CB 101.97 -5.0 58 ASN ( 61-) A ND2 CG OD1 118.35 -4.2 61 HIS ( 64-) A N CA CB 149.24 22.8 61 HIS ( 64-) A C CA CB 92.89 -9.1 61 HIS ( 64-) A CA CB CG 100.75 -13.0 61 HIS ( 64-) A CG ND1 CE1 109.90 4.3And so on for a total of 123 lines.
Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.
Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.
33 HIS ( 36-) A C -9.0 -13.33 0.15 55 ARG ( 58-) A CA 6.6 44.71 33.91 61 HIS ( 64-) A CA -11.3 13.36 34.11 65 VAL ( 68-) A CB -7.0 -42.19 -32.96 163 ILE ( 167-) A CB 6.0 40.15 32.31 181 LEU ( 185-) A C 7.1 11.46 0.20 201 GLU ( 205-) A C -7.6 -11.01 -0.03 235 GLU ( 239-) A C -6.1 -8.81 -0.03 The average deviation= 2.430
Improper dihedral RMS Z-score : 2.055
Error: Tau angle problems
The side chains of the residues listed in the table below contain a tau
angle (N-Calpha-C) that was found to deviate from te expected value by
more than 4.0 times the expected standard deviation. The number in the
table is the number of standard deviations this RMS value deviates from
the expected value.
203 VAL ( 207-) A 5.26
91 HIS ( 94-) A 4.70 93 HIS ( 96-) A 4.26 133 GLN ( 137-) A 4.10 61 HIS ( 64-) A 4.04
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.
80 PRO ( 83-) A -2.6 187 TYR ( 191-) A -2.4 77 LYS ( 80-) A -2.3 163 ILE ( 167-) A -2.3 108 LYS ( 111-) A -2.2 212 ILE ( 216-) A -2.1 172 PHE ( 176-) A -2.1 159 VAL ( 163-) A -2.1 150 LYS ( 154-) A -2.1 147 GLY ( 151-) A -2.1 89 GLN ( 92-) A -2.1 47 SER ( 50-) A -2.1 57 LEU ( 60-) A -2.0 198 PRO ( 202-) 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 61 HIS ( 64-) A Impossible psi 62 ALA ( 65-) A Impossible phi 107 ASP ( 110-) 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 201 GLU ( 205-) A Poor phi/psi, omega poor 202 CYS ( 206-) A omega poor 239 ASP ( 243-) A Poor phi/psi 248 LYS ( 252-) A Poor phi/psi 249 ASN ( 253-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -1.825
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 11 GLU ( 14-) 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 35 ALA ( 38-) A 0 47 SER ( 50-) A 0 49 ASP ( 52-) A 0 50 GLN ( 53-) A 0 51 ALA ( 54-) 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 73 LYS ( 76-) A 0 74 ALA ( 77-) A 0 77 LYS ( 80-) A 0 80 PRO ( 83-) A 0 82 ASP ( 85-) A 0And so on for a total of 117 lines.
18 PRO ( 21-) A 0.18 LOW 43 PRO ( 46-) A 0.19 LOW 151 PRO ( 155-) A 0.20 LOW 177 PRO ( 181-) A 0.19 LOW 191 PRO ( 195-) A 0.18 LOW 211 PRO ( 215-) A 0.20 LOW 233 PRO ( 237-) A 0.06 LOW 243 PRO ( 247-) A 0.06 LOW
