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 pdb1ggh.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 : 0.700
CA-only RMS fit for the two chains : 0.421

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 : 0.719
CA-only RMS fit for the two chains : 0.447

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 : 0.670
CA-only RMS fit for the two chains : 0.397

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 : 0.535
CA-only RMS fit for the two chains : 0.220

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 : 0.608
CA-only RMS fit for the two chains : 0.242

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

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.

2913 HEM   ( 760-)  A  -
2914 HEM   ( 760-)  B  -
2915 HEM   ( 760-)  C  -
2916 HEM   ( 760-)  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: Occupancies atoms do not add up to 1.0.

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

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

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

 495 ARG   ( 521-)  A    0.50
1070 ARG   ( 369-)  B    0.50
1949 ARG   ( 521-)  C    0.50
2300 SER   ( 145-)  D    0.50

Warning: What type of B-factor?

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

Obviously, the temperature at which the X-ray data was collected has some importance too:

Crystal temperature (K) :120.000

Warning: More than 5 percent of buried atoms has low B-factor

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

Percentage of buried atoms with B less than 5 : 18.87

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.

 252 ARG   ( 278-)  A
 287 ARG   ( 313-)  A
 343 ARG   ( 369-)  A
 396 ARG   ( 422-)  A
 510 ARG   ( 536-)  A
 586 ARG   ( 612-)  A
 610 ARG   ( 636-)  A
 812 ARG   ( 111-)  B
 866 ARG   ( 165-)  B
 884 ARG   ( 183-)  B
 961 ARG   ( 260-)  B
1172 ARG   ( 471-)  B
1210 ARG   ( 509-)  B
1489 ARG   (  61-)  C
1539 ARG   ( 111-)  C
1611 ARG   ( 183-)  C
1706 ARG   ( 278-)  C
1850 ARG   ( 422-)  C
1899 ARG   ( 471-)  C
1937 ARG   ( 509-)  C
1964 ARG   ( 536-)  C
1970 ARG   ( 542-)  C
2216 ARG   (  61-)  D
2266 ARG   ( 111-)  D
2338 ARG   ( 183-)  D
2422 ARG   ( 267-)  D
2433 ARG   ( 278-)  D
2626 ARG   ( 471-)  D
2691 ARG   ( 536-)  D
2767 ARG   ( 612-)  D
2857 ARG   ( 702-)  D

Warning: Tyrosine convention problem

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

 111 TYR   ( 137-)  A
 115 TYR   ( 141-)  A
 164 TYR   ( 190-)  A
 308 TYR   ( 334-)  A
 389 TYR   ( 415-)  A
 414 TYR   ( 440-)  A
 434 TYR   ( 460-)  A
 657 TYR   ( 683-)  A
 838 TYR   ( 137-)  B
 842 TYR   ( 141-)  B
1035 TYR   ( 334-)  B
1116 TYR   ( 415-)  B
1141 TYR   ( 440-)  B
1161 TYR   ( 460-)  B
1384 TYR   ( 683-)  B
1565 TYR   ( 137-)  C
1569 TYR   ( 141-)  C
1762 TYR   ( 334-)  C
1843 TYR   ( 415-)  C
1868 TYR   ( 440-)  C
1888 TYR   ( 460-)  C
2111 TYR   ( 683-)  C
2292 TYR   ( 137-)  D
2296 TYR   ( 141-)  D
2345 TYR   ( 190-)  D
2570 TYR   ( 415-)  D
2595 TYR   ( 440-)  D
2615 TYR   ( 460-)  D
2838 TYR   ( 683-)  D

