WHAT IF Check report

This file was created 2012-01-31 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 pdb2rve.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    =  68.500  B   =  79.600  C    =  66.400
    Alpha=  90.000  Beta= 104.600  Gamma=  90.000

Dimensions of a reduced cell

    A    =  66.400  B   =  68.500  C    =  79.600
    Alpha=  90.000  Beta=  90.000  Gamma= 104.600

Dimensions of the conventional cell

    A    =  66.400  B   =  79.600  C    =  68.500
    Alpha=  90.000  Beta= 104.600  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. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

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

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

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

Warning: Tyrosine convention problem

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

  44 TYR   (  18-)  A
  57 TYR   (  31-)  A
  87 TYR   (  61-)  A
 104 TYR   (  78-)  A
 136 TYR   ( 110-)  A
 154 TYR   ( 128-)  A
 168 TYR   ( 151-)  A
 180 TYR   ( 163-)  A
 210 TYR   ( 196-)  A
 233 TYR   ( 219-)  A
 268 TYR   (  31-)  B
 315 TYR   (  78-)  B
 347 TYR   ( 110-)  B
 373 TYR   ( 136-)  B
 379 TYR   ( 151-)  B
 421 TYR   ( 196-)  B
 446 TYR   ( 230-)  B
 452 TYR   ( 236-)  B
 457 TYR   ( 241-)  B

Warning: Phenylalanine convention problem

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

  73 PHE   (  47-)  A
 101 PHE   (  75-)  A
 131 PHE   ( 105-)  A
 151 PHE   ( 125-)  A
 186 PHE   ( 169-)  A
 213 PHE   ( 199-)  A
 226 PHE   ( 212-)  A
 284 PHE   (  47-)  B
 312 PHE   (  75-)  B
 342 PHE   ( 105-)  B
 397 PHE   ( 169-)  B
 437 PHE   ( 212-)  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.

  45 ASP   (  19-)  A
  62 ASP   (  36-)  A
 152 ASP   ( 126-)  A
 189 ASP   ( 172-)  A
 212 ASP   ( 198-)  A
 224 ASP   ( 210-)  A
 228 ASP   ( 214-)  A
 435 ASP   ( 210-)  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.

  83 GLU   (  57-)  A
  90 GLU   (  64-)  A
  91 GLU   (  65-)  A
 108 GLU   (  82-)  A
 172 GLU   ( 155-)  A
 175 GLU   ( 158-)  A
 225 GLU   ( 211-)  A
 240 GLU   ( 235-)  A
 294 GLU   (  57-)  B
 301 GLU   (  64-)  B
 302 GLU   (  65-)  B
 383 GLU   ( 155-)  B
 445 GLU   ( 220-)  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.

   1 DCYT  (   1-)  C      N1   C6    1.33   -7.0
   3 DADE  (   3-)  C      C3'  O3'   1.36   -5.2
   3 DADE  (   3-)  C      N3   C4    1.32   -4.1
   3 DADE  (   3-)  C      C6   N1    1.31   -5.1
   4 DGUA  (   4-)  C      O5'  C5'   1.37   -4.7
   5 DCYT  (   5-)  C      C5   C4    1.46    4.1
   7 DCYT  (   7-)  C      C1'  N1    1.42   -4.2
   7 DCYT  (   7-)  C      N1   C6    1.34   -4.5
  11 DADE  (   3-)  D      C5'  C4'   1.54    4.1
  13 DCYT  (   5-)  D      C1'  N1    1.54    5.6
  17 DCYT  (   1-)  E      C3'  O3'   1.36   -5.3
  17 DCYT  (   1-)  E      C4'  C3'   1.49   -4.3
  17 DCYT  (   1-)  E      C1'  N1    1.42   -4.1
  17 DCYT  (   1-)  E      N1   C6    1.33   -6.7
  19 DADE  (   3-)  E      P    O5'   1.53   -5.8
  19 DADE  (   3-)  E      N3   C4    1.31   -5.0
  20 DGUA  (   4-)  E      O5'  C5'   1.36   -5.2
  24 DGUA  (   8-)  E      P    O5'   1.55   -4.4
  27 DADE  (   3-)  F      N3   C4    1.31   -6.2
  29 DCYT  (   5-)  F      C3'  O3'   1.37   -4.9
  29 DCYT  (   5-)  F      C5'  C4'   1.47   -4.6
  31 DCYT  (   7-)  F      O5'  C5'   1.38   -4.0
  45 ASP   (  19-)  A      CG   OD1   1.33    4.2
  83 GLU   (  57-)  A      CD   OE1   1.33    4.3
 116 ASP   (  90-)  A      CG   OD2   1.34    5.0
 175 GLU   ( 158-)  A      CD   OE1   1.33    4.3
 250 ASP   (   6-)  B      CG   OD2   1.33    4.3
 264 GLU   (  27-)  B      CD   OE2   1.33    4.2
 301 GLU   (  64-)  B      CD   OE1   1.33    4.1
 327 ASP   (  90-)  B      CG   OD2   1.34    4.8
 432 ASP   ( 207-)  B      CG   OD2   1.34    4.8

