WHAT IF Check report

This file was created 2011-12-16 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

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

Verification log for pdb3ln1.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 : 0.149
CA-only RMS fit for the two chains : 0.101

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 : 0.085
CA-only RMS fit for the two chains : 0.057

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 : 0.124
CA-only RMS fit for the two chains : 0.078

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 : 0.140
CA-only RMS fit for the two chains : 0.099

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 : 0.113
CA-only RMS fit for the two chains : 0.062

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

2229 CEL   ( 682-)  A  -
2230 BOG   ( 703-)  B  -
2232 CEL   ( 682-)  B  -
2234 CEL   ( 682-)  C  -
2237 BOG   ( 703-)  D  -
2238 CEL   ( 682-)  D  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

2210 NAG   ( 671-)  A  -   O4  bound to 2211 NAG   ( 672-)  A  -   C1
2211 NAG   ( 672-)  A  -   O4  bound to 2212 NAG   ( 673-)  A  -   C1
2215 NAG   ( 671-)  B  -   O4  bound to 2216 NAG   ( 672-)  B  -   C1
2216 NAG   ( 672-)  B  -   O4  bound to 2217 NAG   ( 673-)  B  -   C1
2220 NAG   ( 671-)  C  -   O4  bound to 2221 NAG   ( 672-)  C  -   C1
2221 NAG   ( 672-)  C  -   O4  bound to 2222 NAG   ( 673-)  C  -   C1
2225 NAG   ( 671-)  D  -   O4  bound to 2226 NAG   ( 672-)  D  -   C1
2226 NAG   ( 672-)  D  -   O4  bound to 2227 NAG   ( 673-)  D  -   C1

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: 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

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

  33 TYR   (  50-)  A
  91 TYR   ( 108-)  A
  99 TYR   ( 116-)  A
 103 TYR   ( 120-)  A
 116 TYR   ( 133-)  A
 223 TYR   ( 240-)  A
 231 TYR   ( 248-)  A
 244 TYR   ( 261-)  A
 342 TYR   ( 359-)  A
 354 TYR   ( 371-)  A
 378 TYR   ( 395-)  A
 444 TYR   ( 461-)  A
 464 TYR   ( 481-)  A
 513 TYR   ( 530-)  A
 585 TYR   (  50-)  B
 611 TYR   (  76-)  B
 643 TYR   ( 108-)  B
 651 TYR   ( 116-)  B
 655 TYR   ( 120-)  B
 657 TYR   ( 122-)  B
 668 TYR   ( 133-)  B
 775 TYR   ( 240-)  B
 783 TYR   ( 248-)  B
 796 TYR   ( 261-)  B
 894 TYR   ( 359-)  B
And so on for a total of 61 lines.

Warning: Phenylalanine convention problem

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

  20 PHE   (  37-)  A
  64 PHE   (  81-)  A
 156 PHE   ( 173-)  A
 170 PHE   ( 187-)  A
 178 PHE   ( 195-)  A
 216 PHE   ( 233-)  A
 254 PHE   ( 271-)  A
 336 PHE   ( 353-)  A
 439 PHE   ( 456-)  A
 447 PHE   ( 464-)  A
 498 PHE   ( 515-)  A
 519 PHE   ( 536-)  A
 546 PHE   ( 563-)  A
 549 PHE   ( 566-)  A
 572 PHE   (  37-)  B
 616 PHE   (  81-)  B
 708 PHE   ( 173-)  B
 722 PHE   ( 187-)  B
 730 PHE   ( 195-)  B
 768 PHE   ( 233-)  B
 806 PHE   ( 271-)  B
 888 PHE   ( 353-)  B
 991 PHE   ( 456-)  B
 999 PHE   ( 464-)  B
1050 PHE   ( 515-)  B
And so on for a total of 55 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.

 142 ASP   ( 159-)  A
 208 ASP   ( 225-)  A
 218 ASP   ( 235-)  A
 362 ASP   ( 379-)  A
 466 ASP   ( 483-)  A
 694 ASP   ( 159-)  B
 760 ASP   ( 225-)  B
 770 ASP   ( 235-)  B
 914 ASP   ( 379-)  B
1018 ASP   ( 483-)  B
1246 ASP   ( 159-)  C
1312 ASP   ( 225-)  C
1322 ASP   ( 235-)  C
1466 ASP   ( 379-)  C
1570 ASP   ( 483-)  C
1798 ASP   ( 159-)  D
1864 ASP   ( 225-)  D
1874 ASP   ( 235-)  D
2018 ASP   ( 379-)  D
2122 ASP   ( 483-)  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.

