WHAT IF Check report

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

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

Verification log for pdb2cxe.ent

Administrative problems that can generate validation failures

Warning: Strange inter-chain connections detected

The pairs of residues listed in the table below seem covalently bound while belonging to different chains in the PDB file.

Sometimes this is unavoidable (e.g. if two protein chains are covalently connected via a Cys-Cys or other bond). But if it can be avoided (e.g. often we observe sugars with one chain identifier connected to protein chains with another chain identifier), it should be avoided. WHAT IF and WHAT-CHECK try to deal with all exceptions thrown at it, but if you want these programs to work optimally (i.e. make as few false error messages as is possible) you should help them by getting as much of the administration correct as is humanly possible.

 847 ARG   (  23-)  C  -   NH1 1263 ARG   (  23-)  D  -   NH2
 847 ARG   (  23-)  C  -   NH2 1263 ARG   (  23-)  D  -   NH1

Warning: Strange inter-chain connections could NOT be corrected

Often inter-chain connections are simple administrative problems. In this case not. The observed inter-chain connection(s) either are real, or they are too strange for WHAT IF to correct. Human inspection seems required.

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

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 GLU   (   9-)  A    High
   2 TRP   (  10-)  A    High
   3 TYR   (  11-)  A    High
   4 LEU   (  12-)  A    High
   5 ASP   (  13-)  A    High
   6 PHE   (  14-)  A    High
   7 VAL   (  15-)  A    High
   8 ASP   (  16-)  A    High
   9 LEU   (  17-)  A    High
  10 ASN   (  18-)  A    High
  11 TYR   (  19-)  A    High
  12 GLU   (  20-)  A    High
  13 PRO   (  21-)  A    High
  14 GLY   (  22-)  A    High
  15 ARG   (  23-)  A    High
  16 ASP   (  24-)  A    High
  29 VAL   (  37-)  A    High
  30 SER   (  38-)  A    High
  31 PRO   (  39-)  A    High
  32 GLU   (  40-)  A    High
  37 ARG   (  45-)  A    High
  45 GLY   (  53-)  A    High
  46 THR   (  54-)  A    High
  47 TRP   (  55-)  A    High
  48 THR   (  56-)  A    High
And so on for a total of 512 lines.

Warning: What type of B-factor?

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

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

Crystal temperature (K) :100.000

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

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

 229 ARG   ( 237-)  A
 353 ARG   ( 361-)  A
 645 ARG   ( 237-)  B
 769 ARG   ( 361-)  B
1061 ARG   ( 237-)  C
1185 ARG   ( 361-)  C
1477 ARG   ( 237-)  D
1601 ARG   ( 361-)  D

Warning: Tyrosine convention problem

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

  66 TYR   (  74-)  A
  74 TYR   (  82-)  A
 167 TYR   ( 175-)  A
 199 TYR   ( 207-)  A
 240 TYR   ( 248-)  A
 255 TYR   ( 263-)  A
 482 TYR   (  74-)  B
 490 TYR   (  82-)  B
 583 TYR   ( 175-)  B
 615 TYR   ( 207-)  B
 656 TYR   ( 248-)  B
 671 TYR   ( 263-)  B
 898 TYR   (  74-)  C
 906 TYR   (  82-)  C
 999 TYR   ( 175-)  C
1031 TYR   ( 207-)  C
1072 TYR   ( 248-)  C
1087 TYR   ( 263-)  C
1314 TYR   (  74-)  D
1322 TYR   (  82-)  D
1415 TYR   ( 175-)  D
1447 TYR   ( 207-)  D
1488 TYR   ( 248-)  D
1503 TYR   ( 263-)  D

Warning: Phenylalanine convention problem

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

  65 PHE   (  73-)  A
 102 PHE   ( 110-)  A
 130 PHE   ( 138-)  A
 138 PHE   ( 146-)  A
 183 PHE   ( 191-)  A
 186 PHE   ( 194-)  A
 336 PHE   ( 344-)  A
 481 PHE   (  73-)  B
 518 PHE   ( 110-)  B
 546 PHE   ( 138-)  B
 554 PHE   ( 146-)  B
 599 PHE   ( 191-)  B
 602 PHE   ( 194-)  B
 752 PHE   ( 344-)  B
 897 PHE   (  73-)  C
 934 PHE   ( 110-)  C
 962 PHE   ( 138-)  C
 970 PHE   ( 146-)  C
1015 PHE   ( 191-)  C
1018 PHE   ( 194-)  C
1168 PHE   ( 344-)  C
1313 PHE   (  73-)  D
1350 PHE   ( 110-)  D
1378 PHE   ( 138-)  D
1386 PHE   ( 146-)  D
1431 PHE   ( 191-)  D
1434 PHE   ( 194-)  D
1584 PHE   ( 344-)  D

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.

   8 ASP   (  16-)  A
  16 ASP   (  24-)  A
 203 ASP   ( 211-)  A
 323 ASP   ( 331-)  A
 372 ASP   ( 380-)  A
 424 ASP   (  16-)  B
 432 ASP   (  24-)  B
 619 ASP   ( 211-)  B
 739 ASP   ( 331-)  B
 788 ASP   ( 380-)  B
 840 ASP   (  16-)  C
 848 ASP   (  24-)  C
1035 ASP   ( 211-)  C
1155 ASP   ( 331-)  C
1204 ASP   ( 380-)  C
1256 ASP   (  16-)  D
1264 ASP   (  24-)  D
1451 ASP   ( 211-)  D
1571 ASP   ( 331-)  D
1620 ASP   ( 380-)  D

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.

