WHAT IF Check report

This file was created 2012-01-31 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

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

Verification log for pdb2vz8.ent

Checks that need to be done early-on in validation

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: P 1 21 1
Number of matrices in space group: 2
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 1
Warning: one pair of SEQRES sequences is sneakingly different
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 4
Z, symmetry, and molecular multiplicity disagree
Could it be that Z must be: 2

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

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.

   1 MET   (   1-)  A    High
   2 GLU   (   2-)  A    High
   3 GLU   (   3-)  A    High
   4 VAL   (   4-)  A    High
   5 VAL   (   5-)  A    High
   7 ALA   (   7-)  A    High
   8 GLY   (   8-)  A    High
   9 MET   (   9-)  A    High
  10 SER   (  10-)  A    High
  12 LYS   (  12-)  A    High
  13 LEU   (  13-)  A    High
  14 PRO   (  14-)  A    High
  15 GLU   (  15-)  A    High
  16 SER   (  16-)  A    High
  17 GLU   (  17-)  A    High
  18 ASN   (  18-)  A    High
  19 LEU   (  19-)  A    High
  20 GLU   (  20-)  A    High
  21 GLU   (  21-)  A    High
  22 PHE   (  22-)  A    High
  23 TRP   (  23-)  A    High
  24 ALA   (  24-)  A    High
  25 ASN   (  25-)  A    High
  26 LEU   (  26-)  A    High
  27 ILE   (  27-)  A    High
And so on for a total of 3426 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: 30

Crystal temperature (K) : 10.000

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

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

 172 TYR   ( 172-)  A
 243 TYR   ( 243-)  A
 289 TYR   ( 289-)  A
 734 TYR   ( 734-)  A
 891 TYR   ( 891-)  A
 993 TYR   ( 993-)  A
1003 TYR   (1003-)  A
1175 TYR   (1255-)  A
1375 TYR   (1506-)  A
1422 TYR   (1553-)  A
1437 TYR   (1568-)  A
1521 TYR   (1652-)  A
1525 TYR   (1656-)  A
1711 TYR   (1842-)  A
1756 TYR   (1887-)  A
1849 TYR   (1996-)  A
1868 TYR   (2015-)  A
2134 TYR   ( 172-)  B
2205 TYR   ( 243-)  B
2251 TYR   ( 289-)  B
2696 TYR   ( 734-)  B
2853 TYR   ( 891-)  B
2955 TYR   ( 993-)  B
2965 TYR   (1003-)  B
3145 TYR   (1255-)  B
3362 TYR   (1506-)  B
3409 TYR   (1553-)  B
3424 TYR   (1568-)  B
3508 TYR   (1652-)  B
3512 TYR   (1656-)  B
3698 TYR   (1842-)  B
3743 TYR   (1887-)  B
3852 TYR   (1996-)  B
3871 TYR   (2015-)  B

Warning: Phenylalanine convention problem

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

  64 PHE   (  64-)  A
 147 PHE   ( 147-)  A
 200 PHE   ( 200-)  A
 215 PHE   ( 215-)  A
 263 PHE   ( 263-)  A
 395 PHE   ( 395-)  A
 450 PHE   ( 450-)  A
 661 PHE   ( 661-)  A
 686 PHE   ( 686-)  A
 730 PHE   ( 730-)  A
 795 PHE   ( 795-)  A
 796 PHE   ( 796-)  A
 821 PHE   ( 821-)  A
 864 PHE   ( 864-)  A
 985 PHE   ( 985-)  A
1007 PHE   (1007-)  A
1096 PHE   (1096-)  A
1238 PHE   (1343-)  A
1251 PHE   (1382-)  A
1265 PHE   (1396-)  A
1271 PHE   (1402-)  A
1284 PHE   (1415-)  A
1292 PHE   (1423-)  A
1383 PHE   (1514-)  A
1401 PHE   (1532-)  A
And so on for a total of 78 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.

