WHAT IF Check report

This file was created 2011-12-17 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 pdb1nsb.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 : 0.464
CA-only RMS fit for the two chains : 0.140

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: Atoms on special positions with too high occupancy

Atoms detected at special positions with too high occupancy. These atoms will upon expansion by applying the symmetry matrices, result in multiple atoms at (nearly) the same position.

Atoms at special positions should have an occupancy that is smaller than 1/N where N is the multiplicity of the symmetry operator. So, an atom on a 2-fold axis should have occupancy less or equal 0.5, for a 3-fold axis this is 0.33, etc. If the occupancy is too high, application of the symmetry matrices will result in the presence of more than one atom at (nearly) the same position. WHAT IF will certainly report this as bumps, but other things will also go wrong. E.g. 3 waters at the same position will make three times more hydrogen bonds, they will be counted three times in packing analysis, etc. So, I suggest you first fix this problem and run WHAT IF again on the fixed PDB file. An atom is considered to be located at a special position if it is within 0.3 Angstrom from one of its own symmetry copies. See also the next check...

 786  CA   (   3-)  B  A  CA

Error: Atoms too close to symmetry axis

The atoms listed in the table below are closer than 0.77 Angstrom to a proper symmetry axis. This creates a bump between the atom and its symmetry relative(s). It is likely that these represent refinement artefacts. The number in the right-hand column is the number of the symmetry matrix that was applied when this problem was detected.

 786  CA   (   3-)  B  A  CA       4

Warning: Chain identifier inconsistency

WHAT IF believes that certain residue(s) have the wrong chain identifier. It has corrected these chain identifiers as indicated in the table. In this table the residues (ligands, drugs, lipids, ions, sugars, etc) that got their chain identifier corrected are listed with the new chain identifier that is used throughout this validation report. WHAT IF does not care about the chain identifiers of water molecules.

 786  CA   (   3-)  B  A

Administrative problems that can generate validation failures

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

 269 ARG   ( 344-)  A  -   CD
 269 ARG   ( 344-)  A  -   NE
 269 ARG   ( 344-)  A  -   CZ
 269 ARG   ( 344-)  A  -   NH1
 269 ARG   ( 344-)  A  -   NH2
 659 ARG   ( 344-)  B  -   CD
 659 ARG   ( 344-)  B  -   NE
 659 ARG   ( 344-)  B  -   CZ
 659 ARG   ( 344-)  B  -   NH1
 659 ARG   ( 344-)  B  -   NH2

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: 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:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Warning: More than 2 percent of buried atoms has low B-factor

For protein structures determined at room temperature, no more than about 1 percent of the B factors of buried atoms is below 5.0.

Percentage of buried atoms with B less than 5 : 3.18

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.

   4 TRP   (  79-)  A      NE1  CE2   1.33   -4.1
  92 GLU   ( 167-)  A      CA   CB    1.45   -4.1
 285 ILE   ( 360-)  A      CA   CB    1.61    4.1
 363 HIS   ( 438-)  A      CG   CD2   1.40    4.1
 497 HIS   ( 182-)  B      CD2  NE2   1.29   -4.1
 546 ILE   ( 231-)  B      CA   CB    1.62    4.3
 667 VAL   ( 352-)  B      CA   CB    1.62    4.6

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

 |  1.002280  0.001321 -0.000316|
 |  0.001321  1.003959 -0.000352|
 | -0.000316 -0.000352  0.996428|
Proposed new scale matrix

 |  0.011215  0.006454  0.000006|
 | -0.000017  0.012938  0.000005|
 |  0.000001  0.000002  0.004504|
With corresponding cell

    A    =  89.100  B   =  89.109  C    = 222.020
    Alpha=  90.017  Beta=  90.036  Gamma= 119.843

The CRYST1 cell dimensions

    A    =  88.900  B   =  88.900  C    = 222.800
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 146.682
(Under-)estimated Z-score: 8.926

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.

