WHAT IF Check report

This file was created 2011-12-28 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 pdb1gt9.ent

Checks that need to be done early-on in validation

Warning: Class of space group could be incorrect

The space group symbol indicates a different class than the unit cell given on the CRYST1 card of the PDB file.

Possible cause: The unit cell may have pseudo-symmetry, or one of the cell dimensions or the space group might be given incorrectly.

Crystal class of the cell: ORTHORHOMBIC

Crystal class of the space group: MONOCLINIC

Space group name: P 1 21 1

Warning: Unconventional cell on CRYST1

The derived `conventional cell' is different from the cell given on the CRYST1 card.

The CRYST1 cell dimensions

    A    =  54.860  B   =  78.250  C    =  73.530
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    =  54.860  B   =  73.530  C    =  78.250
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    =  54.860  B   =  73.530  C    =  78.250
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

 | -1.000000  0.000000  0.000000|
 |  0.000000  0.000000  1.000000|
 |  0.000000  1.000000  0.000000|

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: 1 and 2

All-atom RMS fit for the two chains : 0.334
CA-only RMS fit for the two chains : 0.158

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: 1 and 2

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.

 717 SO4   (1359-)  1  -
 718 SO4   (1359-)  2  -

Administrative problems that can generate validation failures

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

  19 GLU   (  19-)  1  -   CD
  19 GLU   (  19-)  1  -   OE1
  19 GLU   (  19-)  1  -   OE2
  39 GLU   (  39-)  1  -   CG
  39 GLU   (  39-)  1  -   CD
  39 GLU   (  39-)  1  -   OE1
  39 GLU   (  39-)  1  -   OE2
  52 SER   (  52-)  1  -   OG
 172 GLN   ( 172-)  1  -   CD
 172 GLN   ( 172-)  1  -   OE1
 172 GLN   ( 172-)  1  -   NE2
 223 ARG   ( 223-)  1  -   CG
 223 ARG   ( 223-)  1  -   CD
 223 ARG   ( 223-)  1  -   NE
 223 ARG   ( 223-)  1  -   CZ
 223 ARG   ( 223-)  1  -   NH1
 223 ARG   ( 223-)  1  -   NH2
 297 LYS   ( 297-)  1  -   CD
 297 LYS   ( 297-)  1  -   CE
 297 LYS   ( 297-)  1  -   NZ
 376 GLU   (  19-)  2  -   CG
 376 GLU   (  19-)  2  -   CD
 376 GLU   (  19-)  2  -   OE1
 376 GLU   (  19-)  2  -   OE2
 396 GLU   (  39-)  2  -   CG
 396 GLU   (  39-)  2  -   CD
 396 GLU   (  39-)  2  -   OE1
 396 GLU   (  39-)  2  -   OE2
 451 LYS   (  94-)  2  -   CE
 451 LYS   (  94-)  2  -   NZ
 529 GLN   ( 172-)  2  -   CD
 529 GLN   ( 172-)  2  -   OE1
 529 GLN   ( 172-)  2  -   NE2
 580 ARG   ( 223-)  2  -   NE
 580 ARG   ( 223-)  2  -   CZ
 580 ARG   ( 223-)  2  -   NH1
 580 ARG   ( 223-)  2  -   NH2
 654 LYS   ( 297-)  2  -   CD
 654 LYS   ( 297-)  2  -   CE
 654 LYS   ( 297-)  2  -   NZ
 686 ARG   ( 329-)  2  -   CZ
 686 ARG   ( 329-)  2  -   NH1
 686 ARG   ( 329-)  2  -   NH2
 710 GLN   ( 353-)  2  -   OE1
 710 GLN   ( 353-)  2  -   NE2

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: 1

Note: Ramachandran plot

Chain identifier: 2

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

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.

 297 LYS   ( 297-)  1    0.26

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:

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: 1

Note: B-factor plot

Chain identifier: 2

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.

