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 pdb2vdi.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 : 0.091
CA-only RMS fit for the two chains : 0.057

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 : 0.122
CA-only RMS fit for the two chains : 0.064

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 : 0.068
CA-only RMS fit for the two chains : 0.050

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 : 0.070
CA-only RMS fit for the two chains : 0.052

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 : 0.115
CA-only RMS fit for the two chains : 0.056

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.

4844 MME   (   1-)  I  -
4846 MME   (   1-)  J  -
4848 MME   (   1-)  K  -
4850 MME   (   1-)  L  -
4852 MME   (   1-)  M  -
4854 MME   (   1-)  N  -
4856 MME   (   1-)  O  -
4860 CAP   (1477-)  A  -
4866 CAP   (1477-)  B  -
4872 CAP   (1477-)  C  -
4877 CAP   (1477-)  D  -
4882 CAP   (1477-)  E  -
4889 CAP   (1477-)  F  -
4897 CAP   (1477-)  G  -
4917 CAP   (1477-)  H  -
4918 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.

3725 MET   (   2-)  I  -   N   bound to 4844 MME   (   1-)  I  -   C
3864 MET   (   2-)  J  -   N   bound to 4846 MME   (   1-)  J  -   C
4003 MET   (   2-)  K  -   N   bound to 4848 MME   (   1-)  K  -   C
4142 MET   (   2-)  L  -   N   bound to 4850 MME   (   1-)  L  -   C
4281 MET   (   2-)  M  -   N   bound to 4852 MME   (   1-)  M  -   C
4420 MET   (   2-)  N  -   N   bound to 4854 MME   (   1-)  N  -   C
4559 MET   (   2-)  O  -   N   bound to 4856 MME   (   1-)  O  -   C
4698 MET   (   2-)  P  -   N   bound to 4918 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: Missing atoms

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

4550 PHE   ( 132-)  N      CZ

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
1110 ARG   ( 187-)  C
1575 ARG   ( 187-)  D
2040 ARG   ( 187-)  E
2505 ARG   ( 187-)  F
2971 ARG   ( 187-)  G
3436 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

  75 TYR   (  85-)  A
  87 TYR   (  97-)  A
  93 TYR   ( 103-)  A
 543 TYR   (  85-)  B
 555 TYR   (  97-)  B
 741 TYR   ( 283-)  B
1008 TYR   (  85-)  C
1026 TYR   ( 103-)  C
1485 TYR   (  97-)  D
1491 TYR   ( 103-)  D
1671 TYR   ( 283-)  D
1938 TYR   (  85-)  E
1956 TYR   ( 103-)  E
2136 TYR   ( 283-)  E
2206 TYR   ( 353-)  E
2403 TYR   (  85-)  F
2421 TYR   ( 103-)  F
2881 TYR   (  97-)  G
2887 TYR   ( 103-)  G
3346 TYR   (  97-)  H
3352 TYR   ( 103-)  H
3774 TYR   (  51-)  I
3790 TYR   (  67-)  I
3913 TYR   (  51-)  J
3929 TYR   (  67-)  J
4052 TYR   (  51-)  K
4068 TYR   (  67-)  K
4105 TYR   ( 104-)  K
4191 TYR   (  51-)  L
4207 TYR   (  67-)  L
4330 TYR   (  51-)  M
4346 TYR   (  67-)  M
4469 TYR   (  51-)  N
4485 TYR   (  67-)  N
4608 TYR   (  51-)  O
4624 TYR   (  67-)  O
4747 TYR   (  51-)  P
4763 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
1325 PHE   ( 402-)  C
1790 PHE   ( 402-)  D
2255 PHE   ( 402-)  E
2720 PHE   ( 402-)  F
3186 PHE   ( 402-)  G
3735 PHE   (  12-)  I
3738 PHE   (  15-)  I
3767 PHE   (  44-)  I
3783 PHE   (  60-)  I
3823 PHE   ( 100-)  I
3855 PHE   ( 132-)  I
3874 PHE   (  12-)  J
3877 PHE   (  15-)  J
3906 PHE   (  44-)  J
3922 PHE   (  60-)  J
3962 PHE   ( 100-)  J
3983 PHE   ( 121-)  J
3994 PHE   ( 132-)  J
4013 PHE   (  12-)  K
4016 PHE   (  15-)  K
4045 PHE   (  44-)  K
4061 PHE   (  60-)  K
4101 PHE   ( 100-)  K
And so on for a total of 57 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.

