WHAT IF Check report

This file was created 2012-01-30 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 pdb3i8f.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: 1
Highest polymer chain multiplicity according to SEQRES: 2
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 4
Polymer chain multiplicity and SEQRES multiplicity disagree 1 2
Z and NCS seem to support the 3D multiplicity

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: 1361301.3
Volume of the Unit Cell V= 58237228.0
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 21.390
Vm by authors and this calculated Vm do not agree very well
SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)
And remember, a matrix counting problem has been reported earlier already

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.

2827 OADE  (2820-)  A  -   O2' 4765 HIS   (   3-)  0  -   CG
2827 OADE  (2820-)  A  -   O2' 4765 HIS   (   3-)  0  -   CD2
2827 OADE  (2820-)  A  -   O2' 4765 HIS   (   3-)  0  -   NE2

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.

Error: Overlapping residues removed

The pairs of residues listed in the table overlapped too much.

The left-hand residue has been removed, and the right hand residue has been kept for validation. Be aware that WHAT IF calls everything a residue. Two residues are defined as overlapping if the two smallest ellipsoids encompassing the two residues interpenetrate by 33% of the longest axis. Many artefacts can actually cause this problem. The most often observed reason is alternative residue conformations expressed by two residues that accidentally both got 1.0 occupancy for all atoms.

2186 OURA  (2167-)  A  -             2185 OGUA  (2165-)  A  -           3.9
Delete overlapping entity 2185 OGUA (2165-) A  -
Delete overlapping entity 2827 OADE (2820-) A  -

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.

2185 OGUA  (2165-)  A  -
2827 OADE  (2820-)  A  -

Please also see the previous check
Please see the user course on the WHAT CHECK website if you want to know why this table and the previous one have not been merged.

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: 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: K

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: 0

Note: Ramachandran plot

Chain identifier: Q

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: 1

Note: Ramachandran plot

Chain identifier: 2

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: U

Note: Ramachandran plot

Chain identifier: V

Note: Ramachandran plot

Chain identifier: 3

Note: Ramachandran plot

Chain identifier: Z

Note: Ramachandran plot

Chain identifier: W

Note: Ramachandran plot

Chain identifier: X

Note: Ramachandran plot

Chain identifier: 4

Note: Ramachandran plot

Chain identifier: 5

Note: Ramachandran plot

Chain identifier: 6

Note: Ramachandran plot

Chain identifier: 7

Note: Ramachandran plot

Chain identifier: 8

Coordinate problems, unexpected atoms, B-factor and occupancy checks

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  (   1-)  A    High
   2 OGUA  (   2-)  A    High
   3 OURA  (   3-)  A    High
   4 OCYT  (   4-)  A    High
   5 OADE  (   5-)  A    High
   6 OADE  (   6-)  A    High
   7 OGUA  (   7-)  A    High
   8 OADE  (   8-)  A    High
   9 OURA  (   9-)  A    High
  10 OGUA  (  10-)  A    High
  11 OGUA  (  11-)  A    High
  12 OURA  (  12-)  A    High
  13 OADE  (  13-)  A    High
  89 OURA  (  90-)  A    High
  90 OADE  (  91-)  A    High
 153 OCYT  ( 153-)  A    High
 154 OGUA  ( 154-)  A    High
 155 OCYT  ( 155-)  A    High
 156 OURA  ( 161-)  A    High
 157 OURA  ( 162-)  A    High
 158 OGUA  ( 171-)  A    High
 159 OCYT  ( 172-)  A    High
 160 OGUA  ( 173-)  A    High
 161 OCYT  ( 174-)  A    High
 215 OADE  ( 228-)  A    High
And so on for a total of 1661 lines.

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: 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: K

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: 0

Note: B-factor plot

Chain identifier: Q

Note: B-factor plot

Chain identifier: R

Note: B-factor plot

Chain identifier: 1

Note: B-factor plot

Chain identifier: 2

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: V

Note: B-factor plot

Chain identifier: 3

Note: B-factor plot

Chain identifier: Z

Note: B-factor plot

Chain identifier: W

Note: B-factor plot

Chain identifier: X

Note: B-factor plot

Chain identifier: 4

Note: B-factor plot

Chain identifier: 5

Note: B-factor plot

Chain identifier: 6

Note: B-factor plot

Chain identifier: 7

Note: B-factor plot

Chain identifier: 8

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.

3268 ARG   ( 239-)  D
3360 ARG   (  58-)  E
3842 ARG   ( 128-)  G
4513 ARG   (  41-)  O
4527 ARG   (  55-)  O
4533 ARG   (  61-)  O
4574 ARG   ( 102-)  O
4583 ARG   ( 111-)  O
4825 ARG   (  64-)  0
4849 ARG   (  88-)  0
5176 ARG   (  50-)  1
5190 ARG   (  64-)  1
5870 ARG   (  32-)  3
6307 ARG   (  37-)  6

Warning: Tyrosine convention problem

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

3091 TYR   (  62-)  D
3113 TYR   (  84-)  D
3462 TYR   ( 160-)  E
3566 TYR   (  59-)  F
3604 TYR   (  97-)  F
3606 TYR   (  99-)  F
4091 TYR   (  25-)  K
4335 TYR   ( 123-)  M
4782 TYR   (  21-)  0
5090 TYR   ( 100-)  R
5150 TYR   (  24-)  1
5171 TYR   (  45-)  1
5173 TYR   (  47-)  1
5354 TYR   (   9-)  S
5415 TYR   (  70-)  S
5420 TYR   (  75-)  S
5482 TYR   (  26-)  T
5604 TYR   (  55-)  U
5655 TYR   (   3-)  V
5660 TYR   (   8-)  V
5661 TYR   (   9-)  V
5864 TYR   (  26-)  3
5965 TYR   (  43-)  Z
5993 TYR   (  71-)  Z
6211 TYR   (  63-)  4
6215 TYR   (  67-)  4
6291 TYR   (  21-)  6
6309 TYR   (  39-)  6

