WHAT IF Check report

This file was created 2011-12-13 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 pdb1bxn.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.

2297 PO4   ( 501-)  A  -
2298 PO4   ( 502-)  A  -
2299 PO4   ( 503-)  C  -
2300 PO4   ( 504-)  C  -
2301 PO4   ( 505-)  E  -
2302 PO4   ( 506-)  E  -
2303 PO4   ( 507-)  G  -
2304 PO4   ( 508-)  G  -

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: I

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: L

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

Warning: What type of B-factor?

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

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

Crystal temperature (K) :100.000

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 : 12.96

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: I

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: L

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

   1 TYR   (  22-)  A
  61 TYR   (  83-)  A
  84 TYR   ( 106-)  A
 166 TYR   ( 188-)  A
 232 TYR   ( 254-)  A
 333 TYR   ( 355-)  A
 482 TYR   (  37-)  I
 575 TYR   (  22-)  C
 635 TYR   (  83-)  C
 658 TYR   ( 106-)  C
 740 TYR   ( 188-)  C
 806 TYR   ( 254-)  C
 907 TYR   ( 355-)  C
1056 TYR   (  37-)  J
1142 TYR   ( 123-)  J
1149 TYR   (  22-)  E
1209 TYR   (  83-)  E
1232 TYR   ( 106-)  E
1314 TYR   ( 188-)  E
1380 TYR   ( 254-)  E
1481 TYR   ( 355-)  E
1630 TYR   (  37-)  K
1716 TYR   ( 123-)  K
1723 TYR   (  22-)  G
1783 TYR   (  83-)  G
1806 TYR   ( 106-)  G
1888 TYR   ( 188-)  G
1954 TYR   ( 254-)  G
2055 TYR   ( 355-)  G
2204 TYR   (  37-)  L
2290 TYR   ( 123-)  L

Warning: Phenylalanine convention problem

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

  21 PHE   (  43-)  A
  78 PHE   ( 100-)  A
  79 PHE   ( 101-)  A
  89 PHE   ( 111-)  A
 121 PHE   ( 143-)  A
 146 PHE   ( 168-)  A
 374 PHE   ( 396-)  A
 453 PHE   (   8-)  I
 520 PHE   (  75-)  I
 543 PHE   (  98-)  I
 595 PHE   (  43-)  C
 652 PHE   ( 100-)  C
 653 PHE   ( 101-)  C
 663 PHE   ( 111-)  C
 695 PHE   ( 143-)  C
 720 PHE   ( 168-)  C
 948 PHE   ( 396-)  C
1027 PHE   (   8-)  J
1094 PHE   (  75-)  J
1117 PHE   (  98-)  J
1169 PHE   (  43-)  E
1226 PHE   ( 100-)  E
1227 PHE   ( 101-)  E
1237 PHE   ( 111-)  E
1269 PHE   ( 143-)  E
1294 PHE   ( 168-)  E
1522 PHE   ( 396-)  E
1601 PHE   (   8-)  K
1668 PHE   (  75-)  K
1691 PHE   (  98-)  K
1743 PHE   (  43-)  G
1800 PHE   ( 100-)  G
1801 PHE   ( 101-)  G
1811 PHE   ( 111-)  G
1843 PHE   ( 143-)  G
1868 PHE   ( 168-)  G
2096 PHE   ( 396-)  G
2175 PHE   (   8-)  L
2242 PHE   (  75-)  L
2265 PHE   (  98-)  L

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.

   7 ASP   (  29-)  A
  14 ASP   (  36-)  A
  27 ASP   (  49-)  A
  53 ASP   (  75-)  A
  69 ASP   (  91-)  A
 184 ASP   ( 206-)  A
 304 ASP   ( 326-)  A
 347 ASP   ( 369-)  A
 416 ASP   ( 438-)  A
 461 ASP   (  16-)  I
 485 ASP   (  40-)  I
 550 ASP   ( 105-)  I
 581 ASP   (  29-)  C
 588 ASP   (  36-)  C
 601 ASP   (  49-)  C
 627 ASP   (  75-)  C
 643 ASP   (  91-)  C
 758 ASP   ( 206-)  C
 878 ASP   ( 326-)  C
 921 ASP   ( 369-)  C
 990 ASP   ( 438-)  C
1035 ASP   (  16-)  J
1059 ASP   (  40-)  J
1124 ASP   ( 105-)  J
1155 ASP   (  29-)  E
1162 ASP   (  36-)  E
1175 ASP   (  49-)  E
1201 ASP   (  75-)  E
1217 ASP   (  91-)  E
1332 ASP   ( 206-)  E
1452 ASP   ( 326-)  E
1495 ASP   ( 369-)  E
1564 ASP   ( 438-)  E
1609 ASP   (  16-)  K
1633 ASP   (  40-)  K
1698 ASP   ( 105-)  K
1729 ASP   (  29-)  G
1736 ASP   (  36-)  G
1749 ASP   (  49-)  G
1775 ASP   (  75-)  G
1791 ASP   (  91-)  G
1906 ASP   ( 206-)  G
2026 ASP   ( 326-)  G
2069 ASP   ( 369-)  G
2138 ASP   ( 438-)  G
2183 ASP   (  16-)  L
2207 ASP   (  40-)  L
2272 ASP   ( 105-)  L

