WHAT IF Check report

This file was created 2011-12-13 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

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

Verification log for pdb1a4g.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 : 0.488
CA-only RMS fit for the two chains : 0.182

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: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

 786 ZMR   ( 466-)  A  -
 789 ZMR   ( 466-)  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: What type of B-factor?

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

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

Crystal temperature (K) :100.000

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 7.86

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

 |  0.999661 -0.000064 -0.000060|
 | -0.000064  0.999061  0.000033|
 | -0.000060  0.000033  0.998139|
Proposed new scale matrix

 |  0.011342  0.006553  0.000000|
 |  0.000000  0.013104  0.000000|
 |  0.000000  0.000000  0.004531|
With corresponding cell

    A    =  88.166  B   =  88.131  C    = 220.681
    Alpha=  90.001  Beta=  90.002  Gamma= 120.017

The CRYST1 cell dimensions

    A    =  88.200  B   =  88.200  C    = 221.100
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 32.260
(Under-)estimated Z-score: 4.186

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.

   1 GLU   (  76-)  A      CA   CB   CG  122.53    4.2
   1 GLU   (  76-)  A      CB   CG   CD  119.41    4.0
   2 PRO   (  77-)  A     -CA  -C    N   124.85    5.3
   3 GLU   (  78-)  A      CA   CB   CG  122.54    4.2
   5 THR   (  80-)  A      N    CA   CB  103.33   -4.2
  17 GLN   (  92-)  A      CG   CD   NE2 124.77    5.6
  17 GLN   (  92-)  A      NE2  CD   OE1 115.01   -7.6
  22 ILE   (  97-)  A      N    CA   C    99.97   -4.0
  25 HIS   ( 100-)  A      CA   CB   CG  109.04   -4.8
  25 HIS   ( 100-)  A      CG   ND1  CE1 111.50    5.9
  25 HIS   ( 100-)  A      ND1  CE1  NE2 105.85   -4.5
  50 GLU   ( 125-)  A      CA   CB   CG  122.47    4.2
  53 HIS   ( 128-)  A      CG   ND1  CE1 110.33    4.7
  58 HIS   ( 133-)  A      CG   ND1  CE1 110.79    5.2
  63 PRO   ( 138-)  A     -CA  -C    N   124.97    5.4
  75 ASN   ( 150-)  A      CA   CB   CG  117.40    4.8
  79 HIS   ( 154-)  A      CG   ND1  CE1 112.05    6.5
  79 HIS   ( 154-)  A      ND1  CE1  NE2 106.33   -4.1
  93 ASN   ( 168-)  A      CB   CG   ND2 122.50    4.1
  95 ILE   ( 170-)  A      C    CA   CB  101.04   -4.8
  97 HIS   ( 172-)  A      CG   ND1  CE1 111.84    6.2
  97 HIS   ( 172-)  A      ND1  CE1  NE2 105.80   -4.5
 107 HIS   ( 182-)  A      CG   ND1  CE1 110.45    4.9
 118 ASP   ( 193-)  A      CA   CB   CG  119.04    6.4
 139 HIS   ( 214-)  A      CG   ND1  CE1 111.12    5.5
And so on for a total of 98 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.

 220 TYR   ( 295-)  A    4.91
 539 GLN   ( 224-)  B    4.47
 149 GLN   ( 224-)  A    4.27
 179 LYS   ( 254-)  A    4.18

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 : 1.554

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.

