WHAT IF Check report

This file was created 2011-12-17 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb3nxq.ent

Checks that need to be done early-on in validation

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.

1233 RX4   ( 700-)  A  -
1234 BMA   ( 636-)  A  -
1236 PEG   ( 706-)  A  -
1239 PEG   ( 710-)  B  -
1240 A11   ( 709-)  A  -
1241 A10   ( 705-)  B  -
1242 PG4   ( 704-)  B  -
1243 BMA   ( 636-)  B  -
1244 RX4   ( 700-)  B  -
1245 P6G   ( 708-)  A  -

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.

1220 NAG   ( 632-)  A  -   O4  bound to 1221 NAG   ( 633-)  A  -   C1
1222 NAG   ( 634-)  A  -   O4  bound to 1223 NAG   ( 635-)  A  -   C1
1223 NAG   ( 635-)  A  -   O4  bound to 1234 BMA   ( 636-)  A  -   C1
1227 NAG   ( 632-)  B  -   O4  bound to 1228 NAG   ( 633-)  B  -   C1
1229 NAG   ( 634-)  B  -   O4  bound to 1230 NAG   ( 635-)  B  -   C1
1230 NAG   ( 635-)  B  -   O4  bound to 1243 BMA   ( 636-)  B  -   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

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

  56 GLU   (  56-)  A      CD
  56 GLU   (  56-)  A      OE1
  56 GLU   (  56-)  A      OE2
  70 GLN   (  70-)  A      CD
  70 GLN   (  70-)  A      OE1
  70 GLN   (  70-)  A      NE2
 129 LEU   ( 129-)  A      CG
 129 LEU   ( 129-)  A      CD1
 129 LEU   ( 129-)  A      CD2
 130 THR   ( 133-)  A      OG1
 130 THR   ( 133-)  A      CG2
 132 THR   ( 135-)  A      OG1
 132 THR   ( 135-)  A      CG2
 270 ASP   ( 273-)  A      CG
 270 ASP   ( 273-)  A      OD1
 270 ASP   ( 273-)  A      OD2
 338 LYS   ( 341-)  A      CD
 338 LYS   ( 341-)  A      CE
 338 LYS   ( 341-)  A      NZ
 400 GLU   ( 403-)  A      CD
 400 GLU   ( 403-)  A      OE1
 400 GLU   ( 403-)  A      OE2
 410 ARG   ( 413-)  A      CG
 410 ARG   ( 413-)  A      CD
 410 ARG   ( 413-)  A      NE
And so on for a total of 91 lines.

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: 10

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

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

  96 ARG   (  96-)  A
 148 ARG   ( 151-)  A
 196 ARG   ( 199-)  A
 228 ARG   ( 231-)  A
 464 ARG   ( 467-)  A
 703 ARG   (  96-)  B
 758 ARG   ( 151-)  B
 806 ARG   ( 199-)  B
 838 ARG   ( 231-)  B
1074 ARG   ( 467-)  B

Warning: Tyrosine convention problem

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

  76 TYR   (  76-)  A
 122 TYR   ( 122-)  A
 150 TYR   ( 153-)  A
 183 TYR   ( 186-)  A
 234 TYR   ( 237-)  A
 238 TYR   ( 241-)  A
 335 TYR   ( 338-)  A
 365 TYR   ( 368-)  A
 366 TYR   ( 369-)  A
 456 TYR   ( 459-)  A
 467 TYR   ( 470-)  A
 498 TYR   ( 501-)  A
 570 TYR   ( 573-)  A
 683 TYR   (  76-)  B
 760 TYR   ( 153-)  B
 793 TYR   ( 186-)  B
 844 TYR   ( 237-)  B
 848 TYR   ( 241-)  B
 945 TYR   ( 338-)  B
 975 TYR   ( 368-)  B
 976 TYR   ( 369-)  B
1066 TYR   ( 459-)  B
1077 TYR   ( 470-)  B
1108 TYR   ( 501-)  B
1180 TYR   ( 573-)  B