Warning: Phenylalanine convention problem

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

 126 PHE   ( 152-)  A
 140 PHE   ( 166-)  A
 180 PHE   ( 206-)  A
 188 PHE   ( 214-)  A
 191 PHE   ( 217-)  A
 251 PHE   ( 277-)  A
 291 PHE   ( 317-)  A
 305 PHE   ( 331-)  A
 312 PHE   ( 338-)  A
 321 PHE   ( 347-)  A
 325 PHE   ( 351-)  A
 356 PHE   ( 382-)  A
 365 PHE   ( 391-)  A
 376 PHE   ( 402-)  A
 417 PHE   ( 443-)  A
 456 PHE   ( 482-)  A
 485 PHE   ( 511-)  A
 492 PHE   ( 518-)  A
 503 PHE   ( 529-)  A
 628 PHE   ( 654-)  A
 678 PHE   ( 704-)  A
 853 PHE   ( 152-)  B
 867 PHE   ( 166-)  B
 907 PHE   ( 206-)  B
 908 PHE   ( 207-)  B
And so on for a total of 89 lines.

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.

  44 ASP   (  70-)  A
  64 ASP   (  90-)  A
  65 ASP   (  91-)  A
  81 ASP   ( 107-)  A
  92 ASP   ( 118-)  A
 120 ASP   ( 146-)  A
 129 ASP   ( 155-)  A
 151 ASP   ( 177-)  A
 155 ASP   ( 181-)  A
 171 ASP   ( 197-)  A
 190 ASP   ( 216-)  A
 233 ASP   ( 259-)  A
 279 ASP   ( 305-)  A
 304 ASP   ( 330-)  A
 326 ASP   ( 352-)  A
 329 ASP   ( 355-)  A
 354 ASP   ( 380-)  A
 375 ASP   ( 401-)  A
 428 ASP   ( 454-)  A
 499 ASP   ( 525-)  A
 519 ASP   ( 545-)  A
 525 ASP   ( 551-)  A
 543 ASP   ( 569-)  A
 552 ASP   ( 578-)  A
 559 ASP   ( 585-)  A
And so on for a total of 139 lines.

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.

   6 GLU   (  32-)  A
  37 GLU   (  63-)  A
  43 GLU   (  69-)  A
  80 GLU   ( 106-)  A
 167 GLU   ( 193-)  A
 222 GLU   ( 248-)  A
 280 GLU   ( 306-)  A
 301 GLU   ( 327-)  A
 307 GLU   ( 333-)  A
 309 GLU   ( 335-)  A
 318 GLU   ( 344-)  A
 320 GLU   ( 346-)  A
 336 GLU   ( 362-)  A
 361 GLU   ( 387-)  A
 404 GLU   ( 430-)  A
 435 GLU   ( 461-)  A
 446 GLU   ( 472-)  A
 457 GLU   ( 483-)  A
 477 GLU   ( 503-)  A
 493 GLU   ( 519-)  A
 515 GLU   ( 541-)  A
 613 GLU   ( 639-)  A
 694 GLU   ( 720-)  A
 764 GLU   (  63-)  B
 770 GLU   (  69-)  B
And so on for a total of 97 lines.

Geometric checks

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

 |  0.998822 -0.000081  0.000588|
 | -0.000081  0.998618  0.000059|
 |  0.000588  0.000059  1.000732|
Proposed new scale matrix

 |  0.010758  0.000000  0.003825|
 |  0.000000  0.007566  0.000000|
 | -0.000005  0.000000  0.008754|
With corresponding cell

    A    =  92.931  B   = 132.162  C    = 121.218
    Alpha=  90.001  Beta= 109.538  Gamma=  90.001

The CRYST1 cell dimensions

    A    =  93.040  B   = 132.340  C    = 121.200
    Alpha=  90.000  Beta= 109.630  Gamma=  90.000

