WHAT IF Check report

This file was created 2014-12-18 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb3zgb.ent

Checks that need to be done early-on in validation

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.

1842 EDO   (1968-)  A  -
1843 SO4   (1969-)  A  -
1844 SO4   (1970-)  A  -
1845 EDO   (1968-)  B  -
1846 SO4   (1969-)  B  -
1847 SO4   (1970-)  B  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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

Warning: 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.

   1 LEU   (   6-)  A    High
   2 GLU   (   7-)  A    High
   3 LYS   (   8-)  A    High
   4 LEU   (   9-)  A    High
   6 SER   (  11-)  A    High
  14 LEU   (  19-)  A    High
  15 VAL   (  20-)  A    High
  16 PRO   (  21-)  A    High
  17 GLY   (  22-)  A    High
  18 LYS   (  23-)  A    High
  19 VAL   (  24-)  A    High
  20 SER   (  25-)  A    High
 194 ASP   ( 199-)  A    High
 195 ILE   ( 200-)  A    High
 221 ARG   ( 226-)  A    High
 222 ARG   ( 227-)  A    High
 223 THR   ( 228-)  A    High
 337 TYR   ( 342-)  A    High
 338 ARG   ( 343-)  A    High
 340 GLN   ( 358-)  A    High
 733 GLY   ( 751-)  A    High
 734 SER   ( 752-)  A    High
 735 ARG   ( 753-)  A    High
 921 ALA   (  10-)  B    High
 922 SER   (  11-)  B    High
And so on for a total of 60 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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 6

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

Nomenclature related problems

Error: Chain names not unique

The chain names listed below are given for more than one protein/DNA molecule in the structure ('-' represents a chain without chain identifier).

Chain identifier(s): A, B

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

  44 HIS   (  49-)  A      CG   CD2   1.40    4.4
  66 HIS   (  71-)  A      CG   CD2   1.40    4.1
 167 HIS   ( 172-)  A      CG   CD2   1.43    7.0
 239 HIS   ( 244-)  A      CG   CD2   1.43    6.4
 243 TRP   ( 248-)  A      NE1  CE2   1.31   -5.0
 278 TRP   ( 283-)  A      NE1  CE2   1.32   -4.2
 367 HIS   ( 385-)  A      CG   CD2   1.41    4.9
 426 LEU   ( 444-)  A      N    CA    1.55    4.8
 457 TRP   ( 475-)  A      NE1  CE2   1.30   -6.4
 530 HIS   ( 548-)  A      CG   CD2   1.41    5.3
 533 HIS   ( 551-)  A      CG   CD2   1.41    4.7
 615 HIS   ( 633-)  A      CG   CD2   1.40    4.4
 641 HIS   ( 659-)  A      CG   CD2   1.44    7.4
 641 HIS   ( 659-)  A      ND1  CE1   1.38    5.0
 753 TRP   ( 775-)  A      NE1  CE2   1.31   -5.5
 772 HIS   ( 794-)  A      CG   CD2   1.40    4.1
 799 ASP   ( 821-)  A      CG   OD1   1.33    4.2
 867 ASP   ( 889-)  A      CG   OD1   1.33    4.0
 890 HIS   ( 912-)  A      CG   CD2   1.41    4.9
1083 HIS   ( 172-)  B      CG   CD2   1.41    4.5
1154 HIS   ( 244-)  B      CG   CD2   1.42    6.0
1288 HIS   ( 389-)  B      CG   CD2   1.40    4.1
1365 HIS   ( 466-)  B      CG   CD2   1.41    4.5
1382 TRP   ( 483-)  B      NE1  CE2   1.32   -4.1
1447 HIS   ( 548-)  B      CG   CD2   1.40    4.3
1450 HIS   ( 551-)  B      CG   CD2   1.41    4.6
1558 HIS   ( 659-)  B      CG   CD2   1.40    4.4
1806 HIS   ( 912-)  B      CG   CD2   1.40    4.1

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.

