WHAT IF Check report

This file was created 2013-12-26 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

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.

Verification log for pdb2xg1.ent

Checks that need to be done early-on in validation

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: P 21 21 21
Number of matrices in space group: 4
Highest polymer chain multiplicity in structure: 2
Highest polymer chain multiplicity according to SEQRES: 2
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 4
Z, symmetry, and molecular multiplicity disagree
Could it be that Z must be: 8

Error: Matthews Coefficient (Vm) very high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Numbers this high are almost always caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all).

Molecular weight of all polymer chains: 841086.875
Volume of the Unit Cell V= 59251464.0
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 35.223
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 2.960 And remember, a matrix counting problem has been reported earlier already

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

5262 A3P   (1493-)  A  -

Administrative problems that can generate validation failures

Warning: Strange inter-chain connections detected

The pairs of residues listed in the table below seem covalently bound while belonging to different chains in the PDB file.

Sometimes this is unavoidable (e.g. if two protein chains are covalently connected via a Cys-Cys or other bond). But if it can be avoided (e.g. often we observe sugars with one chain identifier connected to protein chains with another chain identifier), it should be avoided. WHAT IF and WHAT-CHECK try to deal with all exceptions thrown at it, but if you want these programs to work optimally (i.e. make as few false error messages as is possible) you should help them by getting as much of the administration correct as is humanly possible.

  33 OGUA  (  35-)  A  -   N2  3161 SER   ( 115-)  L  -   CB
2488 VAL   (  80-)  G  -   C   4056 OADE  (  12-)  X  -   N1
2489 GLY   (  81-)  G  -   N   4056 OADE  (  12-)  X  -   C2
2489 GLY   (  81-)  G  -   CA  4056 OADE  (  12-)  X  -   C2
2489 GLY   (  81-)  G  -   CA  4056 OADE  (  12-)  X  -   N3
3937 OADE  (  35-)  V  -   C6  4061 OURA  (  17-)  X  -   O4
3937 OADE  (  35-)  V  -   N6  4061 OURA  (  17-)  X  -   O4
3937 OADE  (  35-)  V  -   C2  4062 OGUA  (  18-)  X  -   C6
3937 OADE  (  35-)  V  -   C2  4062 OGUA  (  18-)  X  -   O6

Warning: Strange inter-chain connections could NOT be corrected

Often inter-chain connections are simple administrative problems. In this case not. The observed inter-chain connection(s) either are real, or they are too strange for WHAT IF to correct. Human inspection seems required.

Warning: Overlapping residues or molecules

This molecule contains residues or molecules that overlap too much while not being (administrated as) alternate atom/residue pairs. The residues or molecules listed in the table below have been removed before the validation continued.

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.

  33 OGUA  (  35-)  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: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: Q

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: U

Note: Ramachandran plot

Chain identifier: Y

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'.

1468 OGUA  (1494-)  A      P
1468 OGUA  (1494-)  A      OP1
1468 OGUA  (1494-)  A      OP2

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 OGUA  (   3-)  A    High
   2 OURA  (   4-)  A    High
   3 OURA  (   5-)  A    High
   4 OGUA  (   6-)  A    High
   5 OGUA  (   7-)  A    High
   6 OADE  (   8-)  A    High
   7 OGUA  (   9-)  A    High
   8 OADE  (  10-)  A    High
   9 OGUA  (  11-)  A    High
  10 OURA  (  12-)  A    High
  11 OURA  (  13-)  A    High
  12 OURA  (  14-)  A    High
  13 OGUA  (  15-)  A    High
  14 OADE  (  16-)  A    High
  15 OURA  (  17-)  A    High
  16 OCYT  (  18-)  A    High
  17 OCYT  (  19-)  A    High
  18 OURA  (  20-)  A    High
  19 OGUA  (  21-)  A    High
  20 OGUA  (  22-)  A    High
  21 OCYT  (  23-)  A    High
  22 OURA  (  24-)  A    High
  23 OCYT  (  25-)  A    High
  24 OADE  (  26-)  A    High
  25 OGUA  (  27-)  A    High
And so on for a total of 4012 lines.

Warning: C-terminal nitrogen atoms detected.

It is becoming habit to indicate that a residue is not the true C-terminus by including only the backbone N of the next residue. This has been observed in this PDB file.

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.

4078 THR   (  15-)  Y
3900 LYS   (  26-)  U
3776 LYS   (  88-)  S
3621 ARG   ( 101-)  Q
3521 ALA   (  84-)  P
3289 GLY   ( 119-)  M
3171 ALA   ( 126-)  L
2928 VAL   ( 101-)  J
2308 GLU   ( 155-)  E
2157 ARG   ( 209-)  D
1949 ILE   ( 208-)  C
1742 GLU   ( 241-)  B

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

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 number.

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

Note: B-factor plot

Chain identifier: Q

Note: B-factor plot

Chain identifier: R

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: T

Note: B-factor plot

Chain identifier: U

Note: B-factor plot

Chain identifier: Y

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

2064 ARG   ( 118-)  D
2099 ARG   ( 153-)  D
3079 ARG   (  38-)  L
3848 ARG   (  89-)  T

Warning: Tyrosine convention problem

The tyrosine residues listed in the table below have their chi-2 not between -90.0 and 90.0

1532 TYR   (  31-)  B
1700 TYR   ( 199-)  B
1769 TYR   (  29-)  C
1973 TYR   (  27-)  D
2052 TYR   ( 106-)  D
2153 TYR   ( 207-)  D
2283 TYR   ( 133-)  E
2354 TYR   (  50-)  F
2367 TYR   (  63-)  F
2448 TYR   (  44-)  G
2489 TYR   (  85-)  G
2555 TYR   ( 151-)  G
2558 TYR   ( 154-)  G
2811 TYR   ( 114-)  I
2822 TYR   ( 125-)  I
2963 TYR   (  50-)  K
3143 TYR   ( 102-)  L
3185 TYR   (  21-)  M
3187 TYR   (  23-)  M
4061 TYR   (   9-)  Y

Warning: Phenylalanine convention problem

The phenylalanine residues listed in the table below have their chi-2 not between -90.0 and 90.0.

