WHAT IF Check report

This file was created 2011-12-28 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

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

Verification log for pdb1ggu.ent

Administrative problems that can generate validation failures

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

  23 GLU   (  30-)  A  -
 489 THR   ( 508-)  A  -
 701 ARG   ( 727-)  A  -
 729 VAL   (  35-)  B  -
1196 THR   ( 508-)  B  -
1408 ARG   ( 727-)  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: 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'.

  23 GLU   (  30-)  A      O
 489 THR   ( 508-)  A      O
 701 ARG   ( 727-)  A      O
 728 VAL   (  34-)  B      CG1
 728 VAL   (  34-)  B      CG2
 729 VAL   (  35-)  B      O
 729 VAL   (  35-)  B      CG1
 729 VAL   (  35-)  B      CG2
1196 THR   ( 508-)  B      O
1408 ARG   ( 727-)  B      O

Warning: What type of B-factor?

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

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

Crystal temperature (K) :100.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: B

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.

 603 ILE   ( 629-)  A      CA   CB    1.63    4.8
 735 VAL   (  47-)  B      CA   CB    1.62    4.4
1075 VAL   ( 387-)  B      CA   CB    1.61    4.0
1307 VAL   ( 626-)  B      CA   CB    1.61    4.2

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.

   3 GLY   (  10-)  A      N    CA   C   125.19    4.4
  32 HIS   (  51-)  A      CG   ND1  CE1 109.68    4.1
  33 LEU   (  52-)  A      N    CA   C    99.86   -4.1
  46 HIS   (  65-)  A      CG   ND1  CE1 110.00    4.4
  67 ILE   (  86-)  A      C    CA   CB  101.34   -4.6
  77 ARG   (  96-)  A      CG   CD   NE  118.15    4.5
  93 ASN   ( 112-)  A     -C    N    CA  129.55    4.4
  99 PRO   ( 118-)  A      N    CA   C   100.96   -4.3
 109 GLY   ( 128-)  A      N    CA   C   124.29    4.1
 147 PRO   ( 166-)  A      N    CA   C   122.73    4.4
 265 ALA   ( 284-)  A      N    CA   C   122.41    4.0
 292 TYR   ( 311-)  A     -C    N    CA  128.94    4.0
 314 ARG   ( 333-)  A      CB   CG   CD  105.89   -4.1
 354 HIS   ( 373-)  A      CG   ND1  CE1 109.86    4.3
 402 HIS   ( 421-)  A      CG   ND1  CE1 109.68    4.1
 421 ILE   ( 440-)  A      C    CA   CB  101.94   -4.3
 431 HIS   ( 450-)  A      CG   ND1  CE1 109.85    4.2
 440 HIS   ( 459-)  A      CG   ND1  CE1 109.61    4.0
 446 VAL   ( 465-)  A      N    CA   CB  102.69   -4.6
 531 ILE   ( 557-)  A      N    CA   C    99.87   -4.0
 556 PHE   ( 582-)  A      N    CA   C    99.48   -4.2
 563 ILE   ( 589-)  A      N    CA   C    99.52   -4.2
 569 MET   ( 595-)  A      N    CA   C   122.53    4.0
 579 HIS   ( 605-)  A      CG   ND1  CE1 109.65    4.1
 590 ARG   ( 616-)  A      CG   CD   NE  117.37    4.0
And so on for a total of 53 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.

 739 HIS   (  51-)  B      C     -6.6    -9.70     0.15
 884 ASP   ( 196-)  B      C     -6.5   -10.05    -0.01
The average deviation= 1.563

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.