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.

  76 GLU   (  98-)  A
 185 GLU   ( 207-)  A
 215 GLU   ( 237-)  A
 405 GLU   ( 427-)  A
 458 GLU   (  13-)  I
 481 GLU   (  36-)  I
 551 GLU   ( 106-)  I
 561 GLU   ( 116-)  I
 571 GLU   ( 126-)  I
 650 GLU   (  98-)  C
 759 GLU   ( 207-)  C
 789 GLU   ( 237-)  C
 979 GLU   ( 427-)  C
1032 GLU   (  13-)  J
1055 GLU   (  36-)  J
1125 GLU   ( 106-)  J
1135 GLU   ( 116-)  J
1145 GLU   ( 126-)  J
1224 GLU   (  98-)  E
1333 GLU   ( 207-)  E
1363 GLU   ( 237-)  E
1553 GLU   ( 427-)  E
1606 GLU   (  13-)  K
1629 GLU   (  36-)  K
1699 GLU   ( 106-)  K
1709 GLU   ( 116-)  K
1719 GLU   ( 126-)  K
1798 GLU   (  98-)  G
1907 GLU   ( 207-)  G
1937 GLU   ( 237-)  G
2127 GLU   ( 427-)  G
2180 GLU   (  13-)  L
2203 GLU   (  36-)  L
2273 GLU   ( 106-)  L
2283 GLU   ( 116-)  L
2293 GLU   ( 126-)  L

Geometric checks

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.

 861 HIS   ( 309-)  C      CG   ND1  CE1 109.61    4.0

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.

   7 ASP   (  29-)  A
  14 ASP   (  36-)  A
  27 ASP   (  49-)  A
  53 ASP   (  75-)  A
  69 ASP   (  91-)  A
  76 GLU   (  98-)  A
 184 ASP   ( 206-)  A
 185 GLU   ( 207-)  A
 215 GLU   ( 237-)  A
 304 ASP   ( 326-)  A
 347 ASP   ( 369-)  A
 405 GLU   ( 427-)  A
 416 ASP   ( 438-)  A
 458 GLU   (  13-)  I
 461 ASP   (  16-)  I
 481 GLU   (  36-)  I
 485 ASP   (  40-)  I
 550 ASP   ( 105-)  I
 551 GLU   ( 106-)  I
 561 GLU   ( 116-)  I
 571 GLU   ( 126-)  I
 581 ASP   (  29-)  C
 588 ASP   (  36-)  C
 601 ASP   (  49-)  C
 627 ASP   (  75-)  C
And so on for a total of 84 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.

 548 PRO   ( 103-)  I      N      7.0    20.45    -2.48
1122 PRO   ( 103-)  J      N      7.0    20.53    -2.48
1696 PRO   ( 103-)  K      N      7.0    20.35    -2.48
2270 PRO   ( 103-)  L      N      7.0    20.49    -2.48
The average deviation= 0.865

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.

 330 ARG   ( 352-)  A    5.07
2052 ARG   ( 352-)  G    4.99
 904 ARG   ( 352-)  C    4.83
1478 ARG   ( 352-)  E    4.81
2275 GLY   ( 108-)  L    4.27
1701 GLY   ( 108-)  K    4.22
1127 GLY   ( 108-)  J    4.20
 553 GLY   ( 108-)  I    4.18

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.

