WHAT IF Check report

This file was created 2012-03-27 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 pdb3rr3.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.

2225 FLR   ( 700-)  A  -
2226 BOG   (   3-)  A  -
2227 BOG   (   6-)  A  -
2229 FLR   ( 700-)  B  -
2230 BOG   (   3-)  B  -
2232 FLR   ( 700-)  C  -
2233 BOG   (   3-)  C  -
2234 BOG   (   6-)  C  -
2237 BOG   (   3-)  D  -
2238 FLR   ( 700-)  D  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: B-factors outside the range 0.0 - 100.0

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

  21 ASP   (  53-)  A    High
  22 GLN   (  54-)  A    High
  42 PHE   (  74-)  A    High
  43 LEU   (  75-)  A    High
  45 ARG   (  77-)  A    High
  47 LYS   (  79-)  A    High
  51 LYS   (  83-)  A    High
  76 PHE   ( 107-)  A    High
  91 TYR   ( 122-)  A    High
 138 LYS   ( 169-)  A    High
 139 GLU   ( 170-)  A    High
 144 LYS   ( 175-)  A    High
 145 GLU   ( 176-)  A    High
 155 GLU   ( 186-)  A    High
 184 LYS   ( 215-)  A    High
 208 ASP   ( 239-)  A    High
 217 LYS   ( 248-)  A    High
 237 ASP   ( 268-)  A    High
 241 GLU   ( 272-)  A    High
 247 HIS   ( 278-)  A    High
 250 GLU   ( 281-)  A    High
 259 GLU   ( 290-)  A    High
 287 GLN   ( 318-)  A    High
 367 GLU   ( 398-)  A    High
 368 ASP   ( 399-)  A    High
And so on for a total of 147 lines.

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 1.627 over 15750 bonds
Average difference in B over a bond : 5.48
RMS difference in B over a bond : 7.44

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   (  65-)  A
  91 TYR   ( 122-)  A
 317 TYR   ( 348-)  A
 342 TYR   ( 373-)  A
 371 TYR   ( 402-)  A
 575 TYR   (  55-)  B
 585 TYR   (  65-)  B
 643 TYR   ( 122-)  B
 869 TYR   ( 348-)  B
 894 TYR   ( 373-)  B
 923 TYR   ( 402-)  B
1127 TYR   (  55-)  C
1137 TYR   (  65-)  C
1195 TYR   ( 122-)  C
1207 TYR   ( 134-)  C
1327 TYR   ( 254-)  C
1421 TYR   ( 348-)  C
1446 TYR   ( 373-)  C
1475 TYR   ( 402-)  C
1679 TYR   (  55-)  D
1689 TYR   (  65-)  D
1747 TYR   ( 122-)  D
1973 TYR   ( 348-)  D
1998 TYR   ( 373-)  D
2027 TYR   ( 402-)  D

Warning: Phenylalanine convention problem

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

 167 PHE   ( 198-)  A
 178 PHE   ( 209-)  A
 719 PHE   ( 198-)  B
 730 PHE   ( 209-)  B
1282 PHE   ( 209-)  C
1823 PHE   ( 198-)  D
1834 PHE   ( 209-)  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.

 237 ASP   ( 268-)  A
 484 ASP   ( 515-)  A
 789 ASP   ( 268-)  B
1036 ASP   ( 515-)  B
1341 ASP   ( 268-)  C
1588 ASP   ( 515-)  C
1893 ASP   ( 268-)  D
2140 ASP   ( 515-)  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.