 109 GLU   ( 126-)  A
 139 GLU   ( 156-)  A
 145 GLU   ( 162-)  A
 277 GLU   ( 294-)  A
 295 GLU   ( 312-)  A
 308 GLU   ( 325-)  A
 333 GLU   ( 350-)  A
 370 GLU   ( 387-)  A
 426 GLU   ( 443-)  A
 449 GLU   ( 466-)  A
 453 GLU   ( 470-)  A
 455 GLU   ( 472-)  A
 459 GLU   ( 476-)  A
 489 GLU   ( 506-)  A
 661 GLU   ( 126-)  B
 691 GLU   ( 156-)  B
 697 GLU   ( 162-)  B
 829 GLU   ( 294-)  B
 847 GLU   ( 312-)  B
 860 GLU   ( 325-)  B
 885 GLU   ( 350-)  B
 922 GLU   ( 387-)  B
 978 GLU   ( 443-)  B
1001 GLU   ( 466-)  B
1005 GLU   ( 470-)  B
And so on for a total of 55 lines.

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.

 610 HIS   (  75-)  B      CG   ND1  CE1 109.68    4.1
1315 HIS   ( 228-)  C      CG   ND1  CE1 109.60    4.0

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.

 109 GLU   ( 126-)  A
 139 GLU   ( 156-)  A
 142 ASP   ( 159-)  A
 145 GLU   ( 162-)  A
 208 ASP   ( 225-)  A
 218 ASP   ( 235-)  A
 277 GLU   ( 294-)  A
 295 GLU   ( 312-)  A
 308 GLU   ( 325-)  A
 333 GLU   ( 350-)  A
 362 ASP   ( 379-)  A
 370 GLU   ( 387-)  A
 426 GLU   ( 443-)  A
 449 GLU   ( 466-)  A
 453 GLU   ( 470-)  A
 455 GLU   ( 472-)  A
 459 GLU   ( 476-)  A
 466 ASP   ( 483-)  A
 489 GLU   ( 506-)  A
 661 GLU   ( 126-)  B
 691 GLU   ( 156-)  B
 694 ASP   ( 159-)  B
 697 GLU   ( 162-)  B
 760 ASP   ( 225-)  B
 770 ASP   ( 235-)  B
And so on for a total of 75 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.

2017 PRO   ( 378-)  D    -2.5
1810 ARG   ( 171-)  D    -2.5
 706 ARG   ( 171-)  B    -2.5
2200 CYS   ( 561-)  D    -2.4
 154 ARG   ( 171-)  A    -2.4
1258 ARG   ( 171-)  C    -2.4
1096 CYS   ( 561-)  B    -2.4
2109 GLU   ( 470-)  D    -2.4
 897 ARG   ( 362-)  B    -2.4
1557 GLU   ( 470-)  C    -2.4
1005 GLU   ( 470-)  B    -2.4
1449 ARG   ( 362-)  C    -2.4
 453 GLU   ( 470-)  A    -2.4
1251 LEU   ( 164-)  C    -2.3
1803 LEU   ( 164-)  D    -2.3
2001 ARG   ( 362-)  D    -2.3
 699 LEU   ( 164-)  B    -2.3
 378 TYR   ( 395-)  A    -2.3
 345 ARG   ( 362-)  A    -2.3
1482 TYR   ( 395-)  C    -2.3
 930 TYR   ( 395-)  B    -2.3
2034 TYR   ( 395-)  D    -2.3
1648 CYS   ( 561-)  C    -2.3
 913 PRO   ( 378-)  B    -2.3
 147 LEU   ( 164-)  A    -2.3
And so on for a total of 76 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.

