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 pdb2uu7.ent

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

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: O

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.

  22 GLU   (  24-)  A    High
  69 GLU   (  71-)  A    High
 104 ARG   ( 106-)  A    High
 117 ARG   ( 119-)  A    High
 261 GLU   ( 263-)  A    High
 266 LYS   ( 268-)  A    High
 284 ARG   ( 286-)  A    High
 303 GLU   ( 305-)  A    High
 317 ARG   ( 319-)  A    High
 364 ASP   ( 366-)  A    High
 365 GLU   ( 367-)  A    High
 366 PRO   ( 368-)  A    High
 367 PHE   ( 369-)  A    High
 368 GLN   ( 370-)  A    High
 392 GLU   (  24-)  B    High
 439 GLU   (  71-)  B    High
 474 ARG   ( 106-)  B    High
 487 ARG   ( 119-)  B    High
 631 GLU   ( 263-)  B    High
 636 LYS   ( 268-)  B    High
 654 ARG   ( 286-)  B    High
 673 GLU   ( 305-)  B    High
 687 ARG   ( 319-)  B    High
 734 ASP   ( 366-)  B    High
 735 GLU   ( 367-)  B    High
And so on for a total of 210 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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first.

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: O

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

  15 TYR   (  17-)  A
  76 TYR   (  78-)  A
 102 TYR   ( 104-)  A
 135 TYR   ( 137-)  A
 159 TYR   ( 161-)  A
 169 TYR   ( 171-)  A
 178 TYR   ( 180-)  A
 183 TYR   ( 185-)  A
 281 TYR   ( 283-)  A
 286 TYR   ( 288-)  A
 472 TYR   ( 104-)  B
 505 TYR   ( 137-)  B
 529 TYR   ( 161-)  B
 539 TYR   ( 171-)  B
 548 TYR   ( 180-)  B
 553 TYR   ( 185-)  B
 651 TYR   ( 283-)  B
 656 TYR   ( 288-)  B
 755 TYR   (  17-)  C
 842 TYR   ( 104-)  C
 875 TYR   ( 137-)  C
 899 TYR   ( 161-)  C
 909 TYR   ( 171-)  C
 918 TYR   ( 180-)  C
 923 TYR   ( 185-)  C
And so on for a total of 131 lines.

Warning: Phenylalanine convention problem

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

  60 PHE   (  62-)  A
  66 PHE   (  68-)  A
  87 PHE   (  89-)  A
 100 PHE   ( 102-)  A
 129 PHE   ( 131-)  A
 230 PHE   ( 232-)  A
 236 PHE   ( 238-)  A
 301 PHE   ( 303-)  A
 310 PHE   ( 312-)  A
 335 PHE   ( 337-)  A
 347 PHE   ( 349-)  A
 430 PHE   (  62-)  B
 436 PHE   (  68-)  B
 457 PHE   (  89-)  B
 470 PHE   ( 102-)  B
 499 PHE   ( 131-)  B
 600 PHE   ( 232-)  B
 606 PHE   ( 238-)  B
 671 PHE   ( 303-)  B
 680 PHE   ( 312-)  B
 705 PHE   ( 337-)  B
 717 PHE   ( 349-)  B
 806 PHE   (  68-)  C
 827 PHE   (  89-)  C
 840 PHE   ( 102-)  C
And so on for a total of 157 lines.

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.

  74 ASP   (  76-)  A
 214 ASP   ( 216-)  A
 237 ASP   ( 239-)  A
 345 ASP   ( 347-)  A
 444 ASP   (  76-)  B
 584 ASP   ( 216-)  B
 715 ASP   ( 347-)  B
 814 ASP   (  76-)  C
 954 ASP   ( 216-)  C
 977 ASP   ( 239-)  C
1085 ASP   ( 347-)  C
1184 ASP   (  76-)  D
1324 ASP   ( 216-)  D
1347 ASP   ( 239-)  D
1455 ASP   ( 347-)  D
1554 ASP   (  76-)  E
1694 ASP   ( 216-)  E
1825 ASP   ( 347-)  E
1924 ASP   (  76-)  F
2064 ASP   ( 216-)  F
2087 ASP   ( 239-)  F
2195 ASP   ( 347-)  F
2294 ASP   (  76-)  G
2434 ASP   ( 216-)  G
2565 ASP   ( 347-)  G
And so on for a total of 57 lines.

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.

