WHAT IF Check report

This file was created 2012-01-31 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 pdb2vdh.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 : 0.105
CA-only RMS fit for the two chains : 0.088

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 : 0.168
CA-only RMS fit for the two chains : 0.081

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 : 0.137
CA-only RMS fit for the two chains : 0.069

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 : 0.143
CA-only RMS fit for the two chains : 0.070

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 : 0.131
CA-only RMS fit for the two chains : 0.078

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.

4849 MME   (   1-)  I  -
4851 MME   (   1-)  J  -
4853 MME   (   1-)  K  -
4855 MME   (   1-)  L  -
4857 MME   (   1-)  M  -
4859 MME   (   1-)  N  -
4861 MME   (   1-)  O  -
4865 CAP   (1477-)  A  -
4872 CAP   (1477-)  B  -
4879 CAP   (1477-)  C  -
4887 CAP   (1477-)  D  -
4894 CAP   (1477-)  E  -
4902 CAP   (1477-)  F  -
4910 CAP   (1477-)  G  -
4936 CAP   (1477-)  H  -
4937 MME   (   1-)  P  -

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.

3730 MET   (   2-)  I  -   N   bound to 4849 MME   (   1-)  I  -   C
3869 MET   (   2-)  J  -   N   bound to 4851 MME   (   1-)  J  -   C
4008 MET   (   2-)  K  -   N   bound to 4853 MME   (   1-)  K  -   C
4147 MET   (   2-)  L  -   N   bound to 4855 MME   (   1-)  L  -   C
4286 MET   (   2-)  M  -   N   bound to 4857 MME   (   1-)  M  -   C
4425 MET   (   2-)  N  -   N   bound to 4859 MME   (   1-)  N  -   C
4564 MET   (   2-)  O  -   N   bound to 4861 MME   (   1-)  O  -   C
4703 MET   (   2-)  P  -   N   bound to 4937 MME   (   1-)  P  -   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: 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

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

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

 146 GLN   ( 156-)  A    0.50
 614 GLN   ( 156-)  B    0.50
1081 GLN   ( 156-)  C    0.50
1546 GLN   ( 156-)  D    0.50
2011 GLN   ( 156-)  E    0.50
2478 GLN   ( 156-)  F    0.50
3410 GLN   ( 156-)  H    0.50

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

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.

 177 ARG   ( 187-)  A
 645 ARG   ( 187-)  B
1112 ARG   ( 187-)  C
1577 ARG   ( 187-)  D
2042 ARG   ( 187-)  E
2509 ARG   ( 187-)  F
2976 ARG   ( 187-)  G
3441 ARG   ( 187-)  H

Warning: Tyrosine convention problem

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

 741 TYR   ( 283-)  B
1028 TYR   ( 103-)  C
1743 TYR   ( 353-)  D
1940 TYR   (  85-)  E
1955 TYR   ( 100-)  E
2407 TYR   (  85-)  F
3339 TYR   (  85-)  H
3357 TYR   ( 103-)  H
3779 TYR   (  51-)  I
3795 TYR   (  67-)  I
3832 TYR   ( 104-)  I
3918 TYR   (  51-)  J
3934 TYR   (  67-)  J
3971 TYR   ( 104-)  J
4057 TYR   (  51-)  K
4073 TYR   (  67-)  K
4196 TYR   (  51-)  L
4212 TYR   (  67-)  L
4335 TYR   (  51-)  M
4351 TYR   (  67-)  M
4388 TYR   ( 104-)  M
4474 TYR   (  51-)  N
4490 TYR   (  67-)  N
4527 TYR   ( 104-)  N
4613 TYR   (  51-)  O
4629 TYR   (  67-)  O
4666 TYR   ( 104-)  O
4752 TYR   (  51-)  P
4768 TYR   (  67-)  P