 636 TYR   ( 321-)  B      CB   4.38
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -1.491

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    -3.1
 751 THR   ( 436-)  B    -2.6
 429 ILE   ( 114-)  B    -2.6
  39 ILE   ( 114-)  A    -2.5
 361 THR   ( 436-)  A    -2.5
 430 ARG   ( 115-)  B    -2.4
 410 LEU   (  95-)  B    -2.4
 538 THR   ( 223-)  B    -2.4
 446 LEU   ( 131-)  B    -2.4
 555 THR   ( 240-)  B    -2.3
 245 THR   ( 320-)  A    -2.3
  40 ARG   ( 115-)  A    -2.3
 176 ARG   ( 251-)  A    -2.3
 471 ILE   ( 156-)  B    -2.2
 148 THR   ( 223-)  A    -2.2
 277 VAL   ( 352-)  A    -2.2
 721 GLY   ( 406-)  B    -2.2
 513 ASN   ( 198-)  B    -2.2
 711 SER   ( 396-)  B    -2.2
 165 THR   ( 240-)  A    -2.2
  81 ILE   ( 156-)  A    -2.1
 331 GLY   ( 406-)  A    -2.1
 667 VAL   ( 352-)  B    -2.1
 673 SER   ( 358-)  B    -2.1
 599 LYS   ( 284-)  B    -2.1
 467 LEU   ( 152-)  B    -2.1
 377 GLN   ( 452-)  A    -2.1
 276 PHE   ( 351-)  A    -2.0
 635 THR   ( 320-)  B    -2.0
 587 HIS   ( 272-)  B    -2.0
 566 ARG   ( 251-)  B    -2.0
 150 GLU   ( 225-)  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.

  59 TYR   ( 134-)  A  Poor phi/psi
  62 GLN   ( 137-)  A  PRO omega poor
 143 ASN   ( 218-)  A  Poor phi/psi
 148 THR   ( 223-)  A  Poor phi/psi
 150 GLU   ( 225-)  A  Poor phi/psi
 182 GLU   ( 257-)  A  Poor phi/psi
 234 ASP   ( 309-)  A  Poor phi/psi
 249 THR   ( 324-)  A  PRO omega poor
 267 LYS   ( 342-)  A  Poor phi/psi
 308 ASP   ( 383-)  A  Poor phi/psi
 332 TRP   ( 407-)  A  Poor phi/psi
 429 ILE   ( 114-)  B  omega poor
 449 TYR   ( 134-)  B  Poor phi/psi
 452 GLN   ( 137-)  B  PRO omega poor
 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
 657 LYS   ( 342-)  B  Poor phi/psi
 688 ARG   ( 373-)  B  Poor phi/psi
 698 ASP   ( 383-)  B  Poor phi/psi
 722 TRP   ( 407-)  B  Poor phi/psi
 754 SER   ( 439-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.885

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
  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
  57 THR   ( 132-)  A      0
  58 HIS   ( 133-)  A      0
  59 TYR   ( 134-)  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 416 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]

   2 PRO   (  77-)  A    0.51 HIGH
  24 PRO   (  99-)  A    0.49 HIGH
  36 PRO   ( 111-)  A    0.46 HIGH
  42 PRO   ( 117-)  A    0.48 HIGH
  48 PRO   ( 123-)  A    0.46 HIGH
 120 PRO   ( 195-)  A    0.46 HIGH
 191 PRO   ( 266-)  A    0.49 HIGH
 225 PRO   ( 300-)  A    0.50 HIGH
 250 PRO   ( 325-)  A    0.48 HIGH
 252 PRO   ( 327-)  A    0.49 HIGH
 260 PRO   ( 335-)  A    0.47 HIGH
 311 PRO   ( 386-)  A    0.51 HIGH
 330 PRO   ( 405-)  A    0.51 HIGH
 347 PRO   ( 422-)  A    0.45 HIGH
 392 PRO   (  77-)  B    0.49 HIGH
 397 PRO   (  82-)  B    0.47 HIGH
 414 PRO   (  99-)  B    0.47 HIGH
 426 PRO   ( 111-)  B    0.48 HIGH
 432 PRO   ( 117-)  B    0.47 HIGH
 438 PRO   ( 123-)  B    0.50 HIGH
 453 PRO   ( 138-)  B    0.49 HIGH
 581 PRO   ( 266-)  B    0.46 HIGH
 615 PRO   ( 300-)  B    0.48 HIGH
 642 PRO   ( 327-)  B    0.50 HIGH
 650 PRO   ( 335-)  B    0.47 HIGH
 701 PRO   ( 386-)  B    0.51 HIGH
 720 PRO   ( 405-)  B    0.51 HIGH

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.

