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 pdb1h38.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 : 1.452
CA-only RMS fit for the two chains : 1.330

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

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 C

All-atom RMS fit for the two chains : 1.105
CA-only RMS fit for the two chains : 0.955

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 C

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 D

All-atom RMS fit for the two chains : 0.925
CA-only RMS fit for the two chains : 0.750

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 D

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: B and C

All-atom RMS fit for the two chains : 0.948
CA-only RMS fit for the two chains : 0.733

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: B and C

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: B and D

All-atom RMS fit for the two chains : 1.760
CA-only RMS fit for the two chains : 1.652

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: B and D

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

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   7 LYS   (   8-)  A    High
   8 ASN   (   9-)  A    High
   9 ASP   (  10-)  A    High
  14 GLU   (  15-)  A    High
  15 LEU   (  16-)  A    High
  16 ALA   (  17-)  A    High
  62 GLU   (  63-)  A    High
  63 VAL   (  64-)  A    High
  64 ALA   (  65-)  A    High
  65 ASP   (  66-)  A    High
  66 ASN   (  67-)  A    High
  67 ALA   (  68-)  A    High
  68 ALA   (  69-)  A    High
  69 ALA   (  70-)  A    High
  75 THR   (  76-)  A    High
  76 LEU   (  77-)  A    High
  77 LEU   (  78-)  A    High
  78 PRO   (  79-)  A    High
  79 LYS   (  80-)  A    High
  80 MET   (  81-)  A    High
  81 ILE   (  82-)  A    High
  82 ALA   (  83-)  A    High
  83 ARG   (  84-)  A    High
  84 ILE   (  85-)  A    High
  85 ASN   (  86-)  A    High
And so on for a total of 706 lines.

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. 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: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

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.

  51 ARG   (  52-)  A
 908 ARG   (  52-)  B
1765 ARG   (  52-)  C
2622 ARG   (  52-)  D

Warning: Tyrosine convention problem

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

  27 TYR   (  28-)  A
 177 TYR   ( 178-)  A
 249 TYR   ( 250-)  A
 307 TYR   ( 308-)  A
 316 TYR   ( 317-)  A
 368 TYR   ( 385-)  A
 820 TYR   ( 846-)  A
 884 TYR   (  28-)  B
 972 TYR   ( 116-)  B
1106 TYR   ( 250-)  B
1164 TYR   ( 308-)  B
1225 TYR   ( 385-)  B
1358 TYR   ( 518-)  B
1463 TYR   ( 623-)  B
1677 TYR   ( 846-)  B
1891 TYR   ( 178-)  C
1963 TYR   ( 250-)  C
2021 TYR   ( 308-)  C
2030 TYR   ( 317-)  C
2215 TYR   ( 518-)  C
2748 TYR   ( 178-)  D
2820 TYR   ( 250-)  D
2939 TYR   ( 385-)  D

Warning: Phenylalanine convention problem

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

  54 PHE   (  55-)  A
 104 PHE   ( 105-)  A
 161 PHE   ( 162-)  A
 181 PHE   ( 182-)  A
 383 PHE   ( 400-)  A
 464 PHE   ( 481-)  A
 497 PHE   ( 514-)  A
 627 PHE   ( 644-)  A
 716 PHE   ( 733-)  A
 823 PHE   ( 849-)  A
 907 PHE   (  51-)  B
 911 PHE   (  55-)  B
 961 PHE   ( 105-)  B
1007 PHE   ( 151-)  B
1018 PHE   ( 162-)  B
1240 PHE   ( 400-)  B
1248 PHE   ( 408-)  B
1256 PHE   ( 416-)  B
1354 PHE   ( 514-)  B
1591 PHE   ( 751-)  B
1656 PHE   ( 825-)  B
1764 PHE   (  51-)  C
1816 PHE   ( 103-)  C
1818 PHE   ( 105-)  C
1875 PHE   ( 162-)  C
2097 PHE   ( 400-)  C
2206 PHE   ( 509-)  C
2341 PHE   ( 644-)  C
2621 PHE   (  51-)  D
2675 PHE   ( 105-)  D
2752 PHE   ( 182-)  D
3068 PHE   ( 514-)  D
3198 PHE   ( 644-)  D
3352 PHE   ( 807-)  D
3359 PHE   ( 814-)  D
3370 PHE   ( 825-)  D

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.

