WHAT IF Check report

This file was created 2013-12-10 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 pdb4bvh.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 : 1.035
CA-only RMS fit for the two chains : 0.592

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

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.

 814 OCZ   (1393-)  A  -
 815 OAD   (1394-)  A  -
 819 OCZ   (1392-)  B  -
 829 OAD   (1395-)  C  -
 830 OCZ   (1394-)  C  -
 831 AR6   (1393-)  B  -

Non-validating, descriptive output paragraph

Warning: Ions bound to the wrong chain

The ions listed in the table have a chain identifier that is the same as one of the protein, nucleic acid, or sugar chains. However, the ion seems bound to protein, nucleic acid, or sugar, with another chain identifier.

Obviously, this is not wrong, but it is confusing for users of this PDB file.

 817  NA   (1396-)  C  -

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: 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.

 149 ARG   ( 269-)  A    High
 174 PHE   ( 294-)  A    High
 413 ARG   ( 261-)  B    High

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

 285 ARG   ( 133-)  B    0.80
 310 ARG   ( 158-)  B    0.80
 421 ARG   ( 269-)  B    0.80
 484 GLU   ( 332-)  B    0.80
 497 ARG   ( 345-)  B    0.80
 681 ARG   ( 261-)  C    0.50

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

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.

 252 SER   ( 372-)  A      N    CA    1.54    4.3
 638 ASP   ( 218-)  C      CG   OD2   1.16   -4.7

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

 |  0.993766  0.000369  0.000371|
 |  0.000369  0.994003 -0.001687|
 |  0.000371 -0.001687  0.995355|
Proposed new scale matrix

 |  0.015794 -0.000006 -0.000006|
 | -0.000006  0.015122  0.000026|
 | -0.000002  0.000008  0.004992|
With corresponding cell

    A    =  63.313  B   =  66.130  C    = 200.313
    Alpha=  90.194  Beta=  89.957  Gamma=  89.958

The CRYST1 cell dimensions

    A    =  63.710  B   =  66.530  C    = 201.240
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 884.632
(Under-)estimated Z-score: 21.920

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.

  13 ARG   ( 133-)  A      CB   CG   CD  104.72   -4.7
  90 HIS   ( 210-)  A      CG   ND1  CE1 109.61    4.0
 128 HIS   ( 248-)  A      CG   ND1  CE1 109.71    4.1
 231 LEU   ( 351-)  A      CA   CB   CG  100.95   -4.4
 285 ARG   ( 133-)  B      CD   NE   CZ  128.94    4.0
 400 HIS   ( 248-)  B      CG   ND1  CE1 109.85    4.3
 432 CYS   ( 280-)  B      CA   CB   SG  126.15    5.1
 478 PRO   ( 326-)  B      N    CA   C   125.30    5.4
 541 ARG   ( 389-)  B      CG   CD   NE  121.09    6.2
 607 HIS   ( 187-)  C      CG   ND1  CE1 109.61    4.0
 639 LYS   ( 219-)  C      CA   CB   CG  105.04   -4.5
 668 HIS   ( 248-)  C      CG   ND1  CE1 109.73    4.1
 771 LEU   ( 351-)  C      CA   CB   CG   99.02   -4.9
 788 HIS   ( 368-)  C      CG   ND1  CE1 109.61    4.0

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.

 571 ILE   ( 148-)  C    5.88
 188 ASP   ( 308-)  A    5.01
 478 PRO   ( 326-)  B    4.88
 590 ASN   ( 167-)  C    4.09

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.

  90 HIS   ( 210-)  A    4.93
 549 GLN   ( 126-)  C    4.45
 369 HIS   ( 217-)  B    4.14

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.

 506 HIS   ( 354-)  B    -2.8
 607 HIS   ( 187-)  C    -2.6
 341 PRO   ( 189-)  B    -2.5
 545 LYS   ( 122-)  C    -2.5
  63 PRO   ( 183-)  A    -2.4
 130 THR   ( 250-)  A    -2.3
 609 PRO   ( 189-)  C    -2.3
 670 THR   ( 250-)  C    -2.3
 402 THR   ( 250-)  B    -2.3
  69 PRO   ( 189-)  A    -2.3
 410 VAL   ( 258-)  B    -2.3
 704 THR   ( 284-)  C    -2.2
 472 THR   ( 320-)  B    -2.2
   2 LYS   ( 122-)  A    -2.2
 740 THR   ( 320-)  C    -2.2
 434 VAL   ( 282-)  B    -2.1
 328 PRO   ( 176-)  B    -2.1
 140 GLN   ( 260-)  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.