Warning: Phenylalanine convention problem

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

3044 PHE   (  15-)  D
3096 PHE   (  67-)  D
3164 PHE   ( 135-)  D
3317 PHE   (  15-)  E
3386 PHE   (  84-)  E
3415 PHE   ( 113-)  E
3590 PHE   (  83-)  F
4018 PHE   ( 123-)  H
4449 PHE   (  99-)  N
4602 PHE   ( 130-)  O
4808 PHE   (  47-)  0
4841 PHE   (  80-)  0
4890 PHE   (  12-)  Q
4907 PHE   (  29-)  Q
4990 PHE   ( 112-)  Q
5047 PHE   (  57-)  R
5051 PHE   (  61-)  R
5066 PHE   (  76-)  R
5158 PHE   (  32-)  1
5166 PHE   (  40-)  1
5183 PHE   (  57-)  1
5205 PHE   (  79-)  1
5609 PHE   (  60-)  U
5741 PHE   (  89-)  V
5756 PHE   ( 104-)  V
5898 PHE   (  60-)  3
6190 PHE   (  42-)  4
6341 PHE   (  18-)  7

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.

3128 ASP   (  99-)  D
3138 ASP   ( 109-)  D
3476 ASP   ( 174-)  E
3870 ASP   ( 156-)  G
4086 ASP   (  20-)  K
4229 ASP   (  17-)  M
4362 ASP   (  12-)  N
4406 ASP   (  56-)  N
4431 ASP   (  81-)  N
4519 ASP   (  47-)  O
4760 ASP   ( 138-)  P
4820 ASP   (  59-)  0
4830 ASP   (  69-)  0
4833 ASP   (  72-)  0
4868 ASP   ( 107-)  0
4966 ASP   (  88-)  Q
5034 ASP   (  44-)  R
5107 ASP   ( 117-)  R
5217 ASP   (  91-)  1
5367 ASP   (  22-)  S
5439 ASP   (  94-)  S
5462 ASP   (   6-)  T
5775 ASP   ( 123-)  V
5806 ASP   ( 154-)  V
5894 ASP   (  56-)  3

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.

3057 GLU   (  28-)  D
3130 GLU   ( 101-)  D
3177 GLU   ( 148-)  D
3389 GLU   (  87-)  E
3481 GLU   ( 179-)  E
3542 GLU   (  35-)  F
3727 GLU   (  13-)  G
3732 GLU   (  18-)  G
3762 GLU   (  48-)  G
3857 GLU   ( 143-)  G
3953 GLU   (  58-)  H
4054 GLU   ( 159-)  H
4062 GLU   ( 167-)  H
4073 GLU   (   7-)  K
4114 GLU   (  48-)  K
4126 GLU   (  60-)  K
4139 GLU   (  73-)  K
4165 GLU   (  99-)  K
4188 GLU   ( 122-)  K
4404 GLU   (  54-)  N
4418 GLU   (  68-)  N
4458 GLU   ( 108-)  N
4546 GLU   (  74-)  O
4702 GLU   (  80-)  P
4804 GLU   (  43-)  0
And so on for a total of 53 lines.

Error: Decreasing residue numbers

At least one residue in each of the chains mentioned below has a residue number that is lower than the previous residue in that chain ('-' represents a chain without chain identifier).

Chain identifier(s): B

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.

  73 OADE  (  74-)  A      N9   C4    1.35   -4.6
  73 OADE  (  74-)  A      C2   N3    1.29   -4.4
 344 OADE  ( 322-)  A      C8   N7    1.34    4.1
 644 OADE  ( 621-)  A      C5   C6    1.37   -4.3
 644 OADE  ( 621-)  A      C6   N6    1.29   -5.3
 685 OGUA  ( 654-)  A      N9   C4    1.41    4.7
 685 OGUA  ( 654-)  A      C2   N3    1.36    4.8
 685 OGUA  ( 654-)  A      C5   C6    1.37   -5.2
 690 OCYT  ( 654-)  A      N1   C2    1.45    5.6
 939 OURA  ( 895-)  A      C4   N3    1.34   -4.6
1403 OADE  (1359-)  A      C5   C6    1.34   -7.3
1416 OURA  (1372-)  A      C3'  O3'   1.35   -5.2
1791 OADE  (1762-)  A      O5'  C5'   1.37   -4.2
2112 OURA  (2092-)  A      O5'  C5'   1.37   -4.2
2674 OADE  (2665-)  A      C5   C6    1.37   -4.1
2674 OADE  (2665-)  A      C6   N6    1.29   -5.7
2991 OGUA  (  81-)  B      C6   N1    1.36   -5.1
6149 MET   (   1-)  4      SD   CE    1.48   -5.2

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

 |  1.001271 -0.000027  0.000094|
 | -0.000027  1.000874 -0.000001|
 |  0.000094 -0.000001  1.001007|
Proposed new scale matrix

 |  0.004768  0.000000  0.000000|
 |  0.000000  0.002239  0.000000|
 |  0.000000  0.000000  0.001603|
With corresponding cell

