WHAT IF Check report

This file was created 2011-12-17 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 pdb4rub.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 : 0.561
CA-only RMS fit for the two chains : 0.544

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 : 0.671
CA-only RMS fit for the two chains : 0.658

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 : 0.386
CA-only RMS fit for the two chains : 0.363

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: S and T

All-atom RMS fit for the two chains : 0.231
CA-only RMS fit for the two chains : 0.087

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 : 0.167
CA-only RMS fit for the two chains : 0.094

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.

2361 CAP   ( 490-)  B  -
2362 CAP   ( 490-)  C  -
2363 CAP   ( 490-)  D  -
2368 CAP   ( 490-)  A  -

Administrative problems that can generate validation failures

Warning: Strange inter-chain connections detected

The pairs of residues listed in the table below seem covalently bound while belonging to different chains in the PDB file.

Sometimes this is unavoidable (e.g. if two protein chains are covalently connected via a Cys-Cys or other bond). But if it can be avoided (e.g. often we observe sugars with one chain identifier connected to protein chains with another chain identifier), it should be avoided. WHAT IF and WHAT-CHECK try to deal with all exceptions thrown at it, but if you want these programs to work optimally (i.e. make as few false error messages as is possible) you should help them by getting as much of the administration correct as is humanly possible.

 827 CYS   ( 247-)  B  -   SG  1415 CYS   ( 247-)  C  -   SG

Warning: Strange inter-chain connections could NOT be corrected

Often inter-chain connections are simple administrative problems. In this case not. The observed inter-chain connection(s) either are real, or they are too strange for WHAT IF to correct. Human inspection seems required.

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.

 193 LYS   ( 201-)  A  -   NZ  bound to 2364 FMT   ( 492-)  A  -   C
 781 LYS   ( 201-)  B  -   NZ  bound to 2365 FMT   ( 492-)  B  -   C
1369 LYS   ( 201-)  C  -   NZ  bound to 2366 FMT   ( 492-)  C  -   C
1957 LYS   ( 201-)  D  -   NZ  bound to 2367 FMT   ( 492-)  D  -   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

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

Warning: C-terminal nitrogen atoms detected.

It is becoming habit to indicate that a residue is not the true C-terminus by including only the backbone N of the next residue. This has been observed in this PDB file.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. In many cases the N- or C-terminal residues are too disordered to see. In case of the N-terminus, you can see from the residue numbers if there are missing residues, but at the C-terminus this is impossible. Therefore, often the position of the backbone nitrogen of the first residue missing at the C-terminal end is calculated and added to indicate that there are missing residues. As a single N causes validation trouble, we remove these single-N-residues before doing the validation. But, if you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or removed N is the cause.

2229 ASP   ( 473-)  D
1641 ASP   ( 473-)  C
1053 ASP   ( 473-)  B
 465 ASP   ( 473-)  A

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:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Warning: More than 2 percent of buried atoms has low B-factor

For protein structures determined at room temperature, no more than about 1 percent of the B factors of buried atoms is below 5.0.

Percentage of buried atoms with B less than 5 : 4.56

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

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.

 311 ARG   ( 319-)  A
 796 ARG   ( 217-)  B
1485 ARG   ( 319-)  C
2072 ARG   ( 319-)  D

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.

