WHAT IF Check report

This file was created 2011-12-18 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

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

Verification log for pdb2xwd.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.

 996 LGS   (1510-)  A  -
1003 LGS   (1510-)  B  -
1004 BMA   (1500-)  B  -
1005 MAN   (1500-)  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.

 986 NAG   (1498-)  A  -   O4  bound to  987 NAG   (1499-)  A  -   C1
 987 NAG   (1499-)  A  -   O4  bound to 1005 MAN   (1500-)  A  -   C1
 989 NAG   (1498-)  B  -   O4  bound to  990 NAG   (1499-)  B  -   C1
 990 NAG   (1499-)  B  -   O4  bound to 1004 BMA   (1500-)  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'.

  30 LEU   (  34-)  A      CG
  30 LEU   (  34-)  A      CD1
  30 LEU   (  34-)  A      CD2
 139 GLN   ( 143-)  A      CG
 139 GLN   ( 143-)  A      CD
 139 GLN   ( 143-)  A      OE1
 139 GLN   ( 143-)  A      NE2
 151 LYS   ( 155-)  A      CE
 151 LYS   ( 155-)  A      NZ
 159 ARG   ( 163-)  A      NE
 159 ARG   ( 163-)  A      CZ
 159 ARG   ( 163-)  A      NH1
 159 ARG   ( 163-)  A      NH2
 273 ARG   ( 277-)  A      NE
 273 ARG   ( 277-)  A      CZ
 273 ARG   ( 277-)  A      NH1
 273 ARG   ( 277-)  A      NH2
 296 GLU   ( 300-)  A      CG
 296 GLU   ( 300-)  A      CD
 296 GLU   ( 300-)  A      OE1
 296 GLU   ( 300-)  A      OE2
 317 LYS   ( 321-)  A      CE
 317 LYS   ( 321-)  A      NZ
 342 LYS   ( 346-)  A      CE
 342 LYS   ( 346-)  A      NZ
And so on for a total of 72 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: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 5.00

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

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.

 107 GLU   ( 111-)  A      CB   CG    1.65    4.4

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

 |  0.997753  0.000063 -0.000507|
 |  0.000063  0.997774  0.000182|
 | -0.000507  0.000182  0.997710|
Proposed new scale matrix

 |  0.014733 -0.000002  0.003596|
 |  0.000000  0.010373 -0.000002|
 |  0.000006 -0.000002  0.012404|
With corresponding cell

    A    =  67.884  B   =  96.403  C    =  82.993
    Alpha=  89.980  Beta= 103.745  Gamma=  89.997

The CRYST1 cell dimensions

    A    =  68.036  B   =  96.617  C    =  83.164
    Alpha=  90.000  Beta= 103.690  Gamma=  90.000

Variance: 172.542
(Under-)estimated Z-score: 9.681

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.

 324 HIS   ( 328-)  A      CG   ND1  CE1 110.29    4.7
 520 PHE   (  26-)  B      N    CA   CB  117.74    4.3
 700 TYR   ( 212-)  B      CA   CB   CG  121.50    4.2
 762 HIS   ( 274-)  B      CG   ND1  CE1 109.64    4.0
 816 HIS   ( 328-)  B      CG   ND1  CE1 110.34    4.7
 910 HIS   ( 422-)  B      CG   ND1  CE1 109.78    4.2
 964 ALA   ( 476-)  B     -C    N    CA  113.40   -4.6

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.

 520 PHE   (  26-)  B      CA    -6.7    23.23    33.98
The average deviation= 1.029

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.

 958 LEU   ( 470-)  B    -2.5
 970 THR   ( 482-)  B    -2.4
 466 LEU   ( 470-)  A    -2.4
 128 THR   ( 132-)  A    -2.4
 620 THR   ( 132-)  B    -2.3
 478 THR   ( 482-)  A    -2.3
 928 GLN   ( 440-)  B    -2.3
 436 GLN   ( 440-)  A    -2.2
 242 PHE   ( 246-)  A    -2.2
 537 MET   (  49-)  B    -2.2
 981 LEU   ( 493-)  B    -2.1
 220 LYS   ( 224-)  A    -2.1
  57 THR   (  61-)  A    -2.1
  49 MET   (  53-)  A    -2.1
 712 LYS   ( 224-)  B    -2.1
 390 VAL   ( 394-)  A    -2.1
 285 PRO   ( 289-)  A    -2.0
 489 LEU   ( 493-)  A    -2.0
 545 GLN   (  57-)  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.

