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 pdb1xld.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.453
CA-only RMS fit for the two chains : 0.207

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

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: Unexpected atoms encountered

While reading the PDB file, at least one atom was encountered that was not expected in the residue. This might be caused by a naming convention problem. It can also mean that a residue was found protonated that normally is not (e.g. aspartic acid). The unexpected atoms have been discarded; in case protons were deleted that actually might be needed, they will later be put back by the hydrogen bond validation software. This normally is not a warning you should worry too much about.

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'.

   2 GLN   (   3-)  A      CG
   2 GLN   (   3-)  A      CD
   2 GLN   (   3-)  A      OE1
   2 GLN   (   3-)  A      NE2
  30 LYS   (  31-)  A      CG
  30 LYS   (  31-)  A      CD
  30 LYS   (  31-)  A      CE
  30 LYS   (  31-)  A      NZ
  63 GLU   (  64-)  A      CG
  63 GLU   (  64-)  A      CD
  63 GLU   (  64-)  A      OE1
  63 GLU   (  64-)  A      OE2
  78 LYS   (  79-)  A      CG
  78 LYS   (  79-)  A      CD
  78 LYS   (  79-)  A      CE
  78 LYS   (  79-)  A      NZ
 395 GLN   (   3-)  B      CG
 395 GLN   (   3-)  B      CD
 395 GLN   (   3-)  B      OE1
 395 GLN   (   3-)  B      NE2
 423 LYS   (  31-)  B      CG
 423 LYS   (  31-)  B      CD
 423 LYS   (  31-)  B      CE
 423 LYS   (  31-)  B      NZ
 456 GLU   (  64-)  B      CG
 456 GLU   (  64-)  B      CD
 456 GLU   (  64-)  B      OE1
 456 GLU   (  64-)  B      OE2
 471 LYS   (  79-)  B      CG
 471 LYS   (  79-)  B      CD
 471 LYS   (  79-)  B      CE
 471 LYS   (  79-)  B      NZ

Warning: Occupancies atoms do not add up to 1.0.

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

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

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

   1 VAL   (   2-)  A    0.50
  43 GLU   (  44-)  A    0.50
  83 LYS   (  84-)  A    0.50
 130 GLU   ( 131-)  A    0.50
 308 LYS   ( 309-)  A    0.50
 329 GLU   ( 330-)  A    0.50
 332 GLU   ( 333-)  A    0.50
 373 GLU   ( 374-)  A    0.50
 394 VAL   (   2-)  B    0.50
 436 GLU   (  44-)  B    0.50
 476 LYS   (  84-)  B    0.50
 523 GLU   ( 131-)  B    0.50
 701 LYS   ( 309-)  B    0.50
 722 GLU   ( 330-)  B    0.50
 725 GLU   ( 333-)  B    0.50
 766 GLU   ( 374-)  B    0.50

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and 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:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

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.

  19 THR   (  20-)  A      CB   OG1   1.50    4.2
 397 THR   (   5-)  B      CB   OG1   1.50    4.3
 473 THR   (  81-)  B      CA   CB    1.63    5.2
 630 GLU   ( 238-)  B      CB   CG    1.64    4.0
 669 GLY   ( 277-)  B      N    CA    1.54    5.8
 690 THR   ( 298-)  B      CA   CB    1.61    4.1
 787 XYL   ( 400-)  A      C1   O5    4.87   67.9
 788 XYL   ( 400-)  B      C1   O5    4.90   68.6

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

 |  0.997820  0.000280 -0.000077|
 |  0.000280  0.995822 -0.000514|
 | -0.000077 -0.000514  0.996888|
Proposed new scale matrix

 |  0.009489  0.005487  0.000004|
 | -0.000003  0.010981  0.000006|
 |  0.000000  0.000003  0.006535|
With corresponding cell

    A    = 105.366  B   = 105.180  C    = 153.014
    Alpha=  90.049  Beta=  90.005  Gamma= 120.023

The CRYST1 cell dimensions

    A    = 105.600  B   = 105.600  C    = 153.500
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 266.236
(Under-)estimated Z-score: 12.025

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.

