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 pdb2v6a.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 : 0.328
CA-only RMS fit for the two chains : 0.257

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 : 0.369
CA-only RMS fit for the two chains : 0.245

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 : 0.387
CA-only RMS fit for the two chains : 0.265

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 : 0.250
CA-only RMS fit for the two chains : 0.107

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 : 0.321
CA-only RMS fit for the two chains : 0.242

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.

4850 MME   (   1-)  I  -
4852 MME   (   1-)  J  -
4854 MME   (   1-)  K  -
4856 MME   (   1-)  L  -
4857 MME   (   1-)  M  -
4859 MME   (   1-)  N  -
4861 MME   (   1-)  O  -
4865 CAP   (1477-)  A  -
4873 CAP   (1477-)  B  -
4880 CAP   (1477-)  C  -
4888 CAP   (1477-)  D  -
4895 CAP   (1477-)  E  -
4901 CAP   (1477-)  F  -
4909 CAP   (1477-)  G  -
4938 CAP   (1477-)  H  -
4939 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 4850 MME   (   1-)  I  -   C
3869 MET   (   2-)  J  -   N   bound to 4852 MME   (   1-)  J  -   C
4008 MET   (   2-)  K  -   N   bound to 4854 MME   (   1-)  K  -   C
4147 MET   (   2-)  L  -   N   bound to 4856 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 4939 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: 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.

 813 VAL   ( 354-)  B
4812 ASP   ( 111-)  P

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.

 239 CYS   ( 247-)  A    0.75
1173 CYS   ( 247-)  C    0.75
1639 CYS   ( 247-)  D    0.75
2116 GLU   ( 259-)  E    0.50
3847 MET   ( 119-)  I    0.50
3986 MET   ( 119-)  J    0.50
4125 MET   ( 119-)  K    0.50
4264 MET   ( 119-)  L    0.50
4403 MET   ( 119-)  M    0.50
4542 MET   ( 119-)  N    0.50
4681 MET   ( 119-)  O    0.50
4820 MET   ( 119-)  P    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: Leucine nomenclature problem

The leucine residues listed in the table below have their C-delta-1 and C-delta-2 swapped.

 211 LEU   ( 219-)  A
 678 LEU   ( 219-)  B

Warning: Arginine nomenclature problem

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

 179 ARG   ( 187-)  A
 646 ARG   ( 187-)  B
1113 ARG   ( 187-)  C
1579 ARG   ( 187-)  D
1752 ARG   ( 360-)  D
2044 ARG   ( 187-)  E
2509 ARG   ( 187-)  F
2974 ARG   ( 187-)  G
3441 ARG   ( 187-)  H
4514 ARG   (  91-)  N

Warning: Tyrosine convention problem

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

 345 TYR   ( 353-)  A
 562 TYR   ( 103-)  B
 812 TYR   ( 353-)  B
2872 TYR   (  85-)  G
3140 TYR   ( 353-)  G
3339 TYR   (  85-)  H
3607 TYR   ( 353-)  H
3779 TYR   (  51-)  I
3795 TYR   (  67-)  I
3918 TYR   (  51-)  J
3934 TYR   (  67-)  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
4474 TYR   (  51-)  N
4490 TYR   (  67-)  N
4613 TYR   (  51-)  O
4629 TYR   (  67-)  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.

 337 PHE   ( 345-)  A
 394 PHE   ( 402-)  A
 804 PHE   ( 345-)  B
1271 PHE   ( 345-)  C
1328 PHE   ( 402-)  C
1737 PHE   ( 345-)  D
1794 PHE   ( 402-)  D
1861 PHE   ( 469-)  D
2202 PHE   ( 345-)  E
2667 PHE   ( 345-)  F
2724 PHE   ( 402-)  F
3132 PHE   ( 345-)  G
3189 PHE   ( 402-)  G
3256 PHE   ( 469-)  G
3599 PHE   ( 345-)  H
3656 PHE   ( 402-)  H
3723 PHE   ( 469-)  H
3740 PHE   (  12-)  I
3743 PHE   (  15-)  I
3772 PHE   (  44-)  I
3788 PHE   (  60-)  I
3828 PHE   ( 100-)  I
3849 PHE   ( 121-)  I
3860 PHE   ( 132-)  I
3879 PHE   (  12-)  J
And so on for a total of 72 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.