    A    = 209.734  B   = 446.619  C    = 623.680
    Alpha=  90.006  Beta=  90.005  Gamma=  90.004

The CRYST1 cell dimensions

    A    = 209.460  B   = 446.200  C    = 623.050
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 1899.131
(Under-)estimated Z-score: 32.118

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  (   1-)  A      N9   C8   N7  113.21    4.2
   2 OGUA  (   2-)  A      N9   C8   N7  113.28    4.4
   4 OCYT  (   4-)  A      O3'  C3'  C4' 121.18    4.1
   5 OADE  (   5-)  A      OP1  P   -O3*  63.31  -13.8
   5 OADE  (   5-)  A      OP2  P   -O3*  65.57  -13.4
   5 OADE  (   5-)  A      O5*  P   -O3* 114.09    5.3
   5 OADE  (   5-)  A      OP1  P    OP2 128.65    6.0
   5 OADE  (   5-)  A      OP1  P    O5'  95.55   -4.3
  10 OGUA  (  10-)  A      N9   C8   N7  113.17    4.1
  15 OGUA  (  15-)  A      C2'  C1'  N9  105.71   -4.8
  16 OGUA  (  16-)  A      N9   C8   N7  113.24    4.3
  23 OGUA  (  23-)  A      N9   C8   N7  113.15    4.1
  26 OGUA  (  26-)  A      N9   C8   N7  113.13    4.1
  28 OADE  (  28-)  A      C3'  C4'  C5' 109.04   -4.3
  30 OGUA  (  30-)  A      N9   C8   N7  113.16    4.1
  35 OGUA  (  35-)  A      N9   C8   N7  113.11    4.0
  47 OGUA  (  48-)  A      C3'  C4'  C5' 109.13   -4.2
  47 OGUA  (  48-)  A      N9   C8   N7  113.23    4.3
  49 OURA  (  50-)  A      C2'  C1'  N1  120.63    4.5
  53 OGUA  (  54-)  A      N9   C8   N7  113.11    4.0
  57 OGUA  (  58-)  A      N9   C8   N7  113.21    4.2
  59 OGUA  (  60-)  A      C2'  C1'  N9  122.65    5.8
  62 OURA  (  63-)  A      C2'  C1'  N1  120.28    4.3
  66 OURA  (  67-)  A      C4   N3   C2  129.79    4.6
  67 OGUA  (  68-)  A      N9   C8   N7  113.18    4.2
And so on for a total of 823 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.

3057 GLU   (  28-)  D
3128 ASP   (  99-)  D
3130 GLU   ( 101-)  D
3138 ASP   ( 109-)  D
3177 GLU   ( 148-)  D
3268 ARG   ( 239-)  D
3360 ARG   (  58-)  E
3389 GLU   (  87-)  E
3476 ASP   ( 174-)  E
3481 GLU   ( 179-)  E
3542 GLU   (  35-)  F
3727 GLU   (  13-)  G
3732 GLU   (  18-)  G
3762 GLU   (  48-)  G
3842 ARG   ( 128-)  G
3857 GLU   ( 143-)  G
3870 ASP   ( 156-)  G
3953 GLU   (  58-)  H
4054 GLU   ( 159-)  H
4062 GLU   ( 167-)  H
4073 GLU   (   7-)  K
4086 ASP   (  20-)  K
4114 GLU   (  48-)  K
4126 GLU   (  60-)  K
4139 GLU   (  73-)  K
And so on for a total of 92 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.

4482 PRO   (  10-)  O      N      6.0    17.36    -2.48
5626 PRO   (  77-)  U      N      6.9    20.06    -2.48
5714 PRO   (  62-)  V      N    -10.1   -35.48    -2.48
5829 PRO   ( 177-)  V      N     12.1    37.06    -2.48
The average deviation= 0.790

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.

6022 GLU   (   5-)  W    7.69
5958 GLY   (  36-)  Z    7.30
4168 SER   ( 102-)  K    7.28
5569 TYR   (  20-)  U    6.37
3253 ALA   ( 224-)  D    5.90
5222 ALA   (  96-)  1    5.74
3363 ARG   (  61-)  E    5.73
4999 LEU   (   9-)  R    5.71
5196 ARG   (  70-)  1    5.36
4537 ARG   (  65-)  O    5.31
4611 LYS   ( 139-)  O    5.21
5325 TYR   (  81-)  2    5.16
3590 PHE   (  83-)  F    5.13
3064 LYS   (  35-)  D    5.05
3372 ALA   (  70-)  E    5.03
3364 PRO   (  62-)  E    5.03
6413 ARG   (  42-)  8    4.99
5618 ALA   (  69-)  U    4.95
3369 PHE   (  67-)  E    4.94
4155 TYR   (  89-)  K    4.92
4535 PRO   (  63-)  O    4.92
3620 ALA   ( 113-)  F    4.90
5756 PHE   ( 104-)  V    4.90
4326 ARG   ( 114-)  M    4.87
3420 LYS   ( 118-)  E    4.86
And so on for a total of 69 lines.

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.606

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

3133 TYR   ( 104-)  D      CB   4.63

Warning: Uncalibrated side chain planarity problems

The residues listed in the table below contain a planar group that was found to deviate from planarity by more than 0.10 Angstrom RMS. Please be aware that this check cannot be callibrated and that the cutoff of 0.10 Angstrom thus is a wild guess.

