WHAT IF Check report

This file was created 2012-04-12 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 pdb2xyd.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.723
CA-only RMS fit for the two chains : 0.612

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

Warning: Topology could not be determined for some ligands

Some ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

1228 3ES   (1611-)  A  -
1229 BMA   (1618-)  A  -         OK
1232 PEG   (1622-)  A  -         OK
1233 PEG   (1623-)  B  -         OK
1234 PEG   (1624-)  A  -         OK
1237 PEG   (1623-)  B  -         OK
1238 P6G   (1622-)  B  -         OK
1239 A10   (1621-)  B  -         OK
1240 BMA   (1618-)  B  -         OK
1241 BMA   (1611-)  B  -         OK
1242 PG4   (1625-)  B  -         OK

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

1217 NAG   (1614-)  A  -   O4  bound to 1218 NAG   (1615-)  A  -   C1
1219 NAG   (1616-)  A  -   O4  bound to 1220 NAG   (1617-)  A  -   C1
1220 NAG   (1617-)  A  -   O4  bound to 1229 BMA   (1618-)  A  -   C1
1224 NAG   (1614-)  B  -   O4  bound to 1225 NAG   (1615-)  B  -   C1
1226 NAG   (1616-)  B  -   O4  bound to 1227 NAG   (1617-)  B  -   C1
1227 NAG   (1617-)  B  -   O4  bound to 1240 BMA   (1618-)  B  -   C1

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'.

  56 GLU   (  56-)  A      CD
  56 GLU   (  56-)  A      OE1
  56 GLU   (  56-)  A      OE2
  70 GLN   (  70-)  A      CD
  70 GLN   (  70-)  A      OE1
  70 GLN   (  70-)  A      NE2
 129 LEU   ( 129-)  A      CG
 129 LEU   ( 129-)  A      CD1
 129 LEU   ( 129-)  A      CD2
 130 THR   ( 133-)  A      OG1
 130 THR   ( 133-)  A      CG2
 132 THR   ( 135-)  A      OG1
 132 THR   ( 135-)  A      CG2
 338 LYS   ( 341-)  A      CD
 338 LYS   ( 341-)  A      CE
 338 LYS   ( 341-)  A      NZ
 400 GLU   ( 403-)  A      CD
 400 GLU   ( 403-)  A      OE1
 400 GLU   ( 403-)  A      OE2
 514 LYS   ( 517-)  A      CE
 514 LYS   ( 517-)  A      NZ
 539 LYS   ( 542-)  A      CE
 539 LYS   ( 542-)  A      NZ
 663 GLU   (  56-)  B      CD
 663 GLU   (  56-)  B      OE1
And so on for a total of 54 lines.

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 0

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: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.997248  0.000471 -0.000953|
 |  0.000471  0.997334 -0.000496|
 | -0.000953 -0.000496  0.996743|
Proposed new scale matrix

 |  0.013762 -0.003475 -0.006972|
 | -0.000005  0.013528  0.001404|
 |  0.000013  0.000007  0.013479|
With corresponding cell

    A    =  72.638  B   =  76.249  C    =  82.634
    Alpha=  89.163  Beta=  64.514  Gamma=  75.821

The CRYST1 cell dimensions

    A    =  72.837  B   =  76.437  C    =  82.954
    Alpha=  89.110  Beta=  64.430  Gamma=  75.870

Variance: 367.545
(Under-)estimated Z-score: 14.129

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.

 965 HIS   ( 361-)  B      CG   ND1  CE1 109.62    4.0

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.

 823 GLU   ( 219-)  B    4.19

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.