Variance: 81.037
(Under-)estimated Z-score: 6.634

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

   1 ASP   (  27-)  A      CA   CB   CG  120.15    7.5
   2 SER   (  28-)  A     -C    N    CA  129.01    4.1
   2 SER   (  28-)  A      N    CA   CB  103.09   -4.4
  11 ARG   (  37-)  A      CD   NE   CZ  130.80    5.1
  35 ARG   (  61-)  A      C    CA   CB  102.17   -4.2
  43 GLU   (  69-)  A      CB   CG   CD  120.01    4.4
  74 ARG   ( 100-)  A     -C    N    CA  129.15    4.1
  74 ARG   ( 100-)  A      CG   CD   NE  120.83    6.1
  82 PHE   ( 108-)  A      CA   CB   CG  119.25    5.4
  95 ARG   ( 121-)  A      CD   NE   CZ  129.87    4.5
 109 HIS   ( 135-)  A      CA   CB   CG  117.86    4.1
 109 HIS   ( 135-)  A      CG   ND1  CE1 110.66    5.1
 113 GLN   ( 139-)  A      CA   CB   CG  122.69    4.3
 129 ASP   ( 155-)  A      CA   CB   CG  118.28    5.7
 131 ASN   ( 157-)  A      CA   CB   CG  108.21   -4.4
 144 GLN   ( 170-)  A      NE2  CD   OE1 117.38   -5.2
 159 PHE   ( 185-)  A      CA   CB   CG  120.94    7.1
 186 HIS   ( 212-)  A      CG   ND1  CE1 110.12    4.5
 191 PHE   ( 217-)  A      CA   CB   CG  108.57   -5.2
 210 HIS   ( 236-)  A      CG   ND1  CE1 110.37    4.8
 214 TRP   ( 240-)  A      CA   CB   CG  106.00   -4.0
 246 PHE   ( 272-)  A      CA   CB   CG  118.09    4.3
 252 ARG   ( 278-)  A      CD   NE   CZ  129.61    4.4
 264 ARG   ( 290-)  A      N    CA   CB  118.25    4.6
 292 HIS   ( 318-)  A      CG   ND1  CE1 110.29    4.7
And so on for a total of 245 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.

   6 GLU   (  32-)  A
  37 GLU   (  63-)  A
  43 GLU   (  69-)  A
  44 ASP   (  70-)  A
  64 ASP   (  90-)  A
  65 ASP   (  91-)  A
  80 GLU   ( 106-)  A
  81 ASP   ( 107-)  A
  92 ASP   ( 118-)  A
 120 ASP   ( 146-)  A
 129 ASP   ( 155-)  A
 151 ASP   ( 177-)  A
 155 ASP   ( 181-)  A
 167 GLU   ( 193-)  A
 171 ASP   ( 197-)  A
 190 ASP   ( 216-)  A
 222 GLU   ( 248-)  A
 233 ASP   ( 259-)  A
 252 ARG   ( 278-)  A
 279 ASP   ( 305-)  A
 280 GLU   ( 306-)  A
 287 ARG   ( 313-)  A
 301 GLU   ( 327-)  A
 304 ASP   ( 330-)  A
 307 GLU   ( 333-)  A
And so on for a total of 267 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.

 904 THR   ( 203-)  B      C     -6.1    -8.91     0.30
2154 GLY   ( 726-)  C      C      8.1    10.80     0.06
2358 THR   ( 203-)  D      C     -6.3    -9.21     0.30
The average deviation= 1.446

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.

 722 ILE   ( 748-)  A    6.96
1115 SER   ( 414-)  B    6.11
2154 GLY   ( 726-)  C    6.03
 388 SER   ( 414-)  A    5.90
2569 SER   ( 414-)  D    5.45
1842 SER   ( 414-)  C    5.37
 570 GLY   ( 596-)  A    4.89
2392 ASP   ( 237-)  D    4.56
1665 ASP   ( 237-)  C    4.50
1005 TRP   ( 304-)  B    4.23
1767 GLN   ( 339-)  C    4.07
1596 THR   ( 168-)  C    4.05

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.