 145 GLU   ( 176-)  A
 308 GLU   ( 339-)  A
 367 GLU   ( 398-)  A
 426 GLU   ( 457-)  A
 455 GLU   ( 486-)  A
 459 GLU   ( 490-)  A
 471 GLU   ( 502-)  A
 493 GLU   ( 524-)  A
 697 GLU   ( 176-)  B
 781 GLU   ( 260-)  B
 860 GLU   ( 339-)  B
 919 GLU   ( 398-)  B
 978 GLU   ( 457-)  B
1007 GLU   ( 486-)  B
1011 GLU   ( 490-)  B
1023 GLU   ( 502-)  B
1045 GLU   ( 524-)  B
1249 GLU   ( 176-)  C
1412 GLU   ( 339-)  C
1471 GLU   ( 398-)  C
1530 GLU   ( 457-)  C
1559 GLU   ( 486-)  C
1563 GLU   ( 490-)  C
1575 GLU   ( 502-)  C
1597 GLU   ( 524-)  C
1801 GLU   ( 176-)  D
1885 GLU   ( 260-)  D
1964 GLU   ( 339-)  D
2023 GLU   ( 398-)  D
2082 GLU   ( 457-)  D
2111 GLU   ( 486-)  D
2115 GLU   ( 490-)  D
2127 GLU   ( 502-)  D
2149 GLU   ( 524-)  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.

 107 SER   ( 138-)  A      N    CA   C   125.08    5.0
 659 SER   ( 138-)  B      N    CA   C   124.69    4.8
 735 HIS   ( 214-)  B      CG   ND1  CE1 109.90    4.3
 753 HIS   ( 232-)  B      CG   ND1  CE1 109.91    4.3
 763 HIS   ( 242-)  B      CG   ND1  CE1 109.63    4.0
1211 SER   ( 138-)  C      N    CA   C   124.40    4.7
1277 HIS   ( 204-)  C      CG   ND1  CE1 109.60    4.0
1305 HIS   ( 232-)  C      CG   ND1  CE1 110.27    4.7
1315 HIS   ( 242-)  C      CG   ND1  CE1 109.65    4.0
1763 SER   ( 138-)  D      N    CA   C   124.87    4.9
1839 HIS   ( 214-)  D      CG   ND1  CE1 110.06    4.5
1857 HIS   ( 232-)  D      CG   ND1  CE1 109.86    4.3
1867 HIS   ( 242-)  D      CG   ND1  CE1 109.76    4.2

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.

 145 GLU   ( 176-)  A
 237 ASP   ( 268-)  A
 308 GLU   ( 339-)  A
 367 GLU   ( 398-)  A
 426 GLU   ( 457-)  A
 455 GLU   ( 486-)  A
 459 GLU   ( 490-)  A
 471 GLU   ( 502-)  A
 484 ASP   ( 515-)  A
 493 GLU   ( 524-)  A
 697 GLU   ( 176-)  B
 781 GLU   ( 260-)  B
 789 ASP   ( 268-)  B
 860 GLU   ( 339-)  B
 919 GLU   ( 398-)  B
 978 GLU   ( 457-)  B
1007 GLU   ( 486-)  B
1011 GLU   ( 490-)  B
1023 GLU   ( 502-)  B
1036 ASP   ( 515-)  B
1045 GLU   ( 524-)  B
1249 GLU   ( 176-)  C
1341 ASP   ( 268-)  C
1412 GLU   ( 339-)  C
1471 GLU   ( 398-)  C
1530 GLU   ( 457-)  C
1559 GLU   ( 486-)  C
1563 GLU   ( 490-)  C
1575 GLU   ( 502-)  C
1588 ASP   ( 515-)  C
1597 GLU   ( 524-)  C
1801 GLU   ( 176-)  D
1885 GLU   ( 260-)  D
1893 ASP   ( 268-)  D
1964 GLU   ( 339-)  D
2023 GLU   ( 398-)  D
2082 GLU   ( 457-)  D
2111 GLU   ( 486-)  D
2115 GLU   ( 490-)  D
2127 GLU   ( 502-)  D
2140 ASP   ( 515-)  D
2149 GLU   ( 524-)  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.

2046 GLN   ( 421-)  D    6.64
1494 GLN   ( 421-)  C    6.59
 390 GLN   ( 421-)  A    6.51
 942 GLN   ( 421-)  B    6.00
 107 SER   ( 138-)  A    5.14
1763 SER   ( 138-)  D    5.06
 659 SER   ( 138-)  B    4.99
1211 SER   ( 138-)  C    4.88
 808 VAL   ( 287-)  B    4.56
1912 VAL   ( 287-)  D    4.52
 150 VAL   ( 181-)  A    4.42
1360 VAL   ( 287-)  C    4.29
1806 VAL   ( 181-)  D    4.17

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.