  12 ASP   (  13-)  A
  65 ASP   (  66-)  A
 188 ASP   ( 189-)  A
 350 ASP   ( 351-)  A
 371 ASP   ( 388-)  A
 489 ASP   ( 506-)  A
 574 ASP   ( 591-)  A
 869 ASP   (  13-)  B
 922 ASP   (  66-)  B
1045 ASP   ( 189-)  B
1207 ASP   ( 351-)  B
1682 ASP   ( 851-)  B
1779 ASP   (  66-)  C
1902 ASP   ( 189-)  C
1921 ASP   ( 208-)  C
2064 ASP   ( 351-)  C
2203 ASP   ( 506-)  C
2583 ASP   (  13-)  D
2636 ASP   (  66-)  D
2700 ASP   ( 130-)  D
2759 ASP   ( 189-)  D
2921 ASP   ( 351-)  D
3060 ASP   ( 506-)  D
3123 ASP   ( 569-)  D
3404 ASP   ( 859-)  D

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.

  14 GLU   (  15-)  A
  34 GLU   (  35-)  A
  39 GLU   (  40-)  A
  89 GLU   (  90-)  A
 157 GLU   ( 158-)  A
 166 GLU   ( 167-)  A
 198 GLU   ( 199-)  A
 217 GLU   ( 218-)  A
 314 GLU   ( 315-)  A
 481 GLU   ( 498-)  A
 487 GLU   ( 504-)  A
 563 GLU   ( 580-)  A
 583 GLU   ( 600-)  A
 587 GLU   ( 604-)  A
 666 GLU   ( 683-)  A
 721 GLU   ( 738-)  A
 742 GLU   ( 768-)  A
 851 GLU   ( 877-)  A
 871 GLU   (  15-)  B
 891 GLU   (  35-)  B
1004 GLU   ( 148-)  B
1014 GLU   ( 158-)  B
1023 GLU   ( 167-)  B
1063 GLU   ( 207-)  B
1074 GLU   ( 218-)  B
And so on for a total of 69 lines.

Warning: Phosphate group convention problem

The nucleic acid residues listed in the table below have the OP1 and OP2 atom names exchanged.

3453 OURA  (   8-)  F
3488 OURA  (   8-)  I
3522 OURA  (   8-)  L
3556 OURA  (   8-)  O

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.

 423 THR   ( 440-)  A      CA   CB    1.43   -4.9
 435 ILE   ( 452-)  A      CA   CB    1.61    4.2
 493 CYS   ( 510-)  A      CB   SG    1.67   -4.0
 556 ILE   ( 573-)  A      CA   CB    1.71    8.9
 596 THR   ( 613-)  A      CA   CB    1.42   -5.7
 613 THR   ( 630-)  A      CA   CB    1.41   -5.8
 637 THR   ( 654-)  A      CA   CB    1.67    7.1
 757 VAL   ( 783-)  A      CA   CB    1.43   -5.0
 790 THR   ( 816-)  A      CA   CB    1.64    5.5
 805 THR   ( 831-)  A      CA   CB    1.44   -4.3
1155 THR   ( 299-)  B      CA   CB    1.45   -4.1
1285 THR   ( 445-)  B      CA   CB    1.43   -4.9
1345 GLN   ( 505-)  B      CB   CG    1.40   -4.1
1407 VAL   ( 567-)  B      CA   CB    1.61    4.1
1413 ILE   ( 573-)  B      CA   CB    1.61    4.2
1423 GLN   ( 583-)  B      CG   CD    1.62    4.1
1528 THR   ( 688-)  B      CA   CB    1.43   -5.0
1529 VAL   ( 689-)  B      CA   CB    1.61    4.0
1609 ILE   ( 778-)  B      CA   CB    1.65    6.0
1627 VAL   ( 796-)  B      CA   CB    1.62    4.3
1717 ILE   (   4-)  C      CA   CB    1.61    4.0
2116 ASN   ( 419-)  C      CB   CG    1.41   -4.0
2589 ILE   (  19-)  D      CA   CB    1.61    4.0
3452 OADE  (   7-)  F      N3   C4    1.32   -4.1
3452 OADE  (   7-)  F      C5   C6    1.36   -5.3
3453 OURA  (   8-)  F      C5   C4    1.47    4.1
3497 DCYT  (   9-)  J      N1   C2    1.44    4.4
3507 DADE  (  11-)  K      C6   N6    1.30   -4.5

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

 |  0.999944  0.000060 -0.000204|
 |  0.000060  0.998607  0.000326|
 | -0.000204  0.000326  1.000234|
Proposed new scale matrix

 |  0.012515  0.004545  0.000766|
 |  0.000000  0.012536  0.000315|
 |  0.000001 -0.000002  0.004958|
With corresponding cell

    A    =  79.908  B   =  84.866  C    = 202.038
    Alpha=  90.312  Beta=  92.992  Gamma= 109.963

The CRYST1 cell dimensions

    A    =  79.907  B   =  84.971  C    = 202.003
    Alpha=  90.360  Beta=  92.970  Gamma= 109.940

Variance: 71.194
(Under-)estimated Z-score: 6.219

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.