   2 PRO   (  77-)  A     -CA  -C    N   127.02    6.7
   3 GLU   (  78-)  A      CA   CB   CG  127.15    6.5
   3 GLU   (  78-)  A      CB   CG   CD  123.01    6.1
   4 TRP   (  79-)  A      CB   CG   CD1 117.65   -6.2
   4 TRP   (  79-)  A      CG   CD1  NE1 104.71   -4.2
   4 TRP   (  79-)  A      CE3  CD2  CG  140.26    6.4
   4 TRP   (  79-)  A      CG   CD2  CE2 101.18   -5.0
   5 THR   (  80-)  A      N    CA   CB   98.06   -7.3
   5 THR   (  80-)  A      C    CA   CB  118.93    4.6
   5 THR   (  80-)  A      CA   CB   OG1 102.97   -4.4
  17 GLN   (  92-)  A      NE2  CD   OE1 118.20   -4.4
  25 HIS   ( 100-)  A      CA   CB   CG  108.48   -5.3
  26 ARG   ( 101-)  A      CB   CG   CD   97.25   -8.4
  26 ARG   ( 101-)  A      NE   CZ   NH2 112.23   -4.1
  33 ASN   ( 108-)  A      CB   CG   ND2 127.23    7.2
  33 ASN   ( 108-)  A      ND2  CG   OD1 115.67   -6.9
  43 PHE   ( 118-)  A      CA   CB   CG  118.04    4.2
  49 LYS   ( 124-)  A      C    CA   CB  101.80   -4.4
  53 HIS   ( 128-)  A      CD2  CG   ND1 110.31    4.2
  58 HIS   ( 133-)  A      CB   CG   ND1 128.86    4.8
  58 HIS   ( 133-)  A      CB   CG   CD2 123.85   -4.0
  63 PRO   ( 138-)  A     -CA  -C    N   125.28    5.6
  79 HIS   ( 154-)  A      CB   CG   ND1 131.59    6.7
  79 HIS   ( 154-)  A      CG   ND1  CE1 110.17    4.6
  79 HIS   ( 154-)  A      CB   CG   CD2 123.22   -4.5
And so on for a total of 224 lines.

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.

 539 GLN   ( 224-)  B    4.92
 618 LYS   ( 303-)  B    4.69
 721 GLY   ( 406-)  B    4.63
 217 ASP   ( 292-)  A    4.41
 331 GLY   ( 406-)  A    4.12

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 : 1.524

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.

 423 ASN   ( 108-)  B    4.89

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

 528 TYR   ( 213-)  B      OH   4.84
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -1.264

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.

 449 TYR   ( 134-)  B    -3.2
  59 TYR   ( 134-)  A    -3.2
 566 ARG   ( 251-)  B    -2.5
  39 ILE   ( 114-)  A    -2.5
 430 ARG   ( 115-)  B    -2.4
 361 THR   ( 436-)  A    -2.4
 538 THR   ( 223-)  B    -2.4
 245 THR   ( 320-)  A    -2.4
  40 ARG   ( 115-)  A    -2.4
 284 LYS   ( 359-)  A    -2.3
 410 LEU   (  95-)  B    -2.3
 555 THR   ( 240-)  B    -2.3
 176 ARG   ( 251-)  A    -2.3
 751 THR   ( 436-)  B    -2.2
 635 THR   ( 320-)  B    -2.2
 277 VAL   ( 352-)  A    -2.2
  56 LEU   ( 131-)  A    -2.2
 467 LEU   ( 152-)  B    -2.2
 599 LYS   ( 284-)  B    -2.2
  81 ILE   ( 156-)  A    -2.2
 674 LYS   ( 359-)  B    -2.2
 721 GLY   ( 406-)  B    -2.1
 331 GLY   ( 406-)  A    -2.1
 421 ARG   ( 106-)  B    -2.1
 243 THR   ( 318-)  A    -2.1
 148 THR   ( 223-)  A    -2.1
 667 VAL   ( 352-)  B    -2.1
 711 SER   ( 396-)  B    -2.1
 513 ASN   ( 198-)  B    -2.1
 221 THR   ( 296-)  A    -2.1
 471 ILE   ( 156-)  B    -2.1
 546 ILE   ( 231-)  B    -2.1
 446 LEU   ( 131-)  B    -2.1
 165 THR   ( 240-)  A    -2.0
 621 VAL   ( 306-)  B    -2.0
 540 GLU   ( 225-)  B    -2.0
 652 GLU   ( 337-)  B    -2.0
 708 LEU   ( 393-)  B    -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.

