WHAT IF Check report

This file was created 2014-05-15 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 pdb4m10.ent

Checks that need to be done early-on in validation

Warning: Nonstandard space group setting

The space group name given represents a non-standard setting.

Space group name: P 2 21 21

Conventional space group : P 21 21 2

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 : 0.365
CA-only RMS fit for the two chains : 0.197

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.375
CA-only RMS fit for the two chains : 0.152

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 0.233
CA-only RMS fit for the two chains : 0.105

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: B and C

All-atom RMS fit for the two chains : 0.334
CA-only RMS fit for the two chains : 0.122

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: B and C

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and D

All-atom RMS fit for the two chains : 0.368
CA-only RMS fit for the two chains : 0.204

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: B and D

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.

2224 ICD   ( 706-)  A  -
2226 ICD   ( 706-)  B  -
2227 BOG   ( 707-)  B  -
2228 BOG   ( 708-)  B  -
2230 ICD   ( 706-)  C  -
2231 BOG   ( 707-)  C  -
2234 BOG   ( 707-)  C  -
2235 ICD   ( 706-)  D  -

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

 288 GLU   ( 319-)  A  -

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

 288 GLU   ( 319-)  A  -

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.

2209 NAG   ( 702-)  A  -   O4  bound to 2210 NAG   ( 703-)  A  -   C1
2213 NAG   ( 702-)  B  -   O4  bound to 2214 NAG   ( 703-)  B  -   C1
2217 NAG   ( 702-)  C  -   O4  bound to 2218 NAG   ( 703-)  C  -   C1
2221 NAG   ( 702-)  D  -   O4  bound to 2222 NAG   ( 703-)  D  -   C1

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 80

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

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.

 191 ARG   ( 222-)  A
 743 ARG   ( 222-)  B
1295 ARG   ( 222-)  C
1846 ARG   ( 222-)  D

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.

 109 GLU   ( 140-)  A
 205 GLU   ( 236-)  A
 241 GLU   ( 272-)  A
 277 GLU   ( 308-)  A
 291 GLU   ( 322-)  A
 308 GLU   ( 339-)  A
 367 GLU   ( 398-)  A
 370 GLU   ( 401-)  A
 393 GLU   ( 424-)  A
 426 GLU   ( 457-)  A
 449 GLU   ( 480-)  A
 455 GLU   ( 486-)  A
 459 GLU   ( 490-)  A
 489 GLU   ( 520-)  A
 661 GLU   ( 140-)  B
 697 GLU   ( 176-)  B
 757 GLU   ( 236-)  B
 793 GLU   ( 272-)  B
 829 GLU   ( 308-)  B
 843 GLU   ( 322-)  B
 860 GLU   ( 339-)  B
 885 GLU   ( 364-)  B
 919 GLU   ( 398-)  B
 922 GLU   ( 401-)  B
 945 GLU   ( 424-)  B
And so on for a total of 57 lines.

Geometric checks

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  0.998210 -0.000045 -0.000044|
 | -0.000045  0.998546  0.000040|
 | -0.000044  0.000040  0.996384|
Proposed new scale matrix

 |  0.008171  0.000000  0.000000|
 |  0.000000  0.007469  0.000000|
 |  0.000000  0.000000  0.005562|
With corresponding cell

    A    = 122.390  B   = 133.889  C    = 179.788
    Alpha=  90.002  Beta=  90.002  Gamma=  90.001

The CRYST1 cell dimensions

    A    = 122.612  B   = 134.077  C    = 180.439
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 429.039
(Under-)estimated Z-score: 15.266

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.

