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.
603 ACT (1634-) A - 604 ACT (1635-) A - 605 ACT (1636-) A - 606 ACT (1637-) A - 607 ACT (1638-) A - 608 BMA (1633-) A - 609 PE4 (1629-) 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.
583 ASP ( 1-) P - 591 VAL ( 3-) P - 592 TYR ( 4-) P - 593 ILE ( 5-) P - 594 HIS ( 6-) P - 595 PRO ( 7-) P -
Warning: Groups attached to potentially hydrogenbonding atoms
Residues were observed with groups attached to (or very near to) atoms that
potentially can form hydrogen bonds. WHAT IF is not very good at dealing
with such exceptional cases (Mainly because it's author is not...). So be
warned that the hydrogenbonding-related analyses of these residues
might be in error.
For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.
585 VAL ( 3-) P - B N bound to 583 ASP ( 1-) P - A C 592 NAG (1631-) A - O4 bound to 593 NAG (1632-) A - C1 593 NAG (1632-) A - O4 bound to 602 BMA (1633-) A - C1
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.
574 PRO ( 617-) 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
Note: Ramachandran plot
Chain identifier: P
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'.
574 PRO ( 617-) A O 583 ASP ( 1-) P CG 583 ASP ( 1-) P OD1 583 ASP ( 1-) P OD2
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.
590 PHE ( 8-) P 584 PRO ( 7-) P
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.
583 ASP ( 1-) P 0.50 584 VAL ( 3-) P 0.50 585 TYR ( 4-) P 0.50 586 ILE ( 5-) P 0.50 587 HIS ( 6-) P 0.50 588 PRO ( 7-) P 0.50 589 NAG (1630-) 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
Warning: Low bond length variability
Bond lengths were found to deviate less than normal from the mean Engh and
Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS
Z-score given below is expected to be near 1.0 for a normally restrained
data set. The fact that it is lower than 0.667 in this structure might
indicate that too-strong restraints have been used in the refinement. This
can only be a problem for high resolution X-ray structures.
RMS Z-score for bond lengths: 0.356
RMS-deviation in bond distances: 0.008
Warning: Possible cell scaling problem
Comparison of bond distances with Engh and Huber [REF] standard values for
protein residues and Parkinson et al [REF] values for DNA/RNA shows a
significant systematic deviation. It could be that the unit cell used in
refinement was not accurate enough. The deformation matrix given below gives
the deviations found: the three numbers on the diagonal represent the
relative corrections needed along the A, B and C cell axis. These values are
1.000 in a normal case, but have significant deviations here (significant at
the 99.99 percent confidence level)
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
| 0.997120 -0.000013 -0.000073| | -0.000013 0.997322 0.000432| | -0.000073 0.000432 0.997123|Proposed new scale matrix
| 0.017750 0.000000 0.000001| | 0.000000 0.011844 -0.000005| | 0.000000 -0.000003 0.007486|With corresponding cell
A = 56.338 B = 84.433 C = 133.591 Alpha= 89.950 Beta= 90.005 Gamma= 90.001
The CRYST1 cell dimensions
A = 56.500 B = 84.660 C = 133.970 Alpha= 90.000 Beta= 90.000 Gamma= 90.000
(Under-)estimated Z-score: 9.404
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.
425 ARG ( 468-) A CB CG CD 105.26 -4.4
RMS Z-score for bond angles: 0.556
RMS-deviation in bond angles: 1.140
Warning: Torsion angle evaluation shows unusual residues
The residues listed in the table below contain bad or abnormal
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.
542 PRO ( 585-) A -2.9 438 TYR ( 481-) A -2.7 124 PRO ( 163-) A -2.5 586 ILE ( 5-) P -2.3 355 TYR ( 394-) A -2.3 478 ILE ( 521-) A -2.3 84 GLU ( 123-) A -2.1 474 SER ( 517-) A -2.1 201 LEU ( 240-) 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.
33 ASN ( 72-) A Poor phi/psi 84 GLU ( 123-) A Poor phi/psi 113 CYS ( 152-) A omega poor 123 GLU ( 162-) A PRO omega poor 124 PRO ( 163-) A omega poor 157 PHE ( 196-) A omega poor 232 PRO ( 271-) A omega poor 317 ALA ( 356-) A omega poor 321 TYR ( 360-) A Poor phi/psi 366 ALA ( 405-) A omega poor 392 ASN ( 431-) A Poor phi/psi 511 GLN ( 554-) A Poor phi/psi 538 ILE ( 581-) A omega poor 543 ASN ( 586-) A omega poor chi-1/chi-2 correlation Z-score : -1.093
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.
180 SER ( 219-) A 0.37 39 SER ( 78-) A 0.39
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!