3854 ASP   ( 131-)  I
3993 ASP   ( 131-)  J
4132 ASP   ( 131-)  K
4271 ASP   ( 131-)  L
4410 ASP   ( 131-)  M
4549 ASP   ( 131-)  N
4688 ASP   ( 131-)  O
4827 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
 450 GLU   ( 460-)  A
 546 GLU   (  88-)  B
 918 GLU   ( 460-)  B
1011 GLU   (  88-)  C
1383 GLU   ( 460-)  C
1476 GLU   (  88-)  D
1848 GLU   ( 460-)  D
1941 GLU   (  88-)  E
2313 GLU   ( 460-)  E
2406 GLU   (  88-)  F
2778 GLU   ( 460-)  F
2872 GLU   (  88-)  G
3244 GLU   ( 460-)  G
3337 GLU   (  88-)  H
3709 GLU   ( 460-)  H
3769 GLU   (  46-)  I
3778 GLU   (  55-)  I
3908 GLU   (  46-)  J
3917 GLU   (  55-)  J
4047 GLU   (  46-)  K
4056 GLU   (  55-)  K
4186 GLU   (  46-)  L
4195 GLU   (  55-)  L
4325 GLU   (  46-)  M
4334 GLU   (  55-)  M
4464 GLU   (  46-)  N
4473 GLU   (  55-)  N
4603 GLU   (  46-)  O
4612 GLU   (  55-)  O
4742 GLU   (  46-)  P
4751 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
1124 KCX   ( 201-)  C      CH     CX
1124 KCX   ( 201-)  C      OX1    OQ1
1124 KCX   ( 201-)  C      OX2    OQ2
1589 KCX   ( 201-)  D      CH     CX
1589 KCX   ( 201-)  D      OX1    OQ1
1589 KCX   ( 201-)  D      OX2    OQ2
2054 KCX   ( 201-)  E      CH     CX
2054 KCX   ( 201-)  E      OX1    OQ1
2054 KCX   ( 201-)  E      OX2    OQ2
2519 KCX   ( 201-)  F      CH     CX
2519 KCX   ( 201-)  F      OX1    OQ1
2519 KCX   ( 201-)  F      OX2    OQ2
2985 KCX   ( 201-)  G      CH     CX
2985 KCX   ( 201-)  G      OX1    OQ1
2985 KCX   ( 201-)  G      OX2    OQ2
3450 KCX   ( 201-)  H      CH     CX
3450 KCX   ( 201-)  H      OX1    OQ1
3450 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.

4837 LEU   ( 475-)  A      SG  -SG*   2.44   10.1
4837 LEU   ( 475-)  A      SG  -SG*   2.44   10.1

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

 |  0.997680  0.000018 -0.000022|
 |  0.000018  0.997445  0.000089|
 | -0.000022  0.000089  0.997550|
Proposed new scale matrix

 |  0.008295  0.000000  0.004367|
 |  0.000000  0.005625  0.000000|
 |  0.000000  0.000000  0.009217|
With corresponding cell

    A    = 120.550  B   = 177.766  C    = 122.617
    Alpha=  90.001  Beta= 117.764  Gamma=  90.001

The CRYST1 cell dimensions

    A    = 120.831  B   = 178.206  C    = 122.917
    Alpha=  90.000  Beta= 117.760  Gamma=  90.000

Variance: 960.796
(Under-)estimated Z-score: 22.844

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.