  16 TYR   (  24-)  A      C    O     1.34    5.5
  18 THR   (  26-)  A      CA   CB    1.61    4.1
  31 ALA   (  39-)  A      C    O     1.32    4.5
  38 PRO   (  46-)  A      CA   CB    1.62    4.3
  39 GLY   (  47-)  A      N    CA    1.52    4.1
  53 SER   (  61-)  A      CA   CB    1.62    4.3
  55 THR   (  63-)  A      CB   OG1   1.51    4.7
  60 THR   (  68-)  A      CB   OG1   1.51    4.8
  63 THR   (  71-)  A      CA   CB    1.61    4.2
  64 ASP   (  72-)  A      C    O     1.35    6.0
  64 ASP   (  72-)  A      CA   CB    1.45   -4.0
  64 ASP   (  72-)  A      CG   OD2   1.35    5.3
  65 GLY   (  73-)  A      N    CA    1.53    5.0
  67 THR   (  75-)  A      CB   OG1   1.50    4.4
  95 TYR   ( 103-)  A      C    O     1.33    4.9
 111 SER   ( 119-)  A      C    O     1.34    5.3
 113 VAL   ( 121-)  A      N    CA    1.54    4.1
 115 ASN   ( 123-)  A      CG   OD1   1.32    4.2
 126 ARG   ( 134-)  A      CZ   NH1   1.43    5.8
 127 LEU   ( 135-)  A      N    CA    1.56    5.2
 140 PHE   ( 148-)  A      C    O     1.14   -4.3
 146 GLY   ( 154-)  A      CA   C     1.45   -4.4
 158 GLY   ( 166-)  A      CA   C     1.45   -4.6
 161 LEU   ( 169-)  A      CA   CB    1.43   -5.2
 165 THR   ( 173-)  A      CB   OG1   1.50    4.5
And so on for a total of 385 lines.

Warning: High bond length deviations

Bond lengths were found to deviate more than normal from the mean standard bond lengths (standard values for protein residues were taken from Engh and Huber [REF], for DNA/RNA these values were taken 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 higher than 1.5 in this structure might indicate that the restraints used in the refinement were not strong enough. This will also occur if a different bond length dictionary is used.

RMS Z-score for bond lengths: 1.601
RMS-deviation in bond distances: 0.034

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

 |  0.998259  0.000665  0.000110|
 |  0.000665  0.996527 -0.000481|
 |  0.000110 -0.000481  0.997701|
Proposed new scale matrix

 |  0.004895  0.002829  0.000000|
 | -0.000004  0.005664  0.000003|
 |  0.000000  0.000004  0.008538|
With corresponding cell

    A    = 204.227  B   = 203.848  C    = 117.129
    Alpha=  90.055  Beta=  89.986  Gamma= 119.985

The CRYST1 cell dimensions

    A    = 204.600  B   = 204.600  C    = 117.400
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 508.927
(Under-)estimated Z-score: 16.626

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.

   2 SER   (  10-)  A      N    CA   CB  121.59    6.5
   3 VAL   (  11-)  A     -O   -C    N   129.46    4.0
   5 PHE   (  13-)  A      N    CA   C    98.35   -4.6
   5 PHE   (  13-)  A      N    CA   CB  117.96    4.4
   5 PHE   (  13-)  A      CA   CB   CG  121.82    8.0
   9 VAL   (  17-)  A      CA   C    O   110.85   -5.9
  10 LYS   (  18-)  A     -CA  -C    N   124.42    4.1
  10 LYS   (  18-)  A     -C    N    CA  133.02    6.3
  11 GLU   (  19-)  A      N    CA   CB  123.30    7.5
  11 GLU   (  19-)  A      CA   CB   CG  123.79    4.8
  16 TYR   (  24-)  A      N    CA   CB   99.25   -6.6
  16 TYR   (  24-)  A      C    CA   CB  123.62    7.1
  17 TYR   (  25-)  A      C    CA   CB  118.81    4.6
  17 TYR   (  25-)  A      CB   CG   CD1 114.68   -4.1
  17 TYR   (  25-)  A      CB   CG   CD2 127.43    4.4
  18 THR   (  26-)  A      N    CA   CB  100.05   -6.1
  18 THR   (  26-)  A      CA   CB   CG2 120.69    6.0
  18 THR   (  26-)  A      CA   CB   OG1 100.21   -6.3
  22 GLN   (  30-)  A     -CA  -C    N   106.12   -5.0
  22 GLN   (  30-)  A      CB   CG   CD  105.10   -4.4
  24 LYS   (  32-)  A      N    CA   CB  119.68    5.4
  24 LYS   (  32-)  A      C    CA   CB  102.43   -4.0
  25 ASP   (  33-)  A      CB   CG   OD2 107.81   -4.6
  27 ASP   (  35-)  A      C    CA   CB   99.07   -5.8
  28 ILE   (  36-)  A      CA   C    O   109.13   -6.9
And so on for a total of 2671 lines.

