WHAT IF Check report

This file was created 2011-12-16 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 pdb1ir2.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.457
CA-only RMS fit for the two chains : 0.268

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.485
CA-only RMS fit for the two chains : 0.331

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 0.465
CA-only RMS fit for the two chains : 0.264

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and E

All-atom RMS fit for the two chains : 0.422
CA-only RMS fit for the two chains : 0.234

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and E

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and F

All-atom RMS fit for the two chains : 0.404
CA-only RMS fit for the two chains : 0.214

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and F

Warning: Ligands for which a topology was generated automatically

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

9690 MME   (   1-)  I  -
9693 MME   (   1-)  J  -
9696 MME   (   1-)  K  -
9699 MME   (   1-)  L  -
9702 MME   (   1-)  M  -
9705 MME   (   1-)  N  -
9708 MME   (   1-)  O  -
9711 MME   (   1-)  P  -
9714 MME   (   1-)  1  -
9717 MME   (   1-)  2  -
9720 MME   (   1-)  3  -
9723 MME   (   1-)  4  -
9726 MME   (   1-)  5  -
9729 MME   (   1-)  6  -
9732 MME   (   1-)  7  -
9737 CAP   ( 501-)  A  -
9740 CAP   ( 501-)  B  -
9745 CAP   ( 501-)  C  -
9749 CAP   ( 501-)  D  -
9753 CAP   ( 501-)  E  -
9758 CAP   ( 501-)  F  -
9762 CAP   ( 501-)  G  -
9767 CAP   ( 501-)  H  -
9772 CAP   ( 501-)  S  -
9777 CAP   ( 501-)  T  -
9781 CAP   ( 501-)  U  -
9785 CAP   ( 501-)  V  -
9789 CAP   ( 501-)  W  -
9793 CAP   ( 501-)  X  -
9798 CAP   ( 501-)  Y  -
9807 CAP   ( 501-)  Z  -
9808 MME   (   1-)  8  -

Administrative problems that can generate validation failures

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.

 469 MET   (   2-)  I  -   N   bound to 9690 MME   (   1-)  I  -   C
1075 MET   (   2-)  J  -   N   bound to 9693 MME   (   1-)  J  -   C
1680 MET   (   2-)  K  -   N   bound to 9696 MME   (   1-)  K  -   C
2286 MET   (   2-)  L  -   N   bound to 9699 MME   (   1-)  L  -   C
2890 MET   (   2-)  M  -   N   bound to 9702 MME   (   1-)  M  -   C
3494 MET   (   2-)  N  -   N   bound to 9705 MME   (   1-)  N  -   C
4099 MET   (   2-)  O  -   N   bound to 9708 MME   (   1-)  O  -   C
4706 MET   (   2-)  P  -   N   bound to 9711 MME   (   1-)  P  -   C
5310 MET   (   2-)  1  -   N   bound to 9714 MME   (   1-)  1  -   C
5915 MET   (   2-)  2  -   N   bound to 9717 MME   (   1-)  2  -   C
6523 MET   (   2-)  3  -   N   bound to 9720 MME   (   1-)  3  -   C
7131 MET   (   2-)  4  -   N   bound to 9723 MME   (   1-)  4  -   C
7736 MET   (   2-)  5  -   N   bound to 9726 MME   (   1-)  5  -   C
8341 MET   (   2-)  6  -   N   bound to 9729 MME   (   1-)  6  -   C
8945 MET   (   2-)  7  -   N   bound to 9732 MME   (   1-)  7  -   C
9550 MET   (   2-)  8  -   N   bound to 9808 MME   (   1-)  8  -   C

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: I

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: 1

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: 2

Note: Ramachandran plot

Chain identifier: U

Note: Ramachandran plot

Chain identifier: 3

Note: Ramachandran plot

Chain identifier: V

Note: Ramachandran plot

Chain identifier: 4

Note: Ramachandran plot

Chain identifier: W

Note: Ramachandran plot

Chain identifier: 5

Note: Ramachandran plot

Chain identifier: X

Note: Ramachandran plot

Chain identifier: 6

Note: Ramachandran plot

Chain identifier: Y

Note: Ramachandran plot

Chain identifier: 7

Note: Ramachandran plot

Chain identifier: Z

Note: Ramachandran plot

Chain identifier: 8

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

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

4779 MET   (  75-)  P
6468 ARG   ( 421-)  U
8584 ASN   ( 115-)  Y

Warning: What type of B-factor?

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

Obviously, the temperature at which the X-ray data was collected has some importance too:

Crystal temperature (K) :100.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: P

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: 1

Note: B-factor plot

Chain identifier: T

Note: B-factor plot

Chain identifier: 2

Note: B-factor plot

Chain identifier: U

Note: B-factor plot

Chain identifier: 3

Note: B-factor plot

Chain identifier: V

Note: B-factor plot

Chain identifier: 4

Note: B-factor plot

Chain identifier: W

Note: B-factor plot

Chain identifier: 5

Note: B-factor plot

Chain identifier: X

Note: B-factor plot

Chain identifier: 6

Note: B-factor plot

Chain identifier: Y

Note: B-factor plot

Chain identifier: 7

Note: B-factor plot

Chain identifier: Z

Note: B-factor plot

Chain identifier: 8

Nomenclature related problems

Warning: Arginine nomenclature problem

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

  14 ARG   (  21-)  A
1509 ARG   ( 305-)  C
2414 ARG   ( 130-)  L
2446 ARG   (  32-)  E
2719 ARG   ( 305-)  E
2972 ARG   (  84-)  M
3050 ARG   (  32-)  F
3622 ARG   ( 130-)  N
3655 ARG   (  32-)  G
5399 ARG   (  91-)  1
5522 ARG   (  83-)  T
5744 ARG   ( 305-)  T
6068 ARG   (  21-)  U
7015 ARG   ( 360-)  V
7259 ARG   ( 130-)  4
7565 ARG   ( 305-)  W
7859 ARG   ( 125-)  5