  44 HIS   (  49-)  A      CG   ND1  CE1 110.00    4.4
 113 ARG   ( 118-)  A      CG   CD   NE  120.35    5.8
 173 ARG   ( 178-)  A      CG   CD   NE  118.82    4.9
 297 VAL   ( 302-)  A      N    CA   CB  117.47    4.1
 426 LEU   ( 444-)  A     -O   -C    N   115.18   -4.9
 426 LEU   ( 444-)  A     -CA  -C    N   126.01    4.9
 426 LEU   ( 444-)  A     -C    N    CA  105.31   -9.1
 428 LYS   ( 446-)  A      CD   CE   NZ   98.80   -4.1
 437 ARG   ( 455-)  A      CG   CD   NE  102.93   -4.5
 437 ARG   ( 455-)  A      CD   NE   CZ  129.90    4.6
 438 HIS   ( 456-)  A      CG   ND1  CE1 110.11    4.5
 533 HIS   ( 551-)  A      CG   ND1  CE1 109.65    4.1
 566 ARG   ( 584-)  A      CG   CD   NE  100.56   -5.8
 567 ILE   ( 585-)  A      CA   CB   CG2 118.04    4.4
 661 HIS   ( 679-)  A      CG   ND1  CE1 109.88    4.3
 671 CYS   ( 689-)  A      CA   CB   SG  104.24   -4.4
 683 ILE   ( 701-)  A      C    CA   CB  118.62    4.5
 890 HIS   ( 912-)  A      CG   ND1  CE1 109.95    4.4
 938 ASP   (  27-)  B      C    CA   CB  101.28   -4.6
 960 HIS   (  49-)  B      CG   ND1  CE1 109.94    4.3
 982 HIS   (  71-)  B      CG   ND1  CE1 109.83    4.2
1029 ARG   ( 118-)  B      CG   CD   NE  119.07    5.0
1114 ASP   ( 203-)  B      N    CA   CB  117.82    4.3
1124 HIS   ( 213-)  B      CG   ND1  CE1 109.61    4.0
1189 GLN   ( 279-)  B      C    CA   CB  102.36   -4.1
1189 GLN   ( 279-)  B      CA   CB   CG  122.90    4.4
1288 HIS   ( 389-)  B      CG   ND1  CE1 109.78    4.2
1343 LEU   ( 444-)  B     -O   -C    N   114.99   -5.0
1343 LEU   ( 444-)  B     -CA  -C    N   125.55    4.7
1343 LEU   ( 444-)  B     -C    N    CA  107.14   -8.1
1365 HIS   ( 466-)  B      CG   ND1  CE1 109.61    4.0
1444 ARG   ( 545-)  B      CB   CG   CD  105.77   -4.2
1483 ARG   ( 584-)  B      CG   CD   NE  101.30   -5.4
1558 HIS   ( 659-)  B      CG   ND1  CE1 109.62    4.0
1570 ILE   ( 671-)  B      N    CA   CB  118.62    4.8
1570 ILE   ( 671-)  B      C    CA   CB  102.34   -4.1
1588 CYS   ( 689-)  B      CA   CB   SG  104.69   -4.2
1596 MET   ( 697-)  B      CG   SD   CE   89.62   -5.1
1806 HIS   ( 912-)  B      CG   ND1  CE1 109.70    4.1
1812 HIS   ( 918-)  B      CG   ND1  CE1 109.71    4.1
1836 ASP   (1967-)  A      C    CA   CB  101.82   -4.4

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.

1113 PRO   ( 202-)  B    4.73
 779 LYS   ( 801-)  A    4.28
 195 ILE   ( 200-)  A    4.22
 378 GLU   ( 396-)  A    4.17
 197 PRO   ( 202-)  A    4.15
 201 GLN   ( 206-)  A    4.14
 790 THR   ( 812-)  A    4.11

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.

