WHAT IF Check report

This file was created 2011-12-16 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 pdb3jym.ent

Checks that need to be done early-on in validation

Warning: Unconventional cell on CRYST1

The derived `conventional cell' is different from the cell given on the CRYST1 card.

The CRYST1 cell dimensions

    A    = 186.956  B   =  31.012  C    =  68.978
    Alpha=  90.000  Beta=  93.590  Gamma=  90.000

Dimensions of a reduced cell

    A    =  31.012  B   =  68.978  C    = 186.956
    Alpha=  86.410  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    =  68.978  B   =  31.012  C    = 186.956
    Alpha=  90.000  Beta=  93.590  Gamma=  90.000

Transformation to conventional cell

 |  0.000000  0.000000 -1.000000|
 |  0.000000 -1.000000  0.000000|
 | -1.000000  0.000000  0.000000|

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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first.

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Error: Threonine nomenclature problem

The threonine residues listed in the table below have their O-gamma-1 and C-gamma-2 swapped.

 183 THR   ( 268-)  A

Warning: Tyrosine convention problem

The tyrosine residues listed in the table below have their chi-2 not between -90.0 and 90.0

 201 TYR   ( 287-)  A
 269 TYR   ( 355-)  A
 319 TYR   (  67-)  B
 576 TYR   ( 355-)  B

Warning: Phenylalanine convention problem

The phenylalanine residues listed in the table below have their chi-2 not between -90.0 and 90.0.

  21 PHE   (  87-)  A
  23 PHE   (  89-)  A
  49 PHE   ( 115-)  A
  55 PHE   ( 140-)  A
 116 PHE   ( 201-)  A
 150 PHE   ( 235-)  A
 224 PHE   ( 310-)  A
 297 PHE   ( 383-)  A
 322 PHE   (  87-)  B
 362 PHE   ( 140-)  B
 423 PHE   ( 201-)  B
 457 PHE   ( 235-)  B
 531 PHE   ( 310-)  B
 604 PHE   ( 383-)  B

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

   7 ASP   (  55-)  A
 495 ASP   ( 273-)  B

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

  16 GLU   (  64-)  A
  45 GLU   ( 111-)  A
  58 GLU   ( 143-)  A
  99 GLU   ( 184-)  A
 112 GLU   ( 197-)  A
 160 GLU   ( 245-)  A
 198 GLU   ( 283-)  A
 202 GLU   ( 288-)  A
 231 GLU   ( 317-)  A
 236 GLU   ( 322-)  A
 246 GLU   ( 332-)  A
 259 GLU   ( 345-)  A
 268 GLU   ( 354-)  A
 305 GLU   (  37-)  B
 314 GLU   (  62-)  B
 316 GLU   (  64-)  B
 346 GLU   ( 111-)  B
 365 GLU   ( 143-)  B
 393 GLU   ( 171-)  B
 410 GLU   ( 188-)  B
 419 GLU   ( 197-)  B
 538 GLU   ( 317-)  B
 543 GLU   ( 322-)  B
 549 GLU   ( 328-)  B
 553 GLU   ( 332-)  B
 566 GLU   ( 345-)  B
 575 GLU   ( 354-)  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.

   5 GLU   (  37-)  A      C    O     1.33    4.9
  51 ILE   ( 117-)  A      CA   CB    1.63    4.9
  74 ILE   ( 159-)  A      CA   CB    1.65    5.8
  79 LEU   ( 164-)  A      N    CA    1.36   -5.2
  80 LYS   ( 165-)  A      CE   NZ    1.62    4.4
  87 ASN   ( 172-)  A      C    O     1.15   -4.1
  89 LYS   ( 174-)  A      CA   C     1.41   -5.3
  91 PRO   ( 176-)  A      CA   C     1.63    4.8
  96 VAL   ( 181-)  A      CA   CB    1.65    6.0
 106 THR   ( 191-)  A      CA   CB    1.61    4.2
 122 HIS   ( 207-)  A      C    O     1.15   -4.2
 124 CYS   ( 209-)  A      CB   SG    1.62   -5.8
 159 GLY   ( 244-)  A      N    CA    1.57    7.3
 172 ILE   ( 257-)  A      CA   CB    1.61    4.1
 183 THR   ( 268-)  A      CA   C     1.61    4.2
 183 THR   ( 268-)  A      CB   OG1   1.32   -6.9
 184 GLU   ( 269-)  A      CA   C     1.42   -4.8
 188 ASP   ( 273-)  A      CB   CG    1.38   -5.3
 194 LYS   ( 279-)  A      CG   CD    1.39   -4.3
 196 LEU   ( 281-)  A      N    CA    1.54    4.1
 198 GLU   ( 283-)  A      CB   CG    1.38   -4.6
 214 ILE   ( 300-)  A      CA   CB    1.62    4.6
 214 ILE   ( 300-)  A      CG1  CD1   1.69    4.6
 219 GLN   ( 305-)  A      C    O     1.14   -4.6
 222 THR   ( 308-)  A      CA   CB    1.62    4.7
And so on for a total of 69 lines.