  76 ASP   (  76-)  A
 971 ASP   ( 971-)  A
1033 ASP   (1033-)  A
1369 ASP   (1500-)  A
1642 ASP   (1773-)  A
2038 ASP   (  76-)  B
2995 ASP   (1033-)  B
3356 ASP   (1500-)  B
3629 ASP   (1773-)  B

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.

 218 GLU   ( 218-)  A
 270 GLU   ( 270-)  A
 660 GLU   ( 660-)  A
1598 GLU   (1729-)  A
1619 GLU   (1750-)  A
1678 GLU   (1809-)  A
2232 GLU   ( 270-)  B
2574 GLU   ( 612-)  B
3585 GLU   (1729-)  B
3606 GLU   (1750-)  B
3665 GLU   (1809-)  B

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.

 703 LEU   ( 703-)  A      N    CA   C    99.52   -4.2
1242 HIS   (1347-)  A      CG   ND1  CE1 109.60    4.0
3062 HIS   (1100-)  B      CG   ND1  CE1 109.61    4.0
3634 HIS   (1778-)  B      CG   ND1  CE1 109.64    4.0
3778 THR   (1922-)  B      C    CA   CB  101.77   -4.4

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.

  76 ASP   (  76-)  A
 218 GLU   ( 218-)  A
 270 GLU   ( 270-)  A
 660 GLU   ( 660-)  A
 971 ASP   ( 971-)  A
1033 ASP   (1033-)  A
1369 ASP   (1500-)  A
1598 GLU   (1729-)  A
1619 GLU   (1750-)  A
1642 ASP   (1773-)  A
1678 GLU   (1809-)  A
2038 ASP   (  76-)  B
2232 GLU   ( 270-)  B
2574 GLU   ( 612-)  B
2995 ASP   (1033-)  B
3356 ASP   (1500-)  B
3585 GLU   (1729-)  B
3606 GLU   (1750-)  B
3629 ASP   (1773-)  B
3665 GLU   (1809-)  B

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.

3504 VAL   (1648-)  B    4.79
 703 LEU   ( 703-)  A    4.76
 663 GLN   ( 663-)  A    4.38
1482 VAL   (1613-)  A    4.20
2093 SER   ( 131-)  B    4.19
1102 SER   (1102-)  A    4.10
3561 ARG   (1705-)  B    4.09
3865 ALA   (2009-)  B    4.07
1522 THR   (1653-)  A    4.04

Torsion-related checks

Error: Ramachandran Z-score very low

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

Ramachandran Z-score : -4.647

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.

3656 PHE   (1800-)  B    -3.5
3216 THR   (1337-)  B    -3.4
1669 PHE   (1800-)  A    -3.3
2257 THR   ( 295-)  B    -3.3
 413 PRO   ( 413-)  A    -3.1
2375 PRO   ( 413-)  B    -3.1
3320 PRO   (1464-)  B    -3.1
1739 PRO   (1870-)  A    -3.1
 295 THR   ( 295-)  A    -3.1
1333 PRO   (1464-)  A    -3.1
3114 PRO   (1224-)  B    -3.1
1734 PRO   (1865-)  A    -3.0
2598 PRO   ( 636-)  B    -3.0
1976 PRO   (  14-)  B    -3.0
2597 PRO   ( 635-)  B    -3.0
3719 PRO   (1863-)  B    -3.0
  14 PRO   (  14-)  A    -3.0
1074 THR   (1074-)  A    -3.0
3036 THR   (1074-)  B    -3.0
 982 THR   ( 982-)  A    -3.0
1518 PRO   (1649-)  A    -2.9
3031 TYR   (1069-)  B    -2.8
1069 TYR   (1069-)  A    -2.8
1186 PRO   (1266-)  A    -2.8
1144 PRO   (1224-)  A    -2.8
And so on for a total of 252 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.