1099 VAL   ( 495-)  B    -2.5
 349 THR   ( 352-)  A    -2.4
 605 PRO   ( 608-)  A    -2.4
 976 TYR   ( 372-)  B    -2.3
 704 THR   (  97-)  B    -2.3
 369 TYR   ( 372-)  A    -2.3
 261 ILE   ( 264-)  A    -2.3
 883 VAL   ( 279-)  B    -2.2
 276 VAL   ( 279-)  A    -2.2
 138 PRO   ( 141-)  A    -2.2
 322 GLY   ( 325-)  A    -2.2
   3 PRO   (   3-)  A    -2.2
 203 THR   ( 206-)  A    -2.2
 492 VAL   ( 495-)  A    -2.2
1015 LEU   ( 411-)  B    -2.2
 559 LEU   ( 562-)  A    -2.2
 233 ARG   ( 236-)  A    -2.2
 745 PRO   ( 141-)  B    -2.1
1022 THR   ( 418-)  B    -2.1
 456 TYR   ( 459-)  A    -2.1
1088 PHE   ( 484-)  B    -2.1
 374 VAL   ( 377-)  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.

  75 LEU   (  75-)  A  omega poor
 137 ASP   ( 140-)  A  PRO omega poor
 138 PRO   ( 141-)  A  omega poor
 200 ASN   ( 203-)  A  Poor phi/psi
 302 GLU   ( 305-)  A  Poor phi/psi
 322 GLY   ( 325-)  A  Poor phi/psi
 335 TYR   ( 338-)  A  Poor phi/psi
 337 ARG   ( 340-)  A  Poor phi/psi
 380 ALA   ( 383-)  A  omega poor
 529 ARG   ( 532-)  A  Poor phi/psi
 556 MET   ( 559-)  A  omega poor
 604 TYR   ( 607-)  A  PRO omega poor
 744 ASP   ( 140-)  B  PRO omega poor
 745 PRO   ( 141-)  B  omega poor
 752 ALA   ( 148-)  B  omega poor
 856 LEU   ( 252-)  B  omega poor
 909 GLU   ( 305-)  B  Poor phi/psi
 942 TYR   ( 338-)  B  Poor phi/psi
 944 ARG   ( 340-)  B  Poor phi/psi
 987 ALA   ( 383-)  B  omega poor
1021 ASP   ( 417-)  B  Poor phi/psi
1136 ARG   ( 532-)  B  Poor phi/psi
1163 MET   ( 559-)  B  omega poor
1179 GLN   ( 575-)  B  Poor phi/psi
1200 GLU   ( 596-)  B  Poor phi/psi
1211 TYR   ( 607-)  B  PRO omega poor
 chi-1/chi-2 correlation Z-score : -1.763

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.

 417 SER   ( 420-)  A    0.34
  61 SER   (  61-)  A    0.35
 116 SER   ( 116-)  A    0.36
  29 GLU   (  29-)  A    0.37
 668 SER   (  61-)  B    0.37

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 GLN   (   9-)  A      0
  12 ALA   (  12-)  A      0
  44 THR   (  44-)  A      0
  45 ASN   (  45-)  A      0
  76 TYR   (  76-)  A      0
  78 PRO   (  78-)  A      0
  83 PHE   (  83-)  A      0
  97 THR   (  97-)  A      0
 100 SER   ( 100-)  A      0
 128 CYS   ( 128-)  A      0
 129 LEU   ( 129-)  A      0
 130 THR   ( 133-)  A      0
 131 ALA   ( 134-)  A      0
 136 LEU   ( 139-)  A      0
 146 SER   ( 149-)  A      0
 147 SER   ( 150-)  A      0
 198 TRP   ( 201-)  A      0
 200 ASN   ( 203-)  A      0
 234 TYR   ( 237-)  A      0
 238 TYR   ( 241-)  A      0
 242 ARG   ( 245-)  A      0
 248 HIS   ( 251-)  A      0
 249 LEU   ( 252-)  A      0
 250 LEU   ( 253-)  A      0
 254 TRP   ( 257-)  A      0
And so on for a total of 360 lines.

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].