  21 GLU   (  29-)  A
  33 GLU   (  41-)  A
  55 GLU   (  63-)  A
 168 GLU   ( 176-)  A
 181 GLU   ( 189-)  A
 192 GLU   ( 200-)  A
 193 GLU   ( 201-)  A
 208 GLU   ( 216-)  A
 236 GLU   ( 244-)  A
 403 GLU   ( 411-)  A
 410 GLU   ( 418-)  A
 437 GLU   (  29-)  B
 449 GLU   (  41-)  B
 471 GLU   (  63-)  B
 584 GLU   ( 176-)  B
 597 GLU   ( 189-)  B
 608 GLU   ( 200-)  B
 609 GLU   ( 201-)  B
 624 GLU   ( 216-)  B
 652 GLU   ( 244-)  B
 819 GLU   ( 411-)  B
 826 GLU   ( 418-)  B
 853 GLU   (  29-)  C
 865 GLU   (  41-)  C
 887 GLU   (  63-)  C
1000 GLU   ( 176-)  C
1013 GLU   ( 189-)  C
1024 GLU   ( 200-)  C
1025 GLU   ( 201-)  C
1040 GLU   ( 216-)  C
1068 GLU   ( 244-)  C
1235 GLU   ( 411-)  C
1242 GLU   ( 418-)  C
1269 GLU   (  29-)  D
1281 GLU   (  41-)  D
1303 GLU   (  63-)  D
1416 GLU   ( 176-)  D
1429 GLU   ( 189-)  D
1440 GLU   ( 200-)  D
1441 GLU   ( 201-)  D
1456 GLU   ( 216-)  D
1484 GLU   ( 244-)  D
1651 GLU   ( 411-)  D
1658 GLU   ( 418-)  D

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 GLU   (   9-)  A      N    CA    1.56    5.3
   2 TRP   (  10-)  A      CG   CD2   1.51    4.3
   2 TRP   (  10-)  A      NE1  CE2   1.42    4.6
   2 TRP   (  10-)  A      CD2  CE3   1.51    7.0
   2 TRP   (  10-)  A      CE2  CZ2   1.53    6.6
   2 TRP   (  10-)  A      CZ2  CH2   1.45    4.6
   3 TYR   (  11-)  A      CA   C     1.43   -4.4
   3 TYR   (  11-)  A      CG   CD1   1.50    5.2
   3 TYR   (  11-)  A      CE2  CZ    1.50    5.0
   4 LEU   (  12-)  A      CB   CG    1.61    4.2
   5 ASP   (  13-)  A      CG   OD2   1.34    4.6
   6 PHE   (  14-)  A      CB   CG    1.40   -4.2
   6 PHE   (  14-)  A      CG   CD2   1.29   -4.6
   7 VAL   (  15-)  A      CB   CG1   1.38   -4.2
   8 ASP   (  16-)  A      CB   CG    1.38   -5.4
   9 LEU   (  17-)  A      CA   C     1.42   -4.8
   9 LEU   (  17-)  A      CG   CD1   1.35   -5.1
  10 ASN   (  18-)  A      CA   C     1.43   -4.6
  10 ASN   (  18-)  A      CB   CG    1.71    7.6
  10 ASN   (  18-)  A      CG   ND2   1.49    7.8
  12 GLU   (  20-)  A      C    O     1.38    7.4
  12 GLU   (  20-)  A      CD   OE1   1.35    5.1
  13 PRO   (  21-)  A      CA   CB    1.65    6.2
  15 ARG   (  23-)  A      NE   CZ    1.39    4.1
  18 LEU   (  26-)  A      CA   C     1.43   -4.4
And so on for a total of 1982 lines.

Warning: High bond length deviations

Bond lengths were found to deviate more than normal from the mean standard bond lengths (standard values for protein residues were taken from Engh and Huber [REF], for DNA/RNA these values were taken from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is higher than 1.5 in this structure might indicate that the restraints used in the refinement were not strong enough. This will also occur if a different bond length dictionary is used.

RMS Z-score for bond lengths: 2.756
RMS-deviation in bond distances: 0.066

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.998778  0.000470  0.001868|
 |  0.000470  0.999726 -0.000453|
 |  0.001868 -0.000453  0.996687|
Proposed new scale matrix

 |  0.005831  0.000000  0.004457|
 | -0.000003  0.006704  0.000003|
 | -0.000022  0.000005  0.011748|
With corresponding cell

    A    = 171.259  B   = 149.168  C    = 106.987
    Alpha=  90.069  Beta= 127.286  Gamma=  89.954

The CRYST1 cell dimensions

    A    = 171.478  B   = 149.207  C    = 107.461
    Alpha=  90.000  Beta= 127.370  Gamma=  90.000

