WHAT IF Check report

This file was created 2013-12-09 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 pdb3s39.ent

Checks that need to be done early-on in validation

Warning: Topology could not be determined for some ligands

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

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

 761 HAS   ( 801-)  A  -         Atom types
 762 CUA   ( 802-)  B  -         Atom types
 767 HEM   ( 800-)  A  -         OK

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: 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.

   1 SER   (   6-)  A    High
   2 GLU   (   7-)  A    High
   3 ILE   (   8-)  A    High
   4 SER   (   9-)  A    High
   5 ARG   (  10-)  A    High
   6 VAL   (  11-)  A    High
   7 TYR   (  12-)  A    High
   8 GLU   (  13-)  A    High
   9 ALA   (  14-)  A    High
  10 TYR   (  15-)  A    High
  11 PRO   (  16-)  A    High
  12 GLU   (  17-)  A    High
  13 LYS   (  18-)  A    High
  14 LYS   (  19-)  A    High
  15 ALA   (  20-)  A    High
  16 THR   (  21-)  A    High
  17 LEU   (  22-)  A    High
  18 TYR   (  23-)  A    High
  19 PHE   (  24-)  A    High
  20 LEU   (  25-)  A    High
  21 VAL   (  26-)  A    High
  22 LEU   (  27-)  A    High
  23 GLY   (  28-)  A    High
  24 PHE   (  29-)  A    High
  25 LEU   (  30-)  A    High
And so on for a total of 756 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: 0

Crystal temperature (K) :100.000

Warning: Low M-factor

The B-factor flatness, the M-factor, is very low. This is very worrisome. I suggest you consult the WHAT CHECK website and/or a seasoned crystallographer.

The M-factor = 0.000

Warning: Average B-factor problem

The average B-factor for all buried protein atoms normally lies between 10-30. Values around 3-10 are expected for X-ray studies performed at liquid nitrogen temperature.

Because of the extreme value for the average B-factor, no further analysis of the B-factors is performed.

Average B-factor for buried atoms : 0.000

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: A

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: B

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: C

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.

   5 ARG   (  10-)  A
  52 ARG   (  57-)  A
  90 ARG   (  95-)  A
  95 ARG   ( 100-)  A
 163 ARG   ( 168-)  A
 164 ARG   ( 169-)  A
 220 ARG   ( 225-)  A
 320 ARG   ( 325-)  A
 322 ARG   ( 327-)  A
 325 ARG   ( 330-)  A
 413 ARG   ( 418-)  A
 444 ARG   ( 449-)  A
 445 ARG   ( 450-)  A
 490 ARG   ( 495-)  A
 513 ARG   ( 518-)  A
 521 ARG   ( 526-)  A
 555 ARG   ( 560-)  A
 607 ARG   (  52-)  B
 614 ARG   (  59-)  B
 691 ARG   ( 136-)  B
 696 ARG   ( 141-)  B
 701 ARG   ( 146-)  B
 755 ARG   (  33-)  C

Warning: Tyrosine convention problem

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

  18 TYR   (  23-)  A
  61 TYR   (  66-)  A
 131 TYR   ( 136-)  A
 141 TYR   ( 146-)  A
 239 TYR   ( 244-)  A
 243 TYR   ( 248-)  A
 368 TYR   ( 373-)  A
 447 TYR   ( 452-)  A
 455 TYR   ( 460-)  A
 645 TYR   (  90-)  B
 692 TYR   ( 137-)  B

Warning: Phenylalanine convention problem

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

  19 PHE   (  24-)  A
  24 PHE   (  29-)  A
 109 PHE   ( 114-)  A
 130 PHE   ( 135-)  A
 189 PHE   ( 194-)  A
 208 PHE   ( 213-)  A
 223 PHE   ( 228-)  A
 233 PHE   ( 238-)  A
 267 PHE   ( 272-)  A
 276 PHE   ( 281-)  A
 280 PHE   ( 285-)  A
 299 PHE   ( 304-)  A
 317 PHE   ( 322-)  A
 364 PHE   ( 369-)  A
 424 PHE   ( 429-)  A
 503 PHE   ( 508-)  A
 526 PHE   ( 531-)  A
 545 PHE   ( 550-)  A
 584 PHE   (  29-)  B
 643 PHE   (  88-)  B
 716 PHE   ( 161-)  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.