 160 HIS   ( 161-)  A      CG   ND1  CE1 109.67    4.1
 175 HIS   ( 176-)  A      CG   ND1  CE1 109.61    4.0
 349 GLU   ( 350-)  A     -C    N    CA  114.09   -4.2
 374 ARG   ( 391-)  A      CB   CG   CD  105.55   -4.3
 402 ASN   ( 419-)  A      C    CA   CB   98.56   -6.1
 438 GLU   ( 455-)  A      N    CA   CB  103.55   -4.1
 469 HIS   ( 486-)  A      CG   ND1  CE1 109.67    4.1
 493 CYS   ( 510-)  A      CA   CB   SG  103.38   -4.8
 528 HIS   ( 545-)  A      CG   ND1  CE1 109.97    4.4
 764 HIS   ( 790-)  A      CG   ND1  CE1 109.69    4.1
 777 GLY   ( 803-)  A     -C    N    CA  113.24   -4.3
 790 THR   ( 816-)  A      N    CA   CB  118.72    4.8
 790 THR   ( 816-)  A      C    CA   CB   99.39   -5.6
 857 ALA   ( 883-)  A      CA   C    O   113.98   -4.0
1171 GLU   ( 315-)  B      CA   CB   CG  105.68   -4.2
1206 GLU   ( 350-)  B     -C    N    CA  114.18   -4.2
1259 ASN   ( 419-)  B      C    CA   CB  101.15   -4.7
1303 HIS   ( 463-)  B      CG   ND1  CE1 109.83    4.2
1312 LYS   ( 472-)  B      CA   CB   CG  106.07   -4.0
1363 HIS   ( 523-)  B      CG   ND1  CE1 109.68    4.1
1367 SER   ( 527-)  B     -C    N    CA  114.47   -4.0
1389 MET   ( 549-)  B      CB   CG   SD   91.82   -7.0
1406 THR   ( 566-)  B     -C    N    CA  113.57   -4.5
1566 HIS   ( 726-)  B      CG   ND1  CE1 109.88    4.3
1615 HIS   ( 784-)  B      CG   ND1  CE1 109.67    4.1
And so on for a total of 80 lines.

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.

  12 ASP   (  13-)  A
  14 GLU   (  15-)  A
  34 GLU   (  35-)  A
  39 GLU   (  40-)  A
  51 ARG   (  52-)  A
  65 ASP   (  66-)  A
  89 GLU   (  90-)  A
 157 GLU   ( 158-)  A
 166 GLU   ( 167-)  A
 188 ASP   ( 189-)  A
 198 GLU   ( 199-)  A
 217 GLU   ( 218-)  A
 314 GLU   ( 315-)  A
 350 ASP   ( 351-)  A
 371 ASP   ( 388-)  A
 481 GLU   ( 498-)  A
 487 GLU   ( 504-)  A
 489 ASP   ( 506-)  A
 563 GLU   ( 580-)  A
 574 ASP   ( 591-)  A
 583 GLU   ( 600-)  A
 587 GLU   ( 604-)  A
 666 GLU   ( 683-)  A
 721 GLU   ( 738-)  A
 742 GLU   ( 768-)  A
And so on for a total of 98 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.

1348 PRO   ( 508-)  B      N      6.5    18.72    -2.48
The average deviation= 0.791

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.

 785 HIS   ( 811-)  A      CB   4.66

Warning: Uncalibrated side chain planarity problems

The residues listed in the table below contain a planar group that was found to deviate from planarity by more than 0.10 Angstrom RMS. Please be aware that this check cannot be callibrated and that the cutoff of 0.10 Angstrom thus is a wild guess.

3475 DCYT  (  13-)  H    0.12
3478 DCYT  (  16-)  H    0.11
3443 DCYT  (  16-)  E    0.11
3440 DCYT  (  13-)  E    0.10
3476 DGUA  (  14-)  H    0.10
 Ramachandran Z-score : -3.712

Torsion-related checks

Warning: Ramachandran Z-score low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is a bit low.

Ramachandran Z-score : -3.712

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.

