WHAT IF Check report

This file was created 2011-12-21 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 pdb1b1y.ent

Checks that need to be done early-on in validation

Warning: Ligands for which a topology was generated automatically

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

 503 BGC   ( 551-)  A  -
 504 BGC   ( 552-)  A  -

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) :291.000

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.

  50 TRP   (  54-)  A      CG   CD2   1.36   -4.1
 463 ILE   ( 467-)  A      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

 |  1.002535  0.000070 -0.000764|
 |  0.000070  1.002661 -0.000333|
 | -0.000764 -0.000333  1.003014|
Proposed new scale matrix

 |  0.013833  0.000000  0.000011|
 |  0.000000  0.013831  0.000005|
 |  0.000003  0.000001  0.003980|
With corresponding cell

    A    =  72.291  B   =  72.300  C    = 251.256
    Alpha=  90.038  Beta=  90.087  Gamma=  90.001

The CRYST1 cell dimensions

    A    =  72.110  B   =  72.110  C    = 250.510
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 129.739
(Under-)estimated Z-score: 8.395

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.

  15 ASP   (  19-)  A      CA   CB   CG  120.94    8.3
  17 VAL   (  21-)  A      N    CA   C    98.15   -4.7
  18 SER   (  22-)  A      N    CA   C   122.55    4.1
  22 ARG   (  26-)  A      CG   CD   NE  117.63    4.2
  48 VAL   (  52-)  A      N    CA   C    97.32   -5.0
  49 TRP   (  53-)  A      CG   CD2  CE2 101.62   -4.6
  50 TRP   (  54-)  A      CG   CD2  CE2 101.99   -4.3
  53 VAL   (  57-)  A      N    CA   CB  102.93   -4.5
  54 GLU   (  58-)  A     -O   -C    N   112.97   -6.3
  54 GLU   (  58-)  A     -CA  -C    N   130.89    7.3
  54 GLU   (  58-)  A      CA   CB   CG  125.22    5.6
  63 TRP   (  67-)  A      CG   CD2  CE2 101.53   -4.7
  70 PHE   (  74-)  A      CA   CB   CG  119.22    5.4
  74 GLN   (  78-)  A      CG   CD   NE2 123.11    4.5
  74 GLN   (  78-)  A      NE2  CD   OE1 117.49   -5.1
  81 GLN   (  85-)  A      N    CA   C    98.36   -4.6
  85 SER   (  89-)  A      N    CA   C   125.29    5.0
  87 HIS   (  91-)  A      CB   CG   ND1 129.65    5.4
  87 HIS   (  91-)  A      CB   CG   CD2 123.69   -4.2
  93 VAL   (  97-)  A      CG1  CB   CG2 101.97   -4.0
  94 GLY   (  98-)  A     -CA  -C    N   106.41   -4.9
 100 PRO   ( 104-)  A     -CA  -C    N   125.19    5.5
 100 PRO   ( 104-)  A      N    CA   CB  107.43    4.0
 101 ILE   ( 105-)  A      CB   CG1  CD1 104.91   -4.2
 104 TRP   ( 108-)  A      CD1  CG   CD2 113.83    4.7
And so on for a total of 134 lines.

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

  93 VAL   (  97-)  A      CB    -7.3   -42.52   -32.96
 484 VAL   ( 488-)  A      CB    -7.6   -42.86   -32.96
 486 PRO   ( 490-)  A      N     -6.3   -23.15    -2.48
The average deviation= 1.406

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.

 422 GLY   ( 426-)  A    7.33
  85 SER   (  89-)  A    6.88
 127 GLU   ( 131-)  A    6.42
 210 ASP   ( 214-)  A    6.16
 344 GLU   ( 348-)  A    5.87
  64 SER   (  68-)  A    5.44
 192 TRP   ( 196-)  A    5.34
 303 ALA   ( 307-)  A    5.33
 205 LYS   ( 209-)  A    5.22
  48 VAL   (  52-)  A    5.19
 390 ARG   ( 394-)  A    5.05
 146 GLN   ( 150-)  A    4.91
   2 LYS   (   6-)  A    4.84
 336 THR   ( 340-)  A    4.66
  17 VAL   (  21-)  A    4.59
  81 GLN   (  85-)  A    4.48
 338 ALA   ( 342-)  A    4.46
 320 ARG   ( 324-)  A    4.39
 387 THR   ( 391-)  A    4.37
 305 GLU   ( 309-)  A    4.36
  89 CYS   (  93-)  A    4.35
 304 ALA   ( 308-)  A    4.32
 126 ILE   ( 130-)  A    4.29
  18 SER   (  22-)  A    4.17
 370 ASN   ( 374-)  A    4.17
  19 VAL   (  23-)  A    4.10

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 : 1.982

Torsion-related checks

Warning: Ramachandran Z-score low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is a bit low.