  15 GLU   (  15-)  A  Poor phi/psi
  40 TRP   (  40-)  A  Poor phi/psi, omega poor
  45 TYR   (  45-)  A  Poor phi/psi
  57 LEU   (  57-)  A  Poor phi/psi
  60 PHE   (  60-)  A  Poor phi/psi
  61 ASP   (  61-)  A  omega poor
  86 THR   (  86-)  A  omega poor
 103 THR   ( 103-)  A  omega poor
 149 ASP   ( 149-)  A  Poor phi/psi
 160 ALA   ( 160-)  A  Poor phi/psi
 162 SER   ( 162-)  A  Poor phi/psi, omega poor
 163 SER   ( 163-)  A  Poor phi/psi
 179 GLU   ( 179-)  A  Poor phi/psi
 215 PHE   ( 215-)  A  Poor phi/psi
 227 ALA   ( 227-)  A  omega poor
 237 SER   ( 237-)  A  Poor phi/psi
 238 LEU   ( 238-)  A  Poor phi/psi
 249 ALA   ( 249-)  A  Poor phi/psi
 252 ASN   ( 252-)  A  Poor phi/psi
 254 ASP   ( 254-)  A  Poor phi/psi
 255 GLY   ( 255-)  A  Poor phi/psi
 277 TYR   ( 277-)  A  Poor phi/psi
 278 ALA   ( 278-)  A  Poor phi/psi
 282 PRO   ( 282-)  A  Poor phi/psi
 296 GLY   ( 296-)  A  Poor phi/psi
And so on for a total of 302 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -5.180

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.

 519 SER   ( 519-)  A    0.36
2481 SER   ( 519-)  B    0.36
1823 SER   (1954-)  A    0.37
3654 SER   (1798-)  B    0.39
3810 SER   (1954-)  B    0.39
1427 SER   (1558-)  A    0.39
 555 SER   ( 555-)  A    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!

  10 SER   (  10-)  A      0
  13 LEU   (  13-)  A      0
  14 PRO   (  14-)  A      0
  15 GLU   (  15-)  A      0
  18 ASN   (  18-)  A      0
  39 ARG   (  39-)  A      0
  40 TRP   (  40-)  A      0
  41 LYS   (  41-)  A      0
  42 ALA   (  42-)  A      0
  44 LEU   (  44-)  A      0
  45 TYR   (  45-)  A      0
  50 ARG   (  50-)  A      0
  51 MET   (  51-)  A      0
  57 LEU   (  57-)  A      0
  62 ALA   (  62-)  A      0
  65 PHE   (  65-)  A      0
  68 HIS   (  68-)  A      0
  74 THR   (  74-)  A      0
 101 ARG   ( 101-)  A      0
 103 THR   ( 103-)  A      0
 104 SER   ( 104-)  A      0
 113 SER   ( 113-)  A      0
 115 ASP   ( 115-)  A      0
 120 LEU   ( 120-)  A      0
 121 SER   ( 121-)  A      0
And so on for a total of 1633 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!

2140 GLY   ( 178-)  B   1.88   22
 178 GLY   ( 178-)  A   1.83   17
1548 GLY   (1679-)  A   1.76   13
 310 ASN   ( 310-)  A   1.69   19
2272 ASN   ( 310-)  B   1.68   19

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].