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

 |  1.000865  0.000454 -0.000696|
 |  0.000454  0.995068  0.000064|
 | -0.000696  0.000064  0.998945|
Proposed new scale matrix

 |  0.005345 -0.000002  0.000340|
 | -0.000015  0.032406 -0.000002|
 |  0.000010  0.000000  0.014541|
With corresponding cell

    A    = 187.113  B   =  30.859  C    =  68.912
    Alpha=  90.000  Beta=  93.681  Gamma=  89.948

The CRYST1 cell dimensions

    A    = 186.956  B   =  31.012  C    =  68.978
    Alpha=  90.000  Beta=  93.590  Gamma=  90.000

Variance: 104.772
(Under-)estimated Z-score: 7.544

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.

  22 LYS   (  88-)  A     -C    N    CA  131.24    5.3
 111 SER   ( 196-)  A     -C    N    CA  112.21   -5.3
 112 GLU   ( 197-)  A      CA   CB   CG  105.57   -4.3
 115 GLU   ( 200-)  A      N    CA   CB  102.72   -4.6
 138 GLU   ( 223-)  A      C    CA   CB  119.93    5.2
 152 GLU   ( 237-)  A     -C    N    CA  129.32    4.2
 153 MET   ( 238-)  A     -C    N    CA  129.29    4.2
 155 ARG   ( 240-)  A     -C    N    CA  113.23   -4.7
 158 ALA   ( 243-)  A      C    CA   CB  116.63    4.1
 159 GLY   ( 244-)  A      N    CA   C   100.20   -4.2
 161 GLY   ( 246-)  A      N    CA   C   124.39    4.1
 162 GLY   ( 247-)  A      N    CA   C    92.80   -6.8
 183 THR   ( 268-)  A      CA   CB   CG2 118.64    4.8
 183 THR   ( 268-)  A      CA   CB   OG1 118.48    5.9
 183 THR   ( 268-)  A      CG2  CB   OG1 121.90    6.3
 188 ASP   ( 273-)  A     -C    N    CA  133.57    6.6
 188 ASP   ( 273-)  A      N    CA   C   124.99    4.9
 188 ASP   ( 273-)  A      N    CA   CB  102.68   -4.6
 188 ASP   ( 273-)  A      C    CA   CB  100.63   -5.0
 194 LYS   ( 279-)  A      CG   CD   CE  100.78   -4.6
 200 GLY   ( 286-)  A     -C    N    CA  127.93    4.3
 200 GLY   ( 286-)  A      N    CA   C   127.71    5.2
 206 GLU   ( 292-)  A      N    CA   C    99.45   -4.2
 210 VAL   ( 296-)  A      N    CA   CB  102.13   -4.9
 211 THR   ( 297-)  A      C    CA   CB  120.49    5.5
And so on for a total of 67 lines.