Warning: Phenylalanine convention problem

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

 392 PHE   ( 402-)  A
 860 PHE   ( 402-)  B
1327 PHE   ( 402-)  C
1394 PHE   ( 469-)  C
1792 PHE   ( 402-)  D
2257 PHE   ( 402-)  E
2724 PHE   ( 402-)  F
3191 PHE   ( 402-)  G
3656 PHE   ( 402-)  H
3721 PHE   ( 467-)  H
3740 PHE   (  12-)  I
3743 PHE   (  15-)  I
3772 PHE   (  44-)  I
3788 PHE   (  60-)  I
3828 PHE   ( 100-)  I
3860 PHE   ( 132-)  I
3879 PHE   (  12-)  J
3882 PHE   (  15-)  J
3911 PHE   (  44-)  J
3927 PHE   (  60-)  J
3967 PHE   ( 100-)  J
3999 PHE   ( 132-)  J
4018 PHE   (  12-)  K
4021 PHE   (  15-)  K
4050 PHE   (  44-)  K
And so on for a total of 60 lines.

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.

3859 ASP   ( 131-)  I
3998 ASP   ( 131-)  J
4137 ASP   ( 131-)  K
4276 ASP   ( 131-)  L
4415 ASP   ( 131-)  M
4554 ASP   ( 131-)  N
4693 ASP   ( 131-)  O
4832 ASP   ( 131-)  P

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.

  78 GLU   (  88-)  A
 326 GLU   ( 336-)  A
 450 GLU   ( 460-)  A
 546 GLU   (  88-)  B
 794 GLU   ( 336-)  B
 918 GLU   ( 460-)  B
1013 GLU   (  88-)  C
1261 GLU   ( 336-)  C
1385 GLU   ( 460-)  C
1478 GLU   (  88-)  D
1850 GLU   ( 460-)  D
1943 GLU   (  88-)  E
2191 GLU   ( 336-)  E
2315 GLU   ( 460-)  E
2410 GLU   (  88-)  F
2658 GLU   ( 336-)  F
2782 GLU   ( 460-)  F
3125 GLU   ( 336-)  G
3249 GLU   ( 460-)  G
3342 GLU   (  88-)  H
3590 GLU   ( 336-)  H
3714 GLU   ( 460-)  H
3774 GLU   (  46-)  I
3783 GLU   (  55-)  I
3913 GLU   (  46-)  J
3922 GLU   (  55-)  J
4052 GLU   (  46-)  K
4061 GLU   (  55-)  K
4191 GLU   (  46-)  L
4200 GLU   (  55-)  L
4330 GLU   (  46-)  M
4339 GLU   (  55-)  M
4469 GLU   (  46-)  N
4478 GLU   (  55-)  N
4608 GLU   (  46-)  O
4617 GLU   (  55-)  O
4747 GLU   (  46-)  P
4756 GLU   (  55-)  P

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.

 191 KCX   ( 201-)  A      CH     CX
 191 KCX   ( 201-)  A      OX1    OQ1
 191 KCX   ( 201-)  A      OX2    OQ2
 659 KCX   ( 201-)  B      CH     CX
 659 KCX   ( 201-)  B      OX1    OQ1
 659 KCX   ( 201-)  B      OX2    OQ2
1126 KCX   ( 201-)  C      CH     CX
1126 KCX   ( 201-)  C      OX1    OQ1
1126 KCX   ( 201-)  C      OX2    OQ2
1591 KCX   ( 201-)  D      CH     CX
1591 KCX   ( 201-)  D      OX1    OQ1
1591 KCX   ( 201-)  D      OX2    OQ2
2056 KCX   ( 201-)  E      CH     CX
2056 KCX   ( 201-)  E      OX1    OQ1
2056 KCX   ( 201-)  E      OX2    OQ2
2523 KCX   ( 201-)  F      CH     CX
2523 KCX   ( 201-)  F      OX1    OQ1
2523 KCX   ( 201-)  F      OX2    OQ2
2990 KCX   ( 201-)  G      CH     CX
2990 KCX   ( 201-)  G      OX1    OQ1
2990 KCX   ( 201-)  G      OX2    OQ2
3455 KCX   ( 201-)  H      CH     CX
3455 KCX   ( 201-)  H      OX1    OQ1
3455 KCX   ( 201-)  H      OX2    OQ2

Geometric checks

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

 |  0.996436  0.000073  0.000162|
 |  0.000073  0.997621  0.000039|
 |  0.000162  0.000039  0.997236|
Proposed new scale matrix

 |  0.008349  0.000000  0.004411|
 |  0.000000  0.005620  0.000000|
 | -0.000002  0.000000  0.009256|
With corresponding cell

    A    = 119.764  B   = 177.924  C    = 122.183
    Alpha=  90.001  Beta= 117.838  Gamma=  90.001

The CRYST1 cell dimensions

    A    = 120.190  B   = 178.349  C    = 122.561
    Alpha=  90.000  Beta= 117.870  Gamma=  90.000

Variance: 1374.791
(Under-)estimated Z-score: 27.327

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.