 959 ASP   (  33-)  C
1486 ASP   (  94-)  D
3287 ASP   (  33-)  H
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.

  80 GLU   (  88-)  A
 452 GLU   ( 460-)  A
 547 GLU   (  88-)  B
 851 GLU   ( 392-)  B
 919 GLU   ( 460-)  B
 923 GLU   ( 464-)  B
1014 GLU   (  88-)  C
1945 GLU   (  88-)  E
2212 GLU   ( 355-)  E
2410 GLU   (  88-)  F
3752 GLU   (  24-)  I
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
4330 GLU   (  46-)  M
4339 GLU   (  55-)  M
4447 GLU   (  24-)  N
4469 GLU   (  46-)  N
4478 GLU   (  55-)  N
4608 GLU   (  46-)  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.

 193 KCX   ( 201-)  A      CH     CX
 193 KCX   ( 201-)  A      OX1    OQ1
 193 KCX   ( 201-)  A      OX2    OQ2
 660 KCX   ( 201-)  B      CH     CX
 660 KCX   ( 201-)  B      OX1    OQ1
 660 KCX   ( 201-)  B      OX2    OQ2
1127 KCX   ( 201-)  C      CH     CX
1127 KCX   ( 201-)  C      OX1    OQ1
1127 KCX   ( 201-)  C      OX2    OQ2
1593 KCX   ( 201-)  D      CH     CX
1593 KCX   ( 201-)  D      OX1    OQ1
1593 KCX   ( 201-)  D      OX2    OQ2
2058 KCX   ( 201-)  E      CH     CX
2058 KCX   ( 201-)  E      OX1    OQ1
2058 KCX   ( 201-)  E      OX2    OQ2
2523 KCX   ( 201-)  F      CH     CX
2523 KCX   ( 201-)  F      OX1    OQ1
2523 KCX   ( 201-)  F      OX2    OQ2
2988 KCX   ( 201-)  G      CH     CX
2988 KCX   ( 201-)  G      OX1    OQ1
2988 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: 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.

4842 LEU   ( 475-)  A      SG  -SG*   2.45   10.2
 451 CYS   ( 459-)  A      SG  -SG*   2.45   10.2
2306 CYS   ( 449-)  E      SG  -SG*   2.42    9.6
2316 CYS   ( 459-)  E      SG  -SG*   2.42    9.6

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: 0.457
RMS-deviation in bond distances: 0.011

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

 |  0.997205  0.000588 -0.000114|
 |  0.000588  0.997442  0.000061|
 | -0.000114  0.000061  0.996851|
Proposed new scale matrix

 |  0.007720 -0.000005  0.000000|
 | -0.000003  0.005099  0.000000|
 |  0.000000  0.000000  0.004968|
With corresponding cell

    A    = 129.541  B   = 196.115  C    = 201.303
    Alpha=  90.002  Beta=  90.002  Gamma=  89.932

The CRYST1 cell dimensions

    A    = 129.906  B   = 196.629  C    = 201.950
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 1312.046
(Under-)estimated Z-score: 26.696

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   ( 325-)  A      C    CA   CB  102.19   -4.2
1717 HIS   ( 325-)  D      C    CA   CB  102.28   -4.1
2647 HIS   ( 325-)  F      C    CA   CB  101.57   -4.5
2649 HIS   ( 327-)  F      CG   ND1  CE1 109.67    4.1
2946 ARG   ( 159-)  G      CB   CG   CD  106.10   -4.0
3054 HIS   ( 267-)  G      CG   ND1  CE1 109.61    4.0
3112 HIS   ( 325-)  G      C    CA   CB  102.21   -4.2

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: 0.654
RMS-deviation in bond angles: 1.321

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.

