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 pdb4m11.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 : 0.590
CA-only RMS fit for the two chains : 0.189

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 : 0.428
CA-only RMS fit for the two chains : 0.153

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 : 0.558
CA-only RMS fit for the two chains : 0.183

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: 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 : 0.587
CA-only RMS fit for the two chains : 0.176

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 : 0.546
CA-only RMS fit for the two chains : 0.131

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: Topology could not be determined for some ligands

Some ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

2225 MXM   ( 606-)  A  -
2227 MXM   ( 606-)  B  -
2228 BOG   ( 607-)  B  -         OK
2231 MXM   ( 606-)  D  -
2233 BOG   ( 607-)  D  -         OK
2234 BOG   ( 606-)  C  -         OK

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

2210 NAG   ( 602-)  A  -   O4  bound to 2211 NAG   ( 603-)  A  -   C1
2214 NAG   ( 602-)  B  -   O4  bound to 2215 NAG   ( 603-)  B  -   C1
2218 NAG   ( 602-)  C  -   O4  bound to 2219 NAG   ( 603-)  C  -   C1
2222 NAG   ( 602-)  D  -   O4  bound to 2223 NAG   ( 603-)  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: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

 597 ARG   (  77-)  B    High
 601 LEU   (  81-)  B    High

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: Tyrosine convention problem

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

 116 TYR   ( 147-)  A
1220 TYR   ( 147-)  C

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.

 241 GLU   ( 272-)  A
 291 GLU   ( 322-)  A
 295 GLU   ( 326-)  A
 308 GLU   ( 339-)  A
 367 GLU   ( 398-)  A
 426 GLU   ( 457-)  A
 455 GLU   ( 486-)  A
 459 GLU   ( 490-)  A
 471 GLU   ( 502-)  A
 493 GLU   ( 524-)  A
 843 GLU   ( 322-)  B
 847 GLU   ( 326-)  B
 860 GLU   ( 339-)  B
 978 GLU   ( 457-)  B
1023 GLU   ( 502-)  B
1045 GLU   ( 524-)  B
1395 GLU   ( 322-)  C
1399 GLU   ( 326-)  C
1412 GLU   ( 339-)  C
1471 GLU   ( 398-)  C
1489 GLU   ( 416-)  C
1530 GLU   ( 457-)  C
1552 GLU   ( 479-)  C
1559 GLU   ( 486-)  C
1563 GLU   ( 490-)  C
1575 GLU   ( 502-)  C
1597 GLU   ( 524-)  C
1811 GLU   ( 186-)  D
1897 GLU   ( 272-)  D
1947 GLU   ( 322-)  D
1951 GLU   ( 326-)  D
1964 GLU   ( 339-)  D
2082 GLU   ( 457-)  D
2111 GLU   ( 486-)  D
2127 GLU   ( 502-)  D
2149 GLU   ( 524-)  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.

 356 TRP   ( 387-)  A      NE1  CE2   1.30   -6.3
 361 PRO   ( 392-)  A      CD   N     1.55    5.5

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.

 877 HIS   ( 356-)  B      CG   ND1  CE1 109.63    4.0

Error: Nomenclature error(s)

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

 241 GLU   ( 272-)  A
 291 GLU   ( 322-)  A
 295 GLU   ( 326-)  A
 308 GLU   ( 339-)  A
 367 GLU   ( 398-)  A
 426 GLU   ( 457-)  A
 455 GLU   ( 486-)  A
 459 GLU   ( 490-)  A
 471 GLU   ( 502-)  A
 493 GLU   ( 524-)  A
 843 GLU   ( 322-)  B
 847 GLU   ( 326-)  B
 860 GLU   ( 339-)  B
 978 GLU   ( 457-)  B
1023 GLU   ( 502-)  B
1045 GLU   ( 524-)  B
1395 GLU   ( 322-)  C
1399 GLU   ( 326-)  C
1412 GLU   ( 339-)  C
1471 GLU   ( 398-)  C
1489 GLU   ( 416-)  C
1530 GLU   ( 457-)  C
1552 GLU   ( 479-)  C
1559 GLU   ( 486-)  C
1563 GLU   ( 490-)  C
1575 GLU   ( 502-)  C
1597 GLU   ( 524-)  C
1811 GLU   ( 186-)  D
1897 GLU   ( 272-)  D
1947 GLU   ( 322-)  D
1951 GLU   ( 326-)  D
1964 GLU   ( 339-)  D
2082 GLU   ( 457-)  D
2111 GLU   ( 486-)  D
2127 GLU   ( 502-)  D
2149 GLU   ( 524-)  D

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.