 317 HIS   ( 327-)  A      CG   ND1  CE1 109.65    4.1
 785 HIS   ( 327-)  B      CG   ND1  CE1 109.62    4.0
1163 HIS   ( 238-)  C      CG   ND1  CE1 109.64    4.0
2153 HIS   ( 298-)  E      CG   ND1  CE1 109.71    4.1
3027 HIS   ( 238-)  G      CG   ND1  CE1 109.65    4.1

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.

  78 GLU   (  88-)  A
 177 ARG   ( 187-)  A
 326 GLU   ( 336-)  A
 450 GLU   ( 460-)  A
 546 GLU   (  88-)  B
 645 ARG   ( 187-)  B
 794 GLU   ( 336-)  B
 918 GLU   ( 460-)  B
1013 GLU   (  88-)  C
1112 ARG   ( 187-)  C
1261 GLU   ( 336-)  C
1385 GLU   ( 460-)  C
1478 GLU   (  88-)  D
1577 ARG   ( 187-)  D
1850 GLU   ( 460-)  D
1943 GLU   (  88-)  E
2042 ARG   ( 187-)  E
2191 GLU   ( 336-)  E
2315 GLU   ( 460-)  E
2410 GLU   (  88-)  F
2509 ARG   ( 187-)  F
2658 GLU   ( 336-)  F
2782 GLU   ( 460-)  F
2976 ARG   ( 187-)  G
3125 GLU   ( 336-)  G
And so on for a total of 54 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.

3556 ASP   ( 302-)  H    4.59
 760 ASP   ( 302-)  B    4.28
2624 ASP   ( 302-)  F    4.27
 292 ASP   ( 302-)  A    4.18
3378 VAL   ( 124-)  H    4.09
2157 ASP   ( 302-)  E    4.07
1227 ASP   ( 302-)  C    4.06
1049 VAL   ( 124-)  C    4.05
3638 VAL   ( 384-)  H    4.05

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.

4838 LYS   ( 137-)  P    -2.4
4151 PRO   (   6-)  L    -2.3
4574 PHE   (  12-)  O    -2.3
4707 PRO   (   6-)  P    -2.3
3985 ILE   ( 118-)  J    -2.3
4402 ILE   ( 118-)  M    -2.3
4680 ILE   ( 118-)  O    -2.3
4541 ILE   ( 118-)  N    -2.3
4124 ILE   ( 118-)  K    -2.3
4819 ILE   ( 118-)  P    -2.3
4290 PRO   (   6-)  M    -2.3
4263 ILE   ( 118-)  L    -2.3
3846 ILE   ( 118-)  I    -2.3
2336 LYS   (  14-)  F    -2.3
3865 LYS   ( 137-)  I    -2.2
3268 LYS   (  14-)  H    -2.2
4282 LYS   ( 137-)  L    -2.2
4646 ARG   (  84-)  O    -2.2
   4 LYS   (  14-)  A    -2.2
1404 LYS   (  14-)  D    -2.2
4012 PRO   (   6-)  K    -2.2
 472 LYS   (  14-)  B    -2.2
2387 THR   (  65-)  F    -2.2
1985 LEU   ( 130-)  E    -2.2
4122 VAL   ( 116-)  K    -2.2
And so on for a total of 91 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.