  22 GLU   (  24-)  A
  48 GLU   (  50-)  A
 132 GLU   ( 134-)  A
 134 GLU   ( 136-)  A
 228 GLU   ( 230-)  A
 262 GLU   ( 264-)  A
 392 GLU   (  24-)  B
 418 GLU   (  50-)  B
 502 GLU   ( 134-)  B
 504 GLU   ( 136-)  B
 598 GLU   ( 230-)  B
 632 GLU   ( 264-)  B
 762 GLU   (  24-)  C
 788 GLU   (  50-)  C
 872 GLU   ( 134-)  C
 874 GLU   ( 136-)  C
 968 GLU   ( 230-)  C
1002 GLU   ( 264-)  C
1132 GLU   (  24-)  D
1158 GLU   (  50-)  D
1242 GLU   ( 134-)  D
1244 GLU   ( 136-)  D
1338 GLU   ( 230-)  D
1372 GLU   ( 264-)  D
1502 GLU   (  24-)  E
And so on for a total of 90 lines.

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 THR   (   3-)  A      CA   CB    1.66    6.4
 371 THR   (   3-)  B      CA   CB    1.71    8.9
 741 THR   (   3-)  C      CA   CB    1.68    7.7
1111 THR   (   3-)  D      CA   CB    1.72    9.3
1481 THR   (   3-)  E      CA   CB    1.70    8.3
1851 THR   (   3-)  F      CA   CB    1.67    7.1
2221 THR   (   3-)  G      CA   CB    1.71    9.0
2591 THR   (   3-)  H      CA   CB    1.69    7.9
2961 THR   (   3-)  I      CA   CB    1.67    6.9
3331 THR   (   3-)  J      CA   CB    1.67    7.1
3701 THR   (   3-)  K      CA   CB    1.72    9.5
4071 THR   (   3-)  L      CA   CB    1.72    9.5
4441 THR   (   3-)  M      CA   CB    1.69    8.0
4811 THR   (   3-)  N      CA   CB    1.68    7.7
5181 THR   (   3-)  O      CA   CB    1.69    7.9

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 THR   (   3-)  A      N    CA   CB  119.60    5.4
  32 ASP   (  34-)  A     -C    N    CA  130.00    4.6
 191 THR   ( 193-)  A      C    CA   CB  100.08   -5.3
 282 HIS   ( 284-)  A      CG   ND1  CE1 109.61    4.0
 371 THR   (   3-)  B      N    CA   CB  119.93    5.5
 402 ASP   (  34-)  B     -C    N    CA  129.84    4.5
 561 THR   ( 193-)  B      C    CA   CB  102.01   -4.3
 594 HIS   ( 226-)  B      CG   ND1  CE1 109.61    4.0
 652 HIS   ( 284-)  B      CG   ND1  CE1 109.67    4.1
 741 THR   (   3-)  C      N    CA   CB  118.35    4.6
 866 HIS   ( 128-)  C      CG   ND1  CE1 109.62    4.0
 931 THR   ( 193-)  C      C    CA   CB   99.64   -5.5
1111 THR   (   3-)  D      N    CA   CB  120.05    5.6
1301 THR   ( 193-)  D      C    CA   CB   99.35   -5.7
1481 THR   (   3-)  E      N    CA   CB  119.69    5.4
1512 ASP   (  34-)  E     -C    N    CA  129.26    4.2
1671 THR   ( 193-)  E      C    CA   CB   97.90   -6.4
1851 THR   (   3-)  F      N    CA   CB  119.75    5.4
1882 ASP   (  34-)  F     -C    N    CA  129.30    4.2
2041 THR   ( 193-)  F      C    CA   CB  100.89   -4.8
2221 THR   (   3-)  G      N    CA   CB  119.38    5.2
2411 THR   ( 193-)  G      C    CA   CB  101.36   -4.6
2591 THR   (   3-)  H      N    CA   CB  119.67    5.4
2622 ASP   (  34-)  H     -C    N    CA  129.26    4.2
2781 THR   ( 193-)  H      C    CA   CB   99.62   -5.5
2961 THR   (   3-)  I      N    CA   CB  118.68    4.8
3151 THR   ( 193-)  I      C    CA   CB  101.42   -4.6
3331 THR   (   3-)  J      N    CA   CB  119.80    5.5
3362 ASP   (  34-)  J      C    CA   CB  101.32   -4.6
3456 HIS   ( 128-)  J      CG   ND1  CE1 109.66    4.1
3521 THR   ( 193-)  J      C    CA   CB   99.95   -5.3
3581 HIS   ( 253-)  J      CG   ND1  CE1 109.63    4.0
3612 HIS   ( 284-)  J      CG   ND1  CE1 109.62    4.0
3701 THR   (   3-)  K      N    CA   CB  120.12    5.7
3732 ASP   (  34-)  K     -C    N    CA  129.20    4.2
3891 THR   ( 193-)  K      C    CA   CB   98.91   -5.9
4071 THR   (   3-)  L      N    CA   CB  120.80    6.1
4261 THR   ( 193-)  L      C    CA   CB   99.01   -5.8
4441 THR   (   3-)  M      N    CA   CB  119.21    5.1
4472 ASP   (  34-)  M     -C    N    CA  129.31    4.2
4631 THR   ( 193-)  M      C    CA   CB   99.31   -5.7
4811 THR   (   3-)  N      N    CA   CB  119.16    5.1
4842 ASP   (  34-)  N     -C    N    CA  129.05    4.1
5001 THR   ( 193-)  N      C    CA   CB   98.63   -6.0
5092 HIS   ( 284-)  N      CG   ND1  CE1 109.78    4.2
5181 THR   (   3-)  O      N    CA   CB  119.71    5.4
5212 ASP   (  34-)  O     -C    N    CA  129.79    4.5
5212 ASP   (  34-)  O      C    CA   CB  102.07   -4.2
5371 THR   ( 193-)  O      C    CA   CB   99.68   -5.5

