WHAT IF Check report

This file was created 2012-01-25 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 pdb2gie.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 1.042
CA-only RMS fit for the two chains : 0.548

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 1.320
CA-only RMS fit for the two chains : 0.869

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 1.162
CA-only RMS fit for the two chains : 0.701

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and C

All-atom RMS fit for the two chains : 1.323
CA-only RMS fit for the two chains : 0.883

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and C

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and D

All-atom RMS fit for the two chains : 1.155
CA-only RMS fit for the two chains : 0.690

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and D

Administrative problems that can generate validation failures

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

 309 LEU   ( 258-)  A  -
 822 LEU   ( 258-)  C  -

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: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

 197 TYR   ( 146-)  A
 477 LEU   ( 169-)  B

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

  67 ILE   (  16-)  A      CD1
  72 LYS   (  21-)  A      CG
  72 LYS   (  21-)  A      CD
  72 LYS   (  21-)  A      CE
  72 LYS   (  21-)  A      NZ
  75 LYS   (  24-)  A      CG
  75 LYS   (  24-)  A      CD
  75 LYS   (  24-)  A      CE
  75 LYS   (  24-)  A      NZ
  90 LYS   (  39-)  A      CG
  90 LYS   (  39-)  A      CD
  90 LYS   (  39-)  A      CE
  90 LYS   (  39-)  A      NZ
 101 SER   (  50-)  A      OG
 153 GLU   ( 102-)  A      CG
 153 GLU   ( 102-)  A      CD
 153 GLU   ( 102-)  A      OE1
 153 GLU   ( 102-)  A      OE2
 210 LYS   ( 159-)  A      CG
 210 LYS   ( 159-)  A      CD
 210 LYS   ( 159-)  A      CE
 210 LYS   ( 159-)  A      NZ
 279 LYS   ( 228-)  A      CG
 279 LYS   ( 228-)  A      CD
 279 LYS   ( 228-)  A      CE
And so on for a total of 176 lines.

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.

  39 DGUA  (  13-)  G    High
 566 SER   (   2-)  C    High
 567 PHE   (   3-)  C    High
 568 ILE   (   4-)  C    High
 569 LYS   (   5-)  C    High
 570 PRO   (   6-)  C    High
 571 ILE   (   7-)  C    High
 572 TYR   (   8-)  C    High
 573 GLN   (   9-)  C    High
 574 ASP   (  10-)  C    High
 575 ILE   (  11-)  C    High
 576 ASN   (  12-)  C    High
 579 LEU   (  15-)  C    High
 580 ILE   (  16-)  C    High
 581 GLY   (  17-)  C    High
 582 GLN   (  18-)  C    High
 583 LYS   (  19-)  C    High
 584 VAL   (  20-)  C    High
 585 LYS   (  21-)  C    High
 586 ARG   (  22-)  C    High
 587 PRO   (  23-)  C    High
 588 LYS   (  24-)  C    High
 589 SER   (  25-)  C    High
 590 GLY   (  26-)  C    High
 591 THR   (  27-)  C    High
And so on for a total of 209 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.

 142 ARG   (  91-)  A

Warning: Tyrosine convention problem

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

  93 TYR   (  42-)  A
 365 TYR   (  57-)  B
 367 TYR   (  59-)  B
 763 TYR   ( 199-)  C

Warning: Phenylalanine convention problem

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

  88 PHE   (  37-)  A
 131 PHE   (  80-)  A
 156 PHE   ( 105-)  A
 242 PHE   ( 191-)  A
 285 PHE   ( 234-)  A
 345 PHE   (  37-)  B
 388 PHE   (  80-)  B
 413 PHE   ( 105-)  B
 495 PHE   ( 187-)  B
 499 PHE   ( 191-)  B
 561 PHE   ( 253-)  B
 567 PHE   (   3-)  C
 601 PHE   (  37-)  C
 728 PHE   ( 164-)  C
 755 PHE   ( 191-)  C
 875 PHE   (  54-)  D
 901 PHE   (  80-)  D
 926 PHE   ( 105-)  D
1012 PHE   ( 191-)  D
1055 PHE   ( 234-)  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.

