WHAT IF Check report

This file was created 2012-10-10 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 pdb2vt0.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.

 991 CBU   (1499-)  A  -
1002 CBU   (1497-)  B  -
1003 MAN   (1502-)  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.

 337 GLU   ( 340-)  A  -   OE2 bound to  991 CBU   (1499-)  A  -   C5
 828 GLU   ( 340-)  B  -   OE2 bound to 1002 CBU   (1497-)  B  -   C5
 985 NAG   (1500-)  A  -   O4  bound to  986 NAG   (1501-)  A  -   C1
 986 NAG   (1501-)  A  -   O4  bound to 1003 MAN   (1502-)  A  -   C1
 988 NAG   (1498-)  B  -   O4  bound to  989 NAG   (1499-)  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'.

   1 GLU   (  -1-)  A      CG
   1 GLU   (  -1-)  A      CD
   1 GLU   (  -1-)  A      OE1
   1 GLU   (  -1-)  A      OE2
  31 LEU   (  34-)  A      CG
  31 LEU   (  34-)  A      CD1
  31 LEU   (  34-)  A      CD2
 166 GLN   ( 169-)  A      CG
 166 GLN   ( 169-)  A      CD
 166 GLN   ( 169-)  A      OE1
 166 GLN   ( 169-)  A      NE2
 221 LYS   ( 224-)  A      CE
 221 LYS   ( 224-)  A      NZ
 297 GLU   ( 300-)  A      CD
 297 GLU   ( 300-)  A      OE1
 297 GLU   ( 300-)  A      OE2
 438 LYS   ( 441-)  A      CG
 438 LYS   ( 441-)  A      CD
 438 LYS   ( 441-)  A      CE
 438 LYS   ( 441-)  A      NZ
 463 LYS   ( 466-)  A      CG
 463 LYS   ( 466-)  A      CD
 463 LYS   ( 466-)  A      CE
 463 LYS   ( 466-)  A      NZ
 497 ARG   (   2-)  B      CZ
And so on for a total of 55 lines.

Warning: C-terminal nitrogen atoms detected.

It is becoming habit to indicate that a residue is not the true C-terminus by including only the backbone N of the next residue. This has been observed in this PDB file.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. In many cases the N- or C-terminal residues are too disordered to see. In case of the N-terminus, you can see from the residue numbers if there are missing residues, but at the C-terminus this is impossible. Therefore, often the position of the backbone nitrogen of the first residue missing at the C-terminal end is calculated and added to indicate that there are missing residues. As a single N causes validation trouble, we remove these single-N-residues before doing the validation. But, if you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or removed N is the cause.

 495 LEU   ( 498-)  A

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

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.

 840 ARG   ( 353-)  B
 920 ARG   ( 433-)  B
 950 ARG   ( 463-)  B

Warning: Tyrosine convention problem

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

  13 TYR   (  11-)  A
  24 TYR   (  22-)  A
 105 TYR   ( 108-)  A
 113 TYR   ( 116-)  A
 130 TYR   ( 133-)  A
 132 TYR   ( 135-)  A
 202 TYR   ( 205-)  A
 209 TYR   ( 212-)  A
 301 TYR   ( 304-)  A
 409 TYR   ( 412-)  A
 415 TYR   ( 418-)  A
 484 TYR   ( 487-)  A
 505 TYR   (  11-)  B
 516 TYR   (  22-)  B
 595 TYR   ( 108-)  B
 603 TYR   ( 116-)  B
 622 TYR   ( 135-)  B
 692 TYR   ( 205-)  B
 699 TYR   ( 212-)  B
 791 TYR   ( 304-)  B
 899 TYR   ( 412-)  B
 974 TYR   ( 487-)  B