Variance: 229.357
(Under-)estimated Z-score: 11.161

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

   1 GLU   (   9-)  A      CG   CD   OE1 106.41   -5.2
   2 TRP   (  10-)  A     -C    N    CA  130.27    4.8
   3 TYR   (  11-)  A      CA   CB   CG  104.33   -4.9
   8 ASP   (  16-)  A      CB   CG   OD2 107.26   -4.8
   9 LEU   (  17-)  A      CA   CB   CG   96.40   -5.7
  10 ASN   (  18-)  A     -O   -C    N   131.06    5.0
  10 ASN   (  18-)  A     -CA  -C    N   104.68   -5.8
  12 GLU   (  20-)  A      N    CA   CB  121.55    6.5
  12 GLU   (  20-)  A      CB   CG   CD  105.60   -4.1
  13 PRO   (  21-)  A     -O   -C    N   128.77    4.8
  13 PRO   (  21-)  A     -CA  -C    N   103.43   -9.0
  13 PRO   (  21-)  A      CG   CD   N   111.97    5.8
  13 PRO   (  21-)  A      CD   N    CA  101.97   -7.2
  14 GLY   (  22-)  A     -O   -C    N   134.01    6.9
  14 GLY   (  22-)  A     -CA  -C    N   105.96   -5.1
  14 GLY   (  22-)  A     -C    N    CA  131.98    6.7
  16 ASP   (  24-)  A     -C    N    CA  131.29    5.3
  17 GLU   (  25-)  A      CA   CB   CG  122.74    4.3
  18 LEU   (  26-)  A     -O   -C    N   129.63    4.1
  18 LEU   (  26-)  A     -CA  -C    N   104.39   -5.9
  18 LEU   (  26-)  A     -C    N    CA  131.11    5.2
  18 LEU   (  26-)  A      C    CA   CB  102.35   -4.1
  18 LEU   (  26-)  A      CA   CB   CG   98.14   -5.2
  19 ILE   (  27-)  A      N    CA   C   124.34    4.7
  19 ILE   (  27-)  A      CA   CB   CG2 100.16   -6.1
And so on for a total of 2010 lines.

Warning: High bond angle deviations

Bond angles were found to deviate more than normal from the mean standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set, and this is indeed observed for very high resolution X-ray structures. The fact that it is higher than 2.0 in this structure might indicate that the restraints used in the refinement were not strong enough. This will also occur if a different bond angle dictionary is used.

RMS Z-score for bond angles: 2.533
RMS-deviation in bond angles: 5.257

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.

   8 ASP   (  16-)  A
  16 ASP   (  24-)  A
  21 GLU   (  29-)  A
  33 GLU   (  41-)  A
  55 GLU   (  63-)  A
 168 GLU   ( 176-)  A
 181 GLU   ( 189-)  A
 192 GLU   ( 200-)  A
 193 GLU   ( 201-)  A
 203 ASP   ( 211-)  A
 208 GLU   ( 216-)  A
 229 ARG   ( 237-)  A
 236 GLU   ( 244-)  A
 323 ASP   ( 331-)  A
 353 ARG   ( 361-)  A
 372 ASP   ( 380-)  A
 403 GLU   ( 411-)  A
 410 GLU   ( 418-)  A
 424 ASP   (  16-)  B
 432 ASP   (  24-)  B
 437 GLU   (  29-)  B
 449 GLU   (  41-)  B
 471 GLU   (  63-)  B
 584 GLU   ( 176-)  B
 597 GLU   ( 189-)  B
And so on for a total of 72 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.

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

  12 GLU   (  20-)  A      C     -6.0    -8.80    -0.03
  20 VAL   (  28-)  A      CA     8.3    45.26    33.23
  31 PRO   (  39-)  A      N     -8.6   -30.69    -2.48
  83 THR   (  91-)  A      C     -6.2    -9.03     0.30
  87 GLU   (  95-)  A      CA    -6.5    23.24    33.96
  93 LEU   ( 101-)  A      CG    -7.3   -45.83   -33.01
 145 PRO   ( 153-)  A      N     -6.7   -24.33    -2.48
 208 GLU   ( 216-)  A      C      7.3    10.51    -0.03
 217 ILE   ( 225-)  A      CB     6.4    40.67    32.31
 225 ILE   ( 233-)  A      CB    -6.2    24.20    32.31
 243 ILE   ( 251-)  A      CB     7.4    41.98    32.31
 245 ILE   ( 253-)  A      CB     7.2    41.70    32.31
 253 LEU   ( 261-)  A      CG     6.2   -22.12   -33.01
 267 ILE   ( 275-)  A      CB    13.5    49.81    32.31
 281 PRO   ( 289-)  A      N     -6.6   -24.25    -2.48
 302 ILE   ( 310-)  A      CB    -8.3    21.53    32.31
 324 PHE   ( 332-)  A      C     -6.5   -10.32     0.23
 337 PRO   ( 345-)  A      N     -6.0   -22.30    -2.48
 349 PRO   ( 357-)  A      N      6.6    19.24    -2.48
 352 ILE   ( 360-)  A      CB     6.7    41.03    32.31
 385 ILE   ( 393-)  A      CB     8.0    42.75    32.31
 428 GLU   (  20-)  B      C     -6.0    -8.78    -0.03
 436 VAL   (  28-)  B      CA     8.3    45.25    33.23
 447 PRO   (  39-)  B      N     -8.6   -30.68    -2.48
 499 THR   (  91-)  B      C     -6.2    -9.05     0.30
And so on for a total of 85 lines.

Warning: High improper dihedral angle deviations

The RMS Z-score for the improper dihedrals in the structure is high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 2.0 worries us a bit. However, we determined the improper normal distribution from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Improper dihedral RMS Z-score : 2.355

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.