  13 THR   (  23-)  A  omega poor
  31 ARG   (  41-)  A  omega poor
  52 SER   (  62-)  A  Poor phi/psi
  53 THR   (  63-)  A  omega poor
  55 THR   (  65-)  A  omega poor
  97 LEU   ( 107-)  A  omega poor
 153 ASN   ( 163-)  A  Poor phi/psi
 165 LYS   ( 175-)  A  PRO omega poor
 189 PHE   ( 199-)  A  omega poor
 197 ASN   ( 207-)  A  Poor phi/psi
 253 PRO   ( 263-)  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
 481 THR   (  23-)  B  omega poor
 499 ARG   (  41-)  B  omega poor
 520 SER   (  62-)  B  Poor phi/psi
 521 THR   (  63-)  B  Poor phi/psi
 539 LYS   (  81-)  B  omega poor
 621 ASN   ( 163-)  B  Poor phi/psi
 633 LYS   ( 175-)  B  PRO omega poor
 654 GLY   ( 196-)  B  Poor phi/psi
 657 PHE   ( 199-)  B  omega poor
 665 ASN   ( 207-)  B  Poor phi/psi
And so on for a total of 187 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.

 269 SER   ( 279-)  A    0.36
 737 SER   ( 279-)  B    0.36
3533 SER   ( 279-)  H    0.37
2302 SER   ( 447-)  E    0.37
2601 SER   ( 279-)  F    0.37
1204 SER   ( 279-)  C    0.37
1669 SER   ( 279-)  D    0.38
3068 SER   ( 279-)  G    0.38

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   5 ALA   (  15-)  A      0
   8 LYS   (  18-)  A      0
  13 THR   (  23-)  A      0
  14 TYR   (  24-)  A      0
  15 TYR   (  25-)  A      0
  16 THR   (  26-)  A      0
  36 PRO   (  46-)  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
  75 TYR   (  85-)  A      0
  76 ASP   (  86-)  A      0
  81 PRO   (  91-)  A      0
  84 ASP   (  94-)  A      0
  85 ASN   (  95-)  A      0
  94 HYP   ( 104-)  A      0
 100 GLU   ( 110-)  A      0
 113 ASN   ( 123-)  A      0
 117 PHE   ( 127-)  A      0
 127 ASP   ( 137-)  A      0
 138 PHE   ( 148-)  A      0
 139 VAL   ( 149-)  A      0
And so on for a total of 1848 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!

3126 GLY   ( 337-)  G   2.36   13
2192 GLY   ( 337-)  E   2.36   11
2659 GLY   ( 337-)  F   2.35   10
1262 GLY   ( 337-)  C   2.34   11
1727 GLY   ( 337-)  D   2.32   13
 327 GLY   ( 337-)  A   2.28   11
3591 GLY   ( 337-)  H   2.24   10
2727 GLY   ( 405-)  F   1.60   80
2260 GLY   ( 405-)  E   1.56   80
 863 GLY   ( 405-)  B   1.55   80
3194 GLY   ( 405-)  G   1.54   80
 395 GLY   ( 405-)  A   1.53   80
3659 GLY   ( 405-)  H   1.51   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]

3886 PRO   (  19-)  J    0.16 LOW
4442 PRO   (  19-)  N    0.19 LOW
4720 PRO   (  19-)  P    0.19 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].

