WHAT IF Check report

This file was created 2013-06-06 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 pdb3w1k.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.558
CA-only RMS fit for the two chains : 0.344

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.530
CA-only RMS fit for the two chains : 0.305

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 1.420
CA-only RMS fit for the two chains : 1.287

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and E

All-atom RMS fit for the two chains : 0.544
CA-only RMS fit for the two chains : 0.285

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: B and C

All-atom RMS fit for the two chains : 0.560
CA-only RMS fit for the two chains : 0.413

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: B and C

Warning: Matthews Coefficient (Vm) high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 400282.656
Volume of the Unit Cell V= 7904565.5
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 4.937
Vm by authors and this calculated Vm agree well
Matthews coefficient read from REMARK 280 Vm= 4.850

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

Note: Ramachandran plot

Chain identifier: E

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

Warning: Artificial side chains detected

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

 285 LLP   ( 285-)  A
 737 LLP   ( 285-)  B
1059 GLU   ( 155-)  C
1189 LLP   ( 285-)  C
1641 LLP   ( 285-)  D
2093 LLP   ( 285-)  E

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 LYS   (   2-)  A    High
   3 SER   (   3-)  A    High
   4 LEU   (   4-)  A    High
   5 LEU   (   5-)  A    High
   6 ARG   (   6-)  A    High
   7 GLN   (   7-)  A    High
   8 ILE   (   8-)  A    High
   9 PRO   (   9-)  A    High
  10 GLN   (  10-)  A    High
  11 ILE   (  11-)  A    High
  12 SER   (  12-)  A    High
  13 LYS   (  13-)  A    High
  14 VAL   (  14-)  A    High
  15 VAL   (  15-)  A    High
  16 GLU   (  16-)  A    High
  17 ILE   (  17-)  A    High
  18 PHE   (  18-)  A    High
  19 ALA   (  19-)  A    High
  20 LYS   (  20-)  A    High
  21 ALA   (  21-)  A    High
  22 TYR   (  22-)  A    High
  23 PRO   (  23-)  A    High
  24 GLU   (  24-)  A    High
  25 ILE   (  25-)  A    High
And so on for a total of 2720 lines.

Warning: What type of B-factor?

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

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

Crystal temperature (K) : 90.000

Warning: Average B-factor problem

The average B-factor for all buried protein atoms normally lies between 10-30. Values around 3-10 are expected for X-ray studies performed at liquid nitrogen temperature.

Because of the extreme value for the average B-factor, no further analysis of the B-factors is performed.

Average B-factor for buried atoms : 0.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

 335 ARG   ( 335-)  A
 343 ARG   ( 343-)  A
 787 ARG   ( 335-)  B
 795 ARG   ( 343-)  B
1239 ARG   ( 335-)  C
1247 ARG   ( 343-)  C
1691 ARG   ( 335-)  D
1699 ARG   ( 343-)  D
2143 ARG   ( 335-)  E
2151 ARG   ( 343-)  E

Warning: Tyrosine convention problem

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

 109 TYR   ( 109-)  A
 220 TYR   ( 220-)  A
 240 TYR   ( 240-)  A
 245 TYR   ( 245-)  A
 331 TYR   ( 331-)  A
 672 TYR   ( 220-)  B
 692 TYR   ( 240-)  B
 697 TYR   ( 245-)  B
 845 TYR   ( 393-)  B
1013 TYR   ( 109-)  C
1124 TYR   ( 220-)  C
1149 TYR   ( 245-)  C
1235 TYR   ( 331-)  C
1465 TYR   ( 109-)  D
1596 TYR   ( 240-)  D
1601 TYR   ( 245-)  D
1917 TYR   ( 109-)  E
2048 TYR   ( 240-)  E
2053 TYR   ( 245-)  E

Warning: Phenylalanine convention problem

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

 147 PHE   ( 147-)  A
 219 PHE   ( 219-)  A
 268 PHE   ( 268-)  A
 599 PHE   ( 147-)  B
 625 PHE   ( 173-)  B
 784 PHE   ( 332-)  B
 887 PHE   ( 435-)  B
1051 PHE   ( 147-)  C
1163 PHE   ( 259-)  C
1172 PHE   ( 268-)  C
1339 PHE   ( 435-)  C
1529 PHE   ( 173-)  D
1580 PHE   ( 224-)  D
1624 PHE   ( 268-)  D
1688 PHE   ( 332-)  D
1791 PHE   ( 435-)  D
1981 PHE   ( 173-)  E
2027 PHE   ( 219-)  E

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.

