WHAT IF Check report

This file was created 2011-12-17 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 pdb3pyt.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: 1331348.9
Volume of the Unit Cell V= 58457504.0
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 21.954
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)

Warning: Chain identifier inconsistency

WHAT IF believes that certain residue(s) have the wrong chain identifier. It has corrected these chain identifiers as indicated in the table. In this table the residues (ligands, drugs, lipids, ions, sugars, etc) that got their chain identifier corrected are listed with the new chain identifier that is used throughout this validation report. WHAT IF does not care about the chain identifiers of water molecules.

6296  MG   (  70-)  K  6
6527  MG   (3013-)  M  A
6822  MG   (3109-)  B  A
6996  MG   ( 770-)  K  P
7284  MG   (1059-)  A  6

Non-validating, descriptive output paragraph

Warning: Ions bound to the wrong chain

The ions listed in the table have a chain identifier that is the same as one of the protein, nucleic acid, or sugar chains. However, the ion seems bound to protein, nucleic acid, or sugar, with another chain identifier.

Obviously, this is not wrong, but it is confusing for users of this PDB file.

6358  MG   (2959-)  A  -
6929  MG   (3150-)  A  -

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: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: Q

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: U

Note: Ramachandran plot

Chain identifier: V

Note: Ramachandran plot

Chain identifier: W

Note: Ramachandran plot

Chain identifier: X

Note: Ramachandran plot

Chain identifier: Y

Note: Ramachandran plot

Chain identifier: Z

Note: Ramachandran plot

Chain identifier: 1

Note: Ramachandran plot

Chain identifier: 2

Note: Ramachandran plot

Chain identifier: 3

Note: Ramachandran plot

Chain identifier: 4

Note: Ramachandran plot

Chain identifier: 5

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

  54 OGUA  (  60-)  A      O3'
2219 OGUA  (2353-)  A      C6

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 OADE  (   6-)  A    High
   2 OGUA  (   7-)  A    High
   3 OADE  (   8-)  A    High
   4 OURA  (   9-)  A    High
   5 OGUA  (  10-)  A    High
   6 OGUA  (  11-)  A    High
   7 OURA  (  12-)  A    High
  29 OCYT  (  34-)  A    High
  44 OURA  (  50-)  A    High
  57 OURA  (  63-)  A    High
  58 OADE  (  64-)  A    High
  84 OURA  (  90-)  A    High
  85 OADE  (  91-)  A    High
  86 OGUA  (  92-)  A    High
  87 OCYT  (  93-)  A    High
  88 OGUA  (  94-)  A    High
  89 OGUA  (  95-)  A    High
  93 OURA  (  99-)  A    High
  94 OGUA  ( 101-)  A    High
  95 OGUA  ( 102-)  A    High
 127 OCYT  ( 134-)  A    High
 128 OGUA  ( 135-)  A    High
 129 OGUA  ( 136-)  A    High
 131 OGUA  ( 137-)  A    High
 132 OGUA  ( 138-)  A    High
And so on for a total of 2764 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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 0

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: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

Note: B-factor plot

Chain identifier: Q

Note: B-factor plot

Chain identifier: R

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: T

Note: B-factor plot

Chain identifier: U

Note: B-factor plot

Chain identifier: V

Note: B-factor plot

Chain identifier: W

Note: B-factor plot

Chain identifier: X

Note: B-factor plot

Chain identifier: Y

Note: B-factor plot

Chain identifier: Z

Note: B-factor plot

Chain identifier: 1

Note: B-factor plot

Chain identifier: 2

Note: B-factor plot

Chain identifier: 3

Note: B-factor plot

Chain identifier: 4

Note: B-factor plot

Chain identifier: 5

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.

3117 ARG   ( 239-)  C
4044 ARG   (   5-)  I
4058 ARG   (  19-)  I
4066 ARG   (  60-)  I
4369 ARG   (  41-)  L
4383 ARG   (  55-)  L
4430 ARG   ( 102-)  L
4439 ARG   ( 111-)  L
4677 ARG   (  64-)  N
4701 ARG   (  88-)  N
5014 ARG   (  50-)  Q

Warning: Tyrosine convention problem

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

2940 TYR   (  62-)  C
3356 TYR   (   7-)  E
3408 TYR   (  59-)  E
3566 TYR   (  11-)  F
3580 TYR   (  25-)  F
3686 TYR   ( 131-)  F
3809 TYR   (  83-)  G
3921 TYR   (  25-)  H
3985 TYR   (  89-)  H
4026 TYR   ( 130-)  H
4408 TYR   (  80-)  L
4610 TYR   ( 137-)  M
4634 TYR   (  21-)  N
4707 TYR   (  94-)  N
4813 TYR   (  92-)  O
4815 TYR   (  94-)  O
4897 TYR   (  68-)  P
4989 TYR   (  24-)  Q
5009 TYR   (  45-)  Q
5011 TYR   (  47-)  Q
5040 TYR   (  76-)  Q
5094 TYR   (  12-)  R
5173 TYR   (  91-)  R
5192 TYR   (   9-)  S
5228 TYR   (  45-)  S
5253 TYR   (  70-)  S
5258 TYR   (  75-)  S
5298 TYR   (   5-)  T
5362 TYR   (  69-)  T
5441 TYR   (  55-)  U
5514 TYR   (  29-)  V
5523 TYR   (  38-)  V
5584 TYR   (  99-)  V
5692 TYR   (  26-)  W
5787 TYR   (  43-)  X
5916 TYR   (  15-)  Z
5976 TYR   (  51-)  1
6055 TYR   (  21-)  3
6197 TYR   (  64-)  5

Warning: Phenylalanine convention problem

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

2884 PHE   (   6-)  C
2893 PHE   (  15-)  C
2899 PHE   (  21-)  C
2945 PHE   (  67-)  C
3217 PHE   (  67-)  D
3234 PHE   (  84-)  D
3246 PHE   (  96-)  D
3263 PHE   ( 113-)  D
3551 PHE   ( 202-)  E
3578 PHE   (  23-)  F
3635 PHE   (  80-)  F
3657 PHE   ( 102-)  F
3672 PHE   ( 117-)  F
3680 PHE   ( 125-)  F
3733 PHE   ( 178-)  F
3835 PHE   ( 109-)  G
4189 PHE   ( 140-)  J
4289 PHE   (  79-)  K
4458 PHE   ( 130-)  L
4502 PHE   (  29-)  M
4505 PHE   (  32-)  M
4577 PHE   ( 104-)  M
4660 PHE   (  47-)  N
4750 PHE   (  29-)  O
4851 PHE   (  22-)  P
4874 PHE   (  45-)  P
4886 PHE   (  57-)  P
4890 PHE   (  61-)  P
4905 PHE   (  76-)  P
4930 PHE   ( 101-)  P
5004 PHE   (  40-)  Q
5021 PHE   (  57-)  Q
5084 PHE   (   2-)  R
5314 PHE   (  21-)  T
5573 PHE   (  88-)  V
5574 PHE   (  89-)  V
5589 PHE   ( 104-)  V
5621 PHE   ( 136-)  V
5726 PHE   (  60-)  W
5735 PHE   (  69-)  W
5804 PHE   (  60-)  X
6104 PHE   (  18-)  4
6181 PHE   (  48-)  5

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.