 628 OURA  ( 607-)  A    0.31
 939 OURA  ( 895-)  A    0.29
2665 OURA  (2656-)  A    0.25
3006 OURA  (  95-)  B    0.21
1293 OURA  (1249-)  A    0.19
1126 OURA  (1082-)  A    0.18
 684 OCYT  ( 654-)  A    0.14
 690 OCYT  ( 654-)  A    0.12
2799 OCYT  (2789-)  A    0.12
2991 OGUA  (  81-)  B    0.11
1803 OCYT  (1774-)  A    0.11
2415 OURA  (2406-)  A    0.11
 428 OURA  ( 403-)  A    0.10
 Ramachandran Z-score : -6.283

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 : -6.283

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.

4582 TYR   ( 110-)  O    -3.9
4890 PHE   (  12-)  Q    -3.8
6215 TYR   (  67-)  4    -3.7
3314 THR   (  12-)  E    -3.4
4529 THR   (  57-)  O    -3.4
6222 HIS   (   4-)  5    -3.3
4643 THR   (  21-)  P    -3.3
4504 THR   (  32-)  O    -3.3
6172 THR   (  24-)  4    -3.1
4398 PRO   (  48-)  N    -3.1
5714 PRO   (  62-)  V    -3.1
5829 PRO   ( 177-)  V    -3.1
4482 PRO   (  10-)  O    -3.1
5760 PRO   ( 108-)  V    -3.1
5626 PRO   (  77-)  U    -3.1
6009 PRO   (  87-)  Z    -3.1
3503 THR   ( 201-)  E    -3.1
6419 PHE   (  48-)  8    -3.1
4535 PRO   (  63-)  O    -3.1
5246 PHE   (   2-)  2    -3.0
3355 PRO   (  53-)  E    -3.0
5798 ILE   ( 146-)  V    -3.0
4306 HIS   (  94-)  M    -3.0
6155 PRO   (   7-)  4    -3.0
3434 HIS   ( 132-)  E    -3.0
And so on for a total of 397 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.

3032 VAL   (   3-)  D  Poor phi/psi
3037 PRO   (   8-)  D  Poor phi/psi
3041 SER   (  12-)  D  Poor phi/psi
3054 THR   (  25-)  D  Poor phi/psi
3055 LYS   (  26-)  D  Poor phi/psi
3056 THR   (  27-)  D  Poor phi/psi
3057 GLU   (  28-)  D  Poor phi/psi
3062 LEU   (  33-)  D  Poor phi/psi
3064 LYS   (  35-)  D  Poor phi/psi, PRO omega poor
3074 ASN   (  45-)  D  Poor phi/psi
3082 PHE   (  53-)  D  Poor phi/psi
3087 HIS   (  58-)  D  Poor phi/psi
3147 VAL   ( 118-)  D  Poor phi/psi
3172 HIS   ( 143-)  D  Poor phi/psi
3173 ALA   ( 144-)  D  Poor phi/psi
3185 ALA   ( 156-)  D  Poor phi/psi
3186 ARG   ( 157-)  D  Poor phi/psi
3188 ALA   ( 159-)  D  Poor phi/psi
3191 SER   ( 162-)  D  Poor phi/psi
3225 VAL   ( 196-)  D  Poor phi/psi
3227 ASN   ( 198-)  D  Poor phi/psi
3254 ALA   ( 225-)  D  Poor phi/psi
3266 GLU   ( 237-)  D  Poor phi/psi
3267 GLY   ( 238-)  D  Poor phi/psi
3268 ARG   ( 239-)  D  Poor phi/psi
And so on for a total of 657 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 : -5.198

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.

6427 GLU   (  56-)  8    0.35
6057 SER   (  40-)  W    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  (   3-)  A      0
   4 OCYT  (   4-)  A      0
   5 OADE  (   5-)  A      0
   6 OADE  (   6-)  A      0
   7 OGUA  (   7-)  A      0
   8 OADE  (   8-)  A      0
   9 OURA  (   9-)  A      0
  10 OGUA  (  10-)  A      0
  11 OGUA  (  11-)  A      0
  12 OURA  (  12-)  A      0
  13 OADE  (  13-)  A      0
  14 OADE  (  14-)  A      0
  15 OGUA  (  15-)  A      0
  16 OGUA  (  16-)  A      0
  17 OGUA  (  17-)  A      0
  18 OCYT  (  18-)  A      0
  19 OCYT  (  19-)  A      0
  20 OCYT  (  20-)  A      0
  21 OADE  (  21-)  A      0
  22 OCYT  (  22-)  A      0
  23 OGUA  (  23-)  A      0
  24 OGUA  (  24-)  A      0
  25 OURA  (  25-)  A      0
  26 OGUA  (  26-)  A      0
  27 OGUA  (  27-)  A      0
And so on for a total of 4797 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 : 1.383

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!

3352 GLY   (  50-)  E   3.36   53
3305 GLY   (   3-)  E   3.14   42
3799 GLY   (  85-)  G   2.95   23
3568 GLY   (  61-)  F   2.83   12
3432 GLY   ( 130-)  E   2.83   22
3488 GLY   ( 186-)  E   2.72   42
3868 GLY   ( 154-)  G   2.39   62
6268 GLY   (  50-)  5   2.24   26
4056 GLY   ( 161-)  H   2.05   11
4506 GLY   (  34-)  O   2.03   12
4684 GLY   (  62-)  P   1.97   14
3285 GLY   ( 256-)  D   1.95   10
3843 GLY   ( 129-)  G   1.82   26
4768 GLY   (   7-)  0   1.79   11
3312 GLY   (  10-)  E   1.76   15
4974 GLY   (  96-)  Q   1.70   10
4900 GLY   (  22-)  Q   1.69   80
3917 GLY   (  22-)  H   1.65   80
3331 GLY   (  29-)  E   1.64   26
4637 GLY   (  15-)  P   1.53   12

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

3433 ALA   ( 131-)  E   2.27
3434 HIS   ( 132-)  E   2.42
3515 GLN   (   8-)  F   1.52
4208 VAL   ( 142-)  K   2.15
6292 ALA   (  22-)  6   2.14

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]

3115 PRO   (  86-)  D    0.45 HIGH
3324 PRO   (  22-)  E    0.47 HIGH
3364 PRO   (  62-)  E    0.46 HIGH
3449 PRO   ( 147-)  E    0.46 HIGH
4535 PRO   (  63-)  O    0.46 HIGH
6245 PRO   (  27-)  5    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].