 406 PRO   ( 432-)  A    -2.9
1410 LYS   ( 709-)  B    -2.8
 423 HIS   ( 449-)  A    -2.7
1860 PRO   ( 432-)  C    -2.7
2183 SER   (  28-)  D    -2.7
2587 PRO   ( 432-)  D    -2.7
1877 HIS   ( 449-)  C    -2.7
1127 PRO   ( 426-)  B    -2.6
2906 ILE   ( 751-)  D    -2.6
2062 TYR   ( 634-)  C    -2.6
 729 SER   (  28-)  B    -2.6
1078 ARG   ( 377-)  B    -2.5
 906 ILE   ( 205-)  B    -2.5
2064 ARG   ( 636-)  C    -2.5
2581 PRO   ( 426-)  D    -2.5
1133 PRO   ( 432-)  B    -2.5
2765 GLU   ( 610-)  D    -2.5
2604 HIS   ( 449-)  D    -2.5
1854 PRO   ( 426-)  C    -2.5
2038 GLU   ( 610-)  C    -2.4
1658 PRO   ( 230-)  C    -2.4
1311 GLU   ( 610-)  B    -2.4
 608 TYR   ( 634-)  A    -2.4
2864 LYS   ( 709-)  D    -2.4
2303 THR   ( 148-)  D    -2.4
And so on for a total of 83 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.

   2 SER   (  28-)  A  Poor phi/psi
  51 ASN   (  77-)  A  Poor phi/psi
 102 ALA   ( 128-)  A  Poor phi/psi
 203 ILE   ( 229-)  A  PRO omega poor
 248 ILE   ( 274-)  A  Poor phi/psi
 304 ASP   ( 330-)  A  Poor phi/psi
 420 ASP   ( 446-)  A  Poor phi/psi
 435 GLU   ( 461-)  A  PRO omega poor
 441 ASP   ( 467-)  A  Poor phi/psi
 442 ASN   ( 468-)  A  Poor phi/psi
 443 TRP   ( 469-)  A  PRO omega poor
 453 ARG   ( 479-)  A  Poor phi/psi
 558 LYS   ( 584-)  A  Poor phi/psi
 666 LEU   ( 692-)  A  Poor phi/psi
 683 LYS   ( 709-)  A  Poor phi/psi
 685 ALA   ( 711-)  A  Poor phi/psi
 713 HIS   ( 739-)  A  Poor phi/psi
 729 SER   (  28-)  B  Poor phi/psi
 778 ASN   (  77-)  B  Poor phi/psi
 829 ALA   ( 128-)  B  Poor phi/psi
 930 ILE   ( 229-)  B  PRO omega poor
 975 ILE   ( 274-)  B  Poor phi/psi
1147 ASP   ( 446-)  B  Poor phi/psi
1162 GLU   ( 461-)  B  PRO omega poor
1169 ASN   ( 468-)  B  Poor phi/psi
And so on for a total of 68 lines.

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.

2068 VAL   ( 640-)  C    0.33
1672 SER   ( 244-)  C    0.35
 945 SER   ( 244-)  B    0.36
2795 VAL   ( 640-)  D    0.38

Warning: Unusual backbone conformations

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

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

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

   3 LEU   (  29-)  A      0
   4 ALA   (  30-)  A      0
   9 SER   (  35-)  A      0
  10 HIS   (  36-)  A      0
  14 ALA   (  40-)  A      0
  16 PRO   (  42-)  A      0
  19 PRO   (  45-)  A      0
  24 THR   (  50-)  A      0
  25 ALA   (  51-)  A      0
  34 THR   (  60-)  A      0
  35 ARG   (  61-)  A      0
  49 SER   (  75-)  A      0
  50 GLU   (  76-)  A      0
  51 ASN   (  77-)  A      0
  58 GLN   (  84-)  A      0
  63 ALA   (  89-)  A      0
  65 ASP   (  91-)  A      0
  66 GLN   (  92-)  A      0
  70 ARG   (  96-)  A      0
  74 ARG   ( 100-)  A      0
  93 HIS   ( 119-)  A      0
  94 GLU   ( 120-)  A      0
 100 ILE   ( 126-)  A      0
 101 VAL   ( 127-)  A      0
 102 ALA   ( 128-)  A      0
And so on for a total of 1133 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 : 3.536

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!