 165 ASP   ( 114-)  A
 171 ASP   ( 120-)  A
 208 ASP   ( 157-)  A
 230 ASP   ( 179-)  A
 265 ASP   ( 214-)  A
 370 ASP   (  62-)  B
 422 ASP   ( 114-)  B
 428 ASP   ( 120-)  B
 470 ASP   ( 162-)  B
 473 ASP   ( 165-)  B
 691 ASP   ( 127-)  C
 726 ASP   ( 162-)  C
 729 ASP   ( 165-)  C
 736 ASP   ( 172-)  C
 948 ASP   ( 127-)  D
1037 ASP   ( 216-)  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.

  89 GLU   (  38-)  A
  98 GLU   (  47-)  A
 125 GLU   (  74-)  A
 148 GLU   (  97-)  A
 157 GLU   ( 106-)  A
 158 GLU   ( 107-)  A
 175 GLU   ( 124-)  A
 225 GLU   ( 174-)  A
 240 GLU   ( 189-)  A
 276 GLU   ( 225-)  A
 290 GLU   ( 239-)  A
 343 GLU   (  35-)  B
 346 GLU   (  38-)  B
 414 GLU   ( 106-)  B
 432 GLU   ( 124-)  B
 468 GLU   ( 160-)  B
 478 GLU   ( 170-)  B
 482 GLU   ( 174-)  B
 505 GLU   ( 197-)  B
 532 GLU   ( 224-)  B
 533 GLU   ( 225-)  B
 602 GLU   (  38-)  C
 688 GLU   ( 124-)  C
 738 GLU   ( 174-)  C
 742 GLU   ( 178-)  C
 758 GLU   ( 194-)  C
 788 GLU   ( 224-)  C
 895 GLU   (  74-)  D
 918 GLU   (  97-)  D
 945 GLU   ( 124-)  D
1015 GLU   ( 194-)  D
1045 GLU   ( 224-)  D
1046 GLU   ( 225-)  D

Geometric checks

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 DGUA  (   1-)  E      N9   C8   N7  113.11    4.0
   4 DGUA  (   4-)  E      N9   C8   N7  113.10    4.0
   7 DTHY  (   7-)  E      C2'  C1'  N1  106.82   -4.6
  10 DCYT  (  10-)  E      C2'  C1'  N1  106.94   -4.5
  14 DGUA  (   1-)  F      C2'  C1'  N9  105.11   -5.7
  18 DGUA  (   5-)  F      N9   C8   N7  113.16    4.1
  20 DTHY  (   7-)  F      C2'  C1'  N1  107.02   -4.5
  23 DCYT  (  10-)  F      C2'  C1'  N1  107.32   -4.3
  30 DGUA  (   4-)  G      N9   C8   N7  113.11    4.0
  39 DGUA  (  13-)  G      N9   C8   N7  113.13    4.1
  44 DGUA  (   5-)  H      N9   C8   N7  113.15    4.1
  52 DGUA  (  13-)  H      N9   C8   N7  113.11    4.0
 106 LYS   (  55-)  A      N    CA   C    98.49   -4.5
 363 LYS   (  55-)  B      N    CA   C    98.89   -4.4
 529 GLY   ( 221-)  B      N    CA   C   124.49    4.1
 773 GLN   ( 209-)  C      N    CA   C   123.26    4.3
1029 ILE   ( 208-)  D      N    CA   C    99.75   -4.1

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.