 629 ASP   ( 177-)  B
 769 ASP   ( 317-)  B
1081 ASP   ( 177-)  C
1221 ASP   ( 317-)  C
1673 ASP   ( 317-)  D
1985 ASP   ( 177-)  E

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.

 158 GLU   ( 158-)  A
 448 GLU   ( 448-)  A
 610 GLU   ( 158-)  B
 900 GLU   ( 448-)  B
1062 GLU   ( 158-)  C
1352 GLU   ( 448-)  C
1514 GLU   ( 158-)  D
1743 GLU   ( 387-)  D
1804 GLU   ( 448-)  D
1966 GLU   ( 158-)  E
2195 GLU   ( 387-)  E
2256 GLU   ( 448-)  E

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

2445 OGUA  (   1-)  H      P    O5'   1.63    4.1

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.

1755 HIS   ( 399-)  D      CG   ND1  CE1 109.66    4.1
2261 OGUA  (   1-)  F      OP1  P    OP2 113.03   -4.4
2263 OGUA  (   3-)  F      N9   C8   N7  113.18    4.2
2265 OGUA  (   5-)  F      N9   C8   N7  113.20    4.2
2273 OGUA  (  12-)  F      N9   C8   N7  113.13    4.1
2283 OGUA  (  22-)  F      N9   C8   N7  113.22    4.2
2326 OGUA  (  48-)  F      N9   C8   N7  113.14    4.1
2327 OGUA  (  49-)  F      N9   C8   N7  113.21    4.2
2352 OGUA  (  73-)  F      N9   C8   N7  113.24    4.3
2353 OGUA  (   1-)  G      OP1  P    OP2 113.28   -4.2
2355 OGUA  (   3-)  G      N9   C8   N7  113.15    4.1
2357 OGUA  (   5-)  G      N9   C8   N7  113.32    4.4
2375 OGUA  (  22-)  G      N9   C8   N7  113.15    4.1
2383 OGUA  (  30-)  G      O5*  P   -O3*  95.81   -4.3
2397 OGUA  (  43-)  G      N9   C8   N7  113.19    4.2
2412 OGUA  (  47-)  G      N9   C8   N7  113.12    4.0
2414 OGUA  (  47-)  G      N9   C8   N7  113.11    4.0
2416 OGUA  (  47-)  G      N9   C8   N7  113.18    4.2
2418 OGUA  (  48-)  G      N9   C8   N7  113.19    4.2
2419 OGUA  (  49-)  G      N9   C8   N7  113.20    4.2
2444 OGUA  (  73-)  G      N9   C8   N7  113.27    4.3
2445 OGUA  (   1-)  H      OP1  P    OP2 112.63   -4.6
2445 OGUA  (   1-)  H      N9   C8   N7  113.15    4.1
2447 OGUA  (   3-)  H      N9   C8   N7  113.20    4.2
2449 OGUA  (   5-)  H      N9   C8   N7  113.25    4.3
And so on for a total of 65 lines.

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.

 158 GLU   ( 158-)  A
 335 ARG   ( 335-)  A
 343 ARG   ( 343-)  A
 448 GLU   ( 448-)  A
 610 GLU   ( 158-)  B
 629 ASP   ( 177-)  B
 769 ASP   ( 317-)  B
 787 ARG   ( 335-)  B
 795 ARG   ( 343-)  B
 900 GLU   ( 448-)  B
1062 GLU   ( 158-)  C
1081 ASP   ( 177-)  C
1221 ASP   ( 317-)  C
1239 ARG   ( 335-)  C
1247 ARG   ( 343-)  C
1352 GLU   ( 448-)  C
1514 GLU   ( 158-)  D
1673 ASP   ( 317-)  D
1691 ARG   ( 335-)  D
1699 ARG   ( 343-)  D
1743 GLU   ( 387-)  D
1804 GLU   ( 448-)  D
1966 GLU   ( 158-)  E
1985 ASP   ( 177-)  E
2143 ARG   ( 335-)  E
2151 ARG   ( 343-)  E
2195 GLU   ( 387-)  E
2256 GLU   ( 448-)  E

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.