3334 PRO   (  32-)  E  -115.5 envelop C-gamma (-108 degrees)
3532 PRO   (  25-)  F  -116.7 envelop C-gamma (-108 degrees)
4323 PRO   ( 111-)  M   102.1 envelop C-beta (108 degrees)
4354 PRO   (   4-)  N  -113.6 envelop C-gamma (-108 degrees)
4398 PRO   (  48-)  N   132.6 half-chair C-beta/C-alpha (126 degrees)
4482 PRO   (  10-)  O   127.0 half-chair C-beta/C-alpha (126 degrees)
5359 PRO   (  14-)  S    99.3 envelop C-beta (108 degrees)
5626 PRO   (  77-)  U   127.4 half-chair C-beta/C-alpha (126 degrees)
5760 PRO   ( 108-)  V   146.1 envelop C-alpha (144 degrees)
5786 PRO   ( 134-)  V  -119.2 half-chair C-delta/C-gamma (-126 degrees)
5810 PRO   ( 158-)  V   136.2 envelop C-alpha (144 degrees)
5829 PRO   ( 177-)  V   167.4 half-chair C-alpha/N (162 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.

 866 OADE  ( 821-)  A      O2'  <->   989 OGUA  ( 946-)  A      OP2  1.21    1.19  INTRA BL
5827 VAL   ( 175-)  V      CG1  <->  5829 PRO   ( 177-)  V      CD   1.08    2.12  INTRA BF
5827 VAL   ( 175-)  V      C    <->  5829 PRO   ( 177-)  V      CD   1.07    2.13  INTRA BF
6311 PRO   (  41-)  6      CG   <->  6315 LYS   (  45-)  6      O    1.03    1.77  INTRA BF
2827 OADE  (2820-)  A      N6   <->  3494 ASN   ( 192-)  E      N    1.01    1.84  INTRA BL
2827 OADE  (2820-)  A      C8   <->  3411 LYS   ( 109-)  E      CE   1.00    2.20  INTRA BL
 989 OGUA  ( 946-)  A      O2'  <->   990 OGUA  ( 947-)  A      C5'  0.97    1.83  INTRA BL
5760 PRO   ( 108-)  V      CB   <->  5793 VAL   ( 141-)  V      O    0.93    1.87  INTRA BF
 482 OGUA  ( 458-)  A      N2   <->   494 OADE  ( 470-)  A      OP2  0.88    1.82  INTRA BL
5767 GLY   ( 115-)  V      CA   <->  5829 PRO   ( 177-)  V      CG   0.86    2.34  INTRA BF
5827 VAL   ( 175-)  V      CG1  <->  5828 PRO   ( 176-)  V      CD   0.86    2.34  INTRA BF
1919 OGUA  (1899-)  A      N2   <->  1922 OCYT  (1902-)  A      N4   0.86    1.99  INTRA BL
2827 OADE  (2820-)  A      N7   <->  3493 PRO   ( 191-)  E      CB   0.85    2.25  INTRA BL
6311 PRO   (  41-)  6      CD   <->  6315 LYS   (  45-)  6      O    0.85    1.95  INTRA BF
6311 PRO   (  41-)  6      CG   <->  6315 LYS   (  45-)  6      C    0.82    2.38  INTRA BF
1944 OCYT  (1924-)  A      C4   <->  1945 OCYT  (1925-)  A      C5   0.81    2.39  INTRA BF
1944 OCYT  (1924-)  A      N3   <->  1945 OCYT  (1925-)  A      C5   0.80    2.30  INTRA BF
2991 OGUA  (  81-)  B      N2   <->  2992 OGUA  (  82-)  B      N7   0.77    2.23  INTRA BF
1944 OCYT  (1924-)  A      C2   <->  1945 OCYT  (1925-)  A      C6   0.76    2.44  INTRA BF
 629 OADE  ( 608-)  A      C4   <->   644 OADE  ( 621-)  A      N6   0.76    2.34  INTRA BF
 492 OGUA  ( 468-)  A      N7   <->  6362 ARG   (  39-)  7      NH2  0.76    2.24  INTRA BL
 606 OGUA  ( 585-)  A      N1   <->  1297 OADE  (1253-)  A      OP1  0.76    1.94  INTRA BL
1948 OADE  (1928-)  A      C2'  <->  1949 OGUA  (1929-)  A      C5'  0.75    2.45  INTRA BL
2950 OURA  (  40-)  B      N3   <->  6149 MET   (   1-)  4      SD   0.75    2.55  INTRA BF
2991 OGUA  (  81-)  B      N7   <->  3007 OGUA  (  96-)  B      C2   0.73    2.37  INTRA BF
And so on for a total of 6602 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: 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: K

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: 0

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: 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: 2

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: V

Note: Inside/Outside RMS Z-score plot

Chain identifier: 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: Z

Note: Inside/Outside RMS Z-score plot

Chain identifier: W

Note: Inside/Outside RMS Z-score plot

Chain identifier: X

Note: Inside/Outside RMS Z-score plot

Chain identifier: 4

Note: Inside/Outside RMS Z-score plot

Chain identifier: 5

Note: Inside/Outside RMS Z-score plot

Chain identifier: 6

Note: Inside/Outside RMS Z-score plot

Chain identifier: 7

Note: Inside/Outside RMS Z-score plot

Chain identifier: 8

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.