Warning: Phenylalanine convention problem

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

  10 PHE   (  10-)  A
 188 PHE   ( 191-)  A
 268 PHE   ( 271-)  A
 297 PHE   ( 300-)  A
 298 PHE   ( 301-)  A
 310 PHE   ( 313-)  A
 340 PHE   ( 343-)  A
 447 PHE   ( 450-)  A
 458 PHE   ( 461-)  A
 506 PHE   ( 509-)  A
 571 PHE   ( 574-)  A
 617 PHE   (  10-)  B
 798 PHE   ( 191-)  B
 878 PHE   ( 271-)  B
 907 PHE   ( 300-)  B
 908 PHE   ( 301-)  B
 950 PHE   ( 343-)  B
1057 PHE   ( 450-)  B
1068 PHE   ( 461-)  B
1116 PHE   ( 509-)  B
1181 PHE   ( 574-)  B

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.

   2 ASP   (   2-)  A
  43 ASP   (  43-)  A
  85 ASP   (  85-)  A
 206 ASP   ( 209-)  A
 339 ASP   ( 342-)  A
 414 ASP   ( 417-)  A
 650 ASP   (  43-)  B
 692 ASP   (  85-)  B
 885 ASP   ( 278-)  B
 949 ASP   ( 342-)  B
1170 ASP   ( 563-)  B

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.

  29 GLU   (  29-)  A
  49 GLU   (  49-)  A
  74 GLU   (  74-)  A
 158 GLU   ( 161-)  A
 205 GLU   ( 208-)  A
 296 GLU   ( 299-)  A
 312 GLU   ( 315-)  A
 478 GLU   ( 481-)  A
 606 GLU   ( 609-)  A
 621 GLU   (  14-)  B
 670 GLU   (  63-)  B
 681 GLU   (  74-)  B
 768 GLU   ( 161-)  B
 791 GLU   ( 184-)  B
 826 GLU   ( 219-)  B
 906 GLU   ( 299-)  B
 934 GLU   ( 327-)  B
1088 GLU   ( 481-)  B
1125 GLU   ( 518-)  B

Geometric checks

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.365
RMS-deviation in bond distances: 0.009

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

 |  0.997442  0.000424 -0.000157|
 |  0.000424  0.997128 -0.000308|
 | -0.000157 -0.000308  0.996840|
Proposed new scale matrix

 |  0.013757 -0.003515 -0.007031|
 | -0.000006  0.013496  0.001306|
 |  0.000002  0.000004  0.013548|
With corresponding cell

    A    =  72.695  B   =  76.483  C    =  82.387
    Alpha=  88.644  Beta=  64.176  Gamma=  75.652

The CRYST1 cell dimensions

    A    =  72.882  B   =  76.685  C    =  82.646
    Alpha=  88.630  Beta=  64.170  Gamma=  75.700

Variance: 350.745
(Under-)estimated Z-score: 13.803

Warning: Low bond angle variability

Bond angles were found to deviate less than normal from the standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond angles: 0.562
RMS-deviation in bond angles: 1.186

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.

   2 ASP   (   2-)  A
  29 GLU   (  29-)  A
  43 ASP   (  43-)  A
  49 GLU   (  49-)  A
  74 GLU   (  74-)  A
  85 ASP   (  85-)  A
  96 ARG   (  96-)  A
 148 ARG   ( 151-)  A
 158 GLU   ( 161-)  A
 196 ARG   ( 199-)  A
 205 GLU   ( 208-)  A
 206 ASP   ( 209-)  A
 228 ARG   ( 231-)  A
 296 GLU   ( 299-)  A
 312 GLU   ( 315-)  A
 339 ASP   ( 342-)  A
 414 ASP   ( 417-)  A
 464 ARG   ( 467-)  A
 478 GLU   ( 481-)  A
 606 GLU   ( 609-)  A
 621 GLU   (  14-)  B
 650 ASP   (  43-)  B
 670 GLU   (  63-)  B
 681 GLU   (  74-)  B
 692 ASP   (  85-)  B
 703 ARG   (  96-)  B
 758 ARG   ( 151-)  B
 768 GLU   ( 161-)  B
 791 GLU   ( 184-)  B
 806 ARG   ( 199-)  B
 826 GLU   ( 219-)  B
 838 ARG   ( 231-)  B
 885 ASP   ( 278-)  B
 906 GLU   ( 299-)  B
 934 GLU   ( 327-)  B
 949 ASP   ( 342-)  B
1074 ARG   ( 467-)  B
1088 GLU   ( 481-)  B
1125 GLU   ( 518-)  B
1170 ASP   ( 563-)  B

Warning: Chirality deviations detected

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

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

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

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

1177 LEU   ( 570-)  B      CG     7.9   -19.06   -33.01
The average deviation= 0.644

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.

