WHAT IF Check report

This file was created 2013-12-09 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 pdb3axm.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    = 110.408  B   = 199.624  C    = 111.169
    Alpha=  90.000  Beta=  91.450  Gamma=  90.000

Dimensions of a reduced cell

    A    = 110.408  B   = 111.169  C    = 199.624
    Alpha=  90.000  Beta=  90.000  Gamma=  88.550

Dimensions of the conventional cell

    A    = 154.685  B   = 158.649  C    = 199.624
    Alpha=  90.000  Beta=  90.000  Gamma=  90.394

Transformation to conventional cell

 |  1.000000  0.000000  1.000000|
 |  1.000000  0.000000 -1.000000|
 |  0.000000  1.000000  0.000000|

Crystal class of the cell: MONOCLINIC

Crystal class of the conventional CELL: ORTHORHOMBIC

Space group name: P 1 21 1

Bravais type of conventional cell is: 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: S and T

All-atom RMS fit for the two chains : 0.224
CA-only RMS fit for the two chains : 0.149

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: S and T

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: S and U

All-atom RMS fit for the two chains : 0.221
CA-only RMS fit for the two chains : 0.144

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: S and U

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: S and V

All-atom RMS fit for the two chains : 0.257
CA-only RMS fit for the two chains : 0.170

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: S and V

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: S and W

All-atom RMS fit for the two chains : 0.273
CA-only RMS fit for the two chains : 0.109

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: S and W

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: S and X

All-atom RMS fit for the two chains : 0.255
CA-only RMS fit for the two chains : 0.183

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: S and X

Warning: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

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.

4530 6PG   ( 479-)  A  -
4532 6PG   ( 479-)  B  -
4534 6PG   ( 479-)  C  -
4536 6PG   ( 479-)  D  -
4538 6PG   ( 479-)  E  -
4540 6PG   ( 479-)  F  -
4542 6PG   ( 479-)  G  -
4544 6PG   ( 479-)  H  -

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.

 445 MET   (   1-)  S  -   N   bound to 4521 NME   (   0-)  S  -   C
1010 MET   (   1-)  T  -   N   bound to 4522 NME   (   0-)  T  -   C
1575 MET   (   1-)  U  -   N   bound to 4523 NME   (   0-)  U  -   C
2141 MET   (   1-)  V  -   N   bound to 4524 NME   (   0-)  V  -   C
2704 MET   (   1-)  W  -   N   bound to 4525 NME   (   0-)  W  -   C
3270 MET   (   1-)  X  -   N   bound to 4526 NME   (   0-)  X  -   C
3833 MET   (   1-)  Y  -   N   bound to 4527 NME   (   0-)  Y  -   C
4399 MET   (   1-)  Z  -   N   bound to 4528 NME   (   0-)  Z  -   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: S

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: U

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: V

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: W

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: X

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: Y

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: Z

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.

 497 GLU   (  54-)  S
3687 PHE   ( 311-)  G
4395 GLU   ( 460-)  H

Warning: What type of B-factor?

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

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

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: T

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: U

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: V

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: W

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: X

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: Y

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: Z

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.

  63 ARG   (  79-)  A
  67 ARG   (  83-)  A
 631 ARG   (  79-)  B
1195 ARG   (  79-)  C
1761 ARG   (  79-)  D
2116 ARG   ( 439-)  D
2326 ARG   (  79-)  E
2598 ARG   ( 358-)  E
2894 ARG   (  83-)  F
3455 ARG   (  79-)  G

Warning: Tyrosine convention problem

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

 169 TYR   ( 185-)  A
 737 TYR   ( 185-)  B
1301 TYR   ( 185-)  C
1867 TYR   ( 185-)  D
2432 TYR   ( 185-)  E
2996 TYR   ( 185-)  F
3561 TYR   ( 185-)  G
4125 TYR   ( 185-)  H

Warning: Phenylalanine convention problem

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

 111 PHE   ( 127-)  A
 541 PHE   (  98-)  S
1106 PHE   (  98-)  T
1112 PHE   ( 104-)  T
1677 PHE   ( 104-)  U
2237 PHE   (  98-)  V
2243 PHE   ( 104-)  V
2715 PHE   (  12-)  W
2800 PHE   (  98-)  W
2806 PHE   ( 104-)  W
3372 PHE   ( 104-)  X
3844 PHE   (  12-)  Y
3935 PHE   ( 104-)  Y
4151 PHE   ( 211-)  H
4410 PHE   (  12-)  Z
4501 PHE   ( 104-)  Z

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.