1518 PHE   (  17-)  B
1529 PHE   (  28-)  B
1653 PHE   ( 152-)  B
1664 PHE   ( 163-)  B
2039 PHE   (  93-)  D
2715 PHE   (  18-)  I
2734 PHE   (  37-)  I
2798 PHE   ( 101-)  I
2834 PHE   (  11-)  J
3356 PHE   (  15-)  O
3675 PHE   (  81-)  R

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

1561 ASP   (  60-)  B
1667 ASP   ( 166-)  B
1696 ASP   ( 195-)  B
1699 ASP   ( 198-)  B
1776 ASP   (  36-)  C
1923 ASP   ( 183-)  C
2387 ASP   (  83-)  F
2419 ASP   (  15-)  G
2449 ASP   (  45-)  G
2633 ASP   (  73-)  H
2757 ASP   (  60-)  I
2772 ASP   (  75-)  I
2835 ASP   (  12-)  J
3024 ASP   ( 111-)  K
3150 ASP   ( 109-)  L
3180 ASP   (  16-)  M
3247 ASP   (  83-)  M
3362 ASP   (  21-)  O
3459 ASP   (  29-)  P
3470 ASP   (  40-)  P
3558 ASP   (  46-)  Q
3627 ASP   (  33-)  R
3691 ASP   (  12-)  S
4056 ASP   (   4-)  Y

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

1510 GLU   (   9-)  B
1553 GLU   (  52-)  B
1617 GLU   ( 116-)  B
1630 GLU   ( 129-)  B
1644 GLU   ( 143-)  B
1671 GLU   ( 170-)  B
1822 GLU   (  82-)  C
1830 GLU   (  90-)  C
1845 GLU   ( 105-)  C
1970 GLU   (  24-)  D
2027 GLU   (  81-)  D
2091 GLU   ( 145-)  D
2109 GLU   ( 163-)  D
2138 GLU   ( 192-)  D
2151 GLU   ( 205-)  D
2158 GLU   (   8-)  E
2261 GLU   ( 111-)  E
2287 GLU   ( 137-)  E
2299 GLU   ( 149-)  E
2326 GLU   (  22-)  F
2346 GLU   (  42-)  F
2382 GLU   (  78-)  F
2471 GLU   (  67-)  G
2478 GLU   (  74-)  G
2543 GLU   ( 139-)  G
2546 GLU   ( 142-)  G
2582 GLU   (  22-)  H
2594 GLU   (  34-)  H
2609 GLU   (  49-)  H
2683 GLU   ( 123-)  H
2906 GLU   (  83-)  J
2918 GLU   (  95-)  J
3054 GLU   (  13-)  L
3196 GLU   (  32-)  M
3327 GLU   (  46-)  N
3348 GLU   (   7-)  O
3382 GLU   (  41-)  O
3424 GLU   (  83-)  O
3484 GLU   (  54-)  P
3560 GLU   (  48-)  Q
3622 GLU   (  28-)  R
3632 GLU   (  38-)  R
3640 GLU   (  46-)  R
3696 GLU   (  17-)  S
3700 GLU   (  21-)  S
3706 GLU   (  27-)  S
3752 GLU   (  73-)  S
3765 GLU   (  86-)  S
3819 GLU   (  60-)  T

Warning: Phosphate group convention problem

The nucleic acid residues listed in the table below have the OP1 and OP2 atom names exchanged.

   2 OURA  (   4-)  A
   5 OGUA  (   7-)  A
  47 OURA  (  49-)  A
  48 OADE  (  50-)  A
  49 OADE  (  51-)  A
  50 OGUA  (  52-)  A
  60 OURA  (  62-)  A
  61 OCYT  (  63-)  A
  63 OURA  (  65-)  A
  75 OGUA  (  79-)  A
  76 OGUA  (  80-)  A
 108 OGUA  ( 117-)  A
 113 OGUA  ( 122-)  A
 165 OURA  ( 173-)  A
 201 OADE  ( 197-)  A
 254 OURA  ( 261-)  A
 255 OADE  ( 262-)  A
 300 OCYT  ( 307-)  A
 318 OADE  ( 325-)  A
 336 OURA  ( 343-)  A
 337 OADE  ( 344-)  A
 338 OCYT  ( 345-)  A
 339 OGUA  ( 346-)  A
 340 OGUA  ( 347-)  A
 341 OGUA  ( 348-)  A
And so on for a total of 124 lines.

Geometric checks

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.