 386 HIS   ( 417-)  A      CG   ND1  CE1 109.63    4.0
 747 HIS   ( 226-)  B      CG   ND1  CE1 110.03    4.4
 753 HIS   ( 232-)  B      CG   ND1  CE1 109.85    4.2
1379 LEU   ( 306-)  C      CA   CB   CG  130.74    4.1
1490 HIS   ( 417-)  C      CG   ND1  CE1 109.61    4.0
2155 LEU   ( 531-)  D      CA   CB   CG  130.52    4.1

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

 109 GLU   ( 140-)  A
 191 ARG   ( 222-)  A
 205 GLU   ( 236-)  A
 241 GLU   ( 272-)  A
 277 GLU   ( 308-)  A
 291 GLU   ( 322-)  A
 308 GLU   ( 339-)  A
 367 GLU   ( 398-)  A
 370 GLU   ( 401-)  A
 393 GLU   ( 424-)  A
 426 GLU   ( 457-)  A
 449 GLU   ( 480-)  A
 455 GLU   ( 486-)  A
 459 GLU   ( 490-)  A
 489 GLU   ( 520-)  A
 661 GLU   ( 140-)  B
 697 GLU   ( 176-)  B
 743 ARG   ( 222-)  B
 757 GLU   ( 236-)  B
 793 GLU   ( 272-)  B
 829 GLU   ( 308-)  B
 843 GLU   ( 322-)  B
 860 GLU   ( 339-)  B
 885 GLU   ( 364-)  B
 919 GLU   ( 398-)  B
And so on for a total of 61 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.

1254 VAL   ( 181-)  C    4.61
 702 VAL   ( 181-)  B    4.08

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.

1482 TYR   ( 409-)  C    -2.8
 602 LEU   (  82-)  B    -2.8
  75 PRO   ( 106-)  A    -2.6
1719 PHE   (  96-)  D    -2.5
 627 PRO   ( 106-)  B    -2.5
 453 GLU   ( 484-)  A    -2.4
1557 GLU   ( 484-)  C    -2.4
2108 GLU   ( 484-)  D    -2.4
1005 GLU   ( 484-)  B    -2.3
  64 PHE   (  96-)  A    -2.3
 906 TYR   ( 385-)  B    -2.3
1745 SER   ( 121-)  D    -2.3
 564 ARG   (  44-)  B    -2.2
2009 TYR   ( 385-)  D    -2.2
 354 TYR   ( 385-)  A    -2.2
1458 TYR   ( 385-)  C    -2.2
 685 GLY   ( 164-)  B    -2.2
2202 THR   ( 578-)  D    -2.2
 133 GLY   ( 164-)  A    -2.2
1237 GLY   ( 164-)  C    -2.2
 751 LEU   ( 230-)  B    -2.2
1788 GLY   ( 164-)  D    -2.2
1854 LEU   ( 230-)  D    -2.2
1099 THR   ( 578-)  B    -2.2
1019 ILE   ( 498-)  B    -2.2
 992 SER   ( 471-)  B    -2.1
1303 LEU   ( 230-)  C    -2.1
1503 ILE   ( 430-)  C    -2.1
 547 THR   ( 578-)  A    -2.1
1915 VAL   ( 291-)  D    -2.1
  92 LEU   ( 123-)  A    -2.1
1651 THR   ( 578-)  C    -2.1
1571 ILE   ( 498-)  C    -2.1
 199 LEU   ( 230-)  A    -2.1
 791 GLN   ( 270-)  B    -2.1
1667 ARG   (  44-)  D    -2.1
1168 PHE   (  96-)  C    -2.1
1343 GLN   ( 270-)  C    -2.1
 118 THR   ( 149-)  A    -2.0
 644 LEU   ( 123-)  B    -2.0
 616 PHE   (  96-)  B    -2.0
 467 ILE   ( 498-)  A    -2.0
1747 LEU   ( 123-)  D    -2.0

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.