Warning: Phenylalanine convention problem

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

   2 PHE   (   0-)  A
  72 PHE   (  75-)  A
  78 PHE   (  81-)  A
 106 PHE   ( 109-)  A
 125 PHE   ( 128-)  A
 139 PHE   ( 142-)  A
 144 PHE   ( 147-)  A
 243 PHE   ( 246-)  A
 313 PHE   ( 316-)  A
 328 PHE   ( 331-)  A
 394 PHE   ( 397-)  A
 408 PHE   ( 411-)  A
 414 PHE   ( 417-)  A
 423 PHE   ( 426-)  A
 562 PHE   (  75-)  B
 568 PHE   (  81-)  B
 596 PHE   ( 109-)  B
 629 PHE   ( 142-)  B
 634 PHE   ( 147-)  B
 803 PHE   ( 316-)  B
 818 PHE   ( 331-)  B
 884 PHE   ( 397-)  B
 898 PHE   ( 411-)  B
 913 PHE   ( 426-)  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.

 150 ASP   ( 153-)  A
 355 ASP   ( 358-)  A
 640 ASP   ( 153-)  B
 845 ASP   ( 358-)  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.

 346 GLU   ( 349-)  A
 836 GLU   ( 349-)  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.

 129 THR   ( 132-)  A      CA   CB    1.61    4.0
 201 ILE   ( 204-)  A      CA   CB    1.63    5.1
 204 GLN   ( 207-)  A      CG   CD    1.62    4.3
 350 ARG   ( 353-)  A      CZ   NH2   1.25   -4.4
 407 THR   ( 410-)  A      CA   CB    1.62    4.7
 484 TYR   ( 487-)  A      C    O     1.37    6.7
 608 VAL   ( 121-)  B      CA   CB    1.63    5.2
 656 GLN   ( 169-)  B      CB   CG    1.65    4.3
 763 VAL   ( 276-)  B      CA   CB    1.64    5.7
 897 THR   ( 410-)  B      CA   CB    1.62    4.4
 974 TYR   ( 487-)  B      C    O     1.34    5.5
  20 CYS   (  18-)  A      SG  -SG*   2.21    4.1
  25 CYS   (  23-)  A      SG  -SG*   2.21    4.1
 512 CYS   (  18-)  B      SG  -SG*   2.23    4.9
 517 CYS   (  23-)  B      SG  -SG*   2.23    4.9

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

 |  0.994800 -0.000425 -0.001873|
 | -0.000425  0.995037  0.000030|
 | -0.001873  0.000030  0.994600|
Proposed new scale matrix

 |  0.014750  0.000006  0.003630|
 |  0.000004  0.010373  0.000000|
 |  0.000023  0.000000  0.012444|
With corresponding cell

    A    =  67.830  B   =  96.400  C    =  82.795
    Alpha=  89.989  Beta= 103.935  Gamma=  90.048

The CRYST1 cell dimensions

    A    =  68.184  B   =  96.884  C    =  83.171
    Alpha=  90.000  Beta= 103.730  Gamma=  90.000

Variance: 928.349
(Under-)estimated Z-score: 22.455

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.

