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 pdb3i8i.ent

Checks that need to be done early-on in validation

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: 1400839.1
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= 10.393
Vm by authors and this calculated Vm do not agree very well

Administrative problems that can generate validation failures

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.

2189 OURA  (2167-)  A  -             2188 OGUA  (2165-)  A  -           4.0
Delete overlapping entity 2188 OGUA (2165-) A  -
Delete overlapping entity 4265 LEU  (  26-) Y  -
Delete overlapping entity 4349 GLY  ( 110-) Y  -

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.

2188 OGUA  (2165-)  A  -
4265 LEU   (  26-)  Y  -
4349 GLY   ( 110-)  Y  -

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: I

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: Y

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: J

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
 155 OCYT  ( 155-)  A    High
 156 OURA  ( 161-)  A    High
 157 OURA  ( 162-)  A    High
 158 OURA  ( 163-)  A    High
 159 OURA  ( 164-)  A    High
 160 OURA  ( 165-)  A    High
 161 OGUA  ( 171-)  A    High
 162 OCYT  ( 172-)  A    High
 219 OADE  ( 229-)  A    High
 265 OGUA  ( 270-)  A    High
 266 OURA  ( 270-)  A    High
 267 OCYT  ( 270-)  A    High
 268 OCYT  ( 270-)  A    High
 269 OGUA  ( 270-)  A    High
 270 OGUA  ( 270-)  A    High
 271 OCYT  ( 270-)  A    High
 272 OURA  ( 270-)  A    High
 273 OURA  ( 270-)  A    High
 274 OGUA  ( 270-)  A    High
And so on for a total of 1042 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: I

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: Y

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: J

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.

3271 ARG   ( 239-)  D
3305 ARG   ( 273-)  D
3363 ARG   (  58-)  E
3384 ARG   (  79-)  E
3839 ARG   ( 128-)  G
4443 ARG   (  63-)  L
4858 ARG   (  41-)  O
4867 ARG   (  50-)  O
4872 ARG   (  55-)  O
4878 ARG   (  61-)  O
4919 ARG   ( 102-)  O
4928 ARG   ( 111-)  O
5172 ARG   (  64-)  0
5196 ARG   (  88-)  0
5523 ARG   (  50-)  1
5531 ARG   (  58-)  1
5537 ARG   (  64-)  1
6230 ARG   (  32-)  3
6239 ARG   (  41-)  3

Warning: Tyrosine convention problem

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

3094 TYR   (  62-)  D
3136 TYR   ( 104-)  D
3349 TYR   (  44-)  E
3465 TYR   ( 160-)  E
3564 TYR   (  59-)  F
4118 TYR   (  25-)  K
4976 TYR   (   9-)  P
4993 TYR   (  26-)  P
5041 TYR   (  74-)  P
5104 TYR   ( 137-)  P
5129 TYR   (  21-)  0
5202 TYR   (  94-)  0
5232 TYR   (   7-)  Q
5405 TYR   (  68-)  R
5437 TYR   ( 100-)  R
5497 TYR   (  24-)  1
5518 TYR   (  45-)  1
5520 TYR   (  47-)  1
5549 TYR   (  76-)  1
5603 TYR   (  12-)  2
5701 TYR   (   9-)  S
5762 TYR   (  70-)  S
5767 TYR   (  75-)  S
5829 TYR   (  26-)  T
5916 TYR   (  20-)  U
5951 TYR   (  55-)  U
6007 TYR   (   8-)  V
6008 TYR   (   9-)  V
6037 TYR   (  38-)  V
6224 TYR   (  26-)  3
6540 TYR   (  32-)  4
6551 TYR   (  43-)  4
6575 TYR   (  67-)  4
6651 TYR   (  21-)  6
6795 TYR   (  64-)  8

Warning: Phenylalanine convention problem

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

3047 PHE   (  15-)  D
3053 PHE   (  21-)  D
3099 PHE   (  67-)  D
3167 PHE   ( 135-)  D
3356 PHE   (  51-)  E
3389 PHE   (  84-)  E
3418 PHE   ( 113-)  E
3734 PHE   (  23-)  G
3813 PHE   ( 102-)  G
4015 PHE   ( 123-)  H
4263 PHE   (  24-)  Y
4290 PHE   (  52-)  Y
4320 PHE   (  82-)  Y
4421 PHE   (  41-)  L
4445 PHE   (  65-)  L
4908 PHE   (  91-)  O
4947 PHE   ( 130-)  O
5036 PHE   (  69-)  P
5071 PHE   ( 104-)  P
5188 PHE   (  80-)  0
5237 PHE   (  12-)  Q
5254 PHE   (  29-)  Q
5394 PHE   (  57-)  R
5398 PHE   (  61-)  R
5513 PHE   (  40-)  1
5530 PHE   (  57-)  1
5824 PHE   (  21-)  T
5850 PHE   (  47-)  T
6047 PHE   (  48-)  V
6087 PHE   (  88-)  V
6088 PHE   (  89-)  V
6103 PHE   ( 104-)  V
6258 PHE   (  60-)  3

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.

3052 ASP   (  20-)  D
3131 ASP   (  99-)  D
3141 ASP   ( 109-)  D
3154 ASP   ( 122-)  D
3262 ASP   ( 230-)  D
3322 ASP   (  17-)  E
3479 ASP   ( 174-)  E
3702 ASP   ( 197-)  F
3867 ASP   ( 156-)  G
4067 ASP   (   4-)  I
4088 ASP   (  25-)  I
4113 ASP   (  20-)  K
4189 ASP   (  96-)  K
4323 ASP   (  85-)  Y
4369 ASP   ( 132-)  Y
4430 ASP   (  50-)  L
4442 ASP   (  62-)  L
4531 ASP   (   4-)  J
4707 ASP   (  12-)  N
4751 ASP   (  56-)  N
4864 ASP   (  47-)  O
5038 ASP   (  71-)  P
5177 ASP   (  69-)  0
5180 ASP   (  72-)  0
5189 ASP   (  81-)  0
5215 ASP   ( 107-)  0
5267 ASP   (  42-)  Q
5313 ASP   (  88-)  Q
5381 ASP   (  44-)  R
5424 ASP   (  87-)  R
5454 ASP   ( 117-)  R
5564 ASP   (  91-)  1
5714 ASP   (  22-)  S
5759 ASP   (  67-)  S
5786 ASP   (  94-)  S
6086 ASP   (  87-)  V
6122 ASP   ( 123-)  V
6139 ASP   ( 140-)  V
6147 ASP   ( 148-)  V
6153 ASP   ( 154-)  V
6254 ASP   (  56-)  3
6269 ASP   (  71-)  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.