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

   7 ASP   (  55-)  A
  16 GLU   (  64-)  A
  45 GLU   ( 111-)  A
  58 GLU   ( 143-)  A
  99 GLU   ( 184-)  A
 112 GLU   ( 197-)  A
 160 GLU   ( 245-)  A
 183 THR   ( 268-)  A
 198 GLU   ( 283-)  A
 202 GLU   ( 288-)  A
 231 GLU   ( 317-)  A
 236 GLU   ( 322-)  A
 246 GLU   ( 332-)  A
 259 GLU   ( 345-)  A
 268 GLU   ( 354-)  A
 305 GLU   (  37-)  B
 314 GLU   (  62-)  B
 316 GLU   (  64-)  B
 346 GLU   ( 111-)  B
 365 GLU   ( 143-)  B
 393 GLU   ( 171-)  B
 410 GLU   ( 188-)  B
 419 GLU   ( 197-)  B
 495 ASP   ( 273-)  B
 538 GLU   ( 317-)  B
 543 GLU   ( 322-)  B
 549 GLU   ( 328-)  B
 553 GLU   ( 332-)  B
 566 GLU   ( 345-)  B
 575 GLU   ( 354-)  B

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.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 183 THR   ( 268-)  A      CB   -12.3     6.59    34.09
 210 VAL   ( 296-)  A      CB     6.3   -24.72   -32.96
 211 THR   ( 297-)  A      CA    -7.7    20.97    33.84
 222 THR   ( 308-)  A      CA    -9.1    18.72    33.84
 508 TYR   ( 287-)  B      CA    -8.7    20.33    34.03
 535 GLY   ( 314-)  B      C     -6.2    -8.16     0.06
 572 ILE   ( 351-)  B      CB     6.5    40.82    32.31
The average deviation= 1.921

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.

 162 GLY   ( 247-)  A    7.46
 323 LYS   (  88-)  B    6.68
 466 GLY   ( 244-)  B    6.42
  34 TRP   ( 100-)  A    5.66
 200 GLY   ( 286-)  A    5.07
 456 GLY   ( 234-)  B    4.83
 159 GLY   ( 244-)  A    4.80
 188 ASP   ( 273-)  A    4.64
 333 LYS   (  98-)  B    4.38
 126 ALA   ( 211-)  A    4.36
 507 GLY   ( 286-)  B    4.34
 468 GLY   ( 246-)  B    4.23
 363 ASP   ( 141-)  B    4.13
 247 GLY   ( 333-)  A    4.13
 206 GLU   ( 292-)  A    4.09
  29 GLN   (  95-)  A    4.09

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 : 1.683

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.

 229 HIS   ( 315-)  A    6.00
 539 GLN   ( 318-)  B    5.72
 536 HIS   ( 315-)  B    5.19
 237 PHE   ( 323-)  A    4.84
 232 GLN   ( 318-)  A    4.82
  95 PHE   ( 180-)  A    4.72
  92 ASP   ( 177-)  A    4.68
 249 ASP   ( 335-)  A    4.48
 285 ASN   ( 371-)  A    4.13

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.

 508 TYR   ( 287-)  B    -3.6
 473 PRO   ( 251-)  B    -2.7
 377 LYS   ( 155-)  B    -2.5
  31 ILE   (  97-)  A    -2.5
 549 GLU   ( 328-)  B    -2.5
 357 ASN   ( 135-)  B    -2.4
 459 GLU   ( 237-)  B    -2.4
 302 GLU   (  34-)  B    -2.4
 200 GLY   ( 286-)  A    -2.4
 112 GLU   ( 197-)  A    -2.3
 355 PRO   ( 133-)  B    -2.3
 352 ILE   ( 117-)  B    -2.3
 391 LYS   ( 169-)  B    -2.3
  33 GLY   (  99-)  A    -2.2
 161 GLY   ( 246-)  A    -2.2
 245 ILE   ( 331-)  A    -2.2
  25 LEU   (  91-)  A    -2.2
 277 LYS   ( 363-)  A    -2.2
 123 LEU   ( 208-)  A    -2.2
 387 LYS   ( 165-)  B    -2.2
 552 ILE   ( 331-)  B    -2.2
 166 PRO   ( 251-)  A    -2.1
 320 THR   (  68-)  B    -2.1
  97 LYS   ( 182-)  A    -2.1
 160 GLU   ( 245-)  A    -2.1
 420 GLY   ( 198-)  B    -2.1
 460 MET   ( 238-)  B    -2.1
 113 GLY   ( 198-)  A    -2.1
   2 GLU   (  34-)  A    -2.1
 146 PRO   ( 231-)  A    -2.1
  10 GLU   (  58-)  A    -2.0
 588 ILE   ( 367-)  B    -2.0
 393 GLU   ( 171-)  B    -2.0
 328 GLN   (  93-)  B    -2.0
 154 GLY   ( 239-)  A    -2.0
 569 LEU   ( 348-)  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.