  80 GLU   (  88-)  A
 179 ARG   ( 187-)  A
 452 GLU   ( 460-)  A
 547 GLU   (  88-)  B
 646 ARG   ( 187-)  B
 851 GLU   ( 392-)  B
 919 GLU   ( 460-)  B
 923 GLU   ( 464-)  B
 959 ASP   (  33-)  C
1014 GLU   (  88-)  C
1113 ARG   ( 187-)  C
1486 ASP   (  94-)  D
1579 ARG   ( 187-)  D
1752 ARG   ( 360-)  D
1945 GLU   (  88-)  E
2044 ARG   ( 187-)  E
2212 GLU   ( 355-)  E
2410 GLU   (  88-)  F
2509 ARG   ( 187-)  F
2974 ARG   ( 187-)  G
3287 ASP   (  33-)  H
3441 ARG   ( 187-)  H
3752 GLU   (  24-)  I
3774 GLU   (  46-)  I
3783 GLU   (  55-)  I
3859 ASP   ( 131-)  I
3913 GLU   (  46-)  J
3922 GLU   (  55-)  J
3998 ASP   ( 131-)  J
4052 GLU   (  46-)  K
4061 GLU   (  55-)  K
4137 ASP   ( 131-)  K
4191 GLU   (  46-)  L
4276 ASP   ( 131-)  L
4330 GLU   (  46-)  M
4339 GLU   (  55-)  M
4415 ASP   ( 131-)  M
4447 GLU   (  24-)  N
4469 GLU   (  46-)  N
4478 GLU   (  55-)  N
4514 ARG   (  91-)  N
4554 ASP   ( 131-)  N
4608 GLU   (  46-)  O
4693 ASP   ( 131-)  O
4747 GLU   (  46-)  P
4756 GLU   (  55-)  P
4832 ASP   ( 131-)  P

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.

2159 ASP   ( 302-)  E    4.34

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.

 550 PRO   (  91-)  B    -2.9
3873 PRO   (   6-)  J    -2.5
2561 TYR   ( 239-)  F    -2.5
1165 TYR   ( 239-)  C    -2.5
3879 PHE   (  12-)  J    -2.4
3026 TYR   ( 239-)  G    -2.4
3493 TYR   ( 239-)  H    -2.4
4429 PRO   (   6-)  N    -2.4
1631 TYR   ( 239-)  D    -2.3
4124 ILE   ( 118-)  K    -2.3
4680 ILE   ( 118-)  O    -2.3
4263 ILE   ( 118-)  L    -2.3
3846 ILE   ( 118-)  I    -2.3
4435 PHE   (  12-)  N    -2.3
4402 ILE   ( 118-)  M    -2.3
2096 TYR   ( 239-)  E    -2.3
4157 PHE   (  12-)  L    -2.3
4819 ILE   ( 118-)  P    -2.3
3985 ILE   ( 118-)  J    -2.3
3858 ARG   ( 130-)  I    -2.3
4541 ILE   ( 118-)  N    -2.3
 698 TYR   ( 239-)  B    -2.3
4296 PHE   (  12-)  M    -2.3
 231 TYR   ( 239-)  A    -2.3
4012 PRO   (   6-)  K    -2.2
And so on for a total of 87 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.

  15 THR   (  23-)  A  omega poor
  54 SER   (  62-)  A  Poor phi/psi
  57 THR   (  65-)  A  omega poor
  87 ASN   (  95-)  A  Poor phi/psi
 155 ASN   ( 163-)  A  Poor phi/psi
 167 LYS   ( 175-)  A  PRO omega poor
 191 PHE   ( 199-)  A  omega poor
 199 ASN   ( 207-)  A  Poor phi/psi
 255 PRO   ( 263-)  A  omega poor
 289 MET   ( 297-)  A  Poor phi/psi
 293 ILE   ( 301-)  A  omega poor
 323 ALA   ( 331-)  A  Poor phi/psi
 342 ARG   ( 350-)  A  omega poor
 362 SER   ( 370-)  A  Poor phi/psi
 482 THR   (  23-)  B  omega poor
 521 SER   (  62-)  B  Poor phi/psi
 522 THR   (  63-)  B  Poor phi/psi
 524 THR   (  65-)  B  omega poor
 540 LYS   (  81-)  B  omega poor
 556 TYR   (  97-)  B  omega poor
 566 LEU   ( 107-)  B  omega poor
 578 SER   ( 119-)  B  omega poor
 622 ASN   ( 163-)  B  Poor phi/psi
 634 LYS   ( 175-)  B  PRO omega poor
 658 PHE   ( 199-)  B  omega poor
And so on for a total of 192 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.

 271 SER   ( 279-)  A    0.35
1671 SER   ( 279-)  D    0.35
3066 SER   ( 279-)  G    0.35
2136 SER   ( 279-)  E    0.35
 738 SER   ( 279-)  B    0.36
3533 SER   ( 279-)  H    0.36
 439 SER   ( 447-)  A    0.36
1373 SER   ( 447-)  C    0.36
1839 SER   ( 447-)  D    0.36
2304 SER   ( 447-)  E    0.36
2769 SER   ( 447-)  F    0.36
1205 SER   ( 279-)  C    0.37
2601 SER   ( 279-)  F    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!