6270 TYR   (  52-)  5      -8.79
4627 ARG   (   5-)  P      -8.62
4399 ARG   (  49-)  N      -8.58
3898 ARG   (   3-)  H      -8.38
5852 ARG   (  14-)  3      -8.18
3581 ARG   (  74-)  F      -8.14
4490 ARG   (  18-)  O      -8.12
3268 ARG   ( 239-)  D      -8.11
5604 TYR   (  55-)  U      -8.06
6273 ARG   (  55-)  5      -8.05
4866 ARG   ( 105-)  0      -8.01
4628 ARG   (   6-)  P      -7.99
4704 ARG   (  82-)  P      -7.97
3273 ARG   ( 244-)  D      -7.97
4065 ARG   ( 170-)  H      -7.92
3451 ARG   ( 149-)  E      -7.74
4636 ARG   (  14-)  P      -7.74
3292 ARG   ( 263-)  D      -7.69
5849 ARG   (  11-)  3      -7.68
4881 ARG   (   3-)  Q      -7.68
4539 MET   (  67-)  O      -7.67
5044 ARG   (  54-)  R      -7.66
6203 ARG   (  55-)  4      -7.66
6370 ARG   (  47-)  7      -7.66
4493 ARG   (  21-)  O      -7.66
And so on for a total of 320 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.

3068 LYS   (  39-)  D      3070 - GLY     41- ( D)         -4.67
3083 ARG   (  54-)  D      3085 - GLY     56- ( D)         -4.75
3087 HIS   (  58-)  D      3089 - ARG     60- ( D)         -4.91
3265 GLY   ( 236-)  D      3268 - ARG    239- ( D)         -5.59
3270 PRO   ( 241-)  D      3273 - ARG    244- ( D)         -6.00
3360 ARG   (  58-)  E      3363 - ARG     61- ( E)         -5.26
3429 ASP   ( 127-)  E      3431 - HIS    129- ( E)         -4.62
3437 HIS   ( 135-)  E      3439 - HIS    137- ( E)         -5.83
3442 SER   ( 140-)  E      3448 - THR    146- ( E)         -5.18
3551 ARG   (  44-)  F      3553 - ARG     46- ( F)         -5.79
3574 GLN   (  67-)  F      3576 - HIS     69- ( F)         -5.36
3897 SER   (   2-)  H      3899 - ILE      4- ( H)         -5.93
3992 ARG   (  97-)  H      3994 - VAL     99- ( H)         -5.65
4004 PHE   ( 109-)  H      4006 - HIS    111- ( H)         -4.97
4397 ILE   (  47-)  N      4399 - ARG     49- ( N)         -5.68
4485 ASN   (  13-)  O      4491 - VAL     19- ( O)         -5.49
4496 GLY   (  24-)  O      4498 - GLY     26- ( O)         -4.27
4521 ARG   (  49-)  O      4524 - GLU     52- ( O)         -4.97
4531 LEU   (  59-)  O      4533 - ARG     61- ( O)         -5.72
4536 LYS   (  64-)  O      4540 - GLN     68- ( O)         -6.25
4547 ILE   (  75-)  O      4549 - ARG     77- ( O)         -5.83
4562 ARG   (  90-)  O      4564 - GLU     92- ( O)         -4.86
4619 LEU   ( 147-)  O      4622 - ALA    150- ( O)         -5.16
4627 ARG   (   5-)  P      4636 - ARG     14- ( P)         -6.46
4638 ARG   (  16-)  P      4640 - LYS     18- ( P)         -5.94
And so on for a total of 52 lines.

Error: Abnormal average packing environment

The average packing score for the structure is very low.

A molecule is certain to be incorrect if the average packing score is below -3.0. Poorly refined molecules, very well energy minimized misthreaded molecules and low homology models give values between -2.0 and -3.0. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].

Average for range 1 - 6436 : -2.163

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: 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: 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: 0

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: 1

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: 2

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: V

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: 3

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: Z

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: W

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: X

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: 4

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: 5

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: 6

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: 7

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: 8

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.

5850 ASN   (  12-)  3   -3.96
3575 LYS   (  68-)  F   -3.85
3676 ASN   ( 169-)  F   -3.49
6403 LEU   (  32-)  8   -3.47
4644 LYS   (  22-)  P   -3.46
4257 ASN   (  45-)  M   -3.46
4487 ARG   (  15-)  O   -3.42
6227 LYS   (   9-)  5   -3.33
6298 ARG   (  28-)  6   -3.30
5131 LYS   (   5-)  1   -3.27
6297 LYS   (  27-)  6   -3.24
3366 LYS   (  64-)  E   -3.23
4631 TYR   (   9-)  P   -3.21
3284 LYS   ( 255-)  D   -3.15
3451 ARG   ( 149-)  E   -3.15
4640 LYS   (  18-)  P   -3.15
5329 LYS   (  85-)  2   -3.13
6223 PRO   (   5-)  5   -3.08
6222 HIS   (   4-)  5   -3.06
6330 PRO   (   7-)  7   -3.06
6326 ARG   (   3-)  7   -3.03
5254 LYS   (  10-)  2   -3.03
5129 ARG   (   3-)  1   -3.02
5842 LYS   (   4-)  3   -3.02
3432 GLY   ( 130-)  E   -3.00
And so on for a total of 129 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.