1215 PRO   ( 608-)  B    -3.0
 605 PRO   ( 608-)  A    -3.0
 492 VAL   ( 495-)  A    -2.6
 349 THR   ( 352-)  A    -2.6
 369 TYR   ( 372-)  A    -2.4
 758 ARG   ( 151-)  B    -2.4
 871 ILE   ( 264-)  B    -2.4
 979 TYR   ( 372-)  B    -2.3
 138 PRO   ( 141-)  A    -2.3
 748 PRO   ( 141-)  B    -2.3
 740 THR   ( 133-)  B    -2.3
 276 VAL   ( 279-)  A    -2.3
 456 TYR   ( 459-)  A    -2.2
 496 ILE   ( 499-)  A    -2.2
 200 ASN   ( 203-)  A    -2.2
1139 ARG   ( 532-)  B    -2.1
 481 PHE   ( 484-)  A    -2.1
1091 PHE   ( 484-)  B    -2.1

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 ALA   (  12-)  A  Poor phi/psi
  79 ILE   (  79-)  A  Poor phi/psi
 137 ASP   ( 140-)  A  PRO omega poor
 200 ASN   ( 203-)  A  Poor phi/psi
 302 GLU   ( 305-)  A  Poor phi/psi
 335 TYR   ( 338-)  A  Poor phi/psi
 337 ARG   ( 340-)  A  Poor phi/psi
 373 PRO   ( 376-)  A  omega poor
 380 ALA   ( 383-)  A  omega poor
 529 ARG   ( 532-)  A  Poor phi/psi
 556 MET   ( 559-)  A  omega poor
 604 TYR   ( 607-)  A  PRO omega poor
 682 LEU   (  75-)  B  omega poor
 740 THR   ( 133-)  B  Poor phi/psi
 747 ASP   ( 140-)  B  PRO omega poor
 748 PRO   ( 141-)  B  omega poor
 912 GLU   ( 305-)  B  Poor phi/psi
 945 TYR   ( 338-)  B  Poor phi/psi
 947 ARG   ( 340-)  B  Poor phi/psi
 983 PRO   ( 376-)  B  omega poor
 990 ALA   ( 383-)  B  omega poor
1139 ARG   ( 532-)  B  Poor phi/psi
1166 MET   ( 559-)  B  omega poor
1214 TYR   ( 607-)  B  PRO omega poor
 chi-1/chi-2 correlation Z-score : -0.497

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.

  29 GLU   (  29-)  A    0.33
 919 GLU   ( 312-)  B    0.33
 888 SER   ( 281-)  B    0.36
  35 SER   (  35-)  A    0.36
  26 SER   (  26-)  A    0.36
 116 SER   ( 116-)  A    0.36
 642 SER   (  35-)  B    0.36
 723 SER   ( 116-)  B    0.37
 179 SER   ( 182-)  A    0.37
 668 SER   (  61-)  B    0.37
 789 SER   ( 182-)  B    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!

   9 GLN   (   9-)  A      0
  12 ALA   (  12-)  A      0
  44 THR   (  44-)  A      0
  45 ASN   (  45-)  A      0
  76 TYR   (  76-)  A      0
  78 PRO   (  78-)  A      0
  79 ILE   (  79-)  A      0
  83 PHE   (  83-)  A      0
  97 THR   (  97-)  A      0
 100 SER   ( 100-)  A      0
 128 CYS   ( 128-)  A      0
 129 LEU   ( 129-)  A      0
 130 THR   ( 133-)  A      0
 131 ALA   ( 134-)  A      0
 136 LEU   ( 139-)  A      0
 146 SER   ( 149-)  A      0
 198 TRP   ( 201-)  A      0
 234 TYR   ( 237-)  A      0
 238 TYR   ( 241-)  A      0
 242 ARG   ( 245-)  A      0
 248 HIS   ( 251-)  A      0
 249 LEU   ( 252-)  A      0
 250 LEU   ( 253-)  A      0
 254 TRP   ( 257-)  A      0
 256 GLN   ( 259-)  A      0
And so on for a total of 366 lines.