Warning: High bond angle deviations

Bond angles were found to deviate more than normal from the mean 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, and this is indeed observed for very high resolution X-ray structures. The fact that it is higher than 2.0 in this structure might indicate that the restraints used in the refinement were not strong enough. This will also occur if a different bond angle dictionary is used.

RMS Z-score for bond angles: 2.435
RMS-deviation in bond angles: 4.530

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.

 311 ARG   ( 319-)  A
 796 ARG   ( 217-)  B
1485 ARG   ( 319-)  C
2072 ARG   ( 319-)  D

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

  38 PRO   (  46-)  A      CA     8.0    49.36    38.15
  53 SER   (  61-)  A      CA     6.5    46.33    34.32
  89 TYR   (  97-)  A      CA     7.2    45.46    34.03
 193 LYS   ( 201-)  A      CA    11.1    52.38    33.92
 324 VAL   ( 332-)  A      CA     8.0    44.77    33.23
 457 ILE   ( 465-)  A      CA     6.7    43.29    33.24
 676 TYR   (  97-)  B      CA     7.1    45.25    34.03
 778 PHE   ( 199-)  B      CA     6.2    43.98    33.98
 780 LYS   ( 201-)  B      CA    13.7    56.59    33.92
 789 PRO   ( 210-)  B      CA    -6.8    28.52    38.15
 845 MET   ( 266-)  B      CA     6.4    45.66    34.17
 911 VAL   ( 332-)  B      CA     7.6    44.18    33.23
1212 PRO   (  46-)  C      CA     8.9    50.77    38.15
1227 SER   (  61-)  C      CA     6.7    46.87    34.32
1367 LYS   ( 201-)  C      CA    12.5    54.69    33.92
1432 MET   ( 266-)  C      CA     7.9    48.45    34.17
1498 VAL   ( 332-)  C      CA     9.1    46.43    33.23
1799 PRO   (  46-)  D      CA     6.5    47.33    38.15
1942 VAL   ( 189-)  D      CB    -6.6   -41.61   -32.96
1952 PHE   ( 199-)  D      CA     6.3    44.04    33.98
1954 LYS   ( 201-)  D      CA    12.5    54.63    33.92
1978 LEU   ( 225-)  D      CG    -6.5   -44.49   -33.01
2085 VAL   ( 332-)  D      CA     8.6    45.67    33.23
The average deviation= 1.821

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.

1218 GLU   (  52-)  C   11.07
 351 SER   ( 359-)  A    8.74
1805 GLU   (  52-)  D    8.11
2112 SER   ( 359-)  D    7.71
 562 TRP   (  98-)  S    7.54
2010 ALA   ( 257-)  D    7.50
 631 GLU   (  52-)  B    7.31
 249 ALA   ( 257-)  A    7.02
2323 TRP   (  98-)  V    7.01
1645 ILE   (   7-)  U    6.90
1019 GLU   ( 440-)  B    6.90
1606 GLU   ( 440-)  C    6.85
1908 ILE   ( 155-)  D    6.66
2055 ASP   ( 302-)  D    6.62
2232 ILE   (   7-)  V    6.61
1567 GLN   ( 401-)  C    6.57
1525 SER   ( 359-)  C    6.47
 881 ASP   ( 302-)  B    6.29
1749 GLN   ( 111-)  U    6.28
 342 ARG   ( 350-)  A    6.24
  44 GLU   (  52-)  A    6.20
1467 ILE   ( 301-)  C    6.18
1608 ASN   ( 442-)  C    6.18
1736 TRP   (  98-)  U    6.17
 939 ARG   ( 360-)  B    6.14
And so on for a total of 226 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 : 2.356

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

1319 HIS   ( 153-)  C    4.56

Torsion-related checks

Warning: Ramachandran Z-score low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is a bit low.