  14 PRO   (  14-)  A   124.7 half-chair C-beta/C-alpha (126 degrees)
 124 PRO   ( 124-)  A    48.2 half-chair C-delta/C-gamma (54 degrees)
 153 PRO   ( 153-)  A   107.3 envelop C-beta (108 degrees)
 194 PRO   ( 194-)  A    50.7 half-chair C-delta/C-gamma (54 degrees)
 282 PRO   ( 282-)  A   115.7 envelop C-beta (108 degrees)
 332 PRO   ( 332-)  A    45.7 half-chair C-delta/C-gamma (54 degrees)
 334 PRO   ( 334-)  A    24.6 half-chair N/C-delta (18 degrees)
 362 PRO   ( 362-)  A   108.8 envelop C-beta (108 degrees)
 367 PRO   ( 367-)  A    41.4 envelop C-delta (36 degrees)
 410 PRO   ( 410-)  A    52.7 half-chair C-delta/C-gamma (54 degrees)
 413 PRO   ( 413-)  A    18.7 half-chair N/C-delta (18 degrees)
 574 PRO   ( 574-)  A    30.5 envelop C-delta (36 degrees)
 617 PRO   ( 617-)  A   107.2 envelop C-beta (108 degrees)
 635 PRO   ( 635-)  A   100.1 envelop C-beta (108 degrees)
 654 PRO   ( 654-)  A   108.5 envelop C-beta (108 degrees)
 818 PRO   ( 818-)  A   121.5 half-chair C-beta/C-alpha (126 degrees)
 828 PRO   ( 828-)  A   105.0 envelop C-beta (108 degrees)
 845 PRO   ( 845-)  A   115.9 envelop C-beta (108 degrees)
 851 PRO   ( 851-)  A    99.6 envelop C-beta (108 degrees)
 911 PRO   ( 911-)  A  -125.1 half-chair C-delta/C-gamma (-126 degrees)
 926 PRO   ( 926-)  A    50.3 half-chair C-delta/C-gamma (54 degrees)
 978 PRO   ( 978-)  A    48.1 half-chair C-delta/C-gamma (54 degrees)
1005 PRO   (1005-)  A   110.0 envelop C-beta (108 degrees)
1043 PRO   (1043-)  A    39.8 envelop C-delta (36 degrees)
1051 PRO   (1051-)  A    44.0 envelop C-delta (36 degrees)
And so on for a total of 92 lines.

Bump checks

Error: Abnormally short interatomic distances

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

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

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

2965 TYR   (1003-)  B      CZ  <-> 2999 HIS   (1037-)  B      CE1    0.53    2.67  INTRA BL
1003 TYR   (1003-)  A      CZ  <-> 1037 HIS   (1037-)  A      CE1    0.50    2.70  INTRA BL
1314 ALA   (1445-)  A      O   <-> 1345 ASN   (1476-)  A      ND2    0.50    2.20  INTRA BF
3212 ASN   (1333-)  B      ND2 <-> 3213 MET   (1334-)  B      SD     0.48    2.82  INTRA BF
 633 ARG   ( 633-)  A      NH2 <->  668 GLU   ( 668-)  A      OE1    0.47    2.23  INTRA BL
1531 ARG   (1662-)  A      NH1 <-> 1661 HIS   (1792-)  A      ND1    0.46    2.54  INTRA BL
1726 ARG   (1857-)  A      NH1 <-> 1738 PRO   (1869-)  A      CB     0.44    2.66  INTRA BF
 856 CYS   ( 856-)  A      SG  <-> 2818 CYS   ( 856-)  B      CB     0.44    2.96  INTRA BF
1205 ALA   (1285-)  A      O   <-> 1209 LEU   (1289-)  A      N      0.43    2.27  INTRA BF
3175 ALA   (1285-)  B      O   <-> 3179 LEU   (1289-)  B      N      0.41    2.29  INTRA BF
3264 THR   (1408-)  B      N   <-> 3265 PRO   (1409-)  B      CD     0.39    2.61  INTRA BF
3193 ASN   (1303-)  B      N   <-> 3194 PRO   (1304-)  B      CD     0.39    2.61  INTRA BF
 856 CYS   ( 856-)  A      SG  <-> 2818 CYS   ( 856-)  B      SG     0.39    3.06  INTRA BF
1603 ARG   (1734-)  A      O   <-> 1605 THR   (1736-)  A      N      0.38    2.32  INTRA BL
 581 SER   ( 581-)  A      O   <->  583 GLY   ( 583-)  A      N      0.37    2.33  INTRA BL
2289 SER   ( 327-)  B      OG  <-> 2318 ASN   ( 356-)  B      ND2    0.36    2.34  INTRA BF
 327 SER   ( 327-)  A      OG  <->  356 ASN   ( 356-)  A      ND2    0.35    2.35  INTRA BL
3302 VAL   (1446-)  B      CA  <-> 3332 ASN   (1476-)  B      ND2    0.35    2.75  INTRA BF
3189 TRP   (1299-)  B      CH2 <-> 3212 ASN   (1333-)  B      ND2    0.35    2.75  INTRA BF
1872 PHE   (2019-)  A      CD2 <-> 1913 TRP   (2060-)  A      NE1    0.34    2.76  INTRA BF
3190 ASP   (1300-)  B      O   <-> 3192 ALA   (1302-)  B      N      0.34    2.36  INTRA BF
3518 ARG   (1662-)  B      NH2 <-> 3649 GLY   (1793-)  B      O      0.34    2.36  INTRA BL
1345 ASN   (1476-)  A      CB  <-> 1355 MET   (1486-)  A      SD     0.34    3.06  INTRA BF
3530 HIS   (1674-)  B      CD2 <-> 3554 THR   (1698-)  B      CG2    0.33    2.87  INTRA BL
3325 ILE   (1469-)  B      CG2 <-> 3327 CYS   (1471-)  B      SG     0.33    3.07  INTRA BF
And so on for a total of 1127 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

