WHAT IF Check report

This file was created 2012-06-08 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 pdb2wvw.ent

Administrative problems that can generate validation failures

Warning: Strange inter-chain connections detected

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

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

  10 LYS   (  18-)  A  -   C   4818 GLU   (  32-)  S  -   CG
  11 ASP   (  19-)  A  -   N   4818 GLU   (  32-)  S  -   CA
  11 ASP   (  19-)  A  -   N   4818 GLU   (  32-)  S  -   CB
  11 ASP   (  19-)  A  -   N   4818 GLU   (  32-)  S  -   CG
  11 ASP   (  19-)  A  -   CA  4818 GLU   (  32-)  S  -   CB
  11 ASP   (  19-)  A  -   CA  4818 GLU   (  32-)  S  -   CG
  11 ASP   (  19-)  A  -   C   4818 GLU   (  32-)  S  -   CB
  11 ASP   (  19-)  A  -   C   4818 GLU   (  32-)  S  -   CG
  11 ASP   (  19-)  A  -   C   4818 GLU   (  32-)  S  -   CD
  11 ASP   (  19-)  A  -   CB  4818 GLU   (  32-)  S  -   CB
  11 ASP   (  19-)  A  -   CG  4815 GLN   (  29-)  S  - A C
  11 ASP   (  19-)  A  -   CG  4815 GLN   (  29-)  S  - A O
  11 ASP   (  19-)  A  -   OD2 4815 GLN   (  29-)  S  - A C
  11 ASP   (  19-)  A  -   OD2 4815 GLN   (  29-)  S  - A O
  12 TYR   (  20-)  A  -   N   4818 GLU   (  32-)  S  -   CD
  12 TYR   (  20-)  A  -   N   4818 GLU   (  32-)  S  -   OE2
  14 LEU   (  22-)  A  -   CG  4818 GLU   (  32-)  S  -   C
  14 LEU   (  22-)  A  -   CG  4818 GLU   (  32-)  S  -   O
  14 LEU   (  22-)  A  -   CG  4819 THR   (  33-)  S  -   CA
  14 LEU   (  22-)  A  -   CD1 4818 GLU   (  32-)  S  -   C
  14 LEU   (  22-)  A  -   CD1 4818 GLU   (  32-)  S  -   O
  14 LEU   (  22-)  A  -   CD2 4819 THR   (  33-)  S  -   CA
  14 LEU   (  22-)  A  -   CD2 4819 THR   (  33-)  S  -   C
  14 LEU   (  22-)  A  -   CD2 4819 THR   (  33-)  S  -   O
  37 GLN   (  45-)  A  -   OE1 4894 LEU   (   3-)  T  -   CD1
And so on for a total of 428 lines.

Warning: Strange inter-chain connections could NOT be corrected

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

Warning: Overlapping residues or molecules

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

Overlapping residues or molecules (for short entities) are occasionally observed in the PDB. Often these are cases like, for example, two sugars that bind equally well in the same active site, are both seen overlapping in the density, and are both entered in the PDB file as separate entities. This can cause some false positive error messsages further down the validation path, and therefore the second of the overlapping entities has been deleted before the validation continued. If you want to validate both situations, make it two PDB files, one for each sugar. And fudge reality a bit by making the occupancy of the sugar atoms 1.0 in both cases, because many validation options are not executed on atoms with low occupancy. If you go for this two-file option, please make sure that any side chains that have alternate locations depending on the sugar bound are selected in each of the two cases in agreement with the sugar that you keep for validation in that particular file.

  11 ASP   (  19-)  A  -
  62 TRP   (  70-)  A  -
 405 ASN   ( 413-)  A  -
 457 ILE   ( 465-)  A  -
 459 PHE   ( 467-)  A  -
 478 ASP   (  19-)  B  -
 481 LEU   (  22-)  B  -
 505 PRO   (  46-)  B  -
 529 TRP   (  70-)  B  -
 872 ASN   ( 413-)  B  -
 924 ILE   ( 465-)  B  -
 926 PHE   ( 467-)  B  -
 945 ASP   (  19-)  C  -
1391 ILE   ( 465-)  C  -
1393 PHE   ( 467-)  C  -
1412 ASP   (  19-)  D  -
1415 LEU   (  22-)  D  -
1858 ILE   ( 465-)  D  -
1860 PHE   ( 467-)  D  -
1879 ASP   (  19-)  E  -
1882 LEU   (  22-)  E  -
1930 TRP   (  70-)  E  -
2273 ASN   ( 413-)  E  -
2325 ILE   ( 465-)  E  -
2346 ASP   (  19-)  F  -
And so on for a total of 66 lines.

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

  11 ASP   (  19-)  A  -   OD2 bound to 4788 GLN   (  29-)  S  - A C
 382 GLU   ( 392-)  A  -   OE2 bound to  428 TYR   ( 438-)  A  -   CG
 455 ILE   ( 465-)  A  -   N   bound to 5201 ARG   (  24-)  W  -   CZ
 456 LYS   ( 466-)  A  -   NZ  bound to  453 LYS   ( 463-)  A  -   CE
 459 PHE   ( 469-)  A  -   N   bound to  460 GLU   ( 470-)  A  -   N
 460 GLU   ( 470-)  A  -   N   bound to  459 PHE   ( 469-)  A  -   N
 476 ASP   (  19-)  B  -   OD2 bound to 4580 GLN   (  29-)  Q  - A C
 849 GLU   ( 392-)  B  -   OE2 bound to  895 TYR   ( 438-)  B  -   CG
 922 ILE   ( 465-)  B  -   N   bound to 4158 ARG   (  24-)  M  -   CZ
 923 LYS   ( 466-)  B  -   NZ  bound to  920 LYS   ( 463-)  B  -   CE
 926 PHE   ( 469-)  B  -   N   bound to  927 GLU   ( 470-)  B  -   N
 927 GLU   ( 470-)  B  -   N   bound to  926 PHE   ( 469-)  B  -   N
 969 GLY   (  47-)  C  -   N   bound to 4209 HIS   (  76-)  M  -   ND1
1313 GLU   ( 392-)  C  -   OE2 bound to 1358 TYR   ( 438-)  C  -   CG
1385 ILE   ( 465-)  C  -   N   bound to 4575 ARG   (  24-)  Q  -   NH2
1386 LYS   ( 466-)  C  -   NZ  bound to 1383 LYS   ( 463-)  C  -   CE
1389 PHE   ( 469-)  C  -   N   bound to 1390 GLU   ( 470-)  C  -   N
1390 GLU   ( 470-)  C  -   N   bound to 1389 PHE   ( 469-)  C  -   N
1406 ASP   (  19-)  D  -   OD2 bound to 4372 GLN   (  29-)  O  - A C
1777 GLU   ( 392-)  D  -   OE2 bound to 1822 TYR   ( 438-)  D  -   CG
1849 ILE   ( 465-)  D  -   N   bound to 3950 ARG   (  24-)  K  -   CZ
1850 LYS   ( 466-)  D  -   NZ  bound to 1847 LYS   ( 463-)  D  -   CE
1853 PHE   ( 469-)  D  -   N   bound to 1854 GLU   ( 470-)  D  -   N
1854 GLU   ( 470-)  D  -   N   bound to 1853 PHE   ( 469-)  D  -   N
2243 GLU   ( 392-)  E  -   OE2 bound to 2289 TYR   ( 438-)  E  -   CG
And so on for a total of 54 lines.