 228 HIS   ( 238-)  A      CG   ND1  CE1 109.63    4.0
 696 HIS   ( 238-)  B      CG   ND1  CE1 109.62    4.0
1292 SMC   ( 369-)  C      N    CA   CB  103.24   -4.3
3516 HIS   ( 267-)  H      CG   ND1  CE1 109.62    4.0

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
 450 GLU   ( 460-)  A
 546 GLU   (  88-)  B
 645 ARG   ( 187-)  B
 918 GLU   ( 460-)  B
1011 GLU   (  88-)  C
1110 ARG   ( 187-)  C
1383 GLU   ( 460-)  C
1476 GLU   (  88-)  D
1575 ARG   ( 187-)  D
1848 GLU   ( 460-)  D
1941 GLU   (  88-)  E
2040 ARG   ( 187-)  E
2313 GLU   ( 460-)  E
2406 GLU   (  88-)  F
2505 ARG   ( 187-)  F
2778 GLU   ( 460-)  F
2872 GLU   (  88-)  G
2971 ARG   ( 187-)  G
3244 GLU   ( 460-)  G
3337 GLU   (  88-)  H
3436 ARG   ( 187-)  H
3709 GLU   ( 460-)  H
3769 GLU   (  46-)  I
3778 GLU   (  55-)  I
3854 ASP   ( 131-)  I
3908 GLU   (  46-)  J
3917 GLU   (  55-)  J
3993 ASP   ( 131-)  J
4047 GLU   (  46-)  K
4056 GLU   (  55-)  K
4132 ASP   ( 131-)  K
4186 GLU   (  46-)  L
4195 GLU   (  55-)  L
4271 ASP   ( 131-)  L
4325 GLU   (  46-)  M
4334 GLU   (  55-)  M
4410 ASP   ( 131-)  M
4464 GLU   (  46-)  N
4473 GLU   (  55-)  N
4549 ASP   ( 131-)  N
4603 GLU   (  46-)  O
4612 GLU   (  55-)  O
4688 ASP   ( 131-)  O
4742 GLU   (  46-)  P
4751 GLU   (  55-)  P
4827 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.

1225 ASP   ( 302-)  C    4.80
3551 ASP   ( 302-)  H    4.60
 760 ASP   ( 302-)  B    4.51
 292 ASP   ( 302-)  A    4.26
1690 ASP   ( 302-)  D    4.24
2620 ASP   ( 302-)  F    4.13
2155 ASP   ( 302-)  E    4.02

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.

1187 ILE   ( 264-)  C    -2.3
3513 ILE   ( 264-)  H    -2.3
3980 ILE   ( 118-)  J    -2.3
2582 ILE   ( 264-)  F    -2.3
4258 ILE   ( 118-)  L    -2.3
4814 ILE   ( 118-)  P    -2.3
3841 ILE   ( 118-)  I    -2.3
4119 ILE   ( 118-)  K    -2.3
4085 ARG   (  84-)  K    -2.3
4397 ILE   ( 118-)  M    -2.3
4536 ILE   ( 118-)  N    -2.3
1453 THR   (  65-)  D    -2.3
4675 ILE   ( 118-)  O    -2.3
 988 THR   (  65-)  C    -2.2
 523 THR   (  65-)  B    -2.2
4563 PRO   (   6-)  O    -2.2
2383 THR   (  65-)  F    -2.2
4812 VAL   ( 116-)  P    -2.2
4277 LYS   ( 137-)  L    -2.2
  55 THR   (  65-)  A    -2.2
4395 VAL   ( 116-)  M    -2.2
3978 VAL   ( 116-)  J    -2.2
3324 THR   (  75-)  H    -2.2
4673 VAL   ( 116-)  O    -2.2
3379 LEU   ( 130-)  H    -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.

  31 ARG   (  41-)  A  omega poor
  52 SER   (  62-)  A  Poor phi/psi
  53 THR   (  63-)  A  Poor phi/psi
  65 THR   (  75-)  A  Poor phi/psi
 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
 581 ASN   ( 123-)  B  omega poor
 621 ASN   ( 163-)  B  Poor phi/psi
 633 LYS   ( 175-)  B  PRO omega poor
 657 PHE   ( 199-)  B  omega poor
 665 ASN   ( 207-)  B  Poor phi/psi
 721 PRO   ( 263-)  B  omega poor
 755 MET   ( 297-)  B  Poor phi/psi
 759 ILE   ( 301-)  B  omega poor
And so on for a total of 171 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.