1176 GLU   ( 488-)  B    7.85
 740 LEU   (  52-)  B    7.68
1278 GLN   ( 597-)  B    6.98
 703 GLY   (   9-)  B    6.50
1002 CYS   ( 314-)  B    6.34
1276 MET   ( 595-)  B    5.77
 894 LEU   ( 206-)  B    5.24
 884 ASP   ( 196-)  B    5.09
 417 ASN   ( 436-)  A    4.88
 469 GLU   ( 488-)  A    4.84
1153 VAL   ( 465-)  B    4.84
  99 PRO   ( 118-)  A    4.83
 185 TYR   ( 204-)  A    4.81
 804 TYR   ( 116-)  B    4.78
 277 VAL   ( 296-)  A    4.75
 295 CYS   ( 314-)  A    4.75
 741 PHE   (  53-)  B    4.75
 657 ILE   ( 683-)  A    4.67
 265 ALA   ( 284-)  A    4.57
 747 THR   (  59-)  B    4.56
1087 PRO   ( 399-)  B    4.54
1039 ASP   ( 351-)  B    4.50
 853 THR   ( 165-)  B    4.50
 728 VAL   (  34-)  B    4.46
 556 PHE   ( 582-)  A    4.40
 972 ALA   ( 284-)  B    4.39
 409 ALA   ( 428-)  A    4.38
1162 MET   ( 474-)  B    4.35
1327 MET   ( 646-)  B    4.30
 571 GLN   ( 597-)  A    4.28
 957 LYS   ( 269-)  B    4.28
1363 GLU   ( 682-)  B    4.21
1238 ILE   ( 557-)  B    4.18
 620 MET   ( 646-)  A    4.17
   3 GLY   (  10-)  A    4.17
 282 GLU   ( 301-)  A    4.14
  33 LEU   (  52-)  A    4.12
 392 PRO   ( 411-)  A    4.10
 922 ILE   ( 234-)  B    4.08
 563 ILE   ( 589-)  A    4.06
 662 THR   ( 688-)  A    4.05
  35 LYS   (  54-)  A    4.05
 446 VAL   ( 465-)  A    4.01
 968 ASP   ( 280-)  B    4.01

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.796

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.

 488 ASN   ( 507-)  A    5.05

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

 911 ARG   ( 223-)  B    -2.6
 550 THR   ( 576-)  A    -2.5
 264 TYR   ( 283-)  A    -2.5
 320 PHE   ( 339-)  A    -2.5
 599 THR   ( 625-)  A    -2.5
  99 PRO   ( 118-)  A    -2.5
 611 ARG   ( 637-)  A    -2.5
 971 TYR   ( 283-)  B    -2.4
 779 PRO   (  91-)  B    -2.4
 806 PRO   ( 118-)  B    -2.4
1396 ARG   ( 715-)  B    -2.4
1170 LYS   ( 482-)  B    -2.4
1212 LYS   ( 531-)  B    -2.4
1151 LEU   ( 463-)  B    -2.4
 463 LYS   ( 482-)  A    -2.4
1027 PHE   ( 339-)  B    -2.4
 444 LEU   ( 463-)  A    -2.3
 826 GLU   ( 138-)  B    -2.3
 825 ARG   ( 137-)  B    -2.3
 132 LYS   ( 151-)  A    -2.3
1320 THR   ( 639-)  B    -2.3
 561 VAL   ( 587-)  A    -2.3
1402 LEU   ( 721-)  B    -2.3
1285 LEU   ( 604-)  B    -2.2
 881 VAL   ( 193-)  B    -2.2
And so on for a total of 66 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.

  26 LEU   (  45-)  A  Poor phi/psi
  46 HIS   (  65-)  A  Poor phi/psi
 120 ASP   ( 139-)  A  Poor phi/psi
 177 ASP   ( 196-)  A  Poor phi/psi
 195 TYR   ( 214-)  A  Poor phi/psi
 251 ASP   ( 270-)  A  Poor phi/psi
 262 ASN   ( 281-)  A  Poor phi/psi
 264 TYR   ( 283-)  A  Poor phi/psi
 287 GLU   ( 306-)  A  Poor phi/psi
 291 ARG   ( 310-)  A  omega poor
 320 PHE   ( 339-)  A  Poor phi/psi
 326 ASP   ( 345-)  A  Poor phi/psi
 327 ALA   ( 346-)  A  Poor phi/psi
 391 GLY   ( 410-)  A  PRO omega poor
 406 GLN   ( 425-)  A  omega poor
 408 ASP   ( 427-)  A  Poor phi/psi
 491 ASN   ( 517-)  A  Poor phi/psi
 554 LEU   ( 580-)  A  Poor phi/psi
 568 TYR   ( 594-)  A  Poor phi/psi
 575 GLN   ( 601-)  A  Poor phi/psi
 586 ILE   ( 612-)  A  Poor phi/psi
 590 ARG   ( 616-)  A  Poor phi/psi
 636 ASN   ( 662-)  A  Poor phi/psi
 660 ASN   ( 686-)  A  Poor phi/psi
 685 SER   ( 711-)  A  Poor phi/psi
And so on for a total of 51 lines.