2963 ASP   (  85-)  C
2977 ASP   (  99-)  C
3000 ASP   ( 122-)  C
3324 ASP   ( 174-)  D
3711 ASP   ( 156-)  F
4089 ASP   (  40-)  J
4222 ASP   (  12-)  K
4266 ASP   (  56-)  K
4291 ASP   (  81-)  K
4333 ASP   (   5-)  L
4375 ASP   (  47-)  L
4498 ASP   (  25-)  M
4672 ASP   (  59-)  N
4682 ASP   (  69-)  N
4685 ASP   (  72-)  N
4720 ASP   ( 107-)  N
4809 ASP   (  88-)  O
4936 ASP   ( 107-)  P
5055 ASP   (  91-)  Q
5205 ASP   (  22-)  S
5246 ASP   (  63-)  S
5277 ASP   (  94-)  S
5525 ASP   (  40-)  V
5530 ASP   (  45-)  V
5625 ASP   ( 140-)  V
5639 ASP   ( 154-)  V
5681 ASP   (  15-)  W

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.

2906 GLU   (  28-)  C
2908 GLU   (  30-)  C
2979 GLU   ( 101-)  C
3024 GLU   ( 146-)  C
3026 GLU   ( 148-)  C
3047 GLU   ( 169-)  C
3059 GLU   ( 181-)  C
3115 GLU   ( 237-)  C
3223 GLU   (  73-)  D
3250 GLU   ( 100-)  D
3321 GLU   ( 171-)  D
3568 GLU   (  13-)  F
3614 GLU   (  59-)  F
3692 GLU   ( 137-)  F
3698 GLU   ( 143-)  F
3812 GLU   (  86-)  G
3830 GLU   ( 104-)  G
3850 GLU   ( 124-)  G
4047 GLU   (   8-)  I
4054 GLU   (  15-)  I
4057 GLU   (  18-)  I
4071 GLU   (  65-)  I
4264 GLU   (  54-)  K
4278 GLU   (  68-)  K
4402 GLU   (  74-)  L
4511 GLU   (  38-)  M
4553 GLU   (  80-)  M
4564 GLU   (  91-)  M
4585 GLU   ( 112-)  M
4656 GLU   (  43-)  N
4764 GLU   (  43-)  O
4785 GLU   (  64-)  O
4865 GLU   (  36-)  P
4963 GLU   ( 134-)  P
5053 GLU   (  89-)  Q
5066 GLU   ( 102-)  Q
5075 GLU   ( 111-)  Q
5235 GLU   (  52-)  S
5249 GLU   (  66-)  S
5331 GLU   (  38-)  T
5415 GLU   (  29-)  U
5426 GLU   (  40-)  U
5528 GLU   (  43-)  V
5545 GLU   (  60-)  V
5623 GLU   ( 138-)  V
5630 GLU   ( 145-)  V
5647 GLU   ( 162-)  V
5663 GLU   ( 178-)  V
5693 GLU   (  27-)  W
5974 GLU   (  49-)  1

Warning: Phosphate group convention problem

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

  55 OGUA  (  61-)  A

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): A

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.

  11 OGUA  (  16-)  A      C1'  N9    1.50    4.2
  11 OGUA  (  16-)  A      C5   C4    1.35   -4.3
  16 OADE  (  21-)  A      N9   C4    1.35   -4.5
  26 OCYT  (  31-)  A      N1   C6    1.33   -6.3
  31 OGUA  (  36-)  A      C5   C4    1.35   -4.5
  65 OADE  (  71-)  A      N9   C4    1.34   -5.8
  96 OADE  ( 103-)  A      N9   C4    1.35   -4.3
 113 OURA  ( 120-)  A      C1'  N1    1.43   -4.2
 132 OGUA  ( 138-)  A      C1'  N9    1.50    4.9
 132 OGUA  ( 138-)  A      N9   C4    1.41    4.4
 135 OADE  ( 141-)  A      N9   C4    1.35   -4.5
 172 OGUA  ( 187-)  A      N1   C2    1.34   -4.6
 177 OCYT  ( 192-)  A      N1   C6    1.32   -7.8
 177 OCYT  ( 192-)  A      C4   N3    1.30   -4.6
 181 OADE  ( 196-)  A      C6   N1    1.32   -5.1
 183 OCYT  ( 198-)  A      C4   N4    1.30   -4.2
 192 OADE  ( 207-)  A      N9   C4    1.35   -4.0
 196 OADE  ( 211-)  A      N3   C4    1.32   -4.1
 229 OADE  ( 244-)  A      N9   C4    1.34   -5.0
 229 OADE  ( 244-)  A      N3   C4    1.31   -5.5
 233 OGUA  ( 248-)  A      C5   C6    1.38   -4.1
 234 OCYT  ( 249-)  A      N1   C6    1.34   -4.1
 250 OADE  ( 265-)  A      N9   C4    1.34   -6.1
 250 OADE  ( 265-)  A      N3   C4    1.32   -4.3
 326 OURA  ( 306-)  A      C4   N3    1.34   -4.0
And so on for a total of 431 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

 |  1.002729  0.000249  0.000153|
 |  0.000249  1.002238  0.000297|
 |  0.000153  0.000297  1.003165|
Proposed new scale matrix

 |  0.004733 -0.000001  0.000000|
 |  0.000000  0.002209  0.000000|
 |  0.000000  0.000000  0.001623|
With corresponding cell

    A    = 211.279  B   = 452.682  C    = 616.194
    Alpha=  90.006  Beta=  90.005  Gamma=  89.988

The CRYST1 cell dimensions

    A    = 210.690  B   = 451.660  C    = 614.250
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 11833.717
(Under-)estimated Z-score: 80.173

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.