 737 SER   ( 279-)  B    0.36
2132 SER   ( 279-)  E    0.37
 269 SER   ( 279-)  A    0.37
1667 SER   ( 279-)  D    0.37
3063 SER   ( 279-)  G    0.38
3528 SER   ( 279-)  H    0.39

Warning: Unusual backbone conformations

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

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

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

   5 ALA   (  15-)  A      0
  13 THR   (  23-)  A      0
  14 TYR   (  24-)  A      0
  15 TYR   (  25-)  A      0
  16 THR   (  26-)  A      0
  19 TYR   (  29-)  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
  65 THR   (  75-)  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
  86 GLN   (  96-)  A      0
  94 HYP   ( 104-)  A      0
 100 GLU   ( 110-)  A      0
 110 ILE   ( 120-)  A      0
 111 VAL   ( 121-)  A      0
 113 ASN   ( 123-)  A      0
And so on for a total of 1856 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!

1260 GLY   ( 337-)  C   2.42   12
2655 GLY   ( 337-)  F   2.38   10
 327 GLY   ( 337-)  A   2.33   13
1725 GLY   ( 337-)  D   2.31   11
3586 GLY   ( 337-)  H   2.29   11
 795 GLY   ( 337-)  B   2.23   13
2190 GLY   ( 337-)  E   2.17   11
3121 GLY   ( 337-)  G   2.14   17
3654 GLY   ( 405-)  H   1.52   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]

  94 HYP   ( 104-)  A    0.09 LOW
 562 HYP   ( 104-)  B    0.08 LOW
1027 HYP   ( 104-)  C    0.06 LOW
1492 HYP   ( 104-)  D    0.13 LOW
1957 HYP   ( 104-)  E    0.13 LOW
2422 HYP   ( 104-)  F    0.10 LOW
2888 HYP   ( 104-)  G    0.09 LOW
3353 HYP   ( 104-)  H    0.13 LOW
3849 PRO   ( 126-)  I    0.05 LOW
3988 PRO   ( 126-)  J    0.04 LOW
4127 PRO   ( 126-)  K    0.09 LOW
4266 PRO   ( 126-)  L    0.03 LOW
4405 PRO   ( 126-)  M    0.10 LOW
4544 PRO   ( 126-)  N    0.07 LOW
4683 PRO   ( 126-)  O    0.08 LOW
4822 PRO   ( 126-)  P    0.08 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].

  34 PRO   (  44-)  A    45.5 half-chair C-delta/C-gamma (54 degrees)
 502 PRO   (  44-)  B    42.1 envelop C-delta (36 degrees)
 967 PRO   (  44-)  C    41.4 envelop C-delta (36 degrees)
1432 PRO   (  44-)  D    43.1 envelop C-delta (36 degrees)
1897 PRO   (  44-)  E    45.4 half-chair C-delta/C-gamma (54 degrees)
2362 PRO   (  44-)  F    36.8 envelop C-delta (36 degrees)
2581 PRO   ( 263-)  F   -65.9 envelop C-beta (-72 degrees)
2728 PRO   ( 410-)  F  -114.7 envelop C-gamma (-108 degrees)
2828 PRO   (  44-)  G    49.9 half-chair C-delta/C-gamma (54 degrees)
3293 PRO   (  44-)  H    52.9 half-chair C-delta/C-gamma (54 degrees)
3340 PRO   (  91-)  H  -114.3 envelop C-gamma (-108 degrees)
3729 PRO   (   6-)  I   -65.3 envelop C-beta (-72 degrees)
4021 PRO   (  20-)  K   103.9 envelop C-beta (108 degrees)
4299 PRO   (  20-)  M   101.5 envelop C-beta (108 degrees)
4319 PRO   (  40-)  M    51.8 half-chair C-delta/C-gamma (54 degrees)
4438 PRO   (  20-)  N    99.2 envelop C-beta (108 degrees)
4563 PRO   (   6-)  O   -60.9 half-chair C-beta/C-alpha (-54 degrees)
4702 PRO   (   6-)  P   -57.2 half-chair C-beta/C-alpha (-54 degrees)
4716 PRO   (  20-)  P   106.0 envelop C-beta (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.