1696 PRO   ( 103-)  K    -3.1
1122 PRO   ( 103-)  J    -3.1
2270 PRO   ( 103-)  L    -3.1
 548 PRO   ( 103-)  I    -3.1
1601 PHE   (   8-)  K    -3.0
1027 PHE   (   8-)  J    -3.0
2175 PHE   (   8-)  L    -3.0
 453 PHE   (   8-)  I    -2.9
1768 THR   (  68-)  G    -2.9
  46 THR   (  68-)  A    -2.9
1194 THR   (  68-)  E    -2.9
 620 THR   (  68-)  C    -2.9
1206 CYS   (  80-)  E    -2.7
1780 CYS   (  80-)  G    -2.7
 632 CYS   (  80-)  C    -2.7
  58 CYS   (  80-)  A    -2.7
 492 TYR   (  47-)  I    -2.7
1640 TYR   (  47-)  K    -2.6
2214 TYR   (  47-)  L    -2.6
1066 TYR   (  47-)  J    -2.6
1467 PRO   ( 341-)  E    -2.6
1637 ARG   (  44-)  K    -2.6
2211 ARG   (  44-)  L    -2.6
 489 ARG   (  44-)  I    -2.6
1063 ARG   (  44-)  J    -2.5
And so on for a total of 89 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 LYS   (  23-)  A  Poor phi/psi
  43 SER   (  65-)  A  Poor phi/psi
  44 THR   (  66-)  A  Poor phi/psi
  57 ALA   (  79-)  A  Poor phi/psi
  58 CYS   (  80-)  A  Poor phi/psi
  59 ASP   (  81-)  A  Poor phi/psi
  66 TYR   (  88-)  A  Poor phi/psi
  73 ASN   (  95-)  A  Poor phi/psi
  76 GLU   (  98-)  A  Poor phi/psi
  92 GLY   ( 114-)  A  Poor phi/psi
 144 ASP   ( 166-)  A  Poor phi/psi
 158 LYS   ( 180-)  A  Poor phi/psi
 160 GLY   ( 182-)  A  Poor phi/psi
 185 GLU   ( 207-)  A  Poor phi/psi
 189 SER   ( 211-)  A  Poor phi/psi
 191 PRO   ( 213-)  A  Poor phi/psi
 275 ARG   ( 297-)  A  Poor phi/psi
 281 TYR   ( 303-)  A  Poor phi/psi
 286 ASN   ( 308-)  A  Poor phi/psi
 302 GLY   ( 324-)  A  Poor phi/psi
 311 ALA   ( 333-)  A  Poor phi/psi
 312 VAL   ( 334-)  A  Poor phi/psi
 349 ALA   ( 371-)  A  Poor phi/psi
 350 SER   ( 372-)  A  Poor phi/psi
 418 LEU   ( 440-)  A  Poor phi/psi
And so on for a total of 172 lines.

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 MET   (  25-)  A      0
   5 TYR   (  27-)  A      0
   9 ASP   (  31-)  A      0
  15 THR   (  37-)  A      0
  22 ARG   (  44-)  A      0
  27 ASP   (  49-)  A      0
  41 GLU   (  63-)  A      0
  42 SER   (  64-)  A      0
  43 SER   (  65-)  A      0
  44 THR   (  66-)  A      0
  45 ALA   (  67-)  A      0
  47 TRP   (  69-)  A      0
  51 TRP   (  73-)  A      0
  56 THR   (  78-)  A      0
  57 ALA   (  79-)  A      0
  58 CYS   (  80-)  A      0
  59 ASP   (  81-)  A      0
  61 TYR   (  83-)  A      0
  66 TYR   (  88-)  A      0
  67 ARG   (  89-)  A      0
  69 ASP   (  91-)  A      0
  72 PRO   (  94-)  A      0
  73 ASN   (  95-)  A      0
  75 PRO   (  97-)  A      0
  76 GLU   (  98-)  A      0
And so on for a total of 894 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.012

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].

 548 PRO   ( 103-)  I   141.5 envelop C-alpha (144 degrees)
 562 PRO   ( 117-)  I  -112.7 envelop C-gamma (-108 degrees)
1122 PRO   ( 103-)  J   141.6 envelop C-alpha (144 degrees)
1696 PRO   ( 103-)  K   141.7 envelop C-alpha (144 degrees)
1710 PRO   ( 117-)  K  -112.5 envelop C-gamma (-108 degrees)
2270 PRO   ( 103-)  L   141.3 envelop C-alpha (144 degrees)
2284 PRO   ( 117-)  L  -113.2 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.