   2 OGUA  (   7-)  A      N9   C8   N7  113.15    4.1
   6 OGUA  (  11-)  A      N9   C8   N7  113.79    5.4
   8 OADE  (  13-)  A      N6   C6   N1  114.86   -6.2
   9 OADE  (  14-)  A      C6   C5   C4  119.29    4.6
  12 OGUA  (  17-)  A      N9   C8   N7  113.35    4.5
  12 OGUA  (  17-)  A      C5   C6   O6  124.34   -7.1
  14 OCYT  (  19-)  A      C5   C4   N3  123.71    4.5
  14 OCYT  (  19-)  A      C4   N3   C2  117.38   -5.0
  17 OCYT  (  22-)  A      N1   C2   O2  116.18   -4.5
  18 OGUA  (  23-)  A      N9   C4   N3  123.14   -4.8
  18 OGUA  (  23-)  A      C5   C4   N3  130.77    4.3
  18 OGUA  (  23-)  A      C2   N3   C4  109.50   -4.8
  18 OGUA  (  23-)  A      N2   C2   N3  116.05   -5.5
  19 OGUA  (  24-)  A      N9   C8   N7  113.95    5.7
  20 OURA  (  25-)  A      C5   C4   O4  128.39    4.2
  21 OGUA  (  26-)  A      N9   C8   N7  113.44    4.7
  25 OGUA  (  30-)  A      N9   C4   C5  103.59   -4.5
  25 OGUA  (  30-)  A      N9   C4   N3  128.43    4.0
  25 OGUA  (  30-)  A      C8   N9   C4  109.21    7.0
  25 OGUA  (  30-)  A      N1   C2   N2  112.31   -4.3
  26 OCYT  (  31-)  A      N1   C6   C5  118.14   -5.7
  26 OCYT  (  31-)  A      C6   N1   C2  123.33    7.6
  26 OCYT  (  31-)  A      C4   N3   C2  117.81   -4.2
  27 OCYT  (  32-)  A      N1   C2   O2  114.12   -8.0
  27 OCYT  (  32-)  A      N3   C2   O2  125.59    5.3
And so on for a total of 3234 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.

2906 GLU   (  28-)  C
2908 GLU   (  30-)  C
2963 ASP   (  85-)  C
2977 ASP   (  99-)  C
2979 GLU   ( 101-)  C
3000 ASP   ( 122-)  C
3024 GLU   ( 146-)  C
3026 GLU   ( 148-)  C
3047 GLU   ( 169-)  C
3059 GLU   ( 181-)  C
3115 GLU   ( 237-)  C
3117 ARG   ( 239-)  C
3223 GLU   (  73-)  D
3250 GLU   ( 100-)  D
3321 GLU   ( 171-)  D
3324 ASP   ( 174-)  D
3568 GLU   (  13-)  F
3614 GLU   (  59-)  F
3692 GLU   ( 137-)  F
3698 GLU   ( 143-)  F
3711 ASP   ( 156-)  F
3812 GLU   (  86-)  G
3830 GLU   ( 104-)  G
3850 GLU   ( 124-)  G
4044 ARG   (   5-)  I
And so on for a total of 88 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.

3413 ILE   (  64-)  E      CA    -6.3    23.74    33.24
4482 TYR   (   9-)  M      CA    -7.8    21.66    34.03
The average deviation= 0.876

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.

4554 VAL   (  81-)  M    7.76
5779 THR   (  35-)  X    7.18
5860 LEU   (  21-)  Y    7.12
5771 GLU   (  27-)  X    6.73
2924 GLN   (  46-)  C    5.93
4974 VAL   (   9-)  Q    5.60
3120 ARG   ( 242-)  C    5.57
5040 TYR   (  76-)  Q    5.56
5022 ARG   (  58-)  Q    5.40
6183 LEU   (  50-)  5    5.15
6105 ARG   (  19-)  4    5.02
5601 VAL   ( 116-)  V    4.78
6101 THR   (  15-)  4    4.78
4187 ARG   ( 138-)  J    4.73
4482 TYR   (   9-)  M    4.67
5857 PRO   (  18-)  Y    4.65
4996 SER   (  31-)  Q    4.59
4690 ARG   (  77-)  N    4.56
6002 LYS   (  13-)  2    4.50
6165 LEU   (  32-)  5    4.45
4359 ALA   (  31-)  L    4.43
3117 ARG   ( 239-)  C    4.39
4390 LEU   (  62-)  L    4.38
5773 GLY   (  29-)  X    4.35
4338 PRO   (  10-)  L    4.35
4365 GLY   (  37-)  L    4.28
5753 GLY   (   9-)  X    4.28
4381 GLY   (  53-)  L    4.24
4652 PRO   (  39-)  N    4.23
4555 ARG   (  82-)  M    4.19
6171 GLY   (  38-)  5    4.17
5075 GLU   ( 111-)  Q    4.15
4366 GLN   (  38-)  L    4.14
5329 LYS   (  36-)  T    4.11
4370 SER   (  42-)  L    4.09
5850 GLU   (  11-)  Y    4.03
5855 LEU   (  16-)  Y    4.03
6094 ASN   (   8-)  4    4.02

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 : -5.435

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.

5993 HIS   (   4-)  2    -3.4
4419 PHE   (  91-)  L    -3.3
4482 TYR   (   9-)  M    -3.2
5804 PHE   (  60-)  X    -3.2
5392 HIS   (   6-)  U    -3.2
4733 PHE   (  12-)  O    -3.2
2905 THR   (  27-)  C    -3.2
4214 PRO   (   4-)  K    -3.1
4379 PHE   (  51-)  L    -3.1
5258 TYR   (  75-)  S    -3.1
4880 ARG   (  51-)  P    -3.0
4338 PRO   (  10-)  L    -3.0
4100 THR   (  51-)  J    -3.0
3397 THR   (  48-)  E    -3.0
4007 PRO   ( 111-)  H    -2.9
4698 PRO   (  85-)  N    -2.9
4756 ILE   (  35-)  O    -2.9
4520 ILE   (  47-)  M    -2.9
3122 ARG   ( 244-)  C    -2.9
5475 PHE   (  89-)  U    -2.9
3626 THR   (  71-)  F    -2.9
4376 PRO   (  48-)  L    -2.9
5812 PRO   (  68-)  X    -2.9
5757 ILE   (  13-)  X    -2.9
6164 HIS   (  31-)  5    -2.8
And so on for a total of 388 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.