2034 TYR   ( 409-)  D    -3.1
 564 ARG   (  44-)  B    -2.7
 119 ARG   ( 150-)  A    -2.4
1258 ARG   ( 185-)  C    -2.4
 930 TYR   ( 409-)  B    -2.4
1557 GLU   ( 484-)  C    -2.4
 453 GLU   ( 484-)  A    -2.4
1005 GLU   ( 484-)  B    -2.4
2109 GLU   ( 484-)  D    -2.3
1775 ARG   ( 150-)  D    -2.3
1168 PHE   (  96-)  C    -2.3
 118 THR   ( 149-)  A    -2.3
1223 ARG   ( 150-)  C    -2.3
1017 SER   ( 496-)  B    -2.3
2121 SER   ( 496-)  D    -2.3
 354 TYR   ( 385-)  A    -2.2
2001 ARG   ( 376-)  D    -2.2
 791 GLN   ( 270-)  B    -2.2
1449 ARG   ( 376-)  C    -2.2
1544 SER   ( 471-)  C    -2.2
1099 THR   ( 578-)  B    -2.2
 685 GLY   ( 164-)  B    -2.2
1222 THR   ( 149-)  C    -2.2
 361 PRO   ( 392-)  A    -2.2
2010 TYR   ( 385-)  D    -2.2
 345 ARG   ( 376-)  A    -2.2
1789 GLY   ( 164-)  D    -2.1
 980 LYS   ( 459-)  B    -2.1
 547 THR   ( 578-)  A    -2.1
1196 LEU   ( 123-)  C    -2.1
1458 TYR   ( 385-)  C    -2.1
1651 THR   ( 578-)  C    -2.1
 906 TYR   ( 385-)  B    -2.1
2017 PRO   ( 392-)  D    -2.1
  64 PHE   (  96-)  A    -2.1
2203 THR   ( 578-)  D    -2.1
 260 VAL   ( 291-)  A    -2.1
 465 SER   ( 496-)  A    -2.1
1116 ARG   (  44-)  C    -2.1
1870 ARG   ( 245-)  D    -2.1
1916 VAL   ( 291-)  D    -2.1
1720 PHE   (  96-)  D    -2.1
1774 THR   ( 149-)  D    -2.1
1143 THR   (  71-)  C    -2.0
1855 LEU   ( 230-)  D    -2.0
 706 ARG   ( 185-)  B    -2.0
1237 GLY   ( 164-)  C    -2.0
  92 LEU   ( 123-)  A    -2.0
 399 ILE   ( 430-)  A    -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
  64 PHE   (  96-)  A  Poor phi/psi
  90 SER   ( 121-)  A  Poor phi/psi
  95 SER   ( 126-)  A  PRO omega poor
  98 THR   ( 129-)  A  Poor phi/psi
 116 TYR   ( 147-)  A  omega poor
 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
 366 ILE   ( 397-)  A  omega poor
 367 GLU   ( 398-)  A  Poor phi/psi
 378 TYR   ( 409-)  A  Poor phi/psi
 428 LYS   ( 459-)  A  Poor phi/psi
 440 SER   ( 471-)  A  Poor phi/psi
 453 GLU   ( 484-)  A  Poor phi/psi
 465 SER   ( 496-)  A  Poor phi/psi
 484 ASP   ( 515-)  A  Poor phi/psi
 563 ASN   (  43-)  B  Poor phi/psi
 564 ARG   (  44-)  B  Poor phi/psi
 581 ARG   (  61-)  B  Poor phi/psi
 589 CYS   (  69-)  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.

2080 SER   ( 455-)  D    0.35
1524 SER   ( 451-)  C    0.36
1498 SER   ( 425-)  C    0.36
 424 SER   ( 455-)  A    0.36
1735 SER   ( 110-)  D    0.37
 301 SER   ( 332-)  A    0.39

Warning: Unusual backbone conformations

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

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

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

   4 CYS   (  36-)  A      0
   5 CYS   (  37-)  A      0
   8 PRO   (  40-)  A      0
  10 GLN   (  42-)  A      0
  11 ASN   (  43-)  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
  36 ASN   (  68-)  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
  89 ARG   ( 120-)  A      0
  90 SER   ( 121-)  A      0
  92 LEU   ( 123-)  A      0
  95 SER   ( 126-)  A      0
And so on for a total of 825 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!

 779 GLY   ( 258-)  B   3.15   15
 227 GLY   ( 258-)  A   3.00   13
 131 PRO   ( 162-)  A   1.58   10
1235 PRO   ( 162-)  C   1.52   11
 683 PRO   ( 162-)  B   1.52   11

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].