  57 ALA   (  79-)  A      C   <->   58 CYS   (  80-)  A      SG     0.30    3.00  INTRA BF
1779 ALA   (  79-)  G      C   <-> 1780 CYS   (  80-)  G      SG     0.30    3.00  INTRA BF
 631 ALA   (  79-)  C      C   <->  632 CYS   (  80-)  C      SG     0.29    3.01  INTRA BF
1205 ALA   (  79-)  E      C   <-> 1206 CYS   (  80-)  E      SG     0.28    3.02  INTRA BF
 802 MET   ( 250-)  C      SD  <->  805 MET   ( 253-)  C      CE     0.21    3.19  INTRA BL
  58 CYS   (  80-)  A      O   <->   60 MET   (  82-)  A      N      0.21    2.49  INTRA BF
1950 MET   ( 250-)  G      SD  <-> 1953 MET   ( 253-)  G      CE     0.21    3.19  INTRA BL
1206 CYS   (  80-)  E      O   <-> 1208 MET   (  82-)  E      N      0.20    2.50  INTRA BF
 632 CYS   (  80-)  C      O   <->  634 MET   (  82-)  C      N      0.20    2.50  INTRA BF
1780 CYS   (  80-)  G      O   <-> 1782 MET   (  82-)  G      N      0.19    2.51  INTRA BF
 228 MET   ( 250-)  A      SD  <->  231 MET   ( 253-)  A      CE     0.18    3.22  INTRA BL
1123 ALA   ( 104-)  J      O   <-> 1125 GLU   ( 106-)  J      N      0.17    2.53  INTRA
2271 ALA   ( 104-)  L      O   <-> 2273 GLU   ( 106-)  L      N      0.17    2.53  INTRA
1697 ALA   ( 104-)  K      O   <-> 1699 GLU   ( 106-)  K      N      0.16    2.54  INTRA
2000 HIS   ( 300-)  G      ND1 <-> 2004 THR   ( 304-)  G      OG1    0.16    2.54  INTRA
 549 ALA   ( 104-)  I      O   <->  551 GLU   ( 106-)  I      N      0.16    2.54  INTRA BF
 152 GLY   ( 174-)  A      C   <->  381 GLN   ( 403-)  A      NE2    0.16    2.94  INTRA
 527 VAL   (  82-)  I      CG2 <->  543 PHE   (  98-)  I      CE2    0.16    3.04  INTRA BF
1675 VAL   (  82-)  K      CG2 <-> 1691 PHE   (  98-)  K      CE2    0.16    3.04  INTRA
1101 VAL   (  82-)  J      CG2 <-> 1117 PHE   (  98-)  J      CE2    0.16    3.04  INTRA
1376 MET   ( 250-)  E      SD  <-> 1379 MET   ( 253-)  E      CE     0.16    3.24  INTRA BL
2249 VAL   (  82-)  L      CG2 <-> 2265 PHE   (  98-)  L      CE2    0.15    3.05  INTRA BF
1066 TYR   (  47-)  J      CA  <-> 1316 ARG   ( 190-)  E      NH2    0.15    2.95  INTRA BL
 278 HIS   ( 300-)  A      ND1 <->  282 THR   ( 304-)  A      OG1    0.14    2.56  INTRA BF
 852 HIS   ( 300-)  C      ND1 <->  856 THR   ( 304-)  C      OG1    0.14    2.56  INTRA BF
And so on for a total of 241 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: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

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.

2226 ARG   (  59-)  L      -6.70
1078 ARG   (  59-)  J      -6.70
 504 ARG   (  59-)  I      -6.69
1652 ARG   (  59-)  K      -6.69
 315 LEU   ( 337-)  A      -6.57
 889 LEU   ( 337-)  C      -6.57
1463 LEU   ( 337-)  E      -6.57
2037 LEU   ( 337-)  G      -6.57
   3 MET   (  25-)  A      -6.50
 577 MET   (  25-)  C      -6.47
1725 MET   (  25-)  G      -6.43
1151 MET   (  25-)  E      -6.43
1138 ARG   ( 119-)  J      -5.92
1307 LEU   ( 181-)  E      -5.92
1881 LEU   ( 181-)  G      -5.91
 733 LEU   ( 181-)  C      -5.89
 159 LEU   ( 181-)  A      -5.87
1712 ARG   ( 119-)  K      -5.84
 564 ARG   ( 119-)  I      -5.83
2286 ARG   ( 119-)  L      -5.81
2113 GLN   ( 413-)  G      -5.81
1539 GLN   ( 413-)  E      -5.78
 391 GLN   ( 413-)  A      -5.75
 647 ASN   (  95-)  C      -5.67
 965 GLN   ( 413-)  C      -5.67
And so on for a total of 71 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: I

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: J

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: E

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: K

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: G

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: L

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.

