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.
389 XLS ( 393-) A -
The left-hand residue has been removed, and the right hand residue has been kept for validation. Be aware that WHAT IF calls everything a residue. Two residues are defined as overlapping if the two smallest ellipsoids encompassing the two residues interpenetrate by 33% of the longest axis. Many artefacts can actually cause this problem. The most often observed reason is alternative residue conformations expressed by two residues that accidentally both got 1.0 occupancy for all atoms.
387 XLS ( 393-) A - 388 MG ( 391-) A - 1.3
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'.
67 GLU ( 69-) A CD 67 GLU ( 69-) A OE1 67 GLU ( 69-) A OE2 68 GLU ( 70-) A CG 68 GLU ( 70-) A CD 68 GLU ( 70-) A OE1 68 GLU ( 70-) A OE2
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.
386 GLY ( 388-) 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.
2 GLN ( 4-) A 0.50 6 GLU ( 8-) A 0.50 8 ARG ( 10-) A 0.50 21 ARG ( 23-) A 0.50 30 ARG ( 32-) A 0.50 36 GLU ( 38-) A 0.50 39 ARG ( 41-) A 0.50 43 GLU ( 45-) A 0.50 66 ARG ( 68-) A 0.80 71 LYS ( 73-) A 0.50 173 ASP ( 175-) A 0.50 205 GLU ( 207-) A 0.50 326 GLU ( 328-) A 0.50 385 ARG ( 387-) A 0.50
Obviously, the temperature at which the X-ray data was collected has some importance too:
Temperature cannot be read from the PDB file. This most likely means that
the temperature is listed as NULL (meaning unknown) in the PDB file.
Error: The B-factors of bonded atoms show signs of over-refinement
For each of the bond types in a protein a distribution was derived for the
difference between the square roots of the B-factors of the two atoms. All
bonds in the current protein were scored against these distributions. The
number given below is the RMS Z-score over the structure. For a structure
with completely restrained B-factors within residues, this value will be
around 0.35, for extremely high resolution structures refined with free
isotropic B-factors this number is expected to be near 1.0. Any value over
1.5 is sign of severe over-refinement of B-factors.
RMS Z-score : 1.736 over 2714 bonds
Average difference in B over a bond : 3.48
RMS difference in B over a bond : 4.99
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.
15 THR ( 17-) A CB OG1 1.51 4.6 21 ARG ( 23-) A CD NE 1.38 -4.5 50 THR ( 52-) A CA CB 1.62 4.4 52 HIS ( 54-) A CA C 1.61 4.3 80 THR ( 82-) A CA CB 1.65 5.9 89 THR ( 91-) A CA CB 1.61 4.1 103 THR ( 105-) A CA CB 1.61 4.2 130 GLU ( 132-) A CG CD 1.41 -4.2 138 ARG ( 140-) A N CA 1.54 4.5 219 GLU ( 221-) A N CA 1.55 5.0 228 HIS ( 230-) A ND1 CE1 1.39 5.7 264 ARG ( 266-) A CD NE 1.38 -4.5 293 ASP ( 295-) A N CA 1.54 4.4 338 ARG ( 340-) A CD NE 1.36 -5.5 383 GLY ( 385-) A N CA 1.52 4.1
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
| 1.003691 0.002854 0.002159| | 0.002854 0.985068 0.000046| | 0.002159 0.000046 0.990071|Proposed new scale matrix
| 0.010527 -0.000030 -0.000023| | -0.000029 0.010155 0.000000| | -0.000021 0.000000 0.009714|With corresponding cell
A = 94.993 B = 98.478 C = 102.940 Alpha= 90.000 Beta= 89.752 Gamma= 89.671
The CRYST1 cell dimensions
A = 94.640 B = 99.970 C = 103.970 Alpha= 90.000 Beta= 90.000 Gamma= 90.000
(Under-)estimated Z-score: 22.904
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.