   5 PHE   (  13-)  A      0
   7 ALA   (  15-)  A      0
  10 LYS   (  18-)  A      0
  15 THR   (  23-)  A      0
  16 TYR   (  24-)  A      0
  17 TYR   (  25-)  A      0
  18 THR   (  26-)  A      0
  38 PRO   (  46-)  A      0
  53 SER   (  61-)  A      0
  54 SER   (  62-)  A      0
  55 THR   (  63-)  A      0
  58 TRP   (  66-)  A      0
  62 TRP   (  70-)  A      0
  66 LEU   (  74-)  A      0
  77 TYR   (  85-)  A      0
  78 ASP   (  86-)  A      0
  83 PRO   (  91-)  A      0
  86 ASP   (  94-)  A      0
  87 ASN   (  95-)  A      0
  88 GLN   (  96-)  A      0
  96 HYP   ( 104-)  A      0
 102 GLU   ( 110-)  A      0
 113 VAL   ( 121-)  A      0
 115 ASN   ( 123-)  A      0
 116 VAL   ( 124-)  A      0
And so on for a total of 1847 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!

3124 GLY   ( 337-)  G   2.66   12
 796 GLY   ( 337-)  B   2.56   10
1263 GLY   ( 337-)  C   2.54   10
1797 GLY   ( 405-)  D   1.60   80
2262 GLY   ( 405-)  E   1.59   80
 397 GLY   ( 405-)  A   1.58   80
1331 GLY   ( 405-)  C   1.56   80
3192 GLY   ( 405-)  G   1.56   80
3659 GLY   ( 405-)  H   1.56   80
 864 GLY   ( 405-)  B   1.54   80
2727 GLY   ( 405-)  F   1.54   80

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

 255 PRO   ( 263-)  A    0.16 LOW
1189 PRO   ( 263-)  C    0.16 LOW
2008 HYP   ( 151-)  E    0.45 HIGH
2120 PRO   ( 263-)  E    0.19 LOW
3907 PRO   (  40-)  J    0.17 LOW
4025 PRO   (  19-)  K    0.15 LOW
4164 PRO   (  19-)  L    0.13 LOW
4271 PRO   ( 126-)  L    0.19 LOW
4303 PRO   (  19-)  M    0.07 LOW
4410 PRO   ( 126-)  M    0.10 LOW
4463 PRO   (  40-)  N    0.12 LOW
4602 PRO   (  40-)  O    0.13 LOW
4827 PRO   ( 126-)  P    0.13 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].