 187 ASP   ( 203-)  A
 469 ASP   (  25-)  S
 755 ASP   ( 203-)  B
1034 ASP   (  25-)  T
1319 ASP   ( 203-)  C
1599 ASP   (  25-)  U
1885 ASP   ( 203-)  D
2165 ASP   (  25-)  V
2728 ASP   (  25-)  W
3014 ASP   ( 203-)  F
3294 ASP   (  25-)  X
3857 ASP   (  25-)  Y
4143 ASP   ( 203-)  H
4423 ASP   (  25-)  Z

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.

  12 GLU   (  28-)  A
  14 GLU   (  30-)  A
  44 GLU   (  60-)  A
  77 GLU   (  93-)  A
 319 GLU   ( 338-)  A
 532 GLU   (  89-)  S
 580 GLU   (  28-)  B
 604 GLU   (  52-)  B
 645 GLU   (  93-)  B
 884 GLU   ( 338-)  B
1097 GLU   (  89-)  T
1144 GLU   (  28-)  C
1209 GLU   (  93-)  C
1449 GLU   ( 338-)  C
1662 GLU   (  89-)  U
1710 GLU   (  28-)  D
1734 GLU   (  52-)  D
1775 GLU   (  93-)  D
2015 GLU   ( 338-)  D
2228 GLU   (  89-)  V
2275 GLU   (  28-)  E
2340 GLU   (  93-)  E
2578 GLU   ( 338-)  E
2791 GLU   (  89-)  W
2839 GLU   (  28-)  F
2904 GLU   (  93-)  F
3144 GLU   ( 338-)  F
3357 GLU   (  89-)  X
3404 GLU   (  28-)  G
3428 GLU   (  52-)  G
3469 GLU   (  93-)  G
3707 GLU   ( 338-)  G
3920 GLU   (  89-)  Y
3968 GLU   (  28-)  H
4033 GLU   (  93-)  H
4144 GLU   ( 204-)  H
4273 GLU   ( 338-)  H
4486 GLU   (  89-)  Z

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.

 185 KCX   ( 201-)  A      CH     CX
 185 KCX   ( 201-)  A      OX1    OQ1
 185 KCX   ( 201-)  A      OX2    OQ2
 753 KCX   ( 201-)  B      CH     CX
 753 KCX   ( 201-)  B      OX1    OQ1
 753 KCX   ( 201-)  B      OX2    OQ2
1317 KCX   ( 201-)  C      CH     CX
1317 KCX   ( 201-)  C      OX1    OQ1
1317 KCX   ( 201-)  C      OX2    OQ2
1883 KCX   ( 201-)  D      CH     CX
1883 KCX   ( 201-)  D      OX1    OQ1
1883 KCX   ( 201-)  D      OX2    OQ2
2448 KCX   ( 201-)  E      CH     CX
2448 KCX   ( 201-)  E      OX1    OQ1
2448 KCX   ( 201-)  E      OX2    OQ2
3012 KCX   ( 201-)  F      CH     CX
3012 KCX   ( 201-)  F      OX1    OQ1
3012 KCX   ( 201-)  F      OX2    OQ2
3577 KCX   ( 201-)  G      CH     CX
3577 KCX   ( 201-)  G      OX1    OQ1
3577 KCX   ( 201-)  G      OX2    OQ2
4141 KCX   ( 201-)  H      CH     CX
4141 KCX   ( 201-)  H      OX1    OQ1
4141 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.

   1 GLY   (  12-)  A      N    CA    1.52    4.3
1132 GLY   (  12-)  C      N    CA    1.62   10.3
1702 VAL   (  17-)  D      CA   CB    1.62    4.5

Warning: Low bond length variability

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

RMS Z-score for bond lengths: 0.276
RMS-deviation in bond distances: 0.007

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  0.998707 -0.000035  0.000062|
 | -0.000035  0.998516 -0.000029|
 |  0.000062 -0.000029  0.998922|
Proposed new scale matrix

 |  0.009069  0.000000  0.000229|
 |  0.000000  0.005016  0.000000|
 |  0.000000  0.000000  0.009008|
With corresponding cell

    A    = 110.269  B   = 199.344  C    = 111.051
    Alpha=  90.002  Beta=  91.445  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 110.408  B   = 199.624  C    = 111.169
    Alpha=  90.000  Beta=  91.450  Gamma=  90.000

Variance: 254.698
(Under-)estimated Z-score: 11.762

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.

