WHAT IF Check report

This file was created 2011-12-18 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 pdb1xq7.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 : 0.545
CA-only RMS fit for the two chains : 0.175

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 : 0.601
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 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 C

All-atom RMS fit for the two chains : 0.479
CA-only RMS fit for the two chains : 0.180

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: D and E

All-atom RMS fit for the two chains : 1.582
CA-only RMS fit for the two chains : 0.334

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: D and E

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: D and F

All-atom RMS fit for the two chains : 1.205
CA-only RMS fit for the two chains : 0.268

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: D and F

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

 517 DAL   (   1-)  D  -
 518 MVA   (   4-)  D  -
 519 BMT   (   5-)  D  -
 520 ABA   (   6-)  D  -
 521 SAR   (   7-)  D  -
 522 DAL   (   1-)  E  -
 523 MVA   (   4-)  E  -
 524 BMT   (   5-)  E  -
 525 ABA   (   6-)  E  -
 526 SAR   (   7-)  E  -
 527 SAR   (   7-)  F  -
 528 ABA   (   6-)  F  -
 529 BMT   (   5-)  F  -
 530 MVA   (   4-)  F  -
 531 DAL   (   1-)  F  -

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.

 499 MLE   (   2-)  D  -   N   bound to  517 DAL   (   1-)  D  -   C
 505 MLE   (   2-)  E  -   N   bound to  522 DAL   (   1-)  E  -   C
 511 MLE   (   2-)  F  -   N   bound to  531 DAL   (   1-)  F  -   C

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

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

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

 499 MLE   (   2-)  D
 500 MLE   (   3-)  D
 501 MLE   (   8-)  D
 503 MLE   (  10-)  D
 505 MLE   (   2-)  E
 506 MLE   (   3-)  E
 507 MLE   (   8-)  E
 509 MLE   (  10-)  E
 511 MLE   (   2-)  F
 512 MLE   (   3-)  F
 513 MLE   (   8-)  F
 515 MLE   (  10-)  F

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

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

  50 TYR   (  50-)  A
 175 TYR   (   9-)  B
 216 TYR   (  50-)  B
 382 TYR   (  50-)  C

Warning: Phenylalanine convention problem

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

  27 PHE   (  27-)  A
 193 PHE   (  27-)  B
 296 PHE   ( 130-)  B
 359 PHE   (  27-)  C
 387 PHE   (  55-)  C

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

  16 ASP   (  16-)  A
 152 ASP   ( 152-)  A
 182 ASP   (  16-)  B
 196 ASP   (  30-)  B
 318 ASP   ( 152-)  B
 348 ASP   (  16-)  C
 362 ASP   (  30-)  C
 484 ASP   ( 152-)  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.

  17 GLU   (  17-)  A
 183 GLU   (  17-)  B
 202 GLU   (  36-)  B
 211 GLU   (  45-)  B
 349 GLU   (  17-)  C

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.

   8 VAL   (   8-)  A      CA   CB    1.62    4.3
 132 LYS   ( 132-)  A      CE   NZ    1.62    4.3
 333 MET   (   1-)  C      CG   SD    1.96    4.6
 431 VAL   (  99-)  C      CA   CB    1.61    4.2

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

 |  0.996985 -0.001411  0.000390|
 | -0.001411  0.993781 -0.000171|
 |  0.000390 -0.000171  0.995766|
Proposed new scale matrix

 |  0.019193  0.005332  0.010007|
 |  0.000022  0.018293  0.009800|
 | -0.000008  0.000003  0.020402|
With corresponding cell

    A    =  52.111  B   =  56.760  C    =  58.514
    Alpha= 110.407  Beta= 108.131  Gamma= 105.599

The CRYST1 cell dimensions

    A    =  52.269  B   =  57.059  C    =  58.807
    Alpha= 110.490  Beta= 108.210  Gamma= 105.400

Variance: 339.839
(Under-)estimated Z-score: 13.586

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.

  94 HIS   (  94-)  A      CG   ND1  CE1 109.80    4.2
 132 LYS   ( 132-)  A      CD   CE   NZ  124.97    4.1
 150 LEU   ( 150-)  A      CA   CB   CG  135.43    5.5
 260 HIS   (  94-)  B      CG   ND1  CE1 109.88    4.3
 312 THR   ( 146-)  B      C    CA   CB  100.51   -5.0
 333 MET   (   1-)  C      CB   CG   SD  124.81    4.0
 459 HIS   ( 127-)  C      CG   ND1  CE1 109.74    4.1
 480 THR   ( 148-)  C      CG2  CB   OG1 100.90   -4.2
 510 ALA   (  11-)  E      N    CA   C   122.67    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.