2886 PRO   (   8-)  C  Poor phi/psi
2888 THR   (  10-)  C  Poor phi/psi
2890 SER   (  12-)  C  Poor phi/psi
2904 LYS   (  26-)  C  Poor phi/psi
2911 LEU   (  33-)  C  Poor phi/psi
2912 VAL   (  34-)  C  Poor phi/psi
2914 PRO   (  36-)  C  omega poor
2915 LEU   (  37-)  C  Poor phi/psi
2920 GLY   (  42-)  C  Poor phi/psi, omega poor
2921 ARG   (  43-)  C  Poor phi/psi, omega poor
2922 ASN   (  44-)  C  omega poor
2923 ASN   (  45-)  C  omega poor
2925 GLY   (  47-)  C  omega poor
2928 THR   (  50-)  C  Poor phi/psi
2930 ARG   (  52-)  C  omega poor
2931 PHE   (  53-)  C  Poor phi/psi
2952 GLY   (  74-)  C  Poor phi/psi
2965 ASN   (  87-)  C  omega poor
2993 GLN   ( 115-)  C  Poor phi/psi
3000 ASP   ( 122-)  C  omega poor
3003 ILE   ( 125-)  C  Poor phi/psi
3012 ARG   ( 134-)  C  Poor phi/psi
3025 LEU   ( 147-)  C  omega poor
3028 LYS   ( 150-)  C  Poor phi/psi
3040 SER   ( 162-)  C  Poor phi/psi
And so on for a total of 491 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 : -5.985

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.

4326 SER   ( 116-)  K    0.36

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 OADE  (   8-)  A      0
   4 OURA  (   9-)  A      0
   5 OGUA  (  10-)  A      0
   6 OGUA  (  11-)  A      0
   7 OURA  (  12-)  A      0
   8 OADE  (  13-)  A      0
   9 OADE  (  14-)  A      0
  10 OGUA  (  15-)  A      0
  11 OGUA  (  16-)  A      0
  12 OGUA  (  17-)  A      0
  13 OCYT  (  18-)  A      0
  14 OCYT  (  19-)  A      0
  15 OCYT  (  20-)  A      0
  16 OADE  (  21-)  A      0
  17 OCYT  (  22-)  A      0
  18 OGUA  (  23-)  A      0
  19 OGUA  (  24-)  A      0
  20 OURA  (  25-)  A      0
  21 OGUA  (  26-)  A      0
  22 OGUA  (  27-)  A      0
  23 OADE  (  28-)  A      0
  24 OURA  (  29-)  A      0
  25 OGUA  (  30-)  A      0
  26 OCYT  (  31-)  A      0
  27 OCYT  (  32-)  A      0
And so on for a total of 4417 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 7.325

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!

5090 GLY   (   8-)  R   3.41   19
5599 GLY   ( 114-)  V   3.05   20
5497 GLY   (  12-)  V   2.44   16
3396 GLY   (  47-)  E   2.37   19
5970 GLY   (  45-)  1   2.20   11
4854 GLY   (  25-)  P   2.01   10
4432 GLY   ( 104-)  L   1.93   11
3308 GLY   ( 158-)  D   1.88   10
3179 GLY   (  29-)  D   1.84   23
4310 GLY   ( 100-)  K   1.82   12
4421 GLY   (  93-)  L   1.74   16
3732 GLY   ( 177-)  F   1.72   21
3819 GLY   (  93-)  G   1.67   80
4800 ALA   (  79-)  O   1.66   44
5694 GLY   (  28-)  W   1.61   80
2925 GLY   (  47-)  C   1.54   80
3215 GLY   (  65-)  D   1.53   80

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...

4482 TYR   (   9-)  M   1.60

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]

4214 PRO   (   4-)  K    0.46 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].

2986 PRO   ( 108-)  C    50.4 half-chair C-delta/C-gamma (54 degrees)
3056 PRO   ( 178-)  C   107.8 envelop C-beta (108 degrees)
3106 PRO   ( 228-)  C   108.2 envelop C-beta (108 degrees)
3110 PRO   ( 232-)  C  -114.5 envelop C-gamma (-108 degrees)
3127 PRO   ( 249-)  C   107.6 envelop C-beta (108 degrees)
3224 PRO   (  74-)  D  -114.7 envelop C-gamma (-108 degrees)
3236 PRO   (  86-)  D    44.8 envelop C-delta (36 degrees)
3363 PRO   (  14-)  E   106.9 envelop C-beta (108 degrees)
3415 PRO   (  66-)  E   161.4 half-chair C-alpha/N (162 degrees)
3557 PRO   (   2-)  F   104.4 envelop C-beta (108 degrees)
3587 PRO   (  32-)  F   104.0 envelop C-beta (108 degrees)
3738 PRO   (  12-)  G   113.4 envelop C-beta (108 degrees)
3781 PRO   (  55-)  G  -121.5 half-chair C-delta/C-gamma (-126 degrees)
3844 PRO   ( 118-)  G  -116.8 envelop C-gamma (-108 degrees)
3852 PRO   ( 126-)  G  -116.7 envelop C-gamma (-108 degrees)
4028 PRO   ( 132-)  H    25.6 half-chair N/C-delta (18 degrees)
4112 PRO   (  63-)  J    52.9 half-chair C-delta/C-gamma (54 degrees)
4116 PRO   (  67-)  J   100.9 envelop C-beta (108 degrees)
4201 PRO   ( 152-)  J   110.5 envelop C-beta (108 degrees)
4214 PRO   (   4-)  K   127.4 half-chair C-beta/C-alpha (126 degrees)
4311 PRO   ( 101-)  K   103.7 envelop C-beta (108 degrees)
4336 PRO   (   8-)  L   101.1 envelop C-beta (108 degrees)
4338 PRO   (  10-)  L   -26.9 half-chair C-alpha/N (-18 degrees)
4376 PRO   (  48-)  L     9.9 half-chair N/C-delta (18 degrees)
4400 PRO   (  72-)  L     9.7 half-chair N/C-delta (18 degrees)
4473 PRO   ( 145-)  L   -61.0 half-chair C-beta/C-alpha (-54 degrees)
4512 PRO   (  39-)  M    48.7 half-chair C-delta/C-gamma (54 degrees)
4546 PRO   (  73-)  M   -34.4 envelop C-alpha (-36 degrees)
4551 PRO   (  78-)  M    26.8 half-chair N/C-delta (18 degrees)
4572 PRO   (  99-)  M   105.5 envelop C-beta (108 degrees)
4698 PRO   (  85-)  N   110.4 envelop C-beta (108 degrees)
4812 PRO   (  91-)  O   114.8 envelop C-beta (108 degrees)
4910 PRO   (  81-)  P    99.6 envelop C-beta (108 degrees)
4967 PRO   (   2-)  Q    -1.2 envelop N (0 degrees)
5067 PRO   ( 103-)  Q  -125.6 half-chair C-delta/C-gamma (-126 degrees)
5111 PRO   (  29-)  R    99.0 envelop C-beta (108 degrees)
5132 PRO   (  50-)  R   104.2 envelop C-beta (108 degrees)
5197 PRO   (  14-)  S   114.4 envelop C-beta (108 degrees)
5270 PRO   (  87-)  S    18.5 half-chair N/C-delta (18 degrees)
5304 PRO   (  11-)  T   -62.8 half-chair C-beta/C-alpha (-54 degrees)
5418 PRO   (  32-)  U    29.9 envelop C-delta (36 degrees)
5452 PRO   (  66-)  U   100.8 envelop C-beta (108 degrees)
5463 PRO   (  77-)  U   119.3 half-chair C-beta/C-alpha (126 degrees)
5500 PRO   (  15-)  V    99.9 envelop C-beta (108 degrees)
5812 PRO   (  68-)  X   111.6 envelop C-beta (108 degrees)
5917 PRO   (  16-)  Z   121.5 half-chair C-beta/C-alpha (126 degrees)
5994 PRO   (   5-)  2    14.1 half-chair N/C-delta (18 degrees)
6093 PRO   (   7-)  4    51.8 half-chair C-delta/C-gamma (54 degrees)
6135 PRO   (   2-)  5    27.2 envelop C-delta (36 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.