1186 PRO   ( 276-)  B    -2.7
 271 PRO   ( 276-)  A    -2.7
 567 ILE   ( 585-)  A    -2.6
1484 ILE   ( 585-)  B    -2.6
 735 ARG   ( 753-)  A    -2.5
1652 ARG   ( 753-)  B    -2.5
 723 PRO   ( 741-)  A    -2.5
1640 PRO   ( 741-)  B    -2.4
 197 PRO   ( 202-)  A    -2.4
1298 VAL   ( 399-)  B    -2.3
1133 THR   ( 222-)  B    -2.3
 381 VAL   ( 399-)  A    -2.3
1649 ILE   ( 750-)  B    -2.2
 646 VAL   ( 664-)  A    -2.2
 732 ILE   ( 750-)  A    -2.2
1136 ILE   ( 225-)  B    -2.2
 576 GLY   ( 594-)  A    -2.1
1493 GLY   ( 594-)  B    -2.1
 506 GLY   ( 524-)  A    -2.1
1423 GLY   ( 524-)  B    -2.1
 373 ILE   ( 391-)  A    -2.1
 757 ARG   ( 779-)  A    -2.1
 221 ARG   ( 226-)  A    -2.1
 641 HIS   ( 659-)  A    -2.1
 283 ARG   ( 288-)  A    -2.1
  20 SER   (  25-)  A    -2.1
1113 PRO   ( 202-)  B    -2.0
 936 SER   (  25-)  B    -2.0
1198 ARG   ( 288-)  B    -2.0
 196 THR   ( 201-)  A    -2.0
 217 THR   ( 222-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

  66 HIS   (  71-)  A  Poor phi/psi
 145 ASN   ( 150-)  A  Poor phi/psi
 170 GLN   ( 175-)  A  Poor phi/psi
 195 ILE   ( 200-)  A  omega poor
 217 THR   ( 222-)  A  omega poor
 219 GLU   ( 224-)  A  omega poor
 321 SER   ( 326-)  A  omega poor
 371 HIS   ( 389-)  A  Poor phi/psi
 427 VAL   ( 445-)  A  omega poor
 429 LEU   ( 447-)  A  omega poor
 450 GLU   ( 468-)  A  Poor phi/psi
 473 LYS   ( 491-)  A  omega poor
 483 LYS   ( 501-)  A  omega poor
 504 CYS   ( 522-)  A  omega poor
 512 MET   ( 530-)  A  Poor phi/psi
 514 THR   ( 532-)  A  Poor phi/psi
 530 HIS   ( 548-)  A  Poor phi/psi
 626 GLY   ( 644-)  A  Poor phi/psi
 638 ASP   ( 656-)  A  Poor phi/psi
 721 ALA   ( 739-)  A  omega poor
 730 MET   ( 748-)  A  omega poor
 734 SER   ( 752-)  A  Poor phi/psi
 735 ARG   ( 753-)  A  PRO omega poor
 757 ARG   ( 779-)  A  Poor phi/psi
 759 HIS   ( 781-)  A  Poor phi/psi
And so on for a total of 61 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.

 588 SER   ( 606-)  A    0.35
1505 SER   ( 606-)  B    0.36
 398 SER   ( 416-)  A    0.37
1010 SER   (  99-)  B    0.38
1282 SER   ( 383-)  B    0.38
  94 SER   (  99-)  A    0.38
1784 SER   ( 890-)  B    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!

   3 LYS   (   8-)  A      0
  19 VAL   (  24-)  A      0
  20 SER   (  25-)  A      0
  23 ASP   (  28-)  A      0
  24 LYS   (  29-)  A      0
  44 HIS   (  49-)  A      0
  65 LYS   (  70-)  A      0
 116 LEU   ( 121-)  A      0
 117 LYS   ( 122-)  A      0
 120 ASP   ( 125-)  A      0
 125 ALA   ( 130-)  A      0
 126 ASN   ( 131-)  A      0
 169 THR   ( 174-)  A      0
 170 GLN   ( 175-)  A      0
 193 LYS   ( 198-)  A      0
 194 ASP   ( 199-)  A      0
 195 ILE   ( 200-)  A      0
 217 THR   ( 222-)  A      0
 218 ASP   ( 223-)  A      0
 219 GLU   ( 224-)  A      0
 221 ARG   ( 226-)  A      0
 222 ARG   ( 227-)  A      0
 237 TYR   ( 242-)  A      0
 241 THR   ( 246-)  A      0
 260 ILE   ( 265-)  A      0
And so on for a total of 433 lines.

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]

 224 PRO   ( 229-)  A    0.16 LOW
 247 PRO   ( 252-)  A    0.18 LOW
 482 PRO   ( 500-)  A    0.18 LOW
 501 PRO   ( 519-)  A    0.08 LOW
 636 PRO   ( 654-)  A    0.18 LOW
1162 PRO   ( 252-)  B    0.20 LOW
1399 PRO   ( 500-)  B    0.18 LOW
1418 PRO   ( 519-)  B    0.07 LOW
1553 PRO   ( 654-)  B    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].