  32 GLY   (  35-)  A     -C    N    CA  128.63    4.7
  46 MET   (  49-)  A      CG   SD   CE   91.69   -4.2
  50 MET   (  53-)  A      CA   CB   CG  105.71   -4.2
 220 HIS   ( 223-)  A      CG   ND1  CE1 109.61    4.0
 252 HIS   ( 255-)  A      CG   ND1  CE1 109.72    4.1
 270 HIS   ( 273-)  A      CG   ND1  CE1 109.69    4.1
 271 HIS   ( 274-)  A      CG   ND1  CE1 110.08    4.5
 287 HIS   ( 290-)  A      CG   ND1  CE1 109.69    4.1
 303 HIS   ( 306-)  A      CG   ND1  CE1 109.66    4.1
 314 LEU   ( 317-)  A      C    CA   CB  101.03   -4.8
 378 TRP   ( 381-)  A      C    CA   CB  119.95    5.2
 430 ARG   ( 433-)  A      CB   CG   CD  104.66   -4.7
 430 ARG   ( 433-)  A      CD   NE   CZ  129.65    4.4
 430 ARG   ( 433-)  A      NE   CZ   NH1 128.92    4.7
 430 ARG   ( 433-)  A      NE   CZ   NH2 111.36   -4.5
 492 HIS   ( 495-)  A      CG   ND1  CE1 109.76    4.2
 494 GLN   ( 497-)  A      C    CA   CB  102.30   -4.1
 534 ARG   (  47-)  B      CB   CG   CD  105.14   -4.5
 536 MET   (  49-)  B      CG   SD   CE   91.65   -4.2
 656 GLN   ( 169-)  B      CB   CG   CD  120.70    4.8
 693 HIS   ( 206-)  B      CG   ND1  CE1 109.66    4.1
 711 LYS   ( 224-)  B     -C    N    CA  129.39    4.3
 761 HIS   ( 274-)  B      CG   ND1  CE1 110.27    4.7
 798 HIS   ( 311-)  B      CG   ND1  CE1 109.74    4.1
 804 LEU   ( 317-)  B      C    CA   CB  102.10   -4.2
 804 LEU   ( 317-)  B      CA   CB   CG  132.79    4.7
 861 HIS   ( 374-)  B      CG   ND1  CE1 109.64    4.0
 868 TRP   ( 381-)  B      C    CA   CB  119.38    4.9
 881 VAL   ( 394-)  B      N    CA   CB  103.47   -4.1
 881 VAL   ( 394-)  B      CA   CB   CG1 119.46    5.3
 944 VAL   ( 457-)  B      CG1  CB   CG2  98.69   -5.5

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.

 150 ASP   ( 153-)  A
 346 GLU   ( 349-)  A
 355 ASP   ( 358-)  A
 640 ASP   ( 153-)  B
 836 GLU   ( 349-)  B
 840 ARG   ( 353-)  B
 845 ASP   ( 358-)  B
 920 ARG   ( 433-)  B
 950 ARG   ( 463-)  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.

 881 VAL   ( 394-)  B      CB     7.1   -23.60   -32.96
The average deviation= 1.423

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.

 749 ARG   ( 262-)  B    4.63

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.

 969 THR   ( 482-)  B    -2.8
 484 TYR   ( 487-)  A    -2.7
 479 THR   ( 482-)  A    -2.7
 467 LEU   ( 470-)  A    -2.6
 957 LEU   ( 470-)  B    -2.6
 974 TYR   ( 487-)  B    -2.4
 480 ILE   ( 483-)  A    -2.3
 637 PRO   ( 150-)  B    -2.3
 970 ILE   ( 483-)  B    -2.3
 286 PRO   ( 289-)  A    -2.1
 776 PRO   ( 289-)  B    -2.1
 804 LEU   ( 317-)  B    -2.1
 603 TYR   ( 116-)  B    -2.1
 147 PRO   ( 150-)  A    -2.1
 733 PHE   ( 246-)  B    -2.1
 127 ILE   ( 130-)  A    -2.1
 863 VAL   ( 376-)  B    -2.1
 309 TRP   ( 312-)  A    -2.1
 881 VAL   ( 394-)  B    -2.0
 934 VAL   ( 447-)  B    -2.0
 243 PHE   ( 246-)  A    -2.0
 799 TRP   ( 312-)  B    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

   6 CYS   (   4-)  A  omega poor
  16 VAL   (  14-)  A  omega poor
  21 ASN   (  19-)  A  Poor phi/psi
  31 LEU   (  34-)  A  omega poor
  34 PHE   (  37-)  A  omega poor
  36 ARG   (  39-)  A  omega poor
  52 PRO   (  55-)  A  omega poor
  72 PHE   (  75-)  A  Poor phi/psi
 105 TYR   ( 108-)  A  omega poor
 121 ALA   ( 124-)  A  Poor phi/psi
 123 CYS   ( 126-)  A  Poor phi/psi
 125 PHE   ( 128-)  A  Poor phi/psi
 130 TYR   ( 133-)  A  omega poor
 137 ASP   ( 140-)  A  Poor phi/psi
 138 ASP   ( 141-)  A  Poor phi/psi
 141 LEU   ( 144-)  A  Poor phi/psi
 150 ASP   ( 153-)  A  omega poor
 177 THR   ( 180-)  A  omega poor
 221 LYS   ( 224-)  A  Poor phi/psi
 230 GLU   ( 233-)  A  Poor phi/psi
 248 PHE   ( 251-)  A  omega poor
 278 LEU   ( 281-)  A  Poor phi/psi
 279 ASP   ( 282-)  A  Poor phi/psi
 285 LEU   ( 288-)  A  PRO omega poor
 308 HIS   ( 311-)  A  omega poor
And so on for a total of 75 lines.