 194 ARG   ( 194-)  1
 204 ARG   ( 204-)  1
 329 ARG   ( 329-)  1
 350 ARG   ( 350-)  1
 551 ARG   ( 194-)  2
 561 ARG   ( 204-)  2
 590 ARG   ( 233-)  2
 686 ARG   ( 329-)  2
 707 ARG   ( 350-)  2

Warning: Tyrosine convention problem

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

   6 TYR   (   6-)  1
  15 TYR   (  15-)  1
  45 TYR   (  45-)  1
 176 TYR   ( 176-)  1
 186 TYR   ( 186-)  1
 263 TYR   ( 263-)  1
 301 TYR   ( 301-)  1
 363 TYR   (   6-)  2
 372 TYR   (  15-)  2
 402 TYR   (  45-)  2
 533 TYR   ( 176-)  2
 543 TYR   ( 186-)  2
 620 TYR   ( 263-)  2
 658 TYR   ( 301-)  2

Warning: Phenylalanine convention problem

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

  99 PHE   (  99-)  1
 107 PHE   ( 107-)  1
 225 PHE   ( 225-)  1
 314 PHE   ( 314-)  1
 456 PHE   (  99-)  2
 464 PHE   ( 107-)  2
 582 PHE   ( 225-)  2
 671 PHE   ( 314-)  2

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.

  10 ASP   (  10-)  1
  62 ASP   (  62-)  1
  71 ASP   (  71-)  1
  76 ASP   (  76-)  1
  82 ASP   (  82-)  1
 117 ASP   ( 117-)  1
 134 ASP   ( 134-)  1
 150 ASP   ( 150-)  1
 164 ASP   ( 164-)  1
 169 ASP   ( 169-)  1
 179 ASP   ( 179-)  1
 210 ASP   ( 210-)  1
 213 ASP   ( 213-)  1
 258 ASP   ( 258-)  1
 268 ASP   ( 268-)  1
 323 ASP   ( 323-)  1
 367 ASP   (  10-)  2
 395 ASP   (  38-)  2
 419 ASP   (  62-)  2
 428 ASP   (  71-)  2
 433 ASP   (  76-)  2
 439 ASP   (  82-)  2
 474 ASP   ( 117-)  2
 507 ASP   ( 150-)  2
 521 ASP   ( 164-)  2
 526 ASP   ( 169-)  2
 536 ASP   ( 179-)  2
 567 ASP   ( 210-)  2
 570 ASP   ( 213-)  2
 615 ASP   ( 258-)  2
 625 ASP   ( 268-)  2
 680 ASP   ( 323-)  2

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.

  19 GLU   (  19-)  1
  80 GLU   (  80-)  1
 232 GLU   ( 232-)  1
 264 GLU   ( 264-)  1
 312 GLU   ( 312-)  1
 376 GLU   (  19-)  2
 437 GLU   (  80-)  2
 528 GLU   ( 171-)  2
 589 GLU   ( 232-)  2
 621 GLU   ( 264-)  2
 669 GLU   ( 312-)  2
 676 GLU   ( 319-)  2

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.

  13 GLN   (  13-)  1      CG   CD    1.67    6.3
  95 ILE   (  95-)  1      CG1  CD1   1.76    6.3
 141 ILE   ( 141-)  1      N   -C     1.48    7.4
 194 ARG   ( 194-)  1      CG   CD    1.66    4.7
 245 GLY   ( 245-)  1      N    CA    1.67   13.5
 245 GLY   ( 245-)  1      N   -C     1.64   15.8
 387 ILE   (  30-)  2      CB   CG1   1.36   -5.2
 503 ARG   ( 146-)  2      CG   CD    1.69    5.6
 503 ARG   ( 146-)  2      CZ   NH1   1.15   -9.6
 522 SER   ( 165-)  2      CB   OG    1.19  -11.5
 528 GLU   ( 171-)  2      CD   OE2   1.66   21.6
 598 ASN   ( 241-)  2      CA   CB    1.75   10.9
 599 PRO   ( 242-)  2      N    CA    1.68   14.0
 599 PRO   ( 242-)  2      CA   CB    1.90   18.4
 599 PRO   ( 242-)  2      CG   CD    1.67    4.8
 599 PRO   ( 242-)  2      CD   N     1.78   22.2

Warning: Low bond length variability

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

RMS Z-score for bond lengths: 0.560
RMS-deviation in bond distances: 0.014

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

 |  0.998907  0.000296  0.000166|
 |  0.000296  0.997238  0.000256|
 |  0.000166  0.000256  0.998560|
Proposed new scale matrix

 |  0.018248 -0.000005 -0.000003|
 | -0.000004  0.012814 -0.000003|
 | -0.000002 -0.000003  0.013620|
With corresponding cell

    A    =  54.801  B   =  78.037  C    =  73.424
    Alpha=  89.971  Beta=  89.981  Gamma=  89.966

The CRYST1 cell dimensions

    A    =  54.860  B   =  78.250  C    =  73.530
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 73.768
(Under-)estimated Z-score: 6.330

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.

