WHAT IF Check report

This file was created 2011-12-16 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 pdb3i12.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    =  85.153  B   =  85.813  C    = 230.893
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    =  85.153  B   =  85.813  C    = 230.893
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    =  85.813  B   =  85.153  C    = 230.893
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

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

Crystal class of the cell: ORTHORHOMBIC

Crystal class of the conventional CELL: TETRAGONAL

Space group name: P 21 21 21

Bravais type of conventional cell is: P

Warning: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

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.

1410 ADP   ( 365-)  A  -
1411 ADP   ( 365-)  B  -
1412 ADP   ( 365-)  C  -
1413 ADP   ( 365-)  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: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

  71 SER   (  72-)  A      OG

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: 4

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: Tyrosine convention problem

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

  56 TYR   (  57-)  A
 287 TYR   ( 290-)  A
 325 TYR   ( 328-)  A
 417 TYR   (  57-)  B
 671 TYR   ( 328-)  B
 762 TYR   (  57-)  C
 980 TYR   ( 290-)  C
1109 TYR   (  57-)  D
1306 TYR   ( 260-)  D
1374 TYR   ( 328-)  D

Warning: Phenylalanine convention problem

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

   9 PHE   (  10-)  A
 102 PHE   ( 103-)  A
 157 PHE   ( 158-)  A
 182 PHE   ( 183-)  A
 211 PHE   ( 212-)  A
 319 PHE   ( 322-)  A
 370 PHE   (  10-)  B
 463 PHE   ( 103-)  B
 518 PHE   ( 158-)  B
 529 PHE   ( 169-)  B
 543 PHE   ( 183-)  B
 572 PHE   ( 212-)  B
 715 PHE   (  10-)  C
 808 PHE   ( 103-)  C
 863 PHE   ( 158-)  C
 888 PHE   ( 183-)  C
 917 PHE   ( 212-)  C
1012 PHE   ( 322-)  C
1062 PHE   (  10-)  D
1155 PHE   ( 103-)  D
1210 PHE   ( 158-)  D
1235 PHE   ( 183-)  D
1264 PHE   ( 212-)  D
1305 PHE   ( 253-)  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.

  28 ASP   (  29-)  A
  61 ASP   (  62-)  A
 130 ASP   ( 131-)  A
 404 ASP   (  44-)  B
 491 ASP   ( 131-)  B
 767 ASP   (  62-)  C
 836 ASP   ( 131-)  C
 855 ASP   ( 150-)  C
1096 ASP   (  44-)  D
1183 ASP   ( 131-)  D
1354 ASP   ( 308-)  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.

 172 GLU   ( 173-)  A
 200 GLU   ( 201-)  A
 220 GLU   ( 221-)  A
 227 GLU   ( 228-)  A
 229 GLU   ( 230-)  A
 533 GLU   ( 173-)  B
 535 GLU   ( 175-)  B
 561 GLU   ( 201-)  B
 588 GLU   ( 228-)  B
 620 GLU   ( 277-)  B
 658 GLU   ( 315-)  B
 695 GLU   ( 352-)  B
 878 GLU   ( 173-)  C
 880 GLU   ( 175-)  C
 918 GLU   ( 213-)  C
 933 GLU   ( 228-)  C
 935 GLU   ( 230-)  C
 967 GLU   ( 277-)  C
1225 GLU   ( 173-)  D
1227 GLU   ( 175-)  D
1265 GLU   ( 213-)  D
1361 GLU   ( 315-)  D
1394 GLU   ( 348-)  D
1398 GLU   ( 352-)  D

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.

  25 ASN   (  26-)  A      CB   CG    1.62    4.2
  42 ILE   (  43-)  A      CG1  CD1   1.34   -4.3
  43 ASP   (  44-)  A      CB   CG    1.36   -6.2
 554 GLY   ( 194-)  B      N    CA    1.53    4.7
 581 GLU   ( 221-)  B      CB   CG    1.39   -4.4
 691 GLU   ( 348-)  B      CB   CG    1.37   -4.9
 749 ASP   (  44-)  C      CB   CG    1.32   -7.9
 753 GLN   (  48-)  C      CG   CD    1.41   -4.1
1180 VAL   ( 128-)  D      CA   CB    1.61    4.1
1206 ASN   ( 154-)  D      CB   CG    1.41   -4.4

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.