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

 |  1.001394 -0.001053  0.000189|
 | -0.001053  1.002952 -0.000350|
 |  0.000189 -0.000350  1.002887|
Proposed new scale matrix

 |  0.014578  0.000017  0.003789|
 |  0.000013  0.012526  0.000004|
 | -0.000003  0.000005  0.015518|
With corresponding cell

    A    =  68.593  B   =  79.834  C    =  66.579
    Alpha=  90.008  Beta= 104.560  Gamma=  90.120

The CRYST1 cell dimensions

    A    =  68.500  B   =  79.600  C    =  66.400
    Alpha=  90.000  Beta= 104.600  Gamma=  90.000

Variance: 174.258
(Under-)estimated Z-score: 9.729

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 DCYT  (   1-)  C      C1'  N1   C6  129.92    7.6
   1 DCYT  (   1-)  C      C1'  N1   C2  108.06   -9.8
   1 DCYT  (   1-)  C      C6   N1   C2  121.96    4.2
   2 DGUA  (   2-)  C      O4'  C1'  N9  111.95    5.2
   2 DGUA  (   2-)  C      N9   C8   N7  113.47    4.7
   4 DGUA  (   4-)  C      N9   C8   N7  113.48    4.8
   5 DCYT  (   5-)  C      P   -C3* -O3* 126.40    5.6
   6 DTHY  (   6-)  C      C6   C5   C7  120.08   -4.7
   7 DCYT  (   7-)  C      C1'  N1   C6  126.16    4.5
   7 DCYT  (   7-)  C      C1'  N1   C2  112.33   -5.9
   8 DGUA  (   8-)  C      C1'  N9   C8  119.48   -5.8
   8 DGUA  (   8-)  C      C1'  N9   C4  134.22    5.9
   9 DCYT  (   1-)  D      C1'  N1   C6  127.37    5.5
   9 DCYT  (   1-)  D      C1'  N1   C2  111.34   -6.8
  10 DGUA  (   2-)  D      C1'  N9   C8  133.18    4.8
  10 DGUA  (   2-)  D      C1'  N9   C4  121.28   -4.0
  10 DGUA  (   2-)  D      N9   C8   N7  114.26    6.3
  12 DGUA  (   4-)  D      P   -C3* -O3* 114.88   -4.0
  12 DGUA  (   4-)  D      P    O5'  C5' 114.12   -4.2
  12 DGUA  (   4-)  D      O4'  C1'  C2' 100.64   -5.0
  12 DGUA  (   4-)  D      C1'  N9   C8  121.05   -4.6
  15 DCYT  (   7-)  D      O4'  C1'  N1  112.91    6.4
  16 DGUA  (   8-)  D      C1'  N9   C4  132.79    4.8
  16 DGUA  (   8-)  D      N9   C8   N7  113.52    4.8
  17 DCYT  (   1-)  E      C1'  N1   C6  138.28   14.6
And so on for a total of 56 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.

  45 ASP   (  19-)  A
  62 ASP   (  36-)  A
  83 GLU   (  57-)  A
  90 GLU   (  64-)  A
  91 GLU   (  65-)  A
 108 GLU   (  82-)  A
 152 ASP   ( 126-)  A
 172 GLU   ( 155-)  A
 175 GLU   ( 158-)  A
 189 ASP   ( 172-)  A
 212 ASP   ( 198-)  A
 224 ASP   ( 210-)  A
 225 GLU   ( 211-)  A
 228 ASP   ( 214-)  A
 240 GLU   ( 235-)  A
 294 GLU   (  57-)  B
 301 GLU   (  64-)  B
 302 GLU   (  65-)  B
 383 GLU   ( 155-)  B
 435 ASP   ( 210-)  B
 445 GLU   ( 220-)  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.

  59 LEU   (  33-)  A      CA    -8.5    21.18    34.19
 177 PRO   ( 160-)  A      N      8.4    25.07    -2.48
 235 TYR   ( 230-)  A      CA   -12.5    14.25    34.03
 277 LEU   (  40-)  B      CA    -6.3    24.59    34.19
 287 PRO   (  50-)  B      N     -6.8   -24.70    -2.48
 320 PRO   (  83-)  B      N      6.6    19.09    -2.48
 388 PRO   ( 160-)  B      N     -6.1   -22.59    -2.48
The average deviation= 1.375

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.