 505 PRO   (  46-)  B  -125.7 half-chair C-delta/C-gamma (-126 degrees)
 550 PRO   (  91-)  B  -152.8 envelop C-delta (-144 degrees)
 972 PRO   (  46-)  C   105.7 envelop C-beta (108 degrees)
 976 PRO   (  50-)  C  -115.7 envelop C-gamma (-108 degrees)
1903 PRO   (  46-)  E  -122.4 half-chair C-delta/C-gamma (-126 degrees)
1907 PRO   (  50-)  E  -115.0 envelop C-gamma (-108 degrees)
2372 PRO   (  50-)  F  -129.0 half-chair C-delta/C-gamma (-126 degrees)
2837 PRO   (  50-)  G  -114.4 envelop C-gamma (-108 degrees)
3300 PRO   (  46-)  H   100.5 envelop C-beta (108 degrees)
3304 PRO   (  50-)  H  -117.2 half-chair C-delta/C-gamma (-126 degrees)
3768 PRO   (  40-)  I    46.8 half-chair C-delta/C-gamma (54 degrees)
3873 PRO   (   6-)  J   -65.4 envelop C-beta (-72 degrees)
4046 PRO   (  40-)  K    51.8 half-chair C-delta/C-gamma (54 degrees)
4185 PRO   (  40-)  L    45.6 half-chair C-delta/C-gamma (54 degrees)
4741 PRO   (  40-)  P    38.0 envelop C-delta (36 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short 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    <->  4939 MME   (   1-)  P      C    1.37    1.33  INTRA B3
4703 MET   (   2-)  P      CA   <->  4939 MME   (   1-)  P      C    0.77    2.43  INTRA
3410 GLN   ( 156-)  H    A NE2  <->  4947 HOH   (1135 )  H      O    0.66    2.04  INTRA
2620 HIS   ( 298-)  F      ND1  <->  2624 ASP   ( 302-)  F      OD2  0.39    2.31  INTRA
 290 HIS   ( 298-)  A      ND1  <->   294 ASP   ( 302-)  A      OD2  0.35    2.35  INTRA
3226 ARG   ( 439-)  G      NH1  <->  4946 HOH   (1285 )  G      O    0.35    2.35  INTRA BF
 757 HIS   ( 298-)  B      ND1  <->   761 ASP   ( 302-)  B      OD2  0.34    2.36  INTRA
2589 HIS   ( 267-)  F      CD2  <->  2599 ASN   ( 277-)  F      ND2  0.33    2.77  INTRA BL
3054 HIS   ( 267-)  G      CD2  <->  3064 ASN   ( 277-)  G      ND2  0.32    2.78  INTRA BL
3521 HIS   ( 267-)  H      CD2  <->  3531 ASN   ( 277-)  H      ND2  0.32    2.78  INTRA BL
 259 HIS   ( 267-)  A      CD2  <->   269 ASN   ( 277-)  A      ND2  0.32    2.78  INTRA BL
1659 HIS   ( 267-)  D      CD2  <->  1669 ASN   ( 277-)  D      ND2  0.31    2.79  INTRA BL
2124 HIS   ( 267-)  E      CD2  <->  2134 ASN   ( 277-)  E      ND2  0.31    2.79  INTRA BL
 726 HIS   ( 267-)  B      CD2  <->   736 ASN   ( 277-)  B      ND2  0.29    2.81  INTRA BL
1690 HIS   ( 298-)  D      ND1  <->  1694 ASP   ( 302-)  D      OD2  0.29    2.41  INTRA
2155 HIS   ( 298-)  E      ND1  <->  2159 ASP   ( 302-)  E      OD2  0.29    2.41  INTRA
3085 HIS   ( 298-)  G      ND1  <->  3089 ASP   ( 302-)  G      OD2  0.29    2.41  INTRA
1193 HIS   ( 267-)  C      CD2  <->  1203 ASN   ( 277-)  C      ND2  0.28    2.82  INTRA BL
3552 HIS   ( 298-)  H      ND1  <->  3556 ASP   ( 302-)  H      OD2  0.27    2.43  INTRA
3412 GLU   ( 158-)  H      OE2  <->  3579 HIS   ( 325-)  H      NE2  0.27    2.43  INTRA BL
1224 HIS   ( 298-)  C      ND1  <->  1228 ASP   ( 302-)  C      OD2  0.26    2.44  INTRA
4477 ASN   (  54-)  N      ND2  <->  4953 HOH   (1046 )  N      O    0.23    2.47  INTRA
 617 GLU   ( 158-)  B      OE2  <->   784 HIS   ( 325-)  B      NE2  0.22    2.48  INTRA BL
3877 LYS   (  10-)  J      NZ   <->  4949 HOH   (1006 )  J      O    0.22    2.48  INTRA
1084 GLU   ( 158-)  C      OE2  <->  1251 HIS   ( 325-)  C      NE2  0.21    2.49  INTRA
And so on for a total of 275 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.

3951 ARG   (  84-)  J      -6.95
4785 ARG   (  84-)  P      -6.89
3812 ARG   (  84-)  I      -6.82
4507 ARG   (  84-)  N      -6.81
4229 ARG   (  84-)  L      -6.81
4090 ARG   (  84-)  K      -6.78
4368 ARG   (  84-)  M      -6.68
4646 ARG   (  84-)  O      -6.55
 431 ARG   ( 439-)  A      -5.80
3226 ARG   ( 439-)  G      -5.79
2296 ARG   ( 439-)  E      -5.78
2761 ARG   ( 439-)  F      -5.78
3693 ARG   ( 439-)  H      -5.77
1365 ARG   ( 439-)  C      -5.76
 443 TRP   ( 451-)  A      -5.67
1377 TRP   ( 451-)  C      -5.66
2773 TRP   ( 451-)  F      -5.66
3705 TRP   ( 451-)  H      -5.65
2308 TRP   ( 451-)  E      -5.65
1843 TRP   ( 451-)  D      -5.64
3238 TRP   ( 451-)  G      -5.63
 910 TRP   ( 451-)  B      -5.62
1871 LYS   (  14-)  E      -5.59
2796 LYS   ( 474-)  F      -5.57
 466 LYS   ( 474-)  A      -5.57
And so on for a total of 100 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.