Ramachandran Z-score : -3.599

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.

 486 PRO   ( 490-)  A    -3.1
 195 PRO   ( 199-)  A    -3.0
 187 PRO   ( 191-)  A    -3.0
 182 ARG   ( 186-)  A    -2.8
 475 PRO   ( 479-)  A    -2.7
 463 ILE   ( 467-)  A    -2.5
 353 PRO   ( 357-)  A    -2.5
 451 LEU   ( 455-)  A    -2.4
 422 GLY   ( 426-)  A    -2.4
 124 ARG   ( 128-)  A    -2.3
 311 TYR   ( 315-)  A    -2.3
 379 ARG   ( 383-)  A    -2.3
 138 LEU   ( 142-)  A    -2.3
 404 GLU   ( 408-)  A    -2.3
 336 THR   ( 340-)  A    -2.3
 115 ILE   ( 119-)  A    -2.3
 137 PRO   ( 141-)  A    -2.3
 130 THR   ( 134-)  A    -2.3
 201 ILE   ( 205-)  A    -2.2
 420 VAL   ( 424-)  A    -2.2
 346 PRO   ( 350-)  A    -2.2
 145 VAL   ( 149-)  A    -2.2
  22 ARG   (  26-)  A    -2.1
 197 ILE   ( 201-)  A    -2.1
 482 LEU   ( 486-)  A    -2.1
 292 GLY   ( 296-)  A    -2.1
 498 THR   ( 502-)  A    -2.1
 476 PHE   ( 480-)  A    -2.0
 492 GLY   ( 496-)  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.

  18 SER   (  22-)  A  Poor phi/psi
  53 VAL   (  57-)  A  Poor phi/psi
  54 GLU   (  58-)  A  Poor phi/psi
  59 LYS   (  63-)  A  Poor phi/psi
  86 PHE   (  90-)  A  Poor phi/psi
 140 HIS   ( 144-)  A  Poor phi/psi
 178 ALA   ( 182-)  A  Poor phi/psi
 182 ARG   ( 186-)  A  Poor phi/psi
 184 PRO   ( 188-)  A  Poor phi/psi
 194 PHE   ( 198-)  A  PRO omega poor
 196 GLY   ( 200-)  A  Poor phi/psi
 245 ASN   ( 249-)  A  Poor phi/psi
 296 TRP   ( 300-)  A  Poor phi/psi
 302 HIS   ( 306-)  A  Poor phi/psi
 330 ARG   ( 334-)  A  Poor phi/psi
 350 MET   ( 354-)  A  Poor phi/psi
 401 GLY   ( 405-)  A  PRO omega poor
 413 LEU   ( 417-)  A  omega poor
 422 GLY   ( 426-)  A  Poor phi/psi
 437 ALA   ( 441-)  A  Poor phi/psi
 438 ASN   ( 442-)  A  Poor phi/psi
 468 GLN   ( 472-)  A  PRO omega poor
 485 GLY   ( 489-)  A  PRO omega poor
 486 PRO   ( 490-)  A  Poor phi/psi
 496 GLY   ( 500-)  A  PRO omega poor
 498 THR   ( 502-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -4.119

Error: chi-1/chi-2 angle correlation Z-score very low

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

chi-1/chi-2 correlation Z-score : -4.119

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!

  17 VAL   (  21-)  A      0
  18 SER   (  22-)  A      0
  20 ASN   (  24-)  A      0
  22 ARG   (  26-)  A      0
  25 LYS   (  29-)  A      0
  42 ASP   (  46-)  A      0
  49 TRP   (  53-)  A      0
  50 TRP   (  54-)  A      0
  54 GLU   (  58-)  A      0
  58 PRO   (  62-)  A      0
  59 LYS   (  63-)  A      0
  60 ALA   (  64-)  A      0
  61 TYR   (  65-)  A      0
  63 TRP   (  67-)  A      0
  84 MET   (  88-)  A      0
  85 SER   (  89-)  A      0
  86 PHE   (  90-)  A      0
  87 HIS   (  91-)  A      0
  89 CYS   (  93-)  A      0
  93 VAL   (  97-)  A      0
 101 ILE   ( 105-)  A      0
 114 ASP   ( 118-)  A      0
 115 ILE   ( 119-)  A      0
 117 TYR   ( 121-)  A      0
 126 ILE   ( 130-)  A      0
And so on for a total of 188 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 3.740