   2 GLU   (  34-)  A  Poor phi/psi
  10 GLU   (  58-)  A  omega poor
  11 VAL   (  59-)  A  Poor phi/psi
  17 VAL   (  65-)  A  omega poor
  22 LYS   (  88-)  A  Poor phi/psi, omega poor
  25 LEU   (  91-)  A  omega poor
  27 GLN   (  93-)  A  Poor phi/psi
  28 GLY   (  94-)  A  omega poor
  31 ILE   (  97-)  A  omega poor
  32 LYS   (  98-)  A  Poor phi/psi, omega poor
  33 GLY   (  99-)  A  Poor phi/psi, omega poor
  35 ASP   ( 101-)  A  omega poor
  43 LYS   ( 109-)  A  Poor phi/psi
  44 GLY   ( 110-)  A  Poor phi/psi, omega poor
  45 GLU   ( 111-)  A  omega poor
  60 LEU   ( 145-)  A  Poor phi/psi, omega poor
  61 SER   ( 146-)  A  omega poor
  62 TRP   ( 147-)  A  omega poor
  67 ASP   ( 152-)  A  omega poor
  70 LYS   ( 155-)  A  Poor phi/psi, omega poor
  71 ASP   ( 156-)  A  Poor phi/psi, omega poor
  84 LYS   ( 169-)  A  Poor phi/psi
  85 TRP   ( 170-)  A  Poor phi/psi
  95 PHE   ( 180-)  A  omega poor
 101 ARG   ( 186-)  A  omega poor
And so on for a total of 103 lines.

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 : -4.479

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 ASN   (  36-)  A      0
   5 GLU   (  37-)  A      0
   6 TRP   (  54-)  A      0
   7 ASP   (  55-)  A      0
  11 VAL   (  59-)  A      0
  19 TYR   (  67-)  A      0
  20 THR   (  68-)  A      0
  21 PHE   (  87-)  A      0
  22 LYS   (  88-)  A      0
  23 PHE   (  89-)  A      0
  25 LEU   (  91-)  A      0
  27 GLN   (  93-)  A      0
  29 GLN   (  95-)  A      0
  30 VAL   (  96-)  A      0
  31 ILE   (  97-)  A      0
  34 TRP   ( 100-)  A      0
  43 LYS   ( 109-)  A      0
  51 ILE   ( 117-)  A      0
  52 PRO   ( 118-)  A      0
  53 LEU   ( 138-)  A      0
  54 GLN   ( 139-)  A      0
  61 SER   ( 146-)  A      0
  66 ARG   ( 151-)  A      0
  68 ILE   ( 153-)  A      0
  69 ALA   ( 154-)  A      0
And so on for a total of 263 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 9.828

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]

  91 PRO   ( 176-)  A    0.16 LOW
 234 PRO   ( 320-)  A    0.15 LOW
 266 PRO   ( 352-)  A    0.17 LOW
 267 PRO   ( 353-)  A    0.14 LOW
 463 PRO   ( 241-)  B    0.17 LOW
 541 PRO   ( 320-)  B    0.14 LOW
 590 PRO   ( 369-)  B    0.05 LOW

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].