  40 LEU   (  41-)  A      CB   CG   CD1 123.14    4.1
  43 ASP   (  44-)  A      C    CA   CB   93.38   -8.8
  84 HIS   (  85-)  A      CG   ND1  CE1 109.73    4.1
 109 LEU   ( 110-)  A     -O   -C    N   116.18   -4.3
 109 LEU   ( 110-)  A     -CA  -C    N   125.08    4.4
 109 LEU   ( 110-)  A     -C    N    CA  108.10   -7.6
 154 ILE   ( 155-)  A      CA   CB   CG2 118.82    4.9
 165 ARG   ( 166-)  A      CB   CG   CD  102.34   -5.9
 165 ARG   ( 166-)  A      CG   CD   NE  120.06    5.6
 312 GLU   ( 315-)  A      CA   CB   CG  122.72    4.3
 324 MET   ( 327-)  A      CG   SD   CE   91.41   -4.3
 350 ARG   ( 353-)  A      CG   CD   NE   94.99   -9.1
 399 VAL   (  39-)  B      C    CA   CB  117.87    4.1
 411 VAL   (  51-)  B      N    CA   CB  117.69    4.2
 411 VAL   (  51-)  B      C    CA   CB  100.79   -4.9
 461 VAL   ( 101-)  B      C    CA   CB   98.62   -6.0
 467 HIS   ( 107-)  B      CG   ND1  CE1 109.61    4.0
 470 LEU   ( 110-)  B     -C    N    CA  111.86   -5.5
 499 MET   ( 139-)  B      CA   CB   CG  122.66    4.3
 499 MET   ( 139-)  B      CG   SD   CE   84.41   -7.5
 520 THR   ( 160-)  B      C    CA   CB  118.21    4.3
 523 ARG   ( 163-)  B      CD   NE   CZ  129.54    4.4
 527 HIS   ( 167-)  B      CG   ND1  CE1 109.71    4.1
 537 ARG   ( 177-)  B      CB   CG   CD  105.76   -4.2
 551 SER   ( 191-)  B      N    CA   C   122.74    4.1
 581 GLU   ( 221-)  B      C    CA   CB  100.28   -5.2
 598 ASN   ( 238-)  B     -C    N    CA  114.21   -4.2
 636 LEU   ( 293-)  B      CA   CB   CG  100.77   -4.4
 658 GLU   ( 315-)  B      CA   CB   CG  122.50    4.2
 722 HIS   (  17-)  C      CG   ND1  CE1 109.86    4.3
 749 ASP   (  44-)  C      C    CA   CB   98.95   -5.9
 749 ASP   (  44-)  C      CA   CB   CG  108.39   -4.2
 749 ASP   (  44-)  C      CB   CG   OD1 102.06   -7.1
 759 ALA   (  54-)  C      N    CA   C   132.42    7.6
 760 GLU   (  55-)  C      N    CA   CB   84.81  -15.1
 770 ALA   (  65-)  C      N    CA   C    99.52   -4.2
 806 VAL   ( 101-)  C      C    CA   CB   99.39   -5.6
 810 ILE   ( 105-)  C      C    CA   CB  118.40    4.4
 860 ILE   ( 155-)  C      C    CA   CB  118.24    4.3
 860 ILE   ( 155-)  C      CA   CB   CG2 118.23    4.5
 932 ARG   ( 227-)  C      CG   CD   NE  117.90    4.4
1043 ARG   ( 353-)  C      CG   CD   NE  102.11   -4.9
1153 VAL   ( 101-)  D      C    CA   CB   98.75   -6.0
1162 LEU   ( 110-)  D     -C    N    CA  111.45   -5.7
1180 VAL   ( 128-)  D      CA   CB   CG1 117.66    4.2
1290 ASN   ( 238-)  D     -C    N    CA  114.50   -4.0
1311 GLY   ( 265-)  D     -C    N    CA  127.44    4.0
1344 MET   ( 298-)  D      CG   SD   CE   84.96   -7.2
1371 ILE   ( 325-)  D      N    CA   CB  103.35   -4.2

