WHAT IF Check report

This file was created 2012-01-19 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 pdb1y7a.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 : 0.641
CA-only RMS fit for the two chains : 0.256

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

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.

 904 PO4   (1456-)  A  -
 908 SO4   (1458-)  A  -
 909 PO4   (1956-)  B  -
 910 SO4   (1958-)  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: 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) : 93.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

  23 ARG   (  23-)  A
  24 ARG   (  24-)  A
  34 ARG   (  34-)  A
  62 ARG   (  62-)  A
 166 ARG   ( 166-)  A
 232 ARG   ( 232-)  A
 267 ARG   ( 267-)  A
 292 ARG   ( 292-)  A
 351 ARG   ( 351-)  A
 418 ARG   ( 418-)  A
 472 ARG   (  23-)  B
 473 ARG   (  24-)  B
 483 ARG   (  34-)  B
 511 ARG   (  62-)  B
 648 ARG   ( 199-)  B
 681 ARG   ( 232-)  B
 716 ARG   ( 267-)  B
 800 ARG   ( 351-)  B
 867 ARG   ( 418-)  B

Warning: Tyrosine convention problem

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

  87 TYR   (  87-)  A
 234 TYR   ( 234-)  A
 275 TYR   ( 275-)  A
 536 TYR   (  87-)  B
 724 TYR   ( 275-)  B

Warning: Phenylalanine convention problem

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

  71 PHE   (  71-)  A
 318 PHE   ( 318-)  A
 520 PHE   (  71-)  B
 767 PHE   ( 318-)  B
 804 PHE   ( 355-)  B

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

  15 ASP   (  15-)  A
  51 ASP   (  51-)  A
 101 ASP   ( 101-)  A
 123 ASP   ( 123-)  A
 201 ASP   ( 201-)  A
 261 ASP   ( 261-)  A
 280 ASP   ( 280-)  A
 344 ASP   ( 344-)  A
 346 ASP   ( 346-)  A
 369 ASP   ( 369-)  A
 380 ASP   ( 380-)  A
 408 ASP   ( 408-)  A
 437 ASP   ( 437-)  A
 464 ASP   (  15-)  B
 484 ASP   (  35-)  B
 504 ASP   (  55-)  B
 550 ASP   ( 101-)  B
 572 ASP   ( 123-)  B
 577 ASP   ( 128-)  B
 650 ASP   ( 201-)  B
 688 ASP   ( 239-)  B
 710 ASP   ( 261-)  B
 729 ASP   ( 280-)  B
 779 ASP   ( 330-)  B
 793 ASP   ( 344-)  B
 795 ASP   ( 346-)  B
 886 ASP   ( 437-)  B

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

  66 GLU   (  66-)  A
 126 GLU   ( 126-)  A
 150 GLU   ( 150-)  A
 176 GLU   ( 176-)  A
 193 GLU   ( 193-)  A
 248 GLU   ( 248-)  A
 341 GLU   ( 341-)  A
 359 GLU   ( 359-)  A
 406 GLU   ( 406-)  A
 515 GLU   (  66-)  B
 575 GLU   ( 126-)  B
 599 GLU   ( 150-)  B
 633 GLU   ( 184-)  B
 662 GLU   ( 213-)  B
 676 GLU   ( 227-)  B
 697 GLU   ( 248-)  B
 757 GLU   ( 308-)  B
 763 GLU   ( 314-)  B
 790 GLU   ( 341-)  B
 808 GLU   ( 359-)  B
 855 GLU   ( 406-)  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.

  46 ILE   (  46-)  A      CG1  CD1   1.67    4.0
 115 THR   ( 115-)  A      CB   CG2   1.67    4.5
 373 ALA   ( 373-)  A      CA   CB    1.65    4.1
 400 MET   ( 400-)  A      CB   CG    1.65    4.4
 605 PRO   ( 156-)  B      CA   C     1.61    4.0
 612 VAL   ( 163-)  B      CA   CB    1.61    4.1
 696 THR   ( 247-)  B      CA   CB    1.62    4.4
 733 VAL   ( 284-)  B      CA   CB    1.62    4.3
 742 ASN   ( 293-)  B      N    CA    1.56    5.5
 829 ASP   ( 380-)  B      CG   OD2   1.33    4.1
 849 MET   ( 400-)  B      CB   CG    1.65    4.2

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

 |  0.994960 -0.000323  0.001078|
 | -0.000323  0.994011 -0.003943|
 |  0.001078 -0.003943  0.993085|
Proposed new scale matrix

 |  0.013188  0.000004 -0.000014|
 |  0.000002  0.006114  0.000024|
 | -0.000006  0.000021  0.005227|
With corresponding cell

    A    =  75.824  B   = 163.571  C    = 191.311
    Alpha=  90.455  Beta=  89.876  Gamma=  90.037

The CRYST1 cell dimensions

    A    =  76.208  B   = 164.564  C    = 192.636
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 1096.481
(Under-)estimated Z-score: 24.404

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.