Ramachandran Z-score : -3.690

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.

 625 PRO   (  46-)  B    -3.1
1212 PRO   (  46-)  C    -3.1
  38 PRO   (  46-)  A    -3.1
1799 PRO   (  46-)  D    -3.1
  18 THR   (  26-)  A    -2.9
1192 THR   (  26-)  C    -2.8
2338 ILE   ( 113-)  V    -2.8
 605 THR   (  26-)  B    -2.7
  59 THR   (  67-)  A    -2.7
1405 TYR   ( 239-)  C    -2.7
 910 VAL   ( 331-)  B    -2.7
1497 VAL   ( 331-)  C    -2.7
 323 VAL   ( 331-)  A    -2.7
2084 VAL   ( 331-)  D    -2.7
1751 ILE   ( 113-)  U    -2.7
 577 ILE   ( 113-)  S    -2.7
1796 THR   (  43-)  D    -2.7
1164 ILE   ( 113-)  T    -2.7
1535 VAL   ( 369-)  C    -2.7
 470 PRO   (   6-)  S    -2.6
1461 ARG   ( 295-)  C    -2.6
1716 THR   (  78-)  U    -2.6
 948 VAL   ( 369-)  B    -2.6
1779 THR   (  26-)  D    -2.6
2231 PRO   (   6-)  V    -2.6
And so on for a total of 169 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 SER   (  10-)  A  Poor phi/psi
   3 VAL   (  11-)  A  Poor phi/psi
   4 GLY   (  12-)  A  Poor phi/psi
  38 PRO   (  46-)  A  Poor phi/psi
  67 THR   (  75-)  A  Poor phi/psi
  78 ARG   (  86-)  A  Poor phi/psi
  87 ASP   (  95-)  A  Poor phi/psi
 114 GLY   ( 122-)  A  Poor phi/psi
 155 ASN   ( 163-)  A  Poor phi/psi
 159 ARG   ( 167-)  A  Poor phi/psi
 167 LYS   ( 175-)  A  PRO omega poor
 188 GLY   ( 196-)  A  Poor phi/psi
 199 ASN   ( 207-)  A  Poor phi/psi
 289 MET   ( 297-)  A  Poor phi/psi
 323 VAL   ( 331-)  A  Poor phi/psi
 361 VAL   ( 369-)  A  Poor phi/psi
 362 SER   ( 370-)  A  Poor phi/psi
 389 ASP   ( 397-)  A  Poor phi/psi
 433 GLY   ( 441-)  A  Poor phi/psi
 477 GLU   (  13-)  S  Poor phi/psi
 479 LEU   (  15-)  S  Poor phi/psi
 511 GLU   (  47-)  S  Poor phi/psi
 535 LYS   (  71-)  S  Poor phi/psi
 557 ALA   (  93-)  S  Poor phi/psi
 573 GLN   ( 109-)  S  Poor phi/psi
And so on for a total of 102 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -5.276

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 VAL   (  11-)  A      0
   7 ALA   (  15-)  A      0
  15 THR   (  23-)  A      0
  16 TYR   (  24-)  A      0
  18 THR   (  26-)  A      0
  20 GLU   (  28-)  A      0
  37 GLN   (  45-)  A      0
  38 PRO   (  46-)  A      0
  53 SER   (  61-)  A      0
  54 SER   (  62-)  A      0
  55 THR   (  63-)  A      0
  58 TRP   (  66-)  A      0
  59 THR   (  67-)  A      0
  62 TRP   (  70-)  A      0
  66 LEU   (  74-)  A      0
  67 THR   (  75-)  A      0
  69 LEU   (  77-)  A      0
  71 ARG   (  79-)  A      0
  75 ARG   (  83-)  A      0
  77 TYR   (  85-)  A      0
  83 VAL   (  91-)  A      0
  86 LYS   (  94-)  A      0
  87 ASP   (  95-)  A      0
 102 GLU   ( 110-)  A      0
 112 ILE   ( 120-)  A      0
And so on for a total of 896 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 : 2.248

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!