6 GLU ( 8-) A CA CB CG 126.58 6.2 6 GLU ( 8-) A CB CG CD 120.74 4.8 8 ARG ( 10-) A CA CB CG 125.74 5.8 15 THR ( 17-) A C CA CB 118.35 4.3 19 GLN ( 21-) A NE2 CD OE1 127.08 4.5 21 ARG ( 23-) A CG CD NE 130.66 11.9 21 ARG ( 23-) A CD NE CZ 138.56 9.4 22 ASP ( 24-) A C CA CB 121.03 5.8 22 ASP ( 24-) A CA CB CG 121.17 8.6 28 THR ( 30-) A CA CB OG1 103.17 -4.3 30 ARG ( 32-) A CG CD NE 118.74 4.8 32 LEU ( 34-) A N CA CB 101.21 -5.5 33 ASP ( 35-) A CA CB CG 118.93 6.3 36 GLU ( 38-) A CB CG CD 126.63 8.3 43 GLU ( 45-) A CA CB CG 127.80 6.8 50 THR ( 52-) A CG2 CB OG1 117.43 4.1 52 HIS ( 54-) A C CA CB 101.12 -4.7 53 ASP ( 55-) A CA CB CG 117.43 4.8 71 LYS ( 73-) A CA CB CG 122.74 4.3 72 ARG ( 74-) A CD NE CZ 136.30 8.1 74 ARG ( 76-) A C CA CB 117.84 4.1 79 ASP ( 81-) A CA CB CG 119.11 6.5 80 THR ( 82-) A CA CB OG1 101.86 -5.2 90 ASN ( 92-) A ND2 CG OD1 117.84 -4.8 96 VAL ( 98-) A -CA -C N 124.56 4.2And so on for a total of 100 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.
167 VAL ( 169-) A CB 6.2 -24.85 -32.96 194 VAL ( 196-) A CB -6.3 -41.19 -32.96 The average deviation= 1.994
99 ASP ( 101-) A 5.46 39 ARG ( 41-) A 5.25 243 ASP ( 245-) A 5.20 139 GLU ( 141-) A 4.75
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.
88 THR ( 90-) A -2.5 286 PHE ( 288-) A -2.4 8 ARG ( 10-) A -2.3 245 ASN ( 247-) A -2.2 184 GLU ( 186-) A -2.1
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 ARG ( 10-) A Poor phi/psi 51 PHE ( 53-) A omega poor 92 PHE ( 94-) A Poor phi/psi 184 GLU ( 186-) A Poor phi/psi, PRO omega poor 191 LEU ( 193-) A Poor phi/psi 332 ARG ( 334-) A Poor phi/psi 369 ALA ( 371-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -0.620
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!
9 PHE ( 11-) A 0 14 TRP ( 16-) A 0 15 THR ( 17-) A 0 18 TRP ( 20-) A 0 19 GLN ( 21-) A 0 21 ARG ( 23-) A 0 22 ASP ( 24-) A 0 24 PHE ( 26-) A 0 26 ASP ( 28-) A 0 29 ARG ( 31-) A 0 44 LEU ( 46-) A 0 47 HIS ( 49-) A 0 59 PHE ( 61-) A 0 82 MET ( 84-) A 0 85 PRO ( 87-) A 0 86 MET ( 88-) A 0 91 LEU ( 93-) A 0 92 PHE ( 94-) A 0 99 ASP ( 101-) A 0 102 PHE ( 104-) A 0 103 THR ( 105-) A 0 104 ALA ( 106-) A 0 105 ASN ( 107-) A 0 127 LEU ( 129-) A 0 130 GLU ( 132-) A 0And so on for a total of 115 lines.
Standard deviation of omega values : 3.292
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]
3 PRO ( 5-) A 0.07 LOW 23 PRO ( 25-) A 0.08 LOW 185 PRO ( 187-) A 0.48 HIGH
85 PRO ( 87-) A 43.2 envelop C-delta (36 degrees) 180 PRO ( 182-) A 38.8 envelop C-delta (36 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.
388 XLS ( 393-) A O1 <-> 389 HOH ( 721 ) A O 1.58 0.72 INTRA 388 XLS ( 393-) A C1 <-> 389 HOH ( 721 ) A O 1.01 1.69 INTRA 213 ASN ( 215-) A ND2 <-> 241 HIS ( 243-) A ND1 0.27 2.73 INTRA BL 39 ARG ( 41-) A NH2 <-> 389 HOH ( 564 ) A O 0.20 2.50 INTRA 329 ARG ( 331-) A NH2 <-> 389 HOH ( 537 ) A O 0.13 2.57 INTRA 150 ARG ( 152-) A NH1 <-> 389 HOH ( 652 ) A O 0.13 2.57 INTRA 326 GLU ( 328-) A OE2 <-> 329 ARG ( 331-) A NH2 0.12 2.58 INTRA 191 LEU ( 193-) A N <-> 192 PRO ( 194-) A CD 0.10 2.90 INTRA BL 287 LYS ( 289-) A NZ <-> 389 HOH ( 642 ) A O 0.10 2.60 INTRA 52 HIS ( 54-) A NE2 <-> 388 XLS ( 393-) A C5 0.05 3.05 INTRA 40 ARG ( 42-) A NH2 <-> 389 HOH ( 665 ) A O 0.05 2.65 INTRA BF 321 ASP ( 323-) A OD2 <-> 385 ARG ( 387-) A A NH2 0.05 2.65 INTRA BL 47 HIS ( 49-) A NE2 <-> 389 HOH ( 581 ) A O 0.04 2.66 INTRA 94 HIS ( 96-) A CD2 <-> 96 VAL ( 98-) A N 0.04 3.06 INTRA BL 75 GLN ( 77-) A NE2 <-> 389 HOH ( 624 ) A O 0.02 2.68 INTRA 40 ARG ( 42-) A NH2 <-> 389 HOH ( 599 ) A O 0.02 2.68 INTRA BF 66 ARG ( 68-) A NH2 <-> 389 HOH ( 480 ) A O 0.02 2.68 INTRA BL 220 GLN ( 222-) A NE2 <-> 389 HOH ( 494 ) A O 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.