  14 SER   (  89-)  A  Poor phi/psi
  39 ILE   ( 114-)  A  omega poor
  59 TYR   ( 134-)  A  Poor phi/psi
  62 GLN   ( 137-)  A  PRO omega poor
 117 VAL   ( 192-)  A  omega poor
 135 THR   ( 210-)  A  Poor phi/psi
 148 THR   ( 223-)  A  Poor phi/psi, omega poor
 150 GLU   ( 225-)  A  Poor phi/psi
 249 THR   ( 324-)  A  PRO omega poor
 296 THR   ( 371-)  A  Poor phi/psi
 308 ASP   ( 383-)  A  Poor phi/psi
 332 TRP   ( 407-)  A  Poor phi/psi
 449 TYR   ( 134-)  B  Poor phi/psi
 452 GLN   ( 137-)  B  PRO omega poor
 488 MET   ( 173-)  B  Poor phi/psi
 538 THR   ( 223-)  B  Poor phi/psi
 540 GLU   ( 225-)  B  Poor phi/psi
 624 ASP   ( 309-)  B  Poor phi/psi
 639 THR   ( 324-)  B  PRO omega poor
 698 ASP   ( 383-)  B  Poor phi/psi
 722 TRP   ( 407-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.361

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 TRP   (  79-)  A      0
   5 THR   (  80-)  A      0
  12 GLN   (  87-)  A      0
  14 SER   (  89-)  A      0
  18 LYS   (  93-)  A      0
  19 ALA   (  94-)  A      0
  20 LEU   (  95-)  A      0
  25 HIS   ( 100-)  A      0
  27 PHE   ( 102-)  A      0
  33 ASN   ( 108-)  A      0
  35 ALA   ( 110-)  A      0
  39 ILE   ( 114-)  A      0
  40 ARG   ( 115-)  A      0
  41 GLU   ( 116-)  A      0
  42 PRO   ( 117-)  A      0
  49 LYS   ( 124-)  A      0
  50 GLU   ( 125-)  A      0
  58 HIS   ( 133-)  A      0
  62 GLN   ( 137-)  A      0
  63 PRO   ( 138-)  A      0
  66 TYR   ( 141-)  A      0
  67 TYR   ( 142-)  A      0
  68 ASN   ( 143-)  A      0
  70 THR   ( 145-)  A      0
  74 ARG   ( 149-)  A      0
And so on for a total of 415 lines.

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

   7 PRO   (  82-)  A    0.46 HIGH
 252 PRO   ( 327-)  A    0.51 HIGH
 510 PRO   ( 195-)  B    0.15 LOW
 642 PRO   ( 327-)  B    0.46 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].

  48 PRO   ( 123-)  A  -134.3 half-chair C-delta/C-gamma (-126 degrees)
 640 PRO   ( 325-)  B   -55.9 half-chair C-beta/C-alpha (-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.