2621 ALA   ( 299-)  F   -2.83
3086 ALA   ( 299-)  G   -2.81
2156 ALA   ( 299-)  E   -2.81
1363 LEU   ( 437-)  C   -2.81
 758 ALA   ( 299-)  B   -2.79
3224 LEU   ( 437-)  G   -2.79
2759 LEU   ( 437-)  F   -2.78
1422 VAL   (  30-)  D   -2.78
1691 ALA   ( 299-)  D   -2.78
3553 ALA   ( 299-)  H   -2.78
1225 ALA   ( 299-)  C   -2.77
3844 VAL   ( 116-)  I   -2.77
2294 LEU   ( 437-)  E   -2.76
 896 LEU   ( 437-)  B   -2.75
1829 LEU   ( 437-)  D   -2.75
 429 LEU   ( 437-)  A   -2.74
 291 ALA   ( 299-)  A   -2.74
3691 LEU   ( 437-)  H   -2.72
2894 LEU   ( 107-)  G   -2.58
 566 LEU   ( 107-)  B   -2.58
1033 LEU   ( 107-)  C   -2.58
1499 LEU   ( 107-)  D   -2.57
  99 LEU   ( 107-)  A   -2.57
1964 LEU   ( 107-)  E   -2.56
3361 LEU   ( 107-)  H   -2.56
2429 LEU   ( 107-)  F   -2.55

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.

4053 ALA   (  47-)  K     - 4056 ALA   (  50-)  K        -1.87
4192 ALA   (  47-)  L     - 4195 ALA   (  50-)  L        -1.86
4331 ALA   (  47-)  M     - 4334 ALA   (  50-)  M        -1.89

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.

4941 HOH   (1270 )  B      O
4944 HOH   (1018 )  E      O
4953 HOH   (1102 )  N      O
4954 HOH   (1105 )  O      O
ERROR. No convergence in HB2STD
Old,New value: 6332.751 6332.768
ERROR. No convergence in HB2STD
Old,New value: 6337.950 6337.961

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.

 148 GLN   ( 156-)  A
 221 GLN   ( 229-)  A
 230 HIS   ( 238-)  A
 233 ASN   ( 241-)  A
 259 HIS   ( 267-)  A
 269 ASN   ( 277-)  A
 296 GLN   ( 304-)  A
 319 HIS   ( 327-)  A
 412 ASN   ( 420-)  A
 424 ASN   ( 432-)  A
 615 GLN   ( 156-)  B
 688 GLN   ( 229-)  B
 697 HIS   ( 238-)  B
 700 ASN   ( 241-)  B
 726 HIS   ( 267-)  B
 736 ASN   ( 277-)  B
 763 GLN   ( 304-)  B
 786 HIS   ( 327-)  B
 845 HIS   ( 386-)  B
 879 ASN   ( 420-)  B
 891 ASN   ( 432-)  B
1082 GLN   ( 156-)  C
1155 GLN   ( 229-)  C
1164 HIS   ( 238-)  C
1167 ASN   ( 241-)  C
And so on for a total of 130 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.

  26 THR   (  34-)  A      N
  57 THR   (  65-)  A      OG1
  59 THR   (  67-)  A      N
  75 ARG   (  83-)  A      NH1
 159 ARG   ( 167-)  A      N
 165 THR   ( 173-)  A      OG1
 167 LYS   ( 175-)  A      N
 167 LYS   ( 175-)  A      NZ
 170 LEU   ( 178-)  A      N
 171 GLY   ( 179-)  A      N
 203 PHE   ( 211-)  A      N
 209 ARG   ( 217-)  A      NH1
 231 TYR   ( 239-)  A      OH
 238 THR   ( 246-)  A      N
 263 THR   ( 271-)  A      OG1
 287 ARG   ( 295-)  A      NE
 287 ARG   ( 295-)  A      NH1
 332 GLU   ( 340-)  A      N
 371 SER   ( 379-)  A      N
 373 GLY   ( 381-)  A      N
 375 HIS   ( 383-)  A      N
 393 GLN   ( 401-)  A      NE2
 396 GLY   ( 404-)  A      N
 405 ASN   ( 413-)  A      ND2
 524 THR   (  65-)  B      OG1
And so on for a total of 240 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.