   3 PRO   (   3-)  A   148.9 envelop C-alpha (144 degrees)
 167 PRO   ( 170-)  A  -114.2 envelop C-gamma (-108 degrees)
 170 PRO   ( 173-)  A  -129.2 half-chair C-delta/C-gamma (-126 degrees)
 373 PRO   ( 376-)  A   124.6 half-chair C-beta/C-alpha (126 degrees)
 434 PRO   ( 437-)  A  -119.9 half-chair C-delta/C-gamma (-126 degrees)
 453 PRO   ( 456-)  A   103.0 envelop C-beta (108 degrees)
 548 PRO   ( 551-)  A  -114.7 envelop C-gamma (-108 degrees)
 592 PRO   ( 595-)  A  -121.5 half-chair C-delta/C-gamma (-126 degrees)
 605 PRO   ( 608-)  A   -57.1 half-chair C-beta/C-alpha (-54 degrees)
 614 PRO   (   7-)  B   -55.5 half-chair C-beta/C-alpha (-54 degrees)
 745 PRO   ( 141-)  B   -65.2 envelop C-beta (-72 degrees)
 777 PRO   ( 173-)  B  -123.3 half-chair C-delta/C-gamma (-126 degrees)
1041 PRO   ( 437-)  B  -126.5 half-chair C-delta/C-gamma (-126 degrees)
1060 PRO   ( 456-)  B    99.1 envelop C-beta (108 degrees)
1199 PRO   ( 595-)  B  -112.3 envelop C-gamma (-108 degrees)
1212 PRO   ( 608-)  B    47.2 half-chair C-delta/C-gamma (54 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.

1227 NAG   (1617-)  B      O4  <-> 1240 BMA   (1618-)  B      C1     0.95    1.45  INTRA BF
 965 HIS   ( 361-)  B      CD2 <-> 1241 BMA   (1611-)  B      O3     0.82    1.98  INTRA BL
1227 NAG   (1617-)  B      C4  <-> 1240 BMA   (1618-)  B      C1     0.81    2.39  INTRA BF
 965 HIS   ( 361-)  B      NE2 <-> 1241 BMA   (1611-)  B      O3     0.67    2.03  INTRA BL
1095 HIS   ( 491-)  B      CE1 <-> 1241 BMA   (1611-)  B      O6     0.59    2.21  INTRA BL
1105 TYR   ( 501-)  B      CE2 <-> 1241 BMA   (1611-)  B      O6     0.51    1.89  INTRA BL
1105 TYR   ( 501-)  B      CZ  <-> 1241 BMA   (1611-)  B      O6     0.41    1.49  INTRA BL
 349 THR   ( 352-)  A      CG2 <->  351 ASP   ( 354-)  A      OD1    0.41    2.39  INTRA BL
 321 ASP   ( 324-)  A      O   <->  323 ARG   ( 326-)  A      N      0.40    2.30  INTRA BF
1105 TYR   ( 501-)  B      OH  <-> 1241 BMA   (1611-)  B      C6     0.39    1.51  INTRA BL
1105 TYR   ( 501-)  B      CE1 <-> 1241 BMA   (1611-)  B      C6     0.26    2.04  INTRA BL
1105 TYR   ( 501-)  B      OH  <-> 1241 BMA   (1611-)  B      C5     0.25    2.15  INTRA BL
 651 THR   (  44-)  B      O   <->  932 VAL   ( 328-)  B      CG1    0.24    2.56  INTRA
 401 HIS   ( 404-)  A      NE2 <-> 1243 HOH   (2080 )  A      O      0.18    2.52  INTRA BL
1105 TYR   ( 501-)  B      CE1 <-> 1241 BMA   (1611-)  B      C4     0.18    3.02  INTRA BL
 835 ARG   ( 231-)  B      NE  <-> 1194 GLU   ( 590-)  B      OE2    0.16    2.54  INTRA
   9 GLN   (   9-)  A      NE2 <->   71 LYS   (  71-)  A      NZ     0.16    2.69  INTRA BF
 863 GLN   ( 259-)  B      OE1 <-> 1093 LYS   ( 489-)  B      NZ     0.15    2.55  INTRA BL
1095 HIS   ( 491-)  B      CE1 <-> 1241 BMA   (1611-)  B      C6     0.15    3.05  INTRA BL
 964 HIS   ( 360-)  B      NE2 <-> 1244 HOH   (2062 )  B      O      0.14    2.56  INTRA BL
 609 ASP   (   2-)  B      CG  <->  610 PRO   (   3-)  B      CD     0.14    3.06  INTRA BF
 429 LYS   ( 432-)  A      NZ  <-> 1243 HOH   (2086 )  A      O      0.13    2.57  INTRA BL
 801 TYR   ( 197-)  B      O   <->  804 SER   ( 200-)  B      OG     0.13    2.27  INTRA
 652 ASN   (  45-)  B      O   <->  657 ASN   (  50-)  B      ND2    0.12    2.58  INTRA
 755 ARG   ( 151-)  B      NH1 <->  871 MET   ( 267-)  B      CG     0.12    2.98  INTRA BF
And so on for a total of 96 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.