 394 OCYT  ( 401-)  A      C4'  C3'   1.58    5.5
3943 OGUA  (  53-)  V      C1'  N9    1.38   -8.3
4045 OADE  (  13-)  X      P    O5'   1.67    7.2
4045 OADE  (  13-)  X      C4'  O4'   1.50    4.1
4045 OADE  (  13-)  X      C3'  C2'   1.60    6.6
4045 OADE  (  13-)  X      C1'  N9    1.38   -8.4
4045 OADE  (  13-)  X      N9   C8    1.33   -5.2
4046 OADE  (  14-)  X      P    O5'   1.66    7.1
4046 OADE  (  14-)  X      O5'  C5'   1.59    9.1
4046 OADE  (  14-)  X      N9   C4    1.33   -6.6
4046 OADE  (  14-)  X      N7   C5    1.36   -4.5
4046 OADE  (  14-)  X      N3   C4    1.30   -7.2
4046 OADE  (  14-)  X      C6   N1    1.32   -4.5
4047 OADE  (  15-)  X      C3'  O3'   1.35   -5.4
4047 OADE  (  15-)  X      C5'  C4'   1.57    4.9
4047 OADE  (  15-)  X      C1'  C2'   1.46   -6.4
4047 OADE  (  15-)  X      C3'  C2'   1.47   -4.9
4047 OADE  (  15-)  X      N9   C4    1.34   -5.5
4047 OADE  (  15-)  X      O2'  C2'   1.36   -4.2
4048 OADE  (  16-)  X      C3'  O3'   1.28  -10.5
4048 OADE  (  16-)  X      C4'  C3'   1.43   -8.7
4048 OADE  (  16-)  X      C4'  O4'   1.37   -6.5
4048 OADE  (  16-)  X      O4'  C1'   1.34   -6.0
4048 OADE  (  16-)  X      C1'  C2'   1.45   -7.7
4048 OADE  (  16-)  X      C3'  C2'   1.46   -5.9
4048 OADE  (  16-)  X      N7   C5    1.35   -6.3
4048 OADE  (  16-)  X      C5   C4    1.35   -4.3
4048 OADE  (  16-)  X      C5   C6    1.34   -6.8
4048 OADE  (  16-)  X      O2'  C2'   1.33   -6.4
4049 OURA  (  17-)  X      O4'  C1'   1.33   -6.7
4049 OURA  (  17-)  X      C1'  C2'   1.48   -4.5
4049 OURA  (  17-)  X      C3'  C2'   1.48   -4.3
4049 OURA  (  17-)  X      C1'  N1    1.41   -6.1
4049 OURA  (  17-)  X      C2'  O2'   1.36   -4.2
4050 OGUA  (  18-)  X      C4'  O4'   1.40   -4.2
4050 OGUA  (  18-)  X      O4'  C1'   1.35   -5.0
4050 OGUA  (  18-)  X      N9   C4    1.34   -4.4
4050 OGUA  (  18-)  X      N1   C2    1.42    5.6
4050 OGUA  (  18-)  X      C5   C6    1.37   -5.2
4051 OGUA  (  19-)  X      C8   N7    1.27   -6.4

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

 |  0.999132 -0.000013  0.000360|
 | -0.000013  0.999471 -0.000117|
 |  0.000360 -0.000117  0.999135|
Proposed new scale matrix

 |  0.004720  0.000000 -0.000002|
 |  0.000000  0.002206  0.000000|
 |  0.000000  0.000000  0.001624|
With corresponding cell

    A    = 211.860  B   = 453.275  C    = 615.610
    Alpha=  90.006  Beta=  89.983  Gamma=  90.004

The CRYST1 cell dimensions

    A    = 212.041  B   = 453.514  C    = 616.103
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 565.603
(Under-)estimated Z-score: 17.528

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.

   1 OGUA  (   3-)  A      N9   C8   N7  113.81    5.4
   4 OGUA  (   6-)  A      N9   C8   N7  113.46    4.7
   7 OGUA  (   9-)  A      N9   C8   N7  113.45    4.7
   9 OGUA  (  11-)  A      N9   C8   N7  113.51    4.8
  13 OGUA  (  15-)  A      N9   C8   N7  113.25    4.3
  19 OGUA  (  21-)  A      N9   C8   N7  113.18    4.2
  20 OGUA  (  22-)  A      N9   C8   N7  113.15    4.1
  25 OGUA  (  27-)  A      N9   C8   N7  113.16    4.1
  26 OGUA  (  28-)  A      N9   C8   N7  113.26    4.3
  27 OGUA  (  29-)  A      N9   C8   N7  113.19    4.2
  33 OGUA  (  35-)  A      N9   C8   N7  113.52    4.8
  36 OGUA  (  38-)  A      N9   C8   N7  113.48    4.8
  40 OGUA  (  42-)  A      N9   C8   N7  113.19    4.2
  42 OGUA  (  44-)  A      N9   C8   N7  113.21    4.2
  44 OGUA  (  46-)  A      N9   C8   N7  113.46    4.7
  50 OGUA  (  52-)  A      N9   C8   N7  113.22    4.2
  59 OGUA  (  61-)  A      N9   C8   N7  113.13    4.1
  64 OGUA  (  66-)  A      N9   C8   N7  113.13    4.1
  67 OGUA  (  69-)  A      N9   C8   N7  113.13    4.1
  73 OGUA  (  77-)  A      N9   C8   N7  113.13    4.1
  74 OGUA  (  78-)  A      N9   C8   N7  113.18    4.2
  75 OGUA  (  79-)  A      N9   C8   N7  113.24    4.3
  76 OGUA  (  80-)  A      N9   C8   N7  113.22    4.2
  86 OGUA  (  93-)  A      N9   C8   N7  113.13    4.1
  88 OGUA  (  97-)  A      N9   C8   N7  113.16    4.1
And so on for a total of 575 lines.

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

1510 GLU   (   9-)  B
1553 GLU   (  52-)  B
1561 ASP   (  60-)  B
1617 GLU   ( 116-)  B
1630 GLU   ( 129-)  B
1644 GLU   ( 143-)  B
1667 ASP   ( 166-)  B
1671 GLU   ( 170-)  B
1696 ASP   ( 195-)  B
1699 ASP   ( 198-)  B
1776 ASP   (  36-)  C
1822 GLU   (  82-)  C
1830 GLU   (  90-)  C
1845 GLU   ( 105-)  C
1923 ASP   ( 183-)  C
1970 GLU   (  24-)  D
2027 GLU   (  81-)  D
2064 ARG   ( 118-)  D
2091 GLU   ( 145-)  D
2099 ARG   ( 153-)  D
2109 GLU   ( 163-)  D
2138 GLU   ( 192-)  D
2151 GLU   ( 205-)  D
2158 GLU   (   8-)  E
2261 GLU   ( 111-)  E
And so on for a total of 77 lines.