  13 GLN   (  13-)  1      CB   CG   CD  103.54   -5.3
 140 SER   ( 140-)  1      CA   C    O   129.44    5.1
 141 ILE   ( 141-)  1     -O   -C    N   114.59   -5.3
 141 ILE   ( 141-)  1      CA   CB   CG2 101.34   -5.4
 141 ILE   ( 141-)  1      CA   CB   CG1 102.16   -4.8
 144 MET   ( 144-)  1      CA   CB   CG  126.87    6.4
 181 PRO   ( 181-)  1      N    CA   C   123.63    4.7
 194 ARG   ( 194-)  1      CB   CG   CD  101.86   -6.1
 245 GLY   ( 245-)  1     -O   -C    N   131.65    5.4
 245 GLY   ( 245-)  1     -CA  -C    N   104.35   -5.9
 245 GLY   ( 245-)  1     -C    N    CA   92.29  -16.7
 245 GLY   ( 245-)  1      N    CA   C    99.46   -4.5
 274 ILE   ( 274-)  1      CG2  CB   CG1  94.32   -5.5
 347 ILE   ( 347-)  1      N    CA   C    98.88   -4.4
 387 ILE   (  30-)  2      CA   CB   CG1 118.56    4.8
 503 ARG   ( 146-)  2      NH1  CZ   NH2   4.17  -64.2
 522 SER   ( 165-)  2      CA   CB   OG  121.08    5.0
 528 GLU   ( 171-)  2      CG   CD   OE2  93.08  -11.0
 538 PRO   ( 181-)  2      N    CA   C   123.82    4.8
 598 ASN   ( 241-)  2      N    CA   CB   98.45   -7.1
 598 ASN   ( 241-)  2      C    CA   CB  101.00   -4.8
 599 PRO   ( 242-)  2      N    CA   C    93.58   -7.3
 599 PRO   ( 242-)  2      N    CA   CB   81.64  -19.4
 599 PRO   ( 242-)  2      C    CA   CB   90.49  -10.3
 599 PRO   ( 242-)  2      CG   CD   N    84.74  -12.3
 599 PRO   ( 242-)  2      CD   N    CA   88.76  -16.6
 704 ILE   ( 347-)  2      N    CA   C    99.40   -4.2

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.

  10 ASP   (  10-)  1
  19 GLU   (  19-)  1
  62 ASP   (  62-)  1
  71 ASP   (  71-)  1
  76 ASP   (  76-)  1
  80 GLU   (  80-)  1
  82 ASP   (  82-)  1
 117 ASP   ( 117-)  1
 134 ASP   ( 134-)  1
 150 ASP   ( 150-)  1
 164 ASP   ( 164-)  1
 169 ASP   ( 169-)  1
 179 ASP   ( 179-)  1
 194 ARG   ( 194-)  1
 204 ARG   ( 204-)  1
 210 ASP   ( 210-)  1
 213 ASP   ( 213-)  1
 232 GLU   ( 232-)  1
 258 ASP   ( 258-)  1
 264 GLU   ( 264-)  1
 268 ASP   ( 268-)  1
 312 GLU   ( 312-)  1
 323 ASP   ( 323-)  1
 329 ARG   ( 329-)  1
 350 ARG   ( 350-)  1
And so on for a total of 53 lines.

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.

 331 TYR   ( 331-)  1      C      7.3    11.66     0.33
The average deviation= 0.988

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.

 599 PRO   ( 242-)  2    7.54
 619 GLY   ( 262-)  2    5.09
 245 GLY   ( 245-)  1    5.07
 348 GLY   ( 348-)  1    4.52
 262 GLY   ( 262-)  1    4.45
 538 PRO   ( 181-)  2    4.29
 181 PRO   ( 181-)  1    4.22
 551 ARG   ( 194-)  2    4.01

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 528 GLU   ( 171-)  2   28.35

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.