3133 GLU   ( 101-)  D
3180 GLU   ( 148-)  D
3201 GLU   ( 169-)  D
3269 GLU   ( 237-)  D
3505 GLU   ( 200-)  E
3524 GLU   (  19-)  F
3625 GLU   ( 120-)  F
3650 GLU   ( 145-)  F
3705 GLU   ( 200-)  F
3724 GLU   (  13-)  G
3729 GLU   (  18-)  G
3759 GLU   (  48-)  G
3910 GLU   (  18-)  H
4051 GLU   ( 159-)  H
4059 GLU   ( 167-)  H
4069 GLU   (   6-)  I
4100 GLU   (   7-)  K
4103 GLU   (  10-)  K
4141 GLU   (  48-)  K
4153 GLU   (  60-)  K
4166 GLU   (  73-)  K
4210 GLU   ( 117-)  K
4254 GLU   (  15-)  Y
4257 GLU   (  18-)  Y
4274 GLU   (  36-)  Y
And so on for a total of 73 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.

  45 OCYT  (  46-)  A      N1   C2    1.36   -4.0
  66 OURA  (  67-)  A      C4   N3    1.34   -4.8
  73 OADE  (  74-)  A      N9   C4    1.34   -6.0
  73 OADE  (  74-)  A      C2   N3    1.29   -4.8
 411 OURA  ( 383-)  A      N1   C2    1.44    6.3
 411 OURA  ( 383-)  A      C2   O2    1.27    5.8
 471 OCYT  ( 444-)  A      N1   C2    1.35   -4.4
 542 OCYT  ( 516-)  A      N1   C2    1.36   -4.1
 561 OCYT  ( 535-)  A      N1   C2    1.36   -4.1
 647 OADE  ( 621-)  A      C5   C6    1.37   -4.3
 647 OADE  ( 621-)  A      C6   N6    1.28   -7.0
 688 OGUA  ( 654-)  A      N9   C4    1.41    4.1
 688 OGUA  ( 654-)  A      C2   N3    1.36    4.8
 688 OGUA  ( 654-)  A      C5   C6    1.36   -5.4
 693 OCYT  ( 654-)  A      N1   C2    1.45    5.4
 722 OGUA  ( 674-)  A      C5   C6    1.37   -4.4
 815 OURA  ( 767-)  A      N1   C2    1.34   -4.9
 928 OGUA  ( 880-)  A      C6   O6    1.20   -4.1
 929 OGUA  ( 881-)  A      C5   C6    1.37   -4.5
 943 OADE  ( 896-)  A      C2   N3    1.28   -5.2
 944 OCYT  ( 897-)  A      N1   C6    1.34   -4.3
 944 OCYT  ( 897-)  A      C5   C4    1.37   -6.6
 964 OADE  ( 917-)  A      C2   N3    1.29   -4.2
 991 OADE  ( 945-)  A      N9   C4    1.42    7.0
 991 OADE  ( 945-)  A      C6   N1    1.32   -4.8
And so on for a total of 67 lines.

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

 |  1.001981 -0.000029 -0.000044|
 | -0.000029  1.001860  0.000016|
 | -0.000044  0.000016  1.001597|
Proposed new scale matrix

 |  0.004765  0.000000  0.000000|
 |  0.000000  0.002237  0.000000|
 |  0.000000  0.000000  0.001602|
With corresponding cell

    A    = 209.883  B   = 447.059  C    = 624.048
    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: 5624.158
(Under-)estimated Z-score: 55.271

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  113.19    4.2
   2 OGUA  (   2-)  A      N9   C8   N7  113.17    4.1
   4 OCYT  (   4-)  A      O3'  C3'  C4' 122.51    4.6
   5 OADE  (   5-)  A      OP1  P   -O3*  64.56  -13.4
   5 OADE  (   5-)  A      OP2  P   -O3*  65.21  -13.5
   5 OADE  (   5-)  A      O5*  P   -O3* 113.82    5.2
   5 OADE  (   5-)  A      OP1  P    OP2 128.89    6.2
  15 OGUA  (  15-)  A      C2'  C1'  N9  106.64   -4.2
  17 OGUA  (  17-)  A      N9   C8   N7  113.34    4.5
  26 OGUA  (  26-)  A      N9   C8   N7  113.15    4.1
  27 OGUA  (  27-)  A      C5'  C4'  O4' 102.00   -5.1
  27 OGUA  (  27-)  A      C2'  C1'  N9  120.49    4.4
  30 OGUA  (  30-)  A      N9   C8   N7  113.25    4.3
  44 OGUA  (  45-)  A      N9   C8   N7  113.22    4.2
  50 OGUA  (  51-)  A      C3'  C4'  C5' 109.32   -4.1
  53 OGUA  (  54-)  A      C3'  C4'  C5' 108.68   -4.5
  53 OGUA  (  54-)  A      N9   C8   N7  113.42    4.6
  54 OGUA  (  55-)  A      N9   C8   N7  113.13    4.1
  57 OGUA  (  58-)  A      N9   C8   N7  113.14    4.1
  59 OGUA  (  60-)  A      C2'  C1'  N9  121.51    5.1
  62 OURA  (  63-)  A      C2'  C1'  N1  120.27    4.3
  66 OURA  (  67-)  A      C5   C4   O4  128.35    4.1
  66 OURA  (  67-)  A      C4   N3   C2  130.26    5.4
  69 OGUA  (  70-)  A      O3'  C3'  C2' 126.37    5.5
  69 OGUA  (  70-)  A      C2'  C1'  N9  123.63    6.4
And so on for a total of 1007 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.