10 PRO ( 13-) A 118.2 half-chair C-beta/C-alpha (126 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.
249 ASN ( 253-) A C <-> 262 HOH ( 364 ) A O 0.77 2.03 INTRA 260 HGB ( 263-) A C6 <-> 262 HOH ( 390 ) A O 0.62 2.18 INTRA 11 GLU ( 14-) A CA <-> 262 HOH ( 372 ) A O 0.25 2.55 INTRA 250 ARG ( 254-) A N <-> 262 HOH ( 364 ) A O 0.25 2.45 INTRA 12 HIS ( 15-) A ND1 <-> 15 LYS ( 18-) A NZ 0.21 2.79 INTRA BL 261 URE ( 264-) A N2 <-> 262 HOH ( 359 ) A O 0.19 2.51 INTRA 260 HGB ( 263-) A C7 <-> 262 HOH ( 390 ) A O 0.19 2.61 INTRA 64 ASN ( 67-) A ND2 <-> 262 HOH ( 348 ) A O 0.15 2.55 INTRA BL 60 GLY ( 63-) A N <-> 61 HIS ( 64-) A N 0.13 2.47 INTRA BL 55 ARG ( 58-) A NE <-> 66 GLU ( 69-) A OE1 0.11 2.59 INTRA BL 38 ASP ( 41-) A OD1 <-> 40 SER ( 43-) A N 0.06 2.64 INTRA 248 LYS ( 252-) A NZ <-> 262 HOH ( 353 ) A O 0.06 2.64 INTRA 114 GLU ( 117-) A OE2 <-> 116 HIS ( 119-) A NE2 0.05 2.65 INTRA BL 100 GLN ( 103-) A NE2 <-> 239 ASP ( 243-) A OD1 0.05 2.65 INTRA BL 34 THR ( 37-) A N <-> 35 ALA ( 38-) A N 0.04 2.56 INTRA BL 158 ASP ( 162-) A OD2 <-> 262 HOH ( 329 ) A O 0.04 2.36 INTRA 19 ILE ( 22-) A C <-> 21 LYS ( 24-) A N 0.04 2.86 INTRA BL 248 LYS ( 252-) A CB <-> 249 ASN ( 253-) A N 0.03 2.67 INTRA BL 104 HIS ( 107-) A NE2 <-> 190 TYR ( 194-) A OH 0.03 2.67 INTRA BL 40 SER ( 43-) A N <-> 41 LEU ( 44-) A N 0.03 2.57 INTRA BL 39 PRO ( 42-) A N <-> 40 SER ( 43-) A N 0.03 2.57 INTRA BL 29 ASP ( 32-) A N <-> 262 HOH ( 274 ) A O 0.03 2.67 INTRA BL 249 ASN ( 253-) A O <-> 262 HOH ( 364 ) A O 0.02 2.38 INTRA 15 LYS ( 18-) A NZ <-> 262 HOH ( 285 ) A O 0.02 2.68 INTRA 17 PHE ( 20-) A CA <-> 18 PRO ( 21-) A CD 0.01 2.79 INTRA BL 232 GLU ( 236-) A CB <-> 233 PRO ( 237-) A CD 0.01 3.09 INTRA 82 ASP ( 85-) A N <-> 262 HOH ( 287 ) A O 0.01 2.69 INTRA BL 19 ILE ( 22-) A O <-> 22 GLY ( 25-) A N 0.01 2.69 INTRA BL 9 GLY ( 12-) A CA <-> 10 PRO ( 13-) A CD 0.01 2.79 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 -5.90 97 LEU ( 100-) A -5.27 33 HIS ( 36-) A -5.07 132 GLN ( 136-) A -5.06
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.
11 GLU ( 14-) A -2.62
Chain identifier: A
Water, ion, and hydrogenbond related checks
Error: Water molecules without hydrogen bonds
The water molecules listed in the table below do not form any hydrogen bonds,
neither with the protein or DNA/RNA, nor with other water molecules. This is
a strong indication of a refinement problem. The last number on each line is
the identifier of the water molecule in the input file.
262 HOH ( 380 ) 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
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 37 TYR ( 40-) A N 55 ARG ( 58-) A NH2 178 ARG ( 182-) A NH1 200 LEU ( 204-) A N 228 ASN ( 232-) A N 240 ASN ( 244-) A ND2 241 TRP ( 245-) A N 256 PHE ( 260-) A N Only metal coordination for 91 HIS ( 94-) A NE2 Only metal coordination for 93 HIS ( 96-) A NE2
235 GLU ( 239-) A H-bonding suggests Gln
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 : -0.458 2nd generation packing quality : 0.518 Ramachandran plot appearance : -1.778 chi-1/chi-2 rotamer normality : -1.825 Backbone conformation : -0.927
Bond lengths : 0.967 Bond angles : 1.893 Omega angle restraints : 0.934 Side chain planarity : 1.544 Improper dihedral distribution : 2.055 (loose) Inside/Outside distribution : 0.948
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 : 1.85
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.1 2nd generation packing quality : -0.0 Ramachandran plot appearance : -2.4 chi-1/chi-2 rotamer normality : -1.5 Backbone conformation : -1.0
Bond lengths : 0.967 Bond angles : 1.893 Omega angle restraints : 0.934 Side chain planarity : 1.544 Improper dihedral distribution : 2.055 (loose) Inside/Outside distribution : 0.948 ==============
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.