  16 PRO   (  21-)  A   -61.5 half-chair C-beta/C-alpha (-54 degrees)
  83 PRO   (  88-)  A    48.9 half-chair C-delta/C-gamma (54 degrees)
 197 PRO   ( 202-)  A   131.4 half-chair C-beta/C-alpha (126 degrees)
 225 PRO   ( 230-)  A     3.9 envelop N (0 degrees)
 291 PRO   ( 296-)  A   110.1 envelop C-beta (108 degrees)
 377 PRO   ( 395-)  A   -58.6 half-chair C-beta/C-alpha (-54 degrees)
 391 PRO   ( 409-)  A  -114.6 envelop C-gamma (-108 degrees)
 637 PRO   ( 655-)  A   102.0 envelop C-beta (108 degrees)
 685 PRO   ( 703-)  A  -114.1 envelop C-gamma (-108 degrees)
 736 PRO   ( 754-)  A   -62.4 half-chair C-beta/C-alpha (-54 degrees)
 792 PRO   ( 814-)  A   103.1 envelop C-beta (108 degrees)
 857 PRO   ( 879-)  A  -124.8 half-chair C-delta/C-gamma (-126 degrees)
 895 PRO   ( 917-)  A  -118.3 half-chair C-delta/C-gamma (-126 degrees)
 932 PRO   (  21-)  B   -63.7 envelop C-beta (-72 degrees)
 999 PRO   (  88-)  B    48.9 half-chair C-delta/C-gamma (54 degrees)
1113 PRO   ( 202-)  B   133.3 half-chair C-beta/C-alpha (126 degrees)
1139 PRO   ( 229-)  B   130.0 half-chair C-beta/C-alpha (126 degrees)
1140 PRO   ( 230-)  B     2.5 envelop N (0 degrees)
1206 PRO   ( 296-)  B   110.6 envelop C-beta (108 degrees)
1294 PRO   ( 395-)  B   -61.4 half-chair C-beta/C-alpha (-54 degrees)
1308 PRO   ( 409-)  B  -114.3 envelop C-gamma (-108 degrees)
1602 PRO   ( 703-)  B  -116.5 envelop C-gamma (-108 degrees)
1653 PRO   ( 754-)  B   -63.0 envelop C-beta (-72 degrees)
1708 PRO   ( 814-)  B   105.4 envelop C-beta (108 degrees)
1773 PRO   ( 879-)  B  -119.1 half-chair C-delta/C-gamma (-126 degrees)
1811 PRO   ( 917-)  B  -113.8 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