Warning: Unusual PRO puckering phases

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

   3 PRO   (   3-)  A   110.9 envelop C-beta (108 degrees)
 138 PRO   ( 141-)  A   -63.7 envelop C-beta (-72 degrees)
 170 PRO   ( 173-)  A  -124.6 half-chair C-delta/C-gamma (-126 degrees)
 434 PRO   ( 437-)  A  -112.3 envelop C-gamma (-108 degrees)
 605 PRO   ( 608-)  A   -22.6 half-chair C-alpha/N (-18 degrees)
 737 PRO   ( 130-)  B  -113.9 envelop C-gamma (-108 degrees)
 748 PRO   ( 141-)  B   -58.2 half-chair C-beta/C-alpha (-54 degrees)
 854 PRO   ( 247-)  B    47.3 half-chair C-delta/C-gamma (54 degrees)
 882 PRO   ( 275-)  B  -126.2 half-chair C-delta/C-gamma (-126 degrees)
1044 PRO   ( 437-)  B  -119.6 half-chair C-delta/C-gamma (-126 degrees)
1063 PRO   ( 456-)  B    99.2 envelop C-beta (108 degrees)
1215 PRO   ( 608-)  B   -29.4 envelop C-alpha (-36 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.

1230 NAG   ( 635-)  B      O4  <-> 1243 BMA   ( 636-)  B      C1     0.96    1.44  INTRA BF
1230 NAG   ( 635-)  B      C4  <-> 1243 BMA   ( 636-)  B      C1     0.83    2.37  INTRA BF
 661 GLN   (  54-)  B      NE2 <-> 1247 HOH   ( 829 )  B      O      0.46    2.24  INTRA
 126 LYS   ( 126-)  A      NZ  <->  324 GLU   ( 327-)  A      OE2    0.25    2.45  INTRA BF
 349 THR   ( 352-)  A      CG2 <->  351 ASP   ( 354-)  A      OD2    0.20    2.60  INTRA
 362 HIS   ( 365-)  A      ND1 <->  385 HIS   ( 388-)  A      ND1    0.20    2.80  INTRA BL
1105 TYR   ( 498-)  B      OH  <-> 1244 RX4   ( 700-)  B      NAD    0.18    2.52  INTRA BL
1205 GLN   ( 598-)  B      NE2 <-> 1247 HOH   ( 779 )  B      O      0.18    2.52  INTRA
 867 SER   ( 260-)  B      OG  <->  869 GLU   ( 262-)  B      OE1    0.18    2.22  INTRA
 401 HIS   ( 404-)  A      NE2 <-> 1246 HOH   ( 876 )  A      O      0.17    2.53  INTRA BL
1011 HIS   ( 404-)  B      NE2 <-> 1247 HOH   ( 839 )  B      O      0.17    2.53  INTRA BL
1060 ARG   ( 453-)  B      NH2 <-> 1242 PG4   ( 704-)  B      O5     0.16    2.54  INTRA
1118 PHE   ( 511-)  B      CD1 <-> 1166 MET   ( 559-)  B      SD     0.16    3.24  INTRA
1096 LYS   ( 489-)  B      NZ  <-> 1244 RX4   ( 700-)  B      NAD    0.16    2.84  INTRA BL
 820 HIS   ( 213-)  B      ND1 <-> 1247 HOH   ( 891 )  B      O      0.15    2.55  INTRA BF
 508 PHE   ( 511-)  A      CD1 <->  556 MET   ( 559-)  A      SD     0.15    3.25  INTRA
 378 ARG   ( 381-)  A      NH2 <-> 1233 RX4   ( 700-)  A      OAK    0.15    2.55  INTRA
 349 THR   ( 352-)  A      CG2 <->  351 ASP   ( 354-)  A      CG     0.15    3.05  INTRA
1039 LYS   ( 432-)  B      NZ  <-> 1247 HOH   ( 887 )  B      O      0.14    2.56  INTRA BL
 409 ASP   ( 412-)  A      O   <->  410 ARG   ( 413-)  A      C      0.14    2.46  INTRA BF
 708 ALA   ( 101-)  B      O   <->  715 ARG   ( 108-)  B      NH2    0.14    2.56  INTRA
 256 GLN   ( 259-)  A      OE1 <->  486 LYS   ( 489-)  A      NZ     0.13    2.57  INTRA BL
  66 GLU   (  66-)  A      CD  <->  108 ARG   ( 108-)  A      NH2    0.13    2.97  INTRA
 938 HIS   ( 331-)  B      O   <->  953 LYS   ( 346-)  B      NZ     0.10    2.60  INTRA BL
 697 ARG   (  90-)  B      NH2 <-> 1247 HOH   ( 675 )  B      O      0.10    2.60  INTRA
And so on for a total of 61 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