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.

3722 ARG   (1866-)  B      -8.68
1735 ARG   (1866-)  A      -8.37
 384 ARG   ( 384-)  A      -8.09
2346 ARG   ( 384-)  B      -8.05
 317 ARG   ( 317-)  A      -7.83
 316 ARG   ( 316-)  A      -7.82
2278 ARG   ( 316-)  B      -7.82
2279 ARG   ( 317-)  B      -7.81
2752 ARG   ( 790-)  B      -7.67
 973 ARG   ( 973-)  A      -7.66
3773 ARG   (1917-)  B      -7.65
 790 ARG   ( 790-)  A      -7.63
1786 ARG   (1917-)  A      -7.56
2638 ARG   ( 676-)  B      -7.53
1730 GLN   (1861-)  A      -7.48
1737 LEU   (1868-)  A      -7.38
3724 LEU   (1868-)  B      -7.37
3266 GLN   (1410-)  B      -7.36
3717 GLN   (1861-)  B      -7.32
3580 ARG   (1724-)  B      -7.23
1593 ARG   (1724-)  A      -7.16
1790 ARG   (1921-)  A      -7.05
3777 ARG   (1921-)  B      -7.03
1279 GLN   (1410-)  A      -6.99
1392 ARG   (1523-)  A      -6.81
And so on for a total of 137 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.

1275 GLN   (1406-)  A      1277 - THR   1408- ( A)         -5.06
1735 ARG   (1866-)  A      1737 - LEU   1868- ( A)         -6.72
3073 HIS   (1111-)  B      3075 - LYS   1113- ( B)         -4.49
3656 PHE   (1800-)  B      3658 - GLU   1802- ( B)         -4.29
3722 ARG   (1866-)  B      3724 - LEU   1868- ( B)         -6.86

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

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.

1743 THR   (1874-)  A   -3.14
3048 LEU   (1086-)  B   -3.03
1086 LEU   (1086-)  A   -2.96
2100 ALA   ( 138-)  B   -2.71
1403 ASN   (1534-)  A   -2.68
 138 ALA   ( 138-)  A   -2.68
3263 GLN   (1407-)  B   -2.64
1257 HIS   (1388-)  A   -2.64
3244 HIS   (1388-)  B   -2.64
3555 VAL   (1699-)  B   -2.62
1127 SER   (1127-)  A   -2.59
1568 VAL   (1699-)  A   -2.59