 145 HIS   ( 153-)  A      NE2
 260 ASP   ( 268-)  A      OD1
 260 ASP   ( 268-)  A      OD2
 284 HIS   ( 292-)  A      NE2
 378 HIS   ( 386-)  A      NE2
 727 ASP   ( 268-)  B      OD1
 727 ASP   ( 268-)  B      OD2
 751 HIS   ( 292-)  B      NE2
1194 ASP   ( 268-)  C      OD1
1194 ASP   ( 268-)  C      OD2
1253 HIS   ( 327-)  C      ND1
1312 HIS   ( 386-)  C      NE2
1660 ASP   ( 268-)  D      OD1
1678 ASP   ( 286-)  D      OD2
1719 HIS   ( 327-)  D      ND1
2125 ASP   ( 268-)  E      OD1
2125 ASP   ( 268-)  E      OD2
2149 HIS   ( 292-)  E      NE2
2590 ASP   ( 268-)  F      OD1
2590 ASP   ( 268-)  F      OD2
2614 HIS   ( 292-)  F      NE2
2859 ASP   (  72-)  G      OD1
3055 ASP   ( 268-)  G      OD1
3055 ASP   ( 268-)  G      OD2
3173 HIS   ( 386-)  G      NE2
3522 ASP   ( 268-)  H      OD1
3546 HIS   ( 292-)  H      NE2
3640 HIS   ( 386-)  H      NE2
4154 ASN   (   9-)  L      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.

4940 HOH   (1124 )  A      O  1.01  K  4 NCS 7/7
4940 HOH   (1143 )  A      O  0.99  K  4 NCS 7/7
4940 HOH   (1163 )  A      O  1.10  K  4 NCS 7/7
4940 HOH   (1173 )  A      O  1.00  K  4 Ion-B NCS 7/7
4940 HOH   (1196 )  A      O  1.06  K  4 NCS 7/7
4940 HOH   (1252 )  A      O  0.87  K  4 NCS 7/7
4940 HOH   (1269 )  A      O  1.01  K  5 Ion-B NCS 7/7
4941 HOH   (1089 )  B      O  0.88  K  5 NCS 7/7
4941 HOH   (1136 )  B      O  0.99  K  4 NCS 7/7
4941 HOH   (1174 )  B      O  1.15  K  4 NCS 7/7
4941 HOH   (1208 )  B      O  0.87  K  4 NCS 7/7
4941 HOH   (1276 )  B      O  1.12  K  4 NCS 7/7
4941 HOH   (1280 )  B      O  1.10  K  4 NCS 7/7
4942 HOH   (1127 )  C      O  1.06  K  4 NCS 7/7
4943 HOH   (1129 )  D      O  1.02  K  4 NCS 7/7
4943 HOH   (1146 )  D      O  1.01  K  4 NCS 7/7
4943 HOH   (1177 )  D      O  0.88  K  4 NCS 7/7
4943 HOH   (1242 )  D      O  0.95  K  4 NCS 7/7
4943 HOH   (1271 )  D      O  0.92  K  4 Ion-B NCS 7/7
4943 HOH   (1291 )  D      O  0.96  K  5 ION-B
4944 HOH   (1058 )  E      O  0.90  K  4 Ion-B NCS 7/7
4944 HOH   (1085 )  E      O  0.87  K  5 NCS 7/7
4944 HOH   (1133 )  E      O  1.00  K  4 NCS 7/7
4944 HOH   (1169 )  E      O  1.14  K  4 NCS 7/7
4944 HOH   (1179 )  E      O  0.85  K  4 NCS 7/7
4944 HOH   (1209 )  E      O  0.87  K  4 NCS 7/7
4944 HOH   (1241 )  E      O  1.01  K  4 NCS 7/7
4944 HOH   (1283 )  E      O  0.94  K  4 NCS 7/7
4944 HOH   (1285 )  E      O  0.87  K  4 NCS 7/7
4945 HOH   (1168 )  F      O  1.13  K  4 NCS 7/7
4945 HOH   (1177 )  F      O  0.91  K  4 Ion-B NCS 7/7
4945 HOH   (1260 )  F      O  0.94  K  5 ION-B NCS 2/2
4945 HOH   (1330 )  F      O  1.03  K  4 ION-B NCS 1/1
4946 HOH   (1052 )  G      O  0.90  K  4 Ion-B NCS 7/7
4946 HOH   (1159 )  G      O  1.15  K  4 NCS 7/7
4946 HOH   (1228 )  G      O  1.14  K  4 NCS 7/7
4946 HOH   (1261 )  G      O  0.96  K  5 NCS 7/7
4946 HOH   (1266 )  G      O  0.89  K  4 NCS 7/7
4947 HOH   (1058 )  H      O  1.06  K  4 Ion-B NCS 7/7
4947 HOH   (1138 )  H      O  1.00  K  4 NCS 7/7
4947 HOH   (1175 )  H      O  1.15  K  4 NCS 7/7
4947 HOH   (1186 )  H      O  0.86  K  4 NCS 7/7
4947 HOH   (1287 )  H      O  0.94  K  4 NCS 7/7
4948 HOH   (1029 )  I      O  0.96  K  4 NCS 7/7
4949 HOH   (1039 )  J      O  0.94  K  4 NCS 7/7
4950 HOH   (1036 )  K      O  0.98  K  4 NCS 7/7
4951 HOH   (1040 )  L      O  0.95  K  4 NCS 7/7
4953 HOH   (1039 )  N      O  0.95  K  4 NCS 7/7
4954 HOH   (1042 )  O      O  0.92  K  4 NCS 7/7
4955 HOH   (1037 )  P      O  1.06  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.