1041 THR   ( 217-)  C   11.63
1457 THR   ( 217-)  D   11.63
 209 THR   ( 217-)  A   11.63
 625 THR   ( 217-)  B   11.62
 513 VAL   ( 105-)  B   10.45
 929 VAL   ( 105-)  C   10.45
  97 VAL   ( 105-)  A   10.45
1345 VAL   ( 105-)  D   10.44
1288 SER   (  48-)  D    9.80
 872 SER   (  48-)  C    9.78
  40 SER   (  48-)  A    9.78
 456 SER   (  48-)  B    9.76
1089 ARG   ( 265-)  C    9.27
 257 ARG   ( 265-)  A    9.24
 673 ARG   ( 265-)  B    9.23
1505 ARG   ( 265-)  D    9.21
1412 GLU   ( 172-)  D    9.07
 996 GLU   ( 172-)  C    9.04
 164 GLU   ( 172-)  A    9.04
 580 GLU   ( 172-)  B    9.00
 322 ASN   ( 330-)  A    8.96
1542 ALA   ( 302-)  D    8.96
 738 ASN   ( 330-)  B    8.95
1570 ASN   ( 330-)  D    8.94
1154 ASN   ( 330-)  C    8.94
And so on for a total of 383 lines.

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 : 3.516

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.

 540 HIS   ( 132-)  B    4.03
 124 HIS   ( 132-)  A    4.02
1372 HIS   ( 132-)  D    4.02

Error: Connections to aromatic rings out of plane

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

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

  47 TRP   (  55-)  A      CB   8.91
1295 TRP   (  55-)  D      CB   8.90
 463 TRP   (  55-)  B      CB   8.90
 879 TRP   (  55-)  C      CB   8.90
 953 TYR   ( 129-)  C      OH   8.86
 121 TYR   ( 129-)  A      OH   8.84
 537 TYR   ( 129-)  B      OH   8.83
1369 TYR   ( 129-)  D      OH   8.83
 951 TYR   ( 127-)  C      OH   8.82
1367 TYR   ( 127-)  D      OH   8.82
 119 TYR   ( 127-)  A      OH   8.82
 535 TYR   ( 127-)  B      OH   8.81
 671 TYR   ( 263-)  B      OH   8.45
1087 TYR   ( 263-)  C      OH   8.44
 255 TYR   ( 263-)  A      OH   8.43
1503 TYR   ( 263-)  D      OH   8.43
 956 HIS   ( 132-)  C      CB   8.10
 199 TYR   ( 207-)  A      OH   7.89
 615 TYR   ( 207-)  B      OH   7.89
1447 TYR   ( 207-)  D      OH   7.88
1031 TYR   ( 207-)  C      OH   7.88
 897 PHE   (  73-)  C      CB   7.61
  65 PHE   (  73-)  A      CB   7.60
1313 PHE   (  73-)  D      CB   7.60
 481 PHE   (  73-)  B      CB   7.59
And so on for a total of 89 lines.

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 : -6.155

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.

1367 TYR   ( 127-)  D    -3.6
 951 TYR   ( 127-)  C    -3.5
 535 TYR   ( 127-)  B    -3.5
 119 TYR   ( 127-)  A    -3.5
 187 PRO   ( 195-)  A    -3.0
1019 PRO   ( 195-)  C    -3.0
 603 PRO   ( 195-)  B    -2.9
1435 PRO   ( 195-)  D    -2.9
1177 PRO   ( 353-)  C    -2.9
 345 PRO   ( 353-)  A    -2.9
 761 PRO   ( 353-)  B    -2.9
1593 PRO   ( 353-)  D    -2.9
1392 ARG   ( 152-)  D    -2.9
 976 ARG   ( 152-)  C    -2.9
 560 ARG   ( 152-)  B    -2.9
 144 ARG   ( 152-)  A    -2.9
  49 THR   (  57-)  A    -2.7
 465 THR   (  57-)  B    -2.7
1297 THR   (  57-)  D    -2.7
 881 THR   (  57-)  C    -2.7
 876 ILE   (  52-)  C    -2.7
  44 ILE   (  52-)  A    -2.7
 460 ILE   (  52-)  B    -2.7
1292 ILE   (  52-)  D    -2.7
 977 PRO   ( 153-)  C    -2.7
And so on for a total of 192 lines.

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.

   3 TYR   (  11-)  A  Poor phi/psi
  34 ALA   (  42-)  A  Poor phi/psi
  35 ALA   (  43-)  A  Poor phi/psi
  40 SER   (  48-)  A  Poor phi/psi
  41 GLU   (  49-)  A  Poor phi/psi
  42 SER   (  50-)  A  Poor phi/psi
  43 SER   (  51-)  A  Poor phi/psi
  47 TRP   (  55-)  A  Poor phi/psi
  49 THR   (  57-)  A  Poor phi/psi
  55 GLU   (  63-)  A  Poor phi/psi
  56 MET   (  64-)  A  Poor phi/psi
  66 TYR   (  74-)  A  Poor phi/psi
  72 GLU   (  80-)  A  Poor phi/psi
  82 LEU   (  90-)  A  Poor phi/psi
  98 ALA   ( 106-)  A  Poor phi/psi
 102 PHE   ( 110-)  A  Poor phi/psi
 103 GLY   ( 111-)  A  Poor phi/psi
 104 MET   ( 112-)  A  Poor phi/psi
 106 ALA   ( 114-)  A  Poor phi/psi
 119 TYR   ( 127-)  A  Poor phi/psi
 120 GLU   ( 128-)  A  Poor phi/psi
 144 ARG   ( 152-)  A  Poor phi/psi
 152 LYS   ( 160-)  A  PRO omega poor
 156 GLY   ( 164-)  A  Poor phi/psi
 160 GLU   ( 168-)  A  Poor phi/psi
And so on for a total of 181 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 : -6.845

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.