 272 THR   ( 272-)  1    -2.9
 629 THR   ( 272-)  2    -2.9
 608 PRO   ( 251-)  2    -2.9
 251 PRO   ( 251-)  1    -2.8
 522 SER   ( 165-)  2    -2.2
 324 ILE   ( 324-)  1    -2.1
 683 ASN   ( 326-)  2    -2.1
 326 ASN   ( 326-)  1    -2.1
 665 GLN   ( 308-)  2    -2.1
 308 GLN   ( 308-)  1    -2.1
 446 LEU   (  89-)  2    -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.

 180 PHE   ( 180-)  1  PRO omega poor
 235 ASN   ( 235-)  1  Poor phi/psi
 244 ALA   ( 244-)  1  Poor phi/psi
 250 VAL   ( 250-)  1  PRO omega poor
 257 ALA   ( 257-)  1  Poor phi/psi
 329 ARG   ( 329-)  1  Poor phi/psi
 330 ILE   ( 330-)  1  omega poor
 537 PHE   ( 180-)  2  PRO omega poor
 592 ASN   ( 235-)  2  Poor phi/psi
 598 ASN   ( 241-)  2  PRO omega poor
 607 VAL   ( 250-)  2  PRO omega poor
 614 ALA   ( 257-)  2  Poor phi/psi
 686 ARG   ( 329-)  2  Poor phi/psi
 687 ILE   ( 330-)  2  omega poor
 705 GLY   ( 348-)  2  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.689

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

  41 SER   (  41-)  1    0.36
 405 SER   (  48-)  2    0.38
  48 SER   (  48-)  1    0.38

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

  17 PHE   (  17-)  1      0
  19 GLU   (  19-)  1      0
  21 LEU   (  21-)  1      0
  22 ASP   (  22-)  1      0
  24 GLN   (  24-)  1      0
  26 GLN   (  26-)  1      0
  53 ALA   (  53-)  1      0
  61 VAL   (  61-)  1      0
  64 ALA   (  64-)  1      0
  66 ASN   (  66-)  1      0
  67 GLN   (  67-)  1      0
  68 PRO   (  68-)  1      0
  69 THR   (  69-)  1      0
 102 ASN   ( 102-)  1      0
 121 LYS   ( 121-)  1      0
 122 PRO   ( 122-)  1      0
 129 TRP   ( 129-)  1      0
 136 TRP   ( 136-)  1      0
 154 LEU   ( 154-)  1      0
 162 ALA   ( 162-)  1      0
 165 SER   ( 165-)  1      0
 167 SER   ( 167-)  1      0
 169 ASP   ( 169-)  1      0
 172 GLN   ( 172-)  1      0
 173 ASP   ( 173-)  1      0
And so on for a total of 250 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 : 2.862

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]

 282 PRO   ( 282-)  1    0.20 LOW
 594 PRO   ( 237-)  2    0.46 HIGH
 599 PRO   ( 242-)  2    0.95 HIGH
 639 PRO   ( 282-)  2    0.17 LOW
 655 PRO   ( 298-)  2    0.46 HIGH

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].

 339 PRO   ( 339-)  1    38.1 envelop C-delta (36 degrees)
 595 PRO   ( 238-)  2  -113.2 envelop C-gamma (-108 degrees)
 599 PRO   ( 242-)  2   175.2 envelop N (180 degrees)
 696 PRO   ( 339-)  2    35.2 envelop C-delta (36 degrees)
 714 PRO   ( 357-)  2  -114.3 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.