Warning: Tyrosine convention problem

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

 518 TYR   (  51-)  I
1124 TYR   (  51-)  J
1177 TYR   ( 104-)  J
1729 TYR   (  51-)  K
2335 TYR   (  51-)  L
2939 TYR   (  51-)  M
3543 TYR   (  51-)  N
3726 TYR   ( 103-)  G
4148 TYR   (  51-)  O
4333 TYR   ( 103-)  H
4755 TYR   (  51-)  P
5359 TYR   (  51-)  1
5964 TYR   (  51-)  2
6572 TYR   (  51-)  3
7785 TYR   (  51-)  5
7838 TYR   ( 104-)  5
8390 TYR   (  51-)  6
8994 TYR   (  51-)  7
9599 TYR   (  51-)  8

Warning: Phenylalanine convention problem

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

 479 PHE   (  12-)  I
 567 PHE   ( 100-)  I
1068 PHE   ( 469-)  B
2279 PHE   ( 469-)  D
2296 PHE   (  12-)  L
2384 PHE   ( 100-)  L
2900 PHE   (  12-)  M
3487 PHE   ( 469-)  F
3504 PHE   (  12-)  N
3592 PHE   ( 100-)  N
4109 PHE   (  12-)  O
4197 PHE   ( 100-)  O
4218 PHE   ( 121-)  O
4716 PHE   (  12-)  P
4804 PHE   ( 100-)  P
5320 PHE   (  12-)  1
5408 PHE   ( 100-)  1
5908 PHE   ( 469-)  T
6516 PHE   ( 469-)  U
7229 PHE   ( 100-)  4
7729 PHE   ( 469-)  W
7746 PHE   (  12-)  5
7834 PHE   ( 100-)  5
8439 PHE   ( 100-)  6
8938 PHE   ( 469-)  Y
8955 PHE   (  12-)  7
9064 PHE   ( 121-)  7
9543 PHE   ( 469-)  Z
9560 PHE   (  12-)  8
9648 PHE   ( 100-)  8

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.

 429 ASP   ( 436-)  A
 598 ASP   ( 131-)  I
1035 ASP   ( 436-)  B
1204 ASP   ( 131-)  J
1640 ASP   ( 436-)  C
1809 ASP   ( 131-)  K
2246 ASP   ( 436-)  D
2415 ASP   ( 131-)  L
2850 ASP   ( 436-)  E
3019 ASP   ( 131-)  M
3112 ASP   (  94-)  F
3454 ASP   ( 436-)  F
3623 ASP   ( 131-)  N
3717 ASP   (  94-)  G
4059 ASP   ( 436-)  G
4228 ASP   ( 131-)  O
4324 ASP   (  94-)  H
4666 ASP   ( 436-)  H
4835 ASP   ( 131-)  P
4928 ASP   (  94-)  S
5270 ASP   ( 436-)  S
5439 ASP   ( 131-)  1
5875 ASP   ( 436-)  T
6044 ASP   ( 131-)  2
6141 ASP   (  94-)  U
6483 ASP   ( 436-)  U
6652 ASP   ( 131-)  3
7091 ASP   ( 436-)  V
7260 ASP   ( 131-)  4
7696 ASP   ( 436-)  W
7865 ASP   ( 131-)  5
8301 ASP   ( 436-)  X
8470 ASP   ( 131-)  6
8905 ASP   ( 436-)  Y
8966 ASP   (  23-)  7
9074 ASP   ( 131-)  7
9510 ASP   ( 436-)  Z
9679 ASP   ( 131-)  8

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.

 242 GLU   ( 249-)  A
 348 GLU   ( 355-)  A
 453 GLU   ( 460-)  A
 692 GLU   (  93-)  B
 848 GLU   ( 249-)  B
 954 GLU   ( 355-)  B
1067 GLU   ( 468-)  B
1297 GLU   (  93-)  C
1453 GLU   ( 249-)  C
1702 GLU   (  24-)  K
1733 GLU   (  55-)  K
1903 GLU   (  93-)  D
2059 GLU   ( 249-)  D
2165 GLU   ( 355-)  D
2308 GLU   (  24-)  L
2330 GLU   (  46-)  L
2502 GLU   (  88-)  E
2507 GLU   (  93-)  E
2663 GLU   ( 249-)  E
2874 GLU   ( 460-)  E
3106 GLU   (  88-)  F
3111 GLU   (  93-)  F
3267 GLU   ( 249-)  F
3410 GLU   ( 392-)  F
3538 GLU   (  46-)  N
And so on for a total of 55 lines.

Warning: Heavy atom naming convention problem

The atoms listed in the table below have nonstandard names in the input file. (Be aware that we sometimes consider an asterix and an apostrophe identical, and thus do not warn for the use of asterixes. Please be aware that the PDB wants us to deliberately make some nomenclature errors; especially in non-canonical amino acids.

 194 KCX   ( 201-)  A      CH     CX
 194 KCX   ( 201-)  A      OX1    OQ1
 194 KCX   ( 201-)  A      OX2    OQ2
 800 KCX   ( 201-)  B      CH     CX
 800 KCX   ( 201-)  B      OX1    OQ1
 800 KCX   ( 201-)  B      OX2    OQ2
1405 KCX   ( 201-)  C      CH     CX
1405 KCX   ( 201-)  C      OX1    OQ1
1405 KCX   ( 201-)  C      OX2    OQ2
2011 KCX   ( 201-)  D      CH     CX
2011 KCX   ( 201-)  D      OX1    OQ1
2011 KCX   ( 201-)  D      OX2    OQ2
2615 KCX   ( 201-)  E      CH     CX
2615 KCX   ( 201-)  E      OX1    OQ1
2615 KCX   ( 201-)  E      OX2    OQ2
3219 KCX   ( 201-)  F      CH     CX
3219 KCX   ( 201-)  F      OX1    OQ1
3219 KCX   ( 201-)  F      OX2    OQ2
3824 KCX   ( 201-)  G      CH     CX
3824 KCX   ( 201-)  G      OX1    OQ1
3824 KCX   ( 201-)  G      OX2    OQ2
4431 KCX   ( 201-)  H      CH     CX
4431 KCX   ( 201-)  H      OX1    OQ1
4431 KCX   ( 201-)  H      OX2    OQ2
5035 KCX   ( 201-)  S      CH     CX
5035 KCX   ( 201-)  S      OX1    OQ1
5035 KCX   ( 201-)  S      OX2    OQ2
5640 KCX   ( 201-)  T      CH     CX
5640 KCX   ( 201-)  T      OX1    OQ1
5640 KCX   ( 201-)  T      OX2    OQ2
6248 KCX   ( 201-)  U      CH     CX
6248 KCX   ( 201-)  U      OX1    OQ1
6248 KCX   ( 201-)  U      OX2    OQ2
6856 KCX   ( 201-)  V      CH     CX
6856 KCX   ( 201-)  V      OX1    OQ1
6856 KCX   ( 201-)  V      OX2    OQ2
7461 KCX   ( 201-)  W      CH     CX
7461 KCX   ( 201-)  W      OX1    OQ1
7461 KCX   ( 201-)  W      OX2    OQ2
8066 KCX   ( 201-)  X      CH     CX
8066 KCX   ( 201-)  X      OX1    OQ1
8066 KCX   ( 201-)  X      OX2    OQ2
8670 KCX   ( 201-)  Y      CH     CX
8670 KCX   ( 201-)  Y      OX1    OQ1
8670 KCX   ( 201-)  Y      OX2    OQ2
9275 KCX   ( 201-)  Z      CH     CX
9275 KCX   ( 201-)  Z      OX1    OQ1
9275 KCX   ( 201-)  Z      OX2    OQ2