 349 GLU   ( 349-)  A    5.46
1705 GLU   ( 349-)  D    5.39
2157 GLU   ( 349-)  E    5.15
1253 GLU   ( 349-)  C    4.70
2031 GLY   ( 223-)  E    4.21
1579 GLY   ( 223-)  D    4.10

Torsion-related checks

Warning: Ramachandran Z-score low

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

Ramachandran Z-score : -3.280

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.

2148 PRO   ( 340-)  E    -3.0
 792 PRO   ( 340-)  B    -3.0
1696 PRO   ( 340-)  D    -3.0
 340 PRO   ( 340-)  A    -3.0
1244 PRO   ( 340-)  C    -3.0
 644 THR   ( 192-)  B    -2.7
2003 THR   ( 195-)  E    -2.7
1817 PRO   (   9-)  E    -2.5
1915 LEU   ( 107-)  E    -2.4
 187 ARG   ( 187-)  A    -2.4
 844 THR   ( 392-)  B    -2.4
1296 THR   ( 392-)  C    -2.4
2200 THR   ( 392-)  E    -2.4
2232 GLU   ( 424-)  E    -2.3
 392 THR   ( 392-)  A    -2.3
1561 ASN   ( 205-)  D    -2.3
1548 THR   ( 192-)  D    -2.3
 192 THR   ( 192-)  A    -2.3
2000 THR   ( 192-)  E    -2.3
1736 PRO   ( 380-)  D    -2.3
1748 THR   ( 392-)  D    -2.3
2027 PHE   ( 219-)  E    -2.3
2013 ASN   ( 205-)  E    -2.2
1551 THR   ( 195-)  D    -2.2
2188 PRO   ( 380-)  E    -2.2
1365 PRO   (   9-)  D    -2.2
 876 GLU   ( 424-)  B    -2.2
 791 ILE   ( 339-)  B    -2.2
1158 ILE   ( 254-)  C    -2.1
 657 ASN   ( 205-)  B    -2.1
 219 PHE   ( 219-)  A    -2.1
 706 ILE   ( 254-)  B    -2.0
1092 GLU   ( 188-)  C    -2.0
 832 PRO   ( 380-)  B    -2.0
2053 TYR   ( 245-)  E    -2.0
 425 ASP   ( 425-)  A    -2.0
1610 ILE   ( 254-)  D    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

   9 PRO   (   9-)  A  Poor phi/psi
  19 ALA   (  19-)  A  Poor phi/psi
  86 ARG   (  86-)  A  Poor phi/psi
 334 LYS   ( 334-)  A  Poor phi/psi
 384 SER   ( 384-)  A  Poor phi/psi
 415 GLU   ( 415-)  A  PRO omega poor
 424 GLU   ( 424-)  A  Poor phi/psi
 471 ALA   (  19-)  B  Poor phi/psi
 538 ARG   (  86-)  B  Poor phi/psi
 657 ASN   ( 205-)  B  Poor phi/psi
 786 LYS   ( 334-)  B  Poor phi/psi
 836 SER   ( 384-)  B  Poor phi/psi
 867 GLU   ( 415-)  B  PRO omega poor
 876 GLU   ( 424-)  B  Poor phi/psi
 923 ALA   (  19-)  C  Poor phi/psi
 990 ARG   (  86-)  C  Poor phi/psi
1238 LYS   ( 334-)  C  Poor phi/psi
1288 SER   ( 384-)  C  Poor phi/psi
1319 GLU   ( 415-)  C  PRO omega poor
1328 GLU   ( 424-)  C  Poor phi/psi
1365 PRO   (   9-)  D  Poor phi/psi
1375 ALA   (  19-)  D  Poor phi/psi
1442 ARG   (  86-)  D  Poor phi/psi
1575 PHE   ( 219-)  D  Poor phi/psi
1690 LYS   ( 334-)  D  Poor phi/psi
1740 SER   ( 384-)  D  Poor phi/psi
1771 GLU   ( 415-)  D  PRO omega poor
1780 GLU   ( 424-)  D  Poor phi/psi
1810 LYS   (   2-)  E  Poor phi/psi
1817 PRO   (   9-)  E  Poor phi/psi
1827 ALA   (  19-)  E  Poor phi/psi
1894 ARG   (  86-)  E  Poor phi/psi
2013 ASN   ( 205-)  E  Poor phi/psi
2192 SER   ( 384-)  E  Poor phi/psi
2223 GLU   ( 415-)  E  PRO omega poor
2232 GLU   ( 424-)  E  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.454