   5 CYS   (   4-)  A  omega poor
  12 TYR   (  11-)  A  omega poor
  20 ASN   (  19-)  A  Poor phi/psi
  71 PHE   (  75-)  A  Poor phi/psi
 104 TYR   ( 108-)  A  omega poor
 120 ALA   ( 124-)  A  Poor phi/psi, omega poor
 122 CYS   ( 126-)  A  Poor phi/psi
 124 PHE   ( 128-)  A  Poor phi/psi
 127 ARG   ( 131-)  A  omega poor
 136 ASP   ( 140-)  A  Poor phi/psi
 137 ASP   ( 141-)  A  Poor phi/psi
 140 LEU   ( 144-)  A  Poor phi/psi
 188 ASN   ( 192-)  A  Poor phi/psi
 220 LYS   ( 224-)  A  Poor phi/psi
 225 ALA   ( 229-)  A  omega poor
 229 GLU   ( 233-)  A  Poor phi/psi
 247 PHE   ( 251-)  A  omega poor
 259 ASP   ( 263-)  A  omega poor
 277 LEU   ( 281-)  A  Poor phi/psi
 278 ASP   ( 282-)  A  Poor phi/psi
 284 LEU   ( 288-)  A  PRO omega poor
 308 TRP   ( 312-)  A  omega poor
 313 LEU   ( 317-)  A  omega poor
 345 GLU   ( 349-)  A  omega poor
 369 TYR   ( 373-)  A  omega poor
And so on for a total of 66 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!

   7 PRO   (   6-)  A      0
  10 PHE   (   9-)  A      0
  12 TYR   (  11-)  A      0
  13 SER   (  12-)  A      0
  19 CYS   (  18-)  A      0
  23 TYR   (  22-)  A      0
  25 ASP   (  24-)  A      0
  26 SER   (  25-)  A      0
  27 PHE   (  26-)  A      0
  28 PRO   (  32-)  A      0
  29 ALA   (  33-)  A      0
  30 LEU   (  34-)  A      0
  41 SER   (  45-)  A      0
  44 ARG   (  48-)  A      0
  45 MET   (  49-)  A      0
  53 GLN   (  57-)  A      0
  55 ASN   (  59-)  A      0
  57 THR   (  61-)  A      0
  61 LEU   (  65-)  A      0
  69 GLN   (  73-)  A      0
  71 PHE   (  75-)  A      0
  75 LYS   (  79-)  A      0
  77 PHE   (  81-)  A      0
  81 MET   (  85-)  A      0
 110 ILE   ( 114-)  A      0
And so on for a total of 431 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]

 167 PRO   ( 171-)  A    0.07 LOW
 659 PRO   ( 171-)  B    0.18 LOW
 973 PRO   ( 485-)  B    0.07 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].

  28 PRO   (  32-)  A  -125.5 half-chair C-delta/C-gamma (-126 degrees)
  51 PRO   (  55-)  A   -40.7 envelop C-alpha (-36 degrees)
 174 PRO   ( 178-)  A   -46.1 half-chair C-beta/C-alpha (-54 degrees)
 178 PRO   ( 182-)  A   130.7 half-chair C-beta/C-alpha (126 degrees)
 471 PRO   ( 475-)  A  -151.0 envelop C-delta (-144 degrees)
 481 PRO   ( 485-)  A    46.5 half-chair C-delta/C-gamma (54 degrees)
 543 PRO   (  55-)  B   -35.5 envelop C-alpha (-36 degrees)
 666 PRO   ( 178-)  B   -29.1 envelop C-alpha (-36 degrees)
 670 PRO   ( 182-)  B   152.5 envelop C-alpha (144 degrees)
 940 PRO   ( 452-)  B  -124.8 half-chair C-delta/C-gamma (-126 degrees)
 963 PRO   ( 475-)  B  -143.2 envelop C-delta (-144 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.