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: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: Q

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: U

Note: Ramachandran plot

Chain identifier: V

Note: Ramachandran plot

Chain identifier: W

Note: Ramachandran plot

Chain identifier: X

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'.

  81 GLN   (  91-)  A      CG
  81 GLN   (  91-)  A      CD
  81 GLN   (  91-)  A      OE1
  81 GLN   (  91-)  A      NE2
 548 GLN   (  91-)  B      CG
 548 GLN   (  91-)  B      CD
 548 GLN   (  91-)  B      OE1
 548 GLN   (  91-)  B      NE2
1012 GLN   (  91-)  C      CG
1012 GLN   (  91-)  C      CD
1012 GLN   (  91-)  C      OE1
1012 GLN   (  91-)  C      NE2
1476 GLN   (  91-)  D      CG
1476 GLN   (  91-)  D      CD
1476 GLN   (  91-)  D      OE1
1476 GLN   (  91-)  D      NE2
1942 GLN   (  91-)  E      CG
1942 GLN   (  91-)  E      CD
1942 GLN   (  91-)  E      OE1
1942 GLN   (  91-)  E      NE2
2406 GLN   (  91-)  F      CG
2406 GLN   (  91-)  F      CD
2406 GLN   (  91-)  F      OE1
2406 GLN   (  91-)  F      NE2
2871 GLN   (  91-)  G      CG
And so on for a total of 432 lines.

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 SER   (   9-)  A    Zero
   2 ALA   (  10-)  A    Zero
   3 ALA   (  11-)  A    Zero
   4 GLY   (  12-)  A    Zero
   5 TYR   (  13-)  A    Zero
   6 LYS   (  14-)  A    Zero
   7 ALA   (  15-)  A    Zero
   8 GLY   (  16-)  A    Zero
   9 VAL   (  17-)  A    Zero
  10 LYS   (  18-)  A    Zero
  11 ASP   (  19-)  A    Zero
  12 TYR   (  20-)  A    Zero
  13 LYS   (  21-)  A    Zero
  14 THR   (  23-)  A    Zero
  15 TYR   (  24-)  A    Zero
  16 TYR   (  25-)  A    Zero
  17 THR   (  26-)  A    Zero
  18 PRO   (  27-)  A    Zero
  19 ASP   (  28-)  A    Zero
  20 TYR   (  29-)  A    Zero
  21 THR   (  30-)  A    Zero
  22 PRO   (  31-)  A    Zero
  23 LYS   (  32-)  A    Zero
  24 ASP   (  33-)  A    Zero
  25 THR   (  34-)  A    Zero
And so on for a total of 5385 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:

Temperature not mentioned in PDB file. This most likely means that the temperature record is absent.
Room temperature assumed

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 100.00

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: A

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: B

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: C

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: D

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: E

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: F

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: G

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: H

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: I

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: J

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: K

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: L

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: M

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: N

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: O

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: P

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: Q

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: R

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: S

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: T

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: U

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: V

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: W

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: X

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.

 124 ARG   ( 134-)  A
 149 ARG   ( 159-)  A
 205 ARG   ( 215-)  A
 207 ARG   ( 217-)  A
 591 ARG   ( 134-)  B
 616 ARG   ( 159-)  B
 672 ARG   ( 215-)  B
 674 ARG   ( 217-)  B
1055 ARG   ( 134-)  C
1080 ARG   ( 159-)  C
1136 ARG   ( 215-)  C
1138 ARG   ( 217-)  C
1519 ARG   ( 134-)  D
1544 ARG   ( 159-)  D
1600 ARG   ( 215-)  D
1602 ARG   ( 217-)  D
1985 ARG   ( 134-)  E
2010 ARG   ( 159-)  E
2066 ARG   ( 215-)  E
2068 ARG   ( 217-)  E
2449 ARG   ( 134-)  F
2474 ARG   ( 159-)  F
2530 ARG   ( 215-)  F
2532 ARG   ( 217-)  F
2914 ARG   ( 134-)  G
2939 ARG   ( 159-)  G
2995 ARG   ( 215-)  G
2997 ARG   ( 217-)  G
3379 ARG   ( 134-)  H
3404 ARG   ( 159-)  H
3460 ARG   ( 215-)  H
3462 ARG   ( 217-)  H
3785 ARG   (  69-)  I
3993 ARG   (  69-)  K
4202 ARG   (  69-)  M
4411 ARG   (  69-)  O
4619 ARG   (  69-)  Q
4828 ARG   (  69-)  S
5036 ARG   (  69-)  U
5245 ARG   (  69-)  W

Warning: Phenylalanine convention problem

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

3776 PHE   (  60-)  I
3881 PHE   (  60-)  J
3984 PHE   (  60-)  K
4089 PHE   (  60-)  L
4193 PHE   (  60-)  M
4298 PHE   (  60-)  N
4402 PHE   (  60-)  O
4507 PHE   (  60-)  P
4610 PHE   (  60-)  Q
4714 PHE   (  60-)  R
4819 PHE   (  60-)  S
4924 PHE   (  60-)  T
5027 PHE   (  60-)  U
5132 PHE   (  60-)  V
5236 PHE   (  60-)  W
5340 PHE   (  60-)  X

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.