3052 ASP   (  20-)  D
3131 ASP   (  99-)  D
3133 GLU   ( 101-)  D
3141 ASP   ( 109-)  D
3154 ASP   ( 122-)  D
3180 GLU   ( 148-)  D
3201 GLU   ( 169-)  D
3262 ASP   ( 230-)  D
3269 GLU   ( 237-)  D
3271 ARG   ( 239-)  D
3305 ARG   ( 273-)  D
3322 ASP   (  17-)  E
3363 ARG   (  58-)  E
3384 ARG   (  79-)  E
3479 ASP   ( 174-)  E
3505 GLU   ( 200-)  E
3524 GLU   (  19-)  F
3625 GLU   ( 120-)  F
3650 GLU   ( 145-)  F
3702 ASP   ( 197-)  F
3705 GLU   ( 200-)  F
3724 GLU   (  13-)  G
3729 GLU   (  18-)  G
3759 GLU   (  48-)  G
3839 ARG   ( 128-)  G
And so on for a total of 134 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.

3327 PRO   (  22-)  E      N     -9.4   -33.21    -2.48
3367 PRO   (  62-)  E      N      8.1    24.08    -2.48
3904 PRO   (  12-)  H      N     -7.7   -27.79    -2.48
4018 PRO   ( 126-)  H      N    -16.0   -55.07    -2.48
4046 PRO   ( 154-)  H      N      9.4    28.39    -2.48
4087 ILE   (  24-)  I      CB    12.5    48.60    32.31
4227 PRO   ( 134-)  K      N      6.9    20.21    -2.48
4289 LEU   (  51-)  Y      CG    -9.6   -49.83   -33.01
4307 PRO   (  69-)  Y      N     -7.6   -27.55    -2.48
4315 PRO   (  77-)  Y      N    -12.7   -44.01    -2.48
4366 PRO   ( 129-)  Y      N    -10.7   -37.59    -2.48
4382 PRO   ( 145-)  Y      N      6.4    18.44    -2.48
4452 PRO   (  72-)  L      N     -6.7   -24.32    -2.48
4530 LEU   (   3-)  J      CG   -11.2   -52.79   -33.01
4544 VAL   (  17-)  J      CB    -9.9   -45.94   -32.96
4827 PRO   (  10-)  O      N      9.2    27.71    -2.48
5973 PRO   (  77-)  U      N      8.0    23.64    -2.48
6060 LEU   (  61-)  V      CG    -6.8   -44.98   -33.01
6176 PRO   ( 177-)  V      N     12.3    37.96    -2.48
6193 PRO   ( 194-)  V      N    -11.1   -38.80    -2.48
The average deviation= 0.956

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.

4073 GLU   (  10-)  I   10.35
4671 ARG   ( 114-)  M    9.15
4311 GLY   (  73-)  Y    9.02
4273 LYS   (  35-)  Y    8.60
4404 GLY   (  24-)  L    8.45
4375 LEU   ( 138-)  Y    8.36
3702 ASP   ( 197-)  F    8.30
4487 ILE   ( 107-)  L    8.20
5054 LYS   (  87-)  P    8.18
6382 GLU   (   5-)  W    8.08
4297 ILE   (  59-)  Y    7.99
6784 PRO   (  53-)  8    7.76
4247 GLU   (   8-)  Y    7.64
4626 GLN   (  69-)  M    7.52
4083 LEU   (  20-)  I    7.42
5460 GLN   ( 123-)  R    7.30
4520 GLY   ( 140-)  L    7.14
4277 ALA   (  39-)  Y    6.83
6108 ALA   ( 109-)  V    6.81
3473 MET   ( 168-)  E    6.74
4550 LEU   (  23-)  J    6.71
5182 LYS   (  74-)  0    6.71
4830 ASN   (  13-)  O    6.58
4529 ALA   (   2-)  J    6.56
4831 LYS   (  14-)  O    6.55
And so on for a total of 168 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 : 1.944

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.

4852 HIS   (  35-)  O      CB   4.07

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.

1948 OCYT  (1925-)  A    0.40
 631 OURA  ( 607-)  A    0.39
2668 OURA  (2656-)  A    0.32
3009 OURA  (  95-)  B    0.24
1129 OURA  (1082-)  A    0.21
1296 OURA  (1249-)  A    0.19
1952 OGUA  (1929-)  A    0.19
1581 OGUA  (1534-)  A    0.16
 647 OADE  ( 621-)  A    0.16
1133 OADE  (1086-)  A    0.14
 693 OCYT  ( 654-)  A    0.13
2802 OCYT  (2789-)  A    0.13
 687 OCYT  ( 654-)  A    0.13
2792 OURA  (2779-)  A    0.12
2994 OGUA  (  81-)  B    0.12
1806 OCYT  (1774-)  A    0.12
1712 OADE  (1664-)  A    0.11
2516 OURA  (2504-)  A    0.11
 413 OCYT  ( 385-)  A    0.11
2054 OADE  (2031-)  A    0.11
  71 OURA  (  72-)  A    0.10
 656 OGUA  ( 630-)  A    0.10
1866 OURA  (1834-)  A    0.10
 Ramachandran Z-score : -6.024

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 : -6.024

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.

4263 PHE   (  24-)  Y    -3.8
5237 PHE   (  12-)  Q    -3.8
6795 TYR   (  64-)  8    -3.7
4171 THR   (  78-)  K    -3.7
4446 THR   (  66-)  L    -3.7
4497 THR   ( 117-)  L    -3.7
4988 THR   (  21-)  P    -3.6
4543 THR   (  16-)  J    -3.6
4398 THR   (  18-)  L    -3.6
6208 THR   (  10-)  3    -3.6
5640 THR   (  49-)  2    -3.6
6575 TYR   (  67-)  4    -3.5
6106 THR   ( 107-)  V    -3.4
6660 THR   (  30-)  6    -3.4
4330 THR   (  92-)  Y    -3.4
6582 HIS   (   4-)  5    -3.4
4275 THR   (  37-)  Y    -3.4
4585 THR   (  28-)  M    -3.4
4849 THR   (  32-)  O    -3.3
4445 PHE   (  65-)  L    -3.3
5377 THR   (  40-)  R    -3.1
4827 PRO   (  10-)  O    -3.1
3904 PRO   (  12-)  H    -3.1
3367 PRO   (  62-)  E    -3.1
4241 PRO   (   2-)  Y    -3.1
And so on for a total of 574 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.