  16 ASP   (  16-)  A
  17 GLU   (  17-)  A
 152 ASP   ( 152-)  A
 182 ASP   (  16-)  B
 183 GLU   (  17-)  B
 196 ASP   (  30-)  B
 202 GLU   (  36-)  B
 211 GLU   (  45-)  B
 318 ASP   ( 152-)  B
 348 ASP   (  16-)  C
 349 GLU   (  17-)  C
 362 ASP   (  30-)  C
 484 ASP   ( 152-)  C

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.

 475 VAL   ( 143-)  C    4.76
 510 ALA   (  11-)  E    4.68

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.

 109 ASN   ( 109-)  A    4.16

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.

  83 THR   (  83-)  A    -2.8
 228 PHE   (  62-)  B    -2.5
  84 ARG   (  84-)  A    -2.5
 410 LYS   (  78-)  C    -2.4
 151 ASN   ( 151-)  A    -2.4
 307 LYS   ( 141-)  B    -2.4
 298 LYS   ( 132-)  B    -2.4
 229 MET   (  63-)  B    -2.4
 394 PHE   (  62-)  C    -2.3
 416 ARG   (  84-)  C    -2.3
  63 MET   (  63-)  A    -2.3
 135 GLU   ( 135-)  A    -2.3
  62 PHE   (  62-)  A    -2.2
 363 VAL   (  31-)  C    -2.2
 257 LYS   (  91-)  B    -2.2
 244 LYS   (  78-)  B    -2.2
 395 MET   (  63-)  C    -2.1
 110 GLY   ( 110-)  A    -2.1
 338 ASP   (   6-)  C    -2.1
  31 VAL   (  31-)  A    -2.1
 442 GLY   ( 110-)  C    -2.1
 467 GLU   ( 135-)  C    -2.1
 276 GLY   ( 110-)  B    -2.1
 181 GLY   (  15-)  B    -2.0
 197 VAL   (  31-)  B    -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.

  12 ILE   (  12-)  A  omega poor
  16 ASP   (  16-)  A  Poor phi/psi
  44 GLY   (  44-)  A  omega poor
  54 ILE   (  54-)  A  omega poor
  61 ASN   (  61-)  A  Poor phi/psi
  62 PHE   (  62-)  A  Poor phi/psi
  72 PHE   (  72-)  A  Poor phi/psi
  85 PHE   (  85-)  A  omega poor
  99 VAL   (  99-)  A  omega poor
 151 ASN   ( 151-)  A  Poor phi/psi
 152 ASP   ( 152-)  A  Poor phi/psi
 182 ASP   (  16-)  B  Poor phi/psi
 215 GLY   (  49-)  B  omega poor
 221 PHE   (  55-)  B  omega poor
 227 ASN   (  61-)  B  Poor phi/psi
 228 PHE   (  62-)  B  Poor phi/psi
 238 PHE   (  72-)  B  Poor phi/psi
 239 ASP   (  73-)  B  Poor phi/psi
 247 TYR   (  81-)  B  omega poor
 256 LEU   (  90-)  B  omega poor
 265 VAL   (  99-)  B  omega poor
 273 ASN   ( 107-)  B  Poor phi/psi
 318 ASP   ( 152-)  B  Poor phi/psi
 324 VAL   ( 158-)  B  omega poor
 331 VAL   ( 165-)  B  omega poor
 348 ASP   (  16-)  C  Poor phi/psi
 386 ILE   (  54-)  C  omega poor
 393 ASN   (  61-)  C  Poor phi/psi
 394 PHE   (  62-)  C  Poor phi/psi
 395 MET   (  63-)  C  omega poor
 404 PHE   (  72-)  C  Poor phi/psi
 413 TYR   (  81-)  C  omega poor
 417 PHE   (  85-)  C  omega poor
 458 ARG   ( 126-)  C  Poor phi/psi
 481 GLY   ( 149-)  C  omega poor
 483 ASN   ( 151-)  C  Poor phi/psi, omega poor
 502 VAL   (   9-)  D  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.030