   7 ASN   (  24-)  A  Poor phi/psi
  12 ARG   (  29-)  A  Poor phi/psi
  29 ARG   (  46-)  A  Poor phi/psi
  95 SER   ( 112-)  A  PRO omega poor
  98 THR   ( 115-)  A  Poor phi/psi
 116 TYR   ( 133-)  A  omega poor
 199 LEU   ( 216-)  A  Poor phi/psi
 216 PHE   ( 233-)  A  Poor phi/psi, omega poor
 218 ASP   ( 235-)  A  Poor phi/psi
 239 GLN   ( 256-)  A  Poor phi/psi
 367 GLU   ( 384-)  A  Poor phi/psi
 428 LYS   ( 445-)  A  Poor phi/psi
 440 SER   ( 457-)  A  Poor phi/psi
 465 SER   ( 482-)  A  Poor phi/psi
 481 PRO   ( 498-)  A  omega poor
 484 ASP   ( 501-)  A  Poor phi/psi
 559 ASN   (  24-)  B  Poor phi/psi
 564 ARG   (  29-)  B  Poor phi/psi
 581 ARG   (  46-)  B  Poor phi/psi
 589 CYS   (  54-)  B  Poor phi/psi
 647 SER   ( 112-)  B  PRO omega poor
 650 THR   ( 115-)  B  Poor phi/psi, omega poor
 663 PHE   ( 128-)  B  omega poor
 668 TYR   ( 133-)  B  omega poor
 705 ARG   ( 170-)  B  omega poor
And so on for a total of 75 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.

1524 SER   ( 437-)  C    0.36
 420 SER   ( 437-)  A    0.38
 424 SER   ( 441-)  A    0.38
 976 SER   ( 441-)  B    0.38
1528 SER   ( 441-)  C    0.38
2080 SER   ( 441-)  D    0.38
1639 SER   ( 552-)  C    0.40

Warning: Unusual backbone conformations

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

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

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

   4 CYS   (  21-)  A      0
   5 CYS   (  22-)  A      0
   6 SER   (  23-)  A      0
   8 PRO   (  25-)  A      0
   9 CYS   (  26-)  A      0
  10 GLN   (  27-)  A      0
  12 ARG   (  29-)  A      0
  18 THR   (  35-)  A      0
  22 GLN   (  39-)  A      0
  28 THR   (  45-)  A      0
  29 ARG   (  46-)  A      0
  30 THR   (  47-)  A      0
  32 PHE   (  49-)  A      0
  33 TYR   (  50-)  A      0
  37 CYS   (  54-)  A      0
  38 THR   (  55-)  A      0
  62 THR   (  79-)  A      0
  63 HIS   (  80-)  A      0
  64 PHE   (  81-)  A      0
  91 TYR   ( 108-)  A      0
  92 LEU   ( 109-)  A      0
  94 ASP   ( 111-)  A      0
  95 SER   ( 112-)  A      0
  96 PRO   ( 113-)  A      0
  97 PRO   ( 114-)  A      0
And so on for a total of 861 lines.

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]

   8 PRO   (  25-)  A    0.15 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].

   3 PRO   (  20-)  A  -116.1 envelop C-gamma (-108 degrees)
  75 PRO   (  92-)  A   105.4 envelop C-beta (108 degrees)
 141 PRO   ( 158-)  A  -130.3 half-chair C-delta/C-gamma (-126 degrees)
 332 PRO   ( 349-)  A   104.2 envelop C-beta (108 degrees)
 361 PRO   ( 378-)  A   -64.6 envelop C-beta (-72 degrees)
 511 PRO   ( 528-)  A   111.0 envelop C-beta (108 degrees)
 516 PRO   ( 533-)  A   106.7 envelop C-beta (108 degrees)
 627 PRO   (  92-)  B   104.4 envelop C-beta (108 degrees)
 693 PRO   ( 158-)  B  -132.1 half-chair C-delta/C-gamma (-126 degrees)
 884 PRO   ( 349-)  B   104.8 envelop C-beta (108 degrees)
1063 PRO   ( 528-)  B   108.9 envelop C-beta (108 degrees)
1068 PRO   ( 533-)  B   107.7 envelop C-beta (108 degrees)
1107 PRO   (  20-)  C  -120.2 half-chair C-delta/C-gamma (-126 degrees)
1179 PRO   (  92-)  C   106.1 envelop C-beta (108 degrees)
1245 PRO   ( 158-)  C  -134.0 half-chair C-delta/C-gamma (-126 degrees)
1436 PRO   ( 349-)  C   103.4 envelop C-beta (108 degrees)
1615 PRO   ( 528-)  C   112.1 envelop C-beta (108 degrees)
1620 PRO   ( 533-)  C   107.0 envelop C-beta (108 degrees)
1731 PRO   (  92-)  D   105.7 envelop C-beta (108 degrees)
1797 PRO   ( 158-)  D  -131.0 half-chair C-delta/C-gamma (-126 degrees)
1988 PRO   ( 349-)  D   104.7 envelop C-beta (108 degrees)
2167 PRO   ( 528-)  D   108.0 envelop C-beta (108 degrees)
2172 PRO   ( 533-)  D   106.2 envelop C-beta (108 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