 407 SER   ( 415-)  A    0.38
 823 SER   ( 415-)  B    0.38
1239 SER   ( 415-)  C    0.38
1655 SER   ( 415-)  D    0.38

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!

   7 VAL   (  15-)  A      0
   9 LEU   (  17-)  A      0
  16 ASP   (  24-)  A      0
  24 PHE   (  32-)  A      0
  27 ASN   (  35-)  A      0
  42 SER   (  50-)  A      0
  43 SER   (  51-)  A      0
  44 ILE   (  52-)  A      0
  46 THR   (  54-)  A      0
  47 TRP   (  55-)  A      0
  48 THR   (  56-)  A      0
  49 THR   (  57-)  A      0
  50 LEU   (  58-)  A      0
  51 TRP   (  59-)  A      0
  56 MET   (  64-)  A      0
  60 SER   (  68-)  A      0
  65 PHE   (  73-)  A      0
  66 TYR   (  74-)  A      0
  67 LEU   (  75-)  A      0
  70 HIS   (  78-)  A      0
  72 GLU   (  80-)  A      0
  82 LEU   (  90-)  A      0
  83 THR   (  91-)  A      0
  84 LEU   (  92-)  A      0
  86 GLU   (  94-)  A      0
And so on for a total of 607 lines.

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!

1223 GLY   ( 399-)  C   1.96   80
 807 GLY   ( 399-)  B   1.96   80
 391 GLY   ( 399-)  A   1.96   80
1639 GLY   ( 399-)  D   1.96   80
 518 PHE   ( 110-)  B   1.51   11
 934 PHE   ( 110-)  C   1.51   11
 102 PHE   ( 110-)  A   1.51   11
1350 PHE   ( 110-)  D   1.51   11

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...

  11 TYR   (  19-)  A   2.57
  46 THR   (  54-)  A   1.57
  47 TRP   (  55-)  A   1.71
  48 THR   (  56-)  A   1.73
 326 LEU   ( 334-)  A   1.87
 427 TYR   (  19-)  B   2.56
 462 THR   (  54-)  B   1.57
 463 TRP   (  55-)  B   1.72
 464 THR   (  56-)  B   1.74
 742 LEU   ( 334-)  B   1.88
 843 TYR   (  19-)  C   2.57
 878 THR   (  54-)  C   1.56
 879 TRP   (  55-)  C   1.72
 880 THR   (  56-)  C   1.74
1158 LEU   ( 334-)  C   1.87
1259 TYR   (  19-)  D   2.57
1294 THR   (  54-)  D   1.57
1295 TRP   (  55-)  D   1.71
1296 THR   (  56-)  D   1.73
1574 LEU   ( 334-)  D   1.85

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]

  13 PRO   (  21-)  A    0.50 HIGH
  26 PRO   (  34-)  A    0.20 LOW
 118 PRO   ( 126-)  A    0.48 HIGH
 187 PRO   ( 195-)  A    0.47 HIGH
 281 PRO   ( 289-)  A    0.55 HIGH
 334 PRO   ( 342-)  A    0.48 HIGH
 337 PRO   ( 345-)  A    0.56 HIGH
 345 PRO   ( 353-)  A    0.45 HIGH
 371 PRO   ( 379-)  A    0.48 HIGH
 402 PRO   ( 410-)  A    0.47 HIGH
 429 PRO   (  21-)  B    0.50 HIGH
 442 PRO   (  34-)  B    0.20 LOW
 534 PRO   ( 126-)  B    0.48 HIGH
 603 PRO   ( 195-)  B    0.47 HIGH
 697 PRO   ( 289-)  B    0.55 HIGH
 750 PRO   ( 342-)  B    0.48 HIGH
 753 PRO   ( 345-)  B    0.56 HIGH
 761 PRO   ( 353-)  B    0.45 HIGH
 787 PRO   ( 379-)  B    0.48 HIGH
 818 PRO   ( 410-)  B    0.47 HIGH
 845 PRO   (  21-)  C    0.50 HIGH
 858 PRO   (  34-)  C    0.20 LOW
 950 PRO   ( 126-)  C    0.48 HIGH
1019 PRO   ( 195-)  C    0.47 HIGH
1113 PRO   ( 289-)  C    0.55 HIGH
1166 PRO   ( 342-)  C    0.48 HIGH
1169 PRO   ( 345-)  C    0.56 HIGH
1177 PRO   ( 353-)  C    0.45 HIGH
1203 PRO   ( 379-)  C    0.48 HIGH
1234 PRO   ( 410-)  C    0.47 HIGH
1261 PRO   (  21-)  D    0.50 HIGH
1274 PRO   (  34-)  D    0.20 LOW
1366 PRO   ( 126-)  D    0.48 HIGH
1435 PRO   ( 195-)  D    0.47 HIGH
1529 PRO   ( 289-)  D    0.55 HIGH
1582 PRO   ( 342-)  D    0.48 HIGH
1585 PRO   ( 345-)  D    0.56 HIGH
1593 PRO   ( 353-)  D    0.45 HIGH
1619 PRO   ( 379-)  D    0.48 HIGH
1650 PRO   ( 410-)  D    0.47 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].