4698 MET   (   2-)  P      N    <->  4918 MME   (   1-)  P      C    1.37    1.33  INTRA B3
4698 MET   (   2-)  P      CA   <->  4918 MME   (   1-)  P      C    0.78    2.42  INTRA
3233 CYS   ( 449-)  G      SG   <->  3243 CYS   ( 459-)  G      SG   0.65    2.80  INTRA
 907 CYS   ( 449-)  B      SG   <->   917 CYS   ( 459-)  B      SG   0.62    2.83  INTRA
2767 CYS   ( 449-)  F      SG   <->  2777 CYS   ( 459-)  F      SG   0.58    2.87  INTRA
1372 CYS   ( 449-)  C      SG   <->  1382 CYS   ( 459-)  C      SG   0.57    2.88  INTRA
3698 CYS   ( 449-)  H      SG   <->  3708 CYS   ( 459-)  H      SG   0.57    2.88  INTRA
 439 CYS   ( 449-)  A      SG   <->   449 CYS   ( 459-)  A      SG   0.55    2.90  INTRA
1837 CYS   ( 449-)  D      SG   <->  1847 CYS   ( 459-)  D      SG   0.55    2.90  INTRA
2120 HIS   ( 267-)  E      CD2  <->  2130 ASN   ( 277-)  E      ND2  0.48    2.62  INTRA BL
2302 CYS   ( 449-)  E      SG   <->  2312 CYS   ( 459-)  E      SG   0.48    2.97  INTRA
3516 HIS   ( 267-)  H      CD2  <->  3526 ASN   ( 277-)  H      ND2  0.39    2.71  INTRA BL
2757 ARG   ( 439-)  F      NH1  <->  4924 HOH   (2128 )  F      O    0.39    2.31  INTRA
 257 HIS   ( 267-)  A      CD2  <->   267 ASN   ( 277-)  A      ND2  0.38    2.72  INTRA BL
 616 GLU   ( 158-)  B      OE2  <->   783 HIS   ( 325-)  B      NE2  0.37    2.33  INTRA BL
1655 HIS   ( 267-)  D      CD2  <->  1665 ASN   ( 277-)  D      ND2  0.35    2.75  INTRA BL
1262 ARG   ( 339-)  C      NE   <->  4921 HOH   (2099 )  C      O    0.34    2.36  INTRA
2585 HIS   ( 267-)  F      CD2  <->  2595 ASN   ( 277-)  F      ND2  0.34    2.76  INTRA BL
 725 HIS   ( 267-)  B      CD2  <->   735 ASN   ( 277-)  B      ND2  0.33    2.77  INTRA BL
1190 HIS   ( 267-)  C      CD2  <->  1200 ASN   ( 277-)  C      ND2  0.33    2.77  INTRA BL
3181 ASP   ( 397-)  G      OD2  <->  4671 LYS   ( 114-)  O      NZ   0.33    2.37  INTRA
3051 HIS   ( 267-)  G      CD2  <->  3061 ASN   ( 277-)  G      ND2  0.33    2.77  INTRA BL
2942 GLU   ( 158-)  G      OE2  <->  3109 HIS   ( 325-)  G      NE2  0.31    2.39  INTRA BL
1546 GLU   ( 158-)  D      OE2  <->  1713 HIS   ( 325-)  D      NE2  0.31    2.39  INTRA BL
4682 ARG   ( 125-)  O      NH1  <->  4933 HOH   (2033 )  O      O    0.30    2.40  INTRA
And so on for a total of 411 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.