  11 ASN   (  43-)  A  Poor phi/psi
  12 ARG   (  44-)  A  Poor phi/psi
  29 ARG   (  61-)  A  Poor phi/psi
  91 TYR   ( 122-)  A  Poor phi/psi
  95 SER   ( 126-)  A  PRO omega poor
  98 THR   ( 129-)  A  Poor phi/psi
 111 PHE   ( 142-)  A  omega poor
 116 TYR   ( 147-)  A  omega poor
 134 VAL   ( 165-)  A  Poor phi/psi
 154 ARG   ( 185-)  A  Poor phi/psi
 199 LEU   ( 230-)  A  Poor phi/psi
 216 PHE   ( 247-)  A  Poor phi/psi
 218 ASP   ( 249-)  A  Poor phi/psi
 239 GLN   ( 270-)  A  Poor phi/psi
 367 GLU   ( 398-)  A  Poor phi/psi
 378 TYR   ( 409-)  A  Poor phi/psi
 407 ARG   ( 438-)  A  Poor phi/psi
 440 SER   ( 471-)  A  Poor phi/psi
 465 SER   ( 496-)  A  Poor phi/psi
 481 PRO   ( 512-)  A  omega poor
 548 SER   ( 579-)  A  Poor phi/psi
 564 ARG   (  44-)  B  Poor phi/psi
 581 ARG   (  61-)  B  Poor phi/psi
 589 CYS   (  69-)  B  Poor phi/psi
 601 LEU   (  81-)  B  Poor phi/psi
And so on for a total of 80 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.

1528 SER   ( 455-)  C    0.35
 976 SER   ( 455-)  B    0.36
2079 SER   ( 455-)  D    0.36
2075 SER   ( 451-)  D    0.37
 424 SER   ( 455-)  A    0.37

Warning: Unusual backbone conformations

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

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

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

   4 CYS   (  36-)  A      0
   8 PRO   (  40-)  A      0
   9 CYS   (  41-)  A      0
  10 GLN   (  42-)  A      0
  12 ARG   (  44-)  A      0
  21 ASP   (  53-)  A      0
  22 GLN   (  54-)  A      0
  27 CYS   (  59-)  A      0
  28 THR   (  60-)  A      0
  29 ARG   (  61-)  A      0
  30 THR   (  62-)  A      0
  32 PHE   (  64-)  A      0
  33 TYR   (  65-)  A      0
  35 GLU   (  67-)  A      0
  37 CYS   (  69-)  A      0
  38 THR   (  70-)  A      0
  62 THR   (  94-)  A      0
  63 HIS   (  95-)  A      0
  64 PHE   (  96-)  A      0
  90 SER   ( 121-)  A      0
  91 TYR   ( 122-)  A      0
  92 LEU   ( 123-)  A      0
  94 ASP   ( 125-)  A      0
  95 SER   ( 126-)  A      0
  96 PRO   ( 127-)  A      0
And so on for a total of 831 lines.

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 131 PRO   ( 162-)  A   1.69   13
1235 PRO   ( 162-)  C   1.51   11
1786 PRO   ( 162-)  D   1.50   11

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]