  31 PRO   (  39-)  A   142.4 envelop C-alpha (144 degrees)
  81 PRO   (  89-)  A   -48.4 half-chair C-beta/C-alpha (-54 degrees)
 117 PRO   ( 125-)  A    18.5 half-chair N/C-delta (18 degrees)
 118 PRO   ( 126-)  A  -115.1 envelop C-gamma (-108 degrees)
 128 PRO   ( 136-)  A   103.2 envelop C-beta (108 degrees)
 151 PRO   ( 159-)  A    42.4 envelop C-delta (36 degrees)
 153 PRO   ( 161-)  A  -117.8 half-chair C-delta/C-gamma (-126 degrees)
 187 PRO   ( 195-)  A   125.4 half-chair C-beta/C-alpha (126 degrees)
 222 PRO   ( 230-)  A   123.4 half-chair C-beta/C-alpha (126 degrees)
 345 PRO   ( 353-)  A  -112.8 envelop C-gamma (-108 degrees)
 349 PRO   ( 357-)  A    38.4 envelop C-delta (36 degrees)
 371 PRO   ( 379-)  A  -116.2 envelop C-gamma (-108 degrees)
 374 PRO   ( 382-)  A   -57.3 half-chair C-beta/C-alpha (-54 degrees)
 447 PRO   (  39-)  B   142.3 envelop C-alpha (144 degrees)
 497 PRO   (  89-)  B   -48.4 half-chair C-beta/C-alpha (-54 degrees)
 533 PRO   ( 125-)  B    18.5 half-chair N/C-delta (18 degrees)
 534 PRO   ( 126-)  B  -115.1 envelop C-gamma (-108 degrees)
 544 PRO   ( 136-)  B   103.1 envelop C-beta (108 degrees)
 567 PRO   ( 159-)  B    42.4 envelop C-delta (36 degrees)
 569 PRO   ( 161-)  B  -117.8 half-chair C-delta/C-gamma (-126 degrees)
 603 PRO   ( 195-)  B   125.4 half-chair C-beta/C-alpha (126 degrees)
 638 PRO   ( 230-)  B   123.3 half-chair C-beta/C-alpha (126 degrees)
 761 PRO   ( 353-)  B  -112.7 envelop C-gamma (-108 degrees)
 765 PRO   ( 357-)  B    38.4 envelop C-delta (36 degrees)
 787 PRO   ( 379-)  B  -116.2 envelop C-gamma (-108 degrees)
And so on for a total of 52 lines.

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short 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.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

1666 HOH   ( 436 )  B      O    <->  1667 HOH   ( 439 )  C      O    2.26    0.14  INTRA BL
1241 ARG   ( 417-)  C      CD   <->  1667 HOH   ( 481 )  C      O    1.15    1.65  INTRA BF
 919 GLU   (  95-)  C      OE2  <->  1371 ARG   ( 131-)  D      NH1  0.89    1.81  INTRA BL
 952 GLU   ( 128-)  C      CG   <->  1368 GLU   ( 128-)  D      CG   0.87    2.33  INTRA BL
1667 HOH   ( 431 )  C      O    <->  1667 HOH   ( 450 )  C      O    0.83    1.37  INTRA BL
1665 HOH   ( 447 )  A      O    <->  1665 HOH   ( 481 )  A      O    0.83    1.37  INTRA BL
1668 HOH   ( 431 )  D      O    <->  1668 HOH   ( 448 )  D      O    0.81    1.39  INTRA BL
 955 ARG   ( 131-)  C      NH1  <->  1335 GLU   (  95-)  D      OE2  0.80    1.90  INTRA BL
1666 HOH   ( 447 )  B      O    <->  1666 HOH   ( 480 )  B      O    0.71    1.49  INTRA BL
1543 ARG   ( 303-)  D      NH2  <->  1582 PRO   ( 342-)  D      CA   0.64    2.46  INTRA BL
 295 ARG   ( 303-)  A      NH2  <->   334 PRO   ( 342-)  A      CA   0.64    2.46  INTRA BL
 711 ARG   ( 303-)  B      NH2  <->   750 PRO   ( 342-)  B      CA   0.64    2.46  INTRA BL
1127 ARG   ( 303-)  C      NH2  <->  1166 PRO   ( 342-)  C      CA   0.64    2.46  INTRA BL
 418 TRP   (  10-)  B      O    <->   420 LEU   (  12-)  B      N    0.63    2.07  INTRA BF
 834 TRP   (  10-)  C      O    <->   836 LEU   (  12-)  C      N    0.63    2.07  INTRA BF
   2 TRP   (  10-)  A      O    <->     4 LEU   (  12-)  A      N    0.63    2.07  INTRA BF
1250 TRP   (  10-)  D      O    <->  1252 LEU   (  12-)  D      N    0.62    2.08  INTRA BF
 852 VAL   (  28-)  C      CG2  <->   912 TYR   (  88-)  C      CE2  0.60    2.60  INTRA BL
  20 VAL   (  28-)  A      CG2  <->    80 TYR   (  88-)  A      CE2  0.60    2.60  INTRA BL
 436 VAL   (  28-)  B      CG2  <->   496 TYR   (  88-)  B      CE2  0.60    2.60  INTRA BL
1268 VAL   (  28-)  D      CG2  <->  1328 TYR   (  88-)  D      CE2  0.60    2.60  INTRA BL
1374 LYS   ( 134-)  D      NZ   <->  1506 GLU   ( 266-)  D      CG   0.57    2.53  INTRA BF
 126 LYS   ( 134-)  A      NZ   <->   258 GLU   ( 266-)  A      CG   0.57    2.53  INTRA BF
 542 LYS   ( 134-)  B      NZ   <->   674 GLU   ( 266-)  B      CG   0.57    2.53  INTRA BF
 958 LYS   ( 134-)  C      NZ   <->  1090 GLU   ( 266-)  C      CG   0.57    2.53  INTRA BF
And so on for a total of 1560 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

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.