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.

  22 GLU   (  24-)  A
  48 GLU   (  50-)  A
  74 ASP   (  76-)  A
 132 GLU   ( 134-)  A
 134 GLU   ( 136-)  A
 214 ASP   ( 216-)  A
 228 GLU   ( 230-)  A
 237 ASP   ( 239-)  A
 262 GLU   ( 264-)  A
 345 ASP   ( 347-)  A
 392 GLU   (  24-)  B
 418 GLU   (  50-)  B
 444 ASP   (  76-)  B
 502 GLU   ( 134-)  B
 504 GLU   ( 136-)  B
 584 ASP   ( 216-)  B
 598 GLU   ( 230-)  B
 632 GLU   ( 264-)  B
 715 ASP   ( 347-)  B
 762 GLU   (  24-)  C
 788 GLU   (  50-)  C
 814 ASP   (  76-)  C
 872 GLU   ( 134-)  C
 874 GLU   ( 136-)  C
 954 ASP   ( 216-)  C
And so on for a total of 147 lines.

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

2286 PHE   (  68-)  G    -2.7
4261 THR   ( 193-)  L    -2.7
3151 THR   ( 193-)  I    -2.7
5371 THR   ( 193-)  O    -2.7
1176 PHE   (  68-)  D    -2.7
4348 ARG   ( 280-)  L    -2.7
1301 THR   ( 193-)  D    -2.7
 191 THR   ( 193-)  A    -2.7
5001 THR   ( 193-)  N    -2.7
2411 THR   ( 193-)  G    -2.7
 278 ARG   ( 280-)  A    -2.7
 561 THR   ( 193-)  B    -2.7
4631 THR   ( 193-)  M    -2.7
4136 PHE   (  68-)  L    -2.7
 931 THR   ( 193-)  C    -2.7
2041 THR   ( 193-)  F    -2.6
5458 ARG   ( 280-)  O    -2.6
4876 PHE   (  68-)  N    -2.6
3521 THR   ( 193-)  J    -2.6
5246 PHE   (  68-)  O    -2.6
1758 ARG   ( 280-)  E    -2.6
3766 PHE   (  68-)  K    -2.6
 648 ARG   ( 280-)  B    -2.6
3238 ARG   ( 280-)  I    -2.6
1671 THR   ( 193-)  E    -2.6
And so on for a total of 215 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.