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  28 ASP   (  29-)  A
  61 ASP   (  62-)  A
 130 ASP   ( 131-)  A
 172 GLU   ( 173-)  A
 200 GLU   ( 201-)  A
 220 GLU   ( 221-)  A
 227 GLU   ( 228-)  A
 229 GLU   ( 230-)  A
 404 ASP   (  44-)  B
 491 ASP   ( 131-)  B
 533 GLU   ( 173-)  B
 535 GLU   ( 175-)  B
 561 GLU   ( 201-)  B
 588 GLU   ( 228-)  B
 620 GLU   ( 277-)  B
 658 GLU   ( 315-)  B
 695 GLU   ( 352-)  B
 767 ASP   (  62-)  C
 836 ASP   ( 131-)  C
 855 ASP   ( 150-)  C
 878 GLU   ( 173-)  C
 880 GLU   ( 175-)  C
 918 GLU   ( 213-)  C
 933 GLU   ( 228-)  C
 935 GLU   ( 230-)  C
 967 GLU   ( 277-)  C
1096 ASP   (  44-)  D
1183 ASP   ( 131-)  D
1225 GLU   ( 173-)  D
1227 GLU   ( 175-)  D
1265 GLU   ( 213-)  D
1354 ASP   ( 308-)  D
1361 GLU   ( 315-)  D
1394 GLU   ( 348-)  D
1398 GLU   ( 352-)  D

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.

  43 ASP   (  44-)  A      CA     7.3    48.25    33.73
  43 ASP   (  44-)  A      C      6.9    10.66    -0.01
 488 VAL   ( 128-)  B      CA    -6.3    24.14    33.23
 488 VAL   ( 128-)  B      CB    10.1   -19.73   -32.96
 503 VAL   ( 143-)  B      CA    -7.8    21.93    33.23
 503 VAL   ( 143-)  B      CB     8.2   -22.24   -32.96
 520 THR   ( 160-)  B      CA    -6.1    23.72    33.84
 759 ALA   (  54-)  C      CA    -9.3    22.27    34.09
 760 GLU   (  55-)  C      CA    10.5    51.20    33.96
1180 VAL   ( 128-)  D      CB     9.8   -20.17   -32.96
1195 VAL   ( 143-)  D      CA    -6.7    23.47    33.23
1195 VAL   ( 143-)  D      CB     6.4   -24.57   -32.96
The average deviation= 1.342

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.

 759 ALA   (  54-)  C    8.72
1311 GLY   ( 265-)  D    5.75
1310 ASN   ( 264-)  D    5.42
  29 ALA   (  30-)  A    5.11
 770 ALA   (  65-)  C    4.93
 390 ALA   (  30-)  B    4.48
 276 ASN   ( 279-)  A    4.47
 551 SER   ( 191-)  B    4.25
 503 VAL   ( 143-)  B    4.02

Error: Side chain planarity problems

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

1363 ASN   ( 317-)  D    6.25
 631 GLN   ( 288-)  B    4.50
 622 ASN   ( 279-)  B    4.41

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.