1035 PRO   ( 514-)  B    -3.1
 483 PRO   ( 514-)  A    -3.1
2139 PRO   ( 514-)  D    -3.1
1587 PRO   ( 514-)  C    -3.1
1668 ARG   (  44-)  D    -3.0
  12 ARG   (  44-)  A    -3.0
 564 ARG   (  44-)  B    -3.0
1116 ARG   (  44-)  C    -2.9
2047 PHE   ( 422-)  D    -2.7
 391 PHE   ( 422-)  A    -2.7
1495 PHE   ( 422-)  C    -2.7
 943 PHE   ( 422-)  B    -2.7
 119 ARG   ( 150-)  A    -2.6
 671 ARG   ( 150-)  B    -2.6
1223 ARG   ( 150-)  C    -2.6
1775 ARG   ( 150-)  D    -2.6
1251 LEU   ( 178-)  C    -2.6
1133 ARG   (  61-)  C    -2.6
1803 LEU   ( 178-)  D    -2.5
 699 LEU   ( 178-)  B    -2.5
  29 ARG   (  61-)  A    -2.5
 147 LEU   ( 178-)  A    -2.5
 906 TYR   ( 385-)  B    -2.5
 581 ARG   (  61-)  B    -2.4
1685 ARG   (  61-)  D    -2.4
And so on for a total of 102 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.

  12 ARG   (  44-)  A  Poor phi/psi
  29 ARG   (  61-)  A  Poor phi/psi
  37 CYS   (  69-)  A  Poor phi/psi
  64 PHE   (  96-)  A  Poor phi/psi
  95 SER   ( 126-)  A  PRO omega poor
  99 TYR   ( 130-)  A  Poor phi/psi
 105 TYR   ( 136-)  A  omega poor
 107 SER   ( 138-)  A  Poor phi/psi
 116 TYR   ( 147-)  A  omega poor
 154 ARG   ( 185-)  A  Poor phi/psi
 164 ASN   ( 195-)  A  Poor phi/psi
 216 PHE   ( 247-)  A  Poor phi/psi
 218 ASP   ( 249-)  A  Poor phi/psi
 226 ILE   ( 257-)  A  omega poor
 228 GLY   ( 259-)  A  omega poor
 239 GLN   ( 270-)  A  Poor phi/psi
 256 VAL   ( 287-)  A  Poor phi/psi
 257 GLY   ( 288-)  A  omega poor
 342 TYR   ( 373-)  A  Poor phi/psi
 366 ILE   ( 397-)  A  omega poor
 367 GLU   ( 398-)  A  Poor phi/psi
 368 ASP   ( 399-)  A  Poor phi/psi
 389 THR   ( 420-)  A  omega poor
 391 PHE   ( 422-)  A  Poor phi/psi
 428 LYS   ( 459-)  A  Poor phi/psi
And so on for a total of 132 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.

 420 SER   ( 451-)  A    0.36
1524 SER   ( 451-)  C    0.36
 972 SER   ( 451-)  B    0.37
2076 SER   ( 451-)  D    0.37
 976 SER   ( 455-)  B    0.38
1528 SER   ( 455-)  C    0.40
2080 SER   ( 455-)  D    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!

   8 PRO   (  40-)  A      0
   9 CYS   (  41-)  A      0
  10 GLN   (  42-)  A      0
  12 ARG   (  44-)  A      0
  18 THR   (  50-)  A      0
  21 ASP   (  53-)  A      0
  22 GLN   (  54-)  A      0
  27 CYS   (  59-)  A      0
  28 THR   (  60-)  A      0
  29 ARG   (  61-)  A      0
  30 THR   (  62-)  A      0
  32 PHE   (  64-)  A      0
  33 TYR   (  65-)  A      0
  35 GLU   (  67-)  A      0
  36 ASN   (  68-)  A      0
  37 CYS   (  69-)  A      0
  38 THR   (  70-)  A      0
  62 THR   (  94-)  A      0
  63 HIS   (  95-)  A      0
  64 PHE   (  96-)  A      0
  91 TYR   ( 122-)  A      0
  95 SER   ( 126-)  A      0
  96 PRO   ( 127-)  A      0
  97 PRO   ( 128-)  A      0
  98 THR   ( 129-)  A      0
And so on for a total of 856 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!