  36 PRO   (  46-)  A  -118.0 half-chair C-delta/C-gamma (-126 degrees)
 504 PRO   (  46-)  B  -118.4 half-chair C-delta/C-gamma (-126 degrees)
 634 PRO   ( 176-)  B  -112.8 envelop C-gamma (-108 degrees)
 971 PRO   (  46-)  C  -118.4 half-chair C-delta/C-gamma (-126 degrees)
1436 PRO   (  46-)  D  -115.8 envelop C-gamma (-108 degrees)
1532 PRO   ( 142-)  D    99.4 envelop C-beta (108 degrees)
1800 PRO   ( 410-)  D  -113.8 envelop C-gamma (-108 degrees)
1901 PRO   (  46-)  E  -115.6 envelop C-gamma (-108 degrees)
1997 PRO   ( 142-)  E    99.5 envelop C-beta (108 degrees)
2265 PRO   ( 410-)  E  -112.7 envelop C-gamma (-108 degrees)
2368 PRO   (  46-)  F  -116.6 envelop C-gamma (-108 degrees)
2835 PRO   (  46-)  G  -121.6 half-chair C-delta/C-gamma (-126 degrees)
3199 PRO   ( 410-)  G  -114.5 envelop C-gamma (-108 degrees)
3300 PRO   (  46-)  H  -125.9 half-chair C-delta/C-gamma (-126 degrees)
3768 PRO   (  40-)  I    50.3 half-chair C-delta/C-gamma (54 degrees)
3907 PRO   (  40-)  J    48.0 half-chair C-delta/C-gamma (54 degrees)
3993 PRO   ( 126-)  J  -114.7 envelop C-gamma (-108 degrees)
4046 PRO   (  40-)  K    51.6 half-chair C-delta/C-gamma (54 degrees)
4151 PRO   (   6-)  L   -61.8 half-chair C-beta/C-alpha (-54 degrees)
4290 PRO   (   6-)  M   -64.5 envelop C-beta (-72 degrees)
4324 PRO   (  40-)  M    52.2 half-chair C-delta/C-gamma (54 degrees)
4410 PRO   ( 126-)  M  -112.9 envelop C-gamma (-108 degrees)
4463 PRO   (  40-)  N    43.4 envelop C-delta (36 degrees)
4602 PRO   (  40-)  O    51.2 half-chair C-delta/C-gamma (54 degrees)
4741 PRO   (  40-)  P    46.1 half-chair C-delta/C-gamma (54 degrees)
4827 PRO   ( 126-)  P  -112.3 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 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.

4703 MET   (   2-)  P      N    <->  4937 MME   (   1-)  P      C    1.38    1.32  INTRA B3
4703 MET   (   2-)  P      CA   <->  4937 MME   (   1-)  P      C    0.80    2.40  INTRA
2947 GLU   ( 158-)  G      OE2  <->  3114 HIS   ( 325-)  G      NE2  0.41    2.29  INTRA
3412 GLU   ( 158-)  H      OE2  <->  3579 HIS   ( 325-)  H      NE2  0.41    2.29  INTRA
4692 ARG   ( 130-)  O      NH1  <->  4952 HOH   (2039 )  O      O    0.38    2.32  INTRA BF
1548 GLU   ( 158-)  D      OE2  <->  1715 HIS   ( 325-)  D      NE2  0.38    2.32  INTRA
3260 THR   ( 471-)  G      OG1  <->  4944 HOH   (2172 )  G      O    0.38    2.02  INTRA
 756 HIS   ( 298-)  B      ND1  <->   760 ASP   ( 302-)  B      OD2  0.36    2.34  INTRA
2758 ASP   ( 436-)  F      OD2  <->  2761 ARG   ( 439-)  F      NH1  0.35    2.35  INTRA
 616 GLU   ( 158-)  B      OE2  <->   783 HIS   ( 325-)  B      NE2  0.34    2.36  INTRA
4826 ARG   ( 125-)  P      NH1  <->  4953 HOH   (2045 )  P      O    0.34    2.36  INTRA
 148 GLU   ( 158-)  A      OE2  <->   315 HIS   ( 325-)  A      NE2  0.34    2.36  INTRA
3056 HIS   ( 267-)  G      CD2  <->  3066 ASN   ( 277-)  G      ND2  0.33    2.77  INTRA BL
1083 GLU   ( 158-)  C      OE2  <->  1250 HIS   ( 325-)  C      NE2  0.31    2.39  INTRA
2013 GLU   ( 158-)  E      OE2  <->  2180 HIS   ( 325-)  E      NE2  0.31    2.39  INTRA
1657 HIS   ( 267-)  D      CD2  <->  1667 ASN   ( 277-)  D      ND2  0.29    2.81  INTRA BL
 288 HIS   ( 298-)  A      ND1  <->   292 ASP   ( 302-)  A      OD2  0.29    2.41  INTRA
3593 ARG   ( 339-)  H      NH1  <->  4945 HOH   (2137 )  H      O    0.28    2.42  INTRA
2620 HIS   ( 298-)  F      ND1  <->  2624 ASP   ( 302-)  F      OD2  0.27    2.43  INTRA
1223 HIS   ( 298-)  C      ND1  <->  1227 ASP   ( 302-)  C      OD2  0.27    2.43  INTRA
 257 HIS   ( 267-)  A      CD2  <->   267 ASN   ( 277-)  A      ND2  0.27    2.83  INTRA BL
2122 HIS   ( 267-)  E      CD2  <->  2132 ASN   ( 277-)  E      ND2  0.27    2.83  INTRA BL
 725 HIS   ( 267-)  B      CD2  <->   735 ASN   ( 277-)  B      ND2  0.26    2.84  INTRA BL
3087 HIS   ( 298-)  G      ND1  <->  3091 ASP   ( 302-)  G      OD2  0.26    2.44  INTRA
3552 HIS   ( 298-)  H      ND1  <->  3556 ASP   ( 302-)  H      OD2  0.26    2.44  INTRA
And so on for a total of 348 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