 235 TYR   ( 230-)  A    5.61
  34 LEU   (   3-)  A    5.35
 363 ASP   ( 126-)  B    4.96
 172 GLU   ( 155-)  A    4.66
 285 SER   (  48-)  B    4.09
 267 ILE   (  30-)  B    4.08

Torsion-related checks

Error: Ramachandran Z-score very low

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

Ramachandran Z-score : -4.083

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.

  99 PRO   (  73-)  A    -3.1
 310 PRO   (  73-)  B    -3.0
 179 PRO   ( 162-)  A    -2.9
 170 ILE   ( 153-)  A    -2.7
 456 ILE   ( 240-)  B    -2.6
 111 LYS   (  85-)  A    -2.6
 384 LEU   ( 156-)  B    -2.6
 376 THR   ( 139-)  B    -2.5
 331 THR   (  94-)  B    -2.4
 140 ILE   ( 114-)  A    -2.4
 199 GLY   ( 182-)  A    -2.4
 180 TYR   ( 163-)  A    -2.4
 217 LYS   ( 203-)  A    -2.4
 108 GLU   (  82-)  A    -2.3
 238 ILE   ( 233-)  A    -2.3
 391 TYR   ( 163-)  B    -2.3
 275 LYS   (  38-)  B    -2.3
  50 ILE   (  24-)  A    -2.3
 401 LYS   ( 173-)  B    -2.2
 109 PRO   (  83-)  A    -2.2
 344 LEU   ( 107-)  B    -2.2
  85 HIS   (  59-)  A    -2.2
 390 PRO   ( 162-)  B    -2.2
 450 SER   ( 234-)  B    -2.2
 383 GLU   ( 155-)  B    -2.2
 396 VAL   ( 168-)  B    -2.2
 147 ILE   ( 121-)  A    -2.2
 398 LEU   ( 170-)  B    -2.2
 370 ILE   ( 133-)  B    -2.2
 120 THR   (  94-)  A    -2.1
 203 ILE   ( 189-)  A    -2.1
 337 ASN   ( 100-)  B    -2.1
  59 LEU   (  33-)  A    -2.1
 408 LEU   ( 180-)  B    -2.1
 106 PRO   (  80-)  A    -2.1
 340 ILE   ( 103-)  B    -2.0
 155 ILE   ( 129-)  A    -2.0
 393 GLY   ( 165-)  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.

  59 LEU   (  33-)  A  Poor phi/psi
  96 ASN   (  70-)  A  Poor phi/psi
  98 TYR   (  72-)  A  PRO omega poor
 124 LYS   (  98-)  A  Poor phi/psi
 126 ASN   ( 100-)  A  Poor phi/psi
 138 SER   ( 112-)  A  Poor phi/psi
 143 ASN   ( 117-)  A  Poor phi/psi
 146 ASN   ( 120-)  A  Poor phi/psi
 180 TYR   ( 163-)  A  Poor phi/psi
 199 GLY   ( 182-)  A  Poor phi/psi
 222 SER   ( 208-)  A  Poor phi/psi
 307 ASN   (  70-)  B  Poor phi/psi
 309 TYR   (  72-)  B  PRO omega poor
 315 TYR   (  78-)  B  Poor phi/psi
 337 ASN   ( 100-)  B  Poor phi/psi
 349 SER   ( 112-)  B  Poor phi/psi
 354 ASN   ( 117-)  B  Poor phi/psi
 357 ASN   ( 120-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -5.708

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 : -5.708

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

 239 SER   ( 234-)  A    0.40

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!

   3 DADE  (   3-)  C      0
   4 DGUA  (   4-)  C      0
   5 DCYT  (   5-)  C      0
   6 DTHY  (   6-)  C      0
   7 DCYT  (   7-)  C      0
   8 DGUA  (   8-)  C      0
   9 DCYT  (   1-)  D      0
  10 DGUA  (   2-)  D      0
  11 DADE  (   3-)  D      0
  12 DGUA  (   4-)  D      0
  13 DCYT  (   5-)  D      0
  14 DTHY  (   6-)  D      0
  15 DCYT  (   7-)  D      0
  16 DGUA  (   8-)  D      0
  17 DCYT  (   1-)  E      0
  18 DGUA  (   2-)  E      0
  19 DADE  (   3-)  E      0
  20 DGUA  (   4-)  E      0
  21 DCYT  (   5-)  E      0
  22 DTHY  (   6-)  E      0
  23 DCYT  (   7-)  E      0
  24 DGUA  (   8-)  E      0
  25 DCYT  (   1-)  F      0
  26 DGUA  (   2-)  F      0
  27 DADE  (   3-)  F      0
And so on for a total of 209 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 : 1.112

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!