3427 PHE   ( 882-)  D    -3.6
2570 PHE   ( 882-)  C    -3.5
 856 PHE   ( 882-)  A    -3.4
 790 THR   ( 816-)  A    -3.3
2504 THR   ( 816-)  C    -3.2
3361 THR   ( 816-)  D    -3.0
2205 PRO   ( 508-)  C    -3.0
1845 THR   ( 132-)  C    -3.0
3062 PRO   ( 508-)  D    -3.0
 491 PRO   ( 508-)  A    -2.9
 734 PHE   ( 751-)  A    -2.9
1510 PRO   ( 670-)  B    -2.9
3224 PRO   ( 670-)  D    -2.9
 728 THR   ( 745-)  A    -2.9
1585 THR   ( 745-)  B    -2.9
 653 PRO   ( 670-)  A    -2.8
2923 PRO   ( 353-)  D    -2.8
1348 PRO   ( 508-)  B    -2.8
 875 ILE   (  19-)  B    -2.7
2367 PRO   ( 670-)  C    -2.7
2066 PRO   ( 353-)  C    -2.6
 940 ARG   (  84-)  B    -2.6
1713 PHE   ( 882-)  B    -2.6
3105 ARG   ( 551-)  D    -2.6
1466 THR   ( 626-)  B    -2.6
And so on for a total of 138 lines.

Warning: Backbone evaluation reveals unusual conformations

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

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

   6 ALA   (   7-)  A  Poor phi/psi
   7 LYS   (   8-)  A  Poor phi/psi
   9 ASP   (  10-)  A  Poor phi/psi
  13 ILE   (  14-)  A  Poor phi/psi
  18 ILE   (  19-)  A  Poor phi/psi
  19 PRO   (  20-)  A  Poor phi/psi
 192 LYS   ( 193-)  A  Poor phi/psi
 193 GLY   ( 194-)  A  Poor phi/psi
 198 GLU   ( 199-)  A  Poor phi/psi
 199 ALA   ( 200-)  A  Poor phi/psi
 200 TRP   ( 201-)  A  Poor phi/psi
 203 TRP   ( 204-)  A  Poor phi/psi
 205 LYS   ( 206-)  A  Poor phi/psi
 232 ASN   ( 233-)  A  Poor phi/psi
 238 GLN   ( 239-)  A  Poor phi/psi
 356 ALA   ( 373-)  A  Poor phi/psi
 396 ALA   ( 413-)  A  Poor phi/psi
 522 SER   ( 539-)  A  Poor phi/psi
 543 ASN   ( 560-)  A  Poor phi/psi
 571 ASN   ( 588-)  A  Poor phi/psi
 625 LYS   ( 642-)  A  Poor phi/psi
 646 LYS   ( 663-)  A  Poor phi/psi
 696 LYS   ( 713-)  A  Poor phi/psi
 697 LYS   ( 714-)  A  Poor phi/psi
 698 THR   ( 715-)  A  Poor phi/psi
And so on for a total of 129 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -4.873

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.

 667 SER   ( 684-)  A    0.36
1473 SER   ( 633-)  B    0.37
2330 SER   ( 633-)  C    0.37
3187 SER   ( 633-)  D    0.38
2951 SER   ( 397-)  D    0.38
 616 SER   ( 633-)  A    0.39

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!

   5 ILE   (   6-)  A      0
   6 ALA   (   7-)  A      0
   7 LYS   (   8-)  A      0
   8 ASN   (   9-)  A      0
   9 ASP   (  10-)  A      0
  13 ILE   (  14-)  A      0
  14 GLU   (  15-)  A      0
  17 ALA   (  18-)  A      0
  18 ILE   (  19-)  A      0
  19 PRO   (  20-)  A      0
  20 PHE   (  21-)  A      0
  21 ASN   (  22-)  A      0
  27 TYR   (  28-)  A      0
  60 ALA   (  61-)  A      0
  62 GLU   (  63-)  A      0
  65 ASP   (  66-)  A      0
  66 ASN   (  67-)  A      0
  93 ALA   (  94-)  A      0
  95 ARG   (  96-)  A      0
 126 THR   ( 127-)  A      0
 128 ALA   ( 129-)  A      0
 129 ASP   ( 130-)  A      0
 130 ASN   ( 131-)  A      0
 131 THR   ( 132-)  A      0
 132 THR   ( 133-)  A      0
And so on for a total of 1209 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 : 1.748

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!

