WHAT IF Check report

This file was created 2013-12-10 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 pdb4jf7.ent

Checks that need to be done early-on in validation

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.

2010 MAN   ( 603-)  D  -
2018 MAN   ( 607-)  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.

1988 NAG   ( 602-)  D  -   O4  bound to 2010 MAN   ( 603-)  D  -   C1
1989 NAG   ( 604-)  D  -   O4  bound to 1988 NAG   ( 602-)  D  -   C1
1990 NAG   ( 605-)  D  -   O4  bound to 2018 MAN   ( 607-)  D  -   C1
1991 NAG   ( 606-)  D  -   O4  bound to 1990 NAG   ( 605-)  D  -   C1
1994 NAG   ( 603-)  A  -   O4  bound to 1995 NAG   ( 604-)  A  -   C1
1996 NAG   ( 605-)  A  -   O4  bound to 1997 NAG   ( 606-)  A  -   C1
1999 NAG   ( 603-)  B  -   O4  bound to 2000 NAG   ( 604-)  B  -   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: D

Note: Ramachandran plot

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

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

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'.

  41 SER   ( 114-)  D      OG
 494 THR   (  62-)  A      OG1
 494 THR   (  62-)  A      CG2
 498 ASN   (  66-)  A      CG
 498 ASN   (  66-)  A      OD1
 498 ASN   (  66-)  A      ND2
 996 ASN   (  67-)  B      CG
 996 ASN   (  67-)  B      OD1
 996 ASN   (  67-)  B      ND2
1268 THR   ( 339-)  B      OG1
1268 THR   ( 339-)  B      CG2
1497 ASN   (  66-)  C      CG
1497 ASN   (  66-)  C      OD1
1497 ASN   (  66-)  C      ND2
1500 LEU   (  69-)  C      CG
1500 LEU   (  69-)  C      CD1
1500 LEU   (  69-)  C      CD2

Warning: B-factors outside the range 0.0 - 100.0

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

   1 THR   (  62-)  D    High
   2 ASP   (  63-)  D    High
   3 LEU   (  64-)  D    High
   4 LEU   (  65-)  D    High
   5 ASN   (  66-)  D    High
   6 ASN   (  67-)  D    High
   7 ILE   (  68-)  D    High
   8 LEU   (  69-)  D    High
   9 SER   (  70-)  D    High
  10 VAL   (  71-)  D    High
  11 ALA   (  72-)  D    High
  12 ASN   (  73-)  D    High
  13 GLN   (  74-)  D    High
  14 ILE   (  75-)  D    High
  15 ILE   (  76-)  D    High
  16 TYR   (  77-)  D    High
  17 ASN   (  78-)  D    High
  18 SER   (  79-)  D    High
  30 GLU   (  91-)  D    High
  37 ILE   (  98-)  D    High
  38 LYS   (  99-)  D    High
  39 SER   ( 100-)  D    High
  40 LEU   ( 101-)  D    High
  41 SER   ( 114-)  D    High
  42 ALA   ( 115-)  D    High
And so on for a total of 180 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: 11

Crystal temperature (K) :200.000

Note: B-factor plot

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

Chain identifier: D

Note: B-factor plot

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

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

 233 TYR   ( 306-)  D
 250 TYR   ( 323-)  D
 428 TYR   ( 501-)  D
 465 TYR   ( 538-)  D
 734 TYR   ( 306-)  A
 751 TYR   ( 323-)  A
 929 TYR   ( 501-)  A
 966 TYR   ( 538-)  A
1235 TYR   ( 306-)  B
1252 TYR   ( 323-)  B
1467 TYR   ( 538-)  B
1508 TYR   (  77-)  C
1728 TYR   ( 306-)  C
1745 TYR   ( 323-)  C

Warning: Phenylalanine convention problem

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

  78 PHE   ( 151-)  D
 121 PHE   ( 194-)  D
 168 PHE   ( 241-)  D
 579 PHE   ( 151-)  A
 669 PHE   ( 241-)  A
1080 PHE   ( 151-)  B
1170 PHE   ( 241-)  B
1181 PHE   ( 252-)  B
1573 PHE   ( 151-)  C
1663 PHE   ( 241-)  C
1975 PHE   ( 553-)  C

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.

  47 ASP   ( 120-)  D
 114 ASP   ( 187-)  D
 548 ASP   ( 120-)  A
 615 ASP   ( 187-)  A
 696 ASP   ( 268-)  A
1049 ASP   ( 120-)  B
1116 ASP   ( 187-)  B
1197 ASP   ( 268-)  B
1690 ASP   ( 268-)  C
1792 ASP   ( 370-)  C

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.