3282 HIS   ( 132-)  D      CD2 <-> 3285 HIS   ( 135-)  D      NE2    0.83    2.27  INTRA BL
 992 OADE  ( 973-)  A      OP2 <-> 5160 LYS   (  78-)  R      NZ     0.79    1.91  INTRA BL
4392 LYS   (  64-)  L      O   <-> 4394 GLY   (  66-)  L      N      0.78    1.92  INTRA BL
7094  MG   ( 868-)  6     MG   <-> 7107  MG   ( 881-)  6     MG      0.76    2.44  INTRA BF
6341  MG   (2951-)  A     MG   <-> 7146  MG   (3226-)  A     MG      0.75    2.45  INTRA BL
  77 OGUA  (  83-)  A      N1  <->   95 OGUA  ( 102-)  A      O2'    0.73    1.97  INTRA BL
2911 LEU   (  33-)  C      O   <-> 2913 LYS   (  35-)  C      N      0.72    1.98  INTRA BL
1631 OCYT  (1658-)  A      OP1 <-> 3282 HIS   ( 132-)  D      ND1    0.72    1.98  INTRA BL
 237 OGUA  ( 252-)  A      OP2 <-> 4378 ARG   (  50-)  L      NH2    0.72    1.98  INTRA BL
1459 OADE  (1486-)  A      N1  <-> 1477 OCYT  (1504-)  A      N4     0.69    2.31  INTRA BF
 754 OGUA  ( 733-)  A      N7  <->  782 OADE  ( 761-)  A      N6     0.66    2.34  INTRA BL
6305  MG   (  79-)  6     MG   <-> 7151  MG   ( 925-)  6     MG      0.65    2.55  INTRA BL
4387 LEU   (  59-)  L      CA  <-> 4389 ARG   (  61-)  L      NE     0.65    2.45  INTRA BL
6260  MG   (  34-)  6     MG   <-> 7053  MG   ( 827-)  6     MG      0.62    2.58  INTRA BL
1332 OADE  (1359-)  A      N7  <-> 1345 OURA  (1372-)  A      N3     0.61    2.39  INTRA BF
6289  MG   (2925-)  A     MG   <-> 7105  MG   (3217-)  A     MG      0.61    2.59  INTRA BL
6167 TRP   (  34-)  5      CG  <-> 6168 GLN   (  35-)  5      N      0.60    2.40  INTRA BF
 754 OGUA  ( 733-)  A      N7  <->  782 OADE  ( 761-)  A      C6     0.60    2.50  INTRA BL
6402  MG   (2971-)  A     MG   <-> 6555  MG   (3026-)  A     MG      0.60    2.60  INTRA BL
6410  MG   ( 184-)  6     MG   <-> 7178  MG   ( 953-)  6     MG      0.59    2.61  INTRA BL
6269  MG   (  43-)  6     MG   <-> 7123  MG   ( 897-)  6     MG      0.59    2.61  INTRA BL
 403 OURA  ( 380-)  A      C2  <-> 5764 ARG   (  20-)  X      NH2    0.58    2.52  INTRA BL
 881 OURA  ( 860-)  A      C5  <->  937 OADE  ( 917-)  A      N7     0.58    2.52  INTRA BL
5056 ARG   (  92-)  Q      CG  <-> 5093 GLN   (  11-)  R      NE2    0.57    2.53  INTRA BF
6345  MG   ( 119-)  6     MG   <-> 7133  MG   ( 907-)  6     MG      0.57    2.63  INTRA BL
And so on for a total of 6234 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: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

Note: Inside/Outside RMS Z-score plot

Chain identifier: Q

Note: Inside/Outside RMS Z-score plot

Chain identifier: R

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Inside/Outside RMS Z-score plot

Chain identifier: U

Note: Inside/Outside RMS Z-score plot

Chain identifier: V

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: Y

Note: Inside/Outside RMS Z-score plot

Chain identifier: Z

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: 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: 4

Note: Inside/Outside RMS Z-score plot

Chain identifier: 5

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.

3117 ARG   ( 239-)  C      -8.71
6041 TYR   (  52-)  2      -8.62
4349 ARG   (  21-)  L      -8.57
4346 ARG   (  18-)  L      -8.23
3883 TYR   ( 157-)  G      -8.21
3122 ARG   ( 244-)  C      -8.10
4555 ARG   (  82-)  M      -8.02
5680 ARG   (  14-)  W      -7.91
3423 ARG   (  74-)  E      -7.89
5825 ARG   (  81-)  X      -7.88
6133 ARG   (  47-)  4      -7.87
4621 ARG   (   8-)  N      -7.73
4487 ARG   (  14-)  M      -7.72
5443 GLN   (  57-)  U      -7.70
4883 ARG   (  54-)  P      -7.68
3299 ARG   ( 149-)  D      -7.68
6053 ARG   (  19-)  3      -7.67
4924 ARG   (  95-)  P      -7.66
5983 TYR   (  58-)  1      -7.66
4482 TYR   (   9-)  M      -7.66
4395 MET   (  67-)  L      -7.65
4438 TYR   ( 110-)  L      -7.62
5686 ARG   (  20-)  W      -7.58
4259 ARG   (  49-)  K      -7.55
3141 ARG   ( 263-)  C      -7.54
And so on for a total of 301 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.