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

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.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

4063 PRO   (  11-)  Y      N     -9.4   -33.24    -2.48
The average deviation= 0.660

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

1557 ARG   (  56-)  B    6.13
3771 ALA   (  12-)  T    5.35
3579 LYS   (  67-)  Q    5.23
3835 ALA   (  76-)  T    4.97
2098 SER   ( 152-)  D    4.88
1673 ILE   ( 172-)  B    4.87
1610 SER   ( 109-)  B    4.80
2549 ALA   ( 145-)  G    4.77
3156 LYS   ( 116-)  L    4.48
2018 GLU   (  72-)  D    4.46
1816 VAL   (  76-)  C    4.41
4066 LYS   (  14-)  Y    4.40
4055 LYS   (   3-)  Y    4.35
1728 GLY   ( 227-)  B    4.34
2551 ALA   ( 147-)  G    4.33
3409 ARG   (  68-)  O    4.20
3773 LYS   (  14-)  T    4.17
2182 VAL   (  32-)  E    4.16
4052 LYS   (   0-)  Y    4.12
2499 ARG   (  95-)  G    4.04
3064 ALA   (  23-)  L    4.04

Torsion-related checks

Error: Ramachandran Z-score very low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is very low.

Ramachandran Z-score : -6.769

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

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.

2584 THR   (  24-)  H    -3.3
4063 PRO   (  11-)  Y    -3.1
3832 HIS   (  73-)  T    -3.0
3794 THR   (  35-)  T    -2.9
2400 PRO   (  96-)  F    -2.8
3090 LEU   (  49-)  L    -2.8
1953 PRO   (   7-)  D    -2.8
2162 LEU   (  12-)  E    -2.8
3228 TRP   (  64-)  M    -2.7
1520 HIS   (  19-)  B    -2.7
3619 THR   (  25-)  R    -2.7
3044 THR   (   3-)  L    -2.7
2268 ILE   ( 118-)  E    -2.7
3065 LEU   (  24-)  L    -2.7
1518 PHE   (  17-)  B    -2.7
2391 ARG   (  87-)  F    -2.7
2954 THR   (  41-)  K    -2.6
3676 THR   (  82-)  R    -2.6
1701 ILE   ( 200-)  B    -2.6
2915 THR   (  92-)  J    -2.6
1679 ARG   ( 178-)  B    -2.6
3452 THR   (  22-)  P    -2.6
2344 VAL   (  40-)  F    -2.6
3062 VAL   (  21-)  L    -2.6
2860 PRO   (  37-)  J    -2.5
And so on for a total of 160 lines.

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

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.

1517 HIS   (  16-)  B  Poor phi/psi
1520 HIS   (  19-)  B  Poor phi/psi
1521 GLU   (  20-)  B  Poor phi/psi
1523 LYS   (  22-)  B  Poor phi/psi
1525 TRP   (  24-)  B  Poor phi/psi
1527 PRO   (  26-)  B  Poor phi/psi
1538 ASN   (  37-)  B  Poor phi/psi
1567 GLY   (  66-)  B  Poor phi/psi
1574 THR   (  73-)  B  Poor phi/psi
1575 LYS   (  74-)  B  Poor phi/psi
1576 LYS   (  75-)  B  Poor phi/psi
1584 MET   (  83-)  B  Poor phi/psi
1602 MET   ( 101-)  B  Poor phi/psi
1607 LYS   ( 106-)  B  Poor phi/psi
1615 ARG   ( 114-)  B  Poor phi/psi
1620 GLU   ( 119-)  B  Poor phi/psi
1626 PRO   ( 125-)  B  Poor phi/psi
1631 ARG   ( 130-)  B  Poor phi/psi
1632 PRO   ( 131-)  B  Poor phi/psi
1651 SER   ( 150-)  B  Poor phi/psi
1654 ARG   ( 153-)  B  Poor phi/psi
1662 ALA   ( 161-)  B  Poor phi/psi
1669 THR   ( 168-)  B  Poor phi/psi
1670 LYS   ( 169-)  B  Poor phi/psi
1682 PHE   ( 181-)  B  Poor phi/psi
And so on for a total of 330 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -4.200

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

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.

3392 HIS   (  51-)  O    0.35
3531 VAL   (  19-)  Q    0.36
3841 SER   (  82-)  T    0.38

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

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 OURA  (   5-)  A      0
   4 OGUA  (   6-)  A      0
   5 OGUA  (   7-)  A      0
   6 OADE  (   8-)  A      0
   7 OGUA  (   9-)  A      0
   8 OADE  (  10-)  A      0
   9 OGUA  (  11-)  A      0
  10 OURA  (  12-)  A      0
  11 OURA  (  13-)  A      0
  12 OURA  (  14-)  A      0
  13 OGUA  (  15-)  A      0
  14 OADE  (  16-)  A      0
  15 OURA  (  17-)  A      0
  16 OCYT  (  18-)  A      0
  17 OCYT  (  19-)  A      0
  18 OURA  (  20-)  A      0
  19 OGUA  (  21-)  A      0
  20 OGUA  (  22-)  A      0
  21 OCYT  (  23-)  A      0
  22 OURA  (  24-)  A      0
  23 OCYT  (  25-)  A      0
  24 OADE  (  26-)  A      0
  25 OGUA  (  27-)  A      0
  26 OGUA  (  28-)  A      0
  27 OGUA  (  29-)  A      0
And so on for a total of 2761 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 0.897

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

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!