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.

  97 HYP   ( 104-)  A      CD   N     1.49    4.7
 144 HYP   ( 151-)  A      CD   N     1.50    4.8
 703 HYP   ( 104-)  B      CD   N     1.49    4.7
 750 HYP   ( 151-)  B      CD   N     1.50    4.8
1308 HYP   ( 104-)  C      CD   N     1.50    4.8
1355 HYP   ( 151-)  C      CD   N     1.50    4.8
1914 HYP   ( 104-)  D      CD   N     1.50    4.9
1961 HYP   ( 151-)  D      CD   N     1.49    4.7
2518 HYP   ( 104-)  E      CD   N     1.50    4.9
2565 HYP   ( 151-)  E      CD   N     1.50    4.9
3122 HYP   ( 104-)  F      CD   N     1.50    4.8
3169 HYP   ( 151-)  F      CD   N     1.50    4.9
3727 HYP   ( 104-)  G      CD   N     1.49    4.7
3774 HYP   ( 151-)  G      CD   N     1.50    4.9
4334 HYP   ( 104-)  H      CD   N     1.49    4.7
4381 HYP   ( 151-)  H      CD   N     1.50    4.9
4938 HYP   ( 104-)  S      CD   N     1.49    4.6
4985 HYP   ( 151-)  S      CD   N     1.50    4.8
5543 HYP   ( 104-)  T      CD   N     1.50    4.8
5590 HYP   ( 151-)  T      CD   N     1.50    4.8
6151 HYP   ( 104-)  U      CD   N     1.50    4.8
6198 HYP   ( 151-)  U      CD   N     1.49    4.7
6759 HYP   ( 104-)  V      CD   N     1.49    4.7
6806 HYP   ( 151-)  V      CD   N     1.49    4.7
7364 HYP   ( 104-)  W      CD   N     1.49    4.7
7411 HYP   ( 151-)  W      CD   N     1.50    4.9
7969 HYP   ( 104-)  X      CD   N     1.50    4.8
8016 HYP   ( 151-)  X      CD   N     1.50    4.8
8573 HYP   ( 104-)  Y      CD   N     1.50    4.9
8620 HYP   ( 151-)  Y      CD   N     1.50    4.8
9178 HYP   ( 104-)  Z      CD   N     1.50    4.8
9225 HYP   ( 151-)  Z      CD   N     1.49    4.5

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.279
RMS-deviation in bond distances: 0.007

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.998549  0.000065  0.000003|
 |  0.000065  0.998514 -0.000006|
 |  0.000003 -0.000006  0.998505|
Proposed new scale matrix

 |  0.007753  0.000000  0.001056|
 |  0.000000  0.005731  0.000000|
 |  0.000000  0.000000  0.004548|
With corresponding cell

    A    = 128.979  B   = 174.504  C    = 221.916
    Alpha=  90.002  Beta=  97.754  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 129.170  B   = 174.750  C    = 222.270
    Alpha=  90.000  Beta=  97.750  Gamma=  90.000

Variance: 704.699
(Under-)estimated Z-score: 19.564

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.

 193 THR   ( 200-)  A      N    CA   C    99.35   -4.2
 256 PRO   ( 263-)  A      N    CA   C   123.10    4.5
 528 GLY   (  61-)  I      N    CA   C    98.56   -4.8
 799 THR   ( 200-)  B      N    CA   C    97.87   -4.8
 862 PRO   ( 263-)  B      N    CA   C   122.66    4.3
1134 GLY   (  61-)  J      N    CA   C    98.13   -5.0
1288 CYS   (  84-)  C      N    CA   C    99.95   -4.0
1404 THR   ( 200-)  C      N    CA   C    98.90   -4.4
1467 PRO   ( 263-)  C      N    CA   C   123.55    4.7
1739 GLY   (  61-)  K      N    CA   C    98.65   -4.8
2010 THR   ( 200-)  D      N    CA   C    98.55   -4.5
2073 PRO   ( 263-)  D      N    CA   C   122.74    4.4
2345 GLY   (  61-)  L      N    CA   C    98.19   -4.9
2614 THR   ( 200-)  E      N    CA   C    98.84   -4.4
2677 PRO   ( 263-)  E      N    CA   C   122.18    4.2
2949 GLY   (  61-)  M      N    CA   C    98.05   -5.0
3218 THR   ( 200-)  F      N    CA   C    98.98   -4.4
3281 PRO   ( 263-)  F      N    CA   C   123.26    4.6
3553 GLY   (  61-)  N      N    CA   C    98.28   -4.9
3823 THR   ( 200-)  G      N    CA   C    98.57   -4.5
3886 PRO   ( 263-)  G      N    CA   C   123.26    4.6
4158 GLY   (  61-)  O      N    CA   C    99.98   -4.3
4430 THR   ( 200-)  H      N    CA   C    98.48   -4.5
4493 PRO   ( 263-)  H      N    CA   C   123.58    4.7
4765 GLY   (  61-)  P      N    CA   C    98.26   -4.9
And so on for a total of 52 lines.