   2 LYS   ( 122-)  A  omega poor
  15 ARG   ( 135-)  A  omega poor
  25 GLY   ( 145-)  A  omega poor
  37 PHE   ( 157-)  A  omega poor
  46 SER   ( 166-)  A  omega poor
 140 GLN   ( 260-)  A  Poor phi/psi
 145 GLY   ( 265-)  A  Poor phi/psi
 155 ASP   ( 275-)  A  Poor phi/psi
 164 THR   ( 284-)  A  Poor phi/psi
 170 ASP   ( 290-)  A  Poor phi/psi
 202 LEU   ( 322-)  A  Poor phi/psi
 205 GLU   ( 325-)  A  PRO omega poor
 228 VAL   ( 348-)  A  omega poor
 236 ARG   ( 356-)  A  omega poor
 242 GLN   ( 362-)  A  omega poor
 259 TRP   ( 379-)  A  omega poor
 271 THR   ( 391-)  A  omega poor
 297 GLY   ( 145-)  B  omega poor
 308 ASP   ( 156-)  B  Poor phi/psi
 309 PHE   ( 157-)  B  omega poor
 324 ASP   ( 172-)  B  Poor phi/psi
 339 HIS   ( 187-)  B  omega poor
 340 ASN   ( 188-)  B  Poor phi/psi
 401 GLY   ( 249-)  B  omega poor
 410 VAL   ( 258-)  B  Poor phi/psi
 412 GLN   ( 260-)  B  Poor phi/psi
 417 GLY   ( 265-)  B  omega poor
 418 GLU   ( 266-)  B  Poor phi/psi
 427 ASP   ( 275-)  B  Poor phi/psi
 428 ARG   ( 276-)  B  omega poor
 442 ASP   ( 290-)  B  Poor phi/psi
 445 PHE   ( 293-)  B  omega poor
 447 GLY   ( 295-)  B  omega poor
 470 LEU   ( 318-)  B  omega poor
 474 LEU   ( 322-)  B  Poor phi/psi
 477 GLU   ( 325-)  B  PRO omega poor
 514 GLN   ( 362-)  B  omega poor
 558 ARG   ( 135-)  C  Poor phi/psi
 568 GLY   ( 145-)  C  omega poor
 580 PHE   ( 157-)  C  omega poor
 584 GLY   ( 161-)  C  omega poor
 589 SER   ( 166-)  C  omega poor
 607 HIS   ( 187-)  C  Poor phi/psi
 669 GLY   ( 249-)  C  omega poor
 680 GLN   ( 260-)  C  Poor phi/psi
 704 THR   ( 284-)  C  Poor phi/psi
 710 ASP   ( 290-)  C  Poor phi/psi
 745 GLU   ( 325-)  C  PRO omega poor
 755 ARG   ( 335-)  C  omega poor
 chi-1/chi-2 correlation Z-score : -1.678

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.

 252 SER   ( 372-)  A    0.36

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!

  15 ARG   ( 135-)  A      0
  16 ALA   ( 136-)  A      0
  17 CYS   ( 137-)  A      0
  18 GLN   ( 138-)  A      0
  19 ARG   ( 139-)  A      0
  32 SER   ( 152-)  A      0
  37 PHE   ( 157-)  A      0
  38 ARG   ( 158-)  A      0
  40 PRO   ( 160-)  A      0
  47 ASN   ( 167-)  A      0
  51 TYR   ( 171-)  A      0
  52 ASP   ( 172-)  A      0
  53 LEU   ( 173-)  A      0
  54 PRO   ( 174-)  A      0
  55 TYR   ( 175-)  A      0
  67 HIS   ( 187-)  A      0
  68 ASN   ( 188-)  A      0
  80 TYR   ( 200-)  A      0
  81 PRO   ( 201-)  A      0
 101 LEU   ( 221-)  A      0
 104 ARG   ( 224-)  A      0
 108 GLN   ( 228-)  A      0
 110 ILE   ( 230-)  A      0
 117 SER   ( 237-)  A      0
 124 LEU   ( 244-)  A      0
And so on for a total of 305 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!

 447 GLY   ( 295-)  B   1.97   80

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]

 158 PRO   ( 278-)  A    0.16 LOW
 303 PRO   ( 151-)  B    0.48 HIGH
 307 PRO   ( 155-)  B    0.49 HIGH
 392 PRO   ( 240-)  B    0.06 LOW
 611 PRO   ( 191-)  C    0.49 HIGH
 698 PRO   ( 278-)  C    0.15 LOW
 775 PRO   ( 355-)  C    0.14 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].