  20 ILE   (  36-)  A      N    CA   C    99.58   -4.2
  47 THR   (  63-)  A      N    CA   C   122.40    4.0
 184 THR   ( 200-)  A      N    CA   C    99.59   -4.1
 247 PRO   ( 263-)  A      N    CA   C   122.55    4.3
 316 VAL   ( 332-)  A     -C    N    CA  130.03    4.6
 316 VAL   ( 332-)  A      N    CA   C   125.82    5.2
 554 GLN   ( 111-)  S      N    CA   C    98.26   -4.6
 570 ALA   (  15-)  B     -C    N    CA  110.02   -6.5
 570 ALA   (  15-)  B      N    CA   C   128.90    6.3
 572 VAL   (  17-)  B     -C    N    CA  131.12    5.2
 879 HIS   ( 327-)  B      CG   ND1  CE1 109.71    4.1
1119 GLN   ( 111-)  T      N    CA   C    98.86   -4.4
1133 PHE   (  13-)  C      N    CA   C    93.14   -6.5
1133 PHE   (  13-)  C      N    CA   CB  119.91    5.5
1152 ILE   (  36-)  C      N    CA   C    99.06   -4.3
1240 VAL   ( 124-)  C      N    CA   C   122.52    4.0
1316 THR   ( 200-)  C      N    CA   C    99.87   -4.0
1379 PRO   ( 263-)  C      N    CA   C   122.37    4.2
1684 GLN   ( 111-)  U      N    CA   C    98.94   -4.4
1702 VAL   (  17-)  D      CA   C    O   112.26   -5.0
1764 GLY   (  82-)  D      N    CA   C   100.31   -4.2
1882 THR   ( 200-)  D      N    CA   C    99.40   -4.2
1945 PRO   ( 263-)  D      N    CA   C   122.49    4.3
2250 GLN   ( 111-)  V      N    CA   C    98.93   -4.4
2283 ILE   (  36-)  E      N    CA   C    99.68   -4.1
2447 THR   ( 200-)  E      N    CA   C    99.62   -4.1
2510 PRO   ( 263-)  E      N    CA   C   122.12    4.1
2813 GLN   ( 111-)  W      N    CA   C    99.42   -4.2
2847 ILE   (  36-)  F      N    CA   C    99.60   -4.1
3011 THR   ( 200-)  F      N    CA   C    99.36   -4.2
3074 PRO   ( 263-)  F      N    CA   C   122.21    4.2
3379 GLN   ( 111-)  X      N    CA   C    99.52   -4.2
3393 PHE   (  13-)  G      N    CA   C   123.11    4.3
3394 LYS   (  14-)  G     -C    N    CA  129.12    4.1
3395 ALA   (  15-)  G      N    CA   C   126.89    5.6
3395 ALA   (  15-)  G      N    CA   CB  103.84   -4.4
3412 ILE   (  36-)  G      N    CA   C    98.89   -4.4
3467 VAL   (  91-)  G      N    CA   C   123.51    4.4
3942 GLN   ( 111-)  Y      N    CA   C    99.28   -4.3
3976 ILE   (  36-)  H      N    CA   C    99.37   -4.2
4022 GLY   (  82-)  H      N    CA   C   100.20   -4.2
4140 THR   ( 200-)  H      N    CA   C    98.71   -4.5
4203 PRO   ( 263-)  H      N    CA   C   122.99    4.5
4508 GLN   ( 111-)  Z      N    CA   C    99.70   -4.1

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: 0.666
RMS-deviation in bond angles: 1.462

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.

  12 GLU   (  28-)  A
  14 GLU   (  30-)  A
  44 GLU   (  60-)  A
  63 ARG   (  79-)  A
  67 ARG   (  83-)  A
  77 GLU   (  93-)  A
 187 ASP   ( 203-)  A
 319 GLU   ( 338-)  A
 469 ASP   (  25-)  S
 532 GLU   (  89-)  S
 580 GLU   (  28-)  B
 604 GLU   (  52-)  B
 631 ARG   (  79-)  B
 645 GLU   (  93-)  B
 755 ASP   ( 203-)  B
 884 GLU   ( 338-)  B
1034 ASP   (  25-)  T
1097 GLU   (  89-)  T
1144 GLU   (  28-)  C
1195 ARG   (  79-)  C
1209 GLU   (  93-)  C
1319 ASP   ( 203-)  C
1449 GLU   ( 338-)  C
1599 ASP   (  25-)  U
1662 GLU   (  89-)  U
And so on for a total of 62 lines.

