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.
261 RCS ( 302-) A - Atom types 262 RCS ( 303-) A - Atom types 264 DMS ( 314-) A - OK
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.
20 ILE ( 22-) A - 50 ASP ( 52-) 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.
20 ILE ( 22-) A - 50 ASP ( 52-) A -
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.
1 HIS ( 3-) 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'.
1 HIS ( 3-) A N 1 HIS ( 3-) A CG 1 HIS ( 3-) A ND1 1 HIS ( 3-) A CD2 1 HIS ( 3-) A CE1 1 HIS ( 3-) A NE2
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.
128 PHE ( 131-) A 0.80 130 LYS ( 133-) A 0.50
Obviously, the temperature at which the X-ray data was collected has some importance too:
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
56 ARG ( 58-) A
112 TYR ( 114-) A
128 PHE ( 131-) A
236 GLU ( 239-) 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.
121 TRP ( 123-) A NE1 CE2 1.42 4.6 192 PRO ( 195-) A CD N 1.53 4.4
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
| 0.995838 0.000321 0.001162| | 0.000321 1.004737 0.001411| | 0.001162 0.001411 0.992895|Proposed new scale matrix
| 0.023765 -0.000016 0.006160| | -0.000008 0.023903 -0.000034| | -0.000017 -0.000020 0.014431|With corresponding cell
A = 42.066 B = 41.836 C = 71.566 Alpha= 89.853 Beta= 104.465 Gamma= 89.963
The CRYST1 cell dimensions
A = 42.243 B = 41.639 C = 72.107 Alpha= 90.000 Beta= 104.550 Gamma= 90.000
(Under-)estimated Z-score: 8.586
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.
2 HIS ( 4-) A CA CB CG 107.89 -5.9 2 HIS ( 4-) A CG ND1 CE1 109.90 4.3 2 HIS ( 4-) A CB CG CD2 135.77 5.1 7 LYS ( 9-) A CB CG CD 120.71 4.1 8 HIS ( 10-) A CA CB CG 108.66 -5.1 8 HIS ( 10-) A CG ND1 CE1 110.00 4.4 17 ASP ( 19-) A CA CB CG 107.18 -5.4 24 GLU ( 26-) A -O -C N 131.14 5.1 25 ARG ( 27-) A CG CD NE 122.52 7.1 25 ARG ( 27-) A NE CZ NH2 111.66 -4.4 32 ASP ( 34-) A CA CB CG 104.04 -8.6 34 HIS ( 36-) A CA CB CG 108.81 -5.0 34 HIS ( 36-) A CB CG CD2 135.01 4.5 41 SER ( 43-) A -O -C N 113.41 -6.0 41 SER ( 43-) A -CA -C N 125.70 4.8 44 PRO ( 46-) A -O -C N 115.36 -4.7 45 LEU ( 47-) A -O -C N 130.24 4.5 68 PHE ( 70-) A CA CB CG 109.65 -4.1 74 LYS ( 76-) A CA CB CG 125.00 5.4 87 ARG ( 89-) A CB CG CD 105.32 -4.4 90 GLN ( 92-) A NE2 CD OE1 117.94 -4.7 91 PHE ( 93-) A CA CB CG 120.05 6.2 92 HIS ( 94-) A CA CB CG 109.27 -4.5 99 ASP ( 101-) A CA CB CG 117.94 5.3 105 HIS ( 107-) A CG ND1 CE1 110.45 4.8 109 LYS ( 111-) A -C N CA 129.09 4.1 109 LYS ( 111-) A CA C O 113.85 -4.1 127 ASP ( 130-) A CA CB CG 120.46 7.9 127 ASP ( 130-) A OD2 CG OD1 110.13 -5.3 133 GLN ( 136-) A NE2 CD OE1 127.68 5.1 156 LYS ( 159-) A CG CD CE 122.39 4.8 159 ASP ( 162-) A -C N CA 112.87 -4.9 159 ASP ( 162-) A CA C O 113.35 -4.4 159 ASP ( 162-) A CB CG OD2 109.07 -4.1 175 ASN ( 178-) A CA CB CG 108.36 -4.2 184 GLU ( 187-) A C CA CB 101.78 -4.4 216 SER ( 219-) A -C N CA 113.79 -4.4 227 ASN ( 230-) A CB CG ND2 124.00 5.1 228 PHE ( 231-) A CA CB CG 118.02 4.2 229 ASN ( 232-) A ND2 CG OD1 118.38 -4.2 235 GLU ( 238-) A -O -C N 130.36 4.6 240 ASP ( 243-) A CA CB CG 107.43 -5.2 241 ASN ( 244-) A ND2 CG OD1 118.00 -4.6 250 ASN ( 253-) A CA C O 113.73 -4.2 250 ASN ( 253-) A CA CB CG 117.58 5.0 251 ARG ( 254-) A -O -C N 134.17 7.0
56 ARG ( 58-) A 236 GLU ( 239-) 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.
199 PRO ( 202-) A -2.2 173 PHE ( 176-) A -2.1 160 VAL ( 163-) A -2.1 148 GLY ( 151-) A -2.1 183 PRO ( 186-) A -2.1 43 LYS ( 45-) 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.