1527 ARG   ( 287-)  D      -7.11
 279 ARG   ( 287-)  A      -7.11
1663 LYS   ( 423-)  D      -6.42
1247 LYS   ( 423-)  C      -6.40
 415 LYS   ( 423-)  A      -6.40
 831 LYS   ( 423-)  B      -6.40
 695 ARG   ( 287-)  B      -6.39
1111 ARG   ( 287-)  C      -6.33
1300 LYS   (  60-)  D      -6.19
  52 LYS   (  60-)  A      -6.18
 155 MET   ( 163-)  A      -6.16
1403 MET   ( 163-)  D      -6.12
1400 LYS   ( 160-)  D      -6.11
 152 LYS   ( 160-)  A      -6.11
1298 LEU   (  58-)  D      -6.03
  50 LEU   (  58-)  A      -6.03
1576 LYS   ( 336-)  D      -5.91
1160 LYS   ( 336-)  C      -5.91
 328 LYS   ( 336-)  A      -5.86
 744 LYS   ( 336-)  B      -5.84
 844 GLU   (  20-)  C      -5.81
1260 GLU   (  20-)  D      -5.81
  12 GLU   (  20-)  A      -5.81
 428 GLU   (  20-)  B      -5.81
 333 ARG   ( 341-)  A      -5.79
And so on for a total of 52 lines.

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.

  50 LEU   (  58-)  A        53 - LEU     61- ( A)         -5.15
1298 LEU   (  58-)  D      1301 - LEU     61- ( D)         -5.15

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: 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: C

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: D

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.

 916 LEU   (  92-)  C   -2.79
1332 LEU   (  92-)  D   -2.78
 500 LEU   (  92-)  B   -2.78
  84 LEU   (  92-)  A   -2.77
 472 MET   (  64-)  B   -2.53
 888 MET   (  64-)  C   -2.53

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

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

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.

1665 HOH   ( 460 )  A      O    -20.89    1.01  -22.83
1665 HOH   ( 461 )  A      O    -23.67   -2.32  -28.57
1666 HOH   ( 459 )  B      O     33.99    5.31    8.95
1666 HOH   ( 460 )  B      O     38.68    0.04    7.53

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.

1665 HOH   ( 432 )  A      O
1665 HOH   ( 433 )  A      O
1665 HOH   ( 434 )  A      O
1665 HOH   ( 435 )  A      O
1665 HOH   ( 440 )  A      O
1665 HOH   ( 454 )  A      O
1665 HOH   ( 459 )  A      O
1665 HOH   ( 460 )  A      O
1665 HOH   ( 462 )  A      O
1665 HOH   ( 468 )  A      O
1665 HOH   ( 470 )  A      O
1665 HOH   ( 472 )  A      O
1665 HOH   ( 478 )  A      O
1665 HOH   ( 479 )  A      O
1666 HOH   ( 432 )  B      O
1666 HOH   ( 433 )  B      O
1666 HOH   ( 434 )  B      O
1666 HOH   ( 435 )  B      O
1666 HOH   ( 440 )  B      O
1666 HOH   ( 454 )  B      O
1666 HOH   ( 458 )  B      O
1666 HOH   ( 459 )  B      O
1666 HOH   ( 461 )  B      O
1666 HOH   ( 465 )  B      O
1666 HOH   ( 467 )  B      O
And so on for a total of 56 lines.

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.

  92 GLN   ( 100-)  A
 109 ASN   ( 117-)  A
 116 HIS   ( 124-)  A
 218 ASN   ( 226-)  A
 235 ASN   ( 243-)  A
 268 HIS   ( 276-)  A
 283 HIS   ( 291-)  A
 362 GLN   ( 370-)  A
 508 GLN   ( 100-)  B
 525 ASN   ( 117-)  B
 634 ASN   ( 226-)  B
 651 ASN   ( 243-)  B
 684 HIS   ( 276-)  B
 699 HIS   ( 291-)  B
 778 GLN   ( 370-)  B
 924 GLN   ( 100-)  C
 941 ASN   ( 117-)  C
 948 HIS   ( 124-)  C
1050 ASN   ( 226-)  C
1067 ASN   ( 243-)  C
1100 HIS   ( 276-)  C
1115 HIS   ( 291-)  C
1133 GLN   ( 309-)  C
1194 GLN   ( 370-)  C
1340 GLN   ( 100-)  D
1357 ASN   ( 117-)  D
1364 HIS   ( 124-)  D
1466 ASN   ( 226-)  D
1483 ASN   ( 243-)  D
1516 HIS   ( 276-)  D
1518 HIS   ( 278-)  D
1531 HIS   ( 291-)  D
1610 GLN   ( 370-)  D

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.