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

1240 VAL   ( 124-)  C    7.51
 570 ALA   (  15-)  B    7.26
1133 PHE   (  13-)  C    6.97
3678 ASP   ( 302-)  G    6.60
3395 ALA   (  15-)  G    6.43
 676 VAL   ( 124-)  B    6.41
4064 VAL   ( 124-)  H    6.29
1806 VAL   ( 124-)  D    6.26
 108 VAL   ( 124-)  A    6.26
3113 ASP   ( 302-)  F    6.19
 316 VAL   ( 332-)  A    6.09
2371 VAL   ( 124-)  E    6.06
2935 VAL   ( 124-)  F    6.06
1418 ASP   ( 302-)  C    6.04
3500 VAL   ( 124-)  G    6.04
1984 ASP   ( 302-)  D    6.02
 286 ASP   ( 302-)  A    5.96
4242 ASP   ( 302-)  H    5.84
 854 ASP   ( 302-)  B    5.68
2549 ASP   ( 302-)  E    5.64
3467 VAL   (  91-)  G    5.20
4209 TYR   ( 269-)  H    5.13
 896 ARG   ( 350-)  B    5.09
 821 TYR   ( 269-)  B    5.07
3080 TYR   ( 269-)  F    5.06
And so on for a total of 93 lines.

Warning: High tau angle deviations

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

Tau angle RMS Z-score : 1.518

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.

3393 PHE   (  13-)  G    -3.0
2886 THR   (  75-)  F    -3.0
4015 THR   (  75-)  H    -3.0
1757 THR   (  75-)  D    -2.9
 627 THR   (  75-)  B    -2.9
 564 PRO   ( 121-)  S    -2.9
1191 THR   (  75-)  C    -2.8
3451 THR   (  75-)  G    -2.8
2322 THR   (  75-)  E    -2.8
  59 THR   (  75-)  A    -2.8
   2 PHE   (  13-)  A    -2.7
1133 PHE   (  13-)  C    -2.6
 316 VAL   ( 332-)  A    -2.6
2814 LEU   ( 112-)  W    -2.6
4270 THR   ( 330-)  H    -2.6
1705 THR   (  23-)  D    -2.6
1447 VAL   ( 331-)  C    -2.6
 315 VAL   ( 331-)  A    -2.5
3394 LYS   (  14-)  G    -2.5
 195 PHE   ( 211-)  A    -2.5
3467 VAL   (  91-)  G    -2.4
 763 PHE   ( 211-)  B    -2.4
2458 PHE   ( 211-)  E    -2.4
1893 PHE   ( 211-)  D    -2.4
 350 VAL   ( 369-)  A    -2.4
And so on for a total of 65 lines.

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

   2 PHE   (  13-)  A  Poor phi/psi
   3 LYS   (  14-)  A  Poor phi/psi
  46 SER   (  62-)  A  Poor phi/psi
  47 THR   (  63-)  A  Poor phi/psi
 147 ASN   ( 163-)  A  Poor phi/psi
 159 LYS   ( 175-)  A  PRO omega poor
 191 ASN   ( 207-)  A  Poor phi/psi
 195 PHE   ( 211-)  A  Poor phi/psi
 281 MET   ( 297-)  A  Poor phi/psi
 314 THR   ( 330-)  A  Poor phi/psi
 315 VAL   ( 331-)  A  Poor phi/psi
 317 GLY   ( 333-)  A  Poor phi/psi
 351 SER   ( 370-)  A  Poor phi/psi
 420 ARG   ( 439-)  A  Poor phi/psi
 422 GLY   ( 441-)  A  Poor phi/psi
 457 GLU   (  13-)  S  Poor phi/psi
 459 LEU   (  15-)  S  Poor phi/psi
 481 LYS   (  37-)  S  Poor phi/psi
 514 LYS   (  71-)  S  Poor phi/psi
 552 GLN   ( 109-)  S  Poor phi/psi
 563 PRO   ( 120-)  S  Poor phi/psi
 570 ALA   (  15-)  B  Poor phi/psi
 575 THR   (  23-)  B  Poor phi/psi
 614 SER   (  62-)  B  Poor phi/psi
 715 ASN   ( 163-)  B  Poor phi/psi
And so on for a total of 139 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.

 780 SER   ( 228-)  B    0.36
1910 SER   ( 228-)  D    0.36
2475 SER   ( 228-)  E    0.36
2526 SER   ( 279-)  E    0.36
3039 SER   ( 228-)  F    0.36
3604 SER   ( 228-)  G    0.36
4168 SER   ( 228-)  H    0.36
4219 SER   ( 279-)  H    0.37
1961 SER   ( 279-)  D    0.38

Warning: Unusual backbone conformations

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

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

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

   3 LYS   (  14-)  A      0
   4 ALA   (  15-)  A      0
   5 GLY   (  16-)  A      0
   6 VAL   (  17-)  A      0
   7 THR   (  23-)  A      0
   8 TYR   (  24-)  A      0
   9 TYR   (  25-)  A      0
  10 THR   (  26-)  A      0
  30 PRO   (  46-)  A      0
  45 SER   (  61-)  A      0
  46 SER   (  62-)  A      0
  47 THR   (  63-)  A      0
  50 TRP   (  66-)  A      0
  54 TRP   (  70-)  A      0
  58 LEU   (  74-)  A      0
  69 TYR   (  85-)  A      0
  72 GLU   (  88-)  A      0
  75 VAL   (  91-)  A      0
  78 ASP   (  94-)  A      0
  79 ASN   (  95-)  A      0
  91 LEU   ( 107-)  A      0
  94 GLU   ( 110-)  A      0
 105 VAL   ( 121-)  A      0
 107 ASN   ( 123-)  A      0
 108 VAL   ( 124-)  A      0
And so on for a total of 1709 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 1.601

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!