2090 GLY   ( 337-)  D   2.00   35
 671 GLY   (  92-)  B   1.88   59
 916 GLY   ( 337-)  B   1.88   25
1845 GLY   (  92-)  D   1.81   72
1258 GLY   (  92-)  C   1.78   59
1503 GLY   ( 337-)  C   1.75   24
 329 GLY   ( 337-)  A   1.74   28
  84 GLY   (  92-)  A   1.62   73
1741 GLY   ( 103-)  U   1.52   57
 984 GLY   ( 405-)  B   1.51   80

Warning: Unusual peptide bond conformations

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

 658 ARG   (  79-)  B   1.57
1652 THR   (  14-)  U   1.50

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]

  38 PRO   (  46-)  A    0.61 HIGH
  42 PRO   (  50-)  A    0.08 LOW
  96 PRO   ( 104-)  A    0.17 LOW
 134 PRO   ( 142-)  A    0.55 HIGH
 144 PRO   ( 152-)  A    0.48 HIGH
 160 PRO   ( 168-)  A    0.46 HIGH
 168 PRO   ( 176-)  A    0.15 LOW
 364 PRO   ( 372-)  A    0.52 HIGH
 368 PRO   ( 376-)  A    0.51 HIGH
 380 PRO   ( 388-)  A    0.16 LOW
 402 PRO   ( 410-)  A    0.47 HIGH
 470 PRO   (   6-)  S    0.46 HIGH
 537 PRO   (  73-)  S    0.18 LOW
 625 PRO   (  46-)  B    0.55 HIGH
 629 PRO   (  50-)  B    0.15 LOW
 683 PRO   ( 104-)  B    0.11 LOW
 721 PRO   ( 142-)  B    0.49 HIGH
 951 PRO   ( 372-)  B    0.45 HIGH
 955 PRO   ( 376-)  B    0.50 HIGH
 989 PRO   ( 410-)  B    0.48 HIGH
1032 PRO   ( 453-)  B    0.10 LOW
1056 PRO   (   5-)  T    0.48 HIGH
1091 PRO   (  40-)  T    0.19 LOW
1124 PRO   (  73-)  T    0.15 LOW
1212 PRO   (  46-)  C    0.61 HIGH
And so on for a total of 51 lines.

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

  36 PRO   (  44-)  A    38.3 envelop C-delta (36 degrees)
  38 PRO   (  46-)  A   139.9 envelop C-alpha (144 degrees)
 255 PRO   ( 263-)  A   -49.3 half-chair C-beta/C-alpha (-54 degrees)
 402 PRO   ( 410-)  A  -113.3 envelop C-gamma (-108 degrees)
 623 PRO   (  44-)  B     8.6 envelop N (0 degrees)
 625 PRO   (  46-)  B   139.3 envelop C-alpha (144 degrees)
 842 PRO   ( 263-)  B   -62.5 half-chair C-beta/C-alpha (-54 degrees)
 989 PRO   ( 410-)  B  -120.6 half-chair C-delta/C-gamma (-126 degrees)
1212 PRO   (  46-)  C   136.1 envelop C-alpha (144 degrees)
1318 PRO   ( 152-)  C   100.2 envelop C-beta (108 degrees)
1429 PRO   ( 263-)  C   -51.1 half-chair C-beta/C-alpha (-54 degrees)
1576 PRO   ( 410-)  C  -119.7 half-chair C-delta/C-gamma (-126 degrees)
1678 PRO   (  40-)  U    52.9 half-chair C-delta/C-gamma (54 degrees)
1797 PRO   (  44-)  D    38.0 envelop C-delta (36 degrees)
1799 PRO   (  46-)  D   136.0 envelop C-alpha (144 degrees)
2016 PRO   ( 263-)  D   -50.2 half-chair C-beta/C-alpha (-54 degrees)
2163 PRO   ( 410-)  D  -117.5 half-chair C-delta/C-gamma (-126 degrees)
2265 PRO   (  40-)  V    34.1 envelop C-delta (36 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