  19 PRO   (  21-)  A  omega poor
  66 PHE   (  68-)  A  Poor phi/psi
  70 GLY   (  72-)  A  Poor phi/psi, omega poor
  89 LYS   (  91-)  A  Poor phi/psi
  90 ASP   (  92-)  A  PRO omega poor
  93 LYS   (  95-)  A  omega poor
 104 ARG   ( 106-)  A  Poor phi/psi
 150 ASN   ( 152-)  A  Poor phi/psi
 198 ALA   ( 200-)  A  Poor phi/psi
 201 GLU   ( 203-)  A  omega poor
 205 GLY   ( 207-)  A  PRO omega poor
 244 ASN   ( 246-)  A  Poor phi/psi
 263 ASN   ( 265-)  A  Poor phi/psi
 302 HIS   ( 304-)  A  Poor phi/psi
 331 LYS   ( 333-)  A  Poor phi/psi
 361 GLU   ( 363-)  A  omega poor
 368 GLN   ( 370-)  A  omega poor
 369 TYR   ( 371-)  A  Poor phi/psi
 389 PRO   (  21-)  B  omega poor
 436 PHE   (  68-)  B  Poor phi/psi
 440 GLY   (  72-)  B  Poor phi/psi, omega poor
 459 LYS   (  91-)  B  Poor phi/psi
 460 ASP   (  92-)  B  PRO omega poor
 463 LYS   (  95-)  B  omega poor
 520 ASN   ( 152-)  B  Poor phi/psi
And so on for a total of 260 lines.

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!

   8 ASN   (  10-)  A      0
  22 GLU   (  24-)  A      0
  30 TRP   (  32-)  A      0
  32 ASP   (  34-)  A      0
  34 THR   (  36-)  A      0
  36 GLU   (  38-)  A      0
  40 CYS   (  42-)  A      0
  46 ASP   (  48-)  A      0
  58 TRP   (  60-)  A      0
  59 ASN   (  61-)  A      0
  65 THR   (  67-)  A      0
  66 PHE   (  68-)  A      0
  67 GLN   (  69-)  A      0
  68 SER   (  70-)  A      0
  71 SER   (  73-)  A      0
  74 ASP   (  76-)  A      0
  79 PRO   (  81-)  A      0
  80 ALA   (  82-)  A      0
  81 ALA   (  83-)  A      0
  88 ARG   (  90-)  A      0
  89 LYS   (  91-)  A      0
  90 ASP   (  92-)  A      0
  91 PRO   (  93-)  A      0
 110 ASN   ( 112-)  A      0
 111 LEU   ( 113-)  A      0
And so on for a total of 2111 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!

4403 GLY   ( 335-)  L   1.93   26
4773 GLY   ( 335-)  M   1.86   25
3663 GLY   ( 335-)  J   1.86   26
1073 GLY   ( 335-)  C   1.85   26
2553 GLY   ( 335-)  G   1.82   26
2183 GLY   ( 335-)  F   1.79   24
3293 GLY   ( 335-)  I   1.79   24
 333 GLY   ( 335-)  A   1.78   24
 703 GLY   ( 335-)  B   1.78   28
1443 GLY   ( 335-)  D   1.77   26
2923 GLY   ( 335-)  H   1.76   24
1813 GLY   ( 335-)  E   1.75   25
5513 GLY   ( 335-)  O   1.72   28
5143 GLY   ( 335-)  N   1.72   31
4033 GLY   ( 335-)  K   1.68   26
2890 GLY   ( 302-)  H   1.61   11
3630 GLY   ( 302-)  J   1.60   10
1410 GLY   ( 302-)  D   1.59   12
2150 GLY   ( 302-)  F   1.58   12
4370 GLY   ( 302-)  L   1.55   16
 670 GLY   ( 302-)  B   1.55   12
3169 GLY   ( 211-)  I   1.54   10
5110 GLY   ( 302-)  N   1.54   10
4740 GLY   ( 302-)  M   1.53   13
1780 GLY   ( 302-)  E   1.53   14
 949 GLY   ( 211-)  C   1.53   10
 300 GLY   ( 302-)  A   1.52   12
3909 GLY   ( 211-)  K   1.52   10
3260 GLY   ( 302-)  I   1.51   17

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]

 127 PRO   ( 129-)  A    0.19 LOW
 497 PRO   ( 129-)  B    0.19 LOW
 867 PRO   ( 129-)  C    0.18 LOW
1237 PRO   ( 129-)  D    0.17 LOW
1607 PRO   ( 129-)  E    0.18 LOW
1977 PRO   ( 129-)  F    0.20 LOW
2347 PRO   ( 129-)  G    0.18 LOW
2717 PRO   ( 129-)  H    0.17 LOW
3087 PRO   ( 129-)  I    0.18 LOW
3457 PRO   ( 129-)  J    0.19 LOW
3827 PRO   ( 129-)  K    0.19 LOW
4197 PRO   ( 129-)  L    0.20 LOW
4567 PRO   ( 129-)  M    0.18 LOW
4937 PRO   ( 129-)  N    0.19 LOW
5307 PRO   ( 129-)  O    0.17 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].