1387 LEU   ( 488-)  B      O   <-> 1444 ARG   ( 545-)  B      NH2    0.59    2.11  INTRA BF
1183 TYR   ( 273-)  B      OH  <-> 1310 GLU   ( 411-)  B      OE2    0.50    1.90  INTRA BF
 173 ARG   ( 178-)  A      NH1 <-> 1843 SO4   (1969-)  A      O2     0.49    2.21  INTRA BF
 268 TYR   ( 273-)  A      OH  <->  393 GLU   ( 411-)  A      OE2    0.48    1.92  INTRA BF
 235 MET   ( 240-)  A      CE  <->  279 MET   ( 284-)  A      CE     0.48    2.72  INTRA BL
1199 ASP   ( 289-)  B      O   <-> 1661 ARG   ( 767-)  B      NH1    0.43    2.27  INTRA BF
 284 ASP   ( 289-)  A      O   <->  745 ARG   ( 767-)  A      NH1    0.42    2.28  INTRA BL
 283 ARG   ( 288-)  A      NH2 <->  294 THR   ( 299-)  A      OG1    0.37    2.33  INTRA BL
1198 ARG   ( 288-)  B      NH2 <-> 1209 THR   ( 299-)  B      OG1    0.34    2.36  INTRA BL
 221 ARG   ( 226-)  A      NH1 <->  223 THR   ( 228-)  A      OG1    0.34    2.36  INTRA BF
1089 ARG   ( 178-)  B      NH1 <-> 1846 SO4   (1969-)  B      O1     0.33    2.37  INTRA BF
 134 GLU   ( 139-)  A      OE2 <->  138 LYS   ( 143-)  A      NZ     0.30    2.40  INTRA BL
1768 LEU   ( 874-)  B      O   <-> 1776 LYS   ( 882-)  B      NZ     0.29    2.41  INTRA BL
 173 ARG   ( 178-)  A      NH1 <-> 1843 SO4   (1969-)  A      S      0.25    3.05  INTRA BF
1494 TYR   ( 595-)  B      OH  <-> 1532 HIS   ( 633-)  B      ND1    0.25    2.45  INTRA BL
 577 TYR   ( 595-)  A      OH  <->  615 HIS   ( 633-)  A      ND1    0.24    2.46  INTRA BL
  82 ASP   (  87-)  A      OD2 <->  896 HIS   ( 918-)  A      ND1    0.23    2.47  INTRA BF
1144 ASP   ( 234-)  B      OD1 <-> 1147 ARG   ( 237-)  B      NH2    0.23    2.47  INTRA BF
1089 ARG   ( 178-)  B      NH1 <-> 1846 SO4   (1969-)  B      S      0.23    3.07  INTRA BF
 229 ASP   ( 234-)  A      OD1 <->  232 ARG   ( 237-)  A      NH2    0.22    2.48  INTRA BF
1514 GLN   ( 615-)  B      NE2 <-> 1552 GLN   ( 653-)  B      NE2    0.22    2.63  INTRA BL
1512 LYS   ( 613-)  B      NZ  <-> 1611 ASP   ( 712-)  B      OD1    0.22    2.48  INTRA BL
1387 LEU   ( 488-)  B      C   <-> 1444 ARG   ( 545-)  B      NH2    0.22    2.88  INTRA BF
1254 THR   ( 344-)  B      O   <-> 1256 ARG   ( 346-)  B      N      0.21    2.49  INTRA BF
1253 ARG   ( 343-)  B      O   <-> 1255 ALA   ( 345-)  B      N      0.21    2.49  INTRA BF
And so on for a total of 164 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 222 ARG   ( 227-)  A      -7.37
 324 ARG   ( 329-)  A      -7.37
1239 ARG   ( 329-)  B      -7.18
1391 ARG   ( 492-)  B      -7.00
 473 LYS   ( 491-)  A      -6.67
1390 LYS   ( 491-)  B      -6.66
 474 ARG   ( 492-)  A      -6.65
1288 HIS   ( 389-)  B      -6.23
 532 LYS   ( 550-)  A      -6.15
 371 HIS   ( 389-)  A      -6.13
 850 ARG   ( 872-)  A      -6.06
1449 LYS   ( 550-)  B      -6.00
 116 LEU   ( 121-)  A      -5.91
1540 ARG   ( 641-)  B      -5.91
1766 ARG   ( 872-)  B      -5.87
 118 ARG   ( 123-)  A      -5.85
1032 LEU   ( 121-)  B      -5.83
1652 ARG   ( 753-)  B      -5.83
1034 ARG   ( 123-)  B      -5.77
 221 ARG   ( 226-)  A      -5.73
 338 ARG   ( 343-)  A      -5.72
1600 ILE   ( 701-)  B      -5.67
 683 ILE   ( 701-)  A      -5.57
 960 HIS   (  49-)  B      -5.53
 623 ARG   ( 641-)  A      -5.52
1136 ILE   ( 225-)  B      -5.44
 735 ARG   ( 753-)  A      -5.39
 885 ARG   ( 907-)  A      -5.34
1801 ARG   ( 907-)  B      -5.34
  44 HIS   (  49-)  A      -5.28
1194 MET   ( 284-)  B      -5.25
 279 MET   ( 284-)  A      -5.20
1450 HIS   ( 551-)  B      -5.18
 259 ASN   ( 264-)  A      -5.15
 533 HIS   ( 551-)  A      -5.15
1174 ASN   ( 264-)  B      -5.13
 499 GLU   ( 517-)  A      -5.07
 265 ARG   ( 270-)  A      -5.06
1416 GLU   ( 517-)  B      -5.06
1155 GLU   ( 245-)  B      -5.05
 890 HIS   ( 912-)  A      -5.04
 240 GLU   ( 245-)  A      -5.02
1806 HIS   ( 912-)  B      -5.02
 710 LYS   ( 728-)  A      -5.01

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.