1331 GLY   ( 258-)  C   3.15   15
 779 GLY   ( 258-)  B   3.15   15
1883 GLY   ( 258-)  D   3.13   15
 227 GLY   ( 258-)  A   3.12   15
1235 PRO   ( 162-)  C   1.78   12
 683 PRO   ( 162-)  B   1.72   13

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].

  54 PRO   (  86-)  A    99.3 envelop C-beta (108 degrees)
  75 PRO   ( 106-)  A    99.5 envelop C-beta (108 degrees)
 141 PRO   ( 172-)  A  -134.4 half-chair C-delta/C-gamma (-126 degrees)
 160 PRO   ( 191-)  A  -122.9 half-chair C-delta/C-gamma (-126 degrees)
 358 PRO   ( 389-)  A   102.9 envelop C-beta (108 degrees)
 483 PRO   ( 514-)  A   116.0 envelop C-beta (108 degrees)
 507 PRO   ( 538-)  A  -121.8 half-chair C-delta/C-gamma (-126 degrees)
 627 PRO   ( 106-)  B   102.4 envelop C-beta (108 degrees)
 693 PRO   ( 172-)  B  -129.4 half-chair C-delta/C-gamma (-126 degrees)
 712 PRO   ( 191-)  B  -123.1 half-chair C-delta/C-gamma (-126 degrees)
 910 PRO   ( 389-)  B   103.0 envelop C-beta (108 degrees)
1035 PRO   ( 514-)  B   115.3 envelop C-beta (108 degrees)
1059 PRO   ( 538-)  B  -124.5 half-chair C-delta/C-gamma (-126 degrees)
1179 PRO   ( 106-)  C   102.1 envelop C-beta (108 degrees)
1245 PRO   ( 172-)  C  -133.1 half-chair C-delta/C-gamma (-126 degrees)
1264 PRO   ( 191-)  C  -122.4 half-chair C-delta/C-gamma (-126 degrees)
1462 PRO   ( 389-)  C   103.1 envelop C-beta (108 degrees)
1587 PRO   ( 514-)  C   116.6 envelop C-beta (108 degrees)
1611 PRO   ( 538-)  C  -123.3 half-chair C-delta/C-gamma (-126 degrees)
1710 PRO   (  86-)  D    99.7 envelop C-beta (108 degrees)
1731 PRO   ( 106-)  D   102.1 envelop C-beta (108 degrees)
1797 PRO   ( 172-)  D  -129.0 half-chair C-delta/C-gamma (-126 degrees)
1816 PRO   ( 191-)  D  -121.4 half-chair C-delta/C-gamma (-126 degrees)
2014 PRO   ( 389-)  D   100.0 envelop C-beta (108 degrees)
2139 PRO   ( 514-)  D   114.5 envelop C-beta (108 degrees)
2163 PRO   ( 538-)  D  -126.6 half-chair C-delta/C-gamma (-126 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.