  89 GLU   (  38-)  A
  98 GLU   (  47-)  A
 125 GLU   (  74-)  A
 142 ARG   (  91-)  A
 148 GLU   (  97-)  A
 157 GLU   ( 106-)  A
 158 GLU   ( 107-)  A
 165 ASP   ( 114-)  A
 171 ASP   ( 120-)  A
 175 GLU   ( 124-)  A
 208 ASP   ( 157-)  A
 225 GLU   ( 174-)  A
 230 ASP   ( 179-)  A
 240 GLU   ( 189-)  A
 265 ASP   ( 214-)  A
 276 GLU   ( 225-)  A
 290 GLU   ( 239-)  A
 343 GLU   (  35-)  B
 346 GLU   (  38-)  B
 370 ASP   (  62-)  B
 414 GLU   ( 106-)  B
 422 ASP   ( 114-)  B
 428 ASP   ( 120-)  B
 432 GLU   ( 124-)  B
 468 GLU   ( 160-)  B
 470 ASP   ( 162-)  B
 473 ASP   ( 165-)  B
 478 GLU   ( 170-)  B
 482 GLU   ( 174-)  B
 505 GLU   ( 197-)  B
 532 GLU   ( 224-)  B
 533 GLU   ( 225-)  B
 602 GLU   (  38-)  C
 688 GLU   ( 124-)  C
 691 ASP   ( 127-)  C
 726 ASP   ( 162-)  C
 729 ASP   ( 165-)  C
 736 ASP   ( 172-)  C
 738 GLU   ( 174-)  C
 742 GLU   ( 178-)  C
 758 GLU   ( 194-)  C
 788 GLU   ( 224-)  C
 895 GLU   (  74-)  D
 918 GLU   (  97-)  D
 945 GLU   ( 124-)  D
 948 ASP   ( 127-)  D
1015 GLU   ( 194-)  D
1037 ASP   ( 216-)  D
1045 GLU   ( 224-)  D
1046 GLU   ( 225-)  D

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.

 140 LEU   (  89-)  A    5.95
 106 LYS   (  55-)  A    5.02
 363 LYS   (  55-)  B    4.84
 773 GLN   ( 209-)  C    4.67
 206 MET   ( 155-)  A    4.46
 104 THR   (  53-)  A    4.36
 909 LEU   (  88-)  D    4.04
 397 LEU   (  89-)  B    4.03
 231 LEU   ( 180-)  A    4.02

Warning: Uncalibrated side chain planarity problems

The residues listed in the table below contain a planar group that was found to deviate from planarity by more than 0.10 Angstrom RMS. Please be aware that this check cannot be callibrated and that the cutoff of 0.10 Angstrom thus is a wild guess.

   9 DADE  (   9-)  E    0.11
 Ramachandran Z-score : -3.990

Torsion-related checks

Warning: Ramachandran Z-score low

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

Ramachandran Z-score : -3.990

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.