3035 VAL   (   3-)  D  Poor phi/psi
3040 PRO   (   8-)  D  Poor phi/psi
3044 SER   (  12-)  D  Poor phi/psi
3046 ARG   (  14-)  D  Poor phi/psi
3047 PHE   (  15-)  D  Poor phi/psi
3059 THR   (  27-)  D  Poor phi/psi
3060 GLU   (  28-)  D  Poor phi/psi
3062 GLU   (  30-)  D  Poor phi/psi
3065 LEU   (  33-)  D  Poor phi/psi
3067 LYS   (  35-)  D  Poor phi/psi, PRO omega poor
3076 ASN   (  44-)  D  Poor phi/psi
3085 PHE   (  53-)  D  Poor phi/psi
3118 PRO   (  86-)  D  Poor phi/psi
3143 LEU   ( 111-)  D  Poor phi/psi
3154 ASP   ( 122-)  D  Poor phi/psi
3155 ALA   ( 123-)  D  Poor phi/psi
3171 GLY   ( 139-)  D  Poor phi/psi
3175 HIS   ( 143-)  D  Poor phi/psi
3176 ALA   ( 144-)  D  Poor phi/psi
3182 LYS   ( 150-)  D  Poor phi/psi
3191 ALA   ( 159-)  D  Poor phi/psi
3194 SER   ( 162-)  D  Poor phi/psi
3230 ASN   ( 198-)  D  Poor phi/psi
3234 LYS   ( 202-)  D  Poor phi/psi
3269 GLU   ( 237-)  D  Poor phi/psi
And so on for a total of 784 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 : -5.759

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.

5169 HIS   (  61-)  0    0.38
5061 VAL   (  94-)  P    0.39
3955 SER   (  63-)  H    0.39

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 5026 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 : 2.227

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!

3435 GLY   ( 130-)  E   3.03   27
6113 GLY   ( 114-)  V   2.28   13
3685 GLY   ( 180-)  F   1.94   22
3865 GLY   ( 154-)  G   1.81   37
3142 GLY   ( 110-)  D   1.81   80
3288 GLY   ( 256-)  D   1.77   39
3576 GLY   (  71-)  F   1.76   28
4634 GLY   (  77-)  M   1.74   10
3447 GLY   ( 142-)  E   1.66   21
5906 GLY   (  10-)  U   1.60   62
5864 GLY   (  61-)  T   1.53   11
3840 GLY   ( 129-)  G   1.53   24
5499 GLY   (  26-)  1   1.52   14
5059 GLY   (  92-)  P   1.51   21
5599 GLY   (   8-)  2   1.51   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...

3473 MET   ( 168-)  E   1.93
4107 ASP   (  14-)  K   1.80
4309 LEU   (  71-)  Y   2.17
6115 VAL   ( 116-)  V   2.91
6675 LYS   (  45-)  6   2.26
6730 ARG   (  47-)  7   2.32

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]

3273 PRO   ( 241-)  D    0.45 HIGH
3358 PRO   (  53-)  E    0.45 HIGH
3367 PRO   (  62-)  E    0.45 HIGH
3443 PRO   ( 138-)  E    0.47 HIGH
3452 PRO   ( 147-)  E    0.45 HIGH
3571 PRO   (  66-)  F    0.49 HIGH
3597 PRO   (  92-)  F    0.46 HIGH
3599 PRO   (  94-)  F    0.46 HIGH
3904 PRO   (  12-)  H    0.46 HIGH
4046 PRO   ( 154-)  H    0.45 HIGH
4204 PRO   ( 111-)  K    0.46 HIGH
4343 PRO   ( 105-)  Y    0.50 HIGH
4382 PRO   ( 145-)  Y    0.54 HIGH
4402 PRO   (  22-)  L    0.45 HIGH
4434 PRO   (  54-)  L    0.48 HIGH
4493 PRO   ( 113-)  L    0.48 HIGH
4522 PRO   ( 142-)  L    0.45 HIGH
4686 PRO   ( 129-)  M    0.46 HIGH
5147 PRO   (  39-)  0    0.45 HIGH
5607 PRO   (  16-)  2    0.45 HIGH
5973 PRO   (  77-)  U    0.46 HIGH
6176 PRO   ( 177-)  V    0.48 HIGH
6784 PRO   (  53-)  8    0.47 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].