1767 PHE   ( 128-)  D      O   <-> 2001 ARG   ( 362-)  D      NH2    0.70    2.00  INTRA BL
 663 PHE   ( 128-)  B      O   <->  897 ARG   ( 362-)  B      NH2    0.70    2.00  INTRA BL
1215 PHE   ( 128-)  C      O   <-> 1449 ARG   ( 362-)  C      NH2    0.67    2.03  INTRA BL
 111 PHE   ( 128-)  A      O   <->  345 ARG   ( 362-)  A      NH2    0.67    2.03  INTRA BL
1925 MET   ( 286-)  D      CE  <-> 2048 VAL   ( 409-)  D      CG2    0.43    2.77  INTRA BL
 821 MET   ( 286-)  B      CE  <->  944 VAL   ( 409-)  B      CG2    0.38    2.82  INTRA BL
 230 VAL   ( 247-)  A      O   <->  276 ARG   ( 293-)  A      NH1    0.35    2.35  INTRA BL
1334 VAL   ( 247-)  C      O   <-> 1380 ARG   ( 293-)  C      NH1    0.34    2.36  INTRA BL
 559 ASN   (  24-)  B      N   <->  560 PRO   (  25-)  B      CD     0.33    2.67  INTRA BF
2013 HIS   ( 374-)  D      N   <-> 2014 PRO   ( 375-)  D      CD     0.33    2.67  INTRA BL
2023 GLU   ( 384-)  D      CG  <-> 2046 GLN   ( 407-)  D      CD     0.32    2.88  INTRA BF
 269 MET   ( 286-)  A      CE  <->  392 VAL   ( 409-)  A      CG2    0.32    2.88  INTRA BL
   7 ASN   (  24-)  A      N   <->    8 PRO   (  25-)  A      CD     0.31    2.69  INTRA BF
1471 GLU   ( 384-)  C      CG  <-> 1494 GLN   ( 407-)  C      CD     0.31    2.89  INTRA BF
 588 ASN   (  53-)  B      ND2 <-> 2214 NAG   ( 661-)  B      C6     0.31    2.79  INTRA BF
1886 VAL   ( 247-)  D      O   <-> 1932 ARG   ( 293-)  D      NH1    0.31    2.39  INTRA BL
 782 VAL   ( 247-)  B      O   <->  828 ARG   ( 293-)  B      NH1    0.30    2.40  INTRA BL
1289 ARG   ( 202-)  C      NH1 <-> 2221 NAG   ( 672-)  C      N2     0.30    2.70  INTRA BF
 367 GLU   ( 384-)  A      CG  <->  390 GLN   ( 407-)  A      CD     0.30    2.90  INTRA BF
 919 GLU   ( 384-)  B      CG  <->  942 GLN   ( 407-)  B      CD     0.30    2.90  INTRA BF
1663 ASN   (  24-)  D      N   <-> 1664 PRO   (  25-)  D      CD     0.29    2.71  INTRA BF
1048 ALA   ( 513-)  B      N   <-> 1049 PRO   ( 514-)  B      CD     0.28    2.72  INTRA BL
 909 HIS   ( 374-)  B      N   <->  910 PRO   ( 375-)  B      CD     0.28    2.72  INTRA BL
1461 HIS   ( 374-)  C      N   <-> 1462 PRO   ( 375-)  C      CD     0.27    2.73  INTRA BL
1692 ASN   (  53-)  D      ND2 <-> 2224 NAG   ( 661-)  D      C6     0.27    2.83  INTRA BF
And so on for a total of 326 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.

1685 ARG   (  46-)  D      -6.79
 581 ARG   (  46-)  B      -6.79
  29 ARG   (  46-)  A      -6.77
1133 ARG   (  46-)  C      -6.77
1903 HIS   ( 264-)  D      -6.58
 247 HIS   ( 264-)  A      -6.57
1351 HIS   ( 264-)  C      -6.56
 799 HIS   ( 264-)  B      -6.55
1676 PHE   (  37-)  D      -6.10
  20 PHE   (  37-)  A      -6.09
1124 PHE   (  37-)  C      -6.00
1098 PHE   ( 563-)  B      -5.95
 572 PHE   (  37-)  B      -5.93
1242 LYS   ( 155-)  C      -5.75
1794 LYS   ( 155-)  D      -5.71
 138 LYS   ( 155-)  A      -5.70
 690 LYS   ( 155-)  B      -5.69
2202 PHE   ( 563-)  D      -5.62
 185 ARG   ( 202-)  A      -5.54
2053 ARG   ( 414-)  D      -5.53
 737 ARG   ( 202-)  B      -5.52
1289 ARG   ( 202-)  C      -5.50
1841 ARG   ( 202-)  D      -5.49
 397 ARG   ( 414-)  A      -5.46
 891 GLN   ( 356-)  B      -5.45
And so on for a total of 65 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.