32 THR ( 71-) A 0 69 GLN ( 108-) A 0 84 GLU ( 123-) A 0 85 ARG ( 124-) A 0 114 HIS ( 153-) A 0 115 PRO ( 154-) A 0 116 ASN ( 155-) A 0 122 LEU ( 161-) A 0 123 GLU ( 162-) A 0 125 ASP ( 164-) A 0 133 SER ( 172-) A 0 149 LYS ( 188-) A 0 175 VAL ( 214-) A 0 186 GLU ( 225-) A 0 220 TYR ( 259-) A 0 224 HIS ( 263-) A 0 234 HIS ( 273-) A 0 235 LEU ( 274-) A 0 240 TRP ( 279-) A 0 242 GLN ( 281-) A 0 243 THR ( 282-) A 0 244 TRP ( 283-) A 0 245 SER ( 284-) A 0 247 ILE ( 286-) A 0 251 VAL ( 290-) A 0And so on for a total of 163 lines.
454 PRO ( 497-) A 0.18 LOW
124 PRO ( 163-) A -52.6 half-chair C-beta/C-alpha (-54 degrees) 258 PRO ( 297-) A -65.1 envelop C-beta (-72 degrees) 273 PRO ( 312-) A 111.4 envelop C-beta (108 degrees) 294 PRO ( 333-) A 106.3 envelop C-beta (108 degrees) 542 PRO ( 585-) A -38.6 envelop C-alpha (-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.
591 NAG (1632-) A O4 <-> 600 BMA (1633-) A C1 0.95 1.45 INTRA B3 591 NAG (1632-) A C4 <-> 600 BMA (1633-) A C1 0.85 2.35 INTRA 425 ARG ( 468-) A NH2 <-> 470 HIS ( 513-) A O 0.27 2.43 INTRA BL 348 HIS ( 387-) A ND1 <-> 371 HIS ( 410-) A ND1 0.24 2.76 INTRA BL 156 GLN ( 195-) A NE2 <-> 602 HOH (2091 ) A O 0.20 2.50 INTRA 226 ASN ( 265-) A ND2 <-> 575 GLN ( 618-) A NE2 0.18 2.67 INTRA 33 ASN ( 72-) A ND2 <-> 589 NAG (1630-) A C2 0.15 2.05 INTRA B2 464 ASP ( 507-) A N <-> 465 PRO ( 508-) A CD 0.15 2.85 INTRA BL 468 LYS ( 511-) A NZ <-> 596 ACT (1635-) A CH3 0.11 2.99 INTRA 400 ASP ( 443-) A OD1 <-> 505 HIS ( 548-) A NE2 0.10 2.60 INTRA 121 GLN ( 160-) A NE2 <-> 602 HOH (2058 ) A O 0.09 2.61 INTRA 46 ASN ( 85-) A ND2 <-> 598 ACT (1637-) A O2 0.08 2.62 INTRA 469 PHE ( 512-) A N <-> 596 ACT (1635-) A CH3 0.08 3.02 INTRA 531 TRP ( 574-) A N <-> 532 PRO ( 575-) A CD 0.08 2.92 INTRA BL 399 HIS ( 442-) A ND1 <-> 602 HOH (2170 ) A O 0.06 2.64 INTRA 263 THR ( 302-) A OG1 <-> 602 HOH (2173 ) A O 0.06 2.34 INTRA 123 GLU ( 162-) A O <-> 304 LYS ( 343-) A NZ 0.06 2.64 INTRA 203 PRO ( 242-) A O <-> 207 ASN ( 246-) A ND2 0.06 2.64 INTRA BL 33 ASN ( 72-) A ND2 <-> 589 NAG (1630-) A N2 0.05 2.55 INTRA B3 427 ARG ( 470-) A NH2 <-> 441 GLU ( 484-) A OE1 0.05 2.65 INTRA 439 ASN ( 482-) A N <-> 602 HOH (2233 ) A O 0.05 2.65 INTRA BL 411 LYS ( 454-) A NZ <-> 602 HOH (2218 ) A O 0.05 2.65 INTRA BL 264 GLU ( 303-) A O <-> 268 LYS ( 307-) A N 0.04 2.66 INTRA 240 TRP ( 279-) A CH2 <-> 596 ACT (1635-) A C 0.04 3.16 INTRA 446 ARG ( 489-) A NH1 <-> 450 GLN ( 493-) A OE1 0.03 2.67 INTRA BL 217 HIS ( 256-) A ND1 <-> 602 HOH (2144 ) A O 0.03 2.67 INTRA 581 ASN ( 624-) A N <-> 602 HOH (2152 ) A O 0.02 2.68 INTRA 321 TYR ( 360-) A OH <-> 583 ASP ( 1-) P A N 0.02 2.68 INTRA 121 GLN ( 160-) A OE1 <-> 304 LYS ( 343-) A NZ 0.02 2.68 INTRA 443 TRP ( 486-) A NE1 <-> 464 ASP ( 507-) A OD2 0.02 2.68 INTRA BL 596 ACT (1635-) A O2 <-> 602 HOH (2070 ) A O 0.02 2.38 INTRA 224 HIS ( 263-) A ND1 <-> 602 HOH (2153 ) A O 0.01 2.69 INTRA BL 314 HIS ( 353-) A NE2 <-> 587 HIS ( 6-) P B O 0.01 2.69 INTRA 214 ARG ( 253-) A NE <-> 569 GLU ( 612-) A OE2 0.01 2.69 INTRA 244 TRP ( 283-) A N <-> 409 LEU ( 452-) A O 0.01 2.69 INTRA BL 213 ARG ( 252-) A NH2 <-> 570 LYS ( 613-) A O 0.01 2.69 INTRA 581 ASN ( 624-) A N <-> 582 SER ( 625-) A N 0.01 2.59 INTRA B3
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.