Warning: Low bond angle variability

Bond angles were found to deviate less than normal from the standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond angles: 0.622
RMS-deviation in bond angles: 1.399

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.

  14 ARG   (  21-)  A
 242 GLU   ( 249-)  A
 348 GLU   ( 355-)  A
 429 ASP   ( 436-)  A
 453 GLU   ( 460-)  A
 598 ASP   ( 131-)  I
 692 GLU   (  93-)  B
 848 GLU   ( 249-)  B
 954 GLU   ( 355-)  B
1035 ASP   ( 436-)  B
1067 GLU   ( 468-)  B
1204 ASP   ( 131-)  J
1297 GLU   (  93-)  C
1453 GLU   ( 249-)  C
1509 ARG   ( 305-)  C
1640 ASP   ( 436-)  C
1702 GLU   (  24-)  K
1733 GLU   (  55-)  K
1809 ASP   ( 131-)  K
1903 GLU   (  93-)  D
2059 GLU   ( 249-)  D
2165 GLU   ( 355-)  D
2246 ASP   ( 436-)  D
2308 GLU   (  24-)  L
2330 GLU   (  46-)  L
And so on for a total of 110 lines.

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.

9274 THR   ( 200-)  Z    7.45
5136 ASP   ( 302-)  S    6.34
2716 ASP   ( 302-)  E    6.27
8771 ASP   ( 302-)  Y    6.14
2112 ASP   ( 302-)  D    6.03
3320 ASP   ( 302-)  F    5.92
1506 ASP   ( 302-)  C    5.87
 295 ASP   ( 302-)  A    5.81
9337 PRO   ( 263-)  Z    5.77
 901 ASP   ( 302-)  B    5.75
4532 ASP   ( 302-)  H    5.74
8167 ASP   ( 302-)  X    5.69
5563 VAL   ( 124-)  T    5.68
4958 VAL   ( 124-)  S    5.67
1934 VAL   ( 124-)  D    5.64
9342 ASP   ( 268-)  Z    5.64
7562 ASP   ( 302-)  W    5.58
6582 GLY   (  61-)  3    5.58
2949 GLY   (  61-)  M    5.57
5741 ASP   ( 302-)  T    5.56
8593 VAL   ( 124-)  Y    5.56
1134 GLY   (  61-)  J    5.54
8400 GLY   (  61-)  6    5.53
2345 GLY   (  61-)  L    5.52
9609 GLY   (  61-)  8    5.52
And so on for a total of 245 lines.

Warning: High tau angle deviations

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

Tau angle RMS Z-score : 1.521

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.

1079 PRO   (   6-)  J    -2.7
1684 PRO   (   6-)  K    -2.7
8949 PRO   (   6-)  7    -2.7
5919 PRO   (   6-)  2    -2.7
 473 PRO   (   6-)  I    -2.7
3498 PRO   (   6-)  N    -2.7
2290 PRO   (   6-)  L    -2.7
7135 PRO   (   6-)  4    -2.6
4103 PRO   (   6-)  O    -2.6
9554 PRO   (   6-)  8    -2.6
4710 PRO   (   6-)  P    -2.6
6527 PRO   (   6-)  3    -2.6
2894 PRO   (   6-)  M    -2.5
7740 PRO   (   6-)  5    -2.5
5314 PRO   (   6-)  1    -2.5
6533 PHE   (  12-)  3    -2.5
6031 ILE   ( 118-)  2    -2.5
8457 ILE   ( 118-)  6    -2.5
8345 PRO   (   6-)  6    -2.5
9061 ILE   ( 118-)  7    -2.4
 585 ILE   ( 118-)  I    -2.4
5426 ILE   ( 118-)  1    -2.4
1191 ILE   ( 118-)  J    -2.4
9666 ILE   ( 118-)  8    -2.4
7247 ILE   ( 118-)  4    -2.4
And so on for a total of 151 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   (   9-)  A  Poor phi/psi
  55 SER   (  62-)  A  Poor phi/psi
  56 THR   (  63-)  A  Poor phi/psi
  68 THR   (  75-)  A  Poor phi/psi
 116 ASN   ( 123-)  A  Poor phi/psi
 156 ASN   ( 163-)  A  Poor phi/psi
 165 CYS   ( 172-)  A  Poor phi/psi
 168 LYS   ( 175-)  A  PRO omega poor
 200 ASN   ( 207-)  A  Poor phi/psi
 290 MET   ( 297-)  A  Poor phi/psi
 324 VAL   ( 331-)  A  Poor phi/psi
 363 SER   ( 370-)  A  Poor phi/psi
 480 GLU   (  13-)  I  Poor phi/psi
 482 PHE   (  15-)  I  Poor phi/psi
 529 SER   (  62-)  I  Poor phi/psi
 533 LEU   (  66-)  I  Poor phi/psi
 537 ASN   (  70-)  I  Poor phi/psi
 544 LYS   (  77-)  I  Poor phi/psi
 661 SER   (  62-)  B  Poor phi/psi
 762 ASN   ( 163-)  B  Poor phi/psi
 774 LYS   ( 175-)  B  PRO omega poor
 806 ASN   ( 207-)  B  Poor phi/psi
 896 MET   ( 297-)  B  Poor phi/psi
 930 VAL   ( 331-)  B  Poor phi/psi
 969 SER   ( 370-)  B  Poor phi/psi
And so on for a total of 229 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.

3902 SER   ( 279-)  G    0.36
3297 SER   ( 279-)  F    0.36
5113 SER   ( 279-)  S    0.36
7539 SER   ( 279-)  W    0.36
8144 SER   ( 279-)  X    0.36
8748 SER   ( 279-)  Y    0.36
5718 SER   ( 279-)  T    0.37

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!