1118 HIS   (  66-)  D    -3.0
1157 ILE   ( 105-)  D    -2.8
 104 ILE   ( 105-)  A    -2.8
 810 ILE   ( 105-)  C    -2.7
 814 THR   ( 109-)  C    -2.7
 551 SER   ( 191-)  B    -2.7
1365 LEU   ( 319-)  D    -2.6
 465 ILE   ( 105-)  B    -2.6
 860 ILE   ( 155-)  C    -2.6
 190 SER   ( 191-)  A    -2.6
 154 ILE   ( 155-)  A    -2.6
1371 ILE   ( 325-)  D    -2.5
 668 ILE   ( 325-)  B    -2.5
 662 LEU   ( 319-)  B    -2.5
 864 ILE   ( 159-)  C    -2.5
1211 ILE   ( 159-)  D    -2.4
 952 ILE   ( 247-)  C    -2.3
  40 LEU   (  41-)  A    -2.3
 552 SER   ( 192-)  B    -2.3
 515 ILE   ( 155-)  B    -2.3
1153 VAL   ( 101-)  D    -2.3
 196 LYS   ( 197-)  A    -2.3
1136 GLN   (  84-)  D    -2.2
1093 LEU   (  41-)  D    -2.2
1015 ILE   ( 325-)  C    -2.2
 461 VAL   ( 101-)  B    -2.2
 100 VAL   ( 101-)  A    -2.2
 806 VAL   ( 101-)  C    -2.2
 426 HIS   (  66-)  B    -2.2
 896 SER   ( 191-)  C    -2.2
 158 ILE   ( 159-)  A    -2.2
 719 SER   (  14-)  C    -2.2
 746 LEU   (  41-)  C    -2.2
 549 GLN   ( 189-)  B    -2.1
 983 LEU   ( 293-)  C    -2.1
 290 LEU   ( 293-)  A    -2.1
 636 LEU   ( 293-)  B    -2.1
 897 SER   ( 192-)  C    -2.1
 322 ILE   ( 325-)  A    -2.1
 617 ILE   ( 274-)  B    -2.1
1108 ASN   (  56-)  D    -2.1
1012 PHE   ( 322-)  C    -2.1
  63 PRO   (  64-)  A    -2.1
 894 GLN   ( 189-)  C    -2.0
1277 LYS   ( 225-)  D    -2.0
 102 PHE   ( 103-)  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.

  35 PHE   (  36-)  A  omega poor
  56 TYR   (  57-)  A  Poor phi/psi
  61 ASP   (  62-)  A  omega poor
  65 HIS   (  66-)  A  Poor phi/psi
  73 ILE   (  74-)  A  omega poor
  80 GLY   (  81-)  A  Poor phi/psi
 107 GLY   ( 108-)  A  omega poor
 130 ASP   ( 131-)  A  Poor phi/psi
 176 ARG   ( 177-)  A  omega poor
 179 LEU   ( 180-)  A  PRO omega poor
 181 LEU   ( 182-)  A  omega poor
 188 GLN   ( 189-)  A  Poor phi/psi, omega poor
 190 SER   ( 191-)  A  Poor phi/psi
 191 SER   ( 192-)  A  Poor phi/psi
 235 ASN   ( 236-)  A  Poor phi/psi
 241 SER   ( 242-)  A  omega poor
 260 ASP   ( 263-)  A  Poor phi/psi
 267 VAL   ( 270-)  A  PRO omega poor
 306 ASN   ( 309-)  A  Poor phi/psi
 362 ALA   (   2-)  B  Poor phi/psi
 410 HIS   (  50-)  B  omega poor
 424 PRO   (  64-)  B  omega poor
 426 HIS   (  66-)  B  Poor phi/psi
 434 ILE   (  74-)  B  omega poor
 455 PRO   (  95-)  B  omega poor
And so on for a total of 83 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.

  22 SER   (  23-)  A    0.34
 725 SER   (  20-)  C    0.35
 134 SER   ( 135-)  A    0.35
1390 SER   ( 344-)  D    0.36
 175 SER   ( 176-)  A    0.36
 536 SER   ( 176-)  B    0.36
1075 SER   (  23-)  D    0.37
1228 SER   ( 176-)  D    0.37
1186 SER   ( 134-)  D    0.38
 133 SER   ( 134-)  A    0.38
 494 SER   ( 134-)  B    0.39
 840 SER   ( 135-)  C    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!

   9 PHE   (  10-)  A      0
  12 LYS   (  13-)  A      0
  34 ARG   (  35-)  A      0
  43 ASP   (  44-)  A      0
  48 TRP   (  49-)  A      0
  55 ASN   (  56-)  A      0
  56 TYR   (  57-)  A      0
  60 ALA   (  61-)  A      0
  66 ILE   (  67-)  A      0
  72 ALA   (  73-)  A      0
  79 PRO   (  80-)  A      0
  81 LYS   (  82-)  A      0
  83 GLN   (  84-)  A      0
  84 HIS   (  85-)  A      0
  85 GLN   (  86-)  A      0
  88 ASN   (  89-)  A      0
  91 ASN   (  92-)  A      0
  97 THR   (  98-)  A      0
 103 PRO   ( 104-)  A      0
 104 ILE   ( 105-)  A      0
 106 HIS   ( 107-)  A      0
 108 THR   ( 109-)  A      0
 109 LEU   ( 110-)  A      0
 111 GLU   ( 112-)  A      0
 112 ASP   ( 113-)  A      0
And so on for a total of 474 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]

 185 PRO   ( 186-)  A    0.13 LOW
 272 PRO   ( 275-)  A    0.10 LOW
 326 PRO   ( 329-)  A    0.02 LOW
 785 PRO   (  80-)  C    0.19 LOW
 891 PRO   ( 186-)  C    0.18 LOW
1156 PRO   ( 104-)  D    0.19 LOW
1238 PRO   ( 186-)  D    0.15 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].