  30 GLU   (  91-)  D
1020 GLU   (  91-)  B
1037 GLU   ( 108-)  B
1187 GLU   ( 258-)  B
1449 GLU   ( 520-)  B
1680 GLU   ( 258-)  C
1942 GLU   ( 520-)  C

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.

 367 VAL   ( 440-)  D      C    CA   CB  118.20    4.3
1107 HIS   ( 178-)  B      CG   ND1  CE1 109.60    4.0
1544 ARG   ( 122-)  C      CB   CG   CD  105.79   -4.2
1862 VAL   ( 440-)  C      C    CA   CB  119.10    4.7

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.

  30 GLU   (  91-)  D
  47 ASP   ( 120-)  D
 114 ASP   ( 187-)  D
 548 ASP   ( 120-)  A
 615 ASP   ( 187-)  A
 696 ASP   ( 268-)  A
1020 GLU   (  91-)  B
1037 GLU   ( 108-)  B
1049 ASP   ( 120-)  B
1116 ASP   ( 187-)  B
1187 GLU   ( 258-)  B
1197 ASP   ( 268-)  B
1449 GLU   ( 520-)  B
1680 GLU   ( 258-)  C
1690 ASP   ( 268-)  C
1792 ASP   ( 370-)  C
1942 GLU   ( 520-)  C

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.

 544 ALA   ( 116-)  A    4.43

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.

 484 PRO   ( 557-)  D    -3.0
1486 PRO   ( 557-)  B    -2.9
1979 PRO   ( 557-)  C    -2.9
1496 LEU   (  65-)  C    -2.9
1340 PRO   ( 411-)  B    -2.8
1794 THR   ( 372-)  C    -2.8
 985 PRO   ( 557-)  A    -2.7
1713 THR   ( 291-)  C    -2.7
 924 ILE   ( 496-)  A    -2.7
1420 THR   ( 491-)  B    -2.7
1093 ILE   ( 164-)  B    -2.7
1220 THR   ( 291-)  B    -2.7
1586 ILE   ( 164-)  C    -2.6
 218 THR   ( 291-)  D    -2.6
 592 ILE   ( 164-)  A    -2.6
 719 THR   ( 291-)  A    -2.6
 919 THR   ( 491-)  A    -2.6
 963 VAL   ( 535-)  A    -2.6
1957 VAL   ( 535-)  C    -2.6
  91 ILE   ( 164-)  D    -2.5
1371 ARG   ( 442-)  B    -2.5
1464 VAL   ( 535-)  B    -2.5
 528 THR   (  96-)  A    -2.5
1913 THR   ( 491-)  C    -2.5
 387 THR   ( 460-)  D    -2.5
And so on for a total of 96 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.

  44 LEU   ( 117-)  D  Poor phi/psi
  50 TYR   ( 123-)  D  Poor phi/psi
  55 ASN   ( 128-)  D  Poor phi/psi
  56 GLN   ( 129-)  D  omega poor
  91 ILE   ( 164-)  D  Poor phi/psi
 117 SER   ( 190-)  D  Poor phi/psi
 167 CYS   ( 240-)  D  omega poor
 195 ASP   ( 268-)  D  Poor phi/psi
 209 ASP   ( 282-)  D  Poor phi/psi
 218 THR   ( 291-)  D  Poor phi/psi
 220 SER   ( 293-)  D  omega poor
 248 ASN   ( 321-)  D  Poor phi/psi
 282 ASN   ( 355-)  D  Poor phi/psi
 285 ILE   ( 358-)  D  omega poor
 311 GLN   ( 384-)  D  omega poor
 335 SER   ( 408-)  D  Poor phi/psi
 361 ASN   ( 434-)  D  omega poor
 366 GLN   ( 439-)  D  omega poor
 367 VAL   ( 440-)  D  Poor phi/psi
 420 THR   ( 493-)  D  Poor phi/psi
 424 ASN   ( 497-)  D  Poor phi/psi
 428 TYR   ( 501-)  D  omega poor
 430 ALA   ( 503-)  D  omega poor
 449 ALA   ( 522-)  D  Poor phi/psi
 462 VAL   ( 535-)  D  Poor phi/psi
And so on for a total of 106 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.

 999 SER   (  70-)  B    0.36

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!