 665 ASN   ( 144-)  B      ND2 <-> 2214 NAG   ( 671-)  B      C1     0.78    2.32  INTRA BL
 113 ASN   ( 144-)  A      ND2 <-> 2210 NAG   ( 671-)  A      C1     0.77    2.33  INTRA BL
1217 ASN   ( 144-)  C      ND2 <-> 2218 NAG   ( 671-)  C      C1     0.73    2.37  INTRA BL
1769 ASN   ( 144-)  D      ND2 <-> 2222 NAG   ( 671-)  D      C1     0.67    2.43  INTRA BL
1692 ASN   (  68-)  D      ND2 <-> 2221 NAG   ( 661-)  D      C1     0.60    2.50  INTRA BF
 931 ASN   ( 410-)  B      ND2 <-> 2215 NAG   ( 681-)  B      C1     0.56    2.54  INTRA BF
 111 PHE   ( 142-)  A      O   <->  345 ARG   ( 376-)  A      NH2    0.55    2.15  INTRA BL
  36 ASN   (  68-)  A      ND2 <-> 2209 NAG   ( 661-)  A      C1     0.52    2.58  INTRA BF
1140 ASN   (  68-)  C      ND2 <-> 2217 NAG   ( 661-)  C      C1     0.51    2.59  INTRA BF
1292 GLY   ( 219-)  C      N   <-> 2241 HOH   ( 619 )  C      O      0.51    2.19  INTRA BL
 588 ASN   (  68-)  B      ND2 <-> 2213 NAG   ( 661-)  B      C1     0.51    2.59  INTRA BF
1767 PHE   ( 142-)  D      O   <-> 2001 ARG   ( 376-)  D      NH2    0.49    2.21  INTRA BL
 663 PHE   ( 142-)  B      O   <->  897 ARG   ( 376-)  B      NH2    0.49    2.21  INTRA BL
1215 PHE   ( 142-)  C      O   <-> 1449 ARG   ( 376-)  C      NH2    0.49    2.21  INTRA BL
2035 ASN   ( 410-)  D      ND2 <-> 2223 NAG   ( 681-)  D      C1     0.48    2.62  INTRA BF
1223 ARG   ( 150-)  C      NH2 <-> 1531 MET   ( 458-)  C      O      0.45    2.25  INTRA BL
 119 ARG   ( 150-)  A      NH2 <->  427 MET   ( 458-)  A      O      0.44    2.26  INTRA BL
1775 ARG   ( 150-)  D      NH2 <-> 2083 MET   ( 458-)  D      O      0.44    2.26  INTRA BL
2035 ASN   ( 410-)  D      ND2 <-> 2223 NAG   ( 681-)  D      O5     0.44    2.26  INTRA BF
2203 THR   ( 578-)  D      O   <-> 2242 HOH   ( 628 )  D      O      0.44    1.96  INTRA BF
 671 ARG   ( 150-)  B      NH2 <->  979 MET   ( 458-)  B      O      0.43    2.27  INTRA BL
1748 LEU   ( 123-)  D      O   <-> 2094 ARG   ( 469-)  D      NH2    0.41    2.29  INTRA BL
 379 ASN   ( 410-)  A      ND2 <-> 2211 NAG   ( 681-)  A      C1     0.41    2.69  INTRA BF
 177 GLN   ( 208-)  A      CB  <->  201 HIS   ( 232-)  A      ND1    0.41    2.69  INTRA BF
1833 GLN   ( 208-)  D      CB  <-> 1857 HIS   ( 232-)  D      ND1    0.40    2.70  INTRA BF
And so on for a total of 361 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   (  61-)  D      -6.59
 581 ARG   (  61-)  B      -6.55
1133 ARG   (  61-)  C      -6.52
  29 ARG   (  61-)  A      -6.45
 247 HIS   ( 278-)  A      -6.41
1351 HIS   ( 278-)  C      -6.39
 799 HIS   ( 278-)  B      -6.38
1903 HIS   ( 278-)  D      -6.37
 572 PHE   (  52-)  B      -5.83
  20 PHE   (  52-)  A      -5.83
 690 LYS   ( 169-)  B      -5.82
1794 LYS   ( 169-)  D      -5.80
1242 LYS   ( 169-)  C      -5.80
 386 HIS   ( 417-)  A      -5.76
 138 LYS   ( 169-)  A      -5.76
2042 HIS   ( 417-)  D      -5.75
 938 HIS   ( 417-)  B      -5.75
1490 HIS   ( 417-)  C      -5.75
1124 PHE   (  52-)  C      -5.70
1676 PHE   (  52-)  D      -5.69
2202 PHE   ( 577-)  D      -5.58
 546 PHE   ( 577-)  A      -5.49
1689 TYR   (  65-)  D      -5.40
  33 TYR   (  65-)  A      -5.39
1650 PHE   ( 577-)  C      -5.35
And so on for a total of 67 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   ( 169-)  A       140 - LEU    171- ( A)         -5.06
 183 HIS   ( 214-)  A       185 - ARG    216- ( A)         -4.86
 690 LYS   ( 169-)  B       692 - LEU    171- ( B)         -5.08
 735 HIS   ( 214-)  B       737 - ARG    216- ( B)         -4.97
1242 LYS   ( 169-)  C      1244 - LEU    171- ( C)         -5.06
1287 HIS   ( 214-)  C      1289 - ARG    216- ( C)         -4.85
1794 LYS   ( 169-)  D      1796 - LEU    171- ( D)         -5.09
1839 HIS   ( 214-)  D      1841 - ARG    216- ( D)         -4.96