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!

   8 PRO   (   6-)  A      0
  11 PHE   (   9-)  A      0
  13 TYR   (  11-)  A      0
  14 SER   (  12-)  A      0
  20 CYS   (  18-)  A      0
  24 TYR   (  22-)  A      0
  25 CYS   (  23-)  A      0
  26 ASP   (  24-)  A      0
  27 SER   (  25-)  A      0
  28 PHE   (  26-)  A      0
  29 PRO   (  32-)  A      0
  30 ALA   (  33-)  A      0
  42 SER   (  45-)  A      0
  45 ARG   (  48-)  A      0
  46 MET   (  49-)  A      0
  54 GLN   (  57-)  A      0
  56 ASN   (  59-)  A      0
  58 THR   (  61-)  A      0
  70 GLN   (  73-)  A      0
  72 PHE   (  75-)  A      0
  76 LYS   (  79-)  A      0
  78 PHE   (  81-)  A      0
  82 MET   (  85-)  A      0
 111 ILE   ( 114-)  A      0
 120 MET   ( 123-)  A      0
And so on for a total of 426 lines.

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]

 316 PRO   ( 319-)  A    0.12 LOW
 482 PRO   ( 485-)  A    0.19 LOW
 585 PRO   (  98-)  B    0.47 HIGH
 626 PRO   ( 139-)  B    0.17 LOW
 658 PRO   ( 171-)  B    0.20 LOW
 786 PRO   ( 299-)  B    0.18 LOW
 806 PRO   ( 319-)  B    0.11 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].