3327 PRO   (  22-)  E   -14.9 half-chair C-alpha/N (-18 degrees)
3367 PRO   (  62-)  E   156.9 half-chair C-alpha/N (162 degrees)
3530 PRO   (  25-)  F   100.8 envelop C-beta (108 degrees)
3535 PRO   (  30-)  F  -113.4 envelop C-gamma (-108 degrees)
3571 PRO   (  66-)  F   101.7 envelop C-beta (108 degrees)
3904 PRO   (  12-)  H   -36.5 envelop C-alpha (-36 degrees)
4018 PRO   ( 126-)  H   -16.0 half-chair C-alpha/N (-18 degrees)
4046 PRO   ( 154-)  H   136.7 envelop C-alpha (144 degrees)
4227 PRO   ( 134-)  K   137.2 envelop C-alpha (144 degrees)
4241 PRO   (   2-)  Y   -46.1 half-chair C-beta/C-alpha (-54 degrees)
4271 PRO   (  33-)  Y   101.0 envelop C-beta (108 degrees)
4339 PRO   ( 101-)  Y   -57.8 half-chair C-beta/C-alpha (-54 degrees)
4366 PRO   ( 129-)  Y     4.0 envelop N (0 degrees)
4393 PRO   (  13-)  L   -64.4 envelop C-beta (-72 degrees)
4452 PRO   (  72-)  L   -32.6 envelop C-alpha (-36 degrees)
4493 PRO   ( 113-)  L   152.6 envelop C-alpha (144 degrees)
4699 PRO   (   4-)  N  -112.2 envelop C-gamma (-108 degrees)
4825 PRO   (   8-)  O    41.3 envelop C-delta (36 degrees)
4827 PRO   (  10-)  O   157.1 half-chair C-alpha/N (162 degrees)
5066 PRO   (  99-)  P   105.2 envelop C-beta (108 degrees)
5641 PRO   (  50-)  2  -143.6 envelop C-delta (-144 degrees)
5681 PRO   (  90-)  2  -112.3 envelop C-gamma (-108 degrees)
5888 PRO   (  85-)  T  -112.7 envelop C-gamma (-108 degrees)
5928 PRO   (  32-)  U  -116.8 envelop C-gamma (-108 degrees)
5973 PRO   (  77-)  U   149.1 envelop C-alpha (144 degrees)
6612 PRO   (  34-)  5  -113.9 envelop C-gamma (-108 degrees)
6625 PRO   (  47-)  5  -127.2 half-chair C-delta/C-gamma (-126 degrees)
6794 PRO   (  63-)  8   103.6 envelop C-beta (108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic 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. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

4387 VAL   (   7-)  L      CB  <-> 4437 ILE   (  57-)  L      CG2    1.55    1.65  INTRA BF
4289 LEU   (  51-)  Y      CD1 <-> 4319 VAL   (  81-)  Y      CG2    1.54    1.66  INTRA BF
4541 GLN   (  14-)  J      NE2 <-> 4546 GLU   (  19-)  J      CG     1.46    1.64  INTRA BF
4267 TYR   (  29-)  Y      N   <-> 4319 VAL   (  81-)  Y      CG1    1.41    1.69  INTRA BF
4387 VAL   (   7-)  L      CG1 <-> 4437 ILE   (  57-)  L      CD1    1.22    1.98  INTRA BF
4267 TYR   (  29-)  Y      O   <-> 4319 VAL   (  81-)  Y      CB     1.20    1.60  INTRA BF
4400 ALA   (  20-)  L      N   <-> 4405 PRO   (  25-)  L      CD     1.19    1.91  INTRA BF
4266 ASN   (  28-)  Y      O   <-> 4318 VAL   (  80-)  Y      CG1    1.18    1.62  INTRA BF
4387 VAL   (   7-)  L      CG1 <-> 4437 ILE   (  57-)  L      CG2    1.17    2.03  INTRA BF
6190 VAL   ( 191-)  V      CG1 <-> 6196 ILE   ( 197-)  V      CG2    1.17    2.03  INTRA BF
4540 SER   (  13-)  J      CB  <-> 4544 VAL   (  17-)  J      CG2    1.17    2.03  INTRA BF
4289 LEU   (  51-)  Y      CD2 <-> 4320 PHE   (  82-)  Y      O      1.17    1.63  INTRA BF
4264 PHE   (  25-)  Y      CD1 <-> 4320 PHE   (  82-)  Y      CD1    1.17    2.03  INTRA BF
4484 VAL   ( 104-)  L      O   <-> 4487 ILE   ( 107-)  L      CG2    1.12    1.68  INTRA BF
4289 LEU   (  51-)  Y      CD1 <-> 4320 PHE   (  82-)  Y      N      1.11    1.99  INTRA BF
4388 VAL   (   8-)  L      O   <-> 4437 ILE   (  57-)  L      CG1    1.11    1.69  INTRA BF
4289 LEU   (  51-)  Y      CD2 <-> 4320 PHE   (  82-)  Y      C      1.08    2.12  INTRA BF
4541 GLN   (  14-)  J      NE2 <-> 4546 GLU   (  19-)  J      CB     1.04    2.06  INTRA BF
4258 ARG   (  19-)  Y      CZ  <-> 4322 GLU   (  84-)  Y      OE1    1.04    1.76  INTRA BF
4400 ALA   (  20-)  L      N   <-> 4405 PRO   (  25-)  L      CG     1.04    2.06  INTRA BF
4255 ASN   (  16-)  Y      CA  <-> 4258 ARG   (  19-)  Y      NH1    1.01    2.09  INTRA BF
4255 ASN   (  16-)  Y      CB  <-> 4258 ARG   (  19-)  Y      NH1    1.00    2.10  INTRA BF
6524 CYS   (  16-)  4      CB  <-> 6544 CYS   (  36-)  4      SG     0.99    2.41  INTRA BF
4281 ALA   (  43-)  Y      CB  <-> 4285 ASN   (  47-)  Y      ND2    0.99    2.11  INTRA BF
4072 LYS   (   9-)  I      O   <-> 4074 GLU   (  11-)  I      N      0.97    1.73  INTRA BF
And so on for a total of 7473 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: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: Y

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

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.

6111 ARG   ( 112-)  V      -8.43
5951 TYR   (  55-)  U      -8.41
4062 ARG   ( 170-)  H      -8.39
6630 TYR   (  52-)  5      -8.35
3271 ARG   ( 239-)  D      -8.35
4972 ARG   (   5-)  P      -8.33
6795 TYR   (  64-)  8      -8.28
4973 ARG   (   6-)  P      -8.09
6212 ARG   (  14-)  3      -8.09
3295 ARG   ( 263-)  D      -8.07
5213 ARG   ( 105-)  0      -8.02
3276 ARG   ( 244-)  D      -7.97
5432 ARG   (  95-)  R      -7.89
6209 ARG   (  11-)  3      -7.89
4835 ARG   (  18-)  O      -7.86
5049 ARG   (  82-)  P      -7.75
6761 ARG   (  30-)  8      -7.73
3895 ARG   (   3-)  H      -7.68
6730 ARG   (  47-)  7      -7.67
4838 ARG   (  21-)  O      -7.63
5391 ARG   (  54-)  R      -7.53
3116 TYR   (  84-)  D      -7.51
4744 ARG   (  49-)  N      -7.48
5953 GLN   (  57-)  U      -7.47
3579 ARG   (  74-)  F      -7.46
And so on for a total of 354 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.