Warning: Abnormal packing Z-score for sequential residues

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

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

 136 GLN   ( 136-)  A     -  139 MET   ( 139-)  A        -1.60
1394 GLU   (1525-)  A     - 1397 THR   (1528-)  A        -1.51
1876 SER   (2023-)  A     - 1879 ARG   (2026-)  A        -1.47
2098 GLN   ( 136-)  B     - 2101 MET   ( 139-)  B        -1.60

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips

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

  25 ASN   (  25-)  A
 136 GLN   ( 136-)  A
 199 GLN   ( 199-)  A
 248 ASN   ( 248-)  A
 417 HIS   ( 417-)  A
 425 GLN   ( 425-)  A
 444 HIS   ( 444-)  A
 483 GLN   ( 483-)  A
 560 GLN   ( 560-)  A
 792 ASN   ( 792-)  A
1111 HIS   (1111-)  A
1156 ASN   (1236-)  A
1185 GLN   (1265-)  A
1429 GLN   (1560-)  A
1578 GLN   (1709-)  A
1646 ASN   (1777-)  A
1693 GLN   (1824-)  A
1903 HIS   (2050-)  A
1925 ASN   (2076-)  A
1987 ASN   (  25-)  B
2098 GLN   ( 136-)  B
2161 GLN   ( 199-)  B
2210 ASN   ( 248-)  B
2322 HIS   ( 360-)  B
2361 ASN   ( 399-)  B
2387 GLN   ( 425-)  B
2406 HIS   ( 444-)  B
2522 GLN   ( 560-)  B
2685 GLN   ( 723-)  B
2754 ASN   ( 792-)  B
3034 GLN   (1072-)  B
3073 HIS   (1111-)  B
3103 GLN   (1141-)  B
3126 ASN   (1236-)  B
3183 HIS   (1293-)  B
3226 HIS   (1347-)  B
3233 GLN   (1377-)  B
3262 GLN   (1406-)  B
3530 HIS   (1674-)  B
3565 GLN   (1709-)  B
3633 ASN   (1777-)  B
3680 GLN   (1824-)  B
3839 GLN   (1983-)  B
3928 ASN   (2076-)  B

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 LEU   (  19-)  A      N
  38 ARG   (  38-)  A      N
  38 ARG   (  38-)  A      NE
  39 ARG   (  39-)  A      N
  39 ARG   (  39-)  A      NH1
  41 LYS   (  41-)  A      N
  50 ARG   (  50-)  A      N
  53 LYS   (  53-)  A      N
  55 LYS   (  55-)  A      N
  56 ASP   (  56-)  A      N
  59 ARG   (  59-)  A      NE
  60 PHE   (  60-)  A      N
  70 LYS   (  70-)  A      N
  80 ARG   (  80-)  A      NH1
  80 ARG   (  80-)  A      NH2
  86 THR   (  86-)  A      OG1
  87 TYR   (  87-)  A      N
 105 THR   ( 105-)  A      N
 105 THR   ( 105-)  A      OG1
 108 TRP   ( 108-)  A      NE1
 112 SER   ( 112-)  A      N
 113 SER   ( 113-)  A      N
 117 SER   ( 117-)  A      N
 122 ARG   ( 122-)  A      N
 123 ASP   ( 123-)  A      N
And so on for a total of 575 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.

  78 GLN   (  78-)  A      OE1
  96 ASN   (  96-)  A      OD1
 189 ASN   ( 189-)  A      OD1
 195 ASN   ( 195-)  A      OD1
 291 GLU   ( 291-)  A      OE1
 293 HIS   ( 293-)  A      ND1
 328 ASN   ( 328-)  A      OD1
 387 ASN   ( 387-)  A      OD1
 407 ASN   ( 407-)  A      OD1
 425 GLN   ( 425-)  A      OE1
 502 GLN   ( 502-)  A      OE1
 560 GLN   ( 560-)  A      OE1
 643 HIS   ( 643-)  A      ND1
 747 GLU   ( 747-)  A      OE1
 804 HIS   ( 804-)  A      ND1
 945 GLU   ( 945-)  A      OE1
 991 ASP   ( 991-)  A      OD2
1033 ASP   (1033-)  A      OD1
1037 HIS   (1037-)  A      ND1
1196 ASP   (1276-)  A      OD2
1289 ASP   (1420-)  A      OD2
1551 GLN   (1682-)  A      OE1
1598 GLU   (1729-)  A      OE1
1717 HIS   (1848-)  A      ND1
1891 ASN   (2038-)  A      OD1
And so on for a total of 62 lines.