2656 GLY   (  96-)  H   2.89   13
3545 GLY   (  33-)  Q   2.42   44
3427 GLY   (  86-)  O   2.00   23
3264 GLY   ( 100-)  M   1.99   53
2719 GLY   (  22-)  I   1.85   18
3862 GLY   ( 103-)  T   1.80   13
2843 ALA   (  20-)  J   1.72   15
1934 GLY   ( 194-)  C   1.69   24
1877 ALA   ( 137-)  C   1.69   25
3648 ARG   (  54-)  R   1.63   11
2812 GLY   ( 115-)  I   1.63   20
2703 GLY   (   6-)  I   1.61   75
3101 GLY   (  60-)  L   1.56   80
2603 GLY   (  43-)  H   1.55   80
2989 GLY   (  76-)  K   1.52   28

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]

2864 PRO   (  41-)  J    0.45 HIGH

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. 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].

1997 PRO   (  51-)  D   109.1 envelop C-beta (108 degrees)
2135 PRO   ( 189-)  D  -118.9 half-chair C-delta/C-gamma (-126 degrees)
2587 PRO   (  27-)  H   102.6 envelop C-beta (108 degrees)
4063 PRO   (  11-)  Y   -14.3 half-chair C-alpha/N (-18 degrees)
4065 PRO   (  13-)  Y    -4.1 envelop N (0 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short distance; each bump is listed in only one direction,

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.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

4467  MG   ( 444-)  Z     MG    <->  5012  MG   (3343-)  Z     MG    3.20    0.00  INTRA BL
  32 OCYT  (  34-)  A      N4   <->   531 OGUA  ( 550-)  A      C2   1.73    1.37  INTRA BF
  32 OCYT  (  34-)  A      N4   <->   531 OGUA  ( 550-)  A      N2   1.63    1.22  INTRA BF
  32 OCYT  (  34-)  A      N4   <->   531 OGUA  ( 550-)  A      N1   1.40    1.45  INTRA BF
  45 OCYT  (  47-)  A      O2   <->   358 OURA  ( 365-)  A      N3   1.34    1.36  INTRA BF
4819  MG   (3100-)  Z     MG    <->  4871  MG   (3164-)  Z     MG    1.33    1.87  INTRA BL
3946 OCYT  (  56-)  V      N4   <->  3947 OADE  (  57-)  V      N6   1.32    1.53  INTRA BF
4209  MG   ( 171-)  Z     MG    <->  4231  MG   ( 196-)  Z     MG    1.28    1.92  INTRA BL
4408  MG   ( 383-)  Z     MG    <->  4903  MG   (3202-)  Z     MG    1.19    2.01  INTRA BL
3265 GLN   ( 101-)  M      CG   <->  4281  MG   ( 250-)  M     MG    1.18    2.02  INTRA BL
4375  MG   ( 350-)  Z     MG    <->  4528  MG   ( 506-)  Z     MG    1.16    2.04  INTRA BL
4462  MG   ( 439-)  Z     MG    <->  4988  MG   (3309-)  Z     MG    1.14    2.06  INTRA BL
  32 OCYT  (  34-)  A      C4   <->   531 OGUA  ( 550-)  A      N2   1.13    1.97  INTRA BF
1491 OGUA  (1517-)  A      C5'  <->  4830  MG   (3111-)  A     MG    1.10    2.10  INTRA BL
1968 LYS   (  22-)  D      CG   <->  4076  ZN   (   1-)  D     ZN    1.04    2.16  INTRA BL
2019 ARG   (  73-)  D      CB   <->  4145  MG   (  88-)  D     MG    1.04    2.16  INTRA BF
3265 GLN   ( 101-)  M      CB   <->  4631  MG   (1761-)  M     MG    1.04    2.16  INTRA BL
4210  MG   ( 172-)  Z     MG    <->  4529  MG   ( 507-)  Z     MG    1.03    2.17  INTRA BL
1040 OCYT  (1060-)  A      C5   <->  1742 GLY   (   2-)  C      N    1.02    2.08  INTRA BL
4321  MG   ( 290-)  Z     MG    <->  4325  MG   ( 294-)  Z     MG    1.01    2.19  INTRA BL
 394 OCYT  ( 401-)  A      P    <->  2019 ARG   (  73-)  D      NH2  1.00    2.30  INTRA BF
  45 OCYT  (  47-)  A      O2   <->   358 OURA  ( 365-)  A      C2   1.00    1.80  INTRA BF
 818 OGUA  ( 837-)  A      C3'  <->  4629  MG   (1759-)  A     MG    1.00    2.20  INTRA BF
 383 OCYT  ( 390-)  A      C5   <->  4641  MG   (1798-)  A     MG    0.99    2.21  INTRA BF
1467 OADE  (1492-)  A      O3'  <->  5249 A3P   (1493-)  A      P2   0.99    1.61  INTRA BF
And so on for a total of 3305 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

Note: Inside/Outside RMS Z-score plot

Chain identifier: Q

Note: Inside/Outside RMS Z-score plot

Chain identifier: R

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Inside/Outside RMS Z-score plot

Chain identifier: U

Note: Inside/Outside RMS Z-score plot

Chain identifier: Y

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.

