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.
382 PO4 ( 499-) A - 383 GOL ( 401-) A - 384 GOL ( 402-) A - 385 GOL ( 403-) A - 386 GOL ( 404-) A - 387 GOL ( 405-) A - 388 GOL ( 406-) 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.
2 LYS ( 5-) A - 7 LYS ( 10-) A - 16 GLN ( 19-) A - 26 SER ( 29-) A - 106 GLN ( 109-) A - 108 ARG ( 111-) A - 150 THR ( 153-) A - 160 ASP ( 163-) A - 274 ASN ( 277-) A - 284 ILE ( 287-) A - 376 LYS ( 379-) 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.
2 LYS ( 5-) A - 7 LYS ( 10-) A - 16 GLN ( 19-) A - 26 SER ( 29-) A - 106 GLN ( 109-) A - 108 ARG ( 111-) A - 150 THR ( 153-) A - 160 ASP ( 163-) A - 274 ASN ( 277-) A - 284 ILE ( 287-) A - 376 LYS ( 379-) A - Delete overlapping entity 1 GLU ( 4-) A -
Overlapping residues or molecules (for short entities) are occasionally observed in the PDB. Often these are cases like, for example, two sugars that bind equally well in the same active site, are both seen overlapping in the density, and are both entered in the PDB file as separate entities. This can cause some false positive error messsages further down the validation path, and therefore the second of the overlapping entities has been deleted before the validation continued. If you want to validate both situations, make it two PDB files, one for each sugar. And fudge reality a bit by making the occupancy of the sugar atoms 1.0 in both cases, because many validation options are not executed on atoms with low occupancy. If you go for this two-file option, please make sure that any side chains that have alternate locations depending on the sugar bound are selected in each of the two cases in agreement with the sugar that you keep for validation in that particular file.
1 GLU ( 4-) A -
Non-validating, descriptive output paragraph
Note: Ramachandran plot
In this Ramachandran plot x-signs represent glycines, squares represent
prolines, and plus-signs represent the other residues. If too many plus-
signs fall outside the contoured areas then the molecule is poorly refined
(or worse). Proline can only occur in the narrow region around phi=-60 that
also falls within the other contour islands.
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: Occupancies atoms do not add up to 1.0.
In principle, the occupancy of all alternates of one atom should add up till
1.0. A valid exception is the missing atom (i.e. an atom not seen in the
electron density) that is allowed to have a 0.0 occupancy. Sometimes this
even happens when there are no alternate atoms given...
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.
1 GLU ( 4-) A 0.51 163 LYS ( 167-) A 0.15
Obviously, the temperature at which the X-ray data was collected has some importance too:
Crystal temperature (K) :100.000
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 : 5.50
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.
19 THR ( 23-) A CB OG1 1.50 4.3
11 HIS ( 15-) A CG ND1 CE1 113.26 7.7 11 HIS ( 15-) A ND1 CE1 NE2 106.19 -4.2 15 GLN ( 19-) A CB CG CD 105.58 -4.1 15 GLN ( 19-) A NE2 CD OE1 131.29 8.7 50 ASP ( 54-) A CA CB CG 119.96 7.4 58 ASP ( 62-) A CA CB CG 118.41 5.8 71 ASP ( 75-) A CA CB CG 116.78 4.2 103 ASN ( 107-) A CB CG ND2 110.00 -4.3 103 ASN ( 107-) A CB CG OD1 135.00 7.1 103 ASN ( 107-) A ND2 CG OD1 113.80 -8.8 107 ARG ( 111-) A CA CB CG 129.61 7.8 107 ARG ( 111-) A CG CD NE 119.78 5.5 137 ASP ( 141-) A CA CB CG 117.39 4.8 174 VAL ( 178-) A -C N CA 129.04 4.1 181 ASN ( 185-) A ND2 CG OD1 127.95 5.3 226 SER ( 230-) A -C N CA 132.28 5.9 229 ASN ( 233-) A CA CB CG 117.98 5.4 234 ASN ( 238-) A ND2 CG OD1 132.01 9.4 235 ALA ( 239-) A N CA CB 104.32 -4.1 251 GLU ( 255-) A N CA CB 117.33 4.0 257 LYS ( 261-) A CG CD CE 125.12 6.0 264 PRO ( 268-) A -CA -C N 123.41 4.3 270 ASP ( 274-) A CA CB CG 118.42 5.8 283 ILE ( 287-) A CA CB CG1 118.63 4.8 287 ASN ( 291-) A ND2 CG OD1 117.65 -4.9 293 HIS ( 297-) A NE2 CD2 CG 110.94 4.4 300 ASN ( 304-) A CA CB CG 116.89 4.3 313 HIS ( 317-) A NE2 CD2 CG 110.85 4.3 321 LYS ( 325-) A N CA CB 121.87 6.7 344 ARG ( 348-) A CA CB CG 123.84 4.9 344 ARG ( 348-) A CB CG CD 104.41 -4.8 347 VAL ( 351-) A C CA CB 118.72 4.5 369 ARG ( 373-) A CG CD NE 117.73 4.3 369 ARG ( 373-) A NH1 CZ NH2 111.73 -4.4 377 TYR ( 381-) A -O -C N 130.87 4.9 377 TYR ( 381-) A -C N CA 110.65 -6.1 377 TYR ( 381-) A N CA CB 103.19 -4.3
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.