3086 ARG   (  54-)  D      3088 - GLY     56- ( D)         -4.71
3268 GLY   ( 236-)  D      3271 - ARG    239- ( D)         -5.53
3274 ARG   ( 242-)  D      3276 - ARG    244- ( D)         -6.56
3432 ASP   ( 127-)  E      3434 - HIS    129- ( E)         -4.49
3440 HIS   ( 135-)  E      3442 - HIS    137- ( E)         -5.45
3445 SER   ( 140-)  E      3451 - THR    146- ( E)         -5.12
3549 ARG   (  44-)  F      3551 - ARG     46- ( F)         -5.45
3572 GLN   (  67-)  F      3574 - HIS     69- ( F)         -5.61
3587 ILE   (  82-)  F      3589 - VAL     84- ( F)         -4.68
4049 TYR   ( 157-)  H      4051 - GLU    159- ( H)         -5.47
4102 LEU   (   9-)  K      4104 - ASN     11- ( K)         -4.88
4196 ARG   ( 103-)  K      4198 - HIS    105- ( K)         -5.43
4267 TYR   (  29-)  Y      4270 - LEU     32- ( Y)         -4.76
4302 LYS   (  64-)  Y      4304 - LEU     66- ( Y)         -5.12
4344 GLN   ( 106-)  Y      4347 - SER    109- ( Y)         -5.83
4352 GLN   ( 115-)  Y      4354 - LEU    117- ( Y)         -5.02
4379 LEU   ( 142-)  Y      4382 - PRO    145- ( Y)         -5.06
4473 ARG   (  93-)  L      4476 - VAL     96- ( L)         -4.73
4524 VAL   ( 144-)  L      4527 - ALA    147- ( L)         -4.79
4831 LYS   (  14-)  O      4835 - ARG     18- ( O)         -5.64
4841 GLY   (  24-)  O      4843 - GLY     26- ( O)         -4.38
4866 ARG   (  49-)  O      4869 - GLU     52- ( O)         -5.07
4881 LYS   (  64-)  O      4885 - GLN     68- ( O)         -5.99
4892 ILE   (  75-)  O      4894 - ARG     77- ( O)         -5.86
4964 LEU   ( 147-)  O      4967 - ALA    150- ( O)         -5.24
4975 LYS   (   8-)  P      4981 - ARG     14- ( P)         -5.99
4983 ARG   (  16-)  P      4985 - LYS     18- ( P)         -5.61
5046 LEU   (  79-)  P      5052 - LYS     85- ( P)         -5.62
5110 ARG   (   2-)  0      5114 - SER      6- ( 0)         -5.37
5118 LEU   (  10-)  0      5120 - ARG     12- ( 0)         -4.84
5211 ARG   ( 103-)  0      5213 - ARG    105- ( 0)         -5.95
5752 ASN   (  60-)  S      5754 - HIS     62- ( S)         -5.24
5802 LYS   ( 110-)  S      5804 - GLY    112- ( S)         -4.90
5945 VAL   (  49-)  U      5947 - VAL     51- ( U)         -4.41
5997 LYS   ( 101-)  U      5999 - GLY    103- ( U)         -4.89
6008 TYR   (   9-)  V      6010 - GLU     11- ( V)         -4.90
6078 ARG   (  79-)  V      6080 - ARG     81- ( V)         -5.28
6196 ILE   ( 197-)  V      6199 - GLY    200- ( V)         -5.42
6201 HIS   (   3-)  3      6207 - SER      9- ( 3)         -5.28
6357 GLU   (  75-)  Z      6360 - LYS     78- ( Z)         -4.86
6446 ARG   (  69-)  W      6449 - ALA     72- ( W)         -5.25
6461 ILE   (  13-)  X      6463 - TYR     15- ( X)         -4.69
6580 ALA   (   2-)  5      6583 - PRO      5- ( 5)         -5.20
6586 LYS   (   8-)  5      6588 - LYS     10- ( 5)         -5.04
6646 CYS   (  16-)  6      6649 - ARG     19- ( 6)         -6.25
6657 LYS   (  27-)  6      6659 - ASN     29- ( 6)         -5.99
6672 TRP   (  42-)  6      6676 - HIS     46- ( 6)         -5.38
6722 ARG   (  39-)  7      6725 - LEU     42- ( 7)         -4.75
6729 VAL   (  46-)  7      6731 - LYS     48- ( 7)         -6.14
6773 ARG   (  42-)  8      6775 - LYS     44- ( 8)         -4.38

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 - 6796 : -2.104

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: 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: Y

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: 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: 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.

6210 ASN   (  12-)  3   -4.04
3573 LYS   (  68-)  F   -3.79
3367 PRO   (  62-)  E   -3.50
4832 ARG   (  15-)  O   -3.44
4688 GLN   ( 131-)  M   -3.43
6657 LYS   (  27-)  6   -3.43
4877 MET   (  60-)  O   -3.42
6587 LYS   (   9-)  5   -3.38
5478 LYS   (   5-)  1   -3.29
5500 LEU   (  27-)  1   -3.28
6360 LYS   (  78-)  Z   -3.25
6762 HIS   (  31-)  8   -3.25
3454 ARG   ( 149-)  E   -3.23
3674 ASN   ( 169-)  F   -3.23
6362 LEU   (  80-)  Z   -3.22
4881 LYS   (  64-)  O   -3.20
3600 ARG   (  95-)  F   -3.18
4495 LEU   ( 115-)  L   -3.14
3439 ILE   ( 134-)  E   -3.13
6690 PRO   (   7-)  7   -3.09
3273 PRO   ( 241-)  D   -3.09
4985 LYS   (  18-)  P   -3.08
6686 ARG   (   3-)  7   -3.07
3579 ARG   (  74-)  F   -3.07
6582 HIS   (   4-)  5   -3.07
And so on for a total of 133 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.