   1 VAL   (   2-)  A      CA   C    O   128.70    4.6
   6 ALA   (   7-)  A     -O   -C    N   111.92   -6.9
   6 ALA   (   7-)  A     -CA  -C    N   124.66    4.2
   6 ALA   (   7-)  A     -C    N    CA  143.38   12.0
   7 ASP   (   8-)  A     -C    N    CA  133.35    6.5
   8 HIS   (   9-)  A      CG   ND1  CE1 111.04    5.4
   8 HIS   (   9-)  A      ND1  CE1  NE2 106.03   -4.4
   9 PHE   (  10-)  A      C    CA   CB  118.04    4.2
  10 THR   (  11-)  A      C    CA   CB  117.70    4.0
  14 TRP   (  15-)  A     -C    N    CA  130.36    4.8
  15 THR   (  16-)  A      CA   CB   OG1 100.92   -5.8
  17 GLY   (  18-)  A     -C    N    CA  131.21    6.2
  19 THR   (  20-)  A     -C    N    CA  132.90    6.2
  19 THR   (  20-)  A      N    CA   CB   98.70   -6.9
  19 THR   (  20-)  A      C    CA   CB  121.31    5.9
  19 THR   (  20-)  A      CA   CB   CG2 119.15    5.1
  19 THR   (  20-)  A      CA   CB   OG1 102.19   -4.9
  19 THR   (  20-)  A      CG2  CB   OG1 119.28    5.0
  22 ASP   (  23-)  A      C    CA   CB  123.54    7.1
  22 ASP   (  23-)  A      CA   CB   CG  116.85    4.2
  24 PHE   (  25-)  A      CA   CB   CG  107.29   -6.5
  27 ALA   (  28-)  A      CA   C    O   111.32   -5.6
  30 LYS   (  31-)  A     -O   -C    N   130.16    4.5
  30 LYS   (  31-)  A      C    CA   CB  119.36    4.9
  31 ASN   (  32-)  A      CA   CB   CG  105.48   -7.1
And so on for a total of 479 lines.

Warning: High bond angle deviations

Bond angles were found to deviate more than normal from the mean standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set, and this is indeed observed for very high resolution X-ray structures. The fact that it is higher than 2.0 in this structure might indicate that the restraints used in the refinement were not strong enough. This will also occur if a different bond angle dictionary is used.

RMS Z-score for bond angles: 2.015
RMS-deviation in bond angles: 3.696

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.

 675 PRO   ( 283-)  B      CA    -6.3    29.28    38.15
The average deviation= 1.747

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.

  64 ALA   (  65-)  A    7.46
 473 THR   (  81-)  B    5.89
 148 ASP   ( 149-)  A    5.86
 541 ASP   ( 149-)  B    5.43
 448 ASP   (  56-)  B    5.36
 351 GLU   ( 352-)  A    4.96
 578 PRO   ( 186-)  B    4.92
 101 GLY   ( 102-)  A    4.71
 656 LEU   ( 264-)  B    4.32
 288 ARG   ( 289-)  A    4.26
  80 THR   (  81-)  A    4.19
 494 GLY   ( 102-)  B    4.18
 728 LYS   ( 336-)  B    4.05
 476 LYS   (  84-)  B    4.02

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.697

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.

 609 THR   ( 217-)  B    -2.9
 216 THR   ( 217-)  A    -2.4
 678 THR   ( 286-)  B    -2.3
 283 LYS   ( 284-)  A    -2.2
 350 GLY   ( 351-)  A    -2.2
 630 GLU   ( 238-)  B    -2.2
 685 TYR   ( 293-)  B    -2.2
 412 THR   (  20-)  B    -2.2
 184 GLU   ( 185-)  A    -2.1
 292 TYR   ( 293-)  A    -2.1
 363 PHE   ( 364-)  A    -2.0
 285 THR   ( 286-)  A    -2.0
  83 LYS   (  84-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

   8 HIS   (   9-)  A  Poor phi/psi
  92 PHE   (  93-)  A  Poor phi/psi
 184 GLU   ( 185-)  A  Poor phi/psi, PRO omega poor
 191 LEU   ( 192-)  A  Poor phi/psi
 237 GLU   ( 238-)  A  Poor phi/psi
 251 LYS   ( 252-)  A  Poor phi/psi
 363 PHE   ( 364-)  A  Poor phi/psi
 377 ALA   ( 378-)  A  Poor phi/psi
 395 GLN   (   3-)  B  Poor phi/psi
 401 HIS   (   9-)  B  Poor phi/psi
 485 PHE   (  93-)  B  Poor phi/psi
 577 GLU   ( 185-)  B  Poor phi/psi, PRO omega poor
 584 LEU   ( 192-)  B  Poor phi/psi
 630 GLU   ( 238-)  B  Poor phi/psi
 644 LYS   ( 252-)  B  Poor phi/psi
 756 PHE   ( 364-)  B  Poor phi/psi
 770 ALA   ( 378-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.733