1502 GLY   (  74-)  C   2.40   41
  48 GLY   (  74-)  A   2.39   38
 775 GLY   (  74-)  B   2.19   44
2229 GLY   (  74-)  D   2.05   31
1125 GLY   ( 424-)  B   1.59   11
 406 PRO   ( 432-)  A   1.56   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]

  16 PRO   (  42-)  A    0.20 LOW
 316 PRO   ( 342-)  A    0.17 LOW
 340 PRO   ( 366-)  A    0.19 LOW
 406 PRO   ( 432-)  A    0.45 HIGH
 431 PRO   ( 457-)  A    0.15 LOW
 549 PRO   ( 575-)  A    0.16 LOW
 551 PRO   ( 577-)  A    0.09 LOW
 568 PRO   ( 594-)  A    0.19 LOW
 632 PRO   ( 658-)  A    0.06 LOW
 720 PRO   ( 746-)  A    0.17 LOW
 739 PRO   (  38-)  B    0.10 LOW
 743 PRO   (  42-)  B    0.18 LOW
 753 PRO   (  52-)  B    0.13 LOW
 857 PRO   ( 156-)  B    0.15 LOW
 926 PRO   ( 225-)  B    0.45 HIGH
 964 PRO   ( 263-)  B    0.06 LOW
1080 PRO   ( 379-)  B    0.07 LOW
1209 PRO   ( 508-)  B    0.20 LOW
1277 PRO   ( 576-)  B    0.16 LOW
1350 PRO   ( 649-)  B    0.17 LOW
1691 PRO   ( 263-)  C    0.13 LOW
1807 PRO   ( 379-)  C    0.11 LOW
1864 PRO   ( 436-)  C    0.14 LOW
1903 PRO   ( 475-)  C    0.20 LOW
2004 PRO   ( 576-)  C    0.15 LOW
2199 PRO   (  44-)  D    0.10 LOW
2295 PRO   ( 140-)  D    0.18 LOW
2497 PRO   ( 342-)  D    0.14 LOW
2629 PRO   ( 474-)  D    0.12 LOW
2632 PRO   ( 477-)  D    0.20 LOW
2730 PRO   ( 575-)  D    0.14 LOW
2741 PRO   ( 586-)  D    0.08 LOW
2813 PRO   ( 658-)  D    0.09 LOW
2901 PRO   ( 746-)  D    0.18 LOW

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

 199 PRO   ( 225-)  A  -112.8 envelop C-gamma (-108 degrees)
 204 PRO   ( 230-)  A   -43.5 envelop C-alpha (-36 degrees)
 406 PRO   ( 432-)  A    99.5 envelop C-beta (108 degrees)
 482 PRO   ( 508-)  A   102.5 envelop C-beta (108 degrees)
 623 PRO   ( 649-)  A    48.9 half-chair C-delta/C-gamma (54 degrees)
 726 PRO   ( 752-)  A   -55.0 half-chair C-beta/C-alpha (-54 degrees)
 841 PRO   ( 140-)  B    31.1 envelop C-delta (36 degrees)
 931 PRO   ( 230-)  B   -50.7 half-chair C-beta/C-alpha (-54 degrees)
1295 PRO   ( 594-)  B    99.7 envelop C-beta (108 degrees)
1453 PRO   ( 752-)  B   -59.9 half-chair C-beta/C-alpha (-54 degrees)
1466 PRO   (  38-)  C    52.4 half-chair C-delta/C-gamma (54 degrees)
1584 PRO   ( 156-)  C  -115.2 envelop C-gamma (-108 degrees)
1658 PRO   ( 230-)  C   -36.0 envelop C-alpha (-36 degrees)
1860 PRO   ( 432-)  C    99.8 envelop C-beta (108 degrees)
1936 PRO   ( 508-)  C   108.8 envelop C-beta (108 degrees)
2022 PRO   ( 594-)  C  -126.8 half-chair C-delta/C-gamma (-126 degrees)
2385 PRO   ( 230-)  D   -38.4 envelop C-alpha (-36 degrees)
2402 PRO   ( 247-)  D  -118.2 half-chair C-delta/C-gamma (-126 degrees)
2749 PRO   ( 594-)  D  -154.9 half-chair N/C-delta (-162 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.