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

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

 608 TYR   (  29-)  B      OH   <->   611 LYS   (  32-)  B      NZ   0.69    2.01  INTRA
1111 GLY   (  60-)  T      O    <->  1116 ARG   (  65-)  T      NH2  0.61    2.09  INTRA BL
1782 TYR   (  29-)  D      OH   <->  1785 LYS   (  32-)  D      NZ   0.57    2.13  INTRA
 541 CYS   (  77-)  S      SG   <->   546 GLN   (  82-)  S      NE2  0.53    2.77  INTRA BF
 757 LEU   ( 178-)  B      CD2  <->   784 ASN   ( 205-)  B      ND2  0.53    2.57  INTRA BL
1924 GLY   ( 171-)  D      O    <->  2155 PHE   ( 402-)  D      N    0.52    2.18  INTRA BL
1128 CYS   (  77-)  T      SG   <->  1133 GLN   (  82-)  T      CD   0.52    2.88  INTRA BF
1128 CYS   (  77-)  T      SG   <->  1133 GLN   (  82-)  T      NE2  0.51    2.79  INTRA BF
2051 HIS   ( 298-)  D      ND1  <->  2055 ASP   ( 302-)  D      OD2  0.49    2.21  INTRA BL
1717 ASP   (  79-)  U      CB   <->  1720 GLN   (  82-)  U      NE2  0.49    2.61  INTRA BF
 491 LEU   (  27-)  S      CD2  <->   495 GLU   (  31-)  S      OE2  0.48    2.32  INTRA BF
 541 CYS   (  77-)  S      SG   <->   546 GLN   (  82-)  S      CD   0.48    2.92  INTRA BF
1945 CYS   ( 192-)  D      SG   <->  2166 ASN   ( 413-)  D      ND2  0.47    2.83  INTRA BL
1126 PHE   (  75-)  T      CD1  <->  1762 ALA   (   9-)  D      CB   0.46    2.74  INTRA BF
  21 TYR   (  29-)  A      OH   <->    24 LYS   (  32-)  A      NZ   0.46    2.24  INTRA
1785 LYS   (  32-)  D      NZ   <->  1788 ASP   (  35-)  D      OD1  0.45    2.25  INTRA
 962 HIS   ( 383-)  B      O    <->   965 HIS   ( 386-)  B      N    0.45    2.25  INTRA BL
2304 ASP   (  79-)  V      CB   <->  2307 GLN   (  82-)  V      NE2  0.45    2.65  INTRA BF
1128 CYS   (  77-)  T      SG   <->  1129 THR   (  78-)  T      N    0.45    2.75  INTRA BF
 773 ARG   ( 194-)  B      NH2  <->  1055 TRP   (   4-)  T      O    0.44    2.26  INTRA
 912 GLY   ( 333-)  B      O    <->  1294 LYS   ( 128-)  C      NZ   0.44    2.26  INTRA BL
1681 GLU   (  43-)  U      OE1  <->  1738 ARG   ( 100-)  U      NH1  0.44    2.26  INTRA
 199 ASN   ( 207-)  A      O    <->   209 ARG   ( 217-)  A      NH2  0.44    2.26  INTRA BL
 186 ARG   ( 194-)  A      NH2  <->   468 TRP   (   4-)  S      O    0.43    2.27  INTRA
 507 GLU   (  43-)  S      OE1  <->   564 ARG   ( 100-)  S      NH1  0.43    2.27  INTRA
And so on for a total of 929 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

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.