321 LYS ( 325-) A CA -6.9 22.48 33.92 The average deviation= 1.490
77 ASN ( 81-) A 6.38 103 ASN ( 107-) A 6.19 350 GLU ( 354-) A 5.25 133 ASP ( 137-) 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.
255 PHE ( 259-) A -3.2 132 PRO ( 136-) A -2.8 34 ILE ( 38-) A -2.7 55 THR ( 59-) A -2.4 377 TYR ( 381-) A -2.4 328 PRO ( 332-) A -2.4 107 ARG ( 111-) A -2.3 335 GLY ( 339-) A -2.1 276 VAL ( 280-) A -2.1 228 ASN ( 232-) A -2.1 347 VAL ( 351-) A -2.1 105 GLN ( 109-) A -2.0 8 GLU ( 12-) A -2.0 204 SER ( 208-) 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.
8 GLU ( 12-) A Poor phi/psi 9 GLY ( 13-) A Poor phi/psi 33 ARG ( 37-) A omega poor 34 ILE ( 38-) A Poor phi/psi 52 ARG ( 56-) A omega poor 61 PHE ( 65-) A omega poor 79 LYS ( 83-) A omega poor 86 ARG ( 90-) A Poor phi/psi 93 ARG ( 97-) A omega poor 94 VAL ( 98-) A omega poor 96 ASP ( 100-) A Poor phi/psi 100 ILE ( 104-) A omega poor 131 ALA ( 135-) A PRO omega poor 136 TRP ( 140-) A omega poor 146 ASP ( 150-) A Poor phi/psi 171 LEU ( 175-) A omega poor 174 VAL ( 178-) A Poor phi/psi 204 SER ( 208-) A Poor phi/psi 224 PHE ( 228-) A Poor phi/psi 226 SER ( 230-) A Poor phi/psi 234 ASN ( 238-) A Poor phi/psi 236 SER ( 240-) A omega poor 240 ASN ( 244-) A omega poor 255 PHE ( 259-) A Poor phi/psi 267 LYS ( 271-) A Poor phi/psi 272 ARG ( 276-) A Poor phi/psi, omega poor 274 HIS ( 278-) A Poor phi/psi 298 ASN ( 302-) A Poor phi/psi 301 ASN ( 305-) A Poor phi/psi 306 SER ( 310-) A omega poor 307 ASP ( 311-) A Poor phi/psi 308 ILE ( 312-) A omega poor 336 ALA ( 340-) A omega poor 347 VAL ( 351-) A Poor phi/psi 354 VAL ( 358-) A omega poor chi-1/chi-2 correlation Z-score : -0.483
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!
3 VAL ( 7-) A 0 5 PHE ( 9-) A 0 7 ALA ( 11-) A 0 8 GLU ( 12-) A 0 16 LYS ( 20-) A 0 25 SER ( 29-) A 0 31 TYR ( 35-) A 0 33 ARG ( 37-) A 0 34 ILE ( 38-) A 0 35 PRO ( 39-) A 0 42 LYS ( 46-) A 0 53 HIS ( 57-) A 0 54 ASN ( 58-) A 0 55 THR ( 59-) A 0 59 GLN ( 63-) A 0 60 SER ( 64-) A 0 61 PHE ( 65-) A 0 74 LYS ( 78-) A 0 75 THR ( 79-) A 0 78 LYS ( 82-) A 0 79 LYS ( 83-) A 0 81 ALA ( 85-) A 0 92 SER ( 96-) A 0 94 VAL ( 98-) A 0 95 MET ( 99-) A 0And so on for a total of 184 lines.
Standard deviation of omega values : 7.188
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]