  40 PRO   (  72-)  A   -61.7 half-chair C-beta/C-alpha (-54 degrees)
 358 PRO   ( 389-)  A  -164.3 half-chair N/C-delta (-162 degrees)
 511 PRO   ( 542-)  A  -126.4 half-chair C-delta/C-gamma (-126 degrees)
 606 PRO   (  86-)  B   108.7 envelop C-beta (108 degrees)
 627 PRO   ( 106-)  B    99.6 envelop C-beta (108 degrees)
 798 PRO   ( 277-)  B  -113.0 envelop C-gamma (-108 degrees)
 910 PRO   ( 389-)  B   100.0 envelop C-beta (108 degrees)
1063 PRO   ( 542-)  B  -121.9 half-chair C-delta/C-gamma (-126 degrees)
1200 PRO   ( 127-)  C  -116.7 envelop C-gamma (-108 degrees)
1245 PRO   ( 172-)  C  -118.6 half-chair C-delta/C-gamma (-126 degrees)
1615 PRO   ( 542-)  C  -120.2 half-chair C-delta/C-gamma (-126 degrees)
1797 PRO   ( 172-)  D  -112.9 envelop C-gamma (-108 degrees)
1902 PRO   ( 277-)  D  -116.4 envelop C-gamma (-108 degrees)
2167 PRO   ( 542-)  D  -116.5 envelop C-gamma (-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.

1600 ALA   ( 527-)  C      CB  <-> 2234 BOG   ( 606-)  C      C1'    1.05    2.15  INTRA BL
2234 BOG   ( 606-)  C      C3' <-> 2237 HOH   ( 961 )  C      O      0.95    1.85  INTRA BL
1600 ALA   ( 527-)  C      CA  <-> 2234 BOG   ( 606-)  C      O2     0.93    0.97  INTRA BL
  12 ARG   (  44-)  A      N   <-> 2235 HOH   ( 824 )  A      O      0.91    1.79  INTRA BF
1603 SER   ( 530-)  C      CB  <-> 2234 BOG   ( 606-)  C      C4     0.91    1.39  INTRA BL
1600 ALA   ( 527-)  C      CA  <-> 2234 BOG   ( 606-)  C      C1     0.91    2.29  INTRA BL
1600 ALA   ( 527-)  C      CA  <-> 2234 BOG   ( 606-)  C      C2     0.87    1.93  INTRA BL
1603 SER   ( 530-)  C      CB  <-> 2234 BOG   ( 606-)  C      C3     0.81    1.49  INTRA BL
1599 GLY   ( 526-)  C      O   <-> 2234 BOG   ( 606-)  C      O3     0.75    1.65  INTRA BL
1432 LEU   ( 359-)  C      CD1 <-> 2234 BOG   ( 606-)  C      C6'    0.68    2.12  INTRA BL
1600 ALA   ( 527-)  C      C   <-> 2234 BOG   ( 606-)  C      O2     0.68    1.72  INTRA BL
1600 ALA   ( 527-)  C      C   <-> 2234 BOG   ( 606-)  C      C2     0.66    2.54  INTRA BL
1428 TYR   ( 355-)  C      CE2 <-> 2234 BOG   ( 606-)  C      C4'    0.62    2.58  INTRA BL
1600 ALA   ( 527-)  C      CB  <-> 2234 BOG   ( 606-)  C      O1     0.61    2.19  INTRA BL
1603 SER   ( 530-)  C      C   <-> 2234 BOG   ( 606-)  C      O4     0.56    1.84  INTRA BL
1767 PHE   ( 142-)  D      O   <-> 2001 ARG   ( 376-)  D      NH2    0.55    2.15  INTRA BL
  65 LYS   (  97-)  A      NZ  <-> 2235 HOH   ( 911 )  A      O      0.55    2.15  INTRA BF
1196 LEU   ( 123-)  C      O   <-> 1542 ARG   ( 469-)  C      NH2    0.53    2.17  INTRA
1603 SER   ( 530-)  C      OG  <-> 2234 BOG   ( 606-)  C      O4     0.52    0.98  INTRA BL
1384 ARG   ( 311-)  C      NH1 <-> 2237 HOH   ( 842 )  C      O      0.50    2.20  INTRA
1600 ALA   ( 527-)  C      C   <-> 2234 BOG   ( 606-)  C      C1     0.50    2.70  INTRA BL
1000 GLU   ( 479-)  B      OE1 <-> 1006 LYS   ( 485-)  B      NZ     0.50    2.20  INTRA BF
  12 ARG   (  44-)  A      CA  <-> 2235 HOH   ( 824 )  A      O      0.49    2.31  INTRA BF
1116 ARG   (  44-)  C      N   <-> 2237 HOH   ( 852 )  C      O      0.48    2.22  INTRA
1422 VAL   ( 349-)  C      CG1 <-> 2234 BOG   ( 606-)  C      C7'    0.47    2.73  INTRA BL
And so on for a total of 418 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.