1704 TYR   (  66-)  U      -8.54
 530 TYR   (  66-)  S      -8.48
 539 PHE   (  75-)  S      -6.15
1713 PHE   (  75-)  U      -6.13
 728 GLN   ( 149-)  B      -5.97
1902 GLN   ( 149-)  D      -5.92
 141 GLN   ( 149-)  A      -5.84
1315 GLN   ( 149-)  C      -5.83
1709 LYS   (  71-)  U      -5.78
 535 LYS   (  71-)  S      -5.78
1018 GLN   ( 439-)  B      -5.75
  71 ARG   (  79-)  A      -5.74
 431 GLN   ( 439-)  A      -5.72
1605 GLN   ( 439-)  C      -5.70
 443 TRP   ( 451-)  A      -5.70
2204 TRP   ( 451-)  D      -5.70
1108 LYS   (  57-)  T      -5.69
1030 TRP   ( 451-)  B      -5.69
 521 LYS   (  57-)  S      -5.65
1245 ARG   (  79-)  C      -5.65
 658 ARG   (  79-)  B      -5.63
1617 TRP   ( 451-)  C      -5.63
2282 LYS   (  57-)  V      -5.62
1832 ARG   (  79-)  D      -5.59
   6 LYS   (  14-)  A      -5.54
And so on for a total of 75 lines.

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.

1947 ARG   ( 194-)  D      1949 - GLY    196- ( D)         -4.48

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

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.

2052 ALA   ( 299-)  D   -2.87
1632 VAL   ( 466-)  C   -2.86
 458 VAL   ( 466-)  A   -2.85
1045 VAL   ( 466-)  B   -2.85
 291 ALA   ( 299-)  A   -2.78
 878 ALA   ( 299-)  B   -2.77
1465 ALA   ( 299-)  C   -2.71
1748 VAL   ( 110-)  U   -2.70
1161 VAL   ( 110-)  T   -2.65
 574 VAL   ( 110-)  S   -2.65
2335 VAL   ( 110-)  V   -2.56
1603 LEU   ( 437-)  C   -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

Water, ion, and hydrogenbond related checks

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.

 145 HIS   ( 153-)  A
 221 GLN   ( 229-)  A
 230 HIS   ( 238-)  A
 233 ASN   ( 241-)  A
 296 GLN   ( 304-)  A
 378 HIS   ( 386-)  A
 393 GLN   ( 401-)  A
 412 ASN   ( 420-)  A
 519 ASN   (  55-)  S
 520 ASN   (  56-)  S
 546 GLN   (  82-)  S
 742 ASN   ( 163-)  B
 808 GLN   ( 229-)  B
 817 HIS   ( 238-)  B
 820 ASN   ( 241-)  B
 883 GLN   ( 304-)  B
 965 HIS   ( 386-)  B
 999 ASN   ( 420-)  B
1087 ASN   (  36-)  T
1106 ASN   (  55-)  T
1107 ASN   (  56-)  T
1133 GLN   (  82-)  T
1329 ASN   ( 163-)  C
1395 GLN   ( 229-)  C
1404 HIS   ( 238-)  C
1407 ASN   ( 241-)  C
1470 GLN   ( 304-)  C
1586 ASN   ( 420-)  C
1663 GLN   (  25-)  U
1674 ASN   (  36-)  U
1693 ASN   (  55-)  U
1694 ASN   (  56-)  U
1720 GLN   (  82-)  U
1916 ASN   ( 163-)  D
1982 GLN   ( 229-)  D
1991 HIS   ( 238-)  D
1994 ASN   ( 241-)  D
2057 GLN   ( 304-)  D
2173 ASN   ( 420-)  D
2250 GLN   (  25-)  V
2261 ASN   (  36-)  V
2280 ASN   (  55-)  V
2307 GLN   (  82-)  V

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.

   8 GLY   (  16-)  A      N
  53 SER   (  61-)  A      N
  57 THR   (  65-)  A      OG1
  58 TRP   (  66-)  A      NE1
  59 THR   (  67-)  A      OG1
  70 ASP   (  78-)  A      N
 111 SER   ( 119-)  A      OG
 115 ASN   ( 123-)  A      ND2
 116 VAL   ( 124-)  A      N
 126 ARG   ( 134-)  A      NH1
 155 ASN   ( 163-)  A      ND2
 159 ARG   ( 167-)  A      N
 165 THR   ( 173-)  A      N
 165 THR   ( 173-)  A      OG1
 167 LYS   ( 175-)  A      NZ
 186 ARG   ( 194-)  A      NH2
 189 LEU   ( 197-)  A      N
 197 ASN   ( 205-)  A      ND2
 207 ARG   ( 215-)  A      NH2
 209 ARG   ( 217-)  A      NE
 209 ARG   ( 217-)  A      NH2
 230 HIS   ( 238-)  A      N
 236 ALA   ( 244-)  A      N
 245 ARG   ( 253-)  A      NH1
 254 VAL   ( 262-)  A      N
And so on for a total of 254 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.