  63 PRO   (  64-)  A   143.2 envelop C-alpha (144 degrees)
  70 PRO   (  71-)  A  -114.5 envelop C-gamma (-108 degrees)
 156 PRO   ( 157-)  A   111.8 envelop C-beta (108 degrees)
 180 PRO   ( 181-)  A   -45.6 half-chair C-beta/C-alpha (-54 degrees)
 424 PRO   (  64-)  B   106.8 envelop C-beta (108 degrees)
 455 PRO   (  95-)  B   -59.8 half-chair C-beta/C-alpha (-54 degrees)
 546 PRO   ( 186-)  B    37.1 envelop C-delta (36 degrees)
 769 PRO   (  64-)  C    19.1 half-chair N/C-delta (18 degrees)
 809 PRO   ( 104-)  C   -49.6 half-chair C-beta/C-alpha (-54 degrees)
1116 PRO   (  64-)  D  -124.6 half-chair C-delta/C-gamma (-126 degrees)
1123 PRO   (  71-)  D  -119.1 half-chair C-delta/C-gamma (-126 degrees)
1375 PRO   ( 329-)  D  -112.0 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 295 MET   ( 298-)  A      CE  <->  325 TYR   ( 328-)  A      CE1    0.86    2.34  INTRA BL
  56 TYR   (  57-)  A      CE2 <->   57 LEU   (  58-)  A      CD1    0.83    2.37  INTRA BF
  56 TYR   (  57-)  A      CE2 <->   57 LEU   (  58-)  A      CG     0.80    2.40  INTRA BF
  56 TYR   (  57-)  A      CZ  <->   57 LEU   (  58-)  A      CD1    0.61    2.59  INTRA BF
 963 GLN   ( 273-)  C      NE2 <-> 1416 HOH   ( 381 )  C      O      0.61    2.09  INTRA BF
  58 GLN   (  59-)  A      NE2 <->   69 ARG   (  70-)  A      CD     0.54    2.56  INTRA BF
  56 TYR   (  57-)  A      CD2 <->   57 LEU   (  58-)  A      CG     0.50    2.70  INTRA BF
 121 VAL   ( 122-)  A      CG2 <->  479 MET   ( 119-)  B      CE     0.49    2.71  INTRA
 295 MET   ( 298-)  A      CE  <->  325 TYR   ( 328-)  A      CZ     0.49    2.71  INTRA BL
 761 ASN   (  56-)  C      C   <->  775 ARG   (  70-)  C      NH1    0.45    2.65  INTRA BF
 896 SER   ( 191-)  C      O   <->  898 VAL   ( 193-)  C      N      0.44    2.26  INTRA BF
 868 ARG   ( 163-)  C      CD  <-> 1416 HOH   ( 407 )  C      O      0.40    2.40  INTRA BF
 360 THR   ( 363-)  A      C   <-> 1414 HOH   ( 454 )  A      O      0.39    2.41  INTRA BF
 552 SER   ( 192-)  B      N   <-> 1411 ADP   ( 365-)  B      O2B    0.38    2.32  INTRA BF
 765 ASN   (  60-)  C      ND2 <->  771 HIS   (  66-)  C      O      0.38    2.32  INTRA BF
1361 GLU   ( 315-)  D      OE2 <-> 1413 ADP   ( 365-)  D      O1A    0.38    2.02  INTRA BL
 307 GLU   ( 310-)  A      CG  <-> 1414 HOH   ( 431 )  A      O      0.36    2.44  INTRA BF
1173 ARG   ( 121-)  D      NH2 <-> 1183 ASP   ( 131-)  D      OD1    0.35    2.35  INTRA BF
 162 ARG   ( 163-)  A      NH1 <->  215 HIS   ( 216-)  A      CD2    0.35    2.75  INTRA BF
 755 HIS   (  50-)  C      CD2 <-> 1416 HOH   ( 380 )  C      O      0.34    2.46  INTRA BL
 130 ASP   ( 131-)  A      OD2 <->  350 ARG   ( 353-)  A      NH2    0.34    2.36  INTRA BL
 641 MET   ( 298-)  B      CE  <->  663 PRO   ( 320-)  B      CG     0.32    2.88  INTRA BL
 988 MET   ( 298-)  C      CE  <-> 1018 TYR   ( 328-)  C      CE2    0.32    2.88  INTRA BL
 223 ILE   ( 224-)  A      N   <-> 1410 ADP   ( 365-)  A      N1     0.32    2.68  INTRA
 958 VAL   ( 268-)  C      CG1 <-> 1017 MET   ( 327-)  C      CE     0.31    2.89  INTRA BF
And so on for a total of 230 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.