1445 GLY   ( 329-)  C   2.32   18
2011 GLY   ( 329-)  D   2.12   18
4269 GLY   ( 329-)  H   2.04   22
3140 GLY   ( 329-)  F   2.02   17
 313 GLY   ( 329-)  A   1.98   31
 881 GLY   ( 329-)  B   1.85   11
3426 PRO   (  50-)  G   1.64   14
2297 PRO   (  50-)  E   1.53   11

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

3394 LYS   (  14-)  G   2.44

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]

1162 PRO   (  46-)  C    0.48 HIGH
2296 PRO   (  49-)  E    0.46 HIGH

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].

3389 PRO   ( 121-)  X  -119.5 half-chair C-delta/C-gamma (-126 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

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

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

3623 CYS   ( 247-)  G      SG   <->  4187 CYS   ( 247-)  H      SG   0.84    2.61  INTRA
1363 CYS   ( 247-)  C      SG   <->  1929 CYS   ( 247-)  D      SG   0.78    2.67  INTRA
 231 CYS   ( 247-)  A      SG   <->   799 CYS   ( 247-)  B      SG   0.76    2.69  INTRA
2494 CYS   ( 247-)  E      SG   <->  3058 CYS   ( 247-)  F      SG   0.75    2.70  INTRA
4545 HOH   ( 949 )  A      O    <->  4547 HOH   (1425 )  B      O    0.64    1.76  INTRA BF
 352 MET   ( 371-)  A      CG   <->  4545 HOH   ( 480 )  A      O    0.57    2.23  INTRA
3395 ALA   (  15-)  G      CB   <->  4557 HOH   ( 591 )  G      O    0.53    2.27  INTRA BF
 352 MET   ( 371-)  A      SD   <->  4545 HOH   ( 483 )  A      O    0.49    2.51  INTRA
 864 ARG   ( 312-)  B      NH2  <->   887 MET   ( 341-)  B      CE   0.49    2.61  INTRA
2018 MET   ( 341-)  D      CE   <->  2037 ARG   ( 360-)  D      C    0.45    2.75  INTRA
4410 PHE   (  12-)  Z      CB   <->  4513 ILE   ( 116-)  Z      CG1  0.44    2.76  INTRA
1452 MET   ( 341-)  C      SD   <->  4549 HOH   ( 480 )  C      O    0.44    2.56  INTRA
3708 ARG   ( 339-)  G      NH2  <->  4557 HOH   (2358 )  G      O    0.43    2.27  INTRA
1701 GLY   (  16-)  D      CA   <->  1750 THR   (  68-)  D      CB   0.43    2.77  INTRA BF
2260 PRO   ( 121-)  V      O    <->  2262 CYS   ( 123-)  V      N    0.43    2.27  INTRA BF
2983 CYS   ( 172-)  F      SG   <->  3213 LEU   ( 407-)  F      CD1  0.43    2.97  INTRA
 134 GLY   ( 150-)  A      CA   <->   352 MET   ( 371-)  A      SD   0.41    2.99  INTRA
2062 TRP   ( 385-)  D      CB   <->  2140 LYS   ( 463-)  D      CD   0.40    2.80  INTRA
1446 THR   ( 330-)  C      CG2  <->  1490 SER   ( 379-)  C      O    0.40    2.40  INTRA
 314 THR   ( 330-)  A      O    <->   316 VAL   ( 332-)  A      N    0.40    2.30  INTRA BF
 171 ARG   ( 187-)  A      NH1  <->  3875 GLU   (  43-)  Y      OE2  0.40    2.30  INTRA
2168 LYS   (  28-)  V      NZ   <->  4552 HOH   (2609 )  V      O    0.39    2.31  INTRA
1699 LYS   (  14-)  D      O    <->  1701 GLY   (  16-)  D      N    0.39    2.31  INTRA BF
2545 HIS   ( 298-)  E      NE2  <->  4538 6PG   ( 479-)  E      O2P  0.39    2.31  INTRA
3145 ARG   ( 339-)  F      NH2  <->  3198 GLU   ( 392-)  F      OE1  0.38    2.32  INTRA
And so on for a total of 796 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: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: U

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: V

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: W

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: X

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: Y

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: Z

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.