 445 ILE   ( 467-)  A   -3.02
2167 ILE   ( 467-)  G   -3.02
1593 ILE   ( 467-)  E   -3.02
1019 ILE   ( 467-)  C   -3.02
 577 MET   (  25-)  C   -2.62
   3 MET   (  25-)  A   -2.62
1236 LEU   ( 110-)  E   -2.60
1810 LEU   ( 110-)  G   -2.57
 662 LEU   ( 110-)  C   -2.55
  88 LEU   ( 110-)  A   -2.55

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.

 854 THR   ( 302-)  C     -  857 ARG   ( 305-)  C        -1.86
1428 THR   ( 302-)  E     - 1431 ARG   ( 305-)  E        -1.88
2002 THR   ( 302-)  G     - 2005 ARG   ( 305-)  G        -1.87

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: I

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: L

Water, ion, and hydrogenbond related checks

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.

 165 ASN   ( 187-)  A
 194 HIS   ( 216-)  A
 258 GLN   ( 280-)  A
 307 HIS   ( 329-)  A
 323 GLN   ( 345-)  A
 412 ASN   ( 434-)  A
 467 GLN   (  22-)  I
 490 ASN   (  45-)  I
 515 ASN   (  70-)  I
 522 ASN   (  77-)  I
 739 ASN   ( 187-)  C
 768 HIS   ( 216-)  C
 881 HIS   ( 329-)  C
 897 GLN   ( 345-)  C
 986 ASN   ( 434-)  C
1041 GLN   (  22-)  J
1064 ASN   (  45-)  J
1096 ASN   (  77-)  J
1313 ASN   ( 187-)  E
1342 HIS   ( 216-)  E
1406 GLN   ( 280-)  E
1455 HIS   ( 329-)  E
1471 GLN   ( 345-)  E
1560 ASN   ( 434-)  E
1615 GLN   (  22-)  K
1638 ASN   (  45-)  K
1887 ASN   ( 187-)  G
1916 HIS   ( 216-)  G
1980 GLN   ( 280-)  G
2029 HIS   ( 329-)  G
2045 GLN   ( 345-)  G
2134 ASN   ( 434-)  G
2189 GLN   (  22-)  L
2212 ASN   (  45-)  L
2244 ASN   (  77-)  L

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 LYS   (  23-)  A      N
   4 GLY   (  26-)  A      N
  32 VAL   (  54-)  A      N
  42 SER   (  64-)  A      N
  43 SER   (  65-)  A      N
  45 ALA   (  67-)  A      N
  46 THR   (  68-)  A      OG1
  47 TRP   (  69-)  A      NE1
  52 THR   (  74-)  A      OG1
  53 ASP   (  75-)  A      N
  58 CYS   (  80-)  A      N
  63 ALA   (  85-)  A      N
  67 ARG   (  89-)  A      N
  77 GLN   (  99-)  A      N
  84 TYR   ( 106-)  A      OH
  93 SER   ( 115-)  A      N
  95 ALA   ( 117-)  A      N
 106 PHE   ( 128-)  A      N
 109 LYS   ( 131-)  A      N
 115 ARG   ( 137-)  A      NE
 115 ARG   ( 137-)  A      NH2
 125 TYR   ( 147-)  A      OH
 138 VAL   ( 160-)  A      N
 142 ARG   ( 164-)  A      NH1
 148 ARG   ( 170-)  A      N
And so on for a total of 335 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.