  45 ASP   (  50-)  A
 160 ASP   ( 165-)  A
 257 ASP   ( 262-)  A
 282 ASP   ( 287-)  A
 367 ASP   ( 372-)  A
 512 ASP   ( 517-)  A
 520 ASP   ( 525-)  A
 666 ASP   ( 111-)  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.

  91 GLU   (  96-)  A
 123 GLU   ( 128-)  A
 198 GLU   ( 203-)  A
 212 GLU   ( 217-)  A
 316 GLU   ( 321-)  A
 570 GLU   (  15-)  B
 606 GLU   (  51-)  B
 674 GLU   ( 119-)  B

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.

   3 ILE   (   8-)  A      CG1  CD1   1.77    6.6
   4 SER   (   9-)  A      N    CA    1.57    5.9
   4 SER   (   9-)  A      CA   C     1.68    7.2
   4 SER   (   9-)  A      C    O     1.36    6.5
   4 SER   (   9-)  A      CA   CB    1.74   10.7
 722 LYS   ( 167-)  B      CE   NZ    1.65    5.5
 723 GLU   ( 168-)  B      CA   CB    1.61    4.2
 723 GLU   ( 168-)  B      CB   CG    1.69    5.8

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

 |  0.997874 -0.000322 -0.000036|
 | -0.000322  0.998545 -0.000048|
 | -0.000036 -0.000048  0.997231|
Proposed new scale matrix

 |  0.008821  0.000003  0.000000|
 |  0.000003  0.008815  0.000000|
 |  0.000000  0.000000  0.005680|
With corresponding cell

    A    = 113.369  B   = 113.445  C    = 176.065
    Alpha=  90.002  Beta=  90.002  Gamma=  90.037

The CRYST1 cell dimensions

    A    = 113.610  B   = 113.610  C    = 176.550
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 115.952
(Under-)estimated Z-score: 7.936

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.

   3 ILE   (   8-)  A     -C    N    CA  129.50    4.3
   3 ILE   (   8-)  A      N    CA   C   122.91    4.2
   4 SER   (   9-)  A      C    CA   CB   98.28   -6.2
 723 GLU   ( 168-)  B      N    CA   C    98.61   -4.5
 723 GLU   ( 168-)  B      N    CA   CB  120.75    6.0
 723 GLU   ( 168-)  B      C    CA   CB  119.42    4.9

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.

   5 ARG   (  10-)  A
  45 ASP   (  50-)  A
  52 ARG   (  57-)  A
  90 ARG   (  95-)  A
  91 GLU   (  96-)  A
  95 ARG   ( 100-)  A
 123 GLU   ( 128-)  A
 160 ASP   ( 165-)  A
 163 ARG   ( 168-)  A
 164 ARG   ( 169-)  A
 198 GLU   ( 203-)  A
 212 GLU   ( 217-)  A
 220 ARG   ( 225-)  A
 257 ASP   ( 262-)  A
 282 ASP   ( 287-)  A
 316 GLU   ( 321-)  A
 320 ARG   ( 325-)  A
 322 ARG   ( 327-)  A
 325 ARG   ( 330-)  A
 367 ASP   ( 372-)  A
 413 ARG   ( 418-)  A
 444 ARG   ( 449-)  A
 445 ARG   ( 450-)  A
 490 ARG   ( 495-)  A
 512 ASP   ( 517-)  A
 513 ARG   ( 518-)  A
 520 ASP   ( 525-)  A
 521 ARG   ( 526-)  A
 555 ARG   ( 560-)  A
 570 GLU   (  15-)  B
 606 GLU   (  51-)  B
 607 ARG   (  52-)  B
 614 ARG   (  59-)  B
 666 ASP   ( 111-)  B
 674 GLU   ( 119-)  B
 691 ARG   ( 136-)  B
 696 ARG   ( 141-)  B
 701 ARG   ( 146-)  B
 755 ARG   (  33-)  C

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.