3781 ASP   (  65-)  I
3872 ASP   (  51-)  J
3989 ASP   (  65-)  K
4080 ASP   (  51-)  L
4198 ASP   (  65-)  M
4289 ASP   (  51-)  N
4407 ASP   (  65-)  O
4498 ASP   (  51-)  P
4615 ASP   (  65-)  Q
4705 ASP   (  51-)  R
4824 ASP   (  65-)  S
4915 ASP   (  51-)  T
5032 ASP   (  65-)  U
5123 ASP   (  51-)  V
5241 ASP   (  65-)  W
5331 ASP   (  51-)  X

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.

3749 GLU   (  32-)  I
3773 GLU   (  57-)  I
3774 GLU   (  58-)  I
3795 GLU   (  79-)  I
3799 GLU   (  83-)  I
3803 GLU   (  87-)  I
3853 GLU   (  32-)  J
3883 GLU   (  62-)  J
3896 GLU   (  75-)  J
3900 GLU   (  79-)  J
3957 GLU   (  32-)  K
3981 GLU   (  57-)  K
3982 GLU   (  58-)  K
4003 GLU   (  79-)  K
4007 GLU   (  83-)  K
4011 GLU   (  87-)  K
4061 GLU   (  32-)  L
4091 GLU   (  62-)  L
4104 GLU   (  75-)  L
4108 GLU   (  79-)  L
4190 GLU   (  57-)  M
4191 GLU   (  58-)  M
4212 GLU   (  79-)  M
4216 GLU   (  83-)  M
4220 GLU   (  87-)  M
And so on for a total of 78 lines.

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 456 LYS   ( 466-)  A      N   -C     1.09  -12.0
 457 PHE   ( 467-)  A      N   -C     1.05  -13.8
 462 MET   ( 472-)  A      N   -C     1.81   23.9
 923 LYS   ( 466-)  B      N   -C     1.09  -12.1
 924 PHE   ( 467-)  B      N   -C     1.05  -13.9
 929 MET   ( 472-)  B      N   -C     1.81   23.8
1386 LYS   ( 466-)  C      N   -C     1.09  -12.1
1387 PHE   ( 467-)  C      N   -C     1.05  -13.8
1392 MET   ( 472-)  C      N   -C     1.81   23.8
1850 LYS   ( 466-)  D      N   -C     1.09  -12.0
1851 PHE   ( 467-)  D      N   -C     1.05  -13.8
1856 MET   ( 472-)  D      N   -C     1.81   23.9
2317 LYS   ( 466-)  E      N   -C     1.09  -12.0
2322 MET   ( 472-)  E      N   -C     1.81   23.8
2780 LYS   ( 466-)  F      N   -C     1.09  -12.0
2781 PHE   ( 467-)  F      N   -C     1.05  -13.9
2786 MET   ( 472-)  F      N   -C     1.81   23.9
3246 LYS   ( 466-)  G      N   -C     1.09  -12.0
3247 PHE   ( 467-)  G      N   -C     1.05  -13.8
3252 MET   ( 472-)  G      N   -C     1.81   23.9
3710 LYS   ( 466-)  H      N   -C     1.09  -12.1
3715 MET   ( 472-)  H      N   -C     1.81   23.8
3744 VAL   (  26-)  I      CA   CB    1.61    4.1
3855 ASN   (  34-)  J      C    O     1.33    5.0
3855 ASN   (  34-)  J      CG   OD1   1.36    6.3
And so on for a total of 80 lines.

Warning: Directionality in bond lengths and no X-ray cell

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] standard values for DNA/RNA shows a significant systematic deviation.

You have most probably seen symmetry problems earlier. Please correct these and rerun this check to see the possible implications on the X-ray cell axes.

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.

  27 LEU   (  36-)  A      CA   CB   CG  130.58    4.1
 257 HIS   ( 267-)  A      CG   ND1  CE1 109.79    4.2
 317 HIS   ( 327-)  A      CG   ND1  CE1 109.72    4.1
 340 ARG   ( 350-)  A      CB   CG   CD  105.08   -4.5
 454 GLU   ( 464-)  A     -O   -C    N    66.79  -35.1
 454 GLU   ( 464-)  A     -CA  -C    N   167.10   25.4
 454 GLU   ( 464-)  A     -C    N    CA  142.43   11.5
 456 LYS   ( 466-)  A     -O   -C    N   103.26  -12.3
 456 LYS   ( 466-)  A     -CA  -C    N   135.05    9.4
 456 LYS   ( 466-)  A     -C    N    CA  130.12    4.7
 457 PHE   ( 467-)  A     -O   -C    N    86.67  -22.7
 457 PHE   ( 467-)  A     -CA  -C    N   152.40   18.1
 462 MET   ( 472-)  A     -O   -C    N   142.59   12.2
 462 MET   ( 472-)  A     -CA  -C    N    96.42   -9.9
 493 LEU   (  36-)  B      CA   CB   CG  130.60    4.1
 724 HIS   ( 267-)  B      CG   ND1  CE1 109.80    4.2
 784 HIS   ( 327-)  B      CG   ND1  CE1 109.72    4.1
 807 ARG   ( 350-)  B      CB   CG   CD  105.08   -4.5
 921 GLU   ( 464-)  B     -O   -C    N    66.79  -35.1
 921 GLU   ( 464-)  B     -CA  -C    N   167.07   25.4
 921 GLU   ( 464-)  B     -C    N    CA  142.43   11.5
 923 LYS   ( 466-)  B     -O   -C    N   103.28  -12.3
 923 LYS   ( 466-)  B     -CA  -C    N   135.08    9.4
 923 LYS   ( 466-)  B     -C    N    CA  130.13    4.7
 924 PHE   ( 467-)  B     -O   -C    N    86.65  -22.7
And so on for a total of 140 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.