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.742

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!

   4 ARG   (  11-)  A      0
   5 ARG   (  12-)  A      0
   6 ALA   (  13-)  A      0
  10 ASN   (  17-)  A      0
  11 ASN   (  18-)  A      0
  13 ASN   (  20-)  A      0
  15 ALA   (  22-)  A      0
  22 VAL   (  29-)  A      0
  23 GLU   (  30-)  A      0
  24 GLU   (  43-)  A      0
  25 PHE   (  44-)  A      0
  26 LEU   (  45-)  A      0
  27 ASN   (  46-)  A      0
  34 PHE   (  53-)  A      0
  35 LYS   (  54-)  A      0
  38 TRP   (  57-)  A      0
  46 HIS   (  65-)  A      0
  47 THR   (  66-)  A      0
  48 ASP   (  67-)  A      0
  50 TYR   (  69-)  A      0
  51 GLU   (  70-)  A      0
  52 ASN   (  71-)  A      0
  59 ARG   (  78-)  A      0
  70 SER   (  89-)  A      0
  71 ARG   (  90-)  A      0
And so on for a total of 628 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 : 2.100

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 643 GLY   ( 669-)  A   1.90   11
 965 GLY   ( 277-)  B   1.55   10

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]

 289 PRO   ( 308-)  A    0.47 HIGH
 710 PRO   (  16-)  B    0.46 HIGH
 779 PRO   (  91-)  B    0.47 HIGH
 864 PRO   ( 176-)  B    0.45 HIGH
 976 PRO   ( 288-)  B    0.46 HIGH
1311 PRO   ( 630-)  B    0.47 HIGH

Warning: Unusual PRO puckering phases

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

  20 PRO   (  27-)  A  -112.5 envelop C-gamma (-108 degrees)
 157 PRO   ( 176-)  A  -114.9 envelop C-gamma (-108 degrees)
 270 PRO   ( 289-)  A   110.8 envelop C-beta (108 degrees)
 367 PRO   ( 386-)  A   101.3 envelop C-beta (108 degrees)
 553 PRO   ( 579-)  A  -113.7 envelop C-gamma (-108 degrees)
 671 PRO   ( 697-)  A  -117.8 half-chair C-delta/C-gamma (-126 degrees)
 779 PRO   (  91-)  B  -116.4 envelop C-gamma (-108 degrees)
 854 PRO   ( 166-)  B  -114.1 envelop C-gamma (-108 degrees)
 977 PRO   ( 289-)  B   105.4 envelop C-beta (108 degrees)
1356 PRO   ( 675-)  B  -124.9 half-chair C-delta/C-gamma (-126 degrees)
1378 PRO   ( 697-)  B  -121.7 half-chair C-delta/C-gamma (-126 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.