   4 SER   (   9-)  A      C     -7.3   -11.60     0.37
The average deviation= 0.647

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.

   3 ILE   (   8-)  A    4.46
 723 GLU   ( 168-)  B    4.38

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.

 364 PHE   ( 369-)  A    -3.4
 643 PHE   (  88-)  B    -3.4
 665 PRO   ( 110-)  B    -2.6
 447 TYR   ( 452-)  A    -2.4
 448 ILE   ( 453-)  A    -2.4
 130 PHE   ( 135-)  A    -2.4
 283 PRO   ( 288-)  A    -2.4
 725 GLU   (   3-)  C    -2.4
 538 GLY   ( 543-)  A    -2.3
 444 ARG   ( 449-)  A    -2.2
 666 ASP   ( 111-)  B    -2.2
 649 PRO   (  94-)  B    -2.1
 663 THR   ( 108-)  B    -2.1
 128 TYR   ( 133-)  A    -2.1
 627 VAL   (  72-)  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.

  43 ASN   (  48-)  A  Poor phi/psi
  93 ASN   (  98-)  A  Poor phi/psi
 122 ASN   ( 127-)  A  Poor phi/psi
 127 LEU   ( 132-)  A  Poor phi/psi
 130 PHE   ( 135-)  A  Poor phi/psi
 132 PRO   ( 137-)  A  PRO omega poor
 273 PRO   ( 278-)  A  Poor phi/psi
 325 ARG   ( 330-)  A  Poor phi/psi
 364 PHE   ( 369-)  A  Poor phi/psi
 372 ASN   ( 377-)  A  Poor phi/psi
 386 SER   ( 391-)  A  Poor phi/psi
 441 ASN   ( 446-)  A  Poor phi/psi
 502 PRO   ( 507-)  A  Poor phi/psi
 513 ARG   ( 518-)  A  Poor phi/psi
 521 ARG   ( 526-)  A  Poor phi/psi
 538 GLY   ( 543-)  A  Poor phi/psi
 559 GLU   (   4-)  B  Poor phi/psi
 642 ALA   (  87-)  B  Poor phi/psi
 643 PHE   (  88-)  B  Poor phi/psi
 646 GLN   (  91-)  B  PRO omega poor
 648 ASN   (  93-)  B  PRO omega poor
 666 ASP   ( 111-)  B  Poor phi/psi
 725 GLU   (   3-)  C  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.104

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.

 314 SER   ( 319-)  A    0.36
 304 SER   ( 309-)  A    0.37
 330 TRP   ( 335-)  A    0.38
 485 SER   ( 490-)  A    0.38

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!

  10 TYR   (  15-)  A      0
  43 ASN   (  48-)  A      0
  46 ALA   (  51-)  A      0
  58 GLN   (  63-)  A      0
  59 SER   (  64-)  A      0
  94 MET   (  99-)  A      0
  97 ASN   ( 102-)  A      0
  98 MET   ( 103-)  A      0
 122 ASN   ( 127-)  A      0
 124 ALA   ( 129-)  A      0
 125 THR   ( 130-)  A      0
 126 VAL   ( 131-)  A      0
 127 LEU   ( 132-)  A      0
 130 PHE   ( 135-)  A      0
 131 TYR   ( 136-)  A      0
 132 PRO   ( 137-)  A      0
 133 PRO   ( 138-)  A      0
 134 LEU   ( 139-)  A      0
 170 PRO   ( 175-)  A      0
 203 LEU   ( 208-)  A      0
 208 PHE   ( 213-)  A      0
 210 LEU   ( 215-)  A      0
 226 THR   ( 231-)  A      0
 244 THR   ( 249-)  A      0
 255 VAL   ( 260-)  A      0
And so on for a total of 180 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].