 987 NAG   (1499-)  A      O4  <-> 1005 MAN   (1500-)  A      C1     0.99    1.41  INTRA BF
 990 NAG   (1499-)  B      O4  <-> 1004 BMA   (1500-)  B      C1     0.99    1.41  INTRA B3
 990 NAG   (1499-)  B      C4  <-> 1004 BMA   (1500-)  B      C1     0.61    2.59  INTRA
 841 ARG   ( 353-)  B      NH1 <->  998 SO4   (1502-)  B      S      0.50    2.80  INTRA
 841 ARG   ( 353-)  B      NH1 <->  998 SO4   (1502-)  B      O1     0.44    2.26  INTRA
 987 NAG   (1499-)  A      C4  <-> 1005 MAN   (1500-)  A      C1     0.42    2.78  INTRA
1006 HOH   (2029 )  A      O   <-> 1006 HOH   (2081 )  A      O      0.36    1.84  INTRA
  60 GLY   (  64-)  A      N   <-> 1006 HOH   (2021 )  A      O      0.31    2.39  INTRA
 506 SER   (  12-)  B      OG  <->  998 SO4   (1502-)  B      O3     0.31    2.09  INTRA BL
 138 PHE   ( 142-)  A      O   <->  207 ARG   ( 211-)  A      NH2    0.29    2.41  INTRA
 731 GLY   ( 243-)  B      N   <-> 1001 SO4   (1505-)  B      O3     0.28    2.42  INTRA
 630 PHE   ( 142-)  B      O   <->  699 ARG   ( 211-)  B      NH2    0.21    2.49  INTRA
 286 HIS   ( 290-)  A      ND1 <-> 1006 HOH   (2085 )  A      O      0.21    2.49  INTRA
1006 HOH   (2107 )  A      O   <-> 1006 HOH   (2108 )  A      O      0.20    2.00  INTRA BL
 202 HIS   ( 206-)  A      NE2 <->  251 HIS   ( 255-)  A      NE2    0.19    2.81  INTRA BL
 342 LYS   ( 346-)  A      N   <->  345 GLU   ( 349-)  A      OE1    0.18    2.52  INTRA
 349 ARG   ( 353-)  A      NH2 <->  995 SO4   (1505-)  A      S      0.18    3.12  INTRA BL
  56 HIS   (  60-)  A      ND1 <->  477 GLU   ( 481-)  A      OE2    0.17    2.53  INTRA
 694 HIS   ( 206-)  B      NE2 <->  743 HIS   ( 255-)  B      NE2    0.17    2.83  INTRA BL
 223 PHE   ( 227-)  A      N   <-> 1006 HOH   (2060 )  A      O      0.16    2.54  INTRA BL
 361 HIS   ( 365-)  A      ND1 <->  441 ASP   ( 445-)  A      OD2    0.15    2.55  INTRA
 179 THR   ( 183-)  A      N   <-> 1006 HOH   (2045 )  A      O      0.15    2.55  INTRA BL
1007 HOH   (2036 )  B      O   <-> 1007 HOH   (2117 )  B      O      0.15    2.05  INTRA BL
 685 LEU   ( 197-)  B      O   <-> 1007 HOH   (2041 )  B      O      0.15    2.25  INTRA BL
 831 VAL   ( 343-)  B      N   <-> 1007 HOH   (2085 )  B      O      0.14    2.56  INTRA BL
And so on for a total of 103 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.

 492 ARG   ( 496-)  A      -7.31
 984 ARG   ( 496-)  B      -7.17
 165 GLN   ( 169-)  A      -6.67
 196 GLN   ( 200-)  A      -6.22
 657 GLN   ( 169-)  B      -6.11
 835 PHE   ( 347-)  B      -6.07
 688 GLN   ( 200-)  B      -5.99
 491 HIS   ( 495-)  A      -5.94
 983 HIS   ( 495-)  B      -5.75
 258 ARG   ( 262-)  A      -5.65
 750 ARG   ( 262-)  B      -5.63
  40 ARG   (  44-)  A      -5.49
 658 ARG   ( 170-)  B      -5.25
 271 ASN   ( 275-)  A      -5.22
 532 ARG   (  44-)  B      -5.22
 190 LYS   ( 194-)  A      -5.19
 618 ILE   ( 130-)  B      -5.18
 682 LYS   ( 194-)  B      -5.17
 459 ARG   ( 463-)  A      -5.10
 126 ILE   ( 130-)  A      -5.06
 611 MET   ( 123-)  B      -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.

  55 ASN   (  59-)  A        57 - THR     61- ( A)         -4.48
 126 ILE   ( 130-)  A       128 - THR    132- ( A)         -4.40
 547 ASN   (  59-)  B       549 - THR     61- ( B)         -4.56
 618 ILE   ( 130-)  B       620 - THR    132- ( B)         -4.43

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.