  44 GLU   (  52-)  A   H-bonding suggests Gln; Ligand-contact
 260 ASP   ( 268-)  A   H-bonding suggests Asn; but Alt-Rotamer
 511 GLU   (  52-)  B   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
 727 ASP   ( 268-)  B   H-bonding suggests Asn; but Alt-Rotamer
 761 ASP   ( 302-)  B   H-bonding suggests Asn
 978 GLU   (  52-)  C   H-bonding suggests Gln; Ligand-contact
1194 ASP   ( 268-)  C   H-bonding suggests Asn; but Alt-Rotamer
1444 GLU   (  52-)  D   H-bonding suggests Gln; Ligand-contact
1660 ASP   ( 268-)  D   H-bonding suggests Asn; but Alt-Rotamer
1694 ASP   ( 302-)  D   H-bonding suggests Asn
1909 GLU   (  52-)  E   H-bonding suggests Gln; Ligand-contact
2017 ASP   ( 160-)  E   H-bonding suggests Asn; but Alt-Rotamer
2125 ASP   ( 268-)  E   H-bonding suggests Asn; but Alt-Rotamer
2159 ASP   ( 302-)  E   H-bonding suggests Asn
2374 GLU   (  52-)  F   H-bonding suggests Gln; Ligand-contact
2590 ASP   ( 268-)  F   H-bonding suggests Asn; but Alt-Rotamer
2624 ASP   ( 302-)  F   H-bonding suggests Asn
2839 GLU   (  52-)  G   H-bonding suggests Gln; Ligand-contact
3055 ASP   ( 268-)  G   H-bonding suggests Asn; but Alt-Rotamer
3089 ASP   ( 302-)  G   H-bonding suggests Asn
3306 GLU   (  52-)  H   H-bonding suggests Gln; Ligand-contact
3414 ASP   ( 160-)  H   H-bonding suggests Asn; but Alt-Rotamer
3522 ASP   ( 268-)  H   H-bonding suggests Asn
3556 ASP   ( 302-)  H   H-bonding suggests Asn
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 :  -0.549
  2nd generation packing quality :  -0.223
  Ramachandran plot appearance   :  -0.035
  chi-1/chi-2 rotamer normality  :  -0.435
  Backbone conformation          :  -0.550

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.457 (tight)
  Bond angles                    :   0.654 (tight)
  Omega angle restraints         :   1.080
  Side chain planarity           :   0.549 (tight)
  Improper dihedral distribution :   0.684
  B-factor distribution          :   0.403
  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 : 1.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -0.7
  Ramachandran plot appearance   :  -0.6
  chi-1/chi-2 rotamer normality  :  -0.9
  Backbone conformation          :  -1.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.457 (tight)
  Bond angles                    :   0.654 (tight)
  Omega angle restraints         :   1.080
  Side chain planarity           :   0.549 (tight)
  Improper dihedral distribution :   0.684
  B-factor distribution          :   0.403
  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.