1197 SER   ( 516-)  B      N   <-> 1412 HOH   (6294 )  B      O      0.38    2.32  INTRA BF
 579 HIS   ( 605-)  A      CE1 <->  596 GLN   ( 622-)  A      NE2    0.33    2.77  INTRA
 155 ARG   ( 174-)  A      NH2 <->  160 ASP   ( 179-)  A      OD1    0.33    2.37  INTRA BL
  76 ARG   (  95-)  A      NH1 <->   77 ARG   (  96-)  A      NH1    0.33    2.52  INTRA BF
 363 ARG   ( 382-)  A      NH2 <->  406 GLN   ( 425-)  A      O      0.31    2.39  INTRA
1106 LYS   ( 418-)  B      NZ  <-> 1167 ASP   ( 479-)  B      O      0.31    2.39  INTRA BL
1070 ARG   ( 382-)  B      NH2 <-> 1099 PRO   ( 411-)  B      O      0.31    2.39  INTRA BL
 440 HIS   ( 459-)  A      NE2 <-> 1411 HOH   (6128 )  A      O      0.28    2.42  INTRA BL
 144 VAL   ( 163-)  A      N   <->  151 LEU   ( 170-)  A      O      0.28    2.42  INTRA
 828 ARG   ( 140-)  B      NH1 <-> 1412 HOH   (6420 )  B      O      0.28    2.42  INTRA BF
 885 ASN   ( 197-)  B      ND2 <->  888 GLU   ( 200-)  B      OE1    0.28    2.42  INTRA BL
 512 THR   ( 538-)  A      CG2 <->  556 PHE   ( 582-)  A      CZ     0.27    2.93  INTRA BF
 337 GLU   ( 356-)  A      O   <->  585 ARG   ( 611-)  A      NE     0.26    2.44  INTRA BF
 533 PHE   ( 559-)  A      CD2 <->  702 PHE   (   8-)  B      CE2    0.25    2.95  INTRA BF
 179 GLU   ( 198-)  A      OE1 <->  182 ARG   ( 201-)  A      NH1    0.25    2.45  INTRA BF
 490 SER   ( 516-)  A      N   <-> 1411 HOH   (6284 )  A      O      0.25    2.45  INTRA BF
1142 ASN   ( 454-)  B      ND2 <-> 1412 HOH   (6060 )  B      O      0.24    2.46  INTRA BF
 781 ASP   (  93-)  B      O   <->  783 ARG   (  95-)  B      N      0.24    2.46  INTRA BF
1163 MET   ( 475-)  B      SD  <-> 1412 HOH   (6299 )  B      O      0.24    2.76  INTRA BF
 523 ILE   ( 549-)  A      CG2 <->  524 THR   ( 550-)  A      N      0.22    2.78  INTRA BF
  87 GLY   ( 106-)  A      N   <-> 1411 HOH   (6126 )  A      O      0.22    2.48  INTRA BL
1316 LYS   ( 635-)  B      O   <-> 1330 THR   ( 649-)  B      N      0.21    2.49  INTRA
 488 ASN   ( 507-)  A      CG  <->  489 THR   ( 508-)  A      N      0.21    2.79  INTRA BF
 336 GLU   ( 355-)  A      O   <->  585 ARG   ( 611-)  A      NH2    0.21    2.49  INTRA BF
1030 HIS   ( 342-)  B      ND1 <-> 1122 GLU   ( 434-)  B      OE2    0.20    2.50  INTRA BL
And so on for a total of 256 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.