 138 LYS   ( 155-)  A       140 - LEU    157- ( A)         -4.98
 183 HIS   ( 200-)  A       185 - ARG    202- ( A)         -4.90
 690 LYS   ( 155-)  B       692 - LEU    157- ( B)         -5.01
1242 LYS   ( 155-)  C      1244 - LEU    157- ( C)         -4.98
1287 HIS   ( 200-)  C      1289 - ARG    202- ( C)         -4.91
1794 LYS   ( 155-)  D      1796 - LEU    157- ( D)         -5.01

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.

1990 LEU   ( 351-)  D   -2.67
 886 LEU   ( 351-)  B   -2.66
 105 TYR   ( 122-)  A   -2.65
 334 LEU   ( 351-)  A   -2.64
1438 LEU   ( 351-)  C   -2.62
 657 TYR   ( 122-)  B   -2.61

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

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.

2239 HOH   (   7 )  A      O
2239 HOH   ( 628 )  A      O
2240 HOH   ( 632 )  B      O
2241 HOH   ( 609 )  C      O
2242 HOH   ( 610 )  D      O
2242 HOH   ( 614 )  D      O
2242 HOH   ( 619 )  D      O
2242 HOH   ( 630 )  D      O
Bound group on Asn; dont flip   36 ASN  (  53-) A
Bound to: 2209 NAG  ( 661-) A
Bound group on Asn; dont flip  113 ASN  ( 130-) A
Bound to: 2210 NAG  ( 671-) A
Bound group on Asn; dont flip  379 ASN  ( 396-) A
Bound to: 2213 NAG  ( 681-) A
Bound group on Asn; dont flip  588 ASN  (  53-) B
Bound to: 2214 NAG  ( 661-) B
Bound group on Asn; dont flip  665 ASN  ( 130-) B
Bound to: 2215 NAG  ( 671-) B
Bound group on Asn; dont flip  931 ASN  ( 396-) B
Bound to: 2218 NAG  ( 681-) B
Bound group on Asn; dont flip 1140 ASN  (  53-) C
Bound to: 2219 NAG  ( 661-) C
Bound group on Asn; dont flip 1217 ASN  ( 130-) C
Bound to: 2220 NAG  ( 671-) C
Bound group on Asn; dont flip 1483 ASN  ( 396-) C
Bound to: 2223 NAG  ( 681-) C
Bound group on Asn; dont flip 1692 ASN  (  53-) D
Bound to: 2224 NAG  ( 661-) D
Bound group on Asn; dont flip 1769 ASN  ( 130-) D
Bound to: 2225 NAG  ( 671-) D
Bound group on Asn; dont flip 2035 ASN  ( 396-) D
Bound to: 2228 NAG  ( 681-) D
Marked this atom as acceptor 2229 CEL  ( 682-) A      F2
Marked this atom as acceptor 2229 CEL  ( 682-) A      F1
Marked this atom as acceptor 2229 CEL  ( 682-) A      F3
Marked this atom as acceptor 2232 CEL  ( 682-) B      F2
Marked this atom as acceptor 2232 CEL  ( 682-) B      F1
Marked this atom as acceptor 2232 CEL  ( 682-) B      F3
Marked this atom as acceptor 2234 CEL  ( 682-) C      F2
Marked this atom as acceptor 2234 CEL  ( 682-) C      F1
Marked this atom as acceptor 2234 CEL  ( 682-) C      F3
Marked this atom as acceptor 2238 CEL  ( 682-) D      F2
Marked this atom as acceptor 2238 CEL  ( 682-) D      F1
Marked this atom as acceptor 2238 CEL  ( 682-) D      F3
Metal-coordinating Histidine residue 357 fixed to   1
Metal-coordinating Histidine residue 909 fixed to   1
Metal-coordinating Histidine residue1461 fixed to   1
Metal-coordinating Histidine residue2013 fixed to   1

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.