  96 PRO   (  99-)  A   108.9 envelop C-beta (108 degrees)
 175 PRO   ( 178-)  A   -51.4 half-chair C-beta/C-alpha (-54 degrees)
 179 PRO   ( 182-)  A   120.3 half-chair C-beta/C-alpha (126 degrees)
 286 PRO   ( 289-)  A   -65.5 envelop C-beta (-72 degrees)
 466 PRO   ( 469-)  A   -64.8 envelop C-beta (-72 degrees)
 497 PRO   (   3-)  B   -49.1 half-chair C-beta/C-alpha (-54 degrees)
 665 PRO   ( 178-)  B   -64.6 envelop C-beta (-72 degrees)
 669 PRO   ( 182-)  B   121.8 half-chair C-beta/C-alpha (126 degrees)
 962 PRO   ( 475-)  B  -113.0 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 985 NAG   (1501-)  A      O4  <-> 1002 MAN   (1502-)  A      C1     0.95    1.45  INTRA BF
 827 GLU   ( 340-)  B      OE2 <-> 1001 CBU   (1497-)  B      C5     0.92    1.48  INTRA BL
 985 NAG   (1501-)  A      C4  <-> 1002 MAN   (1502-)  A      C1     0.86    2.34  INTRA BF
 827 GLU   ( 340-)  B      CD  <-> 1001 CBU   (1497-)  B      C5     0.79    2.41  INTRA BL
 484 TYR   ( 487-)  A      C   <-> 1003 HOH   (2222 )  A      O      0.44    2.36  INTRA
1004 HOH   (2049 )  B      O   <-> 1004 HOH   (2126 )  B      O      0.43    1.77  INTRA
 496 ARG   (   2-)  B      NE  <-> 1004 HOH   (2001 )  B      O      0.42    2.28  INTRA
 927 GLN   ( 440-)  B      NE2 <-> 1004 HOH   (2204 )  B      O      0.40    2.30  INTRA
 484 TYR   ( 487-)  A      CA  <-> 1003 HOH   (2222 )  A      O      0.37    2.43  INTRA
 392 ARG   ( 395-)  A      NH1 <-> 1003 HOH   (2185 )  A      O      0.36    2.34  INTRA
 430 ARG   ( 433-)  A      NH2 <-> 1003 HOH   (2201 )  A      O      0.33    2.37  INTRA
1003 HOH   (2102 )  A      O   <-> 1003 HOH   (2122 )  A      O      0.31    1.89  INTRA
 730 GLY   ( 243-)  B      N   <->  999 SO4   (1502-)  B      O2     0.29    2.41  INTRA
 693 HIS   ( 206-)  B      NE2 <->  742 HIS   ( 255-)  B      NE2    0.29    2.71  INTRA BL
 485 SER   ( 488-)  A      N   <-> 1003 HOH   (2222 )  A      O      0.28    2.42  INTRA
 166 GLN   ( 169-)  A      N   <-> 1003 HOH   (2075 )  A      O      0.28    2.42  INTRA
 191 LYS   ( 194-)  A      N   <->  993 SO4   (1505-)  A      O1     0.26    2.44  INTRA
 437 GLN   ( 440-)  A      NE2 <-> 1003 HOH   (2206 )  A      O      0.25    2.45  INTRA
 295 ASP   ( 298-)  A      OD2 <-> 1003 HOH   (2128 )  A      O      0.24    2.16  INTRA
 323 GLU   ( 326-)  A      OE2 <->  326 ARG   ( 329-)  A      NH2    0.24    2.46  INTRA
 423 PHE   ( 426-)  A      O   <->  448 HIS   ( 451-)  A      NE2    0.23    2.47  INTRA
1003 HOH   (2153 )  A      O   <-> 1003 HOH   (2159 )  A      O      0.22    1.98  INTRA
 556 LEU   (  69-)  B      CD1 <->  935 ALA   ( 448-)  B      CB     0.22    2.98  INTRA
 803 PHE   ( 316-)  B      CZ  <->  804 LEU   ( 317-)  B      CD2    0.20    3.00  INTRA
 705 ASP   ( 218-)  B      OD1 <->  760 HIS   ( 273-)  B      NE2    0.20    2.50  INTRA
And so on for a total of 112 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.

 656 GLN   ( 169-)  B      -6.53
 197 GLN   ( 200-)  A      -6.32
 493 ARG   ( 496-)  A      -6.06
 687 GLN   ( 200-)  B      -5.76
 259 ARG   ( 262-)  A      -5.66
 749 ARG   ( 262-)  B      -5.63
 982 HIS   ( 495-)  B      -5.58
 544 GLN   (  57-)  B      -5.58
  41 ARG   (  44-)  A      -5.35
 531 ARG   (  44-)  B      -5.16
 547 HIS   (  60-)  B      -5.12
 681 LYS   ( 194-)  B      -5.07
 191 LYS   ( 194-)  A      -5.03

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.

 953 LYS   ( 466-)  B   -2.90
 166 GLN   ( 169-)  A   -2.78
 804 LEU   ( 317-)  B   -2.61
  31 LEU   (  34-)  A   -2.58
 657 ARG   ( 170-)  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.

1003 HOH   (2001 )  A      O
1003 HOH   (2145 )  A      O
1003 HOH   (2167 )  A      O
1004 HOH   (2069 )  B      O
Bound group on Asn; dont flip   21 ASN  (  19-) A
Bound to:  984 NAG  (1500-) A
Bound group on Asn; dont flip  513 ASN  (  19-) B
Bound to:  987 NAG  (1498-) B

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.

 163 GLN   ( 166-)  A
 220 HIS   ( 223-)  A
 347 GLN   ( 350-)  A
 362 HIS   ( 365-)  A
 544 GLN   (  57-)  B
 633 ASN   ( 146-)  B
 710 HIS   ( 223-)  B
 815 HIS   ( 328-)  B
 837 GLN   ( 350-)  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.