Warning: Backbone oxygen evaluation

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

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

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

 492 GLY   ( 496-)  A   2.01   25

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]

 102 PRO   ( 106-)  A    0.50 HIGH
 177 PRO   ( 181-)  A    0.45 HIGH
 347 PRO   ( 351-)  A    0.46 HIGH
 382 PRO   ( 386-)  A    0.48 HIGH
 452 PRO   ( 456-)  A    0.46 HIGH
 475 PRO   ( 479-)  A    0.49 HIGH
 486 PRO   ( 490-)  A    0.45 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].

  13 PRO   (  17-)  A  -139.4 envelop C-delta (-144 degrees)
 187 PRO   ( 191-)  A   -41.3 envelop C-alpha (-36 degrees)
 346 PRO   ( 350-)  A  -128.0 half-chair C-delta/C-gamma (-126 degrees)
 378 PRO   ( 382-)  A  -113.2 envelop C-gamma (-108 degrees)
 443 PRO   ( 447-)  A    41.8 envelop C-delta (36 degrees)
 469 PRO   ( 473-)  A    49.7 half-chair C-delta/C-gamma (54 degrees)
 475 PRO   ( 479-)  A  -117.8 half-chair C-delta/C-gamma (-126 degrees)
 486 PRO   ( 490-)  A   -13.4 half-chair C-alpha/N (-18 degrees)
 497 PRO   ( 501-)  A  -114.9 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

  89 CYS   (  93-)  A      SG  <->   97 VAL   ( 101-)  A      CG1    0.23    3.17  INTRA
  11 MET   (  15-)  A      CE  <->   45 MET   (  49-)  A      SD     0.22    3.18  INTRA
 152 MET   ( 156-)  A      SD  <->  275 ALA   ( 279-)  A      CB     0.12    3.28  INTRA BL
 499 CYS   ( 503-)  A      SG  <->  500 GLY   ( 504-)  A      N      0.12    3.08  INTRA BF
  80 LEU   (  84-)  A      N   <->  167 VAL   ( 171-)  A      O      0.11    2.59  INTRA
  53 VAL   (  57-)  A      O   <->   55 GLY   (  59-)  A      N      0.11    2.59  INTRA BL
 446 ASP   ( 450-)  A      N   <->  447 PRO   ( 451-)  A      CD     0.10    2.90  INTRA BF
 311 TYR   ( 315-)  A      O   <->  316 ARG   ( 320-)  A      NH1    0.08    2.62  INTRA BL
 350 MET   ( 354-)  A      N   <->  351 SER   ( 355-)  A      N      0.07    2.53  INTRA BL
 341 ARG   ( 345-)  A      NH2 <->  478 GLU   ( 482-)  A      O      0.07    2.63  INTRA BL
  83 ILE   (  87-)  A      O   <->   85 SER   (  89-)  A      N      0.07    2.63  INTRA BL
 466 ALA   ( 470-)  A      N   <->  467 ALA   ( 471-)  A      N      0.07    2.53  INTRA BL
 177 PRO   ( 181-)  A      C   <->  179 GLY   ( 183-)  A      N      0.06    2.84  INTRA BL
 471 ILE   ( 475-)  A      CG2 <->  472 GLN   ( 476-)  A      N      0.05    2.95  INTRA BL
 243 ARG   ( 247-)  A      O   <->  246 GLY   ( 250-)  A      N      0.05    2.65  INTRA
 195 PRO   ( 199-)  A      O   <->  296 TRP   ( 300-)  A      NE1    0.05    2.65  INTRA BL
 193 SER   ( 197-)  A      N   <->  233 ASN   ( 237-)  A      ND2    0.05    2.80  INTRA
 139 PHE   ( 143-)  A      CB  <->  147 MET   ( 151-)  A      SD     0.05    3.35  INTRA BL
 274 GLU   ( 278-)  A      O   <->  277 LYS   ( 281-)  A      N      0.04    2.66  INTRA BL
 430 THR   ( 434-)  A      OG1 <->  434 ARG   ( 438-)  A      NH2    0.04    2.66  INTRA
 125 ASN   ( 129-)  A      ND2 <->  127 GLU   ( 131-)  A      CG     0.04    3.06  INTRA
  38 GLU   (  42-)  A      N   <->   39 ALA   (  43-)  A      N      0.03    2.57  INTRA B3
 338 ALA   ( 342-)  A      O   <->  391 ASN   ( 395-)  A      ND2    0.03    2.67  INTRA
  39 ALA   (  43-)  A      N   <->   40 GLY   (  44-)  A      N      0.03    2.57  INTRA B3
  42 ASP   (  46-)  A      OD1 <->  436 HIS   ( 440-)  A      NE2    0.03    2.67  INTRA
 366 ARG   ( 370-)  A      CZ  <->  471 ILE   ( 475-)  A      CG2    0.03    3.17  INTRA BL
 192 TRP   ( 196-)  A      CG  <->  193 SER   ( 197-)  A      N      0.02    2.98  INTRA
 154 SER   ( 158-)  A      O   <->  158 ASN   ( 162-)  A      ND2    0.02    2.68  INTRA
 433 ASP   ( 437-)  A      O   <->  438 ASN   ( 442-)  A      N      0.02    2.68  INTRA
  13 PRO   (  17-)  A      C   <->   15 ASP   (  19-)  A      N      0.02    2.88  INTRA
  46 VAL   (  50-)  A      CG2 <->   47 ASP   (  51-)  A      N      0.02    2.98  INTRA BL
 195 PRO   ( 199-)  A      O   <->  295 TRP   ( 299-)  A      CD1    0.01    2.79  INTRA BL
 187 PRO   ( 191-)  A      C   <->  189 SER   ( 193-)  A      N      0.01    2.89  INTRA
 387 THR   ( 391-)  A      O   <->  391 ASN   ( 395-)  A      ND2    0.01    2.69  INTRA
 115 ILE   ( 119-)  A      N   <->  116 PHE   ( 120-)  A      N      0.01    2.59  INTRA BL
  50 TRP   (  54-)  A      CD1 <->  151 TYR   ( 155-)  A      CD2    0.01    3.19  INTRA BL