567 HIS ( 610-) A -6.16 570 LYS ( 613-) A -5.87 116 ASN ( 155-) A -5.82 460 GLN ( 503-) A -5.76 581 ASN ( 624-) A -5.70 576 TYR ( 619-) A -5.69 219 HIS ( 258-) A -5.55 223 GLN ( 262-) A -5.51 67 GLN ( 106-) A -5.49 450 GLN ( 493-) A -5.16 587 HIS ( 6-) P -5.15 227 LEU ( 266-) A -5.02
The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.
218 ARG ( 257-) A 220 - TYR 259- ( A) -4.75
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.
184 MET ( 223-) A -3.05 83 LEU ( 122-) A -2.91
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.
602 HOH (2019 ) A O 602 HOH (2113 ) A O 602 HOH (2176 ) A O 602 HOH (2177 ) A O 602 HOH (2223 ) A O 602 HOH (2276 ) A O 602 HOH (2277 ) A O 602 HOH (2280 ) A O Bound group on Asn; dont flip 33 ASN ( 72-) A Bound to: 589 NAG (1630-) A Bound group on Asn; dont flip 70 ASN ( 109-) A Bound to: 590 NAG (1631-) A Marked this atom as acceptor 592 CL (1626-) A CL Marked this atom as acceptor 594 CL (1628-) A CL Metal-coordinating Histidine residue 344 fixed to 1 Metal-coordinating Histidine residue 348 fixed to 1
52 HIS ( 91-) A 67 GLN ( 106-) A 209 HIS ( 248-) A 389 HIS ( 428-) A 567 HIS ( 610-) A 575 GLN ( 618-) A 581 ASN ( 624-) 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.
46 ASN ( 85-) A ND2 75 ARG ( 114-) A NH2 85 ARG ( 124-) A NH1 176 ASP ( 215-) A N 226 ASN ( 265-) A ND2 234 HIS ( 273-) A N 234 HIS ( 273-) A ND1 238 ASN ( 277-) A N 243 THR ( 282-) A N 245 SER ( 284-) A N 272 THR ( 311-) A N 309 ARG ( 348-) A NE 324 LYS ( 363-) A N 325 ASP ( 364-) A N 361 ALA ( 400-) A N 367 ASN ( 406-) A N 376 ASP ( 415-) A N 399 HIS ( 442-) A N 406 LYS ( 449-) A NZ 417 PHE ( 460-) A N 434 THR ( 477-) A OG1 446 ARG ( 489-) A NE 456 VAL ( 499-) A N 458 ARG ( 501-) A NH2 479 ARG ( 522-) A N 481 PHE ( 524-) A N 483 SER ( 526-) A OG 536 GLN ( 579-) A NE2 579 THR ( 622-) A N Only metal coordination for 344 HIS ( 383-) A NE2 Only metal coordination for 348 HIS ( 387-) A NE2 Only metal coordination for 372 GLU ( 411-) A OE1
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.
148 ASP ( 187-) A OD1 234 HIS ( 273-) A NE2 264 GLU ( 303-) A OE2 314 HIS ( 353-) A NE2 330 GLN ( 369-) A OE1 345 GLU ( 384-) A OE1 345 GLU ( 384-) A OE2 587 HIS ( 6-) P B 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+.
593 ZN (1627-) A -.- -.- Too few ligands (3)
148 ASP ( 187-) A H-bonding suggests Asn; but Alt-Rotamer 193 ASP ( 232-) A H-bonding suggests Asn; but Alt-Rotamer 264 GLU ( 303-) A H-bonding suggests Gln 282 ASP ( 321-) A H-bonding suggests Asn; but Alt-Rotamer 376 ASP ( 415-) A H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact 430 ASP ( 473-) A H-bonding suggests Asn
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 : -0.065 2nd generation packing quality : -1.075 Ramachandran plot appearance : 0.458 chi-1/chi-2 rotamer normality : -1.093 Backbone conformation : 0.014
Bond lengths : 0.356 (tight) Bond angles : 0.556 (tight) Omega angle restraints : 0.906 Side chain planarity : 0.288 (tight) Improper dihedral distribution : 0.516 B-factor distribution : 0.335 Inside/Outside distribution : 1.005
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 : 1.99
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.3 2nd generation packing quality : -0.7 Ramachandran plot appearance : 0.9 chi-1/chi-2 rotamer normality : -0.3 Backbone conformation : -0.2
Bond lengths : 0.356 (tight) Bond angles : 0.556 (tight) Omega angle restraints : 0.906 Side chain planarity : 0.288 (tight) Improper dihedral distribution : 0.516 B-factor distribution : 0.335 Inside/Outside distribution : 1.005 ==============
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.