   6 PHE   (  13-)  A      0
   8 ALA   (  15-)  A      0
  10 VAL   (  17-)  A      0
  16 THR   (  23-)  A      0
  17 TYR   (  24-)  A      0
  18 TYR   (  25-)  A      0
  19 THR   (  26-)  A      0
  22 TYR   (  29-)  A      0
  39 PRO   (  46-)  A      0
  54 SER   (  61-)  A      0
  55 SER   (  62-)  A      0
  56 THR   (  63-)  A      0
  59 TRP   (  66-)  A      0
  63 TRP   (  70-)  A      0
  67 LEU   (  74-)  A      0
  76 ARG   (  83-)  A      0
  78 TYR   (  85-)  A      0
  79 ASP   (  86-)  A      0
  84 PRO   (  91-)  A      0
  87 ASP   (  94-)  A      0
  88 ASN   (  95-)  A      0
  89 GLN   (  96-)  A      0
  97 HYP   ( 104-)  A      0
 103 GLU   ( 110-)  A      0
 114 VAL   ( 121-)  A      0
And so on for a total of 3765 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 1.411

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!

1004 GLY   ( 405-)  B   1.60   80
7060 GLY   ( 405-)  V   1.55   80
4028 GLY   ( 405-)  G   1.54   80
8270 GLY   ( 405-)  X   1.53   80
3423 GLY   ( 405-)  F   1.53   80
 398 GLY   ( 405-)  A   1.53   80
9479 GLY   ( 405-)  Z   1.53   80
7665 GLY   ( 405-)  W   1.51   80
4635 GLY   ( 405-)  H   1.50   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...

 481 THR   (  14-)  I   1.63
1692 THR   (  14-)  K   1.53
2298 THR   (  14-)  L   1.79
2902 THR   (  14-)  M   1.57
3506 THR   (  14-)  N   1.52
4111 THR   (  14-)  O   1.56
5322 THR   (  14-)  1   1.77
5927 THR   (  14-)  2   1.54
6535 THR   (  14-)  3   1.76
8957 THR   (  14-)  7   1.68

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].

6097 PRO   (  50-)  U  -115.3 envelop C-gamma (-108 degrees)
9446 PRO   ( 372-)  Z  -112.1 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

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

9550 MET   (   2-)  8      N   <-> 9808 MME   (   1-)  8      C      1.37    1.33  INTRA B3
9550 MET   (   2-)  8      CA  <-> 9808 MME   (   1-)  8      C      0.78    2.42  INTRA
1451 CYS   ( 247-)  C      SG  <-> 3870 CYS   ( 247-)  G      SG     0.73    2.72  INTRA
6902 CYS   ( 247-)  V      SG  <-> 9321 CYS   ( 247-)  Z      SG     0.69    2.76  INTRA
 240 CYS   ( 247-)  A      SG  <-> 2661 CYS   ( 247-)  E      SG     0.69    2.76  INTRA
5081 CYS   ( 247-)  S      SG  <-> 7507 CYS   ( 247-)  W      SG     0.68    2.77  INTRA
6294 CYS   ( 247-)  U      SG  <-> 8716 CYS   ( 247-)  Y      SG     0.68    2.77  INTRA
5686 CYS   ( 247-)  T      SG  <-> 8112 CYS   ( 247-)  X      SG     0.66    2.79  INTRA
 846 CYS   ( 247-)  B      SG  <-> 3265 CYS   ( 247-)  F      SG     0.66    2.79  INTRA
2057 CYS   ( 247-)  D      SG  <-> 4477 CYS   ( 247-)  H      SG     0.65    2.80  INTRA
6055 LYS   (   8-)  U      CG  <-> 6056 ALA   (   9-)  U      N      0.42    2.58  INTRA BF
6055 LYS   (   8-)  U      CD  <-> 9632 ARG   (  84-)  8      NH1    0.36    2.74  INTRA BF
9068 ARG   ( 125-)  7      NH1 <-> 9838 HOH   ( 143 )  7      O      0.35    2.35  INTRA
6574 SER   (  53-)  3      CB  <-> 6576 GLU   (  55-)  3      OE2    0.34    2.46  INTRA
1814 ASN   ( 136-)  K      ND2 <-> 1815 LYS   ( 137-)  K      CD     0.34    2.76  INTRA
7139 LYS   (  10-)  4      NZ  <-> 9832 HOH   ( 235 )  4      O      0.30    2.40  INTRA
4992 GLU   ( 158-)  S      OE2 <-> 5159 HIS   ( 325-)  S      NE2    0.30    2.40  INTRA BL
6811 GLN   ( 156-)  V      NE2 <-> 9831 HOH   (1069 )  V      O      0.29    2.41  INTRA
4244 LYS   (  14-)  H      NZ  <-> 9823 HOH   (1068 )  H      O      0.29    2.41  INTRA
5597 GLU   ( 158-)  T      OE2 <-> 5764 HIS   ( 325-)  T      NE2    0.28    2.42  INTRA BL
5361 SER   (  53-)  1      CB  <-> 5363 GLU   (  55-)  1      OE2    0.27    2.53  INTRA
2572 GLU   ( 158-)  E      OE2 <-> 2739 HIS   ( 325-)  E      NE2    0.27    2.43  INTRA BL
8447 VAL   ( 108-)  6      C   <-> 8458 MET   ( 119-)  6      CE     0.27    2.93  INTRA
1362 GLU   ( 158-)  C      OE2 <-> 1529 HIS   ( 325-)  C      NE2    0.27    2.43  INTRA BL
4224 LYS   ( 127-)  O      O   <-> 4227 ARG   ( 130-)  O      NH2    0.27    2.43  INTRA
And so on for a total of 1072 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: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Inside/Outside RMS Z-score plot