3072 THR   (  40-)  D     - 3075 ARG   (  43-)  D        -1.89
3076 ASN   (  44-)  D     - 3084 ARG   (  52-)  D        -2.02
3255 GLY   ( 223-)  D     - 3261 VAL   ( 229-)  D        -2.30
3267 GLY   ( 235-)  D     - 3276 ARG   ( 244-)  D        -2.42
3291 THR   ( 259-)  D     - 3296 LYS   ( 264-)  D        -2.11
3363 ARG   (  58-)  E     - 3367 PRO   (  62-)  E        -2.24
3432 ASP   ( 127-)  E     - 3435 GLY   ( 130-)  E        -2.26
3436 ALA   ( 131-)  E     - 3439 ILE   ( 134-)  E        -2.56
3442 HIS   ( 137-)  E     - 3445 SER   ( 140-)  E        -2.10
3446 ILE   ( 141-)  E     - 3450 LYS   ( 145-)  E        -2.52
3451 THR   ( 146-)  E     - 3454 ARG   ( 149-)  E        -2.51
3804 THR   (  93-)  G     - 3807 ARG   (  96-)  G        -1.85
3893 LYS   ( 182-)  G     - 3896 ILE   (   4-)  H        -1.75
4047 SER   ( 155-)  H     - 4050 HIS   ( 158-)  H        -2.34
4241 PRO   (   2-)  Y     - 4244 ARG   (   5-)  Y        -2.40
4266 ASN   (  28-)  Y     - 4270 LEU   (  32-)  Y        -1.70
4288 ARG   (  50-)  Y     - 4291 VAL   (  53-)  Y        -1.90
4383 LYS   (   3-)  L     - 4386 ALA   (   6-)  L        -1.33
4561 TYR   (   4-)  M     - 4564 LYS   (   7-)  M        -1.51
4687 HIS   ( 130-)  M     - 4690 GLN   ( 133-)  M        -2.22
4721 LYS   (  26-)  N     - 4724 ASN   (  29-)  N        -2.18
4833 ARG   (  16-)  O     - 4842 SER   (  25-)  O        -2.17
4845 GLY   (  28-)  O     - 4848 ALA   (  31-)  O        -2.08
4865 PRO   (  48-)  O     - 4868 PHE   (  51-)  O        -1.81
4876 LEU   (  59-)  O     - 4879 LEU   (  62-)  O        -2.36
4880 PRO   (  63-)  O     - 4890 GLY   (  73-)  O        -2.39
4979 GLN   (  12-)  P     - 4985 LYS   (  18-)  P        -2.38
5042 THR   (  75-)  P     - 5046 LEU   (  79-)  P        -1.88
5047 GLU   (  80-)  P     - 5052 LYS   (  85-)  P        -2.05
5108 GLN   ( 141-)  P     - 5113 LYS   (   5-)  0        -2.37
5116 ARG   (   8-)  0     - 5119 ASN   (  11-)  0        -2.16
5212 ARG   ( 104-)  0     - 5215 ASP   ( 107-)  0        -1.92
5431 ALA   (  94-)  R     - 5435 LYS   (  98-)  R        -2.36
5474 LYS   ( 137-)  R     - 5480 GLY   (   7-)  1        -2.62
5598 THR   (   7-)  2     - 5601 LYS   (  10-)  2        -1.93
5667 LYS   (  76-)  2     - 5672 TYR   (  81-)  2        -2.27
5766 ALA   (  74-)  S     - 5769 ASP   (  77-)  S        -1.57
5778 LEU   (  86-)  S     - 5781 ALA   (  89-)  S        -1.89
5964 HIS   (  68-)  U     - 5967 LYS   (  71-)  U        -1.75
6076 ASP   (  77-)  V     - 6079 ARG   (  80-)  V        -2.14
6192 GLU   ( 193-)  V     - 6196 ILE   ( 197-)  V        -1.86
6201 HIS   (   3-)  3     - 6204 GLY   (   6-)  3        -2.02
6214 SER   (  16-)  3     - 6218 ARG   (  20-)  3        -2.23
6579 ARG   (  71-)  4     - 6589 THR   (  11-)  5        -2.50
6687 THR   (   4-)  7     - 6690 PRO   (   7-)  7        -2.37
6760 LYS   (  29-)  8     - 6763 LEU   (  32-)  8        -2.37
6792 LEU   (  61-)  8     - 6795 TYR   (  64-)  8        -1.96

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: I

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: Y

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: J

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.

3128 HIS   (  96-)  D
3230 ASN   ( 198-)  D
3426 ASN   ( 121-)  E
3440 HIS   ( 135-)  E
3536 HIS   (  31-)  F
3545 GLN   (  40-)  F
3572 GLN   (  67-)  F
3574 HIS   (  69-)  F
3752 GLN   (  41-)  G
4031 GLN   ( 139-)  H
4039 ASN   ( 147-)  H
4121 ASN   (  28-)  K
4167 ASN   (  74-)  K
4276 HIS   (  38-)  Y
4285 ASN   (  47-)  Y
4602 ASN   (  45-)  M
4613 ASN   (  56-)  M
4724 ASN   (  29-)  N
4777 ASN   (  82-)  N
4852 HIS   (  35-)  O
4885 GLN   (  68-)  O
5108 GLN   ( 141-)  P
5111 HIS   (   3-)  0
5124 HIS   (  16-)  0
5131 ASN   (  23-)  0
And so on for a total of 53 lines.

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.