2883 LYS   (   5-)  C      2885 - LYS      7- ( C)         -4.34
2916 LYS   (  38-)  C      2921 - ARG     43- ( C)         -5.31
2932 ARG   (  54-)  C      2934 - GLY     56- ( C)         -4.86
2936 HIS   (  58-)  C      2938 - ARG     60- ( C)         -5.15
3119 PRO   ( 241-)  C      3122 - ARG    244- ( C)         -5.71
3277 ASP   ( 127-)  D      3279 - HIS    129- ( D)         -5.14
3290 SER   ( 140-)  D      3296 - THR    146- ( D)         -5.07
3352 LYS   ( 202-)  D      3354 - ALA    204- ( D)         -5.38
3393 ARG   (  44-)  E      3395 - ARG     46- ( E)         -5.40
3416 GLN   (  67-)  E      3418 - HIS     69- ( E)         -5.96
3431 ILE   (  82-)  E      3433 - VAL     84- ( E)         -4.68
3835 PHE   ( 109-)  G      3837 - HIS    111- ( G)         -4.29
3883 TYR   ( 157-)  G      3885 - GLU    159- ( G)         -5.54
4257 ILE   (  47-)  K      4259 - ARG     49- ( K)         -5.35
4342 LYS   (  14-)  L      4344 - ARG     16- ( L)         -5.67
4369 ARG   (  41-)  L      4371 - GLY     43- ( L)         -5.21
4377 ARG   (  49-)  L      4380 - GLU     52- ( L)         -5.07
4382 GLY   (  54-)  L      4384 - SER     56- ( L)         -4.89
4387 LEU   (  59-)  L      4390 - LEU     62- ( L)         -4.72
4395 MET   (  67-)  L      4399 - VAL     71- ( L)         -6.37
4403 ILE   (  75-)  L      4405 - ARG     77- ( L)         -5.66
4475 LEU   ( 147-)  L      4477 - GLU    149- ( L)         -5.32
4480 MET   (   7-)  M      4487 - ARG     14- ( M)         -6.79
4489 ARG   (  16-)  M      4491 - LYS     18- ( M)         -5.68
4552 LEU   (  79-)  M      4556 - MET     83- ( M)         -6.43
And so on for a total of 51 lines.

Warning: Structural average packing environment a bit worrysome

The structural average packing score is a bit low.

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

Average for range 1 - 6197 : -1.988

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: G

Note: Quality value plot

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

Chain identifier: H

Note: Quality value plot

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

Chain identifier: I

Note: Quality value plot

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

Chain identifier: J

Note: Quality value plot

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

Chain identifier: K

Note: Quality value plot

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

Chain identifier: L

Note: Quality value plot

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

Chain identifier: M

Note: Quality value plot

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

Chain identifier: N

Note: Quality value plot

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

Chain identifier: O

Note: Quality value plot

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

Chain identifier: P

Note: Quality value plot

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

Chain identifier: Q

Note: Quality value plot

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

Chain identifier: R

Note: Quality value plot

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

Chain identifier: S

Note: Quality value plot

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

Chain identifier: T

Note: Quality value plot

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

Chain identifier: U

Note: Quality value plot

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

Chain identifier: 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: 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: 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: 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: 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: 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: 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

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.

5678 ASN   (  12-)  W   -4.04
4239 ASN   (  29-)  K   -3.36
3444 ARG   (  95-)  E   -3.30
3518 ASN   ( 169-)  E   -3.30
2924 GLN   (  46-)  C   -3.28
6165 LEU   (  32-)  5   -3.26
3299 ARG   ( 149-)  D   -3.26
4970 LYS   (   5-)  Q   -3.25
4349 ARG   (  21-)  L   -3.20
5159 ALA   (  77-)  R   -3.16
4392 LYS   (  64-)  L   -3.16
4486 GLN   (  13-)  M   -3.15
3267 MET   ( 117-)  D   -3.14
6093 PRO   (   7-)  4   -3.08
4383 ARG   (  55-)  L   -3.07
4618 LYS   (   5-)  N   -3.07
4398 GLN   (  70-)  L   -3.07
3848 THR   ( 122-)  G   -3.06
4118 VAL   (  69-)  J   -3.06
6089 ARG   (   3-)  4   -3.05
5994 PRO   (   5-)  2   -3.03
4555 ARG   (  82-)  M   -3.02
3121 GLY   ( 243-)  C   -3.02
5993 HIS   (   4-)  2   -3.01
3104 MET   ( 226-)  C   -3.01
And so on for a total of 137 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.

2884 PHE   (   6-)  C     - 2887 TYR   (   9-)  C        -1.79
2919 GLY   (  41-)  C     - 2926 ARG   (  48-)  C        -2.08
2927 ILE   (  49-)  C     - 2930 ARG   (  52-)  C        -2.06
3114 GLY   ( 236-)  C     - 3122 ARG   ( 244-)  C        -2.46
3278 SER   ( 128-)  D     - 3285 HIS   ( 135-)  D        -2.33
3287 HIS   ( 137-)  D     - 3295 LYS   ( 145-)  D        -2.44
3296 THR   ( 146-)  D     - 3299 ARG   ( 149-)  D        -2.47
3405 GLU   (  56-)  E     - 3409 SER   (  60-)  E        -1.95
3415 PRO   (  66-)  E     - 3418 HIS   (  69-)  E        -2.04
3627 ARG   (  72-)  F     - 3630 LYS   (  75-)  F        -1.58
3649 LEU   (  94-)  F     - 3652 ASP   (  97-)  F        -1.90
4151 PRO   ( 102-)  J     - 4154 LEU   ( 105-)  J        -1.76
4212 ILE   (   2-)  K     - 4215 GLN   (   5-)  K        -1.99
4237 GLY   (  27-)  K     - 4241 LYS   (  31-)  K        -2.41
4342 LYS   (  14-)  L     - 4346 ARG   (  18-)  L        -2.09
4365 GLY   (  37-)  L     - 4368 SER   (  40-)  L        -2.12
4370 SER   (  42-)  L     - 4373 LEU   (  45-)  L        -1.96
4380 GLU   (  52-)  L     - 4383 ARG   (  55-)  L        -2.64
4386 THR   (  58-)  L     - 4390 LEU   (  62-)  L        -2.18
4391 PRO   (  63-)  L     - 4395 MET   (  67-)  L        -2.57
4396 GLN   (  68-)  L     - 4401 GLY   (  73-)  L        -2.31
4483 ARG   (  10-)  M     - 4487 ARG   (  14-)  M        -2.29
4488 GLY   (  15-)  M     - 4495 LYS   (  22-)  M        -2.25
4548 THR   (  75-)  M     - 4552 LEU   (  79-)  M        -2.00
4614 GLN   ( 141-)  M     - 4620 GLY   (   7-)  N        -2.28
4622 LYS   (   9-)  N     - 4625 ARG   (  12-)  N        -1.77
4775 LEU   (  54-)  O     - 4778 LYS   (  57-)  O        -2.03
4922 ARG   (  93-)  P     - 4927 LYS   (  98-)  P        -2.31
4966 LYS   ( 137-)  P     - 4973 VAL   (   8-)  Q        -2.42
5016 ARG   (  52-)  Q     - 5019 ARG   (  55-)  Q        -1.71
5158 LYS   (  76-)  R     - 5163 TYR   (  81-)  R        -2.51
5268 VAL   (  85-)  S     - 5271 ARG   (  88-)  S        -1.86
5352 VAL   (  59-)  T     - 5355 LYS   (  62-)  T        -1.60
5389 VAL   (   3-)  U     - 5395 LYS   (   9-)  U        -2.15
5679 GLY   (  13-)  W     - 5682 SER   (  16-)  W        -2.01
5683 GLN   (  17-)  W     - 5686 ARG   (  20-)  W        -2.45
5981 GLU   (  56-)  1     - 5984 VAL   (  59-)  1        -1.92
5990 CYS   (  65-)  1     - 6000 THR   (  11-)  2        -2.39
6086 VAL   (  52-)  3     - 6089 ARG   (   3-)  4        -1.83
6090 THR   (   4-)  4     - 6093 PRO   (   7-)  4        -2.29
6135 PRO   (   2-)  5     - 6138 LYS   (   5-)  5        -2.04
6161 GLY   (  28-)  5     - 6166 ASN   (  33-)  5        -2.30