3035 PHE   (   6-)  D     - 3038 TYR   (   9-)  D        -1.65
3069 THR   (  40-)  D     - 3072 ARG   (  43-)  D        -1.92
3073 ASN   (  44-)  D     - 3077 ARG   (  48-)  D        -2.16
3078 ILE   (  49-)  D     - 3082 PHE   (  53-)  D        -1.85
3254 ALA   ( 225-)  D     - 3259 ASP   ( 230-)  D        -2.04
3264 GLY   ( 235-)  D     - 3273 ARG   ( 244-)  D        -2.39
3283 THR   ( 254-)  D     - 3287 LYS   ( 258-)  D        -2.34
3363 ARG   (  61-)  E     - 3366 LYS   (  64-)  E        -2.47
3429 ASP   ( 127-)  E     - 3437 HIS   ( 135-)  E        -2.41
3443 ILE   ( 141-)  E     - 3447 LYS   ( 145-)  E        -2.43
3448 THR   ( 146-)  E     - 3451 ARG   ( 149-)  E        -2.47
3552 ARG   (  45-)  F     - 3556 ALA   (  49-)  F        -1.85
3566 TYR   (  59-)  F     - 3570 LYS   (  63-)  F        -2.03
3588 PRO   (  81-)  F     - 3591 VAL   (  84-)  F        -2.38
3807 THR   (  93-)  G     - 3810 ARG   (  96-)  G        -1.93
4275 THR   (  63-)  M     - 4278 LYS   (  66-)  M        -1.69
4488 ARG   (  16-)  O     - 4491 VAL   (  19-)  O        -2.07
4499 HIS   (  27-)  O     - 4503 ALA   (  31-)  O        -1.91
4504 THR   (  32-)  O     - 4508 LYS   (  36-)  O        -1.99
4516 GLY   (  44-)  O     - 4527 ARG   (  55-)  O        -2.09
4535 PRO   (  63-)  O     - 4545 GLY   (  73-)  O        -2.28
4633 LYS   (  11-)  P     - 4636 ARG   (  14-)  P        -2.33
4637 GLY   (  15-)  P     - 4641 GLY   (  19-)  P        -2.30
4769 ARG   (   8-)  0     - 4772 ASN   (  11-)  0        -2.13
4865 ARG   ( 104-)  0     - 4868 ASP   ( 107-)  0        -1.73
And so on for a total of 52 lines.

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: 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: K

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: 0

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: 1

Note: Second generation quality Z-score plot

Chain identifier: 2

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: V

Note: Second generation quality Z-score plot

Chain identifier: 3

Note: Second generation quality Z-score plot

Chain identifier: Z

Note: Second generation quality Z-score plot

Chain identifier: W

Note: Second generation quality Z-score plot

Chain identifier: X

Note: Second generation quality Z-score plot

Chain identifier: 4

Note: Second generation quality Z-score plot

Chain identifier: 5

Note: Second generation quality Z-score plot

Chain identifier: 6

Note: Second generation quality Z-score plot

Chain identifier: 7

Note: Second generation quality Z-score plot

Chain identifier: 8

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.

3227 ASN   ( 198-)  D
3423 ASN   ( 121-)  E
3445 ASN   ( 143-)  E
3494 ASN   ( 192-)  E
3835 ASN   ( 121-)  G
3969 ASN   (  74-)  H
4077 ASN   (  11-)  K
4257 ASN   (  45-)  M
4306 HIS   (  94-)  M
4432 ASN   (  82-)  N
4485 ASN   (  13-)  O
4556 ASN   (  84-)  O
4679 HIS   (  57-)  P
4772 ASN   (  11-)  0
4777 HIS   (  16-)  0
4784 ASN   (  23-)  0
4822 HIS   (  61-)  0
5113 GLN   ( 123-)  R
5192 ASN   (  66-)  1
5198 HIS   (  72-)  1
5243 GLN   ( 117-)  1
5308 HIS   (  64-)  2
5402 ASN   (  57-)  S
5447 HIS   ( 102-)  S
5543 GLN   (  87-)  T
5684 HIS   (  32-)  V
5707 HIS   (  55-)  V
5908 GLN   (  70-)  3
5988 HIS   (  66-)  Z
6073 GLN   (  56-)  W
6107 GLN   (  19-)  X
6140 HIS   (  52-)  X
6154 HIS   (   6-)  4
6195 GLN   (  47-)  4
6331 ASN   (   8-)  7
6414 GLN   (  43-)  8

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.

  10 OGUA  (  10-)  A      N1
  44 OGUA  (  45-)  A      N2
  48 OADE  (  49-)  A      N6
  50 OGUA  (  51-)  A      N2
  69 OGUA  (  70-)  A      N2
  71 OURA  (  72-)  A      N3
  83 OADE  (  84-)  A      N6
 138 OGUA  ( 139-)  A      N2
 140 OADE  ( 141-)  A      N6
 187 OURA  ( 200-)  A      N3
 207 OGUA  ( 220-)  A      N2
 209 OADE  ( 222-)  A      N6
 213 OGUA  ( 226-)  A      N1
 233 OCYT  ( 246-)  A      N4
 235 OGUA  ( 248-)  A      N2
 241 OGUA  ( 254-)  A      N2
 246 OGUA  ( 259-)  A      N2
 252 OADE  ( 265-)  A      N6
 329 OGUA  ( 307-)  A      N2
 331 OGUA  ( 309-)  A      N1
 345 OGUA  ( 323-)  A      N2
 349 OGUA  ( 327-)  A      N2
 352 OADE  ( 330-)  A      N6
 368 OADE  ( 346-)  A      N6
 399 OADE  ( 374-)  A      O2'
And so on for a total of 869 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.