4363 ARG   (  84-)  M      -7.54
4224 ARG   (  84-)  L      -7.22
4780 ARG   (  84-)  P      -7.03
3807 ARG   (  84-)  I      -7.03
3946 ARG   (  84-)  J      -6.90
4548 ARG   ( 130-)  N      -6.90
4502 ARG   (  84-)  N      -6.72
4085 ARG   (  84-)  K      -6.66
1362 ARG   ( 439-)  C      -6.50
4641 ARG   (  84-)  O      -6.29
2757 ARG   ( 439-)  F      -5.80
 429 ARG   ( 439-)  A      -5.79
3223 ARG   ( 439-)  G      -5.79
1827 ARG   ( 439-)  D      -5.77
2292 ARG   ( 439-)  E      -5.77
 897 ARG   ( 439-)  B      -5.74
4634 LYS   (  77-)  O      -5.54
3723 LYS   ( 474-)  H      -5.52
 937 LYS   (  14-)  C      -5.52
1862 LYS   ( 474-)  D      -5.52
3688 ARG   ( 439-)  H      -5.51
4217 LYS   (  77-)  L      -5.51
1374 TRP   ( 451-)  C      -5.50
2332 LYS   (  14-)  F      -5.50
 464 LYS   ( 474-)  A      -5.50
And so on for a total of 94 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.

3548 ALA   ( 299-)  H   -2.81
4534 VAL   ( 116-)  N   -2.81
2152 ALA   ( 299-)  E   -2.81
1687 ALA   ( 299-)  D   -2.78
 757 ALA   ( 299-)  B   -2.78
4117 VAL   ( 116-)  K   -2.78
2617 ALA   ( 299-)  F   -2.78
3083 ALA   ( 299-)  G   -2.78
1222 ALA   ( 299-)  C   -2.77
2755 LEU   ( 437-)  F   -2.77
2290 LEU   ( 437-)  E   -2.77
1825 LEU   ( 437-)  D   -2.76
 289 ALA   ( 299-)  A   -2.75
3221 LEU   ( 437-)  G   -2.73
1030 LEU   ( 107-)  C   -2.60
1495 LEU   ( 107-)  D   -2.59
1960 LEU   ( 107-)  E   -2.59
  97 LEU   ( 107-)  A   -2.57
2891 LEU   ( 107-)  G   -2.57
2425 LEU   ( 107-)  F   -2.57
 565 LEU   ( 107-)  B   -2.56
3356 LEU   ( 107-)  H   -2.55
4008 VAL   (   7-)  K   -2.50

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.

4920 HOH   (2010 )  B      O
4920 HOH   (2116 )  B      O
4922 HOH   (2036 )  D      O
4922 HOH   (2141 )  D      O
4922 HOH   (2147 )  D      O
4924 HOH   (2044 )  F      O
4925 HOH   (2153 )  G      O
4929 HOH   (2031 )  K      O
4930 HOH   (2001 )  L      O
4933 HOH   (2009 )  O      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.

 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
 614 GLN   ( 156-)  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
 859 GLN   ( 401-)  B
 878 ASN   ( 420-)  B
 890 ASN   ( 432-)  B
1076 HIS   ( 153-)  C
1079 GLN   ( 156-)  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.

  55 THR   (  65-)  A      OG1
  57 THR   (  67-)  A      N
  86 GLN   (  96-)  A      N
 114 VAL   ( 124-)  A      N
 151 LYS   ( 161-)  A      NZ
 157 ARG   ( 167-)  A      N
 163 THR   ( 173-)  A      N
 165 LYS   ( 175-)  A      N
 165 LYS   ( 175-)  A      NZ
 168 LEU   ( 178-)  A      N
 169 GLY   ( 179-)  A      N
 191 KCX   ( 201-)  A      OX2
 201 PHE   ( 211-)  A      N
 207 ARG   ( 217-)  A      NH1
 229 TYR   ( 239-)  A      OH
 285 ARG   ( 295-)  A      NE
 285 ARG   ( 295-)  A      NH1
 293 ARG   ( 303-)  A      NE
 363 GLY   ( 373-)  A      N
 371 GLY   ( 381-)  A      N
 391 GLN   ( 401-)  A      NE2
 393 GLY   ( 403-)  A      N
 394 GLY   ( 404-)  A      N
 403 ASN   ( 413-)  A      ND2
 419 GLN   ( 429-)  A      NE2
And so on for a total of 316 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.