1319 GLN   ( 273-)  D      -6.72
  69 ARG   (  70-)  A      -6.71
 270 GLN   ( 273-)  A      -6.52
 963 GLN   ( 273-)  C      -6.48
 894 GLN   ( 189-)  C      -6.13
 718 LYS   (  13-)  C      -5.90
 451 GLN   (  91-)  B      -5.83
 585 LYS   ( 225-)  B      -5.81
  90 GLN   (  91-)  A      -5.78
1135 HIS   (  83-)  D      -5.74
 616 GLN   ( 273-)  B      -5.71
1277 LYS   ( 225-)  D      -5.71
 188 GLN   ( 189-)  A      -5.71
1143 GLN   (  91-)  D      -5.67
 788 HIS   (  83-)  C      -5.67
 882 ARG   ( 177-)  C      -5.66
 224 LYS   ( 225-)  A      -5.66
  82 HIS   (  83-)  A      -5.65
1009 LEU   ( 319-)  C      -5.64
 930 LYS   ( 225-)  C      -5.62
1229 ARG   ( 177-)  D      -5.60
 537 ARG   ( 177-)  B      -5.60
 443 HIS   (  83-)  B      -5.58
 176 ARG   ( 177-)  A      -5.54
 373 LYS   (  13-)  B      -5.42
1241 GLN   ( 189-)  D      -5.24
1310 ASN   ( 264-)  D      -5.23
 162 ARG   ( 163-)  A      -5.13

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.

 260 ASP   ( 263-)  A       262 - GLY    265- ( A)         -4.40
1309 ASP   ( 263-)  D      1311 - GLY    265- ( D)         -4.55

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.

 721 GLU   (  16-)  C   -2.63

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

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.

1414 HOH   ( 442 )  A      O
1415 HOH   ( 414 )  B      O
1416 HOH   ( 400 )  C      O
1416 HOH   ( 423 )  C      O
1417 HOH   ( 387 )  D      O
1417 HOH   ( 419 )  D      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.

  25 ASN   (  26-)  A
  55 ASN   (  56-)  A
 106 HIS   ( 107-)  A
 153 ASN   ( 154-)  A
 164 ASN   ( 165-)  A
 187 ASN   ( 188-)  A
 188 GLN   ( 189-)  A
 215 HIS   ( 216-)  A
 239 GLN   ( 240-)  A
 270 GLN   ( 273-)  A
 382 GLN   (  22-)  B
 412 ASN   (  52-)  B
 438 GLN   (  78-)  B
 451 GLN   (  91-)  B
 454 GLN   (  94-)  B
 467 HIS   ( 107-)  B
 484 ASN   ( 124-)  B
 548 ASN   ( 188-)  B
 549 GLN   ( 189-)  B
 576 HIS   ( 216-)  B
 582 GLN   ( 222-)  B
 596 ASN   ( 236-)  B
 622 ASN   ( 279-)  B
 731 ASN   (  26-)  C
 753 GLN   (  48-)  C
 755 HIS   (  50-)  C
 757 ASN   (  52-)  C
 788 HIS   (  83-)  C
 799 GLN   (  94-)  C
 859 ASN   ( 154-)  C
 870 ASN   ( 165-)  C
 893 ASN   ( 188-)  C
 894 GLN   ( 189-)  C
 921 HIS   ( 216-)  C
 945 GLN   ( 240-)  C
 981 GLN   ( 291-)  C
1078 ASN   (  26-)  D
1100 GLN   (  48-)  D
1130 GLN   (  78-)  D
1143 GLN   (  91-)  D
1159 HIS   ( 107-)  D
1240 ASN   ( 188-)  D
1268 HIS   ( 216-)  D
1274 GLN   ( 222-)  D
1288 ASN   ( 236-)  D
1319 GLN   ( 273-)  D
1325 ASN   ( 279-)  D
1370 ASN   ( 324-)  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.