  53 ASP   (  75-)  A      OD1
  53 ASP   (  75-)  A      OD2
 139 GLU   ( 161-)  A      OE1
 183 ASP   ( 205-)  A      OD2
 184 ASP   ( 206-)  A      OD2
 272 HIS   ( 294-)  A      NE2
 284 GLN   ( 306-)  A      OE1
 372 HIS   ( 394-)  A      ND1
 376 ASP   ( 398-)  A      OD1
 523 HIS   (  78-)  I      ND1
 537 GLU   (  92-)  I      OE1
 627 ASP   (  75-)  C      OD1
 627 ASP   (  75-)  C      OD2
 713 GLU   ( 161-)  C      OE1
 757 ASP   ( 205-)  C      OD1
 757 ASP   ( 205-)  C      OD2
 758 ASP   ( 206-)  C      OD2
 762 ASN   ( 210-)  C      OD1
 846 HIS   ( 294-)  C      NE2
 858 GLN   ( 306-)  C      OE1
 946 HIS   ( 394-)  C      ND1
 950 ASP   ( 398-)  C      OD1
1097 HIS   (  78-)  J      ND1
1111 GLU   (  92-)  J      OE1
1201 ASP   (  75-)  E      OD1
1201 ASP   (  75-)  E      OD2
1287 GLU   ( 161-)  E      OE1
1331 ASP   ( 205-)  E      OD2
1332 ASP   ( 206-)  E      OD2
1420 HIS   ( 294-)  E      NE2
1432 GLN   ( 306-)  E      OE1
1520 HIS   ( 394-)  E      ND1
1524 ASP   ( 398-)  E      OD1
1671 HIS   (  78-)  K      ND1
1685 GLU   (  92-)  K      OE1
1775 ASP   (  75-)  G      OD1
1775 ASP   (  75-)  G      OD2
1861 GLU   ( 161-)  G      OE1
1905 ASP   ( 205-)  G      OD2
1906 ASP   ( 206-)  G      OD2
1994 HIS   ( 294-)  G      NE2
2000 HIS   ( 300-)  G      NE2
2006 GLN   ( 306-)  G      OE1
2094 HIS   ( 394-)  G      ND1
2098 ASP   ( 398-)  G      OD1
2245 HIS   (  78-)  L      ND1
2259 GLU   (  92-)  L      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.

  16 ASP   (  38-)  A   H-bonding suggests Asn; but Alt-Rotamer
  69 ASP   (  91-)  A   H-bonding suggests Asn; but Alt-Rotamer
 184 ASP   ( 206-)  A   H-bonding suggests Asn
 427 ASP   ( 449-)  A   H-bonding suggests Asn; but Alt-Rotamer
 440 ASP   ( 462-)  A   H-bonding suggests Asn
 458 GLU   (  13-)  I   H-bonding suggests Gln
 590 ASP   (  38-)  C   H-bonding suggests Asn; but Alt-Rotamer
 643 ASP   (  91-)  C   H-bonding suggests Asn; but Alt-Rotamer
 758 ASP   ( 206-)  C   H-bonding suggests Asn
1001 ASP   ( 449-)  C   H-bonding suggests Asn; but Alt-Rotamer
1014 ASP   ( 462-)  C   H-bonding suggests Asn
1032 GLU   (  13-)  J   H-bonding suggests Gln
1164 ASP   (  38-)  E   H-bonding suggests Asn; but Alt-Rotamer
1217 ASP   (  91-)  E   H-bonding suggests Asn; but Alt-Rotamer
1332 ASP   ( 206-)  E   H-bonding suggests Asn
1575 ASP   ( 449-)  E   H-bonding suggests Asn; but Alt-Rotamer
1588 ASP   ( 462-)  E   H-bonding suggests Asn
1606 GLU   (  13-)  K   H-bonding suggests Gln
1738 ASP   (  38-)  G   H-bonding suggests Asn; but Alt-Rotamer
1791 ASP   (  91-)  G   H-bonding suggests Asn; but Alt-Rotamer
1906 ASP   ( 206-)  G   H-bonding suggests Asn
2149 ASP   ( 449-)  G   H-bonding suggests Asn; but Alt-Rotamer
2162 ASP   ( 462-)  G   H-bonding suggests Asn
2180 GLU   (  13-)  L   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.835
  2nd generation packing quality :  -1.227
  Ramachandran plot appearance   :  -2.965
  chi-1/chi-2 rotamer normality  :  -2.473
  Backbone conformation          :  -0.164

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.285 (tight)
  Bond angles                    :   0.597 (tight)
  Omega angle restraints         :   0.184 (tight)
  Side chain planarity           :   0.265 (tight)
  Improper dihedral distribution :   0.724
  Inside/Outside distribution    :   1.082

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 : 2.70


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.2
  2nd generation packing quality :   0.4
  Ramachandran plot appearance   :  -0.2
  chi-1/chi-2 rotamer normality  :  -0.2
  Backbone conformation          :   0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.285 (tight)
  Bond angles                    :   0.597 (tight)
  Omega angle restraints         :   0.184 (tight)
  Side chain planarity           :   0.265 (tight)
  Improper dihedral distribution :   0.724
  Inside/Outside distribution    :   1.082
==============

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.