3760 ARG   (  81-)  S      -8.25
3888 ARG   (  24-)  U      -8.15
1819 ARG   (  79-)  C      -8.05
4061 TYR   (   9-)  Y      -8.00
2408 ARG   (   4-)  G      -7.89
1995 ARG   (  49-)  D      -7.84
3429 ARG   (  88-)  O      -7.84
3033 ARG   ( 120-)  K      -7.61
3268 ARG   ( 104-)  M      -7.60
2559 ARG   ( 155-)  G      -7.54
2763 ARG   (  66-)  I      -7.49
1988 GLN   (  42-)  D      -7.46
3458 ARG   (  28-)  P      -7.43
1950 TYR   (   4-)  D      -7.40
1912 ARG   ( 172-)  C      -7.25
4057 TYR   (   5-)  Y      -7.21
3512 GLN   (  82-)  P      -7.21
3759 TYR   (  80-)  S      -7.19
1996 ARG   (  50-)  D      -7.17
2483 ARG   (  79-)  G      -7.16
1984 TYR   (  38-)  D      -7.15
3263 ARG   (  99-)  M      -7.14
2407 ARG   (   3-)  G      -7.14
2628 ARG   (  68-)  H      -7.14
2874 ARG   (  51-)  J      -7.13
And so on for a total of 194 lines.

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.

1516 VAL   (  15-)  B      1518 - PHE     17- ( B)         -4.79
1537 ARG   (  36-)  B      1539 - GLY     38- ( B)         -4.95
1597 ARG   (  96-)  B      1599 - LEU     98- ( B)         -5.24
1629 GLU   ( 128-)  B      1631 - ARG    130- ( B)         -4.67
1657 LYS   ( 156-)  B      1659 - LEU    158- ( B)         -5.48
1730 VAL   ( 229-)  B      1732 - GLU    231- ( B)         -4.55
1742 GLY   (   2-)  C      1745 - ILE      5- ( C)         -5.14
1910 GLN   ( 170-)  C      1912 - ARG    172- ( C)         -5.35
1991 GLN   (  45-)  D      1993 - ARG     47- ( D)         -5.63
2030 LYS   (  84-)  D      2032 - LYS     86- ( D)         -5.62
2168 ARG   (  18-)  E      2171 - ALA     21- ( E)         -5.58
2302 ARG   ( 152-)  E      2304 - GLY    154- ( E)         -5.23
2407 ARG   (   3-)  G      2410 - ARG      6- ( G)         -6.75
2414 ARG   (  10-)  G      2417 - GLN     13- ( G)         -5.05
2628 ARG   (  68-)  H      2630 - GLN     70- ( H)         -6.50
2664 ARG   ( 104-)  H      2666 - GLY    106- ( H)         -4.98
2706 ARG   (   9-)  I      2708 - LYS     11- ( I)         -4.64
2806 VAL   ( 109-)  I      2811 - TYR    114- ( I)         -5.02
2877 PHE   (  54-)  J      2880 - LYS     57- ( J)         -5.47
3055 LYS   (  14-)  L      3057 - ARG     16- ( L)         -4.81
3110 GLY   (  69-)  L      3112 - GLY     71- ( L)         -4.77
3163 LYS   ( 123-)  L      3165 - ALA    125- ( L)         -5.17
3263 ARG   (  99-)  M      3266 - ARG    102- ( M)         -5.53
3278 ARG   ( 114-)  M      3282 - ALA    118- ( M)         -4.66
3354 GLN   (  13-)  O      3356 - PHE     15- ( O)         -4.56
3442 LYS   (  12-)  P      3444 - ASN     14- ( P)         -5.33
3683 SER   (   4-)  S      3686 - LYS      7- ( S)         -5.41
3707 LYS   (  28-)  S      3709 - LEU     30- ( S)         -5.78
3757 ARG   (  78-)  S      3762 - HIS     83- ( S)         -6.09
3764 LYS   (  85-)  S      3766 - ALA     87- ( S)         -5.63
3863 LEU   ( 104-)  T      3865 - ALA    106- ( T)         -4.69
4060 ASP   (   8-)  Y      4062 - HIS     10- ( Y)         -6.00

Warning: Structural average packing environment a bit worrysome

The structural average packing score is a bit low.

The protein is probably threaded correctly, but either poorly refined, or it is just a protein with an unusual (but correct) structure. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].

Average for range 1 - 4066 : -1.929

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: B

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: C

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: D

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: E

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: F

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: G

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: H

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: I

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: J

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: K

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: L

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: M

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: N

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: O

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: P

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: Q

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: R

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: S

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: T

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: U

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: Y

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.

1743 ASN   (   3-)  C   -3.93
3270 ASN   ( 106-)  M   -3.72
2878 LYS   (  55-)  J   -3.32
2824 LYS   ( 127-)  I   -3.12
2923 THR   ( 100-)  J   -3.11
2821 GLN   ( 124-)  I   -3.10
3129 LYS   (  88-)  L   -3.09
2939 ASN   (  26-)  K   -3.05
3312 ARG   (  31-)  N   -3.02
2877 PHE   (  54-)  J   -3.00
3757 ARG   (  78-)  S   -2.99
2485 GLY   (  81-)  G   -2.96
3771 ALA   (  12-)  T   -2.95
3769 LEU   (  10-)  T   -2.94
3733 GLY   (  54-)  S   -2.90
3302 TYR   (  21-)  N   -2.89
2880 LYS   (  57-)  J   -2.88
2708 LYS   (  11-)  I   -2.88
1949 ARG   (   3-)  D   -2.88
2810 LYS   ( 113-)  I   -2.87
1742 GLY   (   2-)  C   -2.84
2879 HIS   (  56-)  J   -2.83
3031 GLY   ( 118-)  K   -2.77
3879 ARG   (  15-)  U   -2.77
1988 GLN   (  42-)  D   -2.75
And so on for a total of 53 lines.