 682 ILE   ( 708-)  A      O   <->  684 ILE   ( 710-)  A      N      0.31    2.39  INTRA
2064 ARG   ( 636-)  C      NH2 <-> 2067 GLU   ( 639-)  C      O      0.30    2.40  INTRA
2643 ARG   ( 488-)  D      NE  <-> 2920 HOH   (1379 )  D      O      0.30    2.40  INTRA
 737 HIS   (  36-)  B      NE2 <->  738 ARG   (  37-)  B      NE     0.30    2.70  INTRA
  13 ALA   (  39-)  A      N   <->   22 GLN   (  48-)  A      OE1    0.30    2.40  INTRA
1625 ASP   ( 197-)  C      OD2 <-> 1823 HIS   ( 395-)  C      ND1    0.29    2.41  INTRA BL
1737 LYS   ( 309-)  C      NZ  <-> 2115 GLU   ( 687-)  C      OE2    0.29    2.41  INTRA BL
1370 CYS   ( 669-)  B      SG  <-> 2918 HOH   (1410 )  B      O      0.29    2.71  INTRA
 960 ASP   ( 259-)  B      OD2 <-> 1223 HIS   ( 522-)  B      ND1    0.28    2.42  INTRA BL
2012 LYS   ( 584-)  C      NZ  <-> 2919 HOH   (1205 )  C      O      0.28    2.42  INTRA
 462 ARG   ( 488-)  A      NE  <->  464 GLU   ( 490-)  A      OE2    0.27    2.43  INTRA BL
 920 HIS   ( 219-)  B      NE2 <-> 1548 GLU   ( 120-)  C      OE2    0.27    2.43  INTRA BL
2824 CYS   ( 669-)  D      SG  <-> 2920 HOH   (1403 )  D      O      0.27    2.73  INTRA
2153 ASP   ( 725-)  C      OD1 <-> 2157 MET   ( 729-)  C      N      0.26    2.44  INTRA
2523 GLN   ( 368-)  D      NE2 <-> 2920 HOH   (1084 )  D      O      0.26    2.44  INTRA
 552 ASP   ( 578-)  A      OD2 <->  557 LYS   ( 583-)  A      NZ     0.25    2.45  INTRA
 586 ARG   ( 612-)  A      NH2 <->  643 CYS   ( 669-)  A      SG     0.24    3.06  INTRA
2414 ASP   ( 259-)  D      OD2 <-> 2677 HIS   ( 522-)  D      ND1    0.24    2.46  INTRA BL
 728 ASP   (  27-)  B      OD2 <-> 2623 ASN   ( 468-)  D      ND2    0.24    2.46  INTRA
 740 ALA   (  39-)  B      N   <->  749 GLN   (  48-)  B      OE1    0.22    2.48  INTRA
1703 HIS   ( 275-)  C      ND1 <-> 1833 ASP   ( 405-)  C      OD2    0.21    2.49  INTRA BL
1237 ARG   ( 536-)  B      NH2 <-> 2918 HOH   (1285 )  B      O      0.20    2.50  INTRA
 821 GLU   ( 120-)  B      OE2 <-> 1647 HIS   ( 219-)  C      NE2    0.20    2.50  INTRA BL
 630 GLY   ( 656-)  A      O   <-> 2688 LYS   ( 533-)  D      NZ     0.19    2.51  INTRA BL
1222 ARG   ( 521-)  B      NH2 <-> 2918 HOH   (1092 )  B      O      0.19    2.51  INTRA
And so on for a total of 385 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.