1065 ARG   (  57-)  T      -7.11
2759 ARG   (  57-)  W      -7.07
3888 ARG   (  57-)  Y      -7.06
 574 LEU   (  22-)  B      -7.05
 500 ARG   (  57-)  S      -7.05
3325 ARG   (  57-)  X      -7.04
2833 LEU   (  22-)  F      -7.00
4454 ARG   (  57-)  Z      -6.99
1630 ARG   (  57-)  U      -6.99
3962 LEU   (  22-)  H      -6.96
2196 ARG   (  57-)  V      -6.93
1704 LEU   (  22-)  D      -6.76
3507 ARG   ( 131-)  G      -6.42
 569 LYS   (  14-)  B      -6.39
1813 ARG   ( 131-)  D      -6.38
 115 ARG   ( 131-)  A      -6.03
1265 GLN   ( 149-)  C      -6.00
1831 GLN   ( 149-)  D      -5.98
4089 GLN   ( 149-)  H      -5.98
2396 GLN   ( 149-)  E      -5.96
2960 GLN   ( 149-)  F      -5.93
3525 GLN   ( 149-)  G      -5.92
 701 GLN   ( 149-)  B      -5.92
 133 GLN   ( 149-)  A      -5.90
2378 ARG   ( 131-)  E      -5.84
And so on for a total of 93 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: S

Note: Quality value plot

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

Chain identifier: 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: T

Note: Quality value plot

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

Chain identifier: 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: U

Note: Quality value plot

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

Chain identifier: 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: V

Note: Quality value plot

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

Chain identifier: 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: W

Note: Quality value plot

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

Chain identifier: 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: X

Note: Quality value plot

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

Chain identifier: 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: Y

Note: Quality value plot

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

Chain identifier: 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: Z

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.

2057 GLY   ( 380-)  D   -2.87
4047 LEU   ( 107-)  H   -2.83
3378 VAL   ( 110-)  X   -2.75
1981 ALA   ( 299-)  D   -2.74
3675 ALA   ( 299-)  G   -2.72
  91 LEU   ( 107-)  A   -2.71
4239 ALA   ( 299-)  H   -2.70
3110 ALA   ( 299-)  F   -2.70
3941 VAL   ( 110-)  Y   -2.69
 851 ALA   ( 299-)  B   -2.69
2546 ALA   ( 299-)  E   -2.68
1415 ALA   ( 299-)  C   -2.67
 283 ALA   ( 299-)  A   -2.66
 926 GLY   ( 380-)  B   -2.66
2620 GLY   ( 380-)  E   -2.66
 659 LEU   ( 107-)  B   -2.65
3483 LEU   ( 107-)  G   -2.65
2354 LEU   ( 107-)  E   -2.65
 553 VAL   ( 110-)  S   -2.65
2249 VAL   ( 110-)  V   -2.64
4507 VAL   ( 110-)  Z   -2.64
1118 VAL   ( 110-)  T   -2.64
1223 LEU   ( 107-)  C   -2.63
2918 LEU   ( 107-)  F   -2.63
3186 GLY   ( 380-)  F   -2.63
1683 VAL   ( 110-)  U   -2.62
4045 LEU   ( 105-)  H   -2.61
1789 LEU   ( 107-)  D   -2.60
1491 GLY   ( 380-)  C   -2.60
1787 LEU   ( 105-)  D   -2.59
2812 VAL   ( 110-)  W   -2.59
4151 PHE   ( 211-)  H   -2.54
 763 PHE   ( 211-)  B   -2.52

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: S

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: T

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: U

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: V

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: W

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: X

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: Y

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: Z

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

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

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

4547 HOH   (2410 )  B      O     84.62  -28.92   45.63
4551 HOH   (2042 )  D      O     45.64  -13.77  -27.71
4555 HOH   (2815 )  F      O     54.96   33.67    6.94
4556 HOH   (2577 )  X      O     51.47   27.80  -13.73

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.

4545 HOH   (2798 )  A      O
4546 HOH   (2810 )  S      O
4547 HOH   (1950 )  B      O
4547 HOH   (2531 )  B      O
4547 HOH   (2772 )  B      O
4548 HOH   (1965 )  T      O
4549 HOH   (2352 )  C      O
4549 HOH   (2588 )  C      O
4550 HOH   (2464 )  U      O
4552 HOH   (1389 )  V      O
4552 HOH   (1914 )  V      O
4552 HOH   (2157 )  V      O
4553 HOH   (1648 )  E      O
4553 HOH   (2105 )  E      O
4553 HOH   (2272 )  E      O
4553 HOH   (2570 )  E      O
4553 HOH   (2681 )  E      O
4554 HOH   (1268 )  W      O
4554 HOH   (2644 )  W      O
4555 HOH   (1890 )  F      O
4556 HOH   (1387 )  X      O
4556 HOH   (2016 )  X      O
4556 HOH   (2374 )  X      O
4556 HOH   (2755 )  X      O
4557 HOH   (2719 )  G      O
4557 HOH   (2807 )  G      O
4558 HOH   (1317 )  Y      O
4559 HOH   (1955 )  H      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.