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 ASP   (   8-)  A      0
  15 THR   (  16-)  A      0
  19 THR   (  20-)  A      0
  21 ALA   (  22-)  A      0
  22 ASP   (  23-)  A      0
  24 PHE   (  25-)  A      0
  27 ALA   (  28-)  A      0
  44 LEU   (  45-)  A      0
  46 ALA   (  47-)  A      0
  47 TYR   (  48-)  A      0
  54 ASN   (  55-)  A      0
  57 ILE   (  58-)  A      0
  85 PRO   (  86-)  A      0
  91 LEU   (  92-)  A      0
  92 PHE   (  93-)  A      0
  93 SER   (  94-)  A      0
  97 PHE   (  98-)  A      0
  99 ASP   ( 100-)  A      0
 102 PHE   ( 103-)  A      0
 103 THR   ( 104-)  A      0
 104 SER   ( 105-)  A      0
 107 ARG   ( 108-)  A      0
 127 MET   ( 128-)  A      0
 129 ALA   ( 130-)  A      0
 130 GLU   ( 131-)  A      0
And so on for a total of 263 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 2.522

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 350 GLY   ( 351-)  A   1.63   69

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]

  34 PRO   (  35-)  A    0.08 LOW
  95 PRO   (  96-)  A    0.18 LOW
 180 PRO   ( 181-)  A    0.20 LOW
 214 PRO   ( 215-)  A    0.18 LOW
 282 PRO   ( 283-)  A    0.10 LOW
 287 PRO   ( 288-)  A    0.02 LOW
 294 PRO   ( 295-)  A    0.47 HIGH
 328 PRO   ( 329-)  A    0.06 LOW
 398 PRO   (   6-)  B    0.47 HIGH
 416 PRO   (  24-)  B    0.08 LOW
 427 PRO   (  35-)  B    0.13 LOW
 575 PRO   ( 183-)  B    0.16 LOW
 680 PRO   ( 288-)  B    0.17 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].

   5 PRO   (   6-)  A   100.4 envelop C-beta (108 degrees)
  85 PRO   (  86-)  A    45.7 half-chair C-delta/C-gamma (54 degrees)
 478 PRO   (  86-)  B    43.8 envelop C-delta (36 degrees)
 573 PRO   ( 181-)  B    46.0 half-chair C-delta/C-gamma (54 degrees)
 675 PRO   ( 283-)  B    16.8 half-chair N/C-delta (18 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.