  25 CYS   (  23-)  A      N
 126 SER   ( 129-)  A      N
 137 ASP   ( 140-)  A      N
 176 TRP   ( 179-)  A      NE1
 181 TRP   ( 184-)  A      N
 187 ALA   ( 190-)  A      N
 230 GLU   ( 233-)  A      N
 243 PHE   ( 246-)  A      N
 338 ALA   ( 341-)  A      N
 339 CYS   ( 342-)  A      N
 345 TRP   ( 348-)  A      N
 363 SER   ( 366-)  A      OG
 374 GLY   ( 377-)  A      N
 378 TRP   ( 381-)  A      NE1
 379 ASN   ( 382-)  A      ND2
 381 ALA   ( 384-)  A      N
 389 ASN   ( 392-)  A      ND2
 430 ARG   ( 433-)  A      NH1
 437 GLN   ( 440-)  A      N
 485 SER   ( 488-)  A      N
 493 ARG   ( 496-)  A      N
 494 GLN   ( 497-)  A      NE2
 523 THR   (  36-)  B      N
 530 THR   (  43-)  B      OG1
 616 SER   ( 129-)  B      N
 627 ASP   ( 140-)  B      N
 666 TRP   ( 179-)  B      NE1
 671 TRP   ( 184-)  B      N
 677 ALA   ( 190-)  B      N
 720 GLU   ( 233-)  B      N
 733 PHE   ( 246-)  B      N
 749 ARG   ( 262-)  B      NE
 827 GLU   ( 340-)  B      N
 828 ALA   ( 341-)  B      N
 829 CYS   ( 342-)  B      N
 835 TRP   ( 348-)  B      N
 849 GLN   ( 362-)  B      NE2
 851 SER   ( 364-)  B      OG
 864 GLY   ( 377-)  B      N
 868 TRP   ( 381-)  B      NE1
 869 ASN   ( 382-)  B      ND2
 871 ALA   ( 384-)  B      N
 879 ASN   ( 392-)  B      ND2
 919 GLN   ( 432-)  B      NE2
 920 ARG   ( 433-)  B      NH2
 927 GLN   ( 440-)  B      N

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

  84 ASP   (  87-)  A      OD1
 416 HIS   ( 419-)  A      NE2
 574 ASP   (  87-)  B      OD1
 656 GLN   ( 169-)  B      OE1
 906 HIS   ( 419-)  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.

1004 HOH   (2081 )  B      O  1.03  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.

 200 ASP   ( 203-)  A   H-bonding suggests Asn
 230 GLU   ( 233-)  A   H-bonding suggests Gln
 377 ASP   ( 380-)  A   H-bonding suggests Asn; but Alt-Rotamer
 690 ASP   ( 203-)  B   H-bonding suggests Asn
 705 ASP   ( 218-)  B   H-bonding suggests Asn; but Alt-Rotamer
 720 GLU   ( 233-)  B   H-bonding suggests Gln
 867 ASP   ( 380-)  B   H-bonding suggests Asn; but Alt-Rotamer

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 :  -0.252
  2nd generation packing quality :  -1.328
  Ramachandran plot appearance   :  -0.776
  chi-1/chi-2 rotamer normality  :  -1.715
  Backbone conformation          :  -0.633

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.069
  Bond angles                    :   0.994
  Omega angle restraints         :   1.270
  Side chain planarity           :   1.209
  Improper dihedral distribution :   1.158
  B-factor distribution          :   0.610
  Inside/Outside distribution    :   1.024

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.15


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :   0.2
  chi-1/chi-2 rotamer normality  :  -0.9
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.069
  Bond angles                    :   0.994
  Omega angle restraints         :   1.270
  Side chain planarity           :   1.209
  Improper dihedral distribution :   1.158
  B-factor distribution          :   0.610
  Inside/Outside distribution    :   1.024
==============

WHAT IF
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      WHAT IF: a molecular modelling and drug design program,
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WHAT_CHECK (verification routines from WHAT IF)
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      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.