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.
381 EV6 ( 393-) A -
Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.
108 ASP ( 106-) A -
In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.
108 ASP ( 106-) A -
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.
3 GLU ( 1-) A - CG 3 GLU ( 1-) A - CD 3 GLU ( 1-) A - OE1 3 GLU ( 1-) A - OE2 9 ARG ( 7-) A - CZ 9 ARG ( 7-) A - NH1 9 ARG ( 7-) A - NH2 66 ARG ( 64-) A - NE 66 ARG ( 64-) A - CZ 66 ARG ( 64-) A - NH1 66 ARG ( 64-) A - NH2 108 ASP ( 106-) A - A CG 108 ASP ( 106-) A - A OD1 108 ASP ( 106-) A - A OD2 109 LYS ( 107-) A - NZ 258 GLN ( 266-) A - CD 258 GLN ( 266-) A - OE1 258 GLN ( 266-) A - NE2 263 GLN ( 271-) A - CG 263 GLN ( 271-) A - CD 263 GLN ( 271-) A - OE1 263 GLN ( 271-) A - NE2 373 ASP ( 381-) A - CG 373 ASP ( 381-) A - OD1 373 ASP ( 381-) A - OD2
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'.
9 ARG ( 7-) A NE 109 LYS ( 107-) A CE 144 LYS ( 142-) A NZ 258 GLN ( 266-) A CG
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. In many cases the N- or C-terminal residues are too disordered to see. In case of the N-terminus, you can see from the residue numbers if there are missing residues, but at the C-terminus this is impossible. Therefore, often the position of the backbone nitrogen of the first residue missing at the C-terminal end is calculated and added to indicate that there are missing residues. As a single N causes validation trouble, we remove these single-N-residues before doing the validation. But, if you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or removed N is the cause.
378 ILE ( 386-) A
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.
79 GLU ( 77-) A 0.50 108 ASP ( 106-) A 1.50 173 HIS ( 181-) A 0.50
Obviously, the temperature at which the X-ray data was collected has some importance too:
Number of TLS groups mentione in PDB file header: 1
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
130 ARG ( 128-) A 339 ARG ( 347-) A
70 TYR ( 68-) A 176 TYR ( 184-) A 182 TYR ( 190-) A 212 TYR ( 220-) A
1 PHE ( -1-) A 249 PHE ( 257-) A 272 PHE ( 280-) A 314 PHE ( 322-) A 366 PHE ( 374-) A
6 ASP ( 4-) A 132 ASP ( 130-) A 140 ASP ( 138-) A 215 ASP ( 223-) A 303 ASP ( 311-) A 309 ASP ( 317-) A 355 ASP ( 363-) A
3 GLU ( 1-) A 19 GLU ( 17-) A 79 GLU ( 77-) A 81 GLU ( 79-) A 136 GLU ( 134-) A 211 GLU ( 219-) A 234 GLU ( 242-) 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.
157 CYS ( 155-) A SG -SG* 2.41 9.2 351 CYS ( 359-) A SG -SG* 2.41 9.2
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
| 0.998378 -0.000505 0.000758| | -0.000505 0.998276 -0.000512| | 0.000758 -0.000512 0.996671|Proposed new scale matrix
| 0.009834 0.005682 -0.000005| | 0.000006 0.011354 0.000006| | -0.000004 0.000003 0.005896|With corresponding cell
A = 101.720 B = 101.752 C = 169.617 Alpha= 90.094 Beta= 89.913 Gamma= 120.047
The CRYST1 cell dimensions
A = 101.880 B = 101.880 C = 170.181 Alpha= 90.000 Beta= 90.000 Gamma= 120.000
(Under-)estimated Z-score: 6.139
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.
3 GLU ( 1-) A CB CG CD 103.77 -5.2
3 GLU ( 1-) A 6 ASP ( 4-) A 19 GLU ( 17-) A 79 GLU ( 77-) A 81 GLU ( 79-) A 130 ARG ( 128-) A 132 ASP ( 130-) A 136 GLU ( 134-) A 140 ASP ( 138-) A 211 GLU ( 219-) A 215 ASP ( 223-) A 234 GLU ( 242-) A 303 ASP ( 311-) A 309 ASP ( 317-) A 339 ARG ( 347-) A 355 ASP ( 363-) 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.
268 PRO ( 276-) A -2.9 151 LEU ( 149-) A -2.4 306 THR ( 314-) A -2.4 77 LYS ( 75-) A -2.4 359 THR ( 367-) A -2.3 259 LEU ( 267-) A -2.2 304 VAL ( 312-) A -2.2 292 ILE ( 300-) A -2.1 189 TRP ( 197-) A -2.1 61 THR ( 59-) A -2.1 66 ARG ( 64-) A -2.1 130 ARG ( 128-) A -2.1 187 ARG ( 195-) A -2.1 298 LEU ( 306-) A -2.1 40 PHE ( 38-) A -2.0 135 LEU ( 133-) 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.