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.

4368 ARG   (  84-)  M      -7.59
4229 ARG   (  84-)  L      -7.57
3812 ARG   (  84-)  I      -6.96
4090 ARG   (  84-)  K      -6.67
3951 ARG   (  84-)  J      -6.66
4785 ARG   (  84-)  P      -6.59
4507 ARG   (  84-)  N      -6.51
4646 ARG   (  84-)  O      -6.21
2294 ARG   ( 439-)  E      -5.80
1364 ARG   ( 439-)  C      -5.78
 897 ARG   ( 439-)  B      -5.78
2761 ARG   ( 439-)  F      -5.77
 429 ARG   ( 439-)  A      -5.75
3228 ARG   ( 439-)  G      -5.73
1829 ARG   ( 439-)  D      -5.69
3705 TRP   ( 451-)  H      -5.63
 909 TRP   ( 451-)  B      -5.62
1376 TRP   ( 451-)  C      -5.61
3240 TRP   ( 451-)  G      -5.60
3263 LYS   ( 474-)  G      -5.58
 441 TRP   ( 451-)  A      -5.58
1841 TRP   ( 451-)  D      -5.57
2803 LYS   (  14-)  G      -5.56
3693 ARG   ( 439-)  H      -5.56
2773 TRP   ( 451-)  F      -5.55
And so on for a total of 107 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

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.

1689 ALA   ( 299-)  D   -2.85
3553 ALA   ( 299-)  H   -2.82
2154 ALA   ( 299-)  E   -2.81
 757 ALA   ( 299-)  B   -2.81
1827 LEU   ( 437-)  D   -2.80
2621 ALA   ( 299-)  F   -2.80
 289 ALA   ( 299-)  A   -2.77
1362 LEU   ( 437-)  C   -2.75
1224 ALA   ( 299-)  C   -2.75
3088 ALA   ( 299-)  G   -2.75
3691 LEU   ( 437-)  H   -2.74
2759 LEU   ( 437-)  F   -2.73
 427 LEU   ( 437-)  A   -2.72
3226 LEU   ( 437-)  G   -2.70
 895 LEU   ( 437-)  B   -2.69
1497 LEU   ( 107-)  D   -2.62
1032 LEU   ( 107-)  C   -2.57
4708 VAL   (   7-)  P   -2.56
 565 LEU   ( 107-)  B   -2.55
4366 GLY   (  82-)  M   -2.55
3361 LEU   ( 107-)  H   -2.55
1962 LEU   ( 107-)  E   -2.54
2429 LEU   ( 107-)  F   -2.53
2896 LEU   ( 107-)  G   -2.52
  97 LEU   ( 107-)  A   -2.52

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

Water, ion, and hydrogenbond related checks

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.

4939 HOH   (2180 )  B      O
4940 HOH   (2148 )  C      O
4941 HOH   (2050 )  D      O
4941 HOH   (2150 )  D      O
4942 HOH   (2011 )  E      O
4942 HOH   (2159 )  E      O
4944 HOH   (2003 )  G      O
4951 HOH   (2037 )  N      O
4951 HOH   (2049 )  N      O
4952 HOH   (2001 )  O      O
4952 HOH   (2037 )  O      O
4952 HOH   (2039 )  O      O
4952 HOH   (2041 )  O      O
4952 HOH   (2043 )  O      O
4953 HOH   (2001 )  P      O