27 SER ( 29-) A PRO omega poor 55 LEU ( 57-) A omega poor 74 LYS ( 76-) A Poor phi/psi 90 GLN ( 92-) A omega poor 109 LYS ( 111-) A Poor phi/psi 175 ASN ( 178-) A Poor phi/psi 194 SER ( 197-) A omega poor 198 PRO ( 201-) A PRO omega poor 200 LEU ( 203-) A Poor phi/psi 204 VAL ( 207-) A omega poor 212 PRO ( 215-) A omega poor 240 ASP ( 243-) A Poor phi/psi 249 LYS ( 252-) A Poor phi/psi chi-1/chi-2 correlation Z-score : 0.433
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 TRP ( 5-) A 0 5 TYR ( 7-) A 0 8 HIS ( 10-) A 0 18 PHE ( 20-) A 0 22 LYS ( 24-) A 0 25 ARG ( 27-) A 0 26 GLN ( 28-) A 0 27 SER ( 29-) A 0 36 ALA ( 38-) A 0 43 LYS ( 45-) A 0 48 SER ( 50-) A 0 50 ASP ( 52-) A 0 51 GLN ( 53-) A 0 52 ALA ( 54-) A 0 60 ASN ( 62-) A 0 62 HIS ( 64-) A 0 70 ASP ( 72-) A 0 71 SER ( 73-) A 0 73 ASP ( 75-) A 0 74 LYS ( 76-) A 0 75 ALA ( 77-) A 0 78 LYS ( 80-) A 0 81 PRO ( 83-) A 0 83 ASP ( 85-) A 0 89 ILE ( 91-) A 0And so on for a total of 121 lines.
For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.
In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!
4 GLY ( 6-) A 1.58 13
234 PRO ( 237-) A 0.49 HIGH 244 PRO ( 247-) A 0.12 LOW
11 PRO ( 13-) A 103.2 envelop C-beta (108 degrees) 19 PRO ( 21-) A -114.6 envelop C-gamma (-108 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.
165 LYS ( 168-) A NZ <-> 265 HOH ( 472 ) A O 0.21 2.49 INTRA 2 HIS ( 4-) A ND1 <-> 265 HOH ( 691 ) A O 0.21 2.49 INTRA BF 254 LYS ( 257-) A NZ <-> 265 HOH ( 613 ) A O 0.20 2.50 INTRA 78 LYS ( 80-) A NZ <-> 265 HOH ( 587 ) A O 0.20 2.50 INTRA 34 HIS ( 36-) A ND1 <-> 265 HOH ( 496 ) A O 0.20 2.50 INTRA 25 ARG ( 27-) A NH2 <-> 265 HOH ( 612 ) A O 0.18 2.52 INTRA 156 LYS ( 159-) A NZ <-> 265 HOH ( 692 ) A O 0.16 2.54 INTRA 211 GLU ( 214-) A OE2 <-> 265 HOH ( 584 ) A O 0.14 2.26 INTRA 184 GLU ( 187-) A OE1 <-> 265 HOH ( 598 ) A O 0.13 2.27 INTRA 24 GLU ( 26-) A OE2 <-> 265 HOH ( 733 ) A O 0.11 2.29 INTRA 5 TYR ( 7-) A O <-> 265 HOH ( 634 ) A O 0.11 2.29 INTRA 172 ASP ( 175-) A A OD2 <-> 265 HOH ( 568 ) A O 0.10 2.30 INTRA 50 ASP ( 52-) A A OD1 <-> 265 HOH ( 616 ) A O 0.10 2.30 INTRA 32 ASP ( 34-) A OD2 <-> 265 HOH ( 668 ) A O 0.10 2.30 INTRA 44 PRO ( 46-) A O <-> 265 HOH ( 671 ) A O 0.10 2.30 INTRA 73 ASP ( 75-) A OD2 <-> 265 HOH ( 635 ) A O 0.10 2.30 INTRA 73 ASP ( 75-) A CG <-> 87 ARG ( 89-) A NH2 0.10 3.00 INTRA 123 THR ( 125-) A OG1 <-> 265 HOH ( 638 ) A O 0.10 2.30 INTRA 159 ASP ( 162-) A OD2 <-> 265 HOH ( 549 ) A O 0.10 2.30 INTRA 262 RCS ( 303-) A O4 <-> 265 HOH ( 538 ) A O 0.10 2.30 INTRA 251 ARG ( 254-) A N <-> 265 HOH ( 703 ) A O 0.10 2.60 INTRA 13 HIS ( 15-) A ND1 <-> 16 LYS ( 18-) A NZ 0.09 2.91 INTRA BL 105 HIS ( 107-) A NE2 <-> 191 TYR ( 194-) A OH 0.09 2.61 INTRA BL 62 HIS ( 64-) A ND1 <-> 265 HOH ( 433 ) A O 0.07 2.63 INTRA BL 1 HIS ( 3-) A CA <-> 2 HIS ( 4-) A CA 0.06 2.74 INTRA B3 250 ASN ( 253-) A OD1 <-> 265 HOH ( 729 ) A O 0.06 