6 ASP ( 4-) A Poor phi/psi 24 SER ( 22-) A PRO omega poor 39 ASN ( 37-) A omega poor 46 PRO ( 44-) A Poor phi/psi 77 LYS ( 75-) A omega poor 117 TRP ( 115-) A omega poor 119 GLY ( 117-) A omega poor 124 ALA ( 122-) A omega poor 130 ARG ( 128-) A PRO omega poor 154 LEU ( 152-) A omega poor 165 SER ( 173-) A omega poor 189 TRP ( 197-) A Poor phi/psi, omega poor 201 ASN ( 209-) A Poor phi/psi 204 ASP ( 212-) A omega poor 206 LYS ( 214-) A Poor phi/psi 214 TYR ( 222-) A omega poor 225 ASN ( 233-) A omega poor 285 ASN ( 293-) A Poor phi/psi 303 ASP ( 311-) A Poor phi/psi, omega poor 304 VAL ( 312-) A Poor phi/psi 305 ALA ( 313-) A omega poor 308 GLN ( 316-) A omega poor 309 ASP ( 317-) A Poor phi/psi 332 GLY ( 340-) A omega poor 355 ASP ( 363-) A Poor phi/psi 364 GLY ( 372-) A PRO omega poor 370 ASP ( 378-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -2.612
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.
211 GLU ( 219-) 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!
5 VAL ( 3-) A 0 6 ASP ( 4-) A 0 7 ASN ( 5-) A 0 9 ARG ( 7-) A 0 11 LYS ( 9-) A 0 12 SER ( 10-) A 0 14 GLN ( 12-) A 0 16 TYR ( 14-) A 0 22 VAL ( 20-) A 0 24 SER ( 22-) A 0 25 PRO ( 23-) A 0 26 PRO ( 24-) A 0 35 THR ( 33-) A 0 44 ALA ( 42-) A 0 50 LEU ( 48-) A 0 51 HIS ( 49-) A 0 56 ARG ( 54-) A 0 66 ARG ( 64-) A 0 74 THR ( 72-) A 0 75 GLN ( 73-) A 0 85 ASP ( 83-) A 0 91 HIS ( 89-) A 0 94 ASN ( 92-) A 0 98 ARG ( 96-) A 0 104 ILE ( 102-) A 0And so on for a total of 183 lines.
Standard deviation of omega values : 7.125
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]
26 PRO ( 24-) A 0.19 LOW 184 PRO ( 192-) A 0.45 HIGH
268 PRO ( 276-) A -18.9 half-chair C-alpha/N (-18 degrees) 294 PRO ( 302-) A 123.6 half-chair C-beta/C-alpha (126 degrees) 365 PRO ( 373-) A -60.7 half-chair C-beta/C-alpha (-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.
259 LEU ( 267-) A CD1 <-> 311 CYS ( 319-) A CB 0.51 2.69 INTRA BF 77 LYS ( 75-) A NZ <-> 79 GLU ( 77-) A OE2 0.35 2.35 INTRA 198 VAL ( 206-) A CG1 <-> 205 LEU ( 213-) A CD1 0.31 2.89 INTRA BF 302 GLU ( 310-) A CG <-> 303 ASP ( 311-) A N 0.30 2.70 INTRA BF 127 GLU ( 125-) A OE2 <-> 187 ARG ( 195-) A NH1 0.27 2.43 INTRA BF 1 PHE ( -1-) A N <-> 381 HOH ( 414 ) A O 0.23 2.47 INTRA BF 56 ARG ( 54-) A NH1 <-> 81 GLU ( 79-) A OE1 0.19 2.51 INTRA BL 381 HOH ( 404 ) A O <-> 381 HOH ( 457 ) A O 0.19 2.01 INTRA BF 158 GLY ( 156-) A CA <-> 162 VAL ( 170-) A CG1 0.19 3.01 INTRA BF 140 ASP ( 138-) A OD1 <-> 339 ARG ( 347-) A NH2 0.18 2.52 INTRA 22 VAL ( 20-) A CG1 <-> 101 ILE ( 99-) A CD1 0.18 3.02 INTRA BL 147 HIS ( 145-) A NE2 <-> 381 HOH ( 445 ) A O 0.18 2.52 INTRA BF 203 GLN ( 211-) A C <-> 204 ASP ( 212-) A O 0.18 2.42 INTRA BF 259 LEU ( 267-) A CD1 <-> 311 CYS ( 319-) A SG 0.18 3.22 INTRA BF 204 ASP ( 212-) A CG <-> 205 LEU ( 213-) A N 0.17 2.83 INTRA BF 302 GLU ( 310-) A CG <-> 303 ASP ( 311-) A OD1 0.17 2.63 INTRA BF 237 VAL ( 245-) A O <-> 241 LYS ( 249-) A N 0.17 2.53 INTRA BF 12 SER ( 10-) A N <-> 160 ALA ( 168-) A O 0.17 2.53 INTRA BF 198 VAL ( 206-) A CB <-> 205 LEU ( 213-) A CD1 0.16 3.04 INTRA BF 69 VAL ( 67-) A CG1 <-> 78 TRP ( 76-) A CZ3 0.14 3.06 INTRA BL 42 VAL ( 40-) A O <-> 104 ILE ( 102-) A N 0.13 2.57 INTRA BL 302 GLU ( 310-) A O <-> 304 VAL ( 312-) A N 0.12 2.58 INTRA BF 158 GLY ( 156-) A CA <-> 162 VAL ( 170-) A CB 0.11 3.09 INTRA BF 32 LEU ( 30-) A O <-> 121 LEU ( 119-) A N 0.11 2.59 INTRA BL 132 ASP ( 130-) A OD1 <-> 134 SER ( 132-) A N 0.10 2.60 INTRA BFAnd so on for a total of 58 lines.