  52 PRO   ( 118-)  A    23.5 half-chair N/C-delta (18 degrees)
 146 PRO   ( 231-)  A   118.0 half-chair C-beta/C-alpha (126 degrees)
 156 PRO   ( 241-)  A   -64.7 envelop C-beta (-72 degrees)
 166 PRO   ( 251-)  A   166.4 half-chair C-alpha/N (162 degrees)
 353 PRO   ( 118-)  B   130.5 half-chair C-beta/C-alpha (126 degrees)
 355 PRO   ( 133-)  B    -9.2 half-chair C-alpha/N (-18 degrees)
 432 PRO   ( 210-)  B   103.6 envelop C-beta (108 degrees)
 473 PRO   ( 251-)  B   133.9 half-chair C-beta/C-alpha (126 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 495 ASP   ( 273-)  B      OD2 <->  497 LYS   ( 275-)  B      CD     0.90    1.90  INTRA
  17 VAL   (  65-)  A      O   <->   21 PHE   (  87-)  A      N      0.70    2.00  INTRA BF
 188 ASP   ( 273-)  A      OD1 <->  190 LYS   ( 275-)  A      CD     0.57    2.23  INTRA
 356 ALA   ( 134-)  B      O   <->  358 ALA   ( 136-)  B      N      0.45    2.25  INTRA BF
  99 GLU   ( 184-)  A      OE1 <->  101 ARG   ( 186-)  A      NH1    0.43    2.27  INTRA BL
 185 ILE   ( 270-)  A      N   <->  191 ILE   ( 276-)  A      O      0.38    2.32  INTRA BL
 422 GLU   ( 200-)  B      OE2 <->  487 LYS   ( 265-)  B      NZ     0.35    2.35  INTRA BL
  31 ILE   (  97-)  A      O   <->   33 GLY   (  99-)  A      N      0.33    2.37  INTRA BF
 465 ALA   ( 243-)  B      CB  <->  466 GLY   ( 244-)  B      CA     0.30    2.70  INTRA BF
 303 GLU   (  35-)  B      OE1 <->  348 ALA   ( 113-)  B      CB     0.29    2.51  INTRA BF
 317 VAL   (  65-)  B      N   <->  322 PHE   (  87-)  B      N      0.28    2.57  INTRA BF
 275 GLU   ( 361-)  A      OE2 <->  277 LYS   ( 363-)  A      NZ     0.26    2.44  INTRA
 545 LYS   ( 324-)  B      CD  <->  548 GLU   ( 327-)  B      OE2    0.22    2.58  INTRA BF
  83 ASP   ( 168-)  A      N   <->  136 LYS   ( 221-)  A      O      0.22    2.48  INTRA
 328 GLN   (  93-)  B      O   <->  330 GLN   (  95-)  B      N      0.22    2.48  INTRA BF
 405 TYR   ( 183-)  B      OH  <->  429 HIS   ( 207-)  B      CE1    0.21    2.59  INTRA BL
 276 SER   ( 362-)  A      O   <->  282 VAL   ( 368-)  A      N      0.20    2.50  INTRA BL
 345 GLY   ( 110-)  B      N   <->  366 LEU   ( 144-)  B      O      0.19    2.51  INTRA BF
 492 ILE   ( 270-)  B      N   <->  498 ILE   ( 276-)  B      O      0.19    2.51  INTRA BL
 115 GLU   ( 200-)  A      OE2 <->  180 LYS   ( 265-)  A      NZ     0.19    2.51  INTRA BL
 514 GLY   ( 293-)  B      O   <->  545 LYS   ( 324-)  B      CG     0.18    2.62  INTRA
  51 ILE   ( 117-)  A      O   <->   53 LEU   ( 138-)  A      N      0.18    2.52  INTRA BF
 510 ARG   ( 289-)  B      NH1 <->  561 ASN   ( 340-)  B      O      0.17    2.53  INTRA
 462 ARG   ( 240-)  B      NH2 <->  469 GLY   ( 247-)  B      O      0.17    2.53  INTRA BL
 583 SER   ( 362-)  B      OG  <->  585 GLN   ( 364-)  B      NE2    0.16    2.54  INTRA
And so on for a total of 107 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.

 508 TYR   ( 287-)  B      -7.65
 201 TYR   ( 287-)  A      -7.55
 153 MET   ( 238-)  A      -6.62
 467 GLU   ( 245-)  B      -6.33
 160 GLU   ( 245-)  A      -6.21
 330 GLN   (  95-)  B      -6.01
 460 MET   ( 238-)  B      -5.91
 219 GLN   ( 305-)  A      -5.64
 454 GLN   ( 232-)  B      -5.63
 147 GLN   ( 232-)  A      -5.57
 526 GLN   ( 305-)  B      -5.52
 377 LYS   ( 155-)  B      -5.49
  70 LYS   ( 155-)  A      -5.41
  27 GLN   (  93-)  A      -5.39
  29 GLN   (  95-)  A      -5.24
 305 GLU   (  37-)  B      -5.23
 392 TRP   ( 170-)  B      -5.18
  11 VAL   (  59-)  A      -5.09

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

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

 157 ALA   ( 242-)  A       160 - GLU    245- ( A)         -4.71
 231 GLU   ( 317-)  A       233 - GLU    319- ( A)         -4.59
 538 GLU   ( 317-)  B       540 - GLU    319- ( B)         -4.50

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

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.