  84 TYR   (  84-)  A      CA   CB   CG  124.25    5.6
  97 ASP   (  97-)  A      N    CA   C    99.18   -4.3
 109 TRP   ( 109-)  A     -C    N    CA  114.48   -4.0
 168 CYS   ( 168-)  A      CA   CB   SG  103.95   -4.5
 267 ARG   ( 267-)  A      CB   CG   CD  105.18   -4.5
 292 ARG   ( 292-)  A      CG   CD   NE  117.40    4.1
 293 ASN   ( 293-)  A      C    CA   CB  100.99   -4.8
 323 GLY   ( 323-)  A      N    CA   C    97.53   -5.2
 351 ARG   ( 351-)  A      CG   CD   NE  100.42   -5.9
 351 ARG   ( 351-)  A      CD   NE   CZ  131.64    5.5
 418 ARG   ( 418-)  A      CB   CG   CD  105.61   -4.2
 449 LYS   ( 449-)  A     -C    N    CA  113.33   -4.6
 455 VAL   (   6-)  B      N    CA   C    98.33   -4.6
 499 GLY   (  50-)  B      N    CA   C   100.10   -4.3
 533 TYR   (  84-)  B      CA   CB   CG  124.02    5.5
 546 ASP   (  97-)  B      N    CA   C    92.97   -6.5
 611 HIS   ( 162-)  B      CG   ND1  CE1 109.60    4.0
 742 ASN   ( 293-)  B     -C    N    CA  136.44    8.2
 742 ASN   ( 293-)  B      N    CA   C   137.40    9.4
 742 ASN   ( 293-)  B      C    CA   CB  100.07   -5.3
 772 GLY   ( 323-)  B      N    CA   C    96.80   -5.4
 800 ARG   ( 351-)  B      CG   CD   NE  119.61    5.4
 878 VAL   ( 429-)  B     -C    N    CA  114.38   -4.1
 898 LYS   ( 449-)  B      N    CA   C    99.26   -4.3

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.

  15 ASP   (  15-)  A
  23 ARG   (  23-)  A
  24 ARG   (  24-)  A
  34 ARG   (  34-)  A
  51 ASP   (  51-)  A
  62 ARG   (  62-)  A
  66 GLU   (  66-)  A
 101 ASP   ( 101-)  A
 123 ASP   ( 123-)  A
 126 GLU   ( 126-)  A
 150 GLU   ( 150-)  A
 166 ARG   ( 166-)  A
 176 GLU   ( 176-)  A
 193 GLU   ( 193-)  A
 201 ASP   ( 201-)  A
 232 ARG   ( 232-)  A
 248 GLU   ( 248-)  A
 261 ASP   ( 261-)  A
 267 ARG   ( 267-)  A
 280 ASP   ( 280-)  A
 292 ARG   ( 292-)  A
 341 GLU   ( 341-)  A
 344 ASP   ( 344-)  A
 346 ASP   ( 346-)  A
 351 ARG   ( 351-)  A
And so on for a total of 67 lines.

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.

 742 ASN   ( 293-)  B    8.41
 609 VAL   ( 160-)  B    6.68
 772 GLY   ( 323-)  B    6.39
 323 GLY   ( 323-)  A    6.07
 546 ASP   (  97-)  B    6.00
 676 GLU   ( 227-)  B    5.88
 177 LYS   ( 177-)  A    5.78
 603 ALA   ( 154-)  B    5.72
 729 ASP   ( 280-)  B    5.59
 775 ILE   ( 326-)  B    5.44
 557 ALA   ( 108-)  B    5.13
  65 ALA   (  65-)  A    5.07
 499 GLY   (  50-)  B    4.95
 330 ASP   ( 330-)  A    4.89
  75 ILE   (  75-)  A    4.76
 898 LYS   ( 449-)  B    4.64
 626 LYS   ( 177-)  B    4.60
 324 ALA   ( 324-)  A    4.53
 455 VAL   (   6-)  B    4.52
  50 GLY   (  50-)  A    4.44
  12 ALA   (  12-)  A    4.43
 685 LEU   ( 236-)  B    4.16
 154 ALA   ( 154-)  A    4.09
 805 ALA   ( 356-)  B    4.09
 483 ARG   (  34-)  B    4.09
 658 LYS   ( 209-)  B    4.08
 402 TYR   ( 402-)  A    4.06

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 : 1.728

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

 819 HIS   ( 370-)  B      CB   6.68
 370 HIS   ( 370-)  A      CB   4.84
 234 TYR   ( 234-)  A      OH   4.22
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -0.624

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.