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.030

Warning: Unusual backbone conformations

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

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

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

   5 THR   (   5-)  A      0
  16 ASP   (  16-)  A      0
  18 PRO   (  18-)  A      0
  19 VAL   (  19-)  A      0
  27 PHE   (  27-)  A      0
  30 ASP   (  30-)  A      0
  31 VAL   (  31-)  A      0
  43 SER   (  43-)  A      0
  45 GLU   (  45-)  A      0
  48 PHE   (  48-)  A      0
  50 TYR   (  50-)  A      0
  51 LYS   (  51-)  A      0
  53 SER   (  53-)  A      0
  54 ILE   (  54-)  A      0
  55 PHE   (  55-)  A      0
  56 HIS   (  56-)  A      0
  57 ARG   (  57-)  A      0
  60 ARG   (  60-)  A      0
  61 ASN   (  61-)  A      0
  62 PHE   (  62-)  A      0
  63 MET   (  63-)  A      0
  70 THR   (  70-)  A      0
  71 ASN   (  71-)  A      0
  72 PHE   (  72-)  A      0
  73 ASP   (  73-)  A      0
And so on for a total of 272 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 7.069

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]

 287 PRO   ( 121-)  B    0.14 LOW
 350 PRO   (  18-)  C    0.18 LOW
 364 PRO   (  32-)  C    0.08 LOW

Warning: Unusual PRO puckering phases

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

  32 PRO   (  32-)  A  -118.0 half-chair C-delta/C-gamma (-126 degrees)
 168 PRO   (   2-)  B  -113.9 envelop C-gamma (-108 degrees)
 334 PRO   (   2-)  C    50.8 half-chair C-delta/C-gamma (54 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.

 529 BMT   (   5-)  F      N   <->  530 MVA   (   4-)  F      C      1.37    1.33  INTRA BL
 527 SAR   (   7-)  F      N   <->  528 ABA   (   6-)  F      C      1.37    1.33  INTRA BL
 516 ALA   (  11-)  F      C   <->  531 DAL   (   1-)  F      N      1.37    1.33  INTRA B3
 528 ABA   (   6-)  F      N   <->  529 BMT   (   5-)  F      C      1.37    1.33  INTRA BL
 512 MLE   (   3-)  F      C   <->  530 MVA   (   4-)  F      N      1.36    1.34  INTRA B3
 513 MLE   (   8-)  F      N   <->  527 SAR   (   7-)  F      C      1.36    1.34  INTRA B3
 511 MLE   (   2-)  F      N   <->  531 DAL   (   1-)  F      C      1.35    1.35  INTRA B3
 523 MVA   (   4-)  E      C   <->  524 BMT   (   5-)  E      N      1.00    2.10  INTRA
 529 BMT   (   5-)  F      CA  <->  530 MVA   (   4-)  F      C      0.81    2.39  INTRA BL
 511 MLE   (   2-)  F      CN  <->  531 DAL   (   1-)  F      C      0.77    2.43  INTRA
 513 MLE   (   8-)  F      CA  <->  527 SAR   (   7-)  F      C      0.76    2.44  INTRA
 529 BMT   (   5-)  F      CN  <->  530 MVA   (   4-)  F      C      0.75    2.45  INTRA BL
 513 MLE   (   8-)  F      CN  <->  527 SAR   (   7-)  F      C      0.75    2.45  INTRA
 132 LYS   ( 132-)  A      CD  <->  533 HOH   (2027 )  B      O      0.72    2.08  INTRA
 511 MLE   (   2-)  F      CA  <->  531 DAL   (   1-)  F      C      0.71    2.49  INTRA
 527 SAR   (   7-)  F      CA  <->  528 ABA   (   6-)  F      C      0.70    2.40  INTRA BL
 516 ALA   (  11-)  F      CA  <->  531 DAL   (   1-)  F      N      0.64    2.46  INTRA
 528 ABA   (   6-)  F      CA  <->  529 BMT   (   5-)  F      C      0.64    2.46  INTRA BL
 512 MLE   (   3-)  F      CA  <->  530 MVA   (   4-)  F      N      0.61    2.49  INTRA
  33 LYS   (  33-)  A      CB  <->  532 HOH   (2053 )  A      O      0.57    2.23  INTRA
 523 MVA   (   4-)  E      CA  <->  524 BMT   (   5-)  E      N      0.56    2.54  INTRA
  84 ARG   (  84-)  A      CZ  <->  532 HOH   (2048 )  A      O      0.55    2.25  INTRA BF
 527 SAR   (   7-)  F      CN  <->  528 ABA   (   6-)  F      C      0.50    2.50  INTRA BL
  84 ARG   (  84-)  A      NH1 <->  532 HOH   (2048 )  A      O      0.46    2.24  INTRA BF
 516 ALA   (  11-)  F      O   <->  531 DAL   (   1-)  F      N      0.44    2.26  INTRA
And so on for a total of 117 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

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.