 143 HIS   ( 153-)  A      NE2
 148 GLU   ( 158-)  A      OE1
 258 ASP   ( 268-)  A      OD1
 258 ASP   ( 268-)  A      OD2
 317 HIS   ( 327-)  A      ND1
 616 GLU   ( 158-)  B      OE1
 726 ASP   ( 268-)  B      OD1
 726 ASP   ( 268-)  B      OD2
 750 HIS   ( 292-)  B      NE2
1081 GLU   ( 158-)  C      OE1
1191 ASP   ( 268-)  C      OD1
1191 ASP   ( 268-)  C      OD2
1250 HIS   ( 327-)  C      ND1
1324 GLN   ( 401-)  C      OE1
1656 ASP   ( 268-)  D      OD1
1656 ASP   ( 268-)  D      OD2
1715 HIS   ( 327-)  D      ND1
1789 GLN   ( 401-)  D      OE1
1925 ASP   (  72-)  E      OD1
2011 GLU   ( 158-)  E      OE1
2121 ASP   ( 268-)  E      OD1
2121 ASP   ( 268-)  E      OD2
2239 HIS   ( 386-)  E      NE2
2254 GLN   ( 401-)  E      OE1
2586 ASP   ( 268-)  F      OD1
2586 ASP   ( 268-)  F      OD2
2645 HIS   ( 327-)  F      ND1
2856 ASP   (  72-)  G      OD1
3052 ASP   ( 268-)  G      OD1
3052 ASP   ( 268-)  G      OD2
3111 HIS   ( 327-)  G      ND1
3185 GLN   ( 401-)  G      OE1
3517 ASP   ( 268-)  H      OD1
3517 ASP   ( 268-)  H      OD2
3576 HIS   ( 327-)  H      ND1
4010 ASN   (   9-)  K      OD1
4149 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.

4923 HOH   (2034 )  E      O  0.99  K  4 Ion-B NCS 1/1
4927 HOH   (2002 )  I      O  0.92  K  4 NCS 3/3
4928 HOH   (2033 )  J      O  0.92  K  4 NCS 5/5
4933 HOH   (2029 )  O      O  0.95  K  4 NCS 5/5

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.

   9 ASP   (  19-)  A   H-bonding suggests Asn; but Alt-Rotamer
  42 GLU   (  52-)  A   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
 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
1191 ASP   ( 268-)  C   H-bonding suggests Asn; but Alt-Rotamer
1440 GLU   (  52-)  D   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
1656 ASP   ( 268-)  D   H-bonding suggests Asn; but Alt-Rotamer
1905 GLU   (  52-)  E   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
2121 ASP   ( 268-)  E   H-bonding suggests Asn; but Alt-Rotamer
2155 ASP   ( 302-)  E   H-bonding suggests Asn
2370 GLU   (  52-)  F   H-bonding suggests Gln; Ligand-contact
2390 ASP   (  72-)  F   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
2586 ASP   ( 268-)  F   H-bonding suggests Asn; but Alt-Rotamer
3052 ASP   ( 268-)  G   H-bonding suggests Asn; but Alt-Rotamer
3301 GLU   (  52-)  H   H-bonding suggests Gln; Ligand-contact
3517 ASP   ( 268-)  H   H-bonding suggests Asn; but Alt-Rotamer
3722 ASP   ( 473-)  H   H-bonding suggests Asn; Ligand-contact
4612 GLU   (  55-)  O   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 :  -0.740
  2nd generation packing quality :  -0.266
  Ramachandran plot appearance   :  -0.887
  chi-1/chi-2 rotamer normality  :  -1.582
  Backbone conformation          :  -0.562

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.426 (tight)
  Bond angles                    :   0.584 (tight)
  Omega angle restraints         :   1.020
  Side chain planarity           :   0.315 (tight)
  Improper dihedral distribution :   0.572
  B-factor distribution          :   0.368
  Inside/Outside distribution    :   1.056

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 : 2.65


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.5
  2nd generation packing quality :   2.0
  Ramachandran plot appearance   :   1.1
  chi-1/chi-2 rotamer normality  :   1.0
  Backbone conformation          :   0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.426 (tight)
  Bond angles                    :   0.584 (tight)
  Omega angle restraints         :   1.020
  Side chain planarity           :   0.315 (tight)
  Improper dihedral distribution :   0.572
  B-factor distribution          :   0.368
  Inside/Outside distribution    :   1.056
==============

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.