 124 ARG   ( 134-)  A
 149 ARG   ( 159-)  A
 205 ARG   ( 215-)  A
 207 ARG   ( 217-)  A
 591 ARG   ( 134-)  B
 616 ARG   ( 159-)  B
 672 ARG   ( 215-)  B
 674 ARG   ( 217-)  B
1055 ARG   ( 134-)  C
1080 ARG   ( 159-)  C
1136 ARG   ( 215-)  C
1138 ARG   ( 217-)  C
1519 ARG   ( 134-)  D
1544 ARG   ( 159-)  D
1600 ARG   ( 215-)  D
1602 ARG   ( 217-)  D
1985 ARG   ( 134-)  E
2010 ARG   ( 159-)  E
2066 ARG   ( 215-)  E
2068 ARG   ( 217-)  E
2449 ARG   ( 134-)  F
2474 ARG   ( 159-)  F
2530 ARG   ( 215-)  F
2532 ARG   ( 217-)  F
2914 ARG   ( 134-)  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.

 327 GLY   ( 337-)  A      C     -6.6    -8.71     0.06
 340 ARG   ( 350-)  A      C     -6.1    -9.21     0.13
 453 LYS   ( 463-)  A      C      6.2     9.50     0.11
 794 GLY   ( 337-)  B      C     -6.7    -8.73     0.06
 807 ARG   ( 350-)  B      C     -6.1    -9.18     0.13
 920 LYS   ( 463-)  B      C      6.2     9.53     0.11
1258 GLY   ( 337-)  C      C     -6.7    -8.74     0.06
1271 ARG   ( 350-)  C      C     -6.2    -9.22     0.13
1383 LYS   ( 463-)  C      C      6.2     9.53     0.11
1722 GLY   ( 337-)  D      C     -6.7    -8.73     0.06
1735 ARG   ( 350-)  D      C     -6.2    -9.25     0.13
1847 LYS   ( 463-)  D      C      6.2     9.43     0.11
2188 GLY   ( 337-)  E      C     -6.7    -8.73     0.06
2201 ARG   ( 350-)  E      C     -6.2    -9.23     0.13
2314 LYS   ( 463-)  E      C      6.2     9.43     0.11
2652 GLY   ( 337-)  F      C     -6.7    -8.77     0.06
2665 ARG   ( 350-)  F      C     -6.2    -9.24     0.13
2777 LYS   ( 463-)  F      C      6.2     9.52     0.11
3117 GLY   ( 337-)  G      C     -6.6    -8.71     0.06
3130 ARG   ( 350-)  G      C     -6.2    -9.26     0.13
3243 LYS   ( 463-)  G      C      6.2     9.51     0.11
3582 GLY   ( 337-)  H      C     -6.6    -8.71     0.06
3595 ARG   ( 350-)  H      C     -6.1    -9.18     0.13
3707 LYS   ( 463-)  H      C      6.2     9.48     0.11
3857 PRO   (  36-)  J      C    -11.1   -17.19     0.42
4065 PRO   (  36-)  L      C    -11.1   -17.19     0.42
4274 PRO   (  36-)  N      C    -11.1   -17.19     0.42
4483 PRO   (  36-)  P      C    -11.1   -17.19     0.42
4690 PRO   (  36-)  R      C    -11.1   -17.19     0.42
4900 PRO   (  36-)  T      C    -11.1   -17.19     0.42
5108 PRO   (  36-)  V      C    -11.1   -17.19     0.42
5316 PRO   (  36-)  X      C    -11.1   -17.19     0.42
The average deviation= 1.449

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.

3547 ASP   ( 302-)  H    4.24
3082 ASP   ( 302-)  G    4.23
1687 ASP   ( 302-)  D    4.23
 292 ASP   ( 302-)  A    4.21
 759 ASP   ( 302-)  B    4.21
1223 ASP   ( 302-)  C    4.21
2617 ASP   ( 302-)  F    4.20
2153 ASP   ( 302-)  E    4.19
4423 ILE   (  81-)  O    4.06
4631 ILE   (  81-)  Q    4.06
3797 ILE   (  81-)  I    4.06
4005 ILE   (  81-)  K    4.06
4840 ILE   (  81-)  S    4.06
5048 ILE   (  81-)  U    4.06
4214 ILE   (  81-)  M    4.06
3902 ILE   (  81-)  J    4.01
4735 ILE   (  81-)  R    4.01
4945 ILE   (  81-)  T    4.01
5361 ILE   (  81-)  X    4.01
4110 ILE   (  81-)  L    4.01
4319 ILE   (  81-)  N    4.01
4528 ILE   (  81-)  P    4.01
5153 ILE   (  81-)  V    4.01

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

2471 GLN   ( 156-)  F    6.81
2936 GLN   ( 156-)  G    6.80
1077 GLN   ( 156-)  C    6.79
3401 GLN   ( 156-)  H    6.77
 146 GLN   ( 156-)  A    6.75
 613 GLN   ( 156-)  B    6.74
2007 GLN   ( 156-)  E    6.73
1541 GLN   ( 156-)  D    6.71
2995 ARG   ( 215-)  G    6.51
1600 ARG   ( 215-)  D    6.48
2939 ARG   ( 159-)  G    6.38
2474 ARG   ( 159-)  F    6.38
3460 ARG   ( 215-)  H    6.36
1544 ARG   ( 159-)  D    6.35
2530 ARG   ( 215-)  F    6.35
 616 ARG   ( 159-)  B    6.30
3404 ARG   ( 159-)  H    6.29
 205 ARG   ( 215-)  A    6.26
1080 ARG   ( 159-)  C    6.25
 149 ARG   ( 159-)  A    6.21
2010 ARG   ( 159-)  E    6.13
2066 ARG   ( 215-)  E    6.10
1136 ARG   ( 215-)  C    6.09
 674 ARG   ( 217-)  B    5.90
2068 ARG   ( 217-)  E    5.89
And so on for a total of 96 lines.

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.

2933 HIS   ( 153-)  G      CB   4.66
2468 HIS   ( 153-)  F      CB   4.66
3398 HIS   ( 153-)  H      CB   4.65
1538 HIS   ( 153-)  D      CB   4.65
 143 HIS   ( 153-)  A      CB   4.65
 610 HIS   ( 153-)  B      CB   4.65
1074 HIS   ( 153-)  C      CB   4.63
2004 HIS   ( 153-)  E      CB   4.63
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -1.093

Torsion-related checks

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.