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.

 334 LEU   ( 365-)  A   -2.76
1990 LEU   ( 365-)  D   -2.76
1438 LEU   ( 365-)  C   -2.74
 886 LEU   ( 365-)  B   -2.73
  92 LEU   ( 123-)  A   -2.67
1748 LEU   ( 123-)  D   -2.66
 644 LEU   ( 123-)  B   -2.64
1196 LEU   ( 123-)  C   -2.64
2199 GLY   ( 574-)  D   -2.63
1095 GLY   ( 574-)  B   -2.58
 657 TYR   ( 136-)  B   -2.56

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.

2239 HOH   ( 623 )  A      O     51.50   11.48  -60.05
2239 HOH   ( 640 )  A      O     68.69  -63.14  -51.82
2240 HOH   ( 597 )  B      O     48.98    8.69  -55.69
2240 HOH   ( 605 )  B      O     37.28  -54.61  -51.34

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   (   8 )  A      O
2239 HOH   (  12 )  A      O
2239 HOH   ( 593 )  A      O
2239 HOH   ( 600 )  A      O
2239 HOH   ( 601 )  A      O
2239 HOH   ( 616 )  A      O
2239 HOH   ( 621 )  A      O
2239 HOH   ( 634 )  A      O
2239 HOH   ( 636 )  A      O
2239 HOH   ( 638 )  A      O
2239 HOH   ( 639 )  A      O
2240 HOH   ( 615 )  B      O
2240 HOH   ( 625 )  B      O
2240 HOH   ( 636 )  B      O
2240 HOH   ( 639 )  B      O
2240 HOH   ( 640 )  B      O
2240 HOH   ( 646 )  B      O
2241 HOH   ( 592 )  C      O
2241 HOH   ( 601 )  C      O
2241 HOH   ( 603 )  C      O
2241 HOH   ( 608 )  C      O
2241 HOH   ( 616 )  C      O
2241 HOH   ( 623 )  C      O
2241 HOH   ( 626 )  C      O
2241 HOH   ( 627 )  C      O
2241 HOH   ( 634 )  C      O
2241 HOH   ( 636 )  C      O
2242 HOH   ( 605 )  D      O
2242 HOH   ( 607 )  D      O
2242 HOH   ( 622 )  D      O
2242 HOH   ( 624 )  D      O
2242 HOH   ( 634 )  D      O
2242 HOH   ( 642 )  D      O
2242 HOH   ( 643 )  D      O
2242 HOH   ( 644 )  D      O
Marked this atom as acceptor 2225 FLR  ( 700-) A      F
Marked this atom as acceptor 2229 FLR  ( 700-) B      F
Marked this atom as acceptor 2232 FLR  ( 700-) C      F
Marked this atom as acceptor 2238 FLR  ( 700-) D      F
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.