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: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: Q

Note: Second generation quality Z-score plot

Chain identifier: R

Note: Second generation quality Z-score plot

Chain identifier: S

Note: Second generation quality Z-score plot

Chain identifier: T

Note: Second generation quality Z-score plot

Chain identifier: U

Note: Second generation quality Z-score plot

Chain identifier: V

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: Y

Note: Second generation quality Z-score plot

Chain identifier: Z

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: 3

Note: Second generation quality Z-score plot

Chain identifier: 4

Note: Second generation quality Z-score plot

Chain identifier: 5

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.

2965 ASN   (  87-)  C
3004 GLN   ( 126-)  C
3111 HIS   ( 233-)  C
3210 ASN   (  60-)  D
3282 HIS   ( 132-)  D
3285 HIS   ( 135-)  D
3416 GLN   (  67-)  E
3418 HIS   (  69-)  E
3509 ASN   ( 160-)  E
3518 ASN   ( 169-)  E
3613 GLN   (  58-)  F
3913 GLN   (  17-)  H
4035 GLN   ( 139-)  H
4128 ASN   (  79-)  J
4213 GLN   (   3-)  K
4292 ASN   (  82-)  K
4409 GLN   (  81-)  L
4562 ASN   (  89-)  M
4596 HIS   ( 123-)  M
4663 HIS   (  50-)  N
4666 HIS   (  53-)  N
4979 HIS   (  14-)  Q
5240 ASN   (  57-)  S
5285 HIS   ( 102-)  S
5334 ASN   (  41-)  T
5348 ASN   (  55-)  T
5380 GLN   (  87-)  T
5478 ASN   (  92-)  U
5763 GLN   (  19-)  X
5789 ASN   (  45-)  X
5877 GLN   (  38-)  Y
5887 HIS   (  48-)  Y
5920 GLN   (  19-)  Z
5933 GLN   (  32-)  Z
5947 ASN   (  46-)  Z
5953 HIS   (  52-)  Z
6011 HIS   (  22-)  2
6080 HIS   (  46-)  3
6094 ASN   (   8-)  4
6164 HIS   (  31-)  5
6166 ASN   (  33-)  5

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.

   4 OURA  (   9-)  A      N3
   5 OGUA  (  10-)  A      N1
  45 OGUA  (  51-)  A      N2
  64 OGUA  (  70-)  A      N2
  77 OGUA  (  83-)  A      N1
  97 OURA  ( 104-)  A      N3
 131 OGUA  ( 137-)  A      N2
 132 OGUA  ( 138-)  A      N1
 133 OGUA  ( 139-)  A      N1
 133 OGUA  ( 139-)  A      N2
 135 OADE  ( 141-)  A      N6
 154 OURA  ( 164-)  A      N3
 155 OURA  ( 165-)  A      N3
 185 OURA  ( 200-)  A      N3
 205 OGUA  ( 220-)  A      N2
 206 OADE  ( 221-)  A      N6
 210 OADE  ( 225-)  A      N6
 211 OGUA  ( 226-)  A      N1
 213 OADE  ( 228-)  A      N6
 231 OCYT  ( 246-)  A      N4
 233 OGUA  ( 248-)  A      N2
 279 OGUA  ( 270-)  A      N1
 279 OGUA  ( 270-)  A      N2
 327 OGUA  ( 307-)  A      N2
 328 OGUA  ( 308-)  A      N2
And so on for a total of 795 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.

2963 ASP   (  85-)  C      OD1
2977 ASP   (  99-)  C      OD2
2993 GLN   ( 115-)  C      OE1
3064 HIS   ( 186-)  C      ND1
3109 HIS   ( 231-)  C      ND1
3279 HIS   ( 129-)  D      ND1
3285 HIS   ( 135-)  D      NE2
3380 HIS   (  31-)  E      ND1
3465 ASP   ( 116-)  E      OD2
3569 GLU   (  14-)  F      OE1
3595 ASN   (  40-)  F      OD1
3596 GLN   (  41-)  F      OE1
3698 GLU   ( 143-)  F      OE1
3698 GLU   ( 143-)  F      OE2
3760 GLU   (  34-)  G      OE1
4110 HIS   (  61-)  J      ND1
4530 HIS   (  57-)  M      ND1
4578 GLU   ( 105-)  M      OE1
4614 GLN   ( 141-)  M      OE1
4629 HIS   (  16-)  N      ND1
4637 GLN   (  24-)  N      OE1
4662 ASP   (  49-)  N      OD1
4672 ASP   (  59-)  N      OD1
4840 GLU   (  11-)  P      OE1
4855 ASP   (  26-)  P      OD1
4908 HIS   (  79-)  P      ND1
5061 ASP   (  97-)  Q      OD2
5261 GLU   (  78-)  S      OE2
5348 ASN   (  55-)  T      OD1
5397 ASP   (  11-)  U      OD1
5570 HIS   (  85-)  V      ND1
5664 ASP   ( 179-)  V      OD1
5771 GLU   (  27-)  X      OE1
5940 ASP   (  39-)  Z      OD1
5974 GLU   (  49-)  1      OE2
6032 HIS   (  43-)  2      ND1
6060 ASN   (  26-)  3      OD1
6168 GLN   (  35-)  5      OE1