 157 ARG   ( 167-)  A    -2.6
2482 ARG   ( 167-)  F    -2.6
1088 ARG   ( 167-)  C    -2.6
1552 ARG   ( 167-)  D    -2.6
2947 ARG   ( 167-)  G    -2.6
2018 ARG   ( 167-)  E    -2.6
 624 ARG   ( 167-)  B    -2.6
3412 ARG   ( 167-)  H    -2.6
3261 LYS   (  14-)  H    -2.5
1865 LYS   (  14-)  E    -2.5
1401 LYS   (  14-)  D    -2.5
   6 LYS   (  14-)  A    -2.5
 471 LYS   (  14-)  B    -2.5
2795 LYS   (  14-)  G    -2.5
 938 LYS   (  14-)  C    -2.5
2331 LYS   (  14-)  F    -2.5
1085 LYS   ( 164-)  C    -2.5
 154 LYS   ( 164-)  A    -2.5
3409 LYS   ( 164-)  H    -2.5
 621 LYS   ( 164-)  B    -2.5
2944 LYS   ( 164-)  G    -2.5
1549 LYS   ( 164-)  D    -2.5
2015 LYS   ( 164-)  E    -2.5
2479 LYS   ( 164-)  F    -2.5
1216 ARG   ( 295-)  C    -2.4
And so on for a total of 120 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.

   2 ALA   (  10-)  A  omega poor
  52 SER   (  62-)  A  Poor phi/psi
  53 THR   (  63-)  A  omega poor
  55 THR   (  65-)  A  omega poor
  85 ASN   (  95-)  A  Poor phi/psi
  87 TYR   (  97-)  A  omega poor
 153 ASN   ( 163-)  A  Poor phi/psi
 155 TYR   ( 165-)  A  omega poor
 165 LYS   ( 175-)  A  PRO omega poor
 189 PHE   ( 199-)  A  omega poor
 197 ASN   ( 207-)  A  Poor phi/psi
 233 THR   ( 243-)  A  omega poor
 287 MET   ( 297-)  A  Poor phi/psi
 291 ILE   ( 301-)  A  omega poor
 321 VAL   ( 331-)  A  Poor phi/psi
 360 SER   ( 370-)  A  Poor phi/psi
 402 GLY   ( 412-)  A  omega poor
 453 LYS   ( 463-)  A  Poor phi/psi, omega poor
 456 LYS   ( 466-)  A  omega poor
 467 ALA   (  10-)  B  omega poor
 480 THR   (  23-)  B  omega poor
 519 SER   (  62-)  B  Poor phi/psi
 520 THR   (  63-)  B  omega poor
 522 THR   (  65-)  B  omega poor
 552 ASN   (  95-)  B  Poor phi/psi
And so on for a total of 183 lines.

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.

3837 SER   (  16-)  J    0.36
4045 SER   (  16-)  L    0.36
4254 SER   (  16-)  N    0.36
4463 SER   (  16-)  P    0.36
4670 SER   (  16-)  R    0.36
4880 SER   (  16-)  T    0.36
5088 SER   (  16-)  V    0.36
5296 SER   (  16-)  X    0.36
 331 SER   ( 341-)  A    0.39
 798 SER   ( 341-)  B    0.39
1262 SER   ( 341-)  C    0.39
1726 SER   ( 341-)  D    0.39
2192 SER   ( 341-)  E    0.39
2656 SER   ( 341-)  F    0.39
3121 SER   ( 341-)  G    0.39
3586 SER   ( 341-)  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 ALA   (  11-)  A      0
   5 TYR   (  13-)  A      0
   7 ALA   (  15-)  A      0
  12 TYR   (  20-)  A      0
  13 LYS   (  21-)  A      0
  14 THR   (  23-)  A      0
  15 TYR   (  24-)  A      0
  16 TYR   (  25-)  A      0
  17 THR   (  26-)  A      0
  35 PRO   (  44-)  A      0
  36 GLN   (  45-)  A      0
  37 GLY   (  47-)  A      0
  38 VAL   (  48-)  A      0
  51 SER   (  61-)  A      0
  52 SER   (  62-)  A      0
  53 THR   (  63-)  A      0
  56 TRP   (  66-)  A      0
  60 TRP   (  70-)  A      0
  64 LEU   (  74-)  A      0
  65 THR   (  75-)  A      0
  75 TYR   (  85-)  A      0
  78 GLU   (  88-)  A      0
  81 GLN   (  91-)  A      0
  84 GLU   (  94-)  A      0
  97 LEU   ( 107-)  A      0
And so on for a total of 1646 lines.

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!

3582 GLY   ( 337-)  H   1.66   20
2188 GLY   ( 337-)  E   1.66   20
3117 GLY   ( 337-)  G   1.66   20
1258 GLY   ( 337-)  C   1.66   20
 327 GLY   ( 337-)  A   1.66   20
 794 GLY   ( 337-)  B   1.66   20
1722 GLY   ( 337-)  D   1.66   20
2652 GLY   ( 337-)  F   1.66   20
1326 GLY   ( 405-)  C   1.54   80
 395 GLY   ( 405-)  A   1.54   80
3185 GLY   ( 405-)  G   1.54   80
1790 GLY   ( 405-)  D   1.54   80
3650 GLY   ( 405-)  H   1.54   80
2256 GLY   ( 405-)  E   1.54   80
2720 GLY   ( 405-)  F   1.54   80
 862 GLY   ( 405-)  B   1.54   80

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]

 405 PRO   ( 415-)  A    0.19 LOW
 872 PRO   ( 415-)  B    0.19 LOW
1335 PRO   ( 415-)  C    0.19 LOW
1799 PRO   ( 415-)  D    0.19 LOW
2266 PRO   ( 415-)  E    0.19 LOW
2729 PRO   ( 415-)  F    0.19 LOW
3195 PRO   ( 415-)  G    0.19 LOW
3659 PRO   ( 415-)  H    0.19 LOW
3802 PRO   (  86-)  I    0.20 LOW
4010 PRO   (  86-)  K    0.20 LOW
4219 PRO   (  86-)  M    0.20 LOW
4428 PRO   (  86-)  O    0.20 LOW
4636 PRO   (  86-)  Q    0.20 LOW
4845 PRO   (  86-)  S    0.20 LOW
5053 PRO   (  86-)  U    0.20 LOW
5261 PRO   (  86-)  W    0.20 LOW

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].