   6 ASN   (  67-)  D      0
  39 SER   ( 100-)  D      0
  40 LEU   ( 101-)  D      0
  41 SER   ( 114-)  D      0
  42 ALA   ( 115-)  D      0
  50 TYR   ( 123-)  D      0
  54 ILE   ( 127-)  D      0
  58 TYR   ( 131-)  D      0
  61 ILE   ( 134-)  D      0
  75 MET   ( 148-)  D      0
  78 PHE   ( 151-)  D      0
  90 ARG   ( 163-)  D      0
  91 ILE   ( 164-)  D      0
 100 HIS   ( 173-)  D      0
 105 HIS   ( 178-)  D      0
 110 ASN   ( 183-)  D      0
 115 HIS   ( 188-)  D      0
 116 VAL   ( 189-)  D      0
 117 SER   ( 190-)  D      0
 124 MET   ( 197-)  D      0
 128 GLU   ( 201-)  D      0
 134 PHE   ( 207-)  D      0
 147 ASP   ( 220-)  D      0
 152 LYS   ( 225-)  D      0
 153 SER   ( 226-)  D      0
And so on for a total of 894 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!

 315 GLY   ( 388-)  D   2.73   12
1089 GLY   ( 160-)  B   1.81   17
1582 GLY   ( 160-)  C   1.76   12
  87 GLY   ( 160-)  D   1.52   16

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]

 705 PRO   ( 277-)  A    0.19 LOW
 706 PRO   ( 278-)  A    0.19 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].

 184 PRO   ( 257-)  D    44.9 envelop C-delta (36 degrees)
 484 PRO   ( 557-)  D   -26.2 half-chair C-alpha/N (-18 degrees)
 685 PRO   ( 257-)  A    45.7 half-chair C-delta/C-gamma (54 degrees)
 985 PRO   ( 557-)  A   -64.5 envelop C-beta (-72 degrees)
1185 PRO   ( 256-)  B   -49.1 half-chair C-beta/C-alpha (-54 degrees)
1207 PRO   ( 278-)  B  -115.7 envelop C-gamma (-108 degrees)
1340 PRO   ( 411-)  B   -62.8 half-chair C-beta/C-alpha (-54 degrees)
1486 PRO   ( 557-)  B   -54.0 half-chair C-beta/C-alpha (-54 degrees)
1678 PRO   ( 256-)  C   -56.1 half-chair C-beta/C-alpha (-54 degrees)
1979 PRO   ( 557-)  C   -59.8 half-chair C-beta/C-alpha (-54 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

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

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

 538 ASN   ( 110-)  A      ND2  <->  1998 NAG   ( 608-)  A      C2   1.19    1.91  INTRA BF
 538 ASN   ( 110-)  A      ND2  <->  1998 NAG   ( 608-)  A      C1   1.13    1.97  INTRA BF
2004 NAG   ( 605-)  C      O4   <->  2005 NAG   ( 606-)  C      C1   0.89    1.71  INTRA BF
1990 NAG   ( 605-)  D      O4   <->  2018 MAN   ( 607-)  D      C1   0.73    1.67  INTRA BF
 538 ASN   ( 110-)  A      CG   <->  1998 NAG   ( 608-)  A      C1   0.64    2.56  INTRA BF
1864 ARG   ( 442-)  C      NH2  <->  1870 CYS   ( 448-)  C      O    0.55    2.15  INTRA BF
1262 CYS   ( 333-)  B      SG   <->  1269 GLN   ( 340-)  B      NE2  0.54    2.76  INTRA BF
 369 ARG   ( 442-)  D      NH2  <->   375 CYS   ( 448-)  D      O    0.52    2.18  INTRA BF
 870 ARG   ( 442-)  A      NH2  <->   876 CYS   ( 448-)  A      O    0.52    2.18  INTRA BF
 538 ASN   ( 110-)  A      ND2  <->  1998 NAG   ( 608-)  A      N2   0.50    2.50  INTRA BF
  43 ALA   ( 116-)  D      O    <->    45 ILE   ( 118-)  D      N    0.50    2.20  INTRA BF
1371 ARG   ( 442-)  B      NH2  <->  1377 CYS   ( 448-)  B      O    0.49    2.21  INTRA BF
1533 CYS   ( 111-)  C      N    <->  2022 HOH   ( 835 )  C      O    0.46    2.24  INTRA BF
1017 ASP   (  88-)  B      OD1  <->  1517 GLN   (  86-)  C      NE2  0.43    2.27  INTRA BF
2004 NAG   ( 605-)  C      C4   <->  2005 NAG   ( 606-)  C      C1   0.40    2.60  INTRA BF
1355 GLN   ( 426-)  B      NE2  <->  2021 HOH   ( 803 )  B      O    0.37    2.33  INTRA BF
2004 NAG   ( 605-)  C      O4   <->  2005 NAG   ( 606-)  C      C2   0.37    2.33  INTRA BF
 544 ALA   ( 116-)  A      O    <->   546 ILE   ( 118-)  A      N    0.36    2.34  INTRA BF
 761 CYS   ( 333-)  A      SG   <->   768 GLN   ( 340-)  A      NE2  0.35    2.95  INTRA BF
 867 GLN   ( 439-)  A      O    <->  2020 HOH   ( 808 )  A      O    0.34    2.06  INTRA BL
 500 ILE   (  68-)  A      O    <->   504 ALA   (  72-)  A      N    0.31    2.39  INTRA BF
1495 LEU   (  64-)  C      O    <->  1497 ASN   (  66-)  C      N    0.31    2.39  INTRA BF
 642 LYS   ( 214-)  A      NZ   <->  2020 HOH   ( 713 )  A      O    0.30    2.40  INTRA BL
1301 THR   ( 372-)  B      OG1  <->  1302 ASN   ( 373-)  B      N    0.30    2.30  INTRA BF
 648 ASP   ( 220-)  A      OD1  <->   652 ARG   ( 224-)  A      NH2  0.29    2.41  INTRA BL
And so on for a total of 214 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: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