 116 LEU   ( 121-)  A       118 - ARG    123- ( A)         -5.40
 220 ILE   ( 225-)  A       223 - THR    228- ( A)         -5.52
1032 LEU   ( 121-)  B      1034 - ARG    123- ( B)         -5.33

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: B

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

 640 ILE   ( 658-)  A   -2.92
1557 ILE   ( 658-)  B   -2.92

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

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.

1849 HOH   (2010 )  B      O

Error: HIS, ASN, GLN side chain flips

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

  95 HIS   ( 100-)  A
 107 GLN   ( 112-)  A
 239 HIS   ( 244-)  A
 312 GLN   ( 317-)  A
 597 GLN   ( 615-)  A
 680 ASN   ( 698-)  A
 759 HIS   ( 781-)  A
1011 HIS   ( 100-)  B
1023 GLN   ( 112-)  B
1154 HIS   ( 244-)  B
1257 GLN   ( 358-)  B
1514 GLN   ( 615-)  B

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

   4 LEU   (   9-)  A      N
  80 SER   (  85-)  A      N
  82 ASP   (  87-)  A      N
 128 THR   ( 133-)  A      OG1
 134 GLU   ( 139-)  A      N
 145 ASN   ( 150-)  A      N
 149 GLU   ( 154-)  A      N
 158 GLN   ( 163-)  A      NE2
 173 ARG   ( 178-)  A      NH1
 175 SER   ( 180-)  A      N
 182 ARG   ( 187-)  A      NE
 184 ARG   ( 189-)  A      NH1
 193 LYS   ( 198-)  A      N
 194 ASP   ( 199-)  A      N
 195 ILE   ( 200-)  A      N
 196 THR   ( 201-)  A      N
 220 ILE   ( 225-)  A      N
 223 THR   ( 228-)  A      N
 237 TYR   ( 242-)  A      N
 264 GLU   ( 269-)  A      N
 283 ARG   ( 288-)  A      NH1
 283 ARG   ( 288-)  A      NH2
 288 ARG   ( 293-)  A      NE
 322 MET   ( 327-)  A      N
 323 TRP   ( 328-)  A      N
And so on for a total of 119 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.

  29 ASP   (  34-)  A      OD1
 101 ASN   ( 106-)  A      OD1
 523 GLU   ( 541-)  A      OE2
 629 HIS   ( 647-)  A      NE2
 724 GLU   ( 742-)  A      OE1
1017 ASN   ( 106-)  B      OD1
1114 ASP   ( 203-)  B      OD1
1440 GLU   ( 541-)  B      OE2
1546 HIS   ( 647-)  B      NE2

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.

  42 ASP   (  47-)  A   H-bonding suggests Asn
 503 ASP   ( 521-)  A   H-bonding suggests Asn
 824 ASP   ( 846-)  A   H-bonding suggests Asn; but Alt-Rotamer
 841 ASP   ( 863-)  A   H-bonding suggests Asn
 958 ASP   (  47-)  B   H-bonding suggests Asn
1420 ASP   ( 521-)  B   H-bonding suggests Asn
1740 ASP   ( 846-)  B   H-bonding suggests Asn; but Alt-Rotamer
1757 ASP   ( 863-)  B   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.302
  2nd generation packing quality :  -0.490
  Ramachandran plot appearance   :  -0.238
  chi-1/chi-2 rotamer normality  :  -2.098
  Backbone conformation          :   0.624

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.808
  Bond angles                    :   0.892
  Omega angle restraints         :   1.077
  Side chain planarity           :   0.839
  Improper dihedral distribution :   0.938
  B-factor distribution          :   0.446
  Inside/Outside distribution    :   1.007

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 : 2.71


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.6
  2nd generation packing quality :   1.0
  Ramachandran plot appearance   :   2.1
  chi-1/chi-2 rotamer normality  :   0.2
  Backbone conformation          :   1.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.808
  Bond angles                    :   0.892
  Omega angle restraints         :   1.077
  Side chain planarity           :   0.839
  Improper dihedral distribution :   0.938
  B-factor distribution          :   0.446
  Inside/Outside distribution    :   1.007
==============

WHAT IF
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      WHAT IF: a molecular modelling and drug design program,
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WHAT_CHECK (verification routines from WHAT IF)
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      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.