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.
376 TYR ( 384-) A -7.79 66 ARG ( 64-) A -7.46 75 GLN ( 73-) A -6.74 357 PHE ( 365-) A -6.32 147 HIS ( 145-) A -6.31 248 LYS ( 256-) A -6.20 214 TYR ( 222-) A -5.80 308 GLN ( 316-) A -5.72 341 ARG ( 349-) A -5.65 130 ARG ( 128-) A -5.58 257 GLU ( 265-) A -5.54 94 ASN ( 92-) A -5.54 145 GLN ( 143-) A -5.41 263 GLN ( 271-) A -5.27 70 TYR ( 68-) A -5.23 369 LEU ( 377-) A -5.22 358 ARG ( 366-) A -5.18 52 ARG ( 50-) A -5.12 51 HIS ( 49-) A -5.11 254 TRP ( 262-) A -5.10 186 ARG ( 194-) A -5.04
The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.
51 HIS ( 49-) A 53 - TYR 51- ( A) -4.81
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.
109 LYS ( 107-) A -2.93
The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.
55 GLN ( 53-) A - 58 LEU ( 56-) A -1.82
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.
381 HOH ( 425 ) A O Marked this atom as acceptor 380 EV6 ( 393-) A CL11
75 GLN ( 73-) A 296 GLN ( 304-) 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.
27 GLN ( 25-) A NE2 45 ALA ( 43-) A N 47 HIS ( 45-) A NE2 52 ARG ( 50-) A N 107 SER ( 105-) A OG 109 LYS ( 107-) A N 112 ILE ( 110-) A N 113 ASN ( 111-) A N 119 GLY ( 117-) A N 125 TYR ( 123-) A OH 130 ARG ( 128-) A NE 132 ASP ( 130-) A N 139 PHE ( 137-) A N 170 GLY ( 178-) A N 187 ARG ( 195-) A N 190 TYR ( 198-) A N 197 ARG ( 205-) A N 216 LYS ( 224-) A N 217 SER ( 225-) A N 231 LYS ( 239-) A N 246 THR ( 254-) A N 254 TRP ( 262-) A N 287 SER ( 295-) A OG 309 ASP ( 317-) A N 316 ILE ( 324-) A N 343 ARG ( 351-) A NH2 376 TYR ( 384-) A N
118 GLU ( 116-) A H-bonding suggests Gln 215 ASP ( 223-) A H-bonding suggests Asn 355 ASP ( 363-) A H-bonding suggests Asn; but Alt-Rotamer
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 : -1.278 2nd generation packing quality : -2.596 Ramachandran plot appearance : -2.261 chi-1/chi-2 rotamer normality : -2.612 Backbone conformation : -1.252
Bond lengths : 0.722 Bond angles : 0.780 Omega angle restraints : 1.295 (loose) Side chain planarity : 0.528 (tight) Improper dihedral distribution : 0.839 B-factor distribution : 0.588 Inside/Outside distribution : 1.004
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 : 2.60
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.6 2nd generation packing quality : -1.2 Ramachandran plot appearance : 0.1 chi-1/chi-2 rotamer normality : -0.4 Backbone conformation : -0.6
Bond lengths : 0.722 Bond angles : 0.780 Omega angle restraints : 1.295 (loose) Side chain planarity : 0.528 (tight) Improper dihedral distribution : 0.839 B-factor distribution : 0.588 Inside/Outside distribution : 1.004 ==============
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.