 875 PHE   (  54-)  D    -3.3
 728 PHE   ( 164-)  C    -2.8
 378 ILE   (  70-)  B    -2.7
 493 THR   ( 185-)  B    -2.6
 194 ILE   ( 143-)  A    -2.6
 618 PHE   (  54-)  C    -2.6
 567 PHE   (   3-)  C    -2.6
 571 ILE   (   7-)  C    -2.6
 441 ILE   ( 133-)  B    -2.6
  58 ILE   (   7-)  A    -2.5
 914 LYS   (  93-)  D    -2.5
 660 THR   (  96-)  C    -2.4
 166 ILE   ( 115-)  A    -2.4
 591 THR   (  27-)  C    -2.4
 557 PHE   ( 249-)  B    -2.4
 184 ILE   ( 133-)  A    -2.4
 613 LEU   (  49-)  C    -2.3
 315 ILE   (   7-)  B    -2.3
 841 VAL   (  20-)  D    -2.3
 912 ARG   (  91-)  D    -2.3
 679 ILE   ( 115-)  C    -2.3
 578 ILE   (  14-)  C    -2.2
 774 PHE   ( 210-)  C    -2.2
 560 PRO   ( 252-)  B    -2.2
 336 LEU   (  28-)  B    -2.2
 987 ILE   ( 166-)  D    -2.2
 641 TYR   (  77-)  C    -2.2
 983 ASP   ( 162-)  D    -2.2
 695 ARG   ( 131-)  C    -2.2
 122 ILE   (  71-)  A    -2.2
1039 GLY   ( 218-)  D    -2.2
 998 GLY   ( 177-)  D    -2.2
 444 SER   ( 136-)  B    -2.2
 176 LEU   ( 125-)  A    -2.2
 439 ARG   ( 131-)  B    -2.1
 807 ILE   ( 243-)  C    -2.1
 211 GLU   ( 160-)  A    -2.1
 892 ILE   (  71-)  D    -2.1
  81 GLY   (  30-)  A    -2.1
 338 GLY   (  30-)  B    -2.0
 410 GLU   ( 102-)  B    -2.0
 261 PHE   ( 210-)  A    -2.0
 468 GLU   ( 160-)  B    -2.0
 294 ILE   ( 243-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  75 LYS   (  24-)  A  Poor phi/psi
  79 LEU   (  28-)  A  Poor phi/psi
  81 GLY   (  30-)  A  Poor phi/psi
  84 ALA   (  33-)  A  Poor phi/psi
  86 GLU   (  35-)  A  Poor phi/psi
 171 ASP   ( 120-)  A  Poor phi/psi
 172 GLN   ( 121-)  A  Poor phi/psi
 210 LYS   ( 159-)  A  Poor phi/psi
 214 LEU   ( 163-)  A  Poor phi/psi
 235 SER   ( 184-)  A  Poor phi/psi
 255 ALA   ( 204-)  A  Poor phi/psi
 306 LYS   ( 255-)  A  Poor phi/psi
 338 GLY   (  30-)  B  Poor phi/psi
 341 ALA   (  33-)  B  Poor phi/psi
 379 ILE   (  71-)  B  Poor phi/psi
 419 ASP   ( 111-)  B  Poor phi/psi
 420 THR   ( 112-)  B  Poor phi/psi
 429 GLN   ( 121-)  B  Poor phi/psi
 512 ALA   ( 204-)  B  Poor phi/psi
 513 ALA   ( 205-)  B  Poor phi/psi
 529 GLY   ( 221-)  B  Poor phi/psi
 531 ARG   ( 223-)  B  Poor phi/psi
 557 PHE   ( 249-)  B  Poor phi/psi
 558 VAL   ( 250-)  B  Poor phi/psi
 568 ILE   (   4-)  C  Poor phi/psi
And so on for a total of 58 lines.

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.

 313 LYS   (   5-)  B    0.33
 280 SER   ( 229-)  A    0.37
 321 SER   (  13-)  B    0.37

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   3 DCYT  (   3-)  E      0
   4 DGUA  (   4-)  E      0
   5 DGUA  (   5-)  E      0
   6 DTHY  (   6-)  E      0
   7 DTHY  (   7-)  E      0
   8 DADE  (   8-)  E      0
   9 DADE  (   9-)  E      0
  10 DCYT  (  10-)  E      0
  11 DCYT  (  11-)  E      0
  12 DGUA  (  12-)  E      0
  13 DGUA  (  13-)  E      0
  14 DGUA  (   1-)  F      0
  15 DCYT  (   2-)  F      0
  16 DCYT  (   3-)  F      0
  17 DGUA  (   4-)  F      0
  18 DGUA  (   5-)  F      0
  19 DTHY  (   6-)  F      0
  20 DTHY  (   7-)  F      0
  21 DADE  (   8-)  F      0
  22 DADE  (   9-)  F      0
  23 DCYT  (  10-)  F      0
  24 DCYT  (  11-)  F      0
  25 DGUA  (  12-)  F      0
  26 DGUA  (  13-)  F      0
  27 DGUA  (   1-)  G      0
And so on for a total of 432 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 1.134

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!

 410 GLU   ( 102-)  B   1.56   11

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]

 191 PRO   ( 140-)  A    0.46 HIGH
 961 PRO   ( 140-)  D    0.45 HIGH

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.