 568 GLY   ( 211-)  2      C   <->  720 HOH   (2191 )  2      O      1.95    0.85  INTRA
 357 PRO   ( 357-)  1      CD  <->  719 HOH   (2283 )  1      O      1.84    0.96  INTRA BF
 150 ASP   ( 150-)  1      O   <->  719 HOH   (2141 )  1      O      1.81    0.59  INTRA
 568 GLY   ( 211-)  2      CA  <->  720 HOH   (2191 )  2      O      1.66    1.14  INTRA
  67 GLN   (  67-)  1      OE1 <->  719 HOH   (2075 )  1      O      1.41    0.99  INTRA BF
 567 ASP   ( 210-)  2      CG  <->  720 HOH   (2188 )  2      O      1.41    1.39  INTRA
 567 ASP   ( 210-)  2      OD2 <->  720 HOH   (2188 )  2      O      1.37    1.03  INTRA
 356 LEU   ( 356-)  1      CB  <->  719 HOH   (2282 )  1      O      1.30    1.50  INTRA
 116 HIS   ( 116-)  1      NE2 <->  719 HOH   (2109 )  1      O      1.30    1.40  INTRA
  67 GLN   (  67-)  1      CD  <->  719 HOH   (2075 )  1      O      1.29    1.51  INTRA BF
 356 LEU   ( 356-)  1      CA  <->  719 HOH   (2282 )  1      O      1.29    1.51  INTRA
 569 PRO   ( 212-)  2      N   <->  720 HOH   (2191 )  2      O      1.28    1.42  INTRA
 150 ASP   ( 150-)  1      C   <->  719 HOH   (2141 )  1      O      1.17    1.63  INTRA
 551 ARG   ( 194-)  2      NE  <->  720 HOH   (2170 )  2      O      1.13    1.57  INTRA
 117 ASP   ( 117-)  1      N   <->  719 HOH   (2111 )  1      O      0.99    1.71  INTRA
 358 ALA   (   1-)  2    A CA  <->  720 HOH   (2001 )  2      O      0.91    1.89  INTRA BF
 116 HIS   ( 116-)  1      CD2 <->  719 HOH   (2109 )  1      O      0.88    1.92  INTRA
 154 LEU   ( 154-)  1      CD1 <->  719 HOH   (2139 )  1      O      0.88    1.92  INTRA
 116 HIS   ( 116-)  1      C   <->  719 HOH   (2111 )  1      O      0.86    1.94  INTRA
 294 LYS   ( 294-)  1      CE  <->  719 HOH   (2237 )  1      O      0.84    1.96  INTRA
 357 PRO   ( 357-)  1      CG  <->  719 HOH   (2283 )  1      O      0.79    2.01  INTRA BF
 118 PRO   ( 118-)  1      CD  <->  719 HOH   (2110 )  1      O      0.77    2.03  INTRA
 356 LEU   ( 356-)  1      C   <->  719 HOH   (2282 )  1      O      0.74    2.06  INTRA BF
 356 LEU   ( 356-)  1      CD2 <->  719 HOH   (2236 )  1      O      0.73    2.07  INTRA
 569 PRO   ( 212-)  2      CD  <->  720 HOH   (2191 )  2      O      0.73    2.07  INTRA
And so on for a total of 117 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: 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: 2

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.

 529 GLN   ( 172-)  2      -7.10
 172 GLN   ( 172-)  1      -6.99
 223 ARG   ( 223-)  1      -6.34
 116 HIS   ( 116-)  1      -6.08
 473 HIS   ( 116-)  2      -6.06
 212 PRO   ( 212-)  1      -5.49
 569 PRO   ( 212-)  2      -5.47
 430 ASN   (  73-)  2      -5.32
  73 ASN   (  73-)  1      -5.14
 580 ARG   ( 223-)  2      -5.14
 102 ASN   ( 102-)  1      -5.14
 459 ASN   ( 102-)  2      -5.12

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.

 212 PRO   ( 212-)  1       214 - GLY    214- ( 1)         -4.71
 569 PRO   ( 212-)  2       571 - GLY    214- ( 2)         -4.70

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: 1

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: 2

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.

 591 ALA   ( 234-)  2   -3.11
 234 ALA   ( 234-)  1   -3.10

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: 1

Note: Second generation quality Z-score plot

Chain identifier: 2

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.

 719 HOH   (2041 )  1      O      9.82    8.78  -19.08
 720 HOH   (2076 )  2      O      6.84   22.63   21.80
 720 HOH   (2091 )  2      O     13.40  -23.99   25.09
 720 HOH   (2258 )  2      O      8.85   -3.07   53.84

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.

 720 HOH   (2091 )  2      O
 720 HOH   (2115 )  2      O

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.

  44 GLN   (  44-)  1
  73 ASN   (  73-)  1
 109 ASN   ( 109-)  1
 120 HIS   ( 120-)  1
 177 HIS   ( 177-)  1
 241 ASN   ( 241-)  1
 303 ASN   ( 303-)  1
 308 GLN   ( 308-)  1
 373 GLN   (  16-)  2
 401 GLN   (  44-)  2
 412 GLN   (  55-)  2
 466 ASN   ( 109-)  2
 502 ASN   ( 145-)  2
 534 HIS   ( 177-)  2
 598 ASN   ( 241-)  2
 660 ASN   ( 303-)  2
 665 GLN   ( 308-)  2

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.

