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.
314 HOH (2034 ) A O 11
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.
313 5EZ (1383-) A - Fragmented
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.
182 ALA ( 220-) A - 236 CYS ( 277-) A - 312 ASN ( 382-) 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'.
182 ALA ( 220-) A C 182 ALA ( 220-) A O 182 ALA ( 220-) A CB 236 CYS ( 277-) A C 236 CYS ( 277-) A O 236 CYS ( 277-) A CB 236 CYS ( 277-) A SG 312 ASN ( 382-) A C 312 ASN ( 382-) A O 312 ASN ( 382-) A CB 312 ASN ( 382-) A CG 312 ASN ( 382-) A OD1 312 ASN ( 382-) A ND2
1 GLU ( 39-) A High 3 GLU ( 41-) A High 6 GLU ( 44-) A High 9 ARG ( 47-) A High 10 LYS ( 48-) A High 13 GLU ( 51-) A High 24 GLU ( 62-) A High 26 LYS ( 64-) A High 31 GLU ( 69-) A High 40 ASN ( 78-) A High 64 GLU ( 102-) A High 70 ARG ( 108-) A High 72 GLN ( 110-) A High 75 ARG ( 113-) A High 76 GLU ( 114-) A High 82 GLU ( 120-) A High 118 LYS ( 156-) A High 143 ARG ( 181-) A High 144 GLU ( 182-) A High 147 LYS ( 185-) A High 151 ARG ( 189-) A High 176 GLN ( 214-) A High 179 ASP ( 217-) A High 180 SER ( 218-) A High 181 MET ( 219-) A High 228 LYS ( 269-) A High 229 GLU ( 270-) A High 231 GLU ( 272-) A High 233 MET ( 274-) A High 278 GLU ( 348-) A High 298 GLU ( 368-) A High
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
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.
20 GLN ( 58-) A CD OE1 1.34 5.4 20 GLN ( 58-) A CD NE2 1.24 -4.1 265 GLN ( 335-) A CD NE2 1.20 -6.2
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
| 0.998141 0.000065 0.001258| | 0.000065 0.996274 0.000348| | 0.001258 0.000348 0.996835|Proposed new scale matrix
| 0.013023 0.007532 -0.000019| | 0.000000 0.015066 -0.000005| | -0.000006 -0.000002 0.004523|With corresponding cell
A = 76.789 B = 76.677 C = 221.077 Alpha= 90.038 Beta= 89.855 Gamma= 120.045
The CRYST1 cell dimensions
A = 76.930 B = 76.930 C = 221.757 Alpha= 90.000 Beta= 90.000 Gamma= 120.000
(Under-)estimated Z-score: 6.994
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.
5 ASP ( 43-) A CA CB CG 117.05 4.5 46 LYS ( 84-) A N CA C 99.82 -4.1 144 GLU ( 182-) A CB CG CD 119.96 4.3 179 ASP ( 217-) A CA CB CG 117.30 4.7 281 ASP ( 351-) A CA CB CG 118.16 5.6
249 ASN ( 319-) A 5.37 46 LYS ( 84-) A 4.41 272 LEU ( 342-) A 4.07
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.
65 ILE ( 103-) A -2.7 197 THR ( 238-) A -2.4 170 ASP ( 208-) A -2.2 240 ILE ( 310-) A -2.2 148 ILE ( 186-) A -2.1 217 VAL ( 258-) A -2.0 101 ILE ( 139-) 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.
151 ARG ( 189-) A Poor phi/psi 170 ASP ( 208-) A Poor phi/psi 200 SER ( 241-) A Poor phi/psi 222 ILE ( 263-) A PRO omega poor chi-1/chi-2 correlation Z-score : -1.526
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.
207 SER ( 248-) A 0.35 294 SER ( 364-) A 0.38
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!
22 VAL ( 60-) A 0 24 GLU ( 62-) A 0 33 ILE ( 71-) A 0 38 ALA ( 76-) A 0 40 ASN ( 78-) A 0 49 HIS ( 87-) A 0 52 SER ( 90-) A 0 84 ASN ( 122-) A 0 87 TYR ( 125-) A 0 92 TYR ( 130-) A 0 97 SER ( 135-) A 0 98 ASP ( 136-) A 0 104 CYS ( 142-) A 0 105 MET ( 143-) A 0 109 ASP ( 147-) A 0 112 SER ( 150-) A 0 120 ALA ( 158-) A 0 122 ARG ( 160-) A 0 145 LYS ( 183-) A 0 146 HIS ( 184-) A 0 151 ARG ( 189-) A 0 152 ASP ( 190-) A 0 153 VAL ( 191-) A 0 154 LYS ( 192-) A 0 163 ARG ( 201-) A 0And so on for a total of 103 lines.