Warning: Unusual ion packing

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

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

6227  MG   (   1-)  6   -.-  -.-  Too few ligands (0)
6228  MG   (   2-)  6   -.-  -.-  Too few ligands (0)
6229  MG   (   3-)  6   -.-  -.-  Too few ligands (0)
6230  MG   (   4-)  A   -.-  -.-  Part of ionic cluster
6230  MG   (   4-)  A   -.-  -.-  Too few ligands (2)
6231  MG   (   5-)  A   -.-  -.-  Too few ligands (1)
6232  MG   (   6-)  6   -.-  -.-  Too few ligands (0)
6233  MG   (   7-)  6   -.-  -.-  Too few ligands (0)
6234  MG   (2898-)  A   -.-  -.-  Too few ligands (2)
6235  MG   (2899-)  A   -.-  -.-  Too few ligands (2)
6236  MG   (  10-)  6   -.-  -.-  Too few ligands (0)
6237  MG   (  11-)  6   -.-  -.-  Too few ligands (0)
6238  MG   (  12-)  6   -.-  -.-  Part of ionic cluster
6238  MG   (  12-)  6   -.-  -.-  Too few ligands (0)
6239  MG   (2900-)  A   -.-  -.-  Part of ionic cluster
6239  MG   (2900-)  A   -.-  -.-  Too few ligands (2)
6240  MG   (  14-)  6   -.-  -.-  Too few ligands (0)
6241  MG   (  15-)  6   -.-  -.-  Too few ligands (0)
6242  MG   (  16-)  6   -.-  -.-  Too few ligands (0)
6243  MG   (2901-)  A   -.-  -.-  Too few ligands (3)
6244  MG   (2902-)  A   -.-  -.-  Too few ligands (3)
6245  MG   (2903-)  A   -.-  -.-  Too few ligands (1)
6246  MG   (2904-)  A   -.-  -.-  Too few ligands (2)
6247  MG   (  21-)  6   -.-  -.-  Part of ionic cluster
6247  MG   (  21-)  6   -.-  -.-  Too few ligands (0)
And so on for a total of 1433 lines.

Warning: Possible wrong residue type

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

2898 ASP   (  20-)  C   H-bonding suggests Asn; but Alt-Rotamer
2908 GLU   (  30-)  C   H-bonding suggests Gln
2979 GLU   ( 101-)  C   H-bonding suggests Gln
3078 ASP   ( 200-)  C   H-bonding suggests Asn
3167 ASP   (  17-)  D   H-bonding suggests Asn; but Alt-Rotamer
3168 ASP   (  18-)  D   H-bonding suggests Asn; but Alt-Rotamer
3233 ASP   (  83-)  D   H-bonding suggests Asn
3250 GLU   ( 100-)  D   H-bonding suggests Gln; but Alt-Rotamer
3487 GLU   ( 138-)  E   H-bonding suggests Gln; but Alt-Rotamer
3569 GLU   (  14-)  F   H-bonding suggests Gln
3681 ASP   ( 126-)  F   H-bonding suggests Asn; but Alt-Rotamer
3698 GLU   ( 143-)  F   H-bonding suggests Gln
3721 ASP   ( 166-)  F   H-bonding suggests Asn; but Alt-Rotamer
3944 GLU   (  48-)  H   H-bonding suggests Gln; but Alt-Rotamer
3981 GLU   (  85-)  H   H-bonding suggests Gln
4199 ASP   ( 150-)  J   H-bonding suggests Asn; but Alt-Rotamer
4219 GLU   (   9-)  K   H-bonding suggests Gln
4247 ASP   (  37-)  K   H-bonding suggests Asn; but Alt-Rotamer
4266 ASP   (  56-)  K   H-bonding suggests Asn
4420 GLU   (  92-)  L   H-bonding suggests Gln
4553 GLU   (  80-)  M   H-bonding suggests Gln; but Alt-Rotamer
4611 ASP   ( 138-)  M   H-bonding suggests Asn
4694 ASP   (  81-)  N   H-bonding suggests Asn; but Alt-Rotamer
4828 GLU   ( 107-)  O   H-bonding suggests Gln
4855 ASP   (  26-)  P   H-bonding suggests Asn
4936 ASP   ( 107-)  P   H-bonding suggests Asn; but Alt-Rotamer
4951 ASP   ( 122-)  P   H-bonding suggests Asn; but Alt-Rotamer
5125 GLU   (  43-)  R   H-bonding suggests Gln
5205 ASP   (  22-)  S   H-bonding suggests Asn; but Alt-Rotamer
5246 ASP   (  63-)  S   H-bonding suggests Asn
5368 ASP   (  75-)  T   H-bonding suggests Asn
5397 ASP   (  11-)  U   H-bonding suggests Asn; but Alt-Rotamer
5426 GLU   (  40-)  U   H-bonding suggests Gln; but Alt-Rotamer
5545 GLU   (  60-)  V   H-bonding suggests Gln; but Alt-Rotamer
5562 ASP   (  77-)  V   H-bonding suggests Asn
5639 ASP   ( 154-)  V   H-bonding suggests Asn; but Alt-Rotamer
5844 GLU   (   5-)  Y   H-bonding suggests Gln; but Alt-Rotamer
5859 GLU   (  20-)  Y   H-bonding suggests Gln
5974 GLU   (  49-)  1   H-bonding suggests Gln
6024 GLU   (  35-)  2   H-bonding suggests Gln
6173 GLU   (  40-)  5   H-bonding suggests Gln
6189 GLU   (  56-)  5   H-bonding suggests Gln; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -3.721
  2nd generation packing quality :  -4.373 (bad)
  Ramachandran plot appearance   :  -5.435 (bad)
  chi-1/chi-2 rotamer normality  :  -5.985 (bad)
  Backbone conformation          :  -0.737

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.015
  Bond angles                    :   1.352
  Omega angle restraints         :   1.332 (loose)
  Side chain planarity           :   0.326 (tight)
  Improper dihedral distribution :   0.788
  B-factor distribution          :   1.417
  Inside/Outside distribution    :   1.019

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 : 3.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -2.2
  2nd generation packing quality :  -1.8
  Ramachandran plot appearance   :  -2.3
  chi-1/chi-2 rotamer normality  :  -3.4 (poor)
  Backbone conformation          :   0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.015
  Bond angles                    :   1.352
  Omega angle restraints         :   1.332 (loose)
  Side chain planarity           :   0.326 (tight)
  Improper dihedral distribution :   0.788
  B-factor distribution          :   1.417
  Inside/Outside distribution    :   1.019
==============

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.