 163 MET   ( 238-)  A      SD  <->  201 CYS   ( 276-)  A      SG     0.21    3.24  INTRA BL
 105 ALA   ( 180-)  A      C   <->  153 CYS   ( 228-)  A      SG     0.13    3.27  INTRA BL
 553 MET   ( 238-)  B      SD  <->  591 CYS   ( 276-)  B      SG     0.13    3.32  INTRA BL
 495 ALA   ( 180-)  B      C   <->  543 CYS   ( 228-)  B      SG     0.10    3.30  INTRA BL
 730 LYS   ( 415-)  B      NZ  <->  791 HOH   ( 640 )  B      O      0.08    2.62  INTRA BF
 681 ARG   ( 366-)  B      C   <->  691 MET   ( 376-)  B      SD     0.08    3.32  INTRA BL
 220 TYR   ( 295-)  A      CE2 <->  790 HOH   ( 674 )  A      O      0.08    2.72  INTRA BF
 472 SER   ( 157-)  B      OG  <->  487 HIS   ( 172-)  B      NE2    0.07    2.63  INTRA BL
 415 HIS   ( 100-)  B      NE2 <->  754 SER   ( 439-)  B      OG     0.03    2.67  INTRA BL
 786 ZMR   ( 466-)  A      NH1 <->  790 HOH   ( 701 )  A      O      0.03    2.67  INTRA BF
 468 ARG   ( 153-)  B      NH2 <->  791 HOH   ( 683 )  B      O      0.03    2.67  INTRA BL
 291 ARG   ( 366-)  A      C   <->  301 MET   ( 376-)  A      SD     0.03    3.37  INTRA BL
  11 CYS   (  86-)  A      SG  <->  344 CYS   ( 419-)  A      C      0.02    3.38  INTRA BL
 416 ARG   ( 101-)  B      N   <->  417 PHE   ( 102-)  B      N      0.02    2.58  INTRA BL
 142 ALA   ( 217-)  A      N   <->  143 ASN   ( 218-)  A      N      0.02    2.58  INTRA BL
 222 ALA   ( 297-)  A      N   <->  223 LYS   ( 298-)  A      N      0.01    2.59  INTRA BL
  77 LEU   ( 152-)  A      O   <->   79 HIS   ( 154-)  A      ND1    0.01    2.69  INTRA BL
 613 LYS   ( 298-)  B      NZ  <->  651 CYS   ( 336-)  B      O      0.01    2.69  INTRA BL
 415 HIS   ( 100-)  B      C   <->  417 PHE   ( 102-)  B      N      0.01    2.89  INTRA BL

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      -7.30
 402 GLN   (  87-)  B      -7.15
  49 LYS   ( 124-)  A      -6.47
 659 ARG   ( 344-)  B      -6.43
  31 ARG   ( 106-)  A      -6.37
 750 LYS   ( 435-)  B      -6.34
 360 LYS   ( 435-)  A      -6.33
 421 ARG   ( 106-)  B      -6.29
 269 ARG   ( 344-)  A      -6.23
 439 LYS   ( 124-)  B      -6.09
 500 ARG   ( 185-)  B      -6.07
 456 TYR   ( 141-)  B      -6.04
 110 ARG   ( 185-)  A      -5.94
 298 ARG   ( 373-)  A      -5.79
 688 ARG   ( 373-)  B      -5.75
 220 TYR   ( 295-)  A      -5.68
  62 GLN   ( 137-)  A      -5.61
  26 ARG   ( 101-)  A      -5.48
 379 LEU   ( 454-)  A      -5.41
 452 GLN   ( 137-)  B      -5.41
 464 ARG   ( 149-)  B      -5.32
 610 TYR   ( 295-)  B      -5.27
  67 TYR   ( 142-)  A      -5.26
 328 LYS   ( 403-)  A      -5.23
 457 TYR   ( 142-)  B      -5.20
 343 LYS   ( 418-)  A      -5.19
 513 ASN   ( 198-)  B      -5.17
 416 ARG   ( 101-)  B      -5.14
 461 ARG   ( 146-)  B      -5.14
  74 ARG   ( 149-)  A      -5.09
 718 LYS   ( 403-)  B      -5.06
 190 PHE   ( 265-)  A      -5.04
  71 ARG   ( 146-)  A      -5.03
 571 ARG   ( 256-)  B      -5.03
 373 MET   ( 448-)  A      -5.02
 733 LYS   ( 418-)  B      -5.01
 580 PHE   ( 265-)  B      -5.00

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.