  69 PRO   ( 189-)  A   -62.5 half-chair C-beta/C-alpha (-54 degrees)
  81 PRO   ( 201-)  A   100.3 envelop C-beta (108 degrees)
 177 PRO   ( 297-)  A  -172.8 envelop N (180 degrees)
 206 PRO   ( 326-)  A   -58.3 half-chair C-beta/C-alpha (-54 degrees)
 230 PRO   ( 350-)  A   107.5 envelop C-beta (108 degrees)
 235 PRO   ( 355-)  A    42.9 envelop C-delta (36 degrees)
 328 PRO   ( 176-)  B   104.7 envelop C-beta (108 degrees)
 335 PRO   ( 183-)  B  -155.3 half-chair N/C-delta (-162 degrees)
 414 PRO   ( 262-)  B    30.4 envelop C-delta (36 degrees)
 433 PRO   ( 281-)  B   106.6 envelop C-beta (108 degrees)
 462 PRO   ( 310-)  B   108.2 envelop C-beta (108 degrees)
 583 PRO   ( 160-)  C   101.3 envelop C-beta (108 degrees)
 621 PRO   ( 201-)  C   153.3 half-chair C-alpha/N (162 degrees)
 682 PRO   ( 262-)  C   -59.9 half-chair C-beta/C-alpha (-54 degrees)
 730 PRO   ( 310-)  C  -115.3 envelop C-gamma (-108 degrees)
 770 PRO   ( 350-)  C   101.8 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.

 409 THR   ( 257-)  B      CB  <->  833 HOH   (2096 )  B      O      0.59    2.21  INTRA BF
  13 ARG   ( 133-)  A      NH1 <->  832 HOH   (2013 )  A      O      0.57    2.13  INTRA
 291 ARG   ( 139-)  B      NH1 <->  463 MET   ( 311-)  B    A CE     0.51    2.59  INTRA BF
 408 CYS   ( 256-)  B      SG  <->  410 VAL   ( 258-)  B      N      0.48    2.82  INTRA BF
   2 LYS   ( 122-)  A      NZ  <->  832 HOH   (2003 )  A      O      0.44    2.26  INTRA BF
 238 ARG   ( 358-)  A      NH1 <->  832 HOH   (2112 )  A      O      0.37    2.33  INTRA
 123 LYS   ( 243-)  A    A NZ  <->  832 HOH   (2050 )  A      O      0.35    2.35  INTRA
 438 VAL   ( 286-)  B      N   <->  833 HOH   (2100 )  B      O      0.34    2.36  INTRA BF
 659 ILE   ( 239-)  C    A CD1 <->  834 HOH   (2064 )  C      O      0.33    2.47  INTRA BL
 411 CYS   ( 259-)  B      SG  <->  432 CYS   ( 280-)  B      SG     0.32    3.13  INTRA BF
  77 LYS   ( 197-)  A      NZ  <->  832 HOH   (2036 )  A      O      0.29    2.41  INTRA BF
 534 GLU   ( 382-)  B      CG  <->  833 HOH   (2153 )  B      O      0.27    2.53  INTRA
 246 VAL   ( 366-)  A      N   <->  815 OAD   (1394-)  A      N1     0.27    2.73  INTRA BL
 432 CYS   ( 280-)  B      SG  <->  435 CYS   ( 283-)  B      SG     0.26    3.19  INTRA BF
 708 LYS   ( 288-)  C      NZ  <->  834 HOH   (2130 )  C      O      0.25    2.45  INTRA
 432 CYS   ( 280-)  B      N   <->  437 GLY   ( 285-)  B      O      0.25    2.45  INTRA BF
 238 ARG   ( 358-)  A      NH2 <->  832 HOH   (2111 )  A      O      0.24    2.46  INTRA
 518 VAL   ( 366-)  B      N   <->  831 AR6   (1393-)  B      N1     0.24    2.76  INTRA BL
 115 ARG   ( 235-)  A      CD  <->  282 GLU   ( 130-)  B      OE2    0.21    2.59  INTRA
 786 VAL   ( 366-)  C      N   <->  829 OAD   (1395-)  C      N1     0.21    2.79  INTRA BL
 832 HOH   (2039 )  A      O   <->  832 HOH   (2040 )  A      O      0.20    2.00  INTRA
 593 LEU   ( 173-)  C      CD1 <->  599 ILE   ( 179-)  C      CG2    0.19    3.01  INTRA BF
 699 ARG   ( 279-)  C      NH1 <->  704 THR   ( 284-)  C      O      0.18    2.52  INTRA
 461 PHE   ( 309-)  B      N   <->  462 PRO   ( 310-)  B      CD     0.18    2.82  INTRA BL
 438 VAL   ( 286-)  B      CG1 <->  833 HOH   (2100 )  B      O      0.16    2.64  INTRA BF
And so on for a total of 98 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.