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
 146 GLN   ( 156-)  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
 376 HIS   ( 386-)  A
 410 ASN   ( 420-)  A
 422 ASN   ( 432-)  A
 611 HIS   ( 153-)  B
 687 GLN   ( 229-)  B
 696 HIS   ( 238-)  B
 699 ASN   ( 241-)  B
 725 HIS   ( 267-)  B
 735 ASN   ( 277-)  B
 762 GLN   ( 304-)  B
 785 HIS   ( 327-)  B
 844 HIS   ( 386-)  B
 878 ASN   ( 420-)  B
 890 ASN   ( 432-)  B
1078 HIS   ( 153-)  C
1081 GLN   ( 156-)  C
1154 GLN   ( 229-)  C
And so on for a total of 129 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.

  20 VAL   (  30-)  A      N
  55 THR   (  65-)  A      OG1
  57 THR   (  67-)  A      N
  86 GLN   (  96-)  A      N
 157 ARG   ( 167-)  A      N
 165 LYS   ( 175-)  A      N
 165 LYS   ( 175-)  A      NZ
 168 LEU   ( 178-)  A      N
 169 GLY   ( 179-)  A      N
 195 ASN   ( 205-)  A      ND2
 201 PHE   ( 211-)  A      N
 205 ARG   ( 215-)  A      NH1
 207 ARG   ( 217-)  A      NH1
 229 TYR   ( 239-)  A      OH
 236 THR   ( 246-)  A      N
 285 ARG   ( 295-)  A      NE
 285 ARG   ( 295-)  A      NH1
 293 ARG   ( 303-)  A      NE
 297 HIS   ( 307-)  A      N
 322 VAL   ( 332-)  A      N
 327 GLY   ( 337-)  A      N
 328 GLU   ( 338-)  A      N
 330 GLU   ( 340-)  A      N
 356 GLN   ( 366-)  A      NE2
 363 GLY   ( 373-)  A      N
And so on for a total of 267 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.

 258 ASP   ( 268-)  A      OD1
 258 ASP   ( 268-)  A      OD2
 317 HIS   ( 327-)  A      ND1
 391 GLN   ( 401-)  A      OE1
 726 ASP   ( 268-)  B      OD1
 726 ASP   ( 268-)  B      OD2
 750 HIS   ( 292-)  B      NE2
1193 ASP   ( 268-)  C      OD1
1193 ASP   ( 268-)  C      OD2
1252 HIS   ( 327-)  C      ND1
1326 GLN   ( 401-)  C      OE1
1658 ASP   ( 268-)  D      OD1
1682 HIS   ( 292-)  D      NE2
1692 ASP   ( 302-)  D      OD2
1791 GLN   ( 401-)  D      OE1
2123 ASP   ( 268-)  E      OD1
2123 ASP   ( 268-)  E      OD2
2256 GLN   ( 401-)  E      OE1
2480 GLU   ( 158-)  F      OE1
2590 ASP   ( 268-)  F      OD1
2614 HIS   ( 292-)  F      NE2
2723 GLN   ( 401-)  F      OE1
3057 ASP   ( 268-)  G      OD1
3057 ASP   ( 268-)  G      OD2
3081 HIS   ( 292-)  G      NE2
3190 GLN   ( 401-)  G      OE1
3412 GLU   ( 158-)  H      OE1
3522 ASP   ( 268-)  H      OD1
3522 ASP   ( 268-)  H      OD2
3548 HIS   ( 294-)  H      NE2
3655 GLN   ( 401-)  H      OE1
3937 ASN   (  70-)  J      OD1
4571 ASN   (   9-)  O      OD1

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: 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.

4939 HOH   (2087 )  B      O  1.08  K  4 Ion-B
4939 HOH   (2115 )  B      O  1.08  K  4 NCS 7/7
4940 HOH   (2067 )  C      O  0.92  K  5 Ion-B NCS 7/7
4942 HOH   (2095 )  E      O  0.97  K  4 Ion-B NCS 2/2
4943 HOH   (2007 )  F      O  0.93  K  4
4944 HOH   (2028 )  G      O  0.98  K  4 Ion-B NCS 1/1
4944 HOH   (2089 )  G      O  1.14  K  4 NCS 6/6
4945 HOH   (2117 )  H      O  1.00  K  4 NCS 6/6
4947 HOH   (2012 )  J      O  1.00  K  4 NCS 7/7
4949 HOH   (2017 )  L      O  0.90  K  4 NCS 6/6
4953 HOH   (2019 )  P      O  0.90  K  4 NCS 7/7

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.