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.

1115 GLN   ( 186-)  B      -7.04
1608 GLN   ( 186-)  C      -6.67
1864 ARG   ( 442-)  C      -5.76
1371 ARG   ( 442-)  B      -5.73
 870 ARG   ( 442-)  A      -5.63
 369 ARG   ( 442-)  D      -5.56
1703 LEU   ( 281-)  C      -5.39
1478 LEU   ( 549-)  B      -5.35
 726 LEU   ( 298-)  A      -5.31
 225 LEU   ( 298-)  D      -5.30
1227 LEU   ( 298-)  B      -5.27
1210 LEU   ( 281-)  B      -5.21
 567 ASN   ( 139-)  A      -5.19
1382 ARG   ( 453-)  B      -5.18
1971 LEU   ( 549-)  C      -5.15
 755 GLN   ( 327-)  A      -5.13
1442 GLN   ( 513-)  B      -5.12
1935 GLN   ( 513-)  C      -5.09
 881 ARG   ( 453-)  A      -5.05
1039 ASN   ( 110-)  B      -5.03
 941 GLN   ( 513-)  A      -5.02
1240 LYS   ( 311-)  B      -5.02

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: 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

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.

 695 ASN   ( 267-)  A   -2.77
1196 ASN   ( 267-)  B   -2.70
 616 HIS   ( 188-)  A   -2.58

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: D

Note: Second generation quality Z-score plot

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

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.

2019 HOH   ( 901 )  D      O     35.31  237.21  -17.31
2021 HOH   ( 802 )  B      O     52.79  165.68   -5.74
2022 HOH   ( 801 )  C      O     61.86  234.60   17.33
2022 HOH   ( 813 )  C      O     62.63  232.15   16.82

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.

2019 HOH   ( 913 )  D      O
2020 HOH   ( 765 )  A      O
Bound group on Asn; dont flip   66 ASN  ( 139-) D
Bound to: 1992 NAG  ( 609-) D
Bound group on Asn; dont flip  194 ASN  ( 267-) D
Bound to: 1989 NAG  ( 604-) D
Bound group on Asn; dont flip  431 ASN  ( 504-) D
Bound to: 1991 NAG  ( 606-) D
Bound group on Asn; dont flip  567 ASN  ( 139-) A
Bound to: 1993 NAG  ( 602-) A
Bound group on Asn; dont flip  695 ASN  ( 267-) A
Bound to: 1994 NAG  ( 603-) A
Bound group on Asn; dont flip  932 ASN  ( 504-) A
Bound to: 1996 NAG  ( 605-) A
Bound group on Asn; dont flip 1196 ASN  ( 267-) B
Bound to: 1999 NAG  ( 603-) B
Bound group on Asn; dont flip 1433 ASN  ( 504-) B
Bound to: 2001 NAG  ( 605-) B
Bound group on Asn; dont flip 1561 ASN  ( 139-) C
Bound to: 2002 NAG  ( 603-) C
Bound group on Asn; dont flip 1689 ASN  ( 267-) C
Bound to: 2003 NAG  ( 604-) C
Bound group on Asn; dont flip 1926 ASN  ( 504-) C
Bound to: 2004 NAG  ( 605-) C

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.