 310 ARG   ( 158-)  B      -6.95
  38 ARG   ( 158-)  A      -6.94
 765 ARG   ( 345-)  C      -6.89
 225 ARG   ( 345-)  A      -6.72
 497 ARG   ( 345-)  B      -6.60
 233 TRP   ( 353-)  A      -6.40
 339 HIS   ( 187-)  B      -6.26
 773 TRP   ( 353-)  C      -6.26
 581 ARG   ( 158-)  C      -6.25
 505 TRP   ( 353-)  B      -6.24
  67 HIS   ( 187-)  A      -6.20
 140 GLN   ( 260-)  A      -5.69
 696 ARG   ( 276-)  C      -5.68
 156 ARG   ( 276-)  A      -5.54
  31 PRO   ( 151-)  A      -5.43
 574 PRO   ( 151-)  C      -5.35
 774 HIS   ( 354-)  C      -5.29
 303 PRO   ( 151-)  B      -5.07
 542 GLU   ( 390-)  B      -5.02
 431 ARG   ( 279-)  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: 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.

 455 LEU   ( 303-)  B   -2.74
 485 ALA   ( 333-)  B   -2.64

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.

 834 HOH   (2193 )  C      O      6.19  -17.40  -11.34

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.

 832 HOH   (2035 )  A      O
 833 HOH   (2086 )  B      O
 833 HOH   (2130 )  B      O
 833 HOH   (2137 )  B      O
 834 HOH   (2029 )  C      O
 834 HOH   (2127 )  C      O
 834 HOH   (2164 )  C      O
 834 HOH   (2197 )  C      O
Marked this atom as acceptor  814 OCZ  (1393-) A     CL
Marked this atom as acceptor  818  CL  (1397-) A     CL
Marked this atom as acceptor  819 OCZ  (1392-) B     CL
Marked this atom as acceptor  822  CL  (1397-) B     CL
Marked this atom as acceptor  830 OCZ  (1394-) C     CL
Metal-coordinating Histidine residue  67 fixed to   1
Metal-coordinating Histidine residue 774 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.

   6 GLN   ( 126-)  A
 242 GLN   ( 362-)  A
 248 HIS   ( 368-)  A
 278 GLN   ( 126-)  B
 355 ASN   ( 203-)  B
 506 HIS   ( 354-)  B
 549 GLN   ( 126-)  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.

  26 ALA   ( 146-)  A      N
  37 PHE   ( 157-)  A      N
  38 ARG   ( 158-)  A      N
  38 ARG   ( 158-)  A      NH1
  45 TYR   ( 165-)  A      OH
  55 TYR   ( 175-)  A      N
  62 LEU   ( 182-)  A      N
 110 ILE   ( 230-)  A      N
 111 ASP   ( 231-)  A      N
 133 SER   ( 253-)  A      N
 194 LEU   ( 314-)  A      N
 200 THR   ( 320-)  A      N
 200 THR   ( 320-)  A      OG1
 201 SER   ( 321-)  A      OG
 214 VAL   ( 334-)  A      N
 224 ASN   ( 344-)  A      ND2
 225 ARG   ( 345-)  A      N
 226 ASP   ( 346-)  A      N
 228 VAL   ( 348-)  A      N
 246 VAL   ( 366-)  A      N
 276 SER   ( 124-)  B      OG
 298 ALA   ( 146-)  B      N
 309 PHE   ( 157-)  B      N
 310 ARG   ( 158-)  B      N
 310 ARG   ( 158-)  B      NH1
And so on for a total of 68 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.

 224 ASN   ( 344-)  A      OD1

Warning: Unusual ion packing

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

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

 817  NA   (1396-)  C   -.-  -.-  Too few ligands (1)

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.

 832 HOH   (2066 )  A      O  1.11  K  5
 832 HOH   (2105 )  A      O  0.90  K  4 Ion-B
 834 HOH   (2039 )  C      O  1.00  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.

 170 ASP   ( 290-)  A   H-bonding suggests Asn
 176 GLU   ( 296-)  A   H-bonding suggests Gln; but Alt-Rotamer
 193 ASP   ( 313-)  A   H-bonding suggests Asn
 442 ASP   ( 290-)  B   H-bonding suggests Asn
 465 ASP   ( 313-)  B   H-bonding suggests Asn
 733 ASP   ( 313-)  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 :  -0.994
  2nd generation packing quality :  -1.844
  Ramachandran plot appearance   :  -1.530
  chi-1/chi-2 rotamer normality  :  -1.678
  Backbone conformation          :  -0.751

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.908
  Bond angles                    :   0.968
  Omega angle restraints         :   1.235
  Side chain planarity           :   1.155
  Improper dihedral distribution :   1.194
  B-factor distribution          :   0.840
  Inside/Outside distribution    :   1.000

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 1.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.5
  2nd generation packing quality :  -1.4
  Ramachandran plot appearance   :  -1.4
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :  -1.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.908
  Bond angles                    :   0.968
  Omega angle restraints         :   1.235
  Side chain planarity           :   1.155
  Improper dihedral distribution :   1.194
  B-factor distribution          :   0.840
  Inside/Outside distribution    :   1.000
==============

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.