  42 GLU   (  52-)  A   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
  62 ASP   (  72-)  A   H-bonding suggests Asn; Ligand-contact
 150 ASP   ( 160-)  A   H-bonding suggests Asn; but Alt-Rotamer
 258 ASP   ( 268-)  A   H-bonding suggests Asn; but Alt-Rotamer
 510 GLU   (  52-)  B   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
 726 ASP   ( 268-)  B   H-bonding suggests Asn; but Alt-Rotamer
 931 ASP   ( 473-)  B   H-bonding suggests Asn; Ligand-contact
 977 GLU   (  52-)  C   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
1193 ASP   ( 268-)  C   H-bonding suggests Asn; but Alt-Rotamer
1398 ASP   ( 473-)  C   H-bonding suggests Asn; Ligand-contact
1442 GLU   (  52-)  D   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
1550 ASP   ( 160-)  D   H-bonding suggests Asn; but Alt-Rotamer
1658 ASP   ( 268-)  D   H-bonding suggests Asn; but Alt-Rotamer
1863 ASP   ( 473-)  D   H-bonding suggests Asn; Ligand-contact
1907 GLU   (  52-)  E   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
2123 ASP   ( 268-)  E   H-bonding suggests Asn; but Alt-Rotamer
2328 ASP   ( 473-)  E   H-bonding suggests Asn; Ligand-contact
2374 GLU   (  52-)  F   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
2482 ASP   ( 160-)  F   H-bonding suggests Asn; but Alt-Rotamer
2590 ASP   ( 268-)  F   H-bonding suggests Asn; but Alt-Rotamer
2841 GLU   (  52-)  G   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
3057 ASP   ( 268-)  G   H-bonding suggests Asn; but Alt-Rotamer
3306 GLU   (  52-)  H   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
3414 ASP   ( 160-)  H   H-bonding suggests Asn; but Alt-Rotamer
3522 ASP   ( 268-)  H   H-bonding suggests Asn; but Alt-Rotamer
3783 GLU   (  55-)  I   H-bonding suggests Gln; Ligand-contact
3922 GLU   (  55-)  J   H-bonding suggests Gln; Ligand-contact
4061 GLU   (  55-)  K   H-bonding suggests Gln; Ligand-contact
4200 GLU   (  55-)  L   H-bonding suggests Gln; Ligand-contact
4339 GLU   (  55-)  M   H-bonding suggests Gln; Ligand-contact
4478 GLU   (  55-)  N   H-bonding suggests Gln; Ligand-contact
4617 GLU   (  55-)  O   H-bonding suggests Gln; Ligand-contact
4756 GLU   (  55-)  P   H-bonding suggests Gln; Ligand-contact

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 :  -0.729
  2nd generation packing quality :  -0.202
  Ramachandran plot appearance   :  -0.702
  chi-1/chi-2 rotamer normality  :  -1.405
  Backbone conformation          :  -0.617

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.494 (tight)
  Bond angles                    :   0.628 (tight)
  Omega angle restraints         :   1.075
  Side chain planarity           :   0.411 (tight)
  Improper dihedral distribution :   0.626
  B-factor distribution          :   0.350
  Inside/Outside distribution    :   1.058

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 : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :   0.4
  Ramachandran plot appearance   :   0.6
  chi-1/chi-2 rotamer normality  :  -0.0
  Backbone conformation          :  -0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.494 (tight)
  Bond angles                    :   0.628 (tight)
  Omega angle restraints         :   1.075
  Side chain planarity           :   0.411 (tight)
  Improper dihedral distribution :   0.626
  B-factor distribution          :   0.350
  Inside/Outside distribution    :   1.058
==============

WHAT IF
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    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

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Bond lengths and angles, DNA/RNA
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DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
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    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
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      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
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      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,
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    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.