2768 GLY   ( 198-)  D   2.83   15
1911 GLY   ( 198-)  C   2.75   13
1054 GLY   ( 198-)  B   2.71   13
 197 GLY   ( 198-)  A   2.64   12
2321 GLY   ( 624-)  C   2.12   10
 607 GLY   ( 624-)  A   2.03   10
1215 THR   ( 375-)  B   1.90   11
2929 THR   ( 375-)  D   1.87   11

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]

 347 PRO   ( 348-)  A    0.47 HIGH
 417 PRO   ( 434-)  A    0.47 HIGH
 491 PRO   ( 508-)  A    0.46 HIGH
 653 PRO   ( 670-)  A    0.46 HIGH
 792 PRO   ( 818-)  A    0.46 HIGH
 967 PRO   ( 111-)  B    0.45 HIGH
1131 PRO   ( 275-)  B    0.50 HIGH
1510 PRO   ( 670-)  B    0.46 HIGH
1574 PRO   ( 734-)  B    0.47 HIGH
1582 PRO   ( 742-)  B    0.49 HIGH
2006 PRO   ( 293-)  C    0.48 HIGH
2027 PRO   ( 314-)  C    0.47 HIGH
2148 PRO   ( 451-)  C    0.45 HIGH
2553 PRO   ( 865-)  C    0.47 HIGH
2844 PRO   ( 274-)  D    0.45 HIGH
3224 PRO   ( 670-)  D    0.45 HIGH
3407 PRO   ( 862-)  D    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].

  19 PRO   (  20-)  A  -112.7 envelop C-gamma (-108 degrees)
 273 PRO   ( 274-)  A    99.6 envelop C-beta (108 degrees)
 400 PRO   ( 417-)  A  -117.6 half-chair C-delta/C-gamma (-126 degrees)
 457 PRO   ( 474-)  A  -113.2 envelop C-gamma (-108 degrees)
 479 PRO   ( 496-)  A  -114.7 envelop C-gamma (-108 degrees)
 653 PRO   ( 670-)  A   102.0 envelop C-beta (108 degrees)
1130 PRO   ( 274-)  B   100.0 envelop C-beta (108 degrees)
1316 PRO   ( 476-)  B  -134.9 half-chair C-delta/C-gamma (-126 degrees)
1336 PRO   ( 496-)  B  -130.2 half-chair C-delta/C-gamma (-126 degrees)
1403 PRO   ( 563-)  B  -125.1 half-chair C-delta/C-gamma (-126 degrees)
1497 PRO   ( 657-)  B  -128.3 half-chair C-delta/C-gamma (-126 degrees)
1611 PRO   ( 780-)  B  -126.8 half-chair C-delta/C-gamma (-126 degrees)
2066 PRO   ( 353-)  C  -162.8 half-chair N/C-delta (-162 degrees)
2114 PRO   ( 417-)  C  -116.9 envelop C-gamma (-108 degrees)
2171 PRO   ( 474-)  C  -136.3 envelop C-delta (-144 degrees)
2205 PRO   ( 508-)  C  -119.0 half-chair C-delta/C-gamma (-126 degrees)
2367 PRO   ( 670-)  C   102.1 envelop C-beta (108 degrees)
2427 PRO   ( 730-)  C   108.5 envelop C-beta (108 degrees)
2439 PRO   ( 742-)  C    38.4 envelop C-delta (36 degrees)
2468 PRO   ( 780-)  C  -126.0 half-chair C-delta/C-gamma (-126 degrees)
2550 PRO   ( 862-)  C  -116.9 envelop C-gamma (-108 degrees)
2642 PRO   (  72-)  D  -115.1 envelop C-gamma (-108 degrees)
2670 PRO   ( 100-)  D  -116.8 envelop C-gamma (-108 degrees)
2844 PRO   ( 274-)  D    99.8 envelop C-beta (108 degrees)
2971 PRO   ( 417-)  D  -129.4 half-chair C-delta/C-gamma (-126 degrees)
3028 PRO   ( 474-)  D  -137.1 envelop C-delta (-144 degrees)
3050 PRO   ( 496-)  D  -121.8 half-chair C-delta/C-gamma (-126 degrees)
3284 PRO   ( 730-)  D   100.5 envelop C-beta (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.