 687 GLN   ( 713-)  A      -7.33
 453 ARG   ( 479-)  A      -7.02
1180 ARG   ( 479-)  B      -6.96
1907 ARG   ( 479-)  C      -6.94
  35 ARG   (  61-)  A      -6.88
 452 LYS   ( 478-)  A      -6.79
2634 ARG   ( 479-)  D      -6.74
1906 LYS   ( 478-)  C      -6.72
2633 LYS   ( 478-)  D      -6.63
1549 ARG   ( 121-)  C      -6.51
1179 LYS   ( 478-)  B      -6.47
1414 GLN   ( 713-)  B      -6.47
  95 ARG   ( 121-)  A      -6.44
2276 ARG   ( 121-)  D      -6.44
 822 ARG   ( 121-)  B      -6.39
1489 ARG   (  61-)  C      -6.36
 762 ARG   (  61-)  B      -6.30
2868 GLN   ( 713-)  D      -6.28
2187 GLU   (  32-)  D      -6.20
2652 ARG   ( 497-)  D      -6.16
1925 ARG   ( 497-)  C      -6.11
2141 GLN   ( 713-)  C      -6.08
 471 ARG   ( 497-)  A      -5.99
1198 ARG   ( 497-)  B      -5.99
2064 ARG   ( 636-)  C      -5.94
And so on for a total of 75 lines.

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.

 203 ILE   ( 229-)  A   -3.28
2906 ILE   ( 751-)  D   -2.55
2649 VAL   ( 494-)  D   -2.53

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.

  18 PRO   (  44-)  A     -   21 ALA   (  47-)  A        -1.42
 319 ASP   ( 345-)  A     -  322 LYS   ( 348-)  A        -1.57
 746 PRO   (  45-)  B     -  749 GLN   (  48-)  B        -1.97
1773 ASP   ( 345-)  C     - 1776 LYS   ( 348-)  C        -1.65
2903 ILE   ( 748-)  D     - 2906 ILE   ( 751-)  D        -2.03

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.

2920 HOH   (1375 )  D      O    -11.46  -30.31  -24.89

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.

2917 HOH   (1436 )  A      O
2919 HOH   (1270 )  C      O
2919 HOH   (1434 )  C      O
2920 HOH   (1401 )  D      O
ERROR. No convergence in HB2STD
Old,New value: 4838.255 4838.278

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.

  10 HIS   (  36-)  A
 342 GLN   ( 368-)  A
 489 GLN   ( 515-)  A
1150 HIS   ( 449-)  B
1330 HIS   ( 629-)  B
1512 GLN   (  84-)  C
1629 ASN   ( 201-)  C
1680 ASN   ( 252-)  C
1796 GLN   ( 368-)  C
2057 HIS   ( 629-)  C
2099 ASN   ( 671-)  C
2141 GLN   ( 713-)  C
2203 GLN   (  48-)  D
2356 ASN   ( 201-)  D
2784 HIS   ( 629-)  D
2826 ASN   ( 671-)  D

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.

   2 SER   (  28-)  A      N
  15 GLU   (  41-)  A      N
  33 ASP   (  59-)  A      N
  51 ASN   (  77-)  A      N
  57 ASN   (  83-)  A      N
  67 ASN   (  93-)  A      N
  99 ARG   ( 125-)  A      NE
 101 VAL   ( 127-)  A      N
 104 ARG   ( 130-)  A      NH2
 139 ARG   ( 165-)  A      NH1
 141 SER   ( 167-)  A      OG
 153 VAL   ( 179-)  A      N
 177 THR   ( 203-)  A      N
 179 ILE   ( 205-)  A      N
 181 PHE   ( 207-)  A      N
 182 ILE   ( 208-)  A      N
 190 ASP   ( 216-)  A      N
 201 TRP   ( 227-)  A      N
 209 ALA   ( 235-)  A      N
 226 ASN   ( 252-)  A      ND2
 234 ARG   ( 260-)  A      NH2
 243 MET   ( 269-)  A      N
 273 LYS   ( 299-)  A      N
 325 PHE   ( 351-)  A      N
 371 VAL   ( 397-)  A      N
And so on for a total of 180 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.