 530 THR   ( 222-)  B      O   <->  532 GLU   ( 224-)  B      N      0.50    2.20  INTRA BL
 378 ILE   (  70-)  B      CG2 <->  379 ILE   (  71-)  B      N      0.44    2.56  INTRA BL
  38 DGUA  (  12-)  G      N1  <->   42 DCYT  (   3-)  H      N3     0.42    2.58  INTRA BL
 534 TRP   ( 226-)  B      N   <-> 1086 HOH   ( 723 )  B      O      0.33    2.37  INTRA BL
 530 THR   ( 222-)  B      C   <-> 1086 HOH   ( 723 )  B      O      0.33    2.47  INTRA BL
 197 TYR   ( 146-)  A      CE2 <->  201 GLN   ( 150-)  A      NE2    0.31    2.79  INTRA BL
   2 DCYT  (   2-)  E      N3  <->   27 DGUA  (   1-)  G      N1     0.30    2.70  INTRA BL
  47 DADE  (   8-)  H      N7  <->  705 ASN   ( 141-)  C      ND2    0.29    2.71  INTRA BL
 530 THR   ( 222-)  B      O   <->  533 GLU   ( 225-)  B      N      0.29    2.41  INTRA BL
 912 ARG   (  91-)  D      NH2 <->  927 GLU   ( 106-)  D      O      0.29    2.41  INTRA BL
 706 ILE   ( 142-)  C      CG1 <->  707 ILE   ( 143-)  C      N      0.28    2.72  INTRA BL
 493 THR   ( 185-)  B      CG2 <->  494 SER   ( 186-)  B      N      0.27    2.73  INTRA BL
 519 HIS   ( 211-)  B      ND1 <-> 1086 HOH   ( 647 )  B      O      0.26    2.44  INTRA BL
  85 GLY   (  34-)  A      O   <->   88 PHE   (  37-)  A      N      0.26    2.44  INTRA BF
 706 ILE   ( 142-)  C      N   <-> 1087 HOH   ( 284 )  C      O      0.25    2.45  INTRA BL
   7 DTHY  (   7-)  E      N3  <->   21 DADE  (   8-)  F      N1     0.25    2.75  INTRA BL
 676 THR   ( 112-)  C      OG1 <->  711 LYS   ( 147-)  C      NZ     0.24    2.46  INTRA BF
  35 DADE  (   9-)  G      N1  <->   45 DTHY  (   6-)  H      N3     0.23    2.77  INTRA BL
   2 DCYT  (   2-)  E      O2  <->   27 DGUA  (   1-)  G      N2     0.23    2.47  INTRA BF
  38 DGUA  (  12-)  G      N2  <->   42 DCYT  (   3-)  H      O2     0.22    2.48  INTRA BL
  34 DADE  (   8-)  G      N7  <->  962 ASN   ( 141-)  D      ND2    0.22    2.78  INTRA BL
 841 VAL   (  20-)  D      CG2 <->  842 LYS   (  21-)  D      N      0.22    2.78  INTRA BF
  10 DCYT  (  10-)  E      N3  <->   18 DGUA  (   5-)  F      N1     0.22    2.78  INTRA BL
 856 GLU   (  35-)  D      N   <->  857 PRO   (  36-)  D      CD     0.22    2.78  INTRA BF
 919 ASN   (  98-)  D      O   <->  924 ASN   ( 103-)  D      ND2    0.21    2.49  INTRA BL
And so on for a total of 282 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.