3059 GLU   (  30-)  D      OE1
3059 GLU   (  30-)  D      OE2
3074 ASN   (  45-)  D      OD1
3125 HIS   (  96-)  D      ND1
3210 GLU   ( 181-)  D      OE2
3215 HIS   ( 186-)  D      ND1
3344 ASP   (  42-)  E      OD2
3471 ASN   ( 169-)  E      OD1
3530 ASP   (  23-)  F      OD1
3582 HIS   (  75-)  F      ND1
3676 ASN   ( 169-)  F      OD1
3754 ASN   (  40-)  G      OD1
3773 GLU   (  59-)  G      OE2
3870 ASP   ( 156-)  G      OD1
3956 HIS   (  61-)  H      ND1
3960 HIS   (  65-)  H      ND1
4132 GLU   (  66-)  K      OE1
4268 ASN   (  56-)  M      OD1
4300 GLU   (  88-)  M      OE1
4524 GLU   (  52-)  O      OE1
4647 ASP   (  25-)  P      OD1
4727 GLU   ( 105-)  P      OE2
4810 ASP   (  49-)  0      OD1
5069 HIS   (  79-)  R      ND1
5217 ASP   (  91-)  1      OD1
5220 ASN   (  94-)  1      OD1
5255 GLN   (  11-)  2      OE1
5259 GLU   (  15-)  2      OE1
5439 ASP   (  94-)  S      OD1
5511 ASN   (  55-)  T      OD1
5589 GLU   (  40-)  U      OE1
5775 ASP   ( 123-)  V      OD1
5797 GLU   ( 145-)  V      OE1
5830 GLU   ( 178-)  V      OE1
5928 GLU   (   6-)  Z      OE1
6261 HIS   (  43-)  5      ND1
6266 GLU   (  48-)  5      OE2
6285 GLU   (  15-)  6      OE2
6319 HIS   (  49-)  6      ND1

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.

3057 GLU   (  28-)  D   H-bonding suggests Gln
3198 GLU   ( 169-)  D   H-bonding suggests Gln
3266 GLU   ( 237-)  D   H-bonding suggests Gln
3344 ASP   (  42-)  E   H-bonding suggests Asn
3405 ASP   ( 103-)  E   H-bonding suggests Asn; but Alt-Rotamer
3510 GLU   (   3-)  F   H-bonding suggests Gln
3526 GLU   (  19-)  F   H-bonding suggests Gln
3530 ASP   (  23-)  F   H-bonding suggests Asn; but Alt-Rotamer
3534 GLU   (  27-)  F   H-bonding suggests Gln
3584 ASP   (  77-)  F   H-bonding suggests Asn
3645 GLU   ( 138-)  F   H-bonding suggests Gln; but Alt-Rotamer
3656 ASP   ( 149-)  F   H-bonding suggests Asn
3759 GLU   (  45-)  G   H-bonding suggests Gln; but Alt-Rotamer
3762 GLU   (  48-)  G   H-bonding suggests Gln; but Alt-Rotamer
3840 ASP   ( 126-)  G   H-bonding suggests Asn; but Alt-Rotamer
3870 ASP   ( 156-)  G   H-bonding suggests Asn; but Alt-Rotamer
3913 GLU   (  18-)  H   H-bonding suggests Gln
3929 GLU   (  34-)  H   H-bonding suggests Gln
4011 GLU   ( 116-)  H   H-bonding suggests Gln
4162 ASP   (  96-)  K   H-bonding suggests Asn
4183 GLU   ( 117-)  K   H-bonding suggests Gln
4188 GLU   ( 122-)  K   H-bonding suggests Gln
4191 GLU   ( 125-)  K   H-bonding suggests Gln
4300 GLU   (  88-)  M   H-bonding suggests Gln; but Alt-Rotamer
4339 ASP   ( 127-)  M   H-bonding suggests Asn; but Alt-Rotamer
And so on for a total of 61 lines.

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 :  -4.158 (poor)
  2nd generation packing quality :  -4.597 (bad)
  Ramachandran plot appearance   :  -6.283 (bad)
  chi-1/chi-2 rotamer normality  :  -5.198 (bad)
  Backbone conformation          :  -0.996

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.557 (tight)
  Bond angles                    :   0.805
  Omega angle restraints         :   0.252 (tight)
  Side chain planarity           :   0.193 (tight)
  Improper dihedral distribution :   0.692
  B-factor distribution          :   0.399
  Inside/Outside distribution    :   1.038

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 : 3.10


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -2.9
  2nd generation packing quality :  -2.2
  Ramachandran plot appearance   :  -3.4 (poor)
  chi-1/chi-2 rotamer normality  :  -2.6
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.557 (tight)
  Bond angles                    :   0.805
  Omega angle restraints         :   0.252 (tight)
  Side chain planarity           :   0.193 (tight)
  Improper dihedral distribution :   0.692
  B-factor distribution          :   0.399
  Inside/Outside distribution    :   1.038
==============

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.