 378 PRO   ( 388-)  A  -124.5 half-chair C-delta/C-gamma (-126 degrees)
 400 PRO   ( 410-)  A  -127.0 half-chair C-delta/C-gamma (-126 degrees)
 503 PRO   (  46-)  B  -124.7 half-chair C-delta/C-gamma (-126 degrees)
 845 PRO   ( 388-)  B  -124.5 half-chair C-delta/C-gamma (-126 degrees)
 867 PRO   ( 410-)  B  -127.0 half-chair C-delta/C-gamma (-126 degrees)
1309 PRO   ( 388-)  C  -124.6 half-chair C-delta/C-gamma (-126 degrees)
1331 PRO   ( 410-)  C  -127.1 half-chair C-delta/C-gamma (-126 degrees)
1773 PRO   ( 388-)  D  -124.5 half-chair C-delta/C-gamma (-126 degrees)
1795 PRO   ( 410-)  D  -127.0 half-chair C-delta/C-gamma (-126 degrees)
1897 PRO   (  46-)  E  -124.7 half-chair C-delta/C-gamma (-126 degrees)
2239 PRO   ( 388-)  E  -124.5 half-chair C-delta/C-gamma (-126 degrees)
2261 PRO   ( 410-)  E  -126.9 half-chair C-delta/C-gamma (-126 degrees)
2703 PRO   ( 388-)  F  -124.5 half-chair C-delta/C-gamma (-126 degrees)
2725 PRO   ( 410-)  F  -127.0 half-chair C-delta/C-gamma (-126 degrees)
3168 PRO   ( 388-)  G  -124.6 half-chair C-delta/C-gamma (-126 degrees)
3190 PRO   ( 410-)  G  -127.1 half-chair C-delta/C-gamma (-126 degrees)
3292 PRO   (  46-)  H  -124.7 half-chair C-delta/C-gamma (-126 degrees)
3633 PRO   ( 388-)  H  -124.4 half-chair C-delta/C-gamma (-126 degrees)
3655 PRO   ( 410-)  H  -126.9 half-chair C-delta/C-gamma (-126 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

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

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

1898 GLY   (  47-)  E      CA   <->  4030 MET   (   1-)  L      SD   1.41    1.99  INTRA BL
3293 GLY   (  47-)  H      CA   <->  5281 MET   (   1-)  X      SD   1.41    1.99  INTRA BL
  13 LYS   (  21-)  A      NZ   <->  4792 THR   (  33-)  S      CG2  1.34    1.76  INTRA BL
 624 ARG   ( 167-)  B      CG   <->   885 VAL   ( 428-)  B      CG2  1.34    1.86  INTRA BL
1088 ARG   ( 167-)  C      CG   <->  1348 VAL   ( 428-)  C      CG2  1.34    1.86  INTRA BL
2018 ARG   ( 167-)  E      CG   <->  2279 VAL   ( 428-)  E      CG2  1.34    1.86  INTRA BL
 157 ARG   ( 167-)  A      CG   <->   418 VAL   ( 428-)  A      CG2  1.34    1.86  INTRA BL
3412 ARG   ( 167-)  H      CG   <->  3672 VAL   ( 428-)  H      CG2  1.34    1.86  INTRA BL
2482 ARG   ( 167-)  F      CG   <->  2742 VAL   ( 428-)  F      CG2  1.34    1.86  INTRA BL
2947 ARG   ( 167-)  G      CG   <->  3208 VAL   ( 428-)  G      CG2  1.34    1.86  INTRA BL
1552 ARG   ( 167-)  D      CG   <->  1812 VAL   ( 428-)  D      CG2  1.34    1.86  INTRA BL
 922 ILE   ( 465-)  B      CD1  <->  4158 ARG   (  24-)  M      CB   1.32    1.88  INTRA BL
 969 GLY   (  47-)  C      CA   <->  4239 MET   (   1-)  N      SD   1.29    2.11  INTRA BL
  13 LYS   (  21-)  A      NZ   <->  4792 THR   (  33-)  S      CB   1.27    1.83  INTRA BL
3636 VAL   ( 391-)  H      CG1  <->  3681 LEU   ( 437-)  H      CD1  1.26    1.94  INTRA BL
1897 PRO   (  46-)  E      CB   <->  4000 HIS   (  76-)  K      CD2  1.26    1.94  INTRA BL
2706 VAL   ( 391-)  F      CG1  <->  2751 LEU   ( 437-)  F      CD1  1.26    1.94  INTRA BL
1312 VAL   ( 391-)  C      CG1  <->  1357 LEU   ( 437-)  C      CD1  1.26    1.94  INTRA BL
 381 VAL   ( 391-)  A      CG1  <->   427 LEU   ( 437-)  A      CD1  1.26    1.94  INTRA BL
2242 VAL   ( 391-)  E      CG1  <->  2288 LEU   ( 437-)  E      CD1  1.26    1.94  INTRA BL
3171 VAL   ( 391-)  G      CG1  <->  3217 LEU   ( 437-)  G      CD1  1.26    1.94  INTRA BL
1776 VAL   ( 391-)  D      CG1  <->  1821 LEU   ( 437-)  D      CD1  1.26    1.94  INTRA BL
 848 VAL   ( 391-)  B      CG1  <->   894 LEU   ( 437-)  B      CD1  1.26    1.94  INTRA BL
  13 LYS   (  21-)  A      CG   <->  4792 THR   (  33-)  S      CG2  1.25    1.95  INTRA BL
 455 ILE   ( 465-)  A      CD1  <->  5201 ARG   (  24-)  W      CB   1.24    1.96  INTRA BL
And so on for a total of 1676 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: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

Note: Inside/Outside RMS Z-score plot

Chain identifier: Q

Note: Inside/Outside RMS Z-score plot

Chain identifier: R

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Inside/Outside RMS Z-score plot

Chain identifier: U

Note: Inside/Outside RMS Z-score plot

Chain identifier: V

Note: Inside/Outside RMS Z-score plot

Chain identifier: W

Note: Inside/Outside RMS Z-score plot

Chain identifier: X

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.