Chain identifier: 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: U

Note: Inside/Outside RMS Z-score plot

Chain identifier: 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: V

Note: Inside/Outside RMS Z-score plot

Chain identifier: 4

Note: Inside/Outside RMS Z-score plot

Chain identifier: W

Note: Inside/Outside RMS Z-score plot

Chain identifier: 5

Note: Inside/Outside RMS Z-score plot

Chain identifier: X

Note: Inside/Outside RMS Z-score plot

Chain identifier: 6

Note: Inside/Outside RMS Z-score plot

Chain identifier: Y

Note: Inside/Outside RMS Z-score plot

Chain identifier: 7

Note: Inside/Outside RMS Z-score plot

Chain identifier: Z

Note: Inside/Outside RMS Z-score plot

Chain identifier: 8

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

7213 ARG   (  84-)  4      -7.29
5392 ARG   (  84-)  1      -7.28
 551 ARG   (  84-)  I      -7.15
2368 ARG   (  84-)  L      -7.12
4181 ARG   (  84-)  O      -6.98
6605 ARG   (  84-)  3      -6.86
1157 ARG   (  84-)  J      -6.85
4788 ARG   (  84-)  P      -6.85
5997 ARG   (  84-)  2      -6.83
9027 ARG   (  84-)  7      -6.80
8423 ARG   (  84-)  6      -6.67
2972 ARG   (  84-)  M      -6.64
9513 ARG   ( 439-)  Z      -6.38
3576 ARG   (  84-)  N      -6.34
6055 LYS   (   8-)  U      -6.04
1762 ARG   (  84-)  K      -6.04
9680 TRP   ( 132-)  8      -6.02
6663 LYS   (   8-)  V      -6.00
2853 ARG   ( 439-)  E      -5.83
6486 ARG   ( 439-)  U      -5.81
2249 ARG   ( 439-)  D      -5.81
7094 ARG   ( 439-)  V      -5.81
4062 ARG   ( 439-)  G      -5.80
7699 ARG   ( 439-)  W      -5.80
8304 ARG   ( 439-)  X      -5.80
And so on for a total of 191 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.

9432 ARG   ( 358-)  Z      9434 - ARG    360- ( Z)         -4.56
9440 GLN   ( 366-)  Z      9442 - TRP    368- ( Z)         -4.56

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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 5

Note: Quality value plot

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

Chain identifier: 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: 6

Note: Quality value plot

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

Chain identifier: 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: 7

Note: Quality value plot

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

Chain identifier: 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: 8

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

5424 VAL   ( 116-)  1   -2.87
1189 VAL   ( 116-)  J   -2.86
 583 VAL   ( 116-)  I   -2.84
6522 LEU   ( 475-)  U   -2.84
8397 ILE   (  58-)  6   -2.84
3608 VAL   ( 116-)  N   -2.83
4820 VAL   ( 116-)  P   -2.82
7850 VAL   ( 116-)  5   -2.82
6637 VAL   ( 116-)  3   -2.82
6029 VAL   ( 116-)  2   -2.80
4213 VAL   ( 116-)  O   -2.78
3004 VAL   ( 116-)  M   -2.78
2400 VAL   ( 116-)  L   -2.77
4667 LEU   ( 437-)  H   -2.77
9059 VAL   ( 116-)  7   -2.75
9664 VAL   ( 116-)  8   -2.75
6954 ALA   ( 299-)  V   -2.74
1794 VAL   ( 116-)  K   -2.72
8455 VAL   ( 116-)  6   -2.72
4529 ALA   ( 299-)  H   -2.69
 292 ALA   ( 299-)  A   -2.68
3922 ALA   ( 299-)  G   -2.68
7559 ALA   ( 299-)  W   -2.68
2109 ALA   ( 299-)  D   -2.67
6346 ALA   ( 299-)  U   -2.67
And so on for a total of 70 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.

2434 TYR   (  20-)  E     - 2437 THR   (  23-)  E        -1.66
6647 PRO   ( 126-)  3     - 6650 ALA   ( 129-)  3        -1.38
6675 TYR   (  20-)  V     - 6678 THR   (  23-)  V        -1.74

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: I

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: S

Note: Second generation quality Z-score plot

Chain identifier: 1

Note: Second generation quality Z-score plot

Chain identifier: T

Note: Second generation quality Z-score plot

Chain identifier: 2

Note: Second generation quality Z-score plot

Chain identifier: U

Note: Second generation quality Z-score plot

Chain identifier: 3

Note: Second generation quality Z-score plot

Chain identifier: V

Note: Second generation quality Z-score plot

Chain identifier: 4

Note: Second generation quality Z-score plot

Chain identifier: W

Note: Second generation quality Z-score plot

Chain identifier: 5

Note: Second generation quality Z-score plot

Chain identifier: X

Note: Second generation quality Z-score plot

Chain identifier: 6

Note: Second generation quality Z-score plot

Chain identifier: Y

Note: Second generation quality Z-score plot

Chain identifier: 7

Note: Second generation quality Z-score plot

Chain identifier: Z

Note: Second generation quality Z-score plot

Chain identifier: 8

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

9809 HOH   ( 930 )  A      O    -13.53  -35.47  107.31
9809 HOH   ( 960 )  A      O      0.55  -39.07  102.40
9809 HOH   ( 966 )  A      O    -15.40  -26.25  109.11
9809 HOH   ( 968 )  A      O      1.90  -41.16  107.71
9809 HOH   (1039 )  A      O      0.21  -39.44  105.83
9812 HOH   ( 252 )  J      O     -6.30   73.55  174.12
9813 HOH   ( 835 )  C      O     32.71   61.53  170.02
9813 HOH   ( 903 )  C      O     32.55   63.45  172.09
9813 HOH   ( 999 )  C      O     30.37   63.77  173.64
9813 HOH   (1001 )  C      O     32.11   60.17  163.20
9813 HOH   (1070 )  C      O     39.49   62.81  170.37
9814 HOH   ( 326 )  K      O    -29.29   49.13  161.36
9818 HOH   ( 283 )  M      O     38.90  -40.47  104.50
9818 HOH   ( 296 )  M      O     57.50  -29.41   92.91
9819 HOH   (1055 )  F      O     -7.17  -38.05  168.85
9821 HOH   (1079 )  G      O     29.16    3.76  248.99
9823 HOH   ( 728 )  H      O     51.57   52.55  114.65
9823 HOH   ( 852 )  H      O     44.20   52.28  122.16
9823 HOH   (1000 )  H      O     42.10   52.70  120.73
9827 HOH   ( 963 )  T      O    -34.25  -34.40  210.24
9828 HOH   ( 263 )  2      O     35.86  -29.55  229.61
9828 HOH   ( 297 )  2      O     29.58  -42.23  206.69
9828 HOH   ( 310 )  2      O     28.71  -39.93  216.22
9828 HOH   ( 311 )  2      O     42.39  -33.42  208.81
9829 HOH   ( 856 )  U      O     32.76   50.95  228.00
9832 HOH   ( 308 )  4      O     58.61  -23.29   59.24
9834 HOH   ( 298 )  5      O     -7.87   59.62   66.58
9834 HOH   ( 300 )  5      O     -6.97   56.58   51.67
9835 HOH   (1039 )  X      O    -31.31  -33.37  209.76
9837 HOH   ( 960 )  Y      O     45.72   -6.55   28.94
9837 HOH   (1012 )  Y      O     37.07    3.23   29.25
9839 HOH   ( 963 )  Z      O     60.10   54.19   49.03
9839 HOH   (1071 )  Z      O     53.90   62.91   53.68