 482 LEU   ( 150-)  C      -5.80
  60 ARG   (  60-)  A      -5.77
 392 ARG   (  60-)  C      -5.70
 226 ARG   (  60-)  B      -5.68
 514 VAL   (   9-)  F      -5.61
 508 VAL   (   9-)  E      -5.48
 502 VAL   (   9-)  D      -5.44
 416 ARG   (  84-)  C      -5.21
 317 ASN   ( 151-)  B      -5.16
 151 ASN   ( 151-)  A      -5.10
 458 ARG   ( 126-)  C      -5.10
 413 TYR   (  81-)  C      -5.06
 292 ARG   ( 126-)  B      -5.05
 250 ARG   (  84-)  B      -5.00

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

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.

 120 THR   ( 120-)  A     -  123 LEU   ( 123-)  A        -1.71
 452 THR   ( 120-)  C     -  455 LEU   ( 123-)  C        -1.79

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

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.

 534 HOH   (2005 )  C      O     61.62   35.81   29.37

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.

 532 HOH   (2012 )  A      O
 532 HOH   (2092 )  A      O
 533 HOH   (2019 )  B      O
 533 HOH   (2077 )  B      O
 534 HOH   (2040 )  C      O
 534 HOH   (2095 )  C      O
 535 HOH   (2002 )  E      O
Unrecognized bound group for 500
  Bound atom=  518 MVA  (   4-) D      N

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.

  46 ASN   (  46-)  A
  89 ASN   (  89-)  A
 151 ASN   ( 151-)  A
 212 ASN   (  46-)  B
 378 ASN   (  46-)  C

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.

  48 PHE   (  48-)  A      N
  89 ASN   (  89-)  A      N
 103 ASN   ( 103-)  A      N
 118 ALA   ( 118-)  A      N
 122 TRP   ( 122-)  A      N
 214 PHE   (  48-)  B      N
 231 GLN   (  65-)  B      NE2
 250 ARG   (  84-)  B      N
 255 ASN   (  89-)  B      N
 257 LYS   (  91-)  B      N
 258 ILE   (  92-)  B      N
 269 ASN   ( 103-)  B      N
 274 SER   ( 108-)  B      N
 284 ALA   ( 118-)  B      N
 288 TRP   ( 122-)  B      N
 329 CYS   ( 163-)  B      N
 380 PHE   (  48-)  C      N
 392 ARG   (  60-)  C      N
 410 LYS   (  78-)  C      N
 421 ASN   (  89-)  C      N
 435 ASN   ( 103-)  C      N
 444 GLN   ( 112-)  C      NE2
 450 ALA   ( 118-)  C      N
 454 TRP   ( 122-)  C      N
 480 THR   ( 148-)  C      N
 484 ASP   ( 152-)  C      N
 502 VAL   (   9-)  D      N
 508 VAL   (   9-)  E      N

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.

 338 ASP   (   6-)  C      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.

 534 HOH   (2076 )  C      O  1.13  K  4 *2 Ion-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.

   6 ASP   (   6-)  A   H-bonding suggests Asn; but Alt-Rotamer
  17 GLU   (  17-)  A   H-bonding suggests Gln
  88 GLU   (  88-)  A   H-bonding suggests Gln; but Alt-Rotamer
 138 ASP   ( 138-)  A   H-bonding suggests Asn
 304 ASP   ( 138-)  B   H-bonding suggests Asn; but Alt-Rotamer
 456 ASP   ( 124-)  C   H-bonding suggests Asn
 484 ASP   ( 152-)  C   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.894
  2nd generation packing quality :  -1.108
  Ramachandran plot appearance   :  -0.807
  chi-1/chi-2 rotamer normality  :  -3.030 (poor)
  Backbone conformation          :  -0.511

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.936
  Bond angles                    :   0.979
  Omega angle restraints         :   1.285 (loose)
  Side chain planarity           :   1.081
  Improper dihedral distribution :   1.105
  B-factor distribution          :   0.640
  Inside/Outside distribution    :   0.959

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 : 2.07


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.5
  2nd generation packing quality :  -0.7
  Ramachandran plot appearance   :  -0.0
  chi-1/chi-2 rotamer normality  :  -1.8
  Backbone conformation          :  -0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.936
  Bond angles                    :   0.979
  Omega angle restraints         :   1.285 (loose)
  Side chain planarity           :   1.081
  Improper dihedral distribution :   1.105
  B-factor distribution          :   0.640
  Inside/Outside distribution    :   0.959
==============

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.