 410 PRO   ( 441-)  A    0.19 LOW
1578 PRO   ( 505-)  C    0.19 LOW

Warning: Unusual PRO puckering phases

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

  75 PRO   ( 106-)  A   102.8 envelop C-beta (108 degrees)
 511 PRO   ( 542-)  A  -132.1 half-chair C-delta/C-gamma (-126 degrees)
 627 PRO   ( 106-)  B   101.9 envelop C-beta (108 degrees)
 693 PRO   ( 172-)  B  -115.1 envelop C-gamma (-108 degrees)
 962 PRO   ( 441-)  B  -114.4 envelop C-gamma (-108 degrees)
1063 PRO   ( 542-)  B  -131.6 half-chair C-delta/C-gamma (-126 degrees)
1349 PRO   ( 276-)  C  -112.8 envelop C-gamma (-108 degrees)
1514 PRO   ( 441-)  C  -116.6 envelop C-gamma (-108 degrees)
1601 PRO   ( 528-)  C  -121.5 half-chair C-delta/C-gamma (-126 degrees)
1615 PRO   ( 542-)  C  -116.8 envelop C-gamma (-108 degrees)
1904 PRO   ( 280-)  D  -113.2 envelop C-gamma (-108 degrees)
2166 PRO   ( 542-)  D   108.5 envelop C-beta (108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic 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. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. 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). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 931 ASN   ( 410-)  B      ND2 <-> 2215 NAG   ( 704-)  B      C1     1.24    1.86  INTRA BF
 931 ASN   ( 410-)  B      CG  <-> 2215 NAG   ( 704-)  B      C1     0.82    2.38  INTRA BF
1676 ASP   (  53-)  D      N   <-> 2239 HOH   (1245 )  D      O      0.49    2.21  INTRA BF
 931 ASN   ( 410-)  B      OD1 <-> 2215 NAG   ( 704-)  B      C1     0.49    2.31  INTRA BF
1289 ARG   ( 216-)  C      NH1 <-> 2218 NAG   ( 703-)  C      O7     0.36    2.34  INTRA BF
 743 ARG   ( 222-)  B      NH1 <->  811 GLU   ( 290-)  B      OE2    0.36    2.34  INTRA BF
 397 ARG   ( 428-)  A      NH1 <-> 2236 HOH   (1138 )  A      O      0.31    2.39  INTRA BF
 932 ASN   ( 411-)  B      ND2 <-> 2237 HOH   (1065 )  B      O      0.30    2.40  INTRA
 600 LEU   (  80-)  B      O   <->  602 LEU   (  82-)  B      N      0.29    2.41  INTRA BF
 931 ASN   ( 410-)  B      ND2 <-> 2215 NAG   ( 704-)  B      O5     0.29    2.41  INTRA BF
 183 HIS   ( 214-)  A      NE2 <-> 2225 HEM   ( 705-)  A      O1A    0.29    2.41  INTRA BF
 970 LYS   ( 449-)  B      NZ  <->  974 ASP   ( 453-)  B      OD2    0.24    2.46  INTRA
 774 LYS   ( 253-)  B      NZ  <-> 2237 HOH   ( 972 )  B      O      0.23    2.47  INTRA BF
1475 TYR   ( 402-)  C      OH  <-> 1490 HIS   ( 417-)  C      NE2    0.22    2.48  INTRA
 176 HIS   ( 207-)  A      NE2 <-> 2236 HOH   ( 952 )  A      O      0.21    2.49  INTRA BL
2097 LYS   ( 473-)  D      NZ  <-> 2239 HOH   (1134 )  D      O      0.21    2.49  INTRA BF
1838 HIS   ( 214-)  D      NE2 <-> 2233 HEM   ( 705-)  D      O1A    0.21    2.49  INTRA BF
 180 LYS   ( 211-)  A      NZ  <->  200 ASN   ( 231-)  A      OD1    0.19    2.51  INTRA BL
1484 ASN   ( 411-)  C      ND2 <-> 2238 HOH   (1171 )  C      O      0.19    2.51  INTRA BF
2104 GLU   ( 480-)  D      OE2 <-> 2239 HOH   (1134 )  D      O      0.19    2.21  INTRA BF
1669 GLU   (  46-)  D      OE1 <-> 2239 HOH   (1195 )  D      O      0.18    2.22  INTRA
 760 ASP   ( 239-)  B      OD1 <-> 2237 HOH   (1141 )  B      O      0.17    2.23  INTRA BF
1280 HIS   ( 207-)  C      NE2 <-> 2238 HOH   ( 831 )  C      O      0.16    2.54  INTRA
2213 NAG   ( 702-)  B      O7  <-> 2237 HOH   ( 964 )  B      O      0.16    2.24  INTRA
1840 ARG   ( 216-)  D      NH1 <-> 2239 HOH   (1246 )  D      O      0.15    2.55  INTRA BF
And so on for a total of 193 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

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.