Standard deviation of omega values : 2.983
Warning: Unusual PRO puckering phases
The proline residues listed in the table below have a puckering phase that is
not expected to occur in protein structures. Puckering parameters were
calculated by the method of Cremer and Pople [REF]. Normal PRO rings
approximately show a so-called envelope conformation with the C-gamma atom
above the plane of the ring (phi=+72 degrees), or a half-chair conformation
with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees).
If phi deviates strongly from these values, this is indicative of a very
strange conformation for a PRO residue, and definitely requires a manual
check of the data. 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].
237 PRO ( 307-) A -127.3 half-chair C-delta/C-gamma (-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.
27 ASP ( 65-) A OD1 <-> 58 ARG ( 96-) A NH2 0.30 2.40 INTRA BF 250 GLU ( 320-) A O <-> 274 LYS ( 344-) A NZ 0.11 2.59 INTRA BF 143 ARG ( 181-) A NH1 <-> 314 HOH (2047 ) A O 0.08 2.62 INTRA BF 85 SER ( 123-) A N <-> 314 HOH (2022 ) A O 0.07 2.63 INTRA BL 109 ASP ( 147-) A OD1 <-> 162 SER ( 200-) A N 0.07 2.63 INTRA BL 265 GLN ( 335-) A NE2 <-> 314 HOH (2072 ) A O 0.05 2.65 INTRA BL 288 HIS ( 358-) A ND1 <-> 290 PHE ( 360-) A N 0.04 2.96 INTRA BL 119 LYS ( 157-) A NZ <-> 314 HOH (2036 ) A O 0.04 2.66 INTRA BF 248 VAL ( 318-) A O <-> 274 LYS ( 344-) A NZ 0.02 2.68 INTRA BF 258 GLY ( 328-) A N <-> 314 HOH (2074 ) A O 0.02 2.68 INTRA BL 152 ASP ( 190-) A O <-> 157 ASN ( 195-) A ND2 0.01 2.69 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.
219 ARG ( 260-) A -6.51 199 TYR ( 240-) A -6.35 254 LYS ( 324-) A -6.15 146 HIS ( 184-) A -5.90 40 ASN ( 78-) A -5.53 249 ASN ( 319-) A -5.32 198 HIS ( 239-) A -5.25 64 GLU ( 102-) 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.
89 VAL ( 127-) A -2.57 182 ALA ( 220-) A -2.55
Chain identifier: A
Water, ion, and hydrogenbond related checks
Warning: Buried unsatisfied hydrogen bond donors
The buried hydrogen bond donors listed in the table below have a hydrogen
atom that is not involved in a hydrogen bond in the optimized hydrogen bond
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.
83 CYS ( 121-) A N 108 MET ( 146-) A N 174 SER ( 212-) A OG 190 SER ( 231-) A OG 196 GLY ( 237-) A N 222 ILE ( 263-) A N 236 CYS ( 277-) A N 241 PHE ( 311-) A N 259 VAL ( 329-) A N 260 PHE ( 330-) A N 282 LEU ( 352-) A N
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.
1 GLU ( 39-) A OE2
165 GLU ( 203-) A H-bonding suggests Gln 298 GLU ( 368-) 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 : -0.428 2nd generation packing quality : -0.666 Ramachandran plot appearance : -0.137 chi-1/chi-2 rotamer normality : -1.526 Backbone conformation : 0.081
Bond lengths : 0.660 (tight) Bond angles : 0.887 Omega angle restraints : 0.542 (tight) Side chain planarity : 1.172 Improper dihedral distribution : 1.187 B-factor distribution : 0.893 Inside/Outside distribution : 1.009
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 : 2.20
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.2 2nd generation packing quality : -0.2 Ramachandran plot appearance : 1.0 chi-1/chi-2 rotamer normality : -0.2 Backbone conformation : 0.1
Bond lengths : 0.660 (tight) Bond angles : 0.887 Omega angle restraints : 0.542 (tight) Side chain planarity : 1.172 Improper dihedral distribution : 1.187 B-factor distribution : 0.893 Inside/Outside distribution : 1.009 ==============
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.