 260 HIS   ( 261-)  A      NE2 <->  776 GLN   ( 384-)  B      NE2    0.29    2.71  INTRA BL
 383 GLN   ( 384-)  A      NE2 <->  653 HIS   ( 261-)  B      NE2    0.27    2.73  INTRA BL
 753 SER   ( 361-)  B      O   <->  758 GLY   ( 366-)  B      N      0.22    2.48  INTRA
 293 LYS   ( 294-)  A      NZ  <->  795 HOH   ( 479 )  A      O      0.22    2.48  INTRA
 678 THR   ( 286-)  B      N   <->  815 HOH   ( 530 )  B      O      0.18    2.52  INTRA
 387 GLU   ( 388-)  A      OE1 <->  393 ARG   ( 394-)  A      NH1    0.17    2.53  INTRA
 447 ASN   (  55-)  B      OD1 <->  509 LYS   ( 117-)  B      NZ     0.17    2.53  INTRA
 576 ASN   ( 184-)  B      ND2 <->  815 HOH   ( 489 )  B      O      0.14    2.56  INTRA BL
 341 GLU   ( 342-)  A      OE2 <->  374 ARG   ( 375-)  A      NH1    0.14    2.56  INTRA
  36 GLU   (  37-)  A      OE2 <->   40 LYS   (  41-)  A      NZ     0.14    2.56  INTRA BF
 161 ASP   ( 162-)  A      OD1 <->  206 HIS   ( 207-)  A      N      0.14    2.56  INTRA
 468 GLN   (  76-)  B      O   <->  472 ASP   (  80-)  B      N      0.13    2.57  INTRA
 360 SER   ( 361-)  A      O   <->  365 GLY   ( 366-)  A      N      0.13    2.57  INTRA
 183 ASN   ( 184-)  A      ND2 <->  795 HOH   ( 489 )  A      O      0.13    2.57  INTRA BL
 554 ASP   ( 162-)  B      OD1 <->  599 HIS   ( 207-)  B      N      0.12    2.58  INTRA
 483 ASN   (  91-)  B      ND2 <->  486 SER   (  94-)  B      OG     0.11    2.59  INTRA BL
 215 GLU   ( 216-)  A      OE2 <->  245 ASN   ( 246-)  A      ND2    0.11    2.59  INTRA BL
  18 TRP   (  19-)  A      O   <->   29 ARG   (  30-)  A      NH2    0.11    2.59  INTRA BL
 142 GLU   ( 143-)  A      OE1 <->  186 ARG   ( 187-)  A      NH2    0.10    2.60  INTRA BL
 329 GLU   ( 330-)  A      OE2 <->  380 ARG   ( 381-)  A      NH2    0.10    2.60  INTRA
 331 GLN   ( 332-)  A      NE2 <->  814 HOH   ( 737 )  A      O      0.09    2.61  INTRA
 670 PHE   ( 278-)  B      O   <->  673 GLY   ( 281-)  B      N      0.09    2.61  INTRA BL
 157 ARG   ( 158-)  A      NE  <->  795 HOH   ( 471 )  A      O      0.08    2.62  INTRA
 412 THR   (  20-)  B      O   <->  421 THR   (  29-)  B      N      0.08    2.62  INTRA BL
 319 GLU   ( 320-)  A      OE2 <->  320 ARG   ( 321-)  A      NH1    0.08    2.62  INTRA
And so on for a total of 81 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.

 641 ARG   ( 249-)  B      -7.45
 248 ARG   ( 249-)  A      -7.33
 417 PHE   (  25-)  B      -7.23
  24 PHE   (  25-)  A      -7.20
 536 TYR   ( 144-)  B      -6.86
 143 TYR   ( 144-)  A      -6.73
 645 TYR   ( 253-)  B      -6.24
 252 TYR   ( 253-)  A      -6.21
 531 ARG   ( 139-)  B      -5.56
 138 ARG   ( 139-)  A      -5.55
 668 ASN   ( 276-)  B      -5.30
 275 ASN   ( 276-)  A      -5.23
 491 LYS   (  99-)  B      -5.15
  98 LYS   (  99-)  A      -5.09

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.

 679 GLY   ( 287-)  B   -3.41
 286 GLY   ( 287-)  A   -3.22
  30 LYS   (  31-)  A   -3.17
 222 ALA   ( 223-)  A   -2.63
 615 ALA   ( 223-)  B   -2.61
 649 LEU   ( 257-)  B   -2.52
 256 LEU   ( 257-)  A   -2.50

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

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

 807 HOH   ( 720 )  A      O     10.11   45.90   35.09
 811 HOH   ( 726 )  A      O     38.50   26.20   23.25
 813 HOH   ( 731 )  A      O     11.38   89.98    4.93
 836 HOH   ( 681 )  B      O     20.09   82.10   37.40

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.

 803 HOH   ( 662 )  A      O
 803 HOH   ( 669 )  A      O
 803 HOH   ( 679 )  A      O
 803 HOH   ( 680 )  A      O
 807 HOH   ( 723 )  A      O
 811 HOH   ( 725 )  A      O
 811 HOH   ( 727 )  A      O
 813 HOH   ( 734 )  A      O
 823 HOH   ( 579 )  B      O
 823 HOH   ( 584 )  B      O
 823 HOH   ( 588 )  B      O
 833 HOH   ( 640 )  B      O
 833 HOH   ( 643 )  B      O
 833 HOH   ( 647 )  B      O
 833 HOH   ( 648 )  B      O
 837 HOH   ( 705 )  B      O
 837 HOH   ( 712 )  B      O
 837 HOH   ( 719 )  B      O
 839 HOH   ( 739 )  B      O
Metal-coordinating Histidine residue 218 fixed to   1
Metal-coordinating Histidine residue 611 fixed to   1

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

  94 HIS   (  95-)  A
 119 HIS   ( 120-)  A
 183 ASN   ( 184-)  A
 220 GLN   ( 221-)  A
 383 GLN   ( 384-)  A
 424 ASN   (  32-)  B
 467 ASN   (  75-)  B
 468 GLN   (  76-)  B
 487 HIS   (  95-)  B
 512 HIS   ( 120-)  B
 576 ASN   ( 184-)  B
 613 GLN   ( 221-)  B
 776 GLN   ( 384-)  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.