3376 ARG   ( 131-)  H      -6.54
1394 LYS   ( 474-)  C      -6.44
2324 LYS   ( 474-)  E      -6.43
 464 LYS   ( 474-)  A      -6.43
2788 LYS   ( 474-)  F      -6.43
3254 LYS   ( 474-)  G      -6.42
1858 LYS   ( 474-)  D      -6.42
3717 LYS   ( 474-)  H      -6.42
 931 LYS   ( 474-)  B      -6.42
1835 TRP   ( 451-)  D      -6.10
1052 ARG   ( 131-)  C      -6.10
1371 TRP   ( 451-)  C      -6.09
3231 TRP   ( 451-)  G      -6.09
 441 TRP   ( 451-)  A      -6.09
2302 TRP   ( 451-)  E      -6.09
2765 TRP   ( 451-)  F      -6.09
 908 TRP   ( 451-)  B      -6.09
3695 TRP   ( 451-)  H      -6.09
2911 ARG   ( 131-)  G      -6.06
1516 ARG   ( 131-)  D      -6.05
1982 ARG   ( 131-)  E      -6.01
2446 ARG   ( 131-)  F      -6.01
 121 ARG   ( 131-)  A      -6.00
 588 ARG   ( 131-)  B      -5.93
2620 ARG   ( 305-)  F      -5.93
And so on for a total of 128 lines.

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: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: G

Note: Quality value plot

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

Chain identifier: H

Note: Quality value plot

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

Chain identifier: I

Note: Quality value plot

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

Chain identifier: J

Note: Quality value plot

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

Chain identifier: K

Note: Quality value plot

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

Chain identifier: L

Note: Quality value plot

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

Chain identifier: M

Note: Quality value plot

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

Chain identifier: N

Note: Quality value plot

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

Chain identifier: O

Note: Quality value plot

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

Chain identifier: P

Note: Quality value plot

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

Chain identifier: Q

Note: Quality value plot

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

Chain identifier: R

Note: Quality value plot

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

Chain identifier: S

Note: Quality value plot

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

Chain identifier: T

Note: Quality value plot

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

Chain identifier: U

Note: Quality value plot

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

Chain identifier: 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

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.

2150 ALA   ( 299-)  E   -2.84
1684 ALA   ( 299-)  D   -2.84
3079 ALA   ( 299-)  G   -2.84
3544 ALA   ( 299-)  H   -2.83
2614 ALA   ( 299-)  F   -2.82
5226 GLN   (  50-)  W   -2.81
1220 ALA   ( 299-)  C   -2.81
 289 ALA   ( 299-)  A   -2.81
 756 ALA   ( 299-)  B   -2.81
4288 GLN   (  50-)  N   -2.78
3974 GLN   (  50-)  K   -2.77
4079 GLN   (  50-)  L   -2.76
5330 GLN   (  50-)  X   -2.76
4183 GLN   (  50-)  M   -2.75
3871 GLN   (  50-)  J   -2.74
5122 GLN   (  50-)  V   -2.73
4497 GLN   (  50-)  P   -2.73
4704 GLN   (  50-)  R   -2.72
4914 GLN   (  50-)  T   -2.72
4028 HIS   ( 104-)  K   -2.68
4863 HIS   ( 104-)  S   -2.68
3820 HIS   ( 104-)  I   -2.68
5071 HIS   ( 104-)  U   -2.68
5279 HIS   ( 104-)  W   -2.68
4237 HIS   ( 104-)  M   -2.68
4446 HIS   ( 104-)  O   -2.68
4654 HIS   ( 104-)  Q   -2.68
5017 GLN   (  50-)  U   -2.65
4392 GLN   (  50-)  O   -2.64
1026 LEU   ( 105-)  C   -2.64
4809 GLN   (  50-)  S   -2.64
  95 LEU   ( 105-)  A   -2.64
2885 LEU   ( 105-)  G   -2.63
1490 LEU   ( 105-)  D   -2.63
4600 GLN   (  50-)  Q   -2.63
3766 GLN   (  50-)  I   -2.63
2420 LEU   ( 105-)  F   -2.63
1956 LEU   ( 105-)  E   -2.63
3350 LEU   ( 105-)  H   -2.63
 562 LEU   ( 105-)  B   -2.63

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: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: Q

Note: Second generation quality Z-score plot

Chain identifier: R

Note: Second generation quality Z-score plot

Chain identifier: S

Note: Second generation quality Z-score plot

Chain identifier: T

Note: Second generation quality Z-score plot

Chain identifier: U

Note: Second generation quality Z-score plot

Chain identifier: V

Note: Second generation quality Z-score plot

Chain identifier: W

Note: Second generation quality Z-score plot

Chain identifier: X

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.

 143 HIS   ( 153-)  A
 202 GLN   ( 212-)  A
 219 GLN   ( 229-)  A
 228 HIS   ( 238-)  A
 231 ASN   ( 241-)  A
 257 HIS   ( 267-)  A
 267 ASN   ( 277-)  A
 294 GLN   ( 304-)  A
 343 HIS   ( 353-)  A
 376 HIS   ( 386-)  A
 669 GLN   ( 212-)  B
 686 GLN   ( 229-)  B
 695 HIS   ( 238-)  B
 698 ASN   ( 241-)  B
 724 HIS   ( 267-)  B
 734 ASN   ( 277-)  B
 761 GLN   ( 304-)  B
 810 HIS   ( 353-)  B
 843 HIS   ( 386-)  B
1074 HIS   ( 153-)  C
1133 GLN   ( 212-)  C
1150 GLN   ( 229-)  C
1159 HIS   ( 238-)  C
1162 ASN   ( 241-)  C
1188 HIS   ( 267-)  C
And so on for a total of 87 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.