217 PRO ( 221-) A 0.19 LOW
132 PRO ( 136-) A -59.0 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.
90 LYS ( 94-) A A NZ <-> 388 HOH ( 796 ) A O 0.21 2.49 INTRA 74 LYS ( 78-) A NZ <-> 388 HOH ( 943 ) A O 0.20 2.50 INTRA BF 78 LYS ( 82-) A NZ <-> 388 HOH ( 894 ) A O 0.20 2.50 INTRA 384 GOL ( 403-) A A O2 <-> 388 HOH ( 825 ) A O 0.20 2.20 INTRA BL 142 LYS ( 146-) A NZ <-> 388 HOH (1049 ) A O 0.15 2.55 INTRA BF 123 THR ( 127-) A OG1 <-> 388 HOH ( 825 ) A O 0.12 2.28 INTRA 383 GOL ( 402-) A O1 <-> 388 HOH ( 982 ) A O 0.12 2.28 INTRA 130 LYS ( 134-) A A NZ <-> 388 HOH ( 780 ) A O 0.11 2.59 INTRA 348 ASP ( 352-) A O <-> 388 HOH ( 950 ) A O 0.10 2.30 INTRA BF 385 GOL ( 404-) A A O1 <-> 388 HOH ( 964 ) A O 0.10 2.30 INTRA 253 LYS ( 257-) A NZ <-> 388 HOH ( 871 ) A O 0.06 2.64 INTRA 370 HIS ( 374-) A ND1 <-> 388 HOH (1059 ) A B O 0.05 2.65 INTRA BL 37 MET ( 41-) A C <-> 99 CYS ( 103-) A SG 0.04 3.36 INTRA BL 351 THR ( 355-) A OG1 <-> 388 HOH (1046 ) A O 0.04 2.36 INTRA 273 ASN ( 277-) A A ND2 <-> 388 HOH ( 770 ) A O 0.04 2.66 INTRA 376 SER ( 380-) A C <-> 377 TYR ( 381-) A A CA 0.03 2.27 INTRA BL 6 LYS ( 10-) A A CD <-> 388 HOH ( 939 ) A O 0.03 2.77 INTRA 130 LYS ( 134-) A A CE <-> 388 HOH ( 780 ) A O 0.02 2.78 INTRA 15 GLN ( 19-) A A CD <-> 388 HOH (1022 ) A O 0.02 2.78 INTRA 38 CYS ( 42-) A SG <-> 99 CYS ( 103-) A C 0.02 3.38 INTRA BL 382 GOL ( 401-) A O3 <-> 388 HOH (1002 ) A O 0.02 2.38 INTRA BF 79 LYS ( 83-) A NZ <-> 388 HOH ( 614 ) A O 0.01 2.69 INTRA 303 TYR ( 307-) A OH <-> 388 HOH (1051 ) A A O 0.01 2.39 INTRA BL 257 LYS ( 261-) A CE <-> 388 HOH (1024 ) A O 0.01 2.79 INTRA BF 158 HIS ( 162-) A NE2 <-> 388 HOH ( 531 ) A O 0.01 2.69 INTRA BL 90 LYS ( 94-) A A CE <-> 388 HOH ( 879 ) A O 0.01 2.79 INTRA
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.
15 GLN ( 19-) A -6.05 303 TYR ( 307-) A -5.31 164 ASN ( 168-) A -5.28 11 HIS ( 15-) A -5.26 316 TYR ( 320-) A -5.20 86 ARG ( 90-) A -5.14 220 TYR ( 224-) A -5.08
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.
91 LEU ( 95-) A -3.48 346 ASN ( 350-) A -3.01 253 LYS ( 257-) A -2.91 16 LYS ( 20-) A -2.76
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.
388 HOH (1059 ) A B O 36.07 47.67 69.60
243 ASN ( 247-) 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.
33 ARG ( 37-) A NH2 39 THR ( 43-) A OG1 59 GLN ( 63-) A NE2 84 ASN ( 88-) A ND2 93 ARG ( 97-) A NE 93 ARG ( 97-) A NH2 101 VAL ( 105-) A N 170 MET ( 174-) A N 179 GLN ( 183-) A N 190 GLN ( 194-) A NE2 205 PHE ( 209-) A N 277 GLN ( 281-) A N 279 SER ( 283-) A OG 296 ALA ( 300-) A N 305 ARG ( 309-) A NH2 369 ARG ( 373-) A NH2
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.
96 ASP ( 100-) A OD2 103 ASN ( 107-) A OD1 325 ASP ( 329-) A OD1 325 ASP ( 329-) A OD2 370 HIS ( 374-) A ND1
The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.
380 K ( 450-) A -.- -.- Low probability ion. Occ=0.50
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.
388 HOH ( 517 ) A O 0.86 K 5 *1 388 HOH ( 527 ) A O 0.92 K 5 *1 388 HOH ( 533 ) A O 1.06 K 4 *1 388 HOH ( 622 ) A O 0.88 K 4 *1 388 HOH ( 627 ) A O 1.02 K 4 *1 388 HOH ( 632 ) A O 1.09 K 4 *1 388 HOH ( 650 ) A O 1.04 K 4 *1 388 HOH ( 700 ) A O 0.87 K 4 *1 Ion-B 388 HOH ( 774 ) A O 1.14 K 4 *1 Ion-B 388 HOH ( 821 ) A O 1.04 K 8 *1 388 HOH ( 916 ) A O 0.89 K 5 *1 Ion-B
137 ASP ( 141-) A H-bonding suggests Asn; Ligand-contact 145 ASP ( 149-) 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 : 0.312 2nd generation packing quality : -1.942 Ramachandran plot appearance : -0.662 chi-1/chi-2 rotamer normality : -0.483 Backbone conformation : -0.901
Bond lengths : 0.693 Bond angles : 1.192 Omega angle restraints : 1.307 (loose) Side chain planarity : 1.694 Improper dihedral distribution : 1.243 Inside/Outside distribution : 0.979
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 : 1.05
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.5 2nd generation packing quality : -1.6 Ramachandran plot appearance : -1.1 chi-1/chi-2 rotamer normality : -1.0 Backbone conformation : -1.1
Bond lengths : 0.693 Bond angles : 1.192 Omega angle restraints : 1.307 (loose) Side chain planarity : 1.694 Improper dihedral distribution : 1.243 Inside/Outside distribution : 0.979 ==============
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.