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.

  92 ASP   (  92-)  A   H-bonding suggests Asn
 216 ASP   ( 216-)  A   H-bonding suggests Asn; but Alt-Rotamer
 288 GLU   ( 288-)  A   H-bonding suggests Gln; but Alt-Rotamer
 291 GLU   ( 291-)  A   H-bonding suggests Gln
 980 ASP   ( 980-)  A   H-bonding suggests Asn; but Alt-Rotamer
 984 GLU   ( 984-)  A   H-bonding suggests Gln
1166 GLU   (1246-)  A   H-bonding suggests Gln
1196 ASP   (1276-)  A   H-bonding suggests Asn; but Alt-Rotamer
1210 GLU   (1290-)  A   H-bonding suggests Gln; but Alt-Rotamer
1300 ASP   (1431-)  A   H-bonding suggests Asn
1637 GLU   (1768-)  A   H-bonding suggests Gln
1642 ASP   (1773-)  A   H-bonding suggests Asn; but Alt-Rotamer
1671 GLU   (1802-)  A   H-bonding suggests Gln
1926 ASP   (2077-)  A   H-bonding suggests Asn
1962 GLU   (2113-)  A   H-bonding suggests Gln
2054 ASP   (  92-)  B   H-bonding suggests Asn
2087 GLU   ( 125-)  B   H-bonding suggests Gln
2253 GLU   ( 291-)  B   H-bonding suggests Gln
2263 ASP   ( 301-)  B   H-bonding suggests Asn
2811 ASP   ( 849-)  B   H-bonding suggests Asn
3136 GLU   (1246-)  B   H-bonding suggests Gln
3267 ASP   (1411-)  B   H-bonding suggests Asn; but Alt-Rotamer
3287 ASP   (1431-)  B   H-bonding suggests Asn
3417 ASP   (1561-)  B   H-bonding suggests Asn
3458 GLU   (1602-)  B   H-bonding suggests Gln
3463 ASP   (1607-)  B   H-bonding suggests Asn; but Alt-Rotamer
3624 GLU   (1768-)  B   H-bonding suggests Gln
3629 ASP   (1773-)  B   H-bonding suggests Asn; but Alt-Rotamer
3658 GLU   (1802-)  B   H-bonding suggests Gln; but Alt-Rotamer
3846 ASP   (1990-)  B   H-bonding suggests Asn
3929 ASP   (2077-)  B   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 :  -1.641
  2nd generation packing quality :  -2.556
  Ramachandran plot appearance   :  -4.647 (bad)
  chi-1/chi-2 rotamer normality  :  -5.180 (bad)
  Backbone conformation          :  -0.372

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.380 (tight)
  Bond angles                    :   0.628 (tight)
  Omega angle restraints         :   1.071
  Side chain planarity           :   0.302 (tight)
  Improper dihedral distribution :   0.636
  B-factor distribution          :   0.829
  Inside/Outside distribution    :   1.001

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 3.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.3
  2nd generation packing quality :  -0.4
  Ramachandran plot appearance   :  -1.7
  chi-1/chi-2 rotamer normality  :  -2.7
  Backbone conformation          :   0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.380 (tight)
  Bond angles                    :   0.628 (tight)
  Omega angle restraints         :   1.071
  Side chain planarity           :   0.302 (tight)
  Improper dihedral distribution :   0.636
  B-factor distribution          :   0.829
  Inside/Outside distribution    :   1.001
==============

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.