24 PHE ( 26-) A -7.12 59 PHE ( 61-) A -6.58 235 TRP ( 237-) A -6.26 252 TYR ( 254-) A -6.20 21 ARG ( 23-) A -6.06 138 ARG ( 140-) A -5.59 98 LYS ( 100-) A -5.49 170 GLN ( 172-) A -5.43 142 GLU ( 144-) A -5.26 30 ARG ( 32-) A -5.05
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.
222 ALA ( 224-) A -2.68
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.
389 HOH ( 622 ) A O 30.58 22.93 67.76 389 HOH ( 632 ) A O 19.19 61.77 27.81 389 HOH ( 643 ) A O 17.26 54.58 30.59 389 HOH ( 660 ) A O 20.41 85.15 45.50 389 HOH ( 705 ) A O 20.93 83.99 37.47 389 HOH ( 717 ) A O 0.46 48.32 41.14 389 HOH ( 720 ) A O 23.78 33.89 18.92 389 HOH ( 756 ) A O 24.99 61.34 29.03
389 HOH ( 700 ) A O Metal-coordinating Histidine residue 218 fixed to 1
69 HIS ( 71-) A 75 GLN ( 77-) A 90 ASN ( 92-) A 94 HIS ( 96-) A 183 ASN ( 185-) A 220 GLN ( 222-) A 228 HIS ( 230-) A 232 GLN ( 234-) A 245 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.
10 THR ( 12-) A OG1 14 TRP ( 16-) A N 20 GLY ( 22-) A N 51 PHE ( 53-) A N 74 ARG ( 76-) A A NE 86 MET ( 88-) A N 120 ASN ( 122-) A ND2 135 TRP ( 137-) A NE1 147 LYS ( 149-) A N 150 ARG ( 152-) A NH1 174 ILE ( 176-) A N 183 ASN ( 185-) A N 186 ARG ( 188-) A N 193 THR ( 195-) A N 193 THR ( 195-) A OG1 203 ARG ( 205-) A A NE 213 ASN ( 215-) A ND2 242 ILE ( 244-) A N 329 ARG ( 331-) A NH1 335 GLU ( 337-) A N 338 ARG ( 340-) A NH2 Only metal coordination for 179 GLU ( 181-) A OE2 Only metal coordination for 215 GLU ( 217-) A OE1 Only metal coordination for 285 ASP ( 287-) A OD2
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.
52 HIS ( 54-) A NE2
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+.
386 MG ( 391-) A -.- -.- Low probability ion. Occ=0.47 387 MG ( 392-) A -.- -.- Low probability ion. Occ=0.27
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.
389 HOH ( 410 ) A O 1.03 K 4 389 HOH ( 413 ) A O 0.85 K 4 389 HOH ( 500 ) A O 0.91 K 6 389 HOH ( 621 ) A O 0.86 NA 4 ION-B 389 HOH ( 746 ) A O 1.04 K 4
130 GLU ( 132-) A H-bonding suggests Gln 188 ASP ( 190-) 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 : -0.700 2nd generation packing quality : 0.621 Ramachandran plot appearance : 0.033 chi-1/chi-2 rotamer normality : -0.620 Backbone conformation : 0.499
Bond lengths : 1.227 Bond angles : 1.616 Omega angle restraints : 0.599 (tight) Side chain planarity : 1.808 Improper dihedral distribution : 1.661 (loose) B-factor distribution : 1.736 (loose) Inside/Outside distribution : 1.050
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 : 1.60
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.5 2nd generation packing quality : -0.4 Ramachandran plot appearance : -0.4 chi-1/chi-2 rotamer normality : -1.0 Backbone conformation : 0.3
Bond lengths : 1.227 Bond angles : 1.616 Omega angle restraints : 0.599 (tight) Side chain planarity : 1.808 Improper dihedral distribution : 1.661 (loose) B-factor distribution : 1.736 (loose) Inside/Outside distribution : 1.050 ==============
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.