 613 LYS   ( 298-)  B      NZ  <->  651 CYS   ( 336-)  B      O      0.23    2.47  INTRA BL
  31 ARG   ( 106-)  A      NH2 <->  788 HOH   (1850 )  A      O      0.18    2.52  INTRA BF
 306 ARG   ( 381-)  A      NH1 <->  317 ALA   ( 392-)  A      O      0.15    2.55  INTRA
 472 SER   ( 157-)  B      OG  <->  487 HIS   ( 172-)  B      NE2    0.14    2.56  INTRA BL
 408 LYS   (  93-)  B      NZ  <->  789 HOH   (1344 )  B      O      0.14    2.56  INTRA BL
 223 LYS   ( 298-)  A      NZ  <->  261 CYS   ( 336-)  A      O      0.13    2.57  INTRA
 306 ARG   ( 381-)  A      NH2 <->  316 ASP   ( 391-)  A      CB     0.12    2.98  INTRA
 107 HIS   ( 182-)  A      ND1 <->  109 GLY   ( 184-)  A      N      0.12    2.88  INTRA BL
 618 LYS   ( 303-)  B      NZ  <->  700 ASP   ( 385-)  B      OD1    0.11    2.59  INTRA BL
 495 ALA   ( 180-)  B      C   <->  543 CYS   ( 228-)  B      SG     0.10    3.30  INTRA BL
 496 CYS   ( 181-)  B      SG  <->  545 CYS   ( 230-)  B      SG     0.10    3.35  INTRA BL
 747 GLY   ( 432-)  B      N   <->  748 GLY   ( 433-)  B      N      0.09    2.51  INTRA B3
 786  CA   (   3-)  B     CA   <->  789 HOH   (1062 )  B      O      0.09    2.71  INTRA
 464 ARG   ( 149-)  B      NH1 <->  789 HOH   (1958 )  B      O      0.08    2.62  INTRA
 508 ASP   ( 193-)  B      CG  <->  517 LYS   ( 202-)  B      NZ     0.08    3.02  INTRA BL
 620 ASN   ( 305-)  B      OD1 <->  622 GLU   ( 307-)  B      N      0.08    2.62  INTRA BL
 228 LYS   ( 303-)  A      NZ  <->  310 ASP   ( 385-)  A      OD1    0.08    2.62  INTRA
 681 ARG   ( 366-)  B      NE  <->  789 HOH   (1933 )  B      O      0.07    2.63  INTRA
 391 GLU   (  76-)  B      CD  <->  500 ARG   ( 185-)  B      NH2    0.07    3.03  INTRA
 163 MET   ( 238-)  A      SD  <->  201 CYS   ( 276-)  A      SG     0.07    3.38  INTRA BL
 230 ASN   ( 305-)  A      OD1 <->  232 GLU   ( 307-)  A      N      0.07    2.63  INTRA
   8 ARG   (  83-)  A      O   <->  280 ARG   ( 355-)  A      NE     0.07    2.63  INTRA BL
 105 ALA   ( 180-)  A      C   <->  153 CYS   ( 228-)  A      SG     0.07    3.33  INTRA BL
 297 GLU   ( 372-)  A      CG  <->  788 HOH   (1804 )  A      O      0.06    2.74  INTRA
 200 GLU   ( 275-)  A      OE1 <->  216 ARG   ( 291-)  A      NH1    0.06    2.64  INTRA BL
And so on for a total of 60 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.

  12 GLN   (  87-)  A      -7.26
 402 GLN   (  87-)  B      -7.05
 659 ARG   ( 344-)  B      -6.70
 269 ARG   ( 344-)  A      -6.40
 421 ARG   ( 106-)  B      -6.33
  49 LYS   ( 124-)  A      -6.33
 750 LYS   ( 435-)  B      -6.29
 360 LYS   ( 435-)  A      -6.27
 439 LYS   ( 124-)  B      -6.13
  31 ARG   ( 106-)  A      -5.97
 110 ARG   ( 185-)  A      -5.96
 500 ARG   ( 185-)  B      -5.94
 456 TYR   ( 141-)  B      -5.91
 452 GLN   ( 137-)  B      -5.90
  62 GLN   ( 137-)  A      -5.89
 688 ARG   ( 373-)  B      -5.84
 298 ARG   ( 373-)  A      -5.74
 379 LEU   ( 454-)  A      -5.58
  26 ARG   ( 101-)  A      -5.48
 328 LYS   ( 403-)  A      -5.27
 416 ARG   ( 101-)  B      -5.23
 123 ASN   ( 198-)  A      -5.22
 457 TYR   ( 142-)  B      -5.20
 343 LYS   ( 418-)  A      -5.13
 513 ASN   ( 198-)  B      -5.13
 449 TYR   ( 134-)  B      -5.11
 464 ARG   ( 149-)  B      -5.04
  74 ARG   ( 149-)  A      -5.03
 461 ARG   ( 146-)  B      -5.02
  67 TYR   ( 142-)  A      -5.02

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: 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.

 788 HOH   (1819 )  A      O     23.88   46.44   -0.64
 789 HOH   (1838 )  B      O     19.88   39.29   -0.24
 789 HOH   (1884 )  B      O     -8.89   37.62   22.79

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.