 173 HIS   ( 204-)  A
 351 ASN   ( 382-)  A
 763 HIS   ( 242-)  B
 903 ASN   ( 382-)  B
1277 HIS   ( 204-)  C
1455 ASN   ( 382-)  C
2007 ASN   ( 382-)  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   (  51-)  A      N
  89 ARG   ( 120-)  A      NE
 100 ASN   ( 131-)  A      ND2
 101 VAL   ( 132-)  A      N
 105 TYR   ( 136-)  A      N
 107 SER   ( 138-)  A      OG
 108 TRP   ( 139-)  A      N
 119 ARG   ( 150-)  A      NE
 119 ARG   ( 150-)  A      NH2
 127 ASP   ( 158-)  A      N
 154 ARG   ( 185-)  A      N
 154 ARG   ( 185-)  A      NE
 154 ARG   ( 185-)  A      NH1
 155 GLU   ( 186-)  A      N
 177 GLN   ( 208-)  A      NE2
 183 HIS   ( 214-)  A      N
 196 GLY   ( 227-)  A      N
 201 HIS   ( 232-)  A      N
 201 HIS   ( 232-)  A      ND1
 208 ASP   ( 239-)  A      N
 209 ARG   ( 240-)  A      NH2
 214 ARG   ( 245-)  A      NH1
 216 PHE   ( 247-)  A      N
 217 LYS   ( 248-)  A      N
 224 GLN   ( 255-)  A      NE2
And so on for a total of 223 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   ( 203-)  A      OE1
 308 GLU   ( 339-)  A      OE2
 351 ASN   ( 382-)  A      OD1
 380 ASN   ( 411-)  A      OD1
 724 GLN   ( 203-)  B      OE1
 725 HIS   ( 204-)  B      ND1
 860 GLU   ( 339-)  B      OE2
 903 ASN   ( 382-)  B      OD1
 932 ASN   ( 411-)  B      OD1
1045 GLU   ( 524-)  B      OE1
1276 GLN   ( 203-)  C      OE1
1305 HIS   ( 232-)  C      ND1
1412 GLU   ( 339-)  C      OE2
1455 ASN   ( 382-)  C      OD1
1484 ASN   ( 411-)  C      OD1
1828 GLN   ( 203-)  D      OE1
1829 HIS   ( 204-)  D      ND1
1907 ASN   ( 282-)  D      OD1
1964 GLU   ( 339-)  D      OE2
2007 ASN   ( 382-)  D      OD1

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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   (  53-)  A   H-bonding suggests Asn; but Alt-Rotamer
 139 GLU   ( 170-)  A   H-bonding suggests Gln
 291 GLU   ( 322-)  A   H-bonding suggests Gln
 316 ASP   ( 347-)  A   H-bonding suggests Asn
 573 ASP   (  53-)  B   H-bonding suggests Asn; but Alt-Rotamer
 691 GLU   ( 170-)  B   H-bonding suggests Gln
 843 GLU   ( 322-)  B   H-bonding suggests Gln
 868 ASP   ( 347-)  B   H-bonding suggests Asn
1125 ASP   (  53-)  C   H-bonding suggests Asn; but Alt-Rotamer
1243 GLU   ( 170-)  C   H-bonding suggests Gln
1395 GLU   ( 322-)  C   H-bonding suggests Gln
1420 ASP   ( 347-)  C   H-bonding suggests Asn
1677 ASP   (  53-)  D   H-bonding suggests Asn; but Alt-Rotamer
1795 GLU   ( 170-)  D   H-bonding suggests Gln
1947 GLU   ( 322-)  D   H-bonding suggests Gln
1972 ASP   ( 347-)  D   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.564
  2nd generation packing quality :  -1.597
  Ramachandran plot appearance   :  -2.423
  chi-1/chi-2 rotamer normality  :  -2.846
  Backbone conformation          :  -0.793

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.380 (tight)
  Bond angles                    :   0.623 (tight)
  Omega angle restraints         :   1.032
  Side chain planarity           :   0.316 (tight)
  Improper dihedral distribution :   0.614
  B-factor distribution          :   1.627 (loose)
  Inside/Outside distribution    :   1.107

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 : 2.84


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.6
  2nd generation packing quality :   0.0
  Ramachandran plot appearance   :  -0.0
  chi-1/chi-2 rotamer normality  :  -0.7
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.380 (tight)
  Bond angles                    :   0.623 (tight)
  Omega angle restraints         :   1.032
  Side chain planarity           :   0.316 (tight)
  Improper dihedral distribution :   0.614
  B-factor distribution          :   1.627 (loose)
  Inside/Outside distribution    :   1.107
==============

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.