  12 GLY   (  13-)  A      N
  14 TRP   (  15-)  A      N
  20 GLY   (  21-)  A      N
  21 ALA   (  22-)  A      N
  60 ASP   (  61-)  A      N
  86 MET   (  87-)  A      N
 135 TRP   ( 136-)  A      NE1
 143 TYR   ( 144-)  A      N
 147 LYS   ( 148-)  A      N
 149 LEU   ( 150-)  A      N
 174 LEU   ( 175-)  A      N
 183 ASN   ( 184-)  A      N
 186 ARG   ( 187-)  A      N
 193 THR   ( 194-)  A      N
 193 THR   ( 194-)  A      OG1
 227 THR   ( 228-)  A      OG1
 245 ASN   ( 246-)  A      N
 251 LYS   ( 252-)  A      N
 261 GLY   ( 262-)  A      N
 289 HIS   ( 290-)  A      N
 292 TYR   ( 293-)  A      N
 310 ASN   ( 311-)  A      ND2
 393 ARG   ( 394-)  A      N
 403 THR   (  11-)  B      OG1
 405 GLY   (  13-)  B      N
 407 TRP   (  15-)  B      N
 413 GLY   (  21-)  B      N
 444 PHE   (  52-)  B      N
 453 ASP   (  61-)  B      N
 455 THR   (  63-)  B      N
 479 MET   (  87-)  B      N
 528 TRP   ( 136-)  B      NE1
 540 LYS   ( 148-)  B      N
 541 ASP   ( 149-)  B      N
 576 ASN   ( 184-)  B      N
 579 ARG   ( 187-)  B      N
 586 THR   ( 194-)  B      N
 586 THR   ( 194-)  B      OG1
 588 GLY   ( 196-)  B      N
 635 ILE   ( 243-)  B      N
 644 LYS   ( 252-)  B      N
 654 GLY   ( 262-)  B      N
 682 HIS   ( 290-)  B      N
 685 TYR   ( 293-)  B      N
 692 GLY   ( 300-)  B      N
 703 ASN   ( 311-)  B      ND2
 776 GLN   ( 384-)  B      NE2
Only metal coordination for  179 GLU  ( 180-) A      OE2
Only metal coordination for  218 HIS  ( 219-) A      NE2
Only metal coordination for  572 GLU  ( 180-) B      OE2

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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.

 795 HOH   ( 492 )  A      O  0.97  K  5
 803 HOH   ( 678 )  A      O  0.99  K  4
 815 HOH   ( 504 )  B      O  0.86  K  4
 823 HOH   ( 601 )  B      O  0.92 NA  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.

 169 ASP   ( 170-)  A   H-bonding suggests Asn
 472 ASP   (  80-)  B   H-bonding suggests Asn; but Alt-Rotamer
 698 ASP   ( 306-)  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 :  -0.836
  2nd generation packing quality :  -0.223
  Ramachandran plot appearance   :  -1.308
  chi-1/chi-2 rotamer normality  :  -2.733
  Backbone conformation          :   0.756

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.012
  Bond angles                    :   2.015 (loose)
  Omega angle restraints         :   0.459 (tight)
  Side chain planarity           :   0.954
  Improper dihedral distribution :   1.456
  B-factor distribution          :   0.468
  Inside/Outside distribution    :   1.048

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 : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.1
  2nd generation packing quality :   0.6
  Ramachandran plot appearance   :   0.5
  chi-1/chi-2 rotamer normality  :  -0.9
  Backbone conformation          :   1.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.012
  Bond angles                    :   2.015 (loose)
  Omega angle restraints         :   0.459 (tight)
  Side chain planarity           :   0.954
  Improper dihedral distribution :   1.456
  B-factor distribution          :   0.468
  Inside/Outside distribution    :   1.048
==============

WHAT IF
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Bond lengths and angles, DNA/RNA
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DSSP
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Hydrogen bond networks
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Matthews' Coefficient
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Protein side chain planarity
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Puckering parameters
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Quality Control
    G.Vriend and C.Sander,
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      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
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      Stereochemistry of Polypeptide Chain Conformations
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Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
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      data bank (PDB) files
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Ion Checks
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      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.