  47 GLN   (  48-)  A      N
  50 VAL   (  51-)  A      N
  51 ASN   (  52-)  A      ND2
  54 GLU   (  55-)  A      N
  56 TYR   (  57-)  A      N
  59 ASN   (  60-)  A      N
  67 ALA   (  68-)  A      N
  77 GLN   (  78-)  A      NE2
  97 THR   (  98-)  A      OG1
 105 VAL   ( 106-)  A      N
 112 ASP   ( 113-)  A      N
 155 ALA   ( 156-)  A      N
 188 GLN   ( 189-)  A      N
 191 SER   ( 192-)  A      N
 216 LYS   ( 217-)  A      N
 223 ILE   ( 224-)  A      N
 248 LEU   ( 249-)  A      N
 252 PHE   ( 253-)  A      N
 257 TYR   ( 260-)  A      N
 264 GLN   ( 267-)  A      NE2
 275 VAL   ( 278-)  A      N
 411 VAL   (  51-)  B      N
 422 ASP   (  62-)  B      N
 430 ARG   (  70-)  B      NH1
 438 GLN   (  78-)  B      NE2
And so on for a total of 71 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.

  16 HIS   (  17-)  A      ND1
  77 GLN   (  78-)  A      OE1
 229 GLU   ( 230-)  A      OE1
 438 GLN   (  78-)  B      OE1
 783 GLN   (  78-)  C      OE1
 788 HIS   (  83-)  C      ND1
1005 GLU   ( 315-)  C      OE2
1282 GLU   ( 230-)  D      OE1

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.

  28 ASP   (  29-)  A   H-bonding suggests Asn
 112 ASP   ( 113-)  A   H-bonding suggests Asn; but Alt-Rotamer
 312 GLU   ( 315-)  A   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
 389 ASP   (  29-)  B   H-bonding suggests Asn
 423 ASP   (  63-)  B   H-bonding suggests Asn
 658 GLU   ( 315-)  B   H-bonding suggests Gln; Ligand-contact
 734 ASP   (  29-)  C   H-bonding suggests Asn
 768 ASP   (  63-)  C   H-bonding suggests Asn; but Alt-Rotamer
1005 GLU   ( 315-)  C   H-bonding suggests Gln; Ligand-contact
1115 ASP   (  63-)  D   H-bonding suggests Asn
1165 ASP   ( 113-)  D   H-bonding suggests Asn; but Alt-Rotamer
1225 GLU   ( 173-)  D   H-bonding suggests Gln; 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 :   0.780
  2nd generation packing quality :  -0.400
  Ramachandran plot appearance   :  -0.076
  chi-1/chi-2 rotamer normality  :  -2.533
  Backbone conformation          :   0.967

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.900
  Bond angles                    :   0.958
  Omega angle restraints         :   1.191
  Side chain planarity           :   1.100
  Improper dihedral distribution :   1.182
  B-factor distribution          :   0.513
  Inside/Outside distribution    :   0.968

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 : 2.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.3
  2nd generation packing quality :   0.0
  Ramachandran plot appearance   :   1.0
  chi-1/chi-2 rotamer normality  :  -1.1
  Backbone conformation          :   0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.900
  Bond angles                    :   0.958
  Omega angle restraints         :   1.191
  Side chain planarity           :   1.100
  Improper dihedral distribution :   1.182
  B-factor distribution          :   0.513
  Inside/Outside distribution    :   0.968
==============

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.