Packing, accessibility and threading

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.

 490 MET   ( 494-)  A      -8.28
 441 ARG   ( 445-)  A      -7.12
 380 TYR   ( 384-)  A      -7.03
 444 TYR   ( 448-)  A      -6.88
 453 ARG   ( 457-)  A      -6.51
 194 PHE   ( 198-)  A      -6.18
 499 CYS   ( 503-)  A      -6.12
 190 HIS   ( 194-)  A      -6.09
 495 GLU   ( 499-)  A      -5.93
 471 ILE   ( 475-)  A      -5.85
 238 ARG   ( 242-)  A      -5.82
 111 ARG   ( 115-)  A      -5.68
 399 GLN   ( 403-)  A      -5.58
 366 ARG   ( 370-)  A      -5.41
 468 GLN   ( 472-)  A      -5.40
 472 GLN   ( 476-)  A      -5.24
 478 GLU   ( 482-)  A      -5.20
 330 ARG   ( 334-)  A      -5.08
 448 MET   ( 452-)  A      -5.07
 344 GLU   ( 348-)  A      -5.02
  93 VAL   (  97-)  A      -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.

 243 ARG   ( 247-)  A       245 - ASN    249- ( A)         -4.40
 498 THR   ( 502-)  A       500 - GLY    504- ( A)         -5.15

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.

 349 ALA   ( 353-)  A   -2.66
 471 ILE   ( 475-)  A   -2.63
 466 ALA   ( 470-)  A   -2.62
 131 LEU   ( 135-)  A   -2.61
  52 LEU   (  56-)  A   -2.50

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

 465 GLN   ( 469-)  A     -  468 GLN   ( 472-)  A        -1.85

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.

 505 HOH   ( 634 )  A      O     19.98   53.22   23.53
 505 HOH   ( 643 )  A      O     45.92   -8.36   46.38
 505 HOH   ( 651 )  A      O     56.56   21.37   27.60
 505 HOH   ( 653 )  A      O     55.36   28.31   20.89
 505 HOH   ( 655 )  A      O     41.41   29.16   61.77
 505 HOH   ( 680 )  A      O     40.61   48.30   60.63
 505 HOH   ( 695 )  A      O     39.43   10.68   70.68

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.