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

9809 HOH   ( 985 )  A      O
9809 HOH   (1002 )  A      O
9809 HOH   (1056 )  A      O
9809 HOH   (1062 )  A      O
9810 HOH   ( 278 )  I      O
9810 HOH   ( 306 )  I      O
9810 HOH   ( 307 )  I      O
9811 HOH   ( 961 )  B      O
9811 HOH   ( 981 )  B      O
9811 HOH   ( 982 )  B      O
9811 HOH   (1016 )  B      O
9812 HOH   ( 291 )  J      O
9812 HOH   ( 297 )  J      O
9813 HOH   (1004 )  C      O
9813 HOH   (1058 )  C      O
9813 HOH   (1079 )  C      O
9815 HOH   ( 840 )  D      O
9815 HOH   (1011 )  D      O
9815 HOH   (1040 )  D      O
9816 HOH   ( 326 )  L      O
9817 HOH   (1074 )  E      O
9817 HOH   (1077 )  E      O
9818 HOH   ( 286 )  M      O
9818 HOH   ( 321 )  M      O
9819 HOH   ( 952 )  F      O
And so on for a total of 88 lines.

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.

  88 ASN   (  95-)  A
 496 GLN   (  29-)  I
 600 GLN   ( 133-)  I
1000 GLN   ( 401-)  B
1102 GLN   (  29-)  J
1197 GLN   ( 124-)  J
1206 GLN   ( 133-)  J
1209 ASN   ( 136-)  J
1590 HIS   ( 386-)  C
1605 GLN   ( 401-)  C
1707 GLN   (  29-)  K
1791 GLN   ( 113-)  K
1802 GLN   ( 124-)  K
2211 GLN   ( 401-)  D
2313 GLN   (  29-)  L
2741 HIS   ( 327-)  E
2815 GLN   ( 401-)  E
2896 ASN   (   8-)  M
2917 GLN   (  29-)  M
2976 GLN   (  88-)  M
3012 GLN   ( 124-)  M
3500 ASN   (   8-)  N
3521 GLN   (  29-)  N
3616 GLN   ( 124-)  N
3625 GLN   ( 133-)  N
And so on for a total of 59 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.

  27 THR   (  34-)  A      N
  56 THR   (  63-)  A      OG1
  58 THR   (  65-)  A      OG1
  60 THR   (  67-)  A      N
 112 SER   ( 119-)  A      OG
 149 GLN   ( 156-)  A      N
 168 LYS   ( 175-)  A      N
 168 LYS   ( 175-)  A      NZ
 171 LEU   ( 178-)  A      N
 172 GLY   ( 179-)  A      N
 194 KCX   ( 201-)  A      OX2
 198 ASN   ( 205-)  A      ND2
 200 ASN   ( 207-)  A      ND2
 204 PHE   ( 211-)  A      N
 210 ARG   ( 217-)  A      NH1
 232 TYR   ( 239-)  A      OH
 239 THR   ( 246-)  A      N
 288 ARG   ( 295-)  A      NE
 296 ARG   ( 303-)  A      NE
 297 GLN   ( 304-)  A      NE2
 372 SER   ( 379-)  A      N
 372 SER   ( 379-)  A      OG
 374 GLY   ( 381-)  A      N
 394 GLN   ( 401-)  A      NE2
 397 GLY   ( 404-)  A      N
And so on for a total of 580 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.

 261 ASP   ( 268-)  A      OD1
 320 HIS   ( 327-)  A      ND1
 394 GLN   ( 401-)  A      OE1
 591 GLN   ( 124-)  I      OE1
 867 ASP   ( 268-)  B      OD1
 926 HIS   ( 327-)  B      ND1
1472 ASP   ( 268-)  C      OD1
1531 HIS   ( 327-)  C      ND1
1590 HIS   ( 386-)  C      NE2
2078 ASP   ( 268-)  D      OD1
2104 HIS   ( 294-)  D      NE2
2137 HIS   ( 327-)  D      ND1
2408 GLN   ( 124-)  L      OE1
2682 ASP   ( 268-)  E      OD1
2682 ASP   ( 268-)  E      OD2
2706 HIS   ( 292-)  E      NE2
3286 ASP   ( 268-)  F      OD1
3312 HIS   ( 294-)  F      NE2
3345 HIS   ( 327-)  F      ND1
3419 GLN   ( 401-)  F      OE1
3891 ASP   ( 268-)  G      OD1
3891 ASP   ( 268-)  G      OD2
3915 HIS   ( 292-)  G      NE2
4024 GLN   ( 401-)  G      OE1
4498 ASP   ( 268-)  H      OD1
And so on for a total of 53 lines.

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+.