 799 HIS   ( 278-)  B      -6.53
 247 HIS   ( 278-)  A      -6.51
1684 ARG   (  61-)  D      -6.45
1902 HIS   ( 278-)  D      -6.45
1351 HIS   ( 278-)  C      -6.44
  29 ARG   (  61-)  A      -6.36
1133 ARG   (  61-)  C      -6.33
 581 ARG   (  61-)  B      -6.32
1675 PHE   (  52-)  D      -6.11
1124 PHE   (  52-)  C      -5.99
 572 PHE   (  52-)  B      -5.89
  20 PHE   (  52-)  A      -5.84
 397 ARG   ( 428-)  A      -5.56
1242 LYS   ( 169-)  C      -5.54
2052 ARG   ( 428-)  D      -5.52
1793 LYS   ( 169-)  D      -5.52
 339 GLN   ( 370-)  A      -5.51
 690 LYS   ( 169-)  B      -5.50
1501 ARG   ( 428-)  C      -5.47
 138 LYS   ( 169-)  A      -5.44
 737 ARG   ( 216-)  B      -5.42
 949 ARG   ( 428-)  B      -5.41
1490 HIS   ( 417-)  C      -5.41
1289 ARG   ( 216-)  C      -5.39
1840 ARG   ( 216-)  D      -5.39
And so on for a total of 51 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.

 690 LYS   ( 169-)  B       692 - LEU    171- ( B)         -4.80
 735 HIS   ( 214-)  B       737 - ARG    216- ( B)         -4.81
1242 LYS   ( 169-)  C      1244 - LEU    171- ( C)         -4.79
1838 HIS   ( 214-)  D      1840 - ARG    216- ( D)         -4.84

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

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.

 194 GLY   ( 225-)  A   -3.18
1298 GLY   ( 225-)  C   -3.15
1849 GLY   ( 225-)  D   -3.13
 657 TYR   ( 136-)  B   -2.94
 602 LEU   (  82-)  B   -2.70
 193 LEU   ( 224-)  A   -2.61
1448 ASN   ( 375-)  C   -2.57
 334 LEU   ( 365-)  A   -2.56
1989 LEU   ( 365-)  D   -2.53
1438 LEU   ( 365-)  C   -2.53

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

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

1256 LEU   ( 183-)  C     - 1259 GLU   ( 186-)  C        -1.89

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

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.

 137 ASN   ( 168-)  A
 172 GLN   ( 203-)  A
 224 GLN   ( 255-)  A
 390 GLN   ( 421-)  A
 610 HIS   (  90-)  B
 724 GLN   ( 203-)  B
1241 ASN   ( 168-)  C
1276 GLN   ( 203-)  C
1455 ASN   ( 382-)  C
1792 ASN   ( 168-)  D
1902 HIS   ( 278-)  D
1906 ASN   ( 282-)  D

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.

  19 GLY   (  51-)  A      N
  22 GLN   (  54-)  A      N
  91 TYR   ( 122-)  A      N
 105 TYR   ( 136-)  A      N
 107 SER   ( 138-)  A      OG
 137 ASN   ( 168-)  A      N
 145 GLU   ( 176-)  A      N
 155 GLU   ( 186-)  A      N
 172 GLN   ( 203-)  A      NE2
 177 GLN   ( 208-)  A      NE2
 217 LYS   ( 248-)  A      N
 224 GLN   ( 255-)  A      NE2
 247 HIS   ( 278-)  A      N
 264 VAL   ( 295-)  A      N
 266 GLY   ( 297-)  A      N
 317 TYR   ( 348-)  A      OH
 326 PHE   ( 357-)  A      N
 339 GLN   ( 370-)  A      N
 357 HIS   ( 388-)  A      N
 446 SER   ( 477-)  A      N
 482 ARG   ( 513-)  A      NH2
 490 THR   ( 521-)  A      N
 532 SER   ( 563-)  A      N
 571 GLY   (  51-)  B      N
 574 GLN   (  54-)  B      N
And so on for a total of 84 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.