 148 TYR   ( 167-)  A      -8.57
 266 TYR   ( 285-)  A      -7.82
 973 TYR   ( 285-)  B      -7.39
 862 ARG   ( 174-)  B      -7.37
 726 GLN   (  32-)  B      -7.36
 155 ARG   ( 174-)  A      -7.05
 783 ARG   (  95-)  B      -6.96
  77 ARG   (  96-)  A      -6.54
   4 ARG   (  11-)  A      -6.29
1194 LEU   ( 506-)  B      -6.24
 705 ARG   (  11-)  B      -6.16
 487 LEU   ( 506-)  A      -6.16
 488 ASN   ( 507-)  A      -6.04
 855 TYR   ( 167-)  B      -6.01
1195 ASN   ( 507-)  B      -5.99
 796 TYR   ( 108-)  B      -5.91
 449 GLN   ( 468-)  A      -5.89
1362 ARG   ( 681-)  B      -5.85
1134 LYS   ( 446-)  B      -5.82
 814 GLN   ( 126-)  B      -5.81
 387 MET   ( 406-)  A      -5.80
1172 GLN   ( 484-)  B      -5.77
1156 GLN   ( 468-)  B      -5.76
 107 GLN   ( 126-)  A      -5.72
  89 TYR   ( 108-)  A      -5.66
1338 LYS   ( 657-)  B      -5.65
 518 HIS   ( 544-)  A      -5.59
1355 ARG   ( 674-)  B      -5.58
 427 LYS   ( 446-)  A      -5.48
 465 GLN   ( 484-)  A      -5.46
 648 ARG   ( 674-)  A      -5.45
 631 LYS   ( 657-)  A      -5.44
  76 ARG   (  95-)  A      -5.42
  88 ARG   ( 107-)  A      -5.41
 800 ASN   ( 112-)  B      -5.39
 752 HIS   (  64-)  B      -5.38
  93 ASN   ( 112-)  A      -5.33
 676 HIS   ( 702-)  A      -5.32
 795 ARG   ( 107-)  B      -5.22
  73 TYR   (  92-)  A      -5.20
1278 GLN   ( 597-)  B      -5.19
1094 MET   ( 406-)  B      -5.15
1075 VAL   ( 387-)  B      -5.12
   5 ARG   (  12-)  A      -5.09
1124 ASN   ( 436-)  B      -5.07
1096 ARG   ( 408-)  B      -5.03
 778 ARG   (  90-)  B      -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.

 387 MET   ( 406-)  A       389 - ARG    408- ( A)         -4.97
 725 LEU   (  31-)  B       727 - GLY     33- ( B)         -5.49
1094 MET   ( 406-)  B      1096 - ARG    408- ( B)         -4.85

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.

1355 ARG   ( 674-)  B   -2.65
 388 TYR   ( 407-)  A   -2.54

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.

  91 GLN   ( 110-)  A     -   94 LYS   ( 113-)  A        -1.52
 798 GLN   ( 110-)  B     -  801 LYS   ( 113-)  B        -1.41

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

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

1412 HOH   (6236 )  B      O      8.18    4.38   79.98
1412 HOH   (6418 )  B      O    -24.61    8.93   37.32
1412 HOH   (6477 )  B      O      4.47  -16.71   79.93
1412 HOH   (6503 )  B      O      9.23  -18.51   73.13

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.

1411 HOH   (6062 )  A      O
1411 HOH   (6114 )  A      O
1411 HOH   (6123 )  A      O
1411 HOH   (6169 )  A      O
1411 HOH   (6228 )  A      O
1411 HOH   (6242 )  A      O
1411 HOH   (6256 )  A      O
1411 HOH   (6265 )  A      O
1411 HOH   (6278 )  A      O
1411 HOH   (6286 )  A      O
1411 HOH   (6328 )  A      O
1411 HOH   (6349 )  A      O
1411 HOH   (6362 )  A      O
1411 HOH   (6365 )  A      O
1411 HOH   (6371 )  A      O
1411 HOH   (6378 )  A      O
1411 HOH   (6379 )  A      O
1411 HOH   (6383 )  A      O
1411 HOH   (6401 )  A      O
1411 HOH   (6403 )  A      O
1411 HOH   (6409 )  A      O
1411 HOH   (6410 )  A      O
1411 HOH   (6412 )  A      O
1411 HOH   (6416 )  A      O
1411 HOH   (6420 )  A      O
1411 HOH   (6428 )  A      O
1412 HOH   (6036 )  B      O
1412 HOH   (6212 )  B      O
1412 HOH   (6249 )  B      O
1412 HOH   (6292 )  B      O
1412 HOH   (6346 )  B      O
1412 HOH   (6373 )  B      O
1412 HOH   (6409 )  B      O
1412 HOH   (6451 )  B      O
1412 HOH   (6472 )  B      O
1412 HOH   (6483 )  B      O
1412 HOH   (6487 )  B      O
1412 HOH   (6528 )  B      O
1412 HOH   (6529 )  B      O
1412 HOH   (6542 )  B      O
1412 HOH   (6550 )  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.