  56 PRO   (  58-)  A  -115.1 envelop C-gamma (-108 degrees)
  79 PRO   (  81-)  A   100.4 envelop C-beta (108 degrees)
  86 PRO   (  88-)  A   -61.5 half-chair C-beta/C-alpha (-54 degrees)
 158 PRO   ( 160-)  A    36.9 envelop C-delta (36 degrees)
 206 PRO   ( 208-)  A    43.2 envelop C-delta (36 degrees)
 426 PRO   (  58-)  B  -115.0 envelop C-gamma (-108 degrees)
 449 PRO   (  81-)  B   105.8 envelop C-beta (108 degrees)
 528 PRO   ( 160-)  B    38.1 envelop C-delta (36 degrees)
 576 PRO   ( 208-)  B    43.0 envelop C-delta (36 degrees)
 796 PRO   (  58-)  C  -112.5 envelop C-gamma (-108 degrees)
 819 PRO   (  81-)  C   103.3 envelop C-beta (108 degrees)
 826 PRO   (  88-)  C   -64.6 envelop C-beta (-72 degrees)
 898 PRO   ( 160-)  C    31.6 envelop C-delta (36 degrees)
 946 PRO   ( 208-)  C    44.5 envelop C-delta (36 degrees)
1166 PRO   (  58-)  D  -115.4 envelop C-gamma (-108 degrees)
1189 PRO   (  81-)  D   102.8 envelop C-beta (108 degrees)
1196 PRO   (  88-)  D   -65.6 envelop C-beta (-72 degrees)
1216 PRO   ( 108-)  D  -112.3 envelop C-gamma (-108 degrees)
1268 PRO   ( 160-)  D    26.7 half-chair N/C-delta (18 degrees)
1316 PRO   ( 208-)  D    42.4 envelop C-delta (36 degrees)
1536 PRO   (  58-)  E  -115.7 envelop C-gamma (-108 degrees)
1559 PRO   (  81-)  E   100.6 envelop C-beta (108 degrees)
1566 PRO   (  88-)  E   -62.2 half-chair C-beta/C-alpha (-54 degrees)
1638 PRO   ( 160-)  E    31.6 envelop C-delta (36 degrees)
1686 PRO   ( 208-)  E    43.0 envelop C-delta (36 degrees)
And so on for a total of 73 lines.

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.

4344 LYS   ( 276-)  L      NZ  <-> 4430 ASN   ( 362-)  L      ND2    0.29    2.56  INTRA BF
4409 ARG   ( 341-)  L      N   <-> 4410 PRO   ( 342-)  L      CD     0.26    2.74  INTRA BL
1908 TRP   (  60-)  F      O   <-> 1927 LEU   (  79-)  F      N      0.26    2.44  INTRA BL
4779 ARG   ( 341-)  M      N   <-> 4780 PRO   ( 342-)  M      CD     0.26    2.74  INTRA BL
1449 ARG   ( 341-)  D      N   <-> 1450 PRO   ( 342-)  D      CD     0.24    2.76  INTRA BL
 471 LYS   ( 103-)  B      NZ  <->  478 GLU   ( 110-)  B      OE2    0.24    2.46  INTRA BF
4039 ARG   ( 341-)  K      N   <-> 4040 PRO   ( 342-)  K      CD     0.24    2.76  INTRA BL
3299 ARG   ( 341-)  I      N   <-> 3300 PRO   ( 342-)  I      CD     0.23    2.77  INTRA BL
 101 LYS   ( 103-)  A      NZ  <->  108 GLU   ( 110-)  A      OE2    0.22    2.48  INTRA BF
 339 ARG   ( 341-)  A      N   <->  340 PRO   ( 342-)  A      CD     0.22    2.78  INTRA BL
 428 TRP   (  60-)  B      O   <->  447 LEU   (  79-)  B      N      0.22    2.48  INTRA BL
2559 ARG   ( 341-)  G      N   <-> 2560 PRO   ( 342-)  G      CD     0.22    2.78  INTRA BL
1079 ARG   ( 341-)  C      N   <-> 1080 PRO   ( 342-)  C      CD     0.21    2.79  INTRA BL
 709 ARG   ( 341-)  B      N   <->  710 PRO   ( 342-)  B      CD     0.21    2.79  INTRA BL
2189 ARG   ( 341-)  F      N   <-> 2190 PRO   ( 342-)  F      CD     0.21    2.79  INTRA BL
5084 LYS   ( 276-)  N      NZ  <-> 5170 ASN   ( 362-)  N      ND2    0.20    2.65  INTRA BF
1819 ARG   ( 341-)  E      N   <-> 1820 PRO   ( 342-)  E      CD     0.20    2.80  INTRA BL
4868 TRP   (  60-)  N      O   <-> 4887 LEU   (  79-)  N      N      0.20    2.50  INTRA BL
3414 ARG   (  86-)  J      NH2 <-> 3420 ASP   (  92-)  J      OD2    0.19    2.51  INTRA BL
3431 LYS   ( 103-)  J      NZ  <-> 3438 GLU   ( 110-)  J      OE2    0.19    2.51  INTRA BF
3974 LYS   ( 276-)  K      NZ  <-> 4060 ASN   ( 362-)  K      ND2    0.19    2.66  INTRA BF
 274 LYS   ( 276-)  A      NZ  <->  360 ASN   ( 362-)  A      ND2    0.19    2.66  INTRA BF
5149 ARG   ( 341-)  N      N   <-> 5150 PRO   ( 342-)  N      CD     0.19    2.81  INTRA BL
5519 ARG   ( 341-)  O      N   <-> 5520 PRO   ( 342-)  O      CD     0.19    2.81  INTRA BL
1384 LYS   ( 276-)  D      NZ  <-> 1470 ASN   ( 362-)  D      ND2    0.19    2.66  INTRA BF
And so on for a total of 390 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