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.

 450 ARG   ( 453-)  A      -6.87
1060 ARG   ( 453-)  B      -6.77
 736 LEU   ( 129-)  B      -6.69
1216 GLU   ( 609-)  B      -6.29
   9 GLN   (   9-)  A      -6.25
 519 GLU   ( 522-)  A      -5.98
 613 GLN   (   6-)  B      -5.98
1214 TYR   ( 607-)  B      -5.97
1128 TYR   ( 521-)  B      -5.86
 616 GLN   (   9-)  B      -5.81
 282 GLN   ( 285-)  A      -5.65
 233 ARG   ( 236-)  A      -5.64
 892 GLN   ( 285-)  B      -5.60
1194 GLN   ( 587-)  B      -5.59
 283 GLN   ( 286-)  A      -5.59
   6 GLN   (   6-)  A      -5.58
 584 GLN   ( 587-)  A      -5.58
 893 GLN   ( 286-)  B      -5.55
 542 ARG   ( 545-)  A      -5.51
 518 TYR   ( 521-)  A      -5.50
 847 ARG   ( 240-)  B      -5.50
1207 HIS   ( 600-)  B      -5.48
 597 HIS   ( 600-)  A      -5.48
1152 ARG   ( 545-)  B      -5.47
 843 ARG   ( 236-)  B      -5.44
1134 GLN   ( 527-)  B      -5.42
 524 GLN   ( 527-)  A      -5.37
 604 TYR   ( 607-)  A      -5.33
 585 ASN   ( 588-)  A      -5.32
 921 TRP   ( 314-)  B      -5.31
 413 ASN   ( 416-)  A      -5.31
  82 GLN   (  82-)  A      -5.29
 947 ARG   ( 340-)  B      -5.27
 102 ASN   ( 102-)  A      -5.26
 311 TRP   ( 314-)  A      -5.26
 689 GLN   (  82-)  B      -5.25
 709 ASN   ( 102-)  B      -5.25
1210 LEU   ( 603-)  B      -5.19
 232 ARG   ( 235-)  A      -5.18
1199 LEU   ( 592-)  B      -5.18
 851 LEU   ( 244-)  B      -5.15
 468 GLN   ( 471-)  A      -5.11
1078 GLN   ( 471-)  B      -5.09
 606 GLU   ( 609-)  A      -5.01

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.

 232 ARG   ( 235-)  A       234 - TYR    237- ( A)         -5.04
 311 TRP   ( 314-)  A       313 - GLY    316- ( A)         -4.52
 842 ARG   ( 235-)  B       844 - TYR    237- ( B)         -4.76
 921 TRP   ( 314-)  B       923 - GLY    316- ( B)         -4.55

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

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.

  98 LEU   (  98-)  A   -3.42
 520 GLY   ( 523-)  A   -3.07
 738 GLN   ( 131-)  B   -2.97
1020 ARG   ( 413-)  B   -2.78
 410 ARG   ( 413-)  A   -2.74
1015 ILE   ( 408-)  B   -2.63
1129 GLU   ( 522-)  B   -2.59
 405 ILE   ( 408-)  A   -2.57
 881 LYS   ( 274-)  B   -2.54
 705 LEU   (  98-)  B   -2.51

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

Water, ion, and hydrogenbond related checks

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.