  32 HIS   (  51-)  A
 596 GLN   ( 622-)  A
1059 ASN   ( 371-)  B
1397 HIS   ( 716-)  B
1407 GLN   ( 726-)  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.

  34 PHE   (  53-)  A      N
  36 GLU   (  55-)  A      N
  41 ASN   (  60-)  A      N
  41 ASN   (  60-)  A      ND2
  50 TYR   (  69-)  A      N
  56 ILE   (  75-)  A      N
  58 ARG   (  77-)  A      NH1
  58 ARG   (  77-)  A      NH2
 130 SER   ( 149-)  A      N
 135 VAL   ( 154-)  A      N
 150 VAL   ( 169-)  A      N
 166 ASN   ( 185-)  A      ND2
 192 VAL   ( 211-)  A      N
 204 ARG   ( 223-)  A      NH2
 211 PHE   ( 230-)  A      N
 262 ASN   ( 281-)  A      ND2
 275 GLY   ( 294-)  A      N
 294 GLN   ( 313-)  A      N
 296 TRP   ( 315-)  A      N
 296 TRP   ( 315-)  A      NE1
 303 ASN   ( 322-)  A      ND2
 324 ASP   ( 343-)  A      N
 330 GLN   ( 349-)  A      N
 340 ASN   ( 359-)  A      N
 353 TYR   ( 372-)  A      N
And so on for a total of 92 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.

  61 GLN   (  80-)  A      OE1
 294 GLN   ( 313-)  A      OE1
 318 ASN   ( 337-)  A      OD1
 323 HIS   ( 342-)  A      ND1
 354 HIS   ( 373-)  A      ND1
 515 ASN   ( 541-)  A      OD1
 545 GLU   ( 571-)  A      OE1
1025 ASN   ( 337-)  B      OD1
1061 HIS   ( 373-)  B      ND1
1142 ASN   ( 454-)  B      OD1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

1409  CA   (2001-)  A     0.88   1.09 Scores about as good as NA (Few ligands (4) )
1410  CA   (2002-)  B     0.50   1.50 Is perhaps  K

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

1411 HOH   (6105 )  A      O  0.91  K  4
1412 HOH   (6388 )  B      O  0.98  K  4 Ion-B
1412 HOH   (6503 )  B      O  1.04  K  5 ION-B

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.

 197 GLU   ( 216-)  A   H-bonding suggests Gln
 278 ASP   ( 297-)  A   H-bonding suggests Asn
 466 GLU   ( 485-)  A   H-bonding suggests Gln; but Alt-Rotamer
 493 ASP   ( 519-)  A   H-bonding suggests Asn
 812 GLU   ( 124-)  B   H-bonding suggests Gln
 904 GLU   ( 216-)  B   H-bonding suggests Gln
 985 ASP   ( 297-)  B   H-bonding suggests Asn
1312 GLU   ( 631-)  B   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 :  -0.640
  2nd generation packing quality :  -2.026
  Ramachandran plot appearance   :  -1.874
  chi-1/chi-2 rotamer normality  :  -3.742 (poor)
  Backbone conformation          :  -0.726

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.742
  Bond angles                    :   0.949
  Omega angle restraints         :   0.382 (tight)
  Side chain planarity           :   0.753
  Improper dihedral distribution :   1.300
  B-factor distribution          :   0.598
  Inside/Outside distribution    :   1.039

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 : 2.10


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.2
  2nd generation packing quality :  -1.4
  Ramachandran plot appearance   :  -0.9
  chi-1/chi-2 rotamer normality  :  -2.3
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.742
  Bond angles                    :   0.949
  Omega angle restraints         :   0.382 (tight)
  Side chain planarity           :   0.753
  Improper dihedral distribution :   1.300
  B-factor distribution          :   0.598
  Inside/Outside distribution    :   1.039
==============

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.