  17 ASN   (  78-)  D
 353 GLN   ( 426-)  D
 361 ASN   ( 434-)  D
 862 ASN   ( 434-)  A
1363 ASN   ( 434-)  B
1758 ASN   ( 336-)  C
1856 ASN   ( 434-)  C

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.

  10 VAL   (  71-)  D      N
  44 LEU   ( 117-)  D      N
  45 ILE   ( 118-)  D      N
  78 PHE   ( 151-)  D      N
  84 THR   ( 157-)  D      OG1
  89 THR   ( 162-)  D      N
  90 ARG   ( 163-)  D      NH2
 123 SER   ( 196-)  D      OG
 134 PHE   ( 207-)  D      N
 137 PHE   ( 210-)  D      N
 239 GLY   ( 312-)  D      N
 277 SER   ( 350-)  D      OG
 281 GLY   ( 354-)  D      N
 302 CYS   ( 375-)  D      N
 312 VAL   ( 385-)  D      N
 337 TRP   ( 410-)  D      NE1
 339 MET   ( 412-)  D      N
 364 THR   ( 437-)  D      N
 366 GLN   ( 439-)  D      N
 369 ARG   ( 442-)  D      NH2
 381 CYS   ( 454-)  D      N
 383 GLY   ( 456-)  D      N
 389 VAL   ( 462-)  D      N
 390 TYR   ( 463-)  D      N
 402 THR   ( 475-)  D      N
And so on for a total of 147 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.

 262 GLN   ( 335-)  D      OE1
 452 HIS   ( 525-)  D      ND1
 538 ASN   ( 110-)  A      OD1
 953 HIS   ( 525-)  A      ND1
1117 HIS   ( 188-)  B      ND1
1264 GLN   ( 335-)  B      OE1
1610 HIS   ( 188-)  C      ND1

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+.

2009  CA   ( 601-)  D   -.-  -.-  Low probability ion. B= 80.0
2012  CA   ( 601-)  A     0.40   1.00 Could be  K
2014  CA   ( 601-)  B   -.-  -.-  Low probability ion. B= 92.4
2016  CA   ( 601-)  C   -.-  -.-  Low probability ion. B= 81.2

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.

2019 HOH   ( 842 )  D      O  0.89  K  4
2020 HOH   ( 711 )  A      O  0.91  K  5 NCS 2/2
2021 HOH   ( 768 )  B      O  1.06  K  4 ION-B NCS 1/1
2022 HOH   ( 723 )  C      O  1.10  K  4 NCS 1/1
2022 HOH   ( 725 )  C      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.

  27 ASP   (  88-)  D   H-bonding suggests Asn
 114 ASP   ( 187-)  D   H-bonding suggests Asn; but Alt-Rotamer
 615 ASP   ( 187-)  A   H-bonding suggests Asn; but Alt-Rotamer
1017 ASP   (  88-)  B   H-bonding suggests Asn; but Alt-Rotamer
1034 ASP   ( 105-)  B   H-bonding suggests Asn
1116 ASP   ( 187-)  B   H-bonding suggests Asn
1312 ASP   ( 383-)  B   H-bonding suggests Asn; but Alt-Rotamer
1796 GLU   ( 374-)  C   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 :  -0.025
  2nd generation packing quality :  -1.179
  Ramachandran plot appearance   :  -1.579
  chi-1/chi-2 rotamer normality  :  -2.168
  Backbone conformation          :  -0.306

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.364 (tight)
  Bond angles                    :   0.566 (tight)
  Omega angle restraints         :   1.097
  Side chain planarity           :   0.364 (tight)
  Improper dihedral distribution :   0.631
  B-factor distribution          :   1.208
  Inside/Outside distribution    :   1.036

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 : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.0
  2nd generation packing quality :  -0.0
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :  -0.4
  Backbone conformation          :   0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.364 (tight)
  Bond angles                    :   0.566 (tight)
  Omega angle restraints         :   1.097
  Side chain planarity           :   0.364 (tight)
  Improper dihedral distribution :   0.631
  B-factor distribution          :   1.208
  Inside/Outside distribution    :   1.036
==============

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.