 367 THR   ( 367-)  A    -3.1
 816 THR   ( 367-)  B    -3.1
 115 THR   ( 115-)  A    -3.0
 564 THR   ( 115-)  B    -2.8
 417 LEU   ( 417-)  A    -2.6
 866 LEU   ( 417-)  B    -2.6
 451 PRO   (   2-)  B    -2.5
 372 HIS   ( 372-)  A    -2.3
 293 ASN   ( 293-)  A    -2.3
 697 GLU   ( 248-)  B    -2.2
 821 HIS   ( 372-)  B    -2.2
 699 ASN   ( 250-)  B    -2.2
  84 TYR   (  84-)  A    -2.2
 860 GLU   ( 411-)  B    -2.1
 533 TYR   (  84-)  B    -2.1
 856 GLU   ( 407-)  B    -2.1
 250 ASN   ( 250-)  A    -2.1
 382 LYS   ( 382-)  A    -2.1
 620 PRO   ( 171-)  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.

  88 ALA   (  88-)  A  Poor phi/psi
 111 THR   ( 111-)  A  Poor phi/psi
 126 GLU   ( 126-)  A  Poor phi/psi
 168 CYS   ( 168-)  A  Poor phi/psi
 292 ARG   ( 292-)  A  Poor phi/psi
 293 ASN   ( 293-)  A  Poor phi/psi
 367 THR   ( 367-)  A  Poor phi/psi
 372 HIS   ( 372-)  A  Poor phi/psi
 425 HIS   ( 425-)  A  Poor phi/psi
 560 THR   ( 111-)  B  Poor phi/psi
 575 GLU   ( 126-)  B  Poor phi/psi
 617 CYS   ( 168-)  B  Poor phi/psi
 671 GLY   ( 222-)  B  Poor phi/psi
 725 HIS   ( 276-)  B  Poor phi/psi
 742 ASN   ( 293-)  B  Poor phi/psi
 816 THR   ( 367-)  B  Poor phi/psi
 874 HIS   ( 425-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.715

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.

 172 SER   ( 172-)  A    0.36
 105 SER   ( 105-)  A    0.36
 554 SER   ( 105-)  B    0.36
 175 SER   ( 175-)  A    0.37
 624 SER   ( 175-)  B    0.37

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!

   3 GLU   (   3-)  A      0
   4 MET   (   4-)  A      0
   8 GLU   (   8-)  A      0
   9 ASN   (   9-)  A      0
  10 ARG   (  10-)  A      0
  12 ALA   (  12-)  A      0
  13 GLN   (  13-)  A      0
  15 ASP   (  15-)  A      0
  18 ALA   (  18-)  A      0
  19 PRO   (  19-)  A      0
  23 ARG   (  23-)  A      0
  26 THR   (  26-)  A      0
  28 ASP   (  28-)  A      0
  29 GLN   (  29-)  A      0
  30 THR   (  30-)  A      0
  39 ASP   (  39-)  A      0
  43 LYS   (  43-)  A      0
  44 ASN   (  44-)  A      0
  51 ASP   (  51-)  A      0
  53 MET   (  53-)  A      0
  77 ALA   (  77-)  A      0
  86 HIS   (  86-)  A      0
  95 LYS   (  95-)  A      0
  98 TYR   (  98-)  A      0
 110 SER   ( 110-)  A      0
And so on for a total of 346 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 : 3.290

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]

 130 PRO   ( 130-)  A    0.46 HIGH
 171 PRO   ( 171-)  A    0.46 HIGH
 379 PRO   ( 379-)  A    0.45 HIGH
 384 PRO   ( 384-)  A    0.49 HIGH
 828 PRO   ( 379-)  B    0.18 LOW
 873 PRO   ( 424-)  B    0.49 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].