1057 ARG   ( 453-)  B      -6.91
 450 ARG   ( 453-)  A      -6.83
   9 GLN   (   9-)  A      -6.42
 616 GLN   (   9-)  B      -6.22
1213 GLU   ( 609-)  B      -6.07
 613 GLN   (   6-)  B      -6.05
 519 GLU   ( 522-)  A      -6.04
1126 GLU   ( 522-)  B      -6.00
 889 GLN   ( 285-)  B      -5.69
 282 GLN   ( 285-)  A      -5.68
 233 ARG   ( 236-)  A      -5.66
   6 GLN   (   6-)  A      -5.63
1191 GLN   ( 587-)  B      -5.61
 584 GLN   ( 587-)  A      -5.60
 283 GLN   ( 286-)  A      -5.56
 840 ARG   ( 236-)  B      -5.56
 890 GLN   ( 286-)  B      -5.55
 597 HIS   ( 600-)  A      -5.54
 542 ARG   ( 545-)  A      -5.50
1125 TYR   ( 521-)  B      -5.49
1204 HIS   ( 600-)  B      -5.46
1149 ARG   ( 545-)  B      -5.44
 524 GLN   ( 527-)  A      -5.41
1131 GLN   ( 527-)  B      -5.40
1020 ASN   ( 416-)  B      -5.38
 518 TYR   ( 521-)  A      -5.31
 413 ASN   ( 416-)  A      -5.31
 689 GLN   (  82-)  B      -5.30
  82 GLN   (  82-)  A      -5.28
 606 GLU   ( 609-)  A      -5.23
 102 ASN   ( 102-)  A      -5.23
 918 TRP   ( 314-)  B      -5.21
 709 ASN   ( 102-)  B      -5.19
 844 ARG   ( 240-)  B      -5.18
 311 TRP   ( 314-)  A      -5.18
 944 ARG   ( 340-)  B      -5.13
 468 GLN   ( 471-)  A      -5.12
 604 TYR   ( 607-)  A      -5.11
1196 LEU   ( 592-)  B      -5.09
1075 GLN   ( 471-)  B      -5.09

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.

 232 ARG   ( 235-)  A       234 - TYR    237- ( A)         -4.96
 918 TRP   ( 314-)  B       920 - GLY    316- ( B)         -4.52

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.

  98 LEU   (  98-)  A   -3.43
 705 LEU   (  98-)  B   -3.41
1211 TYR   ( 607-)  B   -3.10
1017 ARG   ( 413-)  B   -2.79
 522 LEU   ( 525-)  A   -2.57
 405 ILE   ( 408-)  A   -2.53