 581 ARG   (  61-)  B      -6.93
1685 ARG   (  61-)  D      -6.60
  29 ARG   (  61-)  A      -6.54
 799 HIS   ( 278-)  B      -6.52
 247 HIS   ( 278-)  A      -6.47
1903 HIS   ( 278-)  D      -6.46
1133 ARG   (  61-)  C      -6.42
1351 HIS   ( 278-)  C      -6.41
 706 ARG   ( 185-)  B      -6.10
1676 PHE   (  52-)  D      -6.00
 572 PHE   (  52-)  B      -6.00
1098 PHE   ( 577-)  B      -5.92
1810 ARG   ( 185-)  D      -5.90
  20 PHE   (  52-)  A      -5.87
 737 ARG   ( 216-)  B      -5.69
1124 PHE   (  52-)  C      -5.64
1650 PHE   ( 577-)  C      -5.63
 154 ARG   ( 185-)  A      -5.60
 938 HIS   ( 417-)  B      -5.59
 397 ARG   ( 428-)  A      -5.59
1258 ARG   ( 185-)  C      -5.58
2053 ARG   ( 428-)  D      -5.57
1501 ARG   ( 428-)  C      -5.51
1794 LYS   ( 169-)  D      -5.48
2202 PHE   ( 577-)  D      -5.46
And so on for a total of 56 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.

 138 LYS   ( 169-)  A       140 - LEU    171- ( A)         -4.62
 183 HIS   ( 214-)  A       185 - ARG    216- ( A)         -4.93
 690 LYS   ( 169-)  B       692 - LEU    171- ( B)         -4.91
 735 HIS   ( 214-)  B       737 - ARG    216- ( B)         -5.08
1242 LYS   ( 169-)  C      1244 - LEU    171- ( C)         -4.80
1287 HIS   ( 214-)  C      1289 - ARG    216- ( C)         -5.06
1794 LYS   ( 169-)  D      1796 - LEU    171- ( D)         -5.04
1839 HIS   ( 214-)  D      1841 - ARG    216- ( D)         -5.02

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.

1298 GLY   ( 225-)  C   -3.18
1850 GLY   ( 225-)  D   -3.15
 657 TYR   ( 136-)  B   -2.92
1761 TYR   ( 136-)  D   -2.90
 252 LEU   ( 283-)  A   -2.72
1438 LEU   ( 365-)  C   -2.55
 334 LEU   ( 365-)  A   -2.54
 886 LEU   ( 365-)  B   -2.54
1209 TYR   ( 136-)  C   -2.51

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.

 152 LEU   ( 183-)  A     -  155 GLU   ( 186-)  A        -2.00

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

Warning: Water molecules need moving

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

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

2235 HOH   ( 922 )  A      O     97.55   35.64   52.42

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

2235 HOH   ( 911 )  A      O
2235 HOH   ( 928 )  A      O
2238 HOH   ( 932 )  D      O
Bound group on Asn; dont flip   36 ASN  (  68-) A
Bound to: 2209 NAG  ( 601-) A
Bound group on Asn; dont flip  113 ASN  ( 144-) A
Bound to: 2210 NAG  ( 602-) A
Bound group on Asn; dont flip  379 ASN  ( 410-) A
Bound to: 2212 NAG  ( 604-) A
Bound group on Asn; dont flip  588 ASN  (  68-) B
Bound to: 2213 NAG  ( 601-) B
Bound group on Asn; dont flip  665 ASN  ( 144-) B
Bound to: 2214 NAG  ( 602-) B
Bound group on Asn; dont flip  931 ASN  ( 410-) B
Bound to: 2216 NAG  ( 604-) B
Bound group on Asn; dont flip 1140 ASN  (  68-) C
Bound to: 2217 NAG  ( 601-) C
Bound group on Asn; dont flip 1217 ASN  ( 144-) C
Bound to: 2218 NAG  ( 602-) C
Bound group on Asn; dont flip 1483 ASN  ( 410-) C
Bound to: 2220 NAG  ( 604-) C
Bound group on Asn; dont flip 1692 ASN  (  68-) D
Bound to: 2221 NAG  ( 601-) D
Bound group on Asn; dont flip 1769 ASN  ( 144-) D
Bound to: 2222 NAG  ( 602-) D
Bound group on Asn; dont flip 2035 ASN  ( 410-) D
Bound to: 2224 NAG  ( 604-) D
Metal-coordinating Histidine residue 357 fixed to   1
Metal-coordinating Histidine residue 909 fixed to   1
Metal-coordinating Histidine residue1461 fixed to   1
Metal-coordinating Histidine residue2013 fixed to   1

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.