 218 GLY   ( 204-)  A   1.68   16
 195 GLY   ( 178-)  A   1.65   17

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

 356 LYS   ( 119-)  B   1.65

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]

  76 PRO   (  50-)  A    0.16 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].

  99 PRO   (  73-)  A   -19.8 half-chair C-alpha/N (-18 degrees)
 106 PRO   (  80-)  A  -156.5 half-chair N/C-delta (-162 degrees)
 109 PRO   (  83-)  A   -47.8 half-chair C-beta/C-alpha (-54 degrees)
 177 PRO   ( 160-)  A   -34.3 envelop C-alpha (-36 degrees)
 179 PRO   ( 162-)  A   -42.8 envelop C-alpha (-36 degrees)
 269 PRO   (  32-)  B    51.5 half-chair C-delta/C-gamma (54 degrees)
 287 PRO   (  50-)  B   144.8 envelop C-alpha (144 degrees)
 310 PRO   (  73-)  B     1.8 envelop N (0 degrees)
 320 PRO   (  83-)  B   -60.3 half-chair C-beta/C-alpha (-54 degrees)
 361 PRO   ( 124-)  B    44.3 envelop C-delta (36 degrees)
 388 PRO   ( 160-)  B  -155.1 half-chair N/C-delta (-162 degrees)
 390 PRO   ( 162-)  B   -43.8 envelop C-alpha (-36 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.

  24 DGUA  (   8-)  E      N1  <->   25 DCYT  (   1-)  F      N3     0.72    2.28  INTRA
  23 DCYT  (   7-)  E      N3  <->   26 DGUA  (   2-)  F      N1     0.57    2.43  INTRA BL
   5 DCYT  (   5-)  C      N3  <->   12 DGUA  (   4-)  D      N1     0.51    2.49  INTRA BL
  24 DGUA  (   8-)  E      N2  <->   25 DCYT  (   1-)  F      O2     0.46    2.24  INTRA
  37 ASP   (   6-)  A      OD2 <->   85 HIS   (  59-)  A      NE2    0.44    2.26  INTRA
 401 LYS   ( 173-)  B      NZ  <->  463 HOH   ( 259 )  B      O      0.41    2.29  INTRA
  24 DGUA  (   8-)  E      O6  <->   25 DCYT  (   1-)  F      N4     0.41    2.29  INTRA
 221 ASP   ( 207-)  A      N   <->  225 GLU   ( 211-)  A      OE1    0.41    2.29  INTRA
 143 ASN   ( 117-)  A      ND2 <->  152 ASP   ( 126-)  A      OD1    0.41    2.29  INTRA BF
 309 TYR   (  72-)  B      OH  <->  368 HIS   ( 131-)  B      ND1    0.40    2.30  INTRA BL
   6 DTHY  (   6-)  C      N3  <->   11 DADE  (   3-)  D      N1     0.40    2.60  INTRA
 129 ILE   ( 103-)  A      N   <->  208 ALA   ( 194-)  A      O      0.38    2.32  INTRA
  85 HIS   (  59-)  A      O   <->  105 LYS   (  79-)  A      NZ     0.37    2.33  INTRA BF
 250 ASP   (   6-)  B      OD2 <->  296 HIS   (  59-)  B      NE2    0.36    2.34  INTRA BL
 188 GLN   ( 171-)  A      NE2 <->  213 PHE   ( 199-)  A      O      0.35    2.35  INTRA
  23 DCYT  (   7-)  E      O2  <->   26 DGUA  (   2-)  F      N2     0.34    2.36  INTRA BL
  18 DGUA  (   2-)  E      O6  <->   31 DCYT  (   7-)  F      N4     0.34    2.36  INTRA BL
  18 DGUA  (   2-)  E      N3  <->  460 HOH   (  60 )  E      O      0.34    2.36  INTRA
  93 LYS   (  67-)  A      N   <->  462 HOH   ( 247 )  A      O      0.33    2.37  INTRA
   7 DCYT  (   7-)  C      N3  <->   10 DGUA  (   2-)  D      N1     0.33    2.67  INTRA
 225 GLU   ( 211-)  A      OE1 <->  242 ARG   ( 237-)  A      NH2    0.31    2.39  INTRA BF
 142 ASN   ( 116-)  A      OD1 <->  145 LYS   ( 119-)  A      N      0.31    2.39  INTRA
 150 PRO   ( 124-)  A      CD  <->  153 GLN   ( 127-)  A      NE2    0.30    2.80  INTRA
 141 ARG   ( 115-)  A      NH1 <->  231 ARG   ( 217-)  A      O      0.30    2.40  INTRA
 286 ARG   (  49-)  B      NH2 <->  302 GLU   (  65-)  B      OE1    0.29    2.41  INTRA BL
And so on for a total of 236 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.