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.

1478 GLN   ( 370-)  D      -6.93
2958 GLN   ( 370-)  H      -6.92
5548 GLN   ( 370-)  O      -6.90
4438 GLN   ( 370-)  L      -6.87
5178 GLN   ( 370-)  N      -6.85
1848 GLN   ( 370-)  E      -6.85
 368 GLN   ( 370-)  A      -6.84
2588 GLN   ( 370-)  G      -6.84
2218 GLN   ( 370-)  F      -6.84
 738 GLN   ( 370-)  B      -6.83
3328 GLN   ( 370-)  I      -6.83
1108 GLN   ( 370-)  C      -6.83
3698 GLN   ( 370-)  J      -6.82
4808 GLN   ( 370-)  M      -6.82
4068 GLN   ( 370-)  K      -6.79
4962 PHE   ( 154-)  N      -6.64
4592 PHE   ( 154-)  M      -6.64
5332 PHE   ( 154-)  O      -6.63
3852 PHE   ( 154-)  K      -6.61
3329 TYR   ( 371-)  I      -6.60
 739 TYR   ( 371-)  B      -6.59
1849 TYR   ( 371-)  E      -6.59
4222 PHE   ( 154-)  L      -6.57
4069 TYR   ( 371-)  K      -6.57
2589 TYR   ( 371-)  G      -6.54
And so on for a total of 165 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.

 301 PHE   ( 303-)  A       303 - GLU    305- ( A)         -4.65
 671 PHE   ( 303-)  B       673 - GLU    305- ( B)         -4.64
1041 PHE   ( 303-)  C      1043 - GLU    305- ( C)         -4.65
1411 PHE   ( 303-)  D      1413 - GLU    305- ( D)         -4.63
1781 PHE   ( 303-)  E      1783 - GLU    305- ( E)         -4.63
2151 PHE   ( 303-)  F      2153 - GLU    305- ( F)         -4.67
2521 PHE   ( 303-)  G      2523 - GLU    305- ( G)         -4.60
2891 PHE   ( 303-)  H      2893 - GLU    305- ( H)         -4.62
3261 PHE   ( 303-)  I      3263 - GLU    305- ( I)         -4.62
3631 PHE   ( 303-)  J      3633 - GLU    305- ( J)         -4.56
4001 PHE   ( 303-)  K      4003 - GLU    305- ( K)         -4.61
4371 PHE   ( 303-)  L      4373 - GLU    305- ( L)         -4.62
4741 PHE   ( 303-)  M      4743 - GLU    305- ( M)         -4.61
5111 PHE   ( 303-)  N      5113 - GLU    305- ( N)         -4.59
5481 PHE   ( 303-)  O      5483 - GLU    305- ( O)         -4.67

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

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: E

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: F

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: G

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: H

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: I

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: J

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: K

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: L

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: M

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: N

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: O

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.