 107 ASN   ( 123-)  A
 282 HIS   ( 298-)  A
 311 HIS   ( 327-)  A
 410 GLN   ( 429-)  A
 473 GLN   (  29-)  S
 498 ASN   (  55-)  S
 554 GLN   ( 111-)  S
 675 ASN   ( 123-)  B
 846 HIS   ( 294-)  B
1038 GLN   (  29-)  T
1119 GLN   ( 111-)  T
1603 GLN   (  29-)  U
1628 ASN   (  55-)  U
1629 HIS   (  56-)  U
1684 GLN   ( 111-)  U
1805 ASN   ( 123-)  D
1838 GLN   ( 156-)  D
2169 GLN   (  29-)  V
2194 ASN   (  55-)  V
2250 GLN   ( 111-)  V
2370 ASN   ( 123-)  E
2545 HIS   ( 298-)  E
2574 HIS   ( 327-)  E
2732 GLN   (  29-)  W
2811 GLN   ( 109-)  W
2813 GLN   ( 111-)  W
2934 ASN   ( 123-)  F
3298 GLN   (  29-)  X
3374 ASN   ( 106-)  X
3379 GLN   ( 111-)  X
3581 ASN   ( 205-)  G
3674 HIS   ( 298-)  G
3861 GLN   (  29-)  Y
3887 HIS   (  56-)  Y
3942 GLN   ( 111-)  Y
4427 GLN   (  29-)  Z
4506 GLN   ( 109-)  Z
4508 GLN   ( 111-)  Z

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.

  35 GLU   (  51-)  A      N
  51 THR   (  67-)  A      N
  80 GLN   (  96-)  A      N
 127 THR   ( 143-)  A      OG1
 140 GLN   ( 156-)  A      N
 151 ARG   ( 167-)  A      N
 157 THR   ( 173-)  A      N
 159 LYS   ( 175-)  A      N
 191 ASN   ( 207-)  A      ND2
 223 TYR   ( 239-)  A      OH
 230 THR   ( 246-)  A      N
 255 THR   ( 271-)  A      OG1
 278 HIS   ( 294-)  A      NE2
 279 ARG   ( 295-)  A      NE
 307 GLY   ( 323-)  A      N
 316 VAL   ( 332-)  A      N
 347 GLN   ( 366-)  A      NE2
 360 SER   ( 379-)  A      OG
 394 ASN   ( 413-)  A      ND2
 435 GLU   ( 454-)  A      N
 446 GLN   (   2-)  S      N
 459 LEU   (  15-)  S      N
 493 PHE   (  50-)  S      N
 505 TYR   (  62-)  S      N
 505 TYR   (  62-)  S      OH
And so on for a total of 212 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.

 276 HIS   ( 292-)  A      NE2
 286 ASP   ( 302-)  A      OD2
 638 HIS   (  86-)  B      NE2
 846 HIS   ( 294-)  B      ND1
1414 HIS   ( 298-)  C      NE2
2515 ASP   ( 268-)  E      OD2
2539 HIS   ( 292-)  E      NE2
2549 ASP   ( 302-)  E      OD2
2746 GLU   (  43-)  W      OE2
3678 ASP   ( 302-)  G      OD2
3707 GLU   ( 338-)  G      OE1
3707 GLU   ( 338-)  G      OE2
3770 GLN   ( 401-)  G      OE1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

4529  MG   ( 478-)  A     0.78   1.40 Scores about as good as CA
4531  MG   ( 478-)  B     0.78   1.40 Scores about as good as CA
4537  MG   ( 478-)  E     0.79   1.41 Scores about as good as CA
4539  MG   ( 478-)  F     0.79   1.41 Scores about as good as CA
4543  MG   ( 478-)  H     0.79   1.41 Scores about as good as CA