 408 LEU   ( 180-)  B      -6.69
  95 GLN   (  69-)  A      -6.34
  93 LYS   (  67-)  A      -6.02
 197 LEU   ( 180-)  A      -5.99
 217 LYS   ( 203-)  A      -5.59
 306 GLN   (  69-)  B      -5.50
 142 ASN   ( 116-)  A      -5.20
 428 LYS   ( 203-)  B      -5.15
 443 ASN   ( 218-)  B      -5.15
 304 LYS   (  67-)  B      -5.12
 215 GLU   ( 201-)  A      -5.03
 426 GLU   ( 201-)  B      -5.01

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.

  95 GLN   (  69-)  A        97 - HIS     71- ( A)         -5.06
 304 LYS   (  67-)  B       307 - ASN     70- ( B)         -4.75

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

 200 SER   ( 183-)  A   -2.99

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

Error: Water molecules without hydrogen bonds

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

 461 HOH   (  36 )  F      O
 462 HOH   ( 250 )  A      O
 462 HOH   ( 254 )  A      O
 463 HOH   ( 253 )  B      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.

  40 ASN   (   9-)  A
  97 HIS   (  71-)  A
 123 ASN   (  97-)  A
 146 ASN   ( 120-)  A
 207 HIS   ( 193-)  A
 296 HIS   (  59-)  B
 306 GLN   (  69-)  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.

  35 ARG   (   4-)  A      NE
  35 ARG   (   4-)  A      NH1
  45 ASP   (  19-)  A      N
  65 VAL   (  39-)  A      N
  74 SER   (  48-)  A      N
 111 LYS   (  85-)  A      N
 124 LYS   (  98-)  A      N
 137 THR   ( 111-)  A      N
 138 SER   ( 112-)  A      N
 140 ILE   ( 114-)  A      N
 149 TYR   ( 123-)  A      N
 171 ASN   ( 154-)  A      N
 173 LEU   ( 156-)  A      N
 211 LYS   ( 197-)  A      N
 222 SER   ( 208-)  A      N
 233 TYR   ( 219-)  A      N
 236 ASN   ( 231-)  A      N
 237 ASN   ( 232-)  A      N
 259 GLY   (  22-)  B      N
 305 GLN   (  68-)  B      N
 313 THR   (  76-)  B      OG1
 345 GLY   ( 108-)  B      N
 351 ILE   ( 114-)  B      N
 354 ASN   ( 117-)  B      N
 355 THR   ( 118-)  B      N
 360 TYR   ( 123-)  B      N
 380 ASN   ( 152-)  B      N
 381 ILE   ( 153-)  B      N
 415 GLY   ( 190-)  B      N
 433 SER   ( 208-)  B      N
 435 ASP   ( 210-)  B      N
 448 ASN   ( 232-)  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.

 202 ASN   ( 188-)  A      OD1
 282 GLU   (  45-)  B      OE2

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.

 100 ASP   (  74-)  A   H-bonding suggests Asn

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 :  -1.373
  2nd generation packing quality :  -1.615
  Ramachandran plot appearance   :  -4.083 (bad)
  chi-1/chi-2 rotamer normality  :  -5.708 (bad)
  Backbone conformation          :  -0.485

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.084
  Bond angles                    :   1.197
  Omega angle restraints         :   0.202 (tight)
  Side chain planarity           :   0.406 (tight)
  Improper dihedral distribution :   1.329
  B-factor distribution          :   0.668
  Inside/Outside distribution    :   0.955

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 : 3.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.3
  2nd generation packing quality :   0.2
  Ramachandran plot appearance   :  -1.4
  chi-1/chi-2 rotamer normality  :  -3.2 (poor)
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.084
  Bond angles                    :   1.197
  Omega angle restraints         :   0.202 (tight)
  Side chain planarity           :   0.406 (tight)
  Improper dihedral distribution :   1.329
  B-factor distribution          :   0.668
  Inside/Outside distribution    :   0.955
==============

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

Ramachandran plot
    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,
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      data bank (PDB) files
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Ion Checks
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      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
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    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      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.