 672 HIS   ( 304-)  B   -2.69
3632 HIS   ( 304-)  J   -2.69
2892 HIS   ( 304-)  H   -2.69
4372 HIS   ( 304-)  L   -2.69
4742 HIS   ( 304-)  M   -2.68
5112 HIS   ( 304-)  N   -2.67
3262 HIS   ( 304-)  I   -2.67
4002 HIS   ( 304-)  K   -2.66
2152 HIS   ( 304-)  F   -2.66
1412 HIS   ( 304-)  D   -2.66
1042 HIS   ( 304-)  C   -2.66
1782 HIS   ( 304-)  E   -2.66
 302 HIS   ( 304-)  A   -2.65
5482 HIS   ( 304-)  O   -2.64
 473 ASN   ( 105-)  B   -2.63
4543 ASN   ( 105-)  M   -2.63
1583 ASN   ( 105-)  E   -2.63
2522 HIS   ( 304-)  G   -2.63
5283 ASN   ( 105-)  O   -2.63
4173 ASN   ( 105-)  L   -2.63
 103 ASN   ( 105-)  A   -2.63
2323 ASN   ( 105-)  G   -2.63
3433 ASN   ( 105-)  J   -2.63
1213 ASN   ( 105-)  D   -2.63
 843 ASN   ( 105-)  C   -2.63
3803 ASN   ( 105-)  K   -2.63
1953 ASN   ( 105-)  F   -2.62
4913 ASN   ( 105-)  N   -2.62
3063 ASN   ( 105-)  I   -2.60

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

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: O

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips

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

 199 GLN   ( 201-)  A
 302 HIS   ( 304-)  A
 360 ASN   ( 362-)  A
 569 GLN   ( 201-)  B
 672 HIS   ( 304-)  B
 730 ASN   ( 362-)  B
 939 GLN   ( 201-)  C
1042 HIS   ( 304-)  C
1100 ASN   ( 362-)  C
1309 GLN   ( 201-)  D
1412 HIS   ( 304-)  D
1470 ASN   ( 362-)  D
1679 GLN   ( 201-)  E
1782 HIS   ( 304-)  E
1840 ASN   ( 362-)  E
2049 GLN   ( 201-)  F
2152 HIS   ( 304-)  F
2210 ASN   ( 362-)  F
2419 GLN   ( 201-)  G
2522 HIS   ( 304-)  G
2580 ASN   ( 362-)  G
2789 GLN   ( 201-)  H
2892 HIS   ( 304-)  H
2950 ASN   ( 362-)  H
3159 GLN   ( 201-)  I
3262 HIS   ( 304-)  I
3320 ASN   ( 362-)  I
3529 GLN   ( 201-)  J
3632 HIS   ( 304-)  J
3690 ASN   ( 362-)  J
3899 GLN   ( 201-)  K
4002 HIS   ( 304-)  K
4060 ASN   ( 362-)  K
4269 GLN   ( 201-)  L
4372 HIS   ( 304-)  L
4430 ASN   ( 362-)  L
4639 GLN   ( 201-)  M
4742 HIS   ( 304-)  M
4800 ASN   ( 362-)  M
5009 GLN   ( 201-)  N
5112 HIS   ( 304-)  N
5170 ASN   ( 362-)  N
5379 GLN   ( 201-)  O
5482 HIS   ( 304-)  O
5540 ASN   ( 362-)  O

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.

  23 LYS   (  25-)  A      N
  30 TRP   (  32-)  A      NE1
  50 LYS   (  52-)  A      N
  51 GLY   (  53-)  A      N
  53 GLU   (  55-)  A      N
  59 ASN   (  61-)  A      N
  66 PHE   (  68-)  A      N
  88 ARG   (  90-)  A      NH1
 103 ASN   ( 105-)  A      N
 136 THR   ( 138-)  A      OG1
 141 ASP   ( 143-)  A      N
 159 TYR   ( 161-)  A      N
 160 TYR   ( 162-)  A      N
 191 THR   ( 193-)  A      OG1
 241 ILE   ( 243-)  A      N
 251 HIS   ( 253-)  A      N
 263 ASN   ( 265-)  A      N
 278 ARG   ( 280-)  A      NH1
 287 ASP   ( 289-)  A      N
 293 ASP   ( 295-)  A      N
 294 ASN   ( 296-)  A      ND2
 301 PHE   ( 303-)  A      N
 316 ASN   ( 318-)  A      N
 320 SER   ( 322-)  A      OG
 334 TYR   ( 336-)  A      N
And so on for a total of 476 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.