  92 ASP   ( 118-)  A      OD2
 186 HIS   ( 212-)  A      ND1
 391 ASP   ( 417-)  A      OD2
 435 GLU   ( 461-)  A      OE2
 569 ASP   ( 595-)  A      OD2
 819 ASP   ( 118-)  B      OD2
 913 HIS   ( 212-)  B      ND1
 953 ASN   ( 252-)  B      OD1
1118 ASP   ( 417-)  B      OD2
1162 GLU   ( 461-)  B      OE2
1223 HIS   ( 522-)  B      ND1
1546 ASP   ( 118-)  C      OD2
1640 HIS   ( 212-)  C      ND1
1823 HIS   ( 395-)  C      ND1
1845 ASP   ( 417-)  C      OD2
1877 HIS   ( 449-)  C      NE2
2273 ASP   ( 118-)  D      OD2
2367 HIS   ( 212-)  D      ND1
2572 ASP   ( 417-)  D      OD2
2574 GLN   ( 419-)  D      OE1
2604 HIS   ( 449-)  D      NE2
2616 GLU   ( 461-)  D      OE2

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.

2917 HOH   ( 765 )  A      O  0.98  K  5

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.

  15 GLU   (  41-)  A   H-bonding suggests Gln
  64 ASP   (  90-)  A   H-bonding suggests Asn; but Alt-Rotamer
  92 ASP   ( 118-)  A   H-bonding suggests Asn; Ligand-contact
 301 GLU   ( 327-)  A   H-bonding suggests Gln
 584 GLU   ( 610-)  A   H-bonding suggests Gln; but Alt-Rotamer
 617 ASP   ( 643-)  A   H-bonding suggests Asn; but Alt-Rotamer
 791 ASP   (  90-)  B   H-bonding suggests Asn; but Alt-Rotamer
 819 ASP   ( 118-)  B   H-bonding suggests Asn; but Alt-Rotamer
1028 GLU   ( 327-)  B   H-bonding suggests Gln
1226 ASP   ( 525-)  B   H-bonding suggests Asn; but Alt-Rotamer
1311 GLU   ( 610-)  B   H-bonding suggests Gln
1518 ASP   (  90-)  C   H-bonding suggests Asn; but Alt-Rotamer
1546 ASP   ( 118-)  C   H-bonding suggests Asn; Ligand-contact
1755 GLU   ( 327-)  C   H-bonding suggests Gln
1953 ASP   ( 525-)  C   H-bonding suggests Asn
2153 ASP   ( 725-)  C   H-bonding suggests Asn
2188 ASP   (  33-)  D   H-bonding suggests Asn
2196 GLU   (  41-)  D   H-bonding suggests Gln
2245 ASP   (  90-)  D   H-bonding suggests Asn; but Alt-Rotamer
2273 ASP   ( 118-)  D   H-bonding suggests Asn; Ligand-contact
2482 GLU   ( 327-)  D   H-bonding suggests Gln
2685 GLU   ( 530-)  D   H-bonding suggests Gln
2832 ASP   ( 677-)  D   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.759
  2nd generation packing quality :  -1.928
  Ramachandran plot appearance   :  -1.074
  chi-1/chi-2 rotamer normality  :  -1.594
  Backbone conformation          :  -0.365

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.413 (tight)
  Bond angles                    :   1.200
  Omega angle restraints         :   0.643 (tight)
  Side chain planarity           :   0.717
  Improper dihedral distribution :   1.228
  Inside/Outside distribution    :   1.067

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 : 2.15


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :  -0.0
  chi-1/chi-2 rotamer normality  :  -0.8
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.413 (tight)
  Bond angles                    :   1.200
  Omega angle restraints         :   0.643 (tight)
  Side chain planarity           :   0.717
  Improper dihedral distribution :   1.228
  Inside/Outside distribution    :   1.067
==============

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.