   4 LEU   (  12-)  A      N
   6 PHE   (  14-)  A      N
  16 ASP   (  24-)  A      N
  32 GLU   (  40-)  A      N
  48 THR   (  56-)  A      N
  51 TRP   (  59-)  A      N
  56 MET   (  64-)  A      N
  59 ARG   (  67-)  A      N
  62 ALA   (  70-)  A      N
  66 TYR   (  74-)  A      N
  83 THR   (  91-)  A      OG1
  85 PHE   (  93-)  A      N
  88 GLY   (  96-)  A      N
  89 SER   (  97-)  A      OG
 102 PHE   ( 110-)  A      N
 105 LYS   ( 113-)  A      N
 111 ARG   ( 119-)  A      NE
 119 TYR   ( 127-)  A      OH
 124 HIS   ( 132-)  A      N
 136 ARG   ( 144-)  A      NH2
 147 THR   ( 155-)  A      OG1
 152 LYS   ( 160-)  A      N
 155 MET   ( 163-)  A      N
 156 GLY   ( 164-)  A      N
 157 TRP   ( 165-)  A      N
And so on for a total of 248 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.

  70 HIS   (  78-)  A      ND1
  87 GLU   (  95-)  A      OE2
 100 ASN   ( 108-)  A      OD1
 160 GLU   ( 168-)  A      OE1
 182 ASN   ( 190-)  A      OD1
 244 ASP   ( 252-)  A      OD1
 330 GLU   ( 338-)  A      OE1
 331 HIS   ( 339-)  A      ND1
 486 HIS   (  78-)  B      ND1
 503 GLU   (  95-)  B      OE2
 576 GLU   ( 168-)  B      OE1
 598 ASN   ( 190-)  B      OD1
 660 ASP   ( 252-)  B      OD1
 746 GLU   ( 338-)  B      OE1
 747 HIS   ( 339-)  B      ND1
 902 HIS   (  78-)  C      ND1
 919 GLU   (  95-)  C      OE2
 932 ASN   ( 108-)  C      OD1
 956 HIS   ( 132-)  C      ND1
 992 GLU   ( 168-)  C      OE1
1014 ASN   ( 190-)  C      OD1
1076 ASP   ( 252-)  C      OD1
1162 GLU   ( 338-)  C      OE1
1163 HIS   ( 339-)  C      ND1
1318 HIS   (  78-)  D      ND1
1335 GLU   (  95-)  D      OE2
1348 ASN   ( 108-)  D      OD1
1408 GLU   ( 168-)  D      OE1
1430 ASN   ( 190-)  D      OD1
1492 ASP   ( 252-)  D      OD1
1578 GLU   ( 338-)  D      OE1
1579 HIS   ( 339-)  D      ND1

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.

   5 ASP   (  13-)  A   H-bonding suggests Asn
  68 GLU   (  76-)  A   H-bonding suggests Gln
  87 GLU   (  95-)  A   H-bonding suggests Gln
 203 ASP   ( 211-)  A   H-bonding suggests Asn
 236 GLU   ( 244-)  A   H-bonding suggests Gln
 244 ASP   ( 252-)  A   H-bonding suggests Asn
 383 ASP   ( 391-)  A   H-bonding suggests Asn
 421 ASP   (  13-)  B   H-bonding suggests Asn
 484 GLU   (  76-)  B   H-bonding suggests Gln
 503 GLU   (  95-)  B   H-bonding suggests Gln
 619 ASP   ( 211-)  B   H-bonding suggests Asn
 652 GLU   ( 244-)  B   H-bonding suggests Gln
 660 ASP   ( 252-)  B   H-bonding suggests Asn
 799 ASP   ( 391-)  B   H-bonding suggests Asn
 837 ASP   (  13-)  C   H-bonding suggests Asn
 900 GLU   (  76-)  C   H-bonding suggests Gln
 919 GLU   (  95-)  C   H-bonding suggests Gln
1035 ASP   ( 211-)  C   H-bonding suggests Asn
1068 GLU   ( 244-)  C   H-bonding suggests Gln
1076 ASP   ( 252-)  C   H-bonding suggests Asn
1215 ASP   ( 391-)  C   H-bonding suggests Asn
1253 ASP   (  13-)  D   H-bonding suggests Asn
1316 GLU   (  76-)  D   H-bonding suggests Gln
1335 GLU   (  95-)  D   H-bonding suggests Gln
1451 ASP   ( 211-)  D   H-bonding suggests Asn
1484 GLU   ( 244-)  D   H-bonding suggests Gln
1492 ASP   ( 252-)  D   H-bonding suggests Asn
1631 ASP   ( 391-)  D   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 :  -1.812
  2nd generation packing quality :  -2.654
  Ramachandran plot appearance   :  -6.155 (bad)
  chi-1/chi-2 rotamer normality  :  -6.845 (bad)
  Backbone conformation          :  -1.010

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   2.756 (loose)
  Bond angles                    :   2.533 (loose)
  Omega angle restraints         :   0.830
  Side chain planarity           :   1.173
  Improper dihedral distribution :   2.355 (loose)
  B-factor distribution          :   0.523
  Inside/Outside distribution    :   1.013

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 :  -0.7
  2nd generation packing quality :  -0.7
  Ramachandran plot appearance   :  -3.4 (poor)
  chi-1/chi-2 rotamer normality  :  -4.2 (bad)
  Backbone conformation          :  -0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   2.756 (loose)
  Bond angles                    :   2.533 (loose)
  Omega angle restraints         :   0.830
  Side chain planarity           :   1.173
  Improper dihedral distribution :   2.355 (loose)
  B-factor distribution          :   0.523
  Inside/Outside distribution    :   1.013
==============

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.