 702 GLN   ( 138-)  C      -7.25
 843 ARG   (  22-)  D      -6.90
 959 GLN   ( 138-)  D      -6.80
 586 ARG   (  22-)  C      -6.77
 446 GLN   ( 138-)  B      -6.67
  73 ARG   (  22-)  A      -6.66
 189 GLN   ( 138-)  A      -6.52
 655 ARG   (  91-)  C      -6.40
 332 LYS   (  24-)  B      -6.05
 912 ARG   (  91-)  D      -5.90
1040 PHE   ( 219-)  D      -5.85
 637 HIS   (  73-)  C      -5.58
 892 ILE   (  71-)  D      -5.57
 784 ASN   ( 220-)  C      -5.49
 635 ILE   (  71-)  C      -5.43
1041 ASN   ( 220-)  D      -5.40
 209 ASN   ( 158-)  A      -5.34
  99 ASN   (  48-)  A      -5.29
 466 ASN   ( 158-)  B      -5.29
 821 ILE   ( 257-)  C      -5.22
 122 ILE   (  71-)  A      -5.22
1020 TYR   ( 199-)  D      -5.20
 665 ILE   ( 101-)  C      -5.18
 389 ASN   (  81-)  B      -5.14
 149 ASN   (  98-)  A      -5.13
 827 PRO   (   6-)  D      -5.10
 528 ASN   ( 220-)  B      -5.06

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.

 161 ASN   ( 110-)  A   -4.12
 931 ASN   ( 110-)  D   -4.12
 418 ASN   ( 110-)  B   -3.95
 657 LYS   (  93-)  C   -3.50
 940 LYS   ( 119-)  D   -3.31
1072 LYS   ( 251-)  D   -3.03
 417 GLN   ( 109-)  B   -2.91
 189 GLN   ( 138-)  A   -2.79
1020 TYR   ( 199-)  D   -2.75
 610 LYS   (  46-)  C   -2.74
 583 LYS   (  19-)  C   -2.74
 930 GLN   ( 109-)  D   -2.70
 160 GLN   ( 109-)  A   -2.66
 959 GLN   ( 138-)  D   -2.66
 854 ALA   (  33-)  D   -2.64
 702 GLN   ( 138-)  C   -2.57
 429 GLN   ( 121-)  B   -2.55
 341 ALA   (  33-)  B   -2.53
 588 LYS   (  24-)  C   -2.51
 845 LYS   (  24-)  D   -2.51
 446 GLN   ( 138-)  B   -2.50

Warning: Abnormal packing Z-score for sequential residues

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

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

 442 SER   ( 134-)  B     -  446 GLN   ( 138-)  B        -1.95

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.

1082 HOH   ( 446 )  F      O     27.70   44.85  199.23
1085 HOH   ( 290 )  A      O     58.86   22.70  199.21
1085 HOH   ( 323 )  A      O     56.63   30.15  190.46
1086 HOH   ( 621 )  B      O     33.95  -24.76  208.63
1086 HOH   ( 683 )  B      O     -7.54   29.45  197.31

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.

1083 HOH   ( 283 )  G      O
1085 HOH   ( 285 )  A      O
1085 HOH   ( 295 )  A      O
1085 HOH   ( 374 )  A      O
1086 HOH   ( 663 )  B      O
1087 HOH   ( 271 )  C      O
1087 HOH   ( 299 )  C      O
1088 HOH   ( 266 )  D      O
1088 HOH   ( 303 )  D      O
1088 HOH   ( 304 )  D      O

Error: HIS, ASN, GLN side chain flips

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

  99 ASN   (  48-)  A
 160 GLN   ( 109-)  A
 262 HIS   ( 211-)  A
 356 ASN   (  48-)  B
 406 ASN   (  98-)  B
 458 GLN   ( 150-)  B
 631 ASN   (  67-)  C
 869 ASN   (  48-)  D
 930 GLN   ( 109-)  D
 931 ASN   ( 110-)  D
1038 GLN   ( 217-)  D
1041 ASN   ( 220-)  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.

   9 DADE  (   9-)  E      N6
  60 GLN   (   9-)  A      N
  61 ASP   (  10-)  A      N
  76 SER   (  25-)  A      N
  80 SER   (  29-)  A      N
 108 TYR   (  57-)  A      N
 143 GLY   (  92-)  A      N
 161 ASN   ( 110-)  A      N
 173 PHE   ( 122-)  A      N
 182 ARG   ( 131-)  A      NH1
 215 PHE   ( 164-)  A      N
 332 LYS   (  24-)  B      N
 359 ASP   (  51-)  B      N
 365 TYR   (  57-)  B      N
 366 GLU   (  58-)  B      N
 379 ILE   (  71-)  B      N
 384 ARG   (  76-)  B      NE
 390 SER   (  82-)  B      OG
 399 ARG   (  91-)  B      NH1
 407 TRP   (  99-)  B      N
 420 THR   ( 112-)  B      N
 446 GLN   ( 138-)  B      NE2
 475 ASN   ( 167-)  B      ND2
 494 SER   ( 186-)  B      OG
 504 SER   ( 196-)  B      N
And so on for a total of 103 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.