   8 GLY   (  16-)  A      N
  37 GLY   (  47-)  A      N
  57 THR   (  67-)  A      N
  57 THR   (  67-)  A      OG1
  86 SER   (  96-)  A      N
  96 ASP   ( 106-)  A      N
 109 SER   ( 119-)  A      OG
 114 VAL   ( 124-)  A      N
 115 PHE   ( 125-)  A      N
 124 ARG   ( 134-)  A      NE
 147 VAL   ( 157-)  A      N
 149 ARG   ( 159-)  A      NE
 157 ARG   ( 167-)  A      N
 162 CYS   ( 172-)  A      N
 163 THR   ( 173-)  A      N
 165 LYS   ( 175-)  A      N
 168 LEU   ( 178-)  A      N
 169 GLY   ( 179-)  A      N
 201 PHE   ( 211-)  A      N
 202 GLN   ( 212-)  A      NE2
 205 ARG   ( 215-)  A      N
 228 HIS   ( 238-)  A      N
 229 TYR   ( 239-)  A      OH
 236 THR   ( 246-)  A      N
 243 ARG   ( 253-)  A      NH1
And so on for a total of 423 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.

 148 GLU   ( 158-)  A      OE1
 258 ASP   ( 268-)  A      OD1
 258 ASP   ( 268-)  A      OD2
 399 HIS   ( 409-)  A      ND1
 410 ASN   ( 420-)  A      OD1
 463 ASP   ( 473-)  A      OD2
 615 GLU   ( 158-)  B      OE1
 725 ASP   ( 268-)  B      OD1
 725 ASP   ( 268-)  B      OD2
 866 HIS   ( 409-)  B      ND1
 877 ASN   ( 420-)  B      OD1
1079 GLU   ( 158-)  C      OE1
1189 ASP   ( 268-)  C      OD1
1189 ASP   ( 268-)  C      OD2
1330 HIS   ( 409-)  C      ND1
1340 ASN   ( 420-)  C      OD1
1543 GLU   ( 158-)  D      OE1
1652 HIS   ( 267-)  D      NE2
1653 ASP   ( 268-)  D      OD1
1653 ASP   ( 268-)  D      OD2
1794 HIS   ( 409-)  D      ND1
1804 ASN   ( 420-)  D      OD1
2009 GLU   ( 158-)  E      OE1
2119 ASP   ( 268-)  E      OD1
2119 ASP   ( 268-)  E      OD2
And so on for a total of 56 lines.

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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.

 150 ASP   ( 160-)  A   H-bonding suggests Asn; but Alt-Rotamer
 258 ASP   ( 268-)  A   H-bonding suggests Asn
 292 ASP   ( 302-)  A   H-bonding suggests Asn
 617 ASP   ( 160-)  B   H-bonding suggests Asn; but Alt-Rotamer
 725 ASP   ( 268-)  B   H-bonding suggests Asn
 759 ASP   ( 302-)  B   H-bonding suggests Asn
1081 ASP   ( 160-)  C   H-bonding suggests Asn; but Alt-Rotamer
1189 ASP   ( 268-)  C   H-bonding suggests Asn
1223 ASP   ( 302-)  C   H-bonding suggests Asn
1545 ASP   ( 160-)  D   H-bonding suggests Asn; but Alt-Rotamer
1653 ASP   ( 268-)  D   H-bonding suggests Asn
1687 ASP   ( 302-)  D   H-bonding suggests Asn
2011 ASP   ( 160-)  E   H-bonding suggests Asn; but Alt-Rotamer
2119 ASP   ( 268-)  E   H-bonding suggests Asn
2153 ASP   ( 302-)  E   H-bonding suggests Asn
2475 ASP   ( 160-)  F   H-bonding suggests Asn; but Alt-Rotamer
2583 ASP   ( 268-)  F   H-bonding suggests Asn
2617 ASP   ( 302-)  F   H-bonding suggests Asn
2940 ASP   ( 160-)  G   H-bonding suggests Asn; but Alt-Rotamer
3048 ASP   ( 268-)  G   H-bonding suggests Asn
3082 ASP   ( 302-)  G   H-bonding suggests Asn
3405 ASP   ( 160-)  H   H-bonding suggests Asn; but Alt-Rotamer
3513 ASP   ( 268-)  H   H-bonding suggests Asn
3547 ASP   ( 302-)  H   H-bonding suggests Asn
3879 GLU   (  58-)  J   H-bonding suggests Gln; but Alt-Rotamer
3908 GLU   (  87-)  J   H-bonding suggests Gln
4087 GLU   (  58-)  L   H-bonding suggests Gln; but Alt-Rotamer
4116 GLU   (  87-)  L   H-bonding suggests Gln
4296 GLU   (  58-)  N   H-bonding suggests Gln; but Alt-Rotamer
4325 GLU   (  87-)  N   H-bonding suggests Gln
4505 GLU   (  58-)  P   H-bonding suggests Gln; but Alt-Rotamer
4534 GLU   (  87-)  P   H-bonding suggests Gln
4712 GLU   (  58-)  R   H-bonding suggests Gln; but Alt-Rotamer
4741 GLU   (  87-)  R   H-bonding suggests Gln
4922 GLU   (  58-)  T   H-bonding suggests Gln; but Alt-Rotamer
4951 GLU   (  87-)  T   H-bonding suggests Gln
5130 GLU   (  58-)  V   H-bonding suggests Gln; but Alt-Rotamer
5159 GLU   (  87-)  V   H-bonding suggests Gln
5338 GLU   (  58-)  X   H-bonding suggests Gln; but Alt-Rotamer
5367 GLU   (  87-)  X   H-bonding suggests Gln

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 :  -0.191
  2nd generation packing quality :   0.283
  Ramachandran plot appearance   :  -1.093
  chi-1/chi-2 rotamer normality  :  -1.959
  Backbone conformation          :  -0.137

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.471 (tight)
  Bond angles                    :   0.645 (tight)
  Omega angle restraints         :   1.075
  Side chain planarity           :   1.437
  Improper dihedral distribution :   1.731 (loose)
  Inside/Outside distribution    :   1.057

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 : 9.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :   0.1
  Ramachandran plot appearance   :  -0.5
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.471 (tight)
  Bond angles                    :   0.645 (tight)
  Omega angle restraints         :   1.075
  Side chain planarity           :   1.437
  Improper dihedral distribution :   1.731 (loose)
  Inside/Outside distribution    :   1.057
==============

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.