  87 ASN   ( 172-)  A
 219 GLN   ( 305-)  A
 429 HIS   ( 207-)  B
 526 GLN   ( 305-)  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 VAL   (  65-)  A      N
  26 GLY   (  92-)  A      N
  29 GLN   (  95-)  A      N
  34 TRP   ( 100-)  A      N
  35 ASP   ( 101-)  A      N
  39 LYS   ( 105-)  A      N
  61 SER   ( 146-)  A      N
  69 ALA   ( 154-)  A      N
  73 GLY   ( 158-)  A      N
  74 ILE   ( 159-)  A      N
  82 GLY   ( 167-)  A      N
  89 LYS   ( 174-)  A      N
 128 ALA   ( 213-)  A      N
 136 LYS   ( 221-)  A      N
 153 MET   ( 238-)  A      N
 154 GLY   ( 239-)  A      N
 190 LYS   ( 275-)  A      N
 219 GLN   ( 305-)  A      N
 228 GLY   ( 314-)  A      N
 241 GLU   ( 327-)  A      N
 243 ALA   ( 329-)  A      N
 257 LYS   ( 343-)  A      N
 271 TYR   ( 357-)  A      N
 274 THR   ( 360-)  A      N
 280 ALA   ( 366-)  A      N
 317 VAL   (  65-)  B      N
 322 PHE   (  87-)  B      N
 331 VAL   (  96-)  B      N
 335 TRP   ( 100-)  B      NE1
 347 ASN   ( 112-)  B      N
 348 ALA   ( 113-)  B      N
 376 ALA   ( 154-)  B      N
 381 ILE   ( 159-)  B      N
 389 GLY   ( 167-)  B      N
 392 TRP   ( 170-)  B      N
 435 ALA   ( 213-)  B      N
 443 LYS   ( 221-)  B      N
 454 GLN   ( 232-)  B      N
 497 LYS   ( 275-)  B      N
 526 GLN   ( 305-)  B      N
 527 ASP   ( 306-)  B      N
 550 ALA   ( 329-)  B      N
 551 VAL   ( 330-)  B      N
 564 LYS   ( 343-)  B      N
 578 TYR   ( 357-)  B      N
 587 ALA   ( 366-)  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.

   3 GLU   (  35-)  A      OE1
  35 ASP   ( 101-)  A      OD1
 249 ASP   ( 335-)  A      OD1
 278 GLN   ( 364-)  A      OE1
 303 GLU   (  35-)  B      OE1
 585 GLN   ( 364-)  B      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.

  10 GLU   (  58-)  A   H-bonding suggests Gln
  71 ASP   ( 156-)  A   H-bonding suggests Asn
 305 GLU   (  37-)  B   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.417
  2nd generation packing quality :  -0.150
  Ramachandran plot appearance   :  -2.656
  chi-1/chi-2 rotamer normality  :  -4.479 (bad)
  Backbone conformation          :  -0.529

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.470
  Bond angles                    :   1.277
  Omega angle restraints         :   1.787 (loose)
  Side chain planarity           :   1.555
  Improper dihedral distribution :   1.671 (loose)
  B-factor distribution          :   0.912
  Inside/Outside distribution    :   1.025

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 : 2.28


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :   0.4
  Ramachandran plot appearance   :  -1.0
  chi-1/chi-2 rotamer normality  :  -2.6
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.470
  Bond angles                    :   1.277
  Omega angle restraints         :   1.787 (loose)
  Side chain planarity           :   1.555
  Improper dihedral distribution :   1.671 (loose)
  B-factor distribution          :   0.912
  Inside/Outside distribution    :   1.025
==============

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.