9736  MG   ( 476-)  A     0.72   1.27 Scores about as good as CA
9739  MG   ( 476-)  B     0.73   1.28 Scores about as good as CA
9744  MG   ( 476-)  C     0.73   1.29 Scores about as good as CA
9748  MG   ( 476-)  D     0.74   1.32 Scores about as good as CA
9752  MG   ( 476-)  E     0.80   1.59 Scores about as good as NA *2
9757  MG   ( 476-)  F     0.71   1.23 Scores about as good as CA
9761  MG   ( 476-)  G     0.73   1.29 Scores about as good as CA
9771  MG   ( 476-)  S     0.73   1.28 Scores about as good as CA
9780  MG   ( 476-)  U     0.75   1.33 Scores about as good as CA
9784  MG   ( 476-)  V     0.80   1.59 Scores about as good as NA *2
9792  MG   ( 476-)  X     0.71   1.23 Scores about as good as CA
9797  MG   ( 476-)  Y     0.72   1.27 Scores about as good as CA

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and 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 nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple 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 method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

9809 HOH   ( 644 )  A      O  0.96  K  4 *2 NCS 7/7
9809 HOH   ( 655 )  A      O  1.17  K  4 *2 NCS 7/7
9809 HOH   ( 672 )  A      O  1.15  K  4 *2 NCS 6/6
9809 HOH   ( 682 )  A      O  1.00  K  4 *2 NCS 7/7
9809 HOH   ( 687 )  A      O  0.85  K  5 *2 NCS 7/7
9809 HOH   ( 813 )  A      O  1.20  K  4 *2 NCS 7/7
9809 HOH   ( 859 )  A      O  0.79  K  4 *2 NCS 7/7
9809 HOH   ( 871 )  A      O  0.96  K  5 *2 Ion-B NCS 6/6
9809 HOH   ( 890 )  A      O  1.11  K  4 *2 NCS 7/7
9809 HOH   ( 898 )  A      O  1.16  K  4 *2 Ion-B NCS 5/5
9809 HOH   ( 906 )  A      O  1.11  K  5 *2 Ion-B NCS 3/3
9809 HOH   ( 939 )  A      O  1.09  K  4 *2 NCS 7/7
9809 HOH   ( 992 )  A      O  0.93  K  4 *2 ION-B
9809 HOH   (1007 )  A      O  0.90  K  4 *2 ION-B
9810 HOH   ( 182 )  I      O  1.05  K  4 *2 NCS 7/7
9811 HOH   ( 643 )  B      O  1.00  K  4 *2 NCS 7/7
9811 HOH   ( 671 )  B      O  1.13  K  4 *2 NCS 7/7
9811 HOH   ( 689 )  B      O  0.92  K  4 *2 NCS 7/7
9811 HOH   ( 738 )  B      O  0.78  K  5 *2 NCS 7/7
9811 HOH   ( 793 )  B      O  0.85  K  4 *2 Ion-B NCS 3/3
9811 HOH   ( 822 )  B      O  1.03  K  4 *2 NCS 7/7
9811 HOH   ( 835 )  B      O  1.14  K  4 *2 NCS 7/7
9811 HOH   ( 840 )  B      O  1.17  K  4 *2 Ion-B NCS 6/6
9811 HOH   ( 860 )  B      O  0.98  K  4 *2 Ion-B NCS 6/6
9811 HOH   ( 878 )  B      O  1.19  K  4 *2 Ion-B NCS 7/7
And so on for a total of 218 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.

 261 ASP   ( 268-)  A   H-bonding suggests Asn; but Alt-Rotamer
 498 ASP   (  31-)  I   H-bonding suggests Asn
 867 ASP   ( 268-)  B   H-bonding suggests Asn; but Alt-Rotamer
 901 ASP   ( 302-)  B   H-bonding suggests Asn
1104 ASP   (  31-)  J   H-bonding suggests Asn
1472 ASP   ( 268-)  C   H-bonding suggests Asn; but Alt-Rotamer
1709 ASP   (  31-)  K   H-bonding suggests Asn
1970 ASP   ( 160-)  D   H-bonding suggests Asn; but Alt-Rotamer
2078 ASP   ( 268-)  D   H-bonding suggests Asn; but Alt-Rotamer
2112 ASP   ( 302-)  D   H-bonding suggests Asn
2315 ASP   (  31-)  L   H-bonding suggests Asn
2574 ASP   ( 160-)  E   H-bonding suggests Asn; but Alt-Rotamer
2682 ASP   ( 268-)  E   H-bonding suggests Asn; but Alt-Rotamer
2700 ASP   ( 286-)  E   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
2716 ASP   ( 302-)  E   H-bonding suggests Asn
2919 ASP   (  31-)  M   H-bonding suggests Asn
3286 ASP   ( 268-)  F   H-bonding suggests Asn; but Alt-Rotamer
3320 ASP   ( 302-)  F   H-bonding suggests Asn; but Alt-Rotamer
3523 ASP   (  31-)  N   H-bonding suggests Asn
3783 ASP   ( 160-)  G   H-bonding suggests Asn; but Alt-Rotamer
3891 ASP   ( 268-)  G   H-bonding suggests Asn; but Alt-Rotamer
3925 ASP   ( 302-)  G   H-bonding suggests Asn
4390 ASP   ( 160-)  H   H-bonding suggests Asn; but Alt-Rotamer
4498 ASP   ( 268-)  H   H-bonding suggests Asn; but Alt-Rotamer
4532 ASP   ( 302-)  H   H-bonding suggests Asn
And so on for a total of 51 lines.

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.720
  2nd generation packing quality :  -0.355
  Ramachandran plot appearance   :  -0.983
  chi-1/chi-2 rotamer normality  :  -1.139
  Backbone conformation          :  -0.682

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.279 (tight)
  Bond angles                    :   0.622 (tight)
  Omega angle restraints         :   0.257 (tight)
  Side chain planarity           :   0.241 (tight)
  Improper dihedral distribution :   0.548
  B-factor distribution          :   0.581
  Inside/Outside distribution    :   1.054

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 : 1.84


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.3
  2nd generation packing quality :  -0.6
  Ramachandran plot appearance   :  -0.9
  chi-1/chi-2 rotamer normality  :  -0.8
  Backbone conformation          :  -0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.279 (tight)
  Bond angles                    :   0.622 (tight)
  Omega angle restraints         :   0.257 (tight)
  Side chain planarity           :   0.241 (tight)
  Improper dihedral distribution :   0.548
  B-factor distribution          :   0.581
  Inside/Outside distribution    :   1.054
==============

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.