 456 TYR   ( 141-)  B       458 - ASN    143- ( B)         -5.32

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.

 790 HOH   ( 669 )  A      O     37.92   30.37  -44.12
 791 HOH   ( 643 )  B      O     38.27   36.68  -39.02

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.

 790 HOH   ( 531 )  A      O
 790 HOH   ( 651 )  A      O
 790 HOH   ( 656 )  A      O
 791 HOH   ( 507 )  B      O
 791 HOH   ( 564 )  B      O
Bound group on Asn; dont flip  208 ASN  ( 283-) A
Bound to:  781 NAG  (   1-) A
Bound group on Asn; dont flip  598 ASN  ( 283-) B
Bound to:  782 NAG  (   1-) B

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
 423 ASN   ( 108-)  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.

  17 GLN   (  92-)  A      NE2
  26 ARG   ( 101-)  A      NE
  40 ARG   ( 115-)  A      NH2
  44 ILE   ( 119-)  A      N
  60 ALA   ( 135-)  A      N
  75 ASN   ( 150-)  A      N
  92 GLU   ( 167-)  A      N
 102 SER   ( 177-)  A      N
 119 GLY   ( 194-)  A      N
 127 LYS   ( 202-)  A      NZ
 134 TYR   ( 209-)  A      N
 143 ASN   ( 218-)  A      N
 143 ASN   ( 218-)  A      ND2
 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
 284 LYS   ( 359-)  A      N
 316 ASP   ( 391-)  A      N
 336 GLY   ( 411-)  A      N
 344 CYS   ( 419-)  A      N
 354 VAL   ( 429-)  A      N
And so on for a total of 51 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.

 197 HIS   ( 272-)  A      NE2
 199 GLU   ( 274-)  A      OE2
 208 ASN   ( 283-)  A      OD1
 232 GLU   ( 307-)  A      OE1
 587 HIS   ( 272-)  B      NE2
 589 GLU   ( 274-)  B      OE2
 598 ASN   ( 283-)  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+.

 785  CA   (   2-)  A     0.74   0.98 Scores about as good as NA
 787  CA   (   2-)  B     0.74   0.98 Scores about as good as NA
 788  CA   (   3-)  B   -.-  -.-  Low probability ion. Occ=0.58

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
 108 ASP   ( 183-)  A   H-bonding suggests Asn; but Alt-Rotamer
 166 ASP   ( 241-)  A   H-bonding suggests Asn
 234 ASP   ( 309-)  A   H-bonding suggests Asn
 462 GLU   ( 147-)  B   H-bonding suggests Gln
 498 ASP   ( 183-)  B   H-bonding suggests Asn; but Alt-Rotamer
 556 ASP   ( 241-)  B   H-bonding suggests Asn
 638 ASP   ( 323-)  B   H-bonding suggests Asn; but Alt-Rotamer
 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 :  -0.973
  2nd generation packing quality :  -1.605
  Ramachandran plot appearance   :  -1.491
  chi-1/chi-2 rotamer normality  :  -1.885
  Backbone conformation          :  -1.033

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.550 (tight)
  Bond angles                    :   1.292
  Omega angle restraints         :   0.869
  Side chain planarity           :   0.482 (tight)
  Improper dihedral distribution :   1.058
  Inside/Outside distribution    :   1.043

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 :  -0.3
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :  -0.2
  chi-1/chi-2 rotamer normality  :  -0.6
  Backbone conformation          :  -0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.550 (tight)
  Bond angles                    :   1.292
  Omega angle restraints         :   0.869
  Side chain planarity           :   0.482 (tight)
  Improper dihedral distribution :   1.058
  Inside/Outside distribution    :   1.043
==============

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.