  17 GLN   (  92-)  A
  58 HIS   ( 133-)  A
  93 ASN   ( 168-)  A
 154 ASN   ( 229-)  A
 423 ASN   ( 108-)  B
 448 HIS   ( 133-)  B
 483 ASN   ( 168-)  B
 544 ASN   ( 229-)  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.

  44 ILE   ( 119-)  A      N
  60 ALA   ( 135-)  A      N
  75 ASN   ( 150-)  A      N
  78 ARG   ( 153-)  A      NE
 119 GLY   ( 194-)  A      N
 121 ASP   ( 196-)  A      N
 134 TYR   ( 209-)  A      N
 149 GLN   ( 224-)  A      NE2
 151 SER   ( 226-)  A      N
 198 THR   ( 273-)  A      OG1
 218 ASN   ( 293-)  A      N
 221 THR   ( 296-)  A      N
 253 ASP   ( 328-)  A      N
 273 LYS   ( 348-)  A      N
 276 PHE   ( 351-)  A      N
 336 GLY   ( 411-)  A      N
 344 CYS   ( 419-)  A      N
 354 VAL   ( 429-)  A      N
 359 LYS   ( 434-)  A      N
 430 ARG   ( 115-)  B      NH2
 434 ILE   ( 119-)  B      N
 450 ALA   ( 135-)  B      N
 457 TYR   ( 142-)  B      N
 465 ASN   ( 150-)  B      N
 483 ASN   ( 168-)  B      N
 502 TRP   ( 187-)  B      NE1
 509 GLY   ( 194-)  B      N
 517 LYS   ( 202-)  B      NZ
 524 TYR   ( 209-)  B      N
 541 SER   ( 226-)  B      N
 608 ASN   ( 293-)  B      N
 609 SER   ( 294-)  B      OG
 611 THR   ( 296-)  B      N
 654 ASN   ( 339-)  B      N
 663 LYS   ( 348-)  B      N
 666 PHE   ( 351-)  B      N
 726 GLY   ( 411-)  B      N
 734 CYS   ( 419-)  B      N
 744 VAL   ( 429-)  B      N

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.

 197 HIS   ( 272-)  A      NE2
 208 ASN   ( 283-)  A      OD1
 587 HIS   ( 272-)  B      NE2
 598 ASN   ( 283-)  B      OD1

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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+.

 786  CA   (   3-)  B     0.62   0.82 Scores about as good as NA *S

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.

 789 HOH   (1615 )  B      O  0.98  K  5 NCS 1/1

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.

   3 GLU   (  78-)  A   H-bonding suggests Gln
  50 GLU   ( 125-)  A   H-bonding suggests Gln
 108 ASP   ( 183-)  A   H-bonding suggests Asn; but Alt-Rotamer
 166 ASP   ( 241-)  A   H-bonding suggests Asn
 462 GLU   ( 147-)  B   H-bonding suggests Gln
 556 ASP   ( 241-)  B   H-bonding suggests Asn
 704 ASP   ( 389-)  B   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.154
  2nd generation packing quality :  -1.647
  Ramachandran plot appearance   :  -1.264
  chi-1/chi-2 rotamer normality  :  -2.361
  Backbone conformation          :  -1.024

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.931
  Bond angles                    :   1.668
  Omega angle restraints         :   1.057
  Side chain planarity           :   0.927
  Improper dihedral distribution :   1.307
  B-factor distribution          :   0.475
  Inside/Outside distribution    :   1.041

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.4
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :  -0.0
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :  -0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.931
  Bond angles                    :   1.668
  Omega angle restraints         :   1.057
  Side chain planarity           :   0.927
  Improper dihedral distribution :   1.307
  B-factor distribution          :   0.475
  Inside/Outside distribution    :   1.041
==============

WHAT IF
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Bond lengths and angles, DNA/RNA
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DSSP
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      Dictionary of protein secondary structure: pattern
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Hydrogen bond networks
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      protein structures
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Matthews' Coefficient
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Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
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Puckering parameters
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Quality Control
    G.Vriend and C.Sander,
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      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
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      Stereochemistry of Polypeptide Chain Conformations
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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.