 493 GLN   ( 497-)  A   -2.89
 139 GLN   ( 143-)  A   -2.86
  60 GLY   (  64-)  A   -2.67
 658 ARG   ( 170-)  B   -2.66

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.

1006 HOH   (2078 )  A      O
1007 HOH   (2122 )  B      O
1007 HOH   (2128 )  B      O
Bound group on Asn; dont flip   20 ASN  (  19-) A
Bound to:  986 NAG  (1498-) A
Bound group on Asn; dont flip  513 ASN  (  19-) B
Bound to:  989 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.

 324 HIS   ( 328-)  A
 631 GLN   ( 143-)  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.

  24 CYS   (  23-)  A      N
 106 SER   ( 110-)  A      OG
 136 ASP   ( 140-)  A      N
 143 PHE   ( 147-)  A      N
 165 GLN   ( 169-)  A      N
 175 TRP   ( 179-)  A      NE1
 229 GLU   ( 233-)  A      N
 235 GLY   ( 239-)  A      N
 242 PHE   ( 246-)  A      N
 250 GLU   ( 254-)  A      N
 337 ALA   ( 341-)  A      N
 338 CYS   ( 342-)  A      N
 362 SER   ( 366-)  A      OG
 373 GLY   ( 377-)  A      N
 377 TRP   ( 381-)  A      NE1
 378 ASN   ( 382-)  A      ND2
 380 ALA   ( 384-)  A      N
 388 ASN   ( 392-)  A      ND2
 429 ARG   ( 433-)  A      NH1
 436 GLN   ( 440-)  A      N
 472 ALA   ( 476-)  A      N
 505 TYR   (  11-)  B      N
 517 CYS   (  23-)  B      N
 540 SER   (  52-)  B      OG
 620 THR   ( 132-)  B      OG1
 628 ASP   ( 140-)  B      N
 635 PHE   ( 147-)  B      N
 667 TRP   ( 179-)  B      NE1
 685 LEU   ( 197-)  B      N
 700 TYR   ( 212-)  B      OH
 727 GLY   ( 239-)  B      N
 734 PHE   ( 246-)  B      N
 750 ARG   ( 262-)  B      NE
 829 ALA   ( 341-)  B      N
 830 CYS   ( 342-)  B      N
 836 TRP   ( 348-)  B      N
 854 SER   ( 366-)  B      OG
 869 TRP   ( 381-)  B      NE1
 870 ASN   ( 382-)  B      ND2
 872 ALA   ( 384-)  B      N
 880 ASN   ( 392-)  B      ND2
 907 HIS   ( 419-)  B      NE2
 921 ARG   ( 433-)  B      NH1
 928 GLN   ( 440-)  B      N
 964 ALA   ( 476-)  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.

  83 ASP   (  87-)  A      OD1
 149 ASP   ( 153-)  A      OD1
 415 HIS   ( 419-)  A      NE2
 862 HIS   ( 374-)  B      NE2

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.

 133 ASP   ( 137-)  A   H-bonding suggests Asn
 199 ASP   ( 203-)  A   H-bonding suggests Asn
 229 GLU   ( 233-)  A   H-bonding suggests Gln
 376 ASP   ( 380-)  A   H-bonding suggests Asn
 691 ASP   ( 203-)  B   H-bonding suggests Asn; but Alt-Rotamer
 721 GLU   ( 233-)  B   H-bonding suggests Gln
 868 ASP   ( 380-)  B   H-bonding suggests Asn; but Alt-Rotamer
 933 ASP   ( 445-)  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 :  -0.321
  2nd generation packing quality :  -1.328
  Ramachandran plot appearance   :  -0.851
  chi-1/chi-2 rotamer normality  :  -2.198
  Backbone conformation          :  -0.473

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.707
  Bond angles                    :   0.793
  Omega angle restraints         :   1.209
  Side chain planarity           :   0.642 (tight)
  Improper dihedral distribution :   0.843
  Inside/Outside distribution    :   1.027

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 : 2.66


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.8
  2nd generation packing quality :   0.3
  Ramachandran plot appearance   :   1.5
  chi-1/chi-2 rotamer normality  :   0.1
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.707
  Bond angles                    :   0.793
  Omega angle restraints         :   1.209
  Side chain planarity           :   0.642 (tight)
  Improper dihedral distribution :   0.843
  Inside/Outside distribution    :   1.027
==============

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.