1247 HOH   ( 815 )  B      O
Bound group on Asn; dont flip   45 ASN  (  45-) A
Bound to: 1220 NAG  ( 632-) A
Bound group on Asn; dont flip  413 ASN  ( 416-) A
Bound to: 1222 NAG  ( 634-) A
Bound group on Asn; dont flip  477 ASN  ( 480-) A
Bound to: 1218 NAG  ( 630-) A
Bound group on Asn; dont flip  652 ASN  (  45-) B
Bound to: 1227 NAG  ( 632-) B
Bound group on Asn; dont flip 1023 ASN  ( 416-) B
Bound to: 1229 NAG  ( 634-) B
Bound group on Asn; dont flip 1087 ASN  ( 480-) B
Bound to: 1225 NAG  ( 630-) B
Marked this atom as acceptor 1235  CL  ( 900-) A     CL
Marked this atom as acceptor 1237  CL  ( 900-) B     CL
Metal-coordinating Histidine residue 358 fixed to   1
Metal-coordinating Histidine residue 362 fixed to   1
Metal-coordinating Histidine residue 968 fixed to   1
Metal-coordinating Histidine residue 972 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.

   9 GLN   (   9-)  A
  25 GLN   (  25-)  A
  87 GLN   (  87-)  A
 368 GLN   ( 371-)  A
 595 GLN   ( 598-)  A
 632 GLN   (  25-)  B
 795 GLN   ( 188-)  B
 962 GLN   ( 355-)  B
1013 HIS   ( 406-)  B
1191 GLN   ( 584-)  B
1205 GLN   ( 598-)  B

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.

  10 PHE   (  10-)  A      N
 122 TYR   ( 122-)  A      OH
 128 CYS   ( 128-)  A      N
 139 ASP   ( 142-)  A      N
 148 ARG   ( 151-)  A      N
 148 ARG   ( 151-)  A      NH1
 190 ASP   ( 193-)  A      N
 203 THR   ( 206-)  A      N
 257 SER   ( 260-)  A      N
 331 ALA   ( 334-)  A      N
 340 PHE   ( 343-)  A      N
 352 GLN   ( 355-)  A      N
 364 GLN   ( 367-)  A      NE2
 370 LYS   ( 373-)  A      N
 381 ASN   ( 384-)  A      N
 390 ASP   ( 393-)  A      N
 414 ASP   ( 417-)  A      N
 432 PHE   ( 435-)  A      N
 441 GLN   ( 444-)  A      NE2
 464 ARG   ( 467-)  A      NE
 474 VAL   ( 477-)  A      N
 476 ARG   ( 479-)  A      NH1
 488 HIS   ( 491-)  A      N
 495 TYR   ( 498-)  A      OH
 520 GLY   ( 523-)  A      N
And so on for a total of 56 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.

  42 HIS   (  42-)  A      NE2
 328 HIS   ( 331-)  A      NE2
 344 GLN   ( 347-)  A      OE1
 359 GLU   ( 362-)  A      OE1
 359 GLU   ( 362-)  A      OE2
 488 HIS   ( 491-)  A      NE2
 938 HIS   ( 331-)  B      NE2
 954 GLN   ( 347-)  B      OE1
 969 GLU   ( 362-)  B      OE1
 969 GLU   ( 362-)  B      OE2
1098 HIS   ( 491-)  B      NE2

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.

1246 HOH   ( 824 )  A      O  0.99  K  4
1246 HOH   ( 921 )  A      O  0.98 NA  4 *2
1247 HOH   ( 756 )  B      O  1.01  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.

 817 ASP   ( 210-)  B   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 :  -0.780
  2nd generation packing quality :  -1.210
  Ramachandran plot appearance   :   0.289
  chi-1/chi-2 rotamer normality  :  -0.497
  Backbone conformation          :  -0.122

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.365 (tight)
  Bond angles                    :   0.562 (tight)
  Omega angle restraints         :   0.884
  Side chain planarity           :   0.337 (tight)
  Improper dihedral distribution :   0.558
  B-factor distribution          :   0.326
  Inside/Outside distribution    :   1.012

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 : 1.99


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.4
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :   0.8
  chi-1/chi-2 rotamer normality  :   0.2
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.365 (tight)
  Bond angles                    :   0.562 (tight)
  Omega angle restraints         :   0.884
  Side chain planarity           :   0.337 (tight)
  Improper dihedral distribution :   0.558
  B-factor distribution          :   0.326
  Inside/Outside distribution    :   1.012
==============

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.