  28 OADE  (  28-)  A      N6
  44 OGUA  (  45-)  A      N2
  48 OADE  (  49-)  A      N6
  50 OGUA  (  51-)  A      N2
  71 OURA  (  72-)  A      N3
  74 OGUA  (  75-)  A      N2
  83 OADE  (  84-)  A      N6
 136 OGUA  ( 137-)  A      N2
 138 OGUA  ( 139-)  A      N1
 138 OGUA  ( 139-)  A      N2
 140 OADE  ( 141-)  A      N6
 189 OADE  ( 199-)  A      N6
 190 OURA  ( 200-)  A      N3
 210 OGUA  ( 220-)  A      N2
 216 OGUA  ( 226-)  A      N1
 238 OGUA  ( 248-)  A      N2
 249 OGUA  ( 259-)  A      N2
 334 OGUA  ( 309-)  A      N1
 355 OADE  ( 330-)  A      N6
 417 OGUA  ( 389-)  A      N1
 439 OGUA  ( 411-)  A      N2
 456 OADE  ( 428-)  A      N6
 491 OURA  ( 464-)  A      O2'
 492 OGUA  ( 465-)  A      N2
 520 OGUA  ( 494-)  A      O2'
And so on for a total of 887 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.

3062 GLU   (  30-)  D      OE2
3076 ASN   (  44-)  D      OD1
3077 ASN   (  45-)  D      OD1
3098 ASP   (  66-)  D      OD2
3115 GLU   (  83-)  D      OE1
3213 GLU   ( 181-)  D      OE2
3218 HIS   ( 186-)  D      ND1
3269 GLU   ( 237-)  D      OE1
3347 ASP   (  42-)  E      OD2
3360 ASN   (  55-)  E      OD1
3378 GLU   (  73-)  E      OE1
3434 HIS   ( 129-)  E      ND1
3580 HIS   (  75-)  F      ND1
3643 GLU   ( 138-)  F      OE1
3700 ASP   ( 195-)  F      OD1
3751 ASN   (  40-)  G      OD1
3770 GLU   (  59-)  G      OE2
3815 GLU   ( 104-)  G      OE1
3867 ASP   ( 156-)  G      OD1
4322 GLU   (  84-)  Y      OE1
4358 ASP   ( 121-)  Y      OD1
4369 ASP   ( 132-)  Y      OD1
4533 GLU   (   6-)  J      OE1
4537 GLU   (  10-)  J      OE1
4537 GLU   (  10-)  J      OE2
4538 GLU   (  11-)  J      OE1
4546 GLU   (  19-)  J      OE2
4685 HIS   ( 128-)  M      ND1
4698 GLN   (   3-)  N      OE1
4945 HIS   ( 128-)  O      ND1
5056 ASN   (  89-)  P      OD1
5058 GLU   (  91-)  P      OE1
5105 ASP   ( 138-)  P      OD2
5157 ASP   (  49-)  0      OD1
5313 ASP   (  88-)  Q      OD1
5416 HIS   (  79-)  R      ND1
5522 HIS   (  49-)  1      ND1
5564 ASP   (  91-)  1      OD1
5581 GLU   ( 108-)  1      OE1
5602 GLN   (  11-)  2      OE1
5655 HIS   (  64-)  2      ND1
5936 GLU   (  40-)  U      OE2
6086 ASP   (  87-)  V      OD2
6177 GLU   ( 178-)  V      OE1
6487 ASP   (  39-)  X      OD1
6679 HIS   (  49-)  6      ND1
6774 GLN   (  43-)  8      OE1

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.

3060 GLU   (  28-)  D   H-bonding suggests Gln
3098 ASP   (  66-)  D   H-bonding suggests Asn; but Alt-Rotamer
3154 ASP   ( 122-)  D   H-bonding suggests Asn; but Alt-Rotamer
3262 ASP   ( 230-)  D   H-bonding suggests Asn
3269 GLU   ( 237-)  D   H-bonding suggests Gln
3345 GLU   (  40-)  E   H-bonding suggests Gln
3347 ASP   (  42-)  E   H-bonding suggests Asn
3394 ASP   (  89-)  E   H-bonding suggests Asn; but Alt-Rotamer
3408 ASP   ( 103-)  E   H-bonding suggests Asn; but Alt-Rotamer
3479 ASP   ( 174-)  E   H-bonding suggests Asn
3484 GLU   ( 179-)  E   H-bonding suggests Gln; but Alt-Rotamer
3505 GLU   ( 200-)  E   H-bonding suggests Gln; but Alt-Rotamer
3625 GLU   ( 120-)  F   H-bonding suggests Gln
3643 GLU   ( 138-)  F   H-bonding suggests Gln
3654 ASP   ( 149-)  F   H-bonding suggests Asn; but Alt-Rotamer
3700 ASP   ( 195-)  F   H-bonding suggests Asn; but Alt-Rotamer
3759 GLU   (  48-)  G   H-bonding suggests Gln
3808 ASP   (  97-)  G   H-bonding suggests Asn
3837 ASP   ( 126-)  G   H-bonding suggests Asn
3858 ASP   ( 147-)  G   H-bonding suggests Asn; but Alt-Rotamer
3910 GLU   (  18-)  H   H-bonding suggests Gln; but Alt-Rotamer
3973 GLU   (  81-)  H   H-bonding suggests Gln
4008 GLU   ( 116-)  H   H-bonding suggests Gln
4069 GLU   (   6-)  I   H-bonding suggests Gln
4092 GLU   (  29-)  I   H-bonding suggests Gln
And so on for a total of 70 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 :  -4.010 (poor)
  2nd generation packing quality :  -4.437 (bad)
  Ramachandran plot appearance   :  -6.024 (bad)
  chi-1/chi-2 rotamer normality  :  -5.759 (bad)
  Backbone conformation          :  -1.136

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.698
  Bond angles                    :   0.914
  Omega angle restraints         :   0.405 (tight)
  Side chain planarity           :   0.255 (tight)
  Improper dihedral distribution :   0.902
  B-factor distribution          :   0.468
  Inside/Outside distribution    :   1.040

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 :  -2.8
  2nd generation packing quality :  -2.1
  Ramachandran plot appearance   :  -3.2 (poor)
  chi-1/chi-2 rotamer normality  :  -3.2 (poor)
  Backbone conformation          :  -0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.698
  Bond angles                    :   0.914
  Omega angle restraints         :   0.405 (tight)
  Side chain planarity           :   0.255 (tight)
  Improper dihedral distribution :   0.902
  B-factor distribution          :   0.468
  Inside/Outside distribution    :   1.040
==============

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.