 308 GLU   ( 339-)  A      OE2
 860 GLU   ( 339-)  B      OE2
 907 HIS   ( 386-)  B      ND1
1412 GLU   ( 339-)  C      OE2
1455 ASN   ( 382-)  C      OD1
1484 ASN   ( 411-)  C      OD1
1827 GLN   ( 203-)  D      OE1
1963 GLU   ( 339-)  D      OE2
2006 ASN   ( 382-)  D      OD1

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.

2236 HOH   ( 857 )  A      O  1.11  K  4 Ion-B
2236 HOH   ( 916 )  A      O  0.92  K  5
2236 HOH   ( 945 )  A      O  0.98  K  4
2236 HOH   ( 947 )  A      O  1.12  K  4 Ion-B
2236 HOH   ( 950 )  A      O  0.86  K  5
2236 HOH   ( 965 )  A      O  0.91  K  4
2236 HOH   (1034 )  A      O  0.94  K  4 Ion-B
2237 HOH   ( 804 )  B      O  0.94  K  5
2237 HOH   ( 865 )  B      O  0.92  K  4
2237 HOH   ( 876 )  B      O  0.91  K  4
2237 HOH   (1018 )  B      O  0.86  K  5
2238 HOH   ( 807 )  C      O  1.02  K  5
2238 HOH   ( 876 )  C      O  0.87  K  6
2238 HOH   ( 905 )  C      O  1.07  K  4
2238 HOH   ( 926 )  C      O  0.93  K  4
2238 HOH   ( 937 )  C      O  1.04  K  4
2238 HOH   ( 968 )  C      O  0.91  K  5
2238 HOH   (1121 )  C      O  0.97  K  4 Ion-B
2238 HOH   (1193 )  C      O  1.03  K  5 Ion-B H2O-B
2238 HOH   (1269 )  C      O  1.07  K  4 ION-B
2239 HOH   ( 913 )  D      O  1.01  K  4
2239 HOH   ( 931 )  D      O  0.96  K  5
2239 HOH   ( 968 )  D      O  0.93  K  5
2239 HOH   (1066 )  D      O  0.89  K  4 Ion-B H2O-B

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.

  21 ASP   (  53-)  A   H-bonding suggests Asn
 291 GLU   ( 322-)  A   H-bonding suggests Gln
 573 ASP   (  53-)  B   H-bonding suggests Asn; but Alt-Rotamer
 691 GLU   ( 170-)  B   H-bonding suggests Gln
 843 GLU   ( 322-)  B   H-bonding suggests Gln
1125 ASP   (  53-)  C   H-bonding suggests Asn; but Alt-Rotamer
1243 GLU   ( 170-)  C   H-bonding suggests Gln
1395 GLU   ( 322-)  C   H-bonding suggests Gln
1676 ASP   (  53-)  D   H-bonding suggests Asn; but Alt-Rotamer
1794 GLU   ( 170-)  D   H-bonding suggests Gln
1860 GLU   ( 236-)  D   H-bonding suggests Gln
1946 GLU   ( 322-)  D   H-bonding suggests Gln

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 :  -1.073
  2nd generation packing quality :  -1.330
  Ramachandran plot appearance   :  -0.265
  chi-1/chi-2 rotamer normality  :  -0.894
  Backbone conformation          :  -1.017

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.429 (tight)
  Bond angles                    :   0.592 (tight)
  Omega angle restraints         :   0.923
  Side chain planarity           :   0.560 (tight)
  Improper dihedral distribution :   0.627
  B-factor distribution          :   0.857
  Inside/Outside distribution    :   1.107

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 : 2.01


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.8
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :  -0.1
  Backbone conformation          :  -1.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.429 (tight)
  Bond angles                    :   0.592 (tight)
  Omega angle restraints         :   0.923
  Side chain planarity           :   0.560 (tight)
  Improper dihedral distribution :   0.627
  B-factor distribution          :   0.857
  Inside/Outside distribution    :   1.107
==============

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.