  48 PRO   (  53-)  A  -117.8 half-chair C-delta/C-gamma (-126 degrees)
 229 PRO   ( 234-)  A  -120.9 half-chair C-delta/C-gamma (-126 degrees)
 283 PRO   ( 288-)  A   -64.2 envelop C-beta (-72 degrees)
 303 PRO   ( 308-)  A   102.6 envelop C-beta (108 degrees)
 335 PRO   ( 340-)  A    49.0 half-chair C-delta/C-gamma (54 degrees)
 649 PRO   (  94-)  B   -54.9 half-chair C-beta/C-alpha (-54 degrees)
 665 PRO   ( 110-)  B   -63.3 envelop C-beta (-72 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.

 228 HIS   ( 233-)  A      NE2 <->  232 TYR   ( 237-)  A      CE2    1.17    1.93  INTRA BF
 228 HIS   ( 233-)  A      CD2 <->  232 TYR   ( 237-)  A      CE2    0.43    2.77  INTRA BF
 228 HIS   ( 233-)  A      CE1 <->  232 TYR   ( 237-)  A      CE2    0.43    2.77  INTRA BF
  67 HIS   (  72-)  A      NE2 <->  767 HEM   ( 800-)  A      NC     0.42    2.58  INTRA BF
 652 VAL   (  97-)  B      O   <->  722 LYS   ( 167-)  B      N      0.41    2.29  INTRA BF
 381 HIS   ( 386-)  A      NE2 <->  767 HEM   ( 800-)  A      NA     0.37    2.63  INTRA BF
 228 HIS   ( 233-)  A      NE2 <->  232 TYR   ( 237-)  A      CZ     0.33    2.77  INTRA BF
 383 GLN   ( 388-)  A      CB  <->  761 HAS   ( 801-)  A      CAC    0.27    2.93  INTRA BF
 651 GLU   (  96-)  B      CB  <->  722 LYS   ( 167-)  B      NZ     0.25    2.85  INTRA BF
 641 PHE   (  86-)  B      O   <->  643 PHE   (  88-)  B      N      0.24    2.46  INTRA BF
  47 TYR   (  52-)  A      N   <->   48 PRO   (  53-)  A      CD     0.21    2.79  INTRA BF
 257 ASP   ( 262-)  A      OD1 <->  261 ARG   ( 266-)  A      NE     0.21    2.49  INTRA BF
 704 CYS   ( 149-)  B      SG  <->  715 MET   ( 160-)  B      SD     0.21    3.24  INTRA BF
 381 HIS   ( 386-)  A      NE2 <->  767 HEM   ( 800-)  A      ND     0.17    2.83  INTRA BF
 337 ASP   ( 342-)  A      O   <->  413 ARG   ( 418-)  A      NH1    0.17    2.53  INTRA BF
 223 PHE   ( 228-)  A      O   <->  227 GLY   ( 232-)  A      N      0.16    2.54  INTRA BF
 400 LEU   ( 405-)  A      N   <->  401 PRO   ( 406-)  A      CD     0.15    2.85  INTRA BF
 431 ALA   ( 436-)  A      O   <->  435 HIS   ( 440-)  A      ND1    0.15    2.55  INTRA BF
 277 HIS   ( 282-)  A      NE2 <->  278 HIS   ( 283-)  A      NE2    0.15    2.85  INTRA BF
 228 HIS   ( 233-)  A      NE2 <->  232 TYR   ( 237-)  A      CD2    0.14    2.96  INTRA BF
 444 ARG   ( 449-)  A      NH2 <->  761 HAS   ( 801-)  A      CGA    0.14    2.96  INTRA BF
 272 THR   ( 277-)  A      N   <->  273 PRO   ( 278-)  A      CD     0.13    2.87  INTRA BF
 361 ASN   ( 366-)  A      CB  <->  761 HAS   ( 801-)  A      CMD    0.13    3.07  INTRA BF
 195 LEU   ( 200-)  A      N   <->  226 THR   ( 231-)  A      OG1    0.13    2.57  INTRA BF
 137 HIS   ( 142-)  A      ND1 <->  139 ALA   ( 144-)  A      N      0.13    2.87  INTRA BF
And so on for a total of 88 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.