 337 ASN   ( 354-)  A
 351 ASN   ( 368-)  A
 550 ASN   ( 567-)  A
 803 ASN   ( 268-)  B
 848 GLN   ( 313-)  B
 889 ASN   ( 354-)  B
 903 ASN   ( 368-)  B
1441 ASN   ( 354-)  C
1455 ASN   ( 368-)  C
1993 ASN   ( 354-)  D
2007 ASN   ( 368-)  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.

  19 GLY   (  36-)  A      N
  22 GLN   (  39-)  A      N
  27 CYS   (  44-)  A      N
  51 LYS   (  68-)  A      N
  55 ASN   (  72-)  A      N
  89 ARG   ( 106-)  A      N
  94 ASP   ( 111-)  A      N
 100 ASN   ( 117-)  A      ND2
 105 TYR   ( 122-)  A      N
 107 SER   ( 124-)  A      OG
 108 TRP   ( 125-)  A      N
 119 ARG   ( 136-)  A      NH2
 135 LYS   ( 152-)  A      N
 154 ARG   ( 171-)  A      N
 154 ARG   ( 171-)  A      NH2
 173 HIS   ( 190-)  A      NE2
 177 GLN   ( 194-)  A      NE2
 194 GLY   ( 211-)  A      N
 214 ARG   ( 231-)  A      NE
 216 PHE   ( 233-)  A      N
 217 LYS   ( 234-)  A      N
 224 GLN   ( 241-)  A      NE2
 247 HIS   ( 264-)  A      N
 262 GLY   ( 279-)  A      N
 266 GLY   ( 283-)  A      N
And so on for a total of 126 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.

 172 GLN   ( 189-)  A      OE1
 308 GLU   ( 325-)  A      OE2
 380 ASN   ( 397-)  A      OD1
 724 GLN   ( 189-)  B      OE1
 860 GLU   ( 325-)  B      OE2
 903 ASN   ( 368-)  B      OD1
 932 ASN   ( 397-)  B      OD1
1011 GLU   ( 476-)  B      OE2
1276 GLN   ( 189-)  C      OE1
1412 GLU   ( 325-)  C      OE2
1455 ASN   ( 368-)  C      OD1
1484 ASN   ( 397-)  C      OD1
1815 ASP   ( 176-)  D      OD1
1828 GLN   ( 189-)  D      OE1
1947 GLU   ( 308-)  D      OE2
1964 GLU   ( 325-)  D      OE2
2007 ASN   ( 368-)  D      OD1
2036 ASN   ( 397-)  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.

2239 HOH   ( 613 )  A      O  0.96  K  4 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.

  21 ASP   (  38-)  A   H-bonding suggests Asn; but Alt-Rotamer
 291 GLU   ( 308-)  A   H-bonding suggests Gln; but Alt-Rotamer
 573 ASP   (  38-)  B   H-bonding suggests Asn; but Alt-Rotamer
 843 GLU   ( 308-)  B   H-bonding suggests Gln
1125 ASP   (  38-)  C   H-bonding suggests Asn; but Alt-Rotamer
1395 GLU   ( 308-)  C   H-bonding suggests Gln; but Alt-Rotamer
1677 ASP   (  38-)  D   H-bonding suggests Asn; but Alt-Rotamer
1947 GLU   ( 308-)  D   H-bonding suggests Gln; 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 :  -1.289
  2nd generation packing quality :  -1.189
  Ramachandran plot appearance   :  -1.552
  chi-1/chi-2 rotamer normality  :  -2.369
  Backbone conformation          :  -1.138

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.493 (tight)
  Bond angles                    :   0.621 (tight)
  Omega angle restraints         :   1.000
  Side chain planarity           :   0.490 (tight)
  Improper dihedral distribution :   0.604
  B-factor distribution          :   0.346
  Inside/Outside distribution    :   1.102

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 : 2.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.6
  2nd generation packing quality :  -0.1
  Ramachandran plot appearance   :   0.2
  chi-1/chi-2 rotamer normality  :  -0.6
  Backbone conformation          :  -0.8

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.493 (tight)
  Bond angles                    :   0.621 (tight)
  Omega angle restraints         :   1.000
  Side chain planarity           :   0.490 (tight)
  Improper dihedral distribution :   0.604
  B-factor distribution          :   0.346
  Inside/Outside distribution    :   1.102
==============

WHAT IF
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      WHAT IF: a molecular modelling and drug design program,
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WHAT_CHECK (verification routines from WHAT IF)
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      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,
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      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.