2120 ARG   ( 423-)  C      NH2 <-> 2472 HIS   ( 784-)  C      ND1    0.82    2.18  INTRA BL
 651 THR   ( 668-)  A      CG2 <->  652 GLN   ( 669-)  A      NE2    0.67    2.43  INTRA BL
1263 ARG   ( 423-)  B      NH2 <-> 1615 HIS   ( 784-)  B      ND1    0.65    2.35  INTRA BL
1621 HIS   ( 790-)  B      CD2 <-> 1662 THR   ( 831-)  B      CG2    0.61    2.59  INTRA BL
2125 ALA   ( 428-)  C      N   <-> 2132 GLN   ( 435-)  C      NE2    0.59    2.26  INTRA BL
 218 MET   ( 219-)  A      SD  <-> 3570 HOH   (2060 )  A      O      0.57    2.43  INTRA BF
1487 ARG   ( 647-)  B      NH2 <-> 1511 ASN   ( 671-)  B      ND2    0.56    2.29  INTRA BL
2977 ARG   ( 423-)  D      NH2 <-> 3329 HIS   ( 784-)  D      ND1    0.55    2.45  INTRA BL
  29 GLU   (  30-)  A      CD  <->   33 ARG   (  34-)  A      NH2    0.54    2.56  INTRA BL
1797 ARG   (  84-)  C      NE  <-> 1935 GLU   ( 222-)  C      OE1    0.54    2.16  INTRA BF
 631 GLN   ( 648-)  A      NE2 <->  635 GLU   ( 652-)  A      OE1    0.54    2.16  INTRA BL
  76 LEU   (  77-)  A      CD2 <->  225 MET   ( 226-)  A      SD     0.53    2.87  INTRA BF
1393 GLU   ( 553-)  B      OE1 <-> 1700 ASN   ( 869-)  B      N      0.52    2.18  INTRA BL
 268 GLN   ( 269-)  A      NE2 <->  390 LYS   ( 407-)  A      NZ     0.52    2.33  INTRA BL
1247 LYS   ( 407-)  B      NZ  <-> 3571 HOH   (2175 )  B      O      0.52    2.18  INTRA BF
2921 ASP   ( 351-)  D      N   <-> 3573 HOH   (2097 )  D      O      0.51    2.19  INTRA BF
 149 ARG   ( 150-)  A      NH1 <-> 3570 HOH   (2075 )  A      O      0.50    2.20  INTRA BF
 406 ARG   ( 423-)  A      NH2 <->  758 HIS   ( 784-)  A      ND1    0.50    2.50  INTRA BL
3027 VAL   ( 473-)  D      O   <-> 3032 ARG   ( 478-)  D      NE     0.50    2.20  INTRA BF
3557 DGUA  (   1-)  P      N2  <-> 3585 HOH   (2001 )  P      O      0.50    2.20  INTRA BF
2060 CYS   ( 347-)  C      SG  <-> 2063 GLU   ( 350-)  C      CG     0.49    2.91  INTRA BF
3105 ARG   ( 551-)  D      NH2 <-> 3381 TYR   ( 836-)  D      O      0.48    2.22  INTRA BF
1621 HIS   ( 790-)  B      NE2 <-> 1662 THR   ( 831-)  B      CG2    0.48    2.62  INTRA BL
2918 PRO   ( 348-)  D      CG  <-> 3573 HOH   (2092 )  D      O      0.48    2.32  INTRA BF
2016 LYS   ( 303-)  C      CE  <-> 2437 LYS   ( 740-)  C      NZ     0.47    2.63  INTRA BL
And so on for a total of 1921 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

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.

1809 ARG   (  96-)  C      -8.64
 952 ARG   (  96-)  B      -8.59
2666 ARG   (  96-)  D      -8.59
  95 ARG   (  96-)  A      -8.32
2004 ARG   ( 291-)  C      -7.70
1147 ARG   ( 291-)  B      -7.66
2861 ARG   ( 291-)  D      -7.58
 290 ARG   ( 291-)  A      -7.48
2025 TYR   ( 312-)  C      -7.21
1168 TYR   ( 312-)  B      -6.94
1052 LEU   ( 196-)  B      -6.73
 311 TYR   ( 312-)  A      -6.67
  97 LYS   (  98-)  A      -6.64
 954 LYS   (  98-)  B      -6.63
1811 LYS   (  98-)  C      -6.63
2668 LYS   (  98-)  D      -6.59
1364 HIS   ( 524-)  B      -6.48
3078 HIS   ( 524-)  D      -6.41
2221 HIS   ( 524-)  C      -6.39
2882 TYR   ( 312-)  D      -6.35
2597 HIS   (  27-)  D      -6.35
2220 HIS   ( 523-)  C      -6.32
 506 HIS   ( 523-)  A      -6.27
 507 HIS   ( 524-)  A      -6.27
  26 HIS   (  27-)  A      -6.24
And so on for a total of 76 lines.

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.

 171 LYS   ( 172-)  A       173 - VAL    174- ( A)         -4.61
 505 GLN   ( 522-)  A       507 - HIS    524- ( A)         -5.57
2219 GLN   ( 522-)  C      2221 - HIS    524- ( C)         -5.59
2440 ILE   ( 743-)  C      2442 - THR    745- ( C)         -5.10
3076 GLN   ( 522-)  D      3078 - HIS    524- ( D)         -5.59
3297 ILE   ( 743-)  D      3301 - LEU    747- ( D)         -4.83

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

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: C

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: D

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.