 124 HIS   (  73-)  A      NE2
 223 ASP   ( 172-)  A      OD1
 366 GLU   (  58-)  B      OE2
 673 GLN   ( 109-)  C      OE1
 688 GLU   ( 124-)  C      OE1
 691 ASP   ( 127-)  C      OD1
 736 ASP   ( 172-)  C      OD1
 852 HIS   (  31-)  D      ND1
 948 ASP   ( 127-)  D      OD1
 962 ASN   ( 141-)  D      OD1
 981 GLU   ( 160-)  D      OE2
 991 GLU   ( 170-)  D      OE2
 993 ASP   ( 172-)  D      OD1

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and 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 nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple 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 method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

1085 HOH   ( 326 )  A      O  0.91  K  4
1085 HOH   ( 356 )  A      O  0.92  K  4
1086 HOH   ( 676 )  B      O  0.91  K  5
1086 HOH   ( 686 )  B      O  0.86  K  7 ION-B
1088 HOH   ( 270 )  D      O  1.13  K  5 ION-B

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.

  86 GLU   (  35-)  A   H-bonding suggests Gln; but Alt-Rotamer
 165 ASP   ( 114-)  A   H-bonding suggests Asn; but Alt-Rotamer
 230 ASP   ( 179-)  A   H-bonding suggests Asn; but Alt-Rotamer
 343 GLU   (  35-)  B   H-bonding suggests Gln; but Alt-Rotamer
 465 ASP   ( 157-)  B   H-bonding suggests Asn
 675 ASP   ( 111-)  C   H-bonding suggests Asn; but Alt-Rotamer
 678 ASP   ( 114-)  C   H-bonding suggests Asn; but Alt-Rotamer
 691 ASP   ( 127-)  C   H-bonding suggests Asn; but Alt-Rotamer
 743 ASP   ( 179-)  C   H-bonding suggests Asn; but Alt-Rotamer
 935 ASP   ( 114-)  D   H-bonding suggests Asn; but Alt-Rotamer
 948 ASP   ( 127-)  D   H-bonding suggests Asn; but Alt-Rotamer

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 :  -0.779
  2nd generation packing quality :  -3.316 (poor)
  Ramachandran plot appearance   :  -3.990 (poor)
  chi-1/chi-2 rotamer normality  :  -2.873
  Backbone conformation          :  -1.316

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.333 (tight)
  Bond angles                    :   0.613 (tight)
  Omega angle restraints         :   0.206 (tight)
  Side chain planarity           :   0.227 (tight)
  Improper dihedral distribution :   0.574
  B-factor distribution          :   0.478
  Inside/Outside distribution    :   1.007

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.60


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.1
  2nd generation packing quality :  -1.9
  Ramachandran plot appearance   :  -1.3
  chi-1/chi-2 rotamer normality  :  -0.6
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.333 (tight)
  Bond angles                    :   0.613 (tight)
  Omega angle restraints         :   0.206 (tight)
  Side chain planarity           :   0.227 (tight)
  Improper dihedral distribution :   0.574
  B-factor distribution          :   0.478
  Inside/Outside distribution    :   1.007
==============

WHAT IF
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Bond lengths and angles, DNA/RNA
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DSSP
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Hydrogen bond networks
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Matthews' Coefficient
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Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
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Puckering parameters
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Quality Control
    G.Vriend and C.Sander,
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      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
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Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
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      data bank (PDB) files
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Ion Checks
    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?
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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.