 325 ARG   ( 330-)  A      -8.14
 696 ARG   ( 141-)  B      -6.76
 492 ARG   ( 497-)  A      -6.59
 490 ARG   ( 495-)  A      -6.11
 695 LYS   ( 140-)  B      -6.04
  58 GLN   (  63-)  A      -6.02
 607 ARG   (  52-)  B      -5.99
 210 LEU   ( 215-)  A      -5.87
 322 ARG   ( 327-)  A      -5.54
 249 GLN   ( 254-)  A      -5.49
 614 ARG   (  59-)  B      -5.45
 444 ARG   ( 449-)  A      -5.35
 131 TYR   ( 136-)  A      -5.32
 555 ARG   ( 560-)  A      -5.26
 278 HIS   ( 283-)  A      -5.15
   3 ILE   (   8-)  A      -5.12
 725 GLU   (   3-)  C      -5.02

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.

 210 LEU   ( 215-)  A       212 - GLU    217- ( A)         -4.88
 614 ARG   (  59-)  B       616 - GLU     61- ( B)         -4.97

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.

 625 ALA   (  70-)  B   -2.57

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.

 367 ASP   ( 372-)  A     -  370 VAL   ( 375-)  A        -2.04

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

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.

 249 GLN   ( 254-)  A
 293 HIS   ( 298-)  A
 560 HIS   (   5-)  B
 646 GLN   (  91-)  B
 672 HIS   ( 117-)  B
 677 ASN   ( 122-)  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.

   2 GLU   (   7-)  A      N
   3 ILE   (   8-)  A      N
   4 SER   (   9-)  A      N
  36 PHE   (  41-)  A      N
  37 GLN   (  42-)  A      NE2
  43 ASN   (  48-)  A      ND2
  46 ALA   (  51-)  A      N
  47 TYR   (  52-)  A      OH
  59 SER   (  64-)  A      N
  60 TYR   (  65-)  A      OH
  71 ASN   (  76-)  A      ND2
  97 ASN   ( 102-)  A      N
 124 ALA   ( 129-)  A      N
 125 THR   ( 130-)  A      N
 128 TYR   ( 133-)  A      N
 128 TYR   ( 133-)  A      OH
 129 THR   ( 134-)  A      OG1
 141 TYR   ( 146-)  A      OH
 206 TRP   ( 211-)  A      NE1
 220 ARG   ( 225-)  A      NE
 232 TYR   ( 237-)  A      OH
 253 LYS   ( 258-)  A      N
 256 SER   ( 261-)  A      N
 257 ASP   ( 262-)  A      N
 272 THR   ( 277-)  A      N
And so on for a total of 72 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.

  37 GLN   (  42-)  A      OE1
 198 GLU   ( 203-)  A      OE1
 279 GLN   ( 284-)  A      OE1
 367 ASP   ( 372-)  A      OD1
 371 HIS   ( 376-)  A      ND1
 383 GLN   ( 388-)  A      OE1
 435 HIS   ( 440-)  A      NE2
 465 ASN   ( 470-)  A      OD1
 563 HIS   (   8-)  B      NE2
 570 GLU   (  15-)  B      OE2
 654 GLN   (  99-)  B      OE1
 672 HIS   ( 117-)  B      NE2
 677 ASN   ( 122-)  B      OD1

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.

 198 GLU   ( 203-)  A   H-bonding suggests Gln
 686 GLU   ( 131-)  B   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.378
  2nd generation packing quality :  -0.409
  Ramachandran plot appearance   :  -2.213
  chi-1/chi-2 rotamer normality  :  -2.104
  Backbone conformation          :   0.618

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.465 (tight)
  Bond angles                    :   0.570 (tight)
  Omega angle restraints         :   0.757
  Side chain planarity           :   0.411 (tight)
  Improper dihedral distribution :   0.591
  Inside/Outside distribution    :   1.156

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 : 4.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.0
  2nd generation packing quality :   1.5
  Ramachandran plot appearance   :   0.7
  chi-1/chi-2 rotamer normality  :   0.3
  Backbone conformation          :   1.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.465 (tight)
  Bond angles                    :   0.570 (tight)
  Omega angle restraints         :   0.757
  Side chain planarity           :   0.411 (tight)
  Improper dihedral distribution :   0.591
  Inside/Outside distribution    :   1.156
==============

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.