 505 HOH   ( 605 )  A      O
 505 HOH   ( 611 )  A      O
 505 HOH   ( 613 )  A      O
 505 HOH   ( 619 )  A      O
 505 HOH   ( 620 )  A      O
 505 HOH   ( 624 )  A      O
 505 HOH   ( 626 )  A      O
 505 HOH   ( 627 )  A      O
 505 HOH   ( 632 )  A      O
 505 HOH   ( 637 )  A      O
 505 HOH   ( 641 )  A      O
 505 HOH   ( 643 )  A      O
 505 HOH   ( 646 )  A      O
 505 HOH   ( 652 )  A      O
 505 HOH   ( 662 )  A      O
 505 HOH   ( 663 )  A      O
 505 HOH   ( 664 )  A      O
 505 HOH   ( 671 )  A      O
 505 HOH   ( 673 )  A      O
 505 HOH   ( 678 )  A      O
 505 HOH   ( 686 )  A      O
 505 HOH   ( 697 )  A      O
 505 HOH   ( 701 )  A      O
 505 HOH   ( 704 )  A      O
 505 HOH   ( 709 )  A      O
 505 HOH   ( 710 )  A      O

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

   7 GLN   (  11-)  A
 146 GLN   ( 150-)  A
 314 HIS   ( 318-)  A
 395 HIS   ( 399-)  A

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.

  15 ASP   (  19-)  A      N
  19 VAL   (  23-)  A      N
  21 ASN   (  25-)  A      N
  26 GLY   (  30-)  A      N
  34 ARG   (  38-)  A      N
  54 GLU   (  58-)  A      N
  61 TYR   (  65-)  A      OH
  62 ASP   (  66-)  A      N
  79 LYS   (  83-)  A      NZ
  81 GLN   (  85-)  A      NE2
  87 HIS   (  91-)  A      N
 101 ILE   ( 105-)  A      N
 106 ARG   ( 110-)  A      NE
 117 TYR   ( 121-)  A      N
 118 THR   ( 122-)  A      N
 120 GLY   ( 124-)  A      N
 124 ARG   ( 128-)  A      N
 125 ASN   ( 129-)  A      ND2
 128 TYR   ( 132-)  A      N
 141 GLY   ( 145-)  A      N
 142 ARG   ( 146-)  A      N
 143 SER   ( 147-)  A      N
 156 ARG   ( 160-)  A      NE
 175 LEU   ( 179-)  A      N
 176 GLY   ( 180-)  A      N
And so on for a total of 63 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.

  32 GLN   (  36-)  A      OE1
 127 GLU   ( 131-)  A      OE1
 170 ASP   ( 174-)  A      OD2
 262 ASN   ( 266-)  A      OD1
 302 HIS   ( 306-)  A      ND1
 355 GLU   ( 359-)  A      OE1
 374 GLU   ( 378-)  A      OE2
 438 ASN   ( 442-)  A      OD1
 468 GLN   ( 472-)  A      OE1

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

  95 ASP   (  99-)  A   H-bonding suggests Asn; but Alt-Rotamer
 164 ASP   ( 168-)  A   H-bonding suggests Asn
 170 ASP   ( 174-)  A   H-bonding suggests Asn; but Alt-Rotamer
 224 GLU   ( 228-)  A   H-bonding suggests Gln; but Alt-Rotamer
 433 ASP   ( 437-)  A   H-bonding suggests Asn
 495 GLU   ( 499-)  A   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 :  -1.561
  2nd generation packing quality :  -1.516
  Ramachandran plot appearance   :  -3.599 (poor)
  chi-1/chi-2 rotamer normality  :  -4.119 (bad)
  Backbone conformation          :  -0.746

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.823
  Bond angles                    :   1.555
  Omega angle restraints         :   0.680 (tight)
  Side chain planarity           :   0.506 (tight)
  Improper dihedral distribution :   1.193
  B-factor distribution          :   1.283
  Inside/Outside distribution    :   0.958

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 : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.7
  2nd generation packing quality :  -0.3
  Ramachandran plot appearance   :  -1.3
  chi-1/chi-2 rotamer normality  :  -2.1
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.823
  Bond angles                    :   1.555
  Omega angle restraints         :   0.680 (tight)
  Side chain planarity           :   0.506 (tight)
  Improper dihedral distribution :   1.193
  B-factor distribution          :   1.283
  Inside/Outside distribution    :   0.958
==============

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.