  33 LEU   (  33-)  1      N
 120 HIS   ( 120-)  1      N
 129 TRP   ( 129-)  1      N
 134 ASP   ( 134-)  1      N
 145 ASN   ( 145-)  1      ND2
 184 SER   ( 184-)  1      OG
 201 ARG   ( 201-)  1      NH1
 246 SER   ( 246-)  1      N
 256 ASN   ( 256-)  1      ND2
 297 LYS   ( 297-)  1      N
 326 ASN   ( 326-)  1      ND2
 359 ALA   (   2-)  2    A N
 390 LEU   (  33-)  2      N
 486 TRP   ( 129-)  2      N
 491 ASP   ( 134-)  2      N
 603 SER   ( 246-)  2      N
 613 ASN   ( 256-)  2      ND2
 654 LYS   ( 297-)  2      N
 683 ASN   ( 326-)  2      ND2
 684 ARG   ( 327-)  2      NH1
 684 ARG   ( 327-)  2      NH2
 685 ALA   ( 328-)  2      N
 686 ARG   ( 329-)  2      NE
 686 ARG   ( 329-)  2      NH2
Only metal coordination for  316 ASP  ( 316-) 1      OD1
Only metal coordination for  673 ASP  ( 316-) 2      OD1

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.

  32 GLU   (  32-)  1      OE2
  38 ASP   (  38-)  1      OD1
  78 GLU   (  78-)  1      OE2
  82 ASP   (  82-)  1      OD1
  84 GLU   (  84-)  1      OE2
 134 ASP   ( 134-)  1      OD1
 268 ASP   ( 268-)  1      OD2
 389 GLU   (  32-)  2      OE2
 435 GLU   (  78-)  2      OE2
 439 ASP   (  82-)  2      OD1
 441 GLU   (  84-)  2      OE2
 477 HIS   ( 120-)  2      ND1
 589 GLU   ( 232-)  2      OE2
 625 ASP   ( 268-)  2      OD2

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.

 719 HOH   (2016 )  1      O  0.97  K  4
 720 HOH   (2072 )  2      O  1.02  K  4 NCS 1/1
 720 HOH   (2194 )  2      O  1.15  K  4 NCS 1/1

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.

  32 GLU   (  32-)  1   H-bonding suggests Gln; but Alt-Rotamer
  82 ASP   (  82-)  1   H-bonding suggests Asn; but Alt-Rotamer
  84 GLU   (  84-)  1   H-bonding suggests Gln; but Alt-Rotamer
 164 ASP   ( 164-)  1   H-bonding suggests Asn; but Alt-Rotamer
 179 ASP   ( 179-)  1   H-bonding suggests Asn
 268 ASP   ( 268-)  1   H-bonding suggests Asn
 435 GLU   (  78-)  2   H-bonding suggests Gln; but Alt-Rotamer
 439 ASP   (  82-)  2   H-bonding suggests Asn; but Alt-Rotamer
 441 GLU   (  84-)  2   H-bonding suggests Gln; but Alt-Rotamer
 507 ASP   ( 150-)  2   H-bonding suggests Asn
 521 ASP   ( 164-)  2   H-bonding suggests Asn; but Alt-Rotamer
 536 ASP   ( 179-)  2   H-bonding suggests Asn
 625 ASP   ( 268-)  2   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 :  -0.656
  2nd generation packing quality :  -1.654
  Ramachandran plot appearance   :  -0.339
  chi-1/chi-2 rotamer normality  :  -1.689
  Backbone conformation          :   0.539

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.560 (tight)
  Bond angles                    :   0.814
  Omega angle restraints         :   0.520 (tight)
  Side chain planarity           :   2.005 (loose)
  Improper dihedral distribution :   0.835
  B-factor distribution          :   0.595
  Inside/Outside distribution    :   0.955

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 1.38


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.3
  2nd generation packing quality :  -1.6
  Ramachandran plot appearance   :  -0.8
  chi-1/chi-2 rotamer normality  :  -2.3
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.560 (tight)
  Bond angles                    :   0.814
  Omega angle restraints         :   0.520 (tight)
  Side chain planarity           :   2.005 (loose)
  Improper dihedral distribution :   0.835
  B-factor distribution          :   0.595
  Inside/Outside distribution    :   0.955
==============

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.