 150 GLU   ( 158-)  A      OE1
 195 ASP   ( 203-)  A      OD2
 259 HIS   ( 267-)  A      NE2
 260 ASP   ( 268-)  A      OD1
 319 HIS   ( 327-)  A      ND1
 500 ASN   (  36-)  S      OD1
 639 GLU   (  60-)  B      OE1
 732 HIS   ( 153-)  B      ND1
 737 GLU   ( 158-)  B      OE1
 782 ASP   ( 203-)  B      OD2
 846 HIS   ( 267-)  B      NE2
 847 ASP   ( 268-)  B      OD1
 906 HIS   ( 327-)  B      ND1
1053 GLN   (   2-)  T      OE1
1226 GLU   (  60-)  C      OE1
1324 GLU   ( 158-)  C      OE1
1369 ASP   ( 203-)  C      OD2
1433 HIS   ( 267-)  C      NE2
1434 ASP   ( 268-)  C      OD1
1434 ASP   ( 268-)  C      OD2
1493 HIS   ( 327-)  C      ND1
1552 HIS   ( 386-)  C      NE2
1956 ASP   ( 203-)  D      OD2
2020 HIS   ( 267-)  D      NE2
2021 ASP   ( 268-)  D      OD1
2080 HIS   ( 327-)  D      ND1
2139 HIS   ( 386-)  D      NE2

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 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+.

2355  MG   ( 491-)  C     0.74   1.26 Scores about as good as CA
Since there are no waters, the water check has been skipped.

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.

 260 ASP   ( 268-)  A   H-bonding suggests Asn; but Alt-Rotamer
 294 ASP   ( 302-)  A   H-bonding suggests Asn; but Alt-Rotamer
 847 ASP   ( 268-)  B   H-bonding suggests Asn
 881 ASP   ( 302-)  B   H-bonding suggests Asn; but Alt-Rotamer
1434 ASP   ( 268-)  C   H-bonding suggests Asn; but Alt-Rotamer
1468 ASP   ( 302-)  C   H-bonding suggests Asn; but Alt-Rotamer
1591 GLU   ( 425-)  C   H-bonding suggests Gln; but Alt-Rotamer
2021 ASP   ( 268-)  D   H-bonding suggests Asn; but Alt-Rotamer
2055 ASP   ( 302-)  D   H-bonding suggests Asn; but Alt-Rotamer
2178 GLU   ( 425-)  D   H-bonding suggests Gln; but Alt-Rotamer

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 :  -1.492
  2nd generation packing quality :  -1.245
  Ramachandran plot appearance   :  -3.690 (poor)
  chi-1/chi-2 rotamer normality  :  -5.276 (bad)
  Backbone conformation          :  -0.661

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.601 (loose)
  Bond angles                    :   2.435 (loose)
  Omega angle restraints         :   0.409 (tight)
  Side chain planarity           :   0.987
  Improper dihedral distribution :   1.609 (loose)
  B-factor distribution          :   0.604
  Inside/Outside distribution    :   1.073

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 : 2.70


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.5
  2nd generation packing quality :   0.4
  Ramachandran plot appearance   :  -0.9
  chi-1/chi-2 rotamer normality  :  -2.8
  Backbone conformation          :  -0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.601 (loose)
  Bond angles                    :   2.435 (loose)
  Omega angle restraints         :   0.409 (tight)
  Side chain planarity           :   0.987
  Improper dihedral distribution :   1.609 (loose)
  B-factor distribution          :   0.604
  Inside/Outside distribution    :   1.073
==============

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.