  85 ASP   (  87-)  A      OD2
 262 GLU   ( 264-)  A      OE2
 864 ASN   ( 126-)  C      OD1
1195 ASP   (  87-)  D      OD2
1372 GLU   ( 264-)  D      OE1
4155 ASP   (  87-)  L      OD2
4331 GLU   ( 263-)  L      OE1
4525 ASP   (  87-)  M      OD2

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

5551  MG   ( 401-)  A     0.69   1.23 Scores about as good as CA (Few ligands (4) )
5553  MG   ( 401-)  B     0.66   1.17 Is perhaps CA (Few ligands (4) )
5555  MG   ( 401-)  C     0.58   0.97 Is perhaps CA (Few ligands (4) )
5557  MG   ( 401-)  D     0.68   1.21 Scores about as good as CA (Few ligands (4) )
5559  MG   ( 401-)  E     0.70   1.23 Scores about as good as CA (Few ligands (4) )
5561  MG   ( 401-)  F     0.56   1.12 Is perhaps NA (Few ligands (4) )
5563  MG   ( 401-)  G     0.66   1.15 Is perhaps CA (Few ligands (4) )
5565  MG   ( 401-)  H     0.75   1.36 Scores about as good as CA (Few ligands (4) )
5567  MG   ( 401-)  I     0.63   1.10 Is perhaps CA (Few ligands (4) )
5569  MG   ( 401-)  J     0.60   1.01 Is perhaps CA (Few ligands (4) )
5571  MG   ( 401-)  K     0.73   1.30 Scores about as good as CA (Few ligands (4) )
5573  MG   ( 401-)  L     0.61   1.03 Is perhaps CA (Few ligands (4) )
5575  MG   ( 401-)  M     0.66   1.16 Is perhaps CA (Few ligands (4) )
5577  MG   ( 401-)  N     0.69   1.25 Scores about as good as CA (Few ligands (4) )
5579  MG   ( 401-)  O     0.69   1.24 Scores about as good as CA (Few ligands (4) )
Since there are no waters, the water check has been skipped.

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.

 120 ASP   ( 122-)  A   H-bonding suggests Asn; but Alt-Rotamer
 269 GLU   ( 271-)  A   H-bonding suggests Gln
 639 GLU   ( 271-)  B   H-bonding suggests Gln
 860 ASP   ( 122-)  C   H-bonding suggests Asn; but Alt-Rotamer
1009 GLU   ( 271-)  C   H-bonding suggests Gln
1230 ASP   ( 122-)  D   H-bonding suggests Asn; but Alt-Rotamer
1379 GLU   ( 271-)  D   H-bonding suggests Gln
1749 GLU   ( 271-)  E   H-bonding suggests Gln
2119 GLU   ( 271-)  F   H-bonding suggests Gln
2489 GLU   ( 271-)  G   H-bonding suggests Gln
2859 GLU   ( 271-)  H   H-bonding suggests Gln
3229 GLU   ( 271-)  I   H-bonding suggests Gln
3450 ASP   ( 122-)  J   H-bonding suggests Asn; but Alt-Rotamer
3599 GLU   ( 271-)  J   H-bonding suggests Gln
3969 GLU   ( 271-)  K   H-bonding suggests Gln
4339 GLU   ( 271-)  L   H-bonding suggests Gln
4709 GLU   ( 271-)  M   H-bonding suggests Gln
5079 GLU   ( 271-)  N   H-bonding suggests Gln
5449 GLU   ( 271-)  O   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.877
  2nd generation packing quality :  -1.160
  Ramachandran plot appearance   :  -1.778
  chi-1/chi-2 rotamer normality  :  -2.496
  Backbone conformation          :  -0.045

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.596 (tight)
  Bond angles                    :   0.717
  Omega angle restraints         :   1.072
  Side chain planarity           :   0.449 (tight)
  Improper dihedral distribution :   0.696
  B-factor distribution          :   0.460
  Inside/Outside distribution    :   1.033

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 :   0.2
  2nd generation packing quality :   0.6
  Ramachandran plot appearance   :   0.8
  chi-1/chi-2 rotamer normality  :  -0.3
  Backbone conformation          :   0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.596 (tight)
  Bond angles                    :   0.717
  Omega angle restraints         :   1.072
  Side chain planarity           :   0.449 (tight)
  Improper dihedral distribution :   0.696
  B-factor distribution          :   0.460
  Inside/Outside distribution    :   1.033
==============

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.