3150 THR   ( 596-)  D   -2.90
1436 THR   ( 596-)  B   -2.89
 579 THR   ( 596-)  A   -2.89
3302 ASN   ( 748-)  D   -2.69
 731 ASN   ( 748-)  A   -2.60

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

 619 THR   ( 636-)  A     -  622 TYR   ( 639-)  A        -1.72
1476 THR   ( 636-)  B     - 1479 TYR   ( 639-)  B        -1.63
2333 THR   ( 636-)  C     - 2336 TYR   ( 639-)  C        -1.67
2988 PRO   ( 434-)  D     - 2991 ASN   ( 437-)  D        -1.50

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

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

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.

3570 HOH   (2006 )  A      O     46.48    2.55  -17.09
3571 HOH   (2002 )  B      O     14.93   24.63   27.70
3571 HOH   (2007 )  B      O     18.32   24.24   28.44
3571 HOH   (2032 )  B      O      0.41  -52.35   68.15
3572 HOH   (2006 )  C      O      1.37  -23.04  -88.03
3573 HOH   (2008 )  D      O    -14.15   -9.63  120.22
3573 HOH   (2010 )  D      O     13.85    2.02  128.19

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.

3570 HOH   (2042 )  A      O
3570 HOH   (2055 )  A      O
3570 HOH   (2058 )  A      O
3570 HOH   (2059 )  A      O
3570 HOH   (2061 )  A      O
3570 HOH   (2066 )  A      O
3570 HOH   (2067 )  A      O
3570 HOH   (2070 )  A      O
3570 HOH   (2072 )  A      O
3570 HOH   (2076 )  A      O
3570 HOH   (2083 )  A      O
3570 HOH   (2087 )  A      O
3570 HOH   (2091 )  A      O
3570 HOH   (2109 )  A      O
3570 HOH   (2111 )  A      O
3570 HOH   (2118 )  A      O
3570 HOH   (2138 )  A      O
3570 HOH   (2139 )  A      O
3570 HOH   (2148 )  A      O
3570 HOH   (2150 )  A      O
3570 HOH   (2151 )  A      O
3570 HOH   (2153 )  A      O
3570 HOH   (2156 )  A      O
3570 HOH   (2184 )  A      O
3570 HOH   (2186 )  A      O
And so on for a total of 113 lines.

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.

 130 ASN   ( 131-)  A
 229 HIS   ( 230-)  A
 268 GLN   ( 269-)  A
 323 GLN   ( 324-)  A
 418 GLN   ( 435-)  A
 446 HIS   ( 463-)  A
 468 ASN   ( 485-)  A
 469 HIS   ( 486-)  A
 506 HIS   ( 523-)  A
 527 GLN   ( 544-)  A
 566 GLN   ( 583-)  A
 720 GLN   ( 737-)  A
 755 ASN   ( 781-)  A
 758 HIS   ( 784-)  A
 785 HIS   ( 811-)  A
1040 GLN   ( 184-)  B
1067 HIS   ( 211-)  B
1086 HIS   ( 230-)  B
1095 GLN   ( 239-)  B
1180 GLN   ( 324-)  B
1275 GLN   ( 435-)  B
1277 ASN   ( 437-)  B
1303 HIS   ( 463-)  B
1325 ASN   ( 485-)  B
1326 HIS   ( 486-)  B
And so on for a total of 64 lines.

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.

  16 ALA   (  17-)  A      N
  21 ASN   (  22-)  A      N
  31 LEU   (  32-)  A      N
  35 GLN   (  36-)  A      NE2
  49 ARG   (  50-)  A      NH1
  63 VAL   (  64-)  A      N
  66 ASN   (  67-)  A      ND2
  72 LEU   (  73-)  A      N
  83 ARG   (  84-)  A      NE
  87 TRP   (  88-)  A      NE1
 108 ILE   ( 109-)  A      N
 111 GLU   ( 112-)  A      N
 132 THR   ( 133-)  A      N
 134 GLN   ( 135-)  A      N
 176 VAL   ( 177-)  A      N
 200 TRP   ( 201-)  A      NE1
 203 TRP   ( 204-)  A      N
 206 GLU   ( 207-)  A      N
 225 MET   ( 226-)  A      N
 229 HIS   ( 230-)  A      N
 231 GLN   ( 232-)  A      NE2
 264 SER   ( 265-)  A      N
 268 GLN   ( 269-)  A      N
 272 VAL   ( 273-)  A      N
 279 GLY   ( 280-)  A      N
And so on for a total of 319 lines.