  19 PRO   (  19-)  A  -150.6 envelop C-delta (-144 degrees)
 179 PRO   ( 179-)  A  -114.8 envelop C-gamma (-108 degrees)
 271 PRO   ( 271-)  A    48.5 half-chair C-delta/C-gamma (54 degrees)
 628 PRO   ( 179-)  B  -112.0 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 166 ARG   ( 166-)  A      NH2 <->  904 PO4   (1456-)  A      O1     0.65    2.05  INTRA BF
 673 THR   ( 224-)  B      CG2 <->  676 GLU   ( 227-)  B      N      0.49    2.61  INTRA BF
 102 SER   ( 102-)  A      OG  <->  904 PO4   (1456-)  A      O3     0.46    1.94  INTRA BF
 244 ASN   ( 244-)  A      ND2 <->  911 HOH   (1656 )  A      O      0.40    2.30  INTRA BF
 128 ASP   ( 128-)  A      OD2 <->  188 LYS   ( 188-)  A      CE     0.37    2.43  INTRA
 615 ARG   ( 166-)  B      NH1 <->  909 PO4   (1956-)  B      O1     0.36    2.34  INTRA BF
 808 GLU   ( 359-)  B      OE1 <->  810 ASN   ( 361-)  B      N      0.31    2.39  INTRA
 861 HIS   ( 412-)  B      CE1 <->  909 PO4   (1956-)  B      P      0.27    3.13  INTRA BF
 489 LYS   (  40-)  B      NZ  <->  912 HOH   (2200 )  B      O      0.27    2.43  INTRA BF
 699 ASN   ( 250-)  B      OD1 <->  701 GLN   ( 252-)  B      CG     0.25    2.55  INTRA BF
 166 ARG   ( 166-)  A      NH1 <->  904 PO4   (1456-)  A      O1     0.24    2.46  INTRA BF
 662 GLU   ( 213-)  B      O   <->  674 LEU   ( 225-)  B      N      0.24    2.46  INTRA BF
 331 HIS   ( 331-)  A      ND1 <->  410 GLN   ( 410-)  A      O      0.23    2.47  INTRA
 166 ARG   ( 166-)  A      CZ  <->  904 PO4   (1456-)  A      O1     0.22    2.58  INTRA BF
 292 ARG   ( 292-)  A      O   <->  293 ASN   ( 293-)  A      CG     0.22    2.48  INTRA BF
 630 ASN   ( 181-)  B      O   <->  638 GLY   ( 189-)  B      N      0.22    2.48  INTRA
 372 HIS   ( 372-)  A      ND1 <->  373 ALA   ( 373-)  A      N      0.21    2.69  INTRA BL
 102 SER   ( 102-)  A      OG  <->  904 PO4   (1456-)  A      P      0.21    2.79  INTRA BF
 188 LYS   ( 188-)  A      CE  <->  911 HOH   (1814 )  A      O      0.21    2.59  INTRA
 583 GLU   ( 134-)  B      OE2 <->  611 HIS   ( 162-)  B      NE2    0.19    2.51  INTRA
 370 HIS   ( 370-)  A      NE2 <->  412 HIS   ( 412-)  A      CE1    0.18    2.92  INTRA BL
   4 MET   (   4-)  A      CE  <->   40 LYS   (  40-)  A      NZ     0.18    2.92  INTRA
 166 ARG   ( 166-)  A      NH2 <->  911 HOH   (1611 )  A      O      0.17    2.53  INTRA
 648 ARG   ( 199-)  B      NE  <->  700 GLN   ( 251-)  B      O      0.17    2.53  INTRA BF
 327 ASP   ( 327-)  A      OD2 <->  911 HOH   (1571 )  A      O      0.16    2.24  INTRA
And so on for a total of 121 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.

 724 TYR   ( 275-)  B      -7.13
 292 ARG   ( 292-)  A      -7.06
 275 TYR   ( 275-)  A      -6.64
 741 ARG   ( 292-)  B      -6.05
 701 GLN   ( 252-)  B      -5.96
 541 LYS   (  92-)  B      -5.83
  92 LYS   (  92-)  A      -5.81
 462 GLN   (  13-)  B      -5.70
 252 GLN   ( 252-)  A      -5.63
 763 GLU   ( 314-)  B      -5.39
   3 GLU   (   3-)  A      -5.16
 314 GLU   ( 314-)  A      -5.12
 359 GLU   ( 359-)  A      -5.00

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.

 324 ALA   ( 324-)  A   -2.73
 773 ALA   ( 324-)  B   -2.71
 476 GLY   (  27-)  B   -2.54

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.

 911 HOH   (1627 )  A      O     78.58   58.36   -0.06

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.