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

1243 HOH   (2014 )  A      O
1243 HOH   (2026 )  A      O
1244 HOH   (2005 )  B      O
Bound group on Asn; dont flip   45 ASN  (  45-) A
Bound to: 1217 NAG  (1614-) A
Bound group on Asn; dont flip  413 ASN  ( 416-) A
Bound to: 1219 NAG  (1616-) A
Bound group on Asn; dont flip  477 ASN  ( 480-) A
Bound to: 1215 NAG  (1612-) A
Bound group on Asn; dont flip  652 ASN  (  45-) B
Bound to: 1224 NAG  (1614-) B
Bound group on Asn; dont flip 1020 ASN  ( 416-) B
Bound to: 1226 NAG  (1616-) B
Bound group on Asn; dont flip 1084 ASN  ( 480-) B
Bound to: 1222 NAG  (1612-) B
Marked this atom as acceptor 1231  CL  (1621-) A     CL
Marked this atom as acceptor 1236  CL  (1620-) B     CL
Metal-coordinating Histidine residue 358 fixed to   1
Metal-coordinating Histidine residue 362 fixed to   1
Metal-coordinating Histidine residue 965 fixed to   1
Metal-coordinating Histidine residue 969 fixed to   1

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.

   9 GLN   (   9-)  A
  25 GLN   (  25-)  A
 368 GLN   ( 371-)  A
 468 GLN   ( 471-)  A
 597 HIS   ( 600-)  A
 632 GLN   (  25-)  B
 959 GLN   ( 355-)  B
 975 GLN   ( 371-)  B
1202 GLN   ( 598-)  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.

  10 PHE   (  10-)  A      N
  13 ASP   (  13-)  A      N
  29 GLU   (  29-)  A      N
  81 GLN   (  81-)  A      N
  96 ARG   (  96-)  A      NH1
  97 THR   (  97-)  A      N
 128 CYS   ( 128-)  A      N
 148 ARG   ( 151-)  A      N
 148 ARG   ( 151-)  A      NH1
 150 TYR   ( 153-)  A      OH
 186 ASP   ( 189-)  A      N
 190 ASP   ( 193-)  A      N
 203 THR   ( 206-)  A      N
 233 ARG   ( 236-)  A      NH1
 238 TYR   ( 241-)  A      N
 248 HIS   ( 251-)  A      NE2
 252 ASP   ( 255-)  A      N
 257 SER   ( 260-)  A      N
 259 GLU   ( 262-)  A      N
 331 ALA   ( 334-)  A      N
 333 ASP   ( 336-)  A      N
 340 PHE   ( 343-)  A      N
 341 ARG   ( 344-)  A      NE
 352 GLN   ( 355-)  A      N
 364 GLN   ( 367-)  A      NE2
And so on for a total of 82 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.

 161 HIS   ( 164-)  A      NE2
 344 GLN   ( 347-)  A      OE1
 359 GLU   ( 362-)  A      OE1
 359 GLU   ( 362-)  A      OE2
 386 GLU   ( 389-)  A      OE2
 488 HIS   ( 491-)  A      NE2
 951 GLN   ( 347-)  B      OE1
 966 GLU   ( 362-)  B      OE1

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.

1244 HOH   (2029 )  B      O  0.90  K  4

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.

 207 ASP   ( 210-)  A   H-bonding suggests Asn
 636 GLU   (  29-)  B   H-bonding suggests Gln
1085 GLU   ( 481-)  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 :  -0.832
  2nd generation packing quality :  -1.264
  Ramachandran plot appearance   :  -0.852
  chi-1/chi-2 rotamer normality  :  -1.763
  Backbone conformation          :  -0.094

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.407 (tight)
  Bond angles                    :   0.590 (tight)
  Omega angle restraints         :   0.954
  Side chain planarity           :   0.380 (tight)
  Improper dihedral distribution :   0.583
  B-factor distribution          :   0.351
  Inside/Outside distribution    :   1.017

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.15


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -0.4
  Ramachandran plot appearance   :   0.1
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.407 (tight)
  Bond angles                    :   0.590 (tight)
  Omega angle restraints         :   0.954
  Side chain planarity           :   0.380 (tight)
  Improper dihedral distribution :   0.583
  B-factor distribution          :   0.351
  Inside/Outside distribution    :   1.017
==============

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Hydrogen bond networks
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Matthews' Coefficient
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Protein side chain planarity
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Puckering parameters
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Quality Control
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Ramachandran plot
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Symmetry Checks
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Ion Checks
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      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
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      Binding Sites
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    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
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Checking checks
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      Who checks the checkers
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