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

1741 GLN   ( 240-)  B     - 1745 ILE   (   5-)  C        -2.43
2406 ALA   (   2-)  G     - 2409 ARG   (   5-)  G        -1.94
2435 MET   (  31-)  G     - 2438 GLY   (  34-)  G        -1.96
2484 VAL   (  80-)  G     - 2487 ALA   (  83-)  G        -1.93
2560 TRP   ( 156-)  G     - 2563 THR   (   3-)  H        -1.89
2807 GLU   ( 110-)  I     - 2812 GLY   ( 115-)  I        -2.37
2815 LYS   ( 118-)  I     - 2818 ARG   ( 121-)  I        -2.00
2820 PRO   ( 123-)  I     - 2825 ARG   ( 128-)  I        -2.48
2876 PRO   (  53-)  J     - 2882 SER   (  59-)  J        -2.52
3028 PRO   ( 115-)  K     - 3033 ARG   ( 120-)  K        -2.11
3262 VAL   (  98-)  M     - 3266 ARG   ( 102-)  M        -2.02
3267 THR   ( 103-)  M     - 3270 ASN   ( 106-)  M        -2.47
3294 THR   (  13-)  N     - 3300 ARG   (  19-)  N        -2.02
3338 ARG   (  57-)  N     - 3341 SER   (  60-)  N        -1.95
3440 GLY   (  10-)  P     - 3443 HIS   (  13-)  P        -2.17
3456 ARG   (  26-)  P     - 3459 ASP   (  29-)  P        -2.08
3710 ILE   (  31-)  S     - 3713 TRP   (  34-)  S        -1.83

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: Q

Note: Second generation quality Z-score plot

Chain identifier: R

Note: Second generation quality Z-score plot

Chain identifier: S

Note: Second generation quality Z-score plot

Chain identifier: T

Note: Second generation quality Z-score plot

Chain identifier: U

Note: Second generation quality Z-score plot

Chain identifier: Y

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

1541 HIS   (  40-)  B
1595 ASN   (  94-)  B
1705 ASN   ( 204-)  B
1743 ASN   (   3-)  C
1777 GLN   (  37-)  C
2008 GLN   (  62-)  D
2023 ASN   (  77-)  D
2075 ASN   ( 129-)  D
2107 ASN   ( 161-)  D
2311 ASN   (   7-)  F
2368 GLN   (  64-)  F
2404 ASN   ( 100-)  F
2441 ASN   (  37-)  G
2638 GLN   (  78-)  H
2770 GLN   (  73-)  I
3006 GLN   (  93-)  K
3030 ASN   ( 117-)  K
3046 ASN   (   5-)  L
3087 ASN   (  46-)  L
3226 ASN   (  62-)  M
3265 GLN   ( 101-)  M
3369 GLN   (  28-)  O
3495 GLN   (  65-)  P
3702 ASN   (  23-)  S
3762 HIS   (  83-)  S
3849 GLN   (  90-)  T

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

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.

  32 OCYT  (  34-)  A      N4
  53 OADE  (  55-)  A      N6
  55 OGUA  (  57-)  A      N2
  71 OGUA  (  73-)  A      N1
  75 OGUA  (  79-)  A      N1
  75 OGUA  (  79-)  A      N2
  87 OURA  (  96-)  A      N3
  99 OGUA  ( 108-)  A      N2
 101 OCYT  ( 110-)  A      N4
 106 OGUA  ( 115-)  A      N2
 142 OCYT  ( 150-)  A      N4
 143 OADE  ( 151-)  A      N6
 152 OADE  ( 160-)  A      N6
 161 OCYT  ( 169-)  A      N4
 173 OGUA  ( 181-)  A      N1
 174 OURA  ( 182-)  A      N3
 181 OGUA  ( 189-)  A      N1
 194 OURA  ( 190-)  A      N3
 203 OGUA  ( 199-)  A      N2
 209 OGUA  ( 216-)  A      N1
 213 OGUA  ( 220-)  A      N2
 222 OURA  ( 229-)  A      N3
 247 OGUA  ( 254-)  A      N2
 259 OGUA  ( 266-)  A      N1
 261 OCYT  ( 268-)  A      N4
And so on for a total of 656 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

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.

1513 GLU   (  12-)  B      OE1
1585 GLU   (  84-)  B      OE1
1667 ASP   ( 166-)  B      OD1
1671 GLU   ( 170-)  B      OE1
1677 GLU   ( 176-)  B      OE1
1690 ASP   ( 189-)  B      OD1
1706 ASP   ( 205-)  B      OD2
1776 ASP   (  36-)  C      OD1
1784 GLU   (  44-)  C      OE1
2023 ASN   (  77-)  D      OD1
2229 GLU   (  79-)  E      OE2
2280 ASN   ( 130-)  E      OD1
2311 ASN   (   7-)  F      OD1
2326 GLU   (  22-)  F      OE1
2419 ASP   (  15-)  G      OD2
2807 GLU   ( 110-)  I      OE1
2980 ASP   (  67-)  K      OD1
3029 HIS   ( 116-)  K      NE2
3047 GLN   (   6-)  L      OE1
3172 GLU   (   8-)  M      OE2
3196 GLU   (  32-)  M      OE1
3327 GLU   (  46-)  N      OE1
3387 HIS   (  46-)  O      NE2
3657 GLN   (  63-)  R      OE1
3702 ASN   (  23-)  S      OD1
3819 GLU   (  60-)  T      OE2
4059 HIS   (   7-)  Y      ND1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

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+.