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

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

4545 HOH   ( 592 )  A      O  0.89  K  4 *2 NCS 7/7
4545 HOH   ( 825 )  A      O  1.11  K  4 *2 NCS 7/7
4545 HOH   (1246 )  A      O  0.92  K  5 *2 Ion-B NCS 7/7
4545 HOH   (2522 )  A      O  0.90  K  4 *2 Ion-B NCS 5/5
4546 HOH   ( 374 )  S      O  0.80  K  4 *2 NCS 7/7
4546 HOH   (2033 )  S      O  1.08  K  4 *2 Ion-B NCS 7/7
4547 HOH   ( 481 )  B      O  0.88  K  4 *2 NCS 7/7
4547 HOH   ( 522 )  B      O  0.93  K  5 *2 NCS 7/7
4547 HOH   ( 527 )  B      O  1.08  K  4 *2 NCS 7/7
4547 HOH   ( 944 )  B      O  0.78  K  5 *2 Ion-B NCS 5/5
4547 HOH   (2203 )  B      O  0.87  K  4 *2 Ion-B NCS 7/7
4547 HOH   (3191 )  B      O  0.82  K  4 *2 NCS 7/7
4548 HOH   ( 704 )  T      O  0.89  K  5 *2 NCS 7/7
4549 HOH   ( 486 )  C      O  0.84  K  4 *2 NCS 8/8
4549 HOH   ( 499 )  C      O  1.19  K  4 *2 NCS 6/6
4549 HOH   ( 517 )  C      O  1.08  K  4 *2 NCS 7/7
4549 HOH   ( 600 )  C      O  1.20  K  4 *2 NCS 7/7
4549 HOH   (1463 )  C      O  0.88  K  5 *2 Ion-B NCS 6/6
4549 HOH   (3491 )  C      O  0.83  K  4 *2 NCS 7/7
4549 HOH   (3526 )  C      O  1.18  K  4 *2 NCS 7/7
4549 HOH   (3528 )  C      O  0.92  K  5 *2 NCS 7/7
4551 HOH   ( 480 )  D      O  0.82  K  4 *2 NCS 8/8
4551 HOH   ( 609 )  D      O  0.87  K  4 *2 NCS 7/7
4551 HOH   (1492 )  D      O  1.02  K  4 *2 Ion-B NCS 5/5
4551 HOH   (1537 )  D      O  0.86  K  4 *2 Ion-B NCS 7/7
And so on for a total of 66 lines.

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

 252 ASP   ( 268-)  A   H-bonding suggests Asn
 270 ASP   ( 286-)  A   H-bonding suggests Asn
 286 ASP   ( 302-)  A   H-bonding suggests Asn
 820 ASP   ( 268-)  B   H-bonding suggests Asn
 854 ASP   ( 302-)  B   H-bonding suggests Asn; but Alt-Rotamer
1384 ASP   ( 268-)  C   H-bonding suggests Asn
1402 ASP   ( 286-)  C   H-bonding suggests Asn; but Alt-Rotamer
1418 ASP   ( 302-)  C   H-bonding suggests Asn
1950 ASP   ( 268-)  D   H-bonding suggests Asn
1968 ASP   ( 286-)  D   H-bonding suggests Asn
1984 ASP   ( 302-)  D   H-bonding suggests Asn
2515 ASP   ( 268-)  E   H-bonding suggests Asn
2549 ASP   ( 302-)  E   H-bonding suggests Asn
3079 ASP   ( 268-)  F   H-bonding suggests Asn
3113 ASP   ( 302-)  F   H-bonding suggests Asn
3644 ASP   ( 268-)  G   H-bonding suggests Asn
3662 ASP   ( 286-)  G   H-bonding suggests Asn; but Alt-Rotamer
3678 ASP   ( 302-)  G   H-bonding suggests Asn
3863 GLU   (  31-)  Y   H-bonding suggests Gln; but Alt-Rotamer
4208 ASP   ( 268-)  H   H-bonding suggests Asn
4242 ASP   ( 302-)  H   H-bonding suggests Asn

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 :  -0.624
  2nd generation packing quality :   0.027
  Ramachandran plot appearance   :  -0.593
  chi-1/chi-2 rotamer normality  :  -0.935
  Backbone conformation          :  -0.643

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.276 (tight)
  Bond angles                    :   0.666
  Omega angle restraints         :   0.291 (tight)
  Side chain planarity           :   0.260 (tight)
  Improper dihedral distribution :   0.594
  B-factor distribution          :   0.534
  Inside/Outside distribution    :   1.063

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 : 1.65


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.4
  2nd generation packing quality :  -0.7
  Ramachandran plot appearance   :  -0.7
  chi-1/chi-2 rotamer normality  :  -1.2
  Backbone conformation          :  -0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.276 (tight)
  Bond angles                    :   0.666
  Omega angle restraints         :   0.291 (tight)
  Side chain planarity           :   0.260 (tight)
  Improper dihedral distribution :   0.594
  B-factor distribution          :   0.534
  Inside/Outside distribution    :   1.063
==============

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.