 176 HIS   ( 207-)  A
 390 GLN   ( 421-)  A
 610 HIS   (  90-)  B
 791 GLN   ( 270-)  B
2208 GLN   ( 583-)  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.

   2 ASN   (  34-)  A      N
   9 CYS   (  41-)  A      N
  12 ARG   (  44-)  A      NH1
  19 GLY   (  51-)  A      N
  22 GLN   (  54-)  A      N
  44 THR   (  76-)  A      N
  90 SER   ( 121-)  A      N
  92 LEU   ( 123-)  A      N
 105 TYR   ( 136-)  A      N
 107 SER   ( 138-)  A      OG
 154 ARG   ( 185-)  A      NH1
 155 GLU   ( 186-)  A      N
 177 GLN   ( 208-)  A      NE2
 181 THR   ( 212-)  A      N
 217 LYS   ( 248-)  A      N
 264 VAL   ( 295-)  A      N
 266 GLY   ( 297-)  A      N
 280 ARG   ( 311-)  A      NH1
 317 TYR   ( 348-)  A      OH
 326 PHE   ( 357-)  A      N
 329 LYS   ( 360-)  A      N
 368 ASP   ( 399-)  A      N
 372 SER   ( 403-)  A      OG
 382 ILE   ( 413-)  A      N
 383 LEU   ( 414-)  A      N
And so on for a total of 123 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.

 155 GLU   ( 186-)  A      OE1
 172 GLN   ( 203-)  A      OE1
 308 GLU   ( 339-)  A      OE2
 724 GLN   ( 203-)  B      OE1
 860 GLU   ( 339-)  B      OE2
1276 GLN   ( 203-)  C      OE1
1455 ASN   ( 382-)  C      OD1
1828 GLN   ( 203-)  D      OE1
1964 GLU   ( 339-)  D      OE2
2007 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.

2235 HOH   ( 834 )  A      O  0.85 NA  4 *2
2236 HOH   ( 706 )  B      O  0.99  K  5
2237 HOH   ( 722 )  C      O  0.87 NA  4 *2
2238 HOH   ( 915 )  D      O  0.87  K  4

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
 205 GLU   ( 236-)  A   H-bonding suggests Gln
 291 GLU   ( 322-)  A   H-bonding suggests Gln
 316 ASP   ( 347-)  A   H-bonding suggests Asn
 573 ASP   (  53-)  B   H-bonding suggests Asn
 843 GLU   ( 322-)  B   H-bonding suggests Gln
 868 ASP   ( 347-)  B   H-bonding suggests Asn
1125 ASP   (  53-)  C   H-bonding suggests Asn
1309 GLU   ( 236-)  C   H-bonding suggests Gln
1395 GLU   ( 322-)  C   H-bonding suggests Gln
1420 ASP   ( 347-)  C   H-bonding suggests Asn
1795 GLU   ( 170-)  D   H-bonding suggests Gln
1947 GLU   ( 322-)  D   H-bonding suggests Gln
1972 ASP   ( 347-)  D   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.231
  2nd generation packing quality :  -1.530
  Ramachandran plot appearance   :  -0.997
  chi-1/chi-2 rotamer normality  :  -1.598
  Backbone conformation          :  -1.180

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.317 (tight)
  Bond angles                    :   0.521 (tight)
  Omega angle restraints         :   0.825
  Side chain planarity           :   0.279 (tight)
  Improper dihedral distribution :   0.502
  B-factor distribution          :   0.543
  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 : 2.45


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.0
  2nd generation packing quality :  -0.1
  Ramachandran plot appearance   :   0.8
  chi-1/chi-2 rotamer normality  :   0.5
  Backbone conformation          :  -1.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.317 (tight)
  Bond angles                    :   0.521 (tight)
  Omega angle restraints         :   0.825
  Side chain planarity           :   0.279 (tight)
  Improper dihedral distribution :   0.502
  B-factor distribution          :   0.543
  Inside/Outside distribution    :   1.107
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    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,
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      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.