2.34 INTRA 236 GLU ( 239-) A OE2 <-> 265 HOH ( 488 ) A O 0.05 2.35 INTRA 1 HIS ( 3-) A O <-> 265 HOH ( 711 ) A O 0.04 2.36 INTRA 262 RCS ( 303-) A C8 <-> 265 HOH ( 693 ) A O 0.03 2.77 INTRA BF 49 TYR ( 51-) A OH <-> 120 HIS ( 122-) A NE2 0.03 2.67 INTRA BL 250 ASN ( 253-) A C <-> 265 HOH ( 703 ) A O 0.02 2.78 INTRA 74 LYS ( 76-) A CB <-> 75 ALA ( 77-) A N 0.01 2.69 INTRA B3 56 ARG ( 58-) A NE <-> 67 GLU ( 69-) A OE1 0.01 2.69 INTRA BL 24 GLU ( 26-) A OE1 <-> 265 HOH ( 681 ) A O 0.01 2.39 INTRA 7 LYS ( 9-) A CE <-> 265 HOH ( 732 ) A O 0.01 2.79 INTRA BF 43 LYS ( 45-) A N <-> 265 HOH ( 637 ) A O 0.01 2.69 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.
8 HIS ( 10-) A -6.42 2 HIS ( 4-) A -6.06 98 LEU ( 100-) A -5.24
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.
1 HIS ( 3-) A -3.37 244 PRO ( 247-) A -2.71 16 LYS ( 18-) A -2.63 8 HIS ( 10-) A -2.51
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.
265 HOH ( 462 ) A O 34.85 2.47 22.83 265 HOH ( 486 ) A O 34.08 -5.43 24.49 265 HOH ( 573 ) A O 21.93 -16.14 -2.09 265 HOH ( 744 ) A O 34.10 -10.12 5.20
265 HOH ( 623 ) A O 265 HOH ( 700 ) A O Metal-coordinating Histidine residue 92 fixed to 1 Metal-coordinating Histidine residue 94 fixed to 1 Metal-coordinating Histidine residue 117 fixed to 1
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.
3 TRP ( 5-) A N 29 VAL ( 31-) A N 72 GLN ( 74-) A N 98 LEU ( 100-) A N 179 ARG ( 182-) A NH1 197 THR ( 200-) A N 201 LEU ( 204-) A N 227 ASN ( 230-) A ND2 241 ASN ( 244-) A ND2 242 TRP ( 245-) A N 257 PHE ( 260-) A N Only metal coordination for 94 HIS ( 96-) A NE2 Only metal coordination for 117 HIS ( 119-) A ND1
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.
265 HOH ( 454 ) A O 0.93 K 5 265 HOH ( 479 ) A O 0.99 K 4 H2O-B 265 HOH ( 488 ) A O 1.04 NA 4 H2O-B 265 HOH ( 499 ) A O 0.86 K 4 265 HOH ( 507 ) A O 1.05 K 5 265 HOH ( 641 ) A O 0.92 K 5 Ion-B 265 HOH ( 668 ) A O 0.89 NA 6 Ion-B
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 : 0.054 2nd generation packing quality : 0.332 Ramachandran plot appearance : -1.398 chi-1/chi-2 rotamer normality : 0.433 Backbone conformation : -1.117
Bond lengths : 0.879 Bond angles : 1.437 Omega angle restraints : 1.192 Side chain planarity : 1.090 Improper dihedral distribution : 0.997 B-factor distribution : 1.248 Inside/Outside distribution : 0.960
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 : 1.20
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.3 2nd generation packing quality : -0.4 Ramachandran plot appearance : -1.7 chi-1/chi-2 rotamer normality : -0.1 Backbone conformation : -1.3
Bond lengths : 0.879 Bond angles : 1.437 Omega angle restraints : 1.192 Side chain planarity : 1.090 Improper dihedral distribution : 0.997 B-factor distribution : 1.248 Inside/Outside distribution : 0.960 ==============
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.