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.

  57 GLN   (  58-)  A      OE1
 145 GLU   ( 146-)  A      OE1
 146 ASP   ( 147-)  A      OD2
 221 GLU   ( 222-)  A      OE1
 449 ASN   ( 466-)  A      OD1
 602 GLN   ( 619-)  A      OE1
 632 GLN   ( 649-)  A      OE1
 785 HIS   ( 811-)  A      ND1
 882 ASP   (  26-)  B      OD1
 883 HIS   (  27-)  B      ND1
 897 HIS   (  41-)  B      ND1
1014 GLU   ( 158-)  B      OE1
1055 GLU   ( 199-)  B      OE2
1096 ASP   ( 240-)  B      OD1
1244 GLN   ( 404-)  B      OE1
1459 GLN   ( 619-)  B      OE1
1642 HIS   ( 811-)  B      NE2
1871 GLU   ( 158-)  C      OE1
2226 ASN   ( 529-)  C      OD1
2718 GLU   ( 148-)  D      OE1
2728 GLU   ( 158-)  D      OE1
2757 GLU   ( 187-)  D      OE1
2810 ASP   ( 240-)  D      OD1
3040 HIS   ( 486-)  D      ND1
3173 GLN   ( 619-)  D      OE1
3356 HIS   ( 811-)  D      ND1

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.

3570 HOH   (2198 )  A      O  0.98  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.

  14 GLU   (  15-)  A   H-bonding suggests Gln; but Alt-Rotamer
  86 ASP   (  87-)  A   H-bonding suggests Asn
  89 GLU   (  90-)  A   H-bonding suggests Gln
  90 GLU   (  91-)  A   H-bonding suggests Gln
 107 GLU   ( 108-)  A   H-bonding suggests Gln; but Alt-Rotamer
 129 ASP   ( 130-)  A   H-bonding suggests Asn; but Alt-Rotamer
 146 ASP   ( 147-)  A   H-bonding suggests Asn; but Alt-Rotamer
 167 GLU   ( 168-)  A   H-bonding suggests Gln
 244 GLU   ( 245-)  A   H-bonding suggests Gln
 251 GLU   ( 252-)  A   H-bonding suggests Gln
 309 ASP   ( 310-)  A   H-bonding suggests Asn; but Alt-Rotamer
 350 ASP   ( 351-)  A   H-bonding suggests Asn; but Alt-Rotamer
 568 ASP   ( 585-)  A   H-bonding suggests Asn
 643 ASP   ( 660-)  A   H-bonding suggests Asn; but Alt-Rotamer
 825 ASP   ( 851-)  A   H-bonding suggests Asn
 871 GLU   (  15-)  B   H-bonding suggests Gln; but Alt-Rotamer
 943 ASP   (  87-)  B   H-bonding suggests Asn
1002 GLU   ( 146-)  B   H-bonding suggests Gln
1003 ASP   ( 147-)  B   H-bonding suggests Asn; but Alt-Rotamer
1014 GLU   ( 158-)  B   H-bonding suggests Gln
1024 GLU   ( 168-)  B   H-bonding suggests Gln
1101 GLU   ( 245-)  B   H-bonding suggests Gln
1207 ASP   ( 351-)  B   H-bonding suggests Asn
1311 ASP   ( 471-)  B   H-bonding suggests Asn; but Alt-Rotamer
1346 ASP   ( 506-)  B   H-bonding suggests Asn
And so on for a total of 57 lines.

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 :  -0.963
  2nd generation packing quality :  -2.102
  Ramachandran plot appearance   :  -3.712 (poor)
  chi-1/chi-2 rotamer normality  :  -4.873 (bad)
  Backbone conformation          :   0.177

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.707
  Bond angles                    :   0.827
  Omega angle restraints         :   0.318 (tight)
  Side chain planarity           :   0.203 (tight)
  Improper dihedral distribution :   0.728
  B-factor distribution          :   0.526
  Inside/Outside distribution    :   1.019

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 : 2.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -0.3
  Ramachandran plot appearance   :  -1.2
  chi-1/chi-2 rotamer normality  :  -2.5
  Backbone conformation          :   0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.707
  Bond angles                    :   0.827
  Omega angle restraints         :   0.318 (tight)
  Side chain planarity           :   0.203 (tight)
  Improper dihedral distribution :   0.728
  B-factor distribution          :   0.526
  Inside/Outside distribution    :   1.019
==============

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.