 911 HOH   (1782 )  A      O
Metal-coordinating Histidine residue 331 fixed to   1
Metal-coordinating Histidine residue 412 fixed to   1
Metal-coordinating Histidine residue 370 fixed to   1
Metal-coordinating Histidine residue 153 fixed to   1
Metal-coordinating Histidine residue 780 fixed to   1
Metal-coordinating Histidine residue 861 fixed to   1
Metal-coordinating Histidine residue 819 fixed to   1
Metal-coordinating Histidine residue 602 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.

  13 GLN   (  13-)  A
  83 GLN   (  83-)  A
 291 GLN   ( 291-)  A
 462 GLN   (  13-)  B
 594 ASN   ( 145-)  B
 601 GLN   ( 152-)  B
 700 GLN   ( 251-)  B
 742 ASN   ( 293-)  B
 762 ASN   ( 313-)  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.

   6 VAL   (   6-)  A      N
  10 ARG   (  10-)  A      N
  27 GLY   (  27-)  A      N
  78 LEU   (  78-)  A      N
  81 THR   (  81-)  A      N
 102 SER   ( 102-)  A      N
 103 ALA   ( 103-)  A      N
 118 GLY   ( 118-)  A      N
 122 VAL   ( 122-)  A      N
 217 ALA   ( 217-)  A      N
 267 ARG   ( 267-)  A      NE
 292 ARG   ( 292-)  A      NH1
 293 ASN   ( 293-)  A      N
 295 SER   ( 295-)  A      N
 326 ILE   ( 326-)  A      N
 459 ARG   (  10-)  B      N
 527 LEU   (  78-)  B      N
 530 THR   (  81-)  B      N
 551 SER   ( 102-)  B      N
 552 ALA   ( 103-)  B      N
 571 VAL   ( 122-)  B      N
 666 ALA   ( 217-)  B      N
 676 GLU   ( 227-)  B      N
 697 GLU   ( 248-)  B      N
 716 ARG   ( 267-)  B      NE
 719 GLY   ( 270-)  B      N
 741 ARG   ( 292-)  B      NH1
 744 SER   ( 295-)  B      N
 761 LYS   ( 312-)  B      N
 799 GLN   ( 350-)  B      NE2
 829 ASP   ( 380-)  B      N
 853 ASN   ( 404-)  B      ND2
 857 ASP   ( 408-)  B      N
 858 SER   ( 409-)  B      N
Only metal coordination for   51 ASP  (  51-) A      OD1
Only metal coordination for  322 GLU  ( 322-) A      OE2
Only metal coordination for  370 HIS  ( 370-) A      NE2
Only metal coordination for  412 HIS  ( 412-) A      NE2
Only metal coordination for  500 ASP  (  51-) B      OD1
Only metal coordination for  771 GLU  ( 322-) B      OE2
Only metal coordination for  819 HIS  ( 370-) B      NE2
Only metal coordination for  861 HIS  ( 412-) B      NE2

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.

 330 ASP   ( 330-)  A      OD2
 779 ASP   ( 330-)  B      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.

 911 HOH   (1534 )  A      O  1.03  K  4
 911 HOH   (1601 )  A      O  0.96  K  4
 911 HOH   (1616 )  A      O  0.99  K  4
 911 HOH   (1655 )  A      O  1.14  K  4 ION-B H2O-B
 911 HOH   (1735 )  A      O  0.89  K  4 ION-B
 912 HOH   (2123 )  B      O  0.95  K  4

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

 411 GLU   ( 411-)  A   H-bonding suggests Gln
 763 GLU   ( 314-)  B   H-bonding suggests Gln
 860 GLU   ( 411-)  B   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.337
  2nd generation packing quality :  -1.139
  Ramachandran plot appearance   :  -0.624
  chi-1/chi-2 rotamer normality  :  -1.715
  Backbone conformation          :  -0.551

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.034
  Bond angles                    :   1.035
  Omega angle restraints         :   0.598 (tight)
  Side chain planarity           :   0.855
  Improper dihedral distribution :   1.096
  B-factor distribution          :   0.527
  Inside/Outside distribution    :   0.943

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 : 1.77


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.0
  2nd generation packing quality :  -1.1
  Ramachandran plot appearance   :  -0.6
  chi-1/chi-2 rotamer normality  :  -1.4
  Backbone conformation          :  -0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.034
  Bond angles                    :   1.035
  Omega angle restraints         :   0.598 (tight)
  Side chain planarity           :   0.855
  Improper dihedral distribution :   1.096
  B-factor distribution          :   0.527
  Inside/Outside distribution    :   0.943
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    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,
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      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
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      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.