4077  MG   (   2-)  Z   -.-  -.-  Part of ionic cluster
4077  MG   (   2-)  Z   -.-  -.-  Too few ligands (0)
4078  MG   (   3-)  Z   -.-  -.-  Low probability ion. Occ=0.46
4079  MG   (   4-)  A   -.-  -.-  Low probability ion. B= 96.3
4080  MG   (   5-)  A   -.-  -.-  Too few ligands (2)
4081  MG   (   6-)  A   -.-  -.-  Low probability ion. B=112.0
4082  MG   (   7-)  A     0.22   0.61 Is perhaps  K (Few ligands (4) )
4083  MG   (   8-)  A   -.-  -.-  Low probability ion. Occ=0.61
4084  MG   (   9-)  Z   -.-  -.-  Too few ligands (0)
4085  MG   (  10-)  A     0.32   0.63 Is perhaps NA (Few ligands (4) )
4086  MG   (  12-)  A   -.-  -.-  Low probability ion. B= 94.1
4087  MG   (  14-)  A   -.-  -.-  Low probability ion. B=124.9
4088  MG   (  15-)  Z   -.-  -.-  Too few ligands (0)
4089  MG   (  16-)  Z   -.-  -.-  Too few ligands (0)
4090  MG   (  18-)  Z   -.-  -.-  Low probability ion. B= 80.1
4091  MG   (  19-)  Z   -.-  -.-  Low probability ion. B= 93.9
4092  MG   (  20-)  Z   -.-  -.-  Low probability ion. B= 83.5
4093  MG   (  21-)  Z   -.-  -.-  Low probability ion. B= 97.5
4094  MG   (  22-)  Z   -.-  -.-  Low probability ion. B= 83.9
4095  MG   (  26-)  V   -.-  -.-  Low probability ion. B= 93.2
4096  MG   (  27-)  V   -.-  -.-  Low probability ion. B= 92.9
4097  MG   (  28-)  V   -.-  -.-  Too few ligands (2)
4098  MG   (  29-)  V   -.-  -.-  Low probability ion. B= 86.9
4099  MG   (  30-)  V   -.-  -.-  Low probability ion. B= 82.4
4100  MG   (  31-)  Z   -.-  -.-  Low probability ion. B=101.2
And so on for a total of 1424 lines.

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

1551 GLU   (  50-)  B   H-bonding suggests Gln
1553 GLU   (  52-)  B   H-bonding suggests Gln
1561 ASP   (  60-)  B   H-bonding suggests Asn
1585 GLU   (  84-)  B   H-bonding suggests Gln
1587 GLU   (  86-)  B   H-bonding suggests Gln
1630 GLU   ( 129-)  B   H-bonding suggests Gln
1644 GLU   ( 143-)  B   H-bonding suggests Gln
1706 ASP   ( 205-)  B   H-bonding suggests Asn
1707 ASP   ( 206-)  B   H-bonding suggests Asn; but Alt-Rotamer
1757 ASP   (  17-)  C   H-bonding suggests Asn
1786 GLU   (  46-)  C   H-bonding suggests Gln
1796 ASP   (  56-)  C   H-bonding suggests Asn; but Alt-Rotamer
1830 GLU   (  90-)  C   H-bonding suggests Gln; but Alt-Rotamer
2090 ASP   ( 144-)  D   H-bonding suggests Asn
2139 ASP   ( 193-)  D   H-bonding suggests Asn
2272 GLU   ( 122-)  E   H-bonding suggests Gln; but Alt-Rotamer
2299 GLU   ( 149-)  E   H-bonding suggests Gln; but Alt-Rotamer
2359 ASP   (  55-)  F   H-bonding suggests Asn
2449 ASP   (  45-)  G   H-bonding suggests Asn
2585 ASP   (  25-)  H   H-bonding suggests Asn
2594 GLU   (  34-)  H   H-bonding suggests Gln
2612 ASP   (  52-)  H   H-bonding suggests Asn
2757 ASP   (  60-)  I   H-bonding suggests Asn
2896 ASP   (  73-)  J   H-bonding suggests Asn; but Alt-Rotamer
2906 GLU   (  83-)  J   H-bonding suggests Gln
2947 ASP   (  34-)  K   H-bonding suggests Asn
3233 GLU   (  69-)  M   H-bonding suggests Gln
3247 ASP   (  83-)  M   H-bonding suggests Asn; but Alt-Rotamer
3327 GLU   (  46-)  N   H-bonding suggests Gln
3567 ASP   (  55-)  Q   H-bonding suggests Asn; but Alt-Rotamer
3608 GLU   (  96-)  Q   H-bonding suggests Gln
3624 ASP   (  30-)  R   H-bonding suggests Asn; but Alt-Rotamer
3677 GLU   (  83-)  R   H-bonding suggests Gln
3691 ASP   (  12-)  S   H-bonding suggests Asn; but Alt-Rotamer
3706 GLU   (  27-)  S   H-bonding suggests Gln; but Alt-Rotamer
3852 GLU   (  93-)  T   H-bonding suggests Gln
4056 ASP   (   4-)  Y   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

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 :  -3.573
  2nd generation packing quality :  -3.901 (poor)
  Ramachandran plot appearance   :  -6.769 (bad)
  chi-1/chi-2 rotamer normality  :  -4.200 (bad)
  Backbone conformation          :  -0.909

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.419 (tight)
  Bond angles                    :   0.671
  Omega angle restraints         :   0.163 (tight)
  Side chain planarity           :   0.167 (tight)
  Improper dihedral distribution :   0.578
  B-factor distribution          :   0.789
  Inside/Outside distribution    :   1.013

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

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 : 3.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -2.2
  2nd generation packing quality :  -1.5
  Ramachandran plot appearance   :  -3.6 (poor)
  chi-1/chi-2 rotamer normality  :  -1.8
  Backbone conformation          :   0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.419 (tight)
  Bond angles                    :   0.671
  Omega angle restraints         :   0.163 (tight)
  Side chain planarity           :   0.167 (tight)
  Improper dihedral distribution :   0.578
  B-factor distribution          :   0.789
  Inside/Outside distribution    :   1.013
==============

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.