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.

 322 SER   ( 322-)  A    0.38
  63 SER   (  63-)  A    0.38
1678 SER   ( 322-)  D    0.39

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!

   7 GLN   (   7-)  A      0
  19 ALA   (  19-)  A      0
  20 LYS   (  20-)  A      0
  21 ALA   (  21-)  A      0
  22 TYR   (  22-)  A      0
  44 GLU   (  44-)  A      0
  46 ALA   (  46-)  A      0
  47 ARG   (  47-)  A      0
  48 ALA   (  48-)  A      0
  50 LEU   (  50-)  A      0
  51 ASN   (  51-)  A      0
  65 MET   (  65-)  A      0
  69 ILE   (  69-)  A      0
  75 ALA   (  75-)  A      0
  76 THR   (  76-)  A      0
  84 LEU   (  84-)  A      0
  86 ARG   (  86-)  A      0
  87 ALA   (  87-)  A      0
 102 ASN   ( 102-)  A      0
 104 TYR   ( 104-)  A      0
 107 LEU   ( 107-)  A      0
 108 GLU   ( 108-)  A      0
 113 GLU   ( 113-)  A      0
 116 ARG   ( 116-)  A      0
 119 ARG   ( 119-)  A      0
And so on for a total of 1191 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 1.447

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]

 290 PRO   ( 290-)  A    0.46 HIGH
 832 PRO   ( 380-)  B    0.45 HIGH
1365 PRO   (   9-)  D    0.46 HIGH
1599 PRO   ( 243-)  D    0.45 HIGH
1817 PRO   (   9-)  E    0.45 HIGH

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].

   9 PRO   (   9-)  A  -125.4 half-chair C-delta/C-gamma (-126 degrees)
 971 PRO   (  67-)  C  -112.0 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

2545 OADE  (   8-)  I      N6  <-> 2558 OURA  (  21-)  I      O4     0.50    2.20  INTRA BF
2269 OADE  (   8-)  F      N6  <-> 2282 OURA  (  21-)  F      O4     0.48    2.22  INTRA BF
 615 ARG   ( 163-)  B      NH1 <-> 1092 GLU   ( 188-)  C      OE1    0.48    2.22  INTRA BF
2384 OADE  (  31-)  G      N7  <-> 2385 OCYT  (  32-)  G      C4     0.46    2.64  INTRA BF
  68 ASN   (  68-)  A      ND2 <->  574 HIS   ( 122-)  B      CD2    0.46    2.64  INTRA BF
1189 LLP   ( 285-)  C      OP3 <-> 1668 ARG   ( 312-)  D      NH2    0.44    2.26  INTRA BL
2637 OADE  (   8-)  J      N6  <-> 2650 OURA  (  21-)  J      O4     0.44    2.26  INTRA BF
 409 ARG   ( 409-)  A      NH1 <->  413 LEU   ( 413-)  A      CD1    0.43    2.67  INTRA BL
 171 GLY   ( 171-)  A      CA  <->  568 ARG   ( 116-)  B      NH2    0.43    2.67  INTRA BL
2361 OADE  (   8-)  G      N6  <-> 2374 OURA  (  21-)  G      O4     0.43    2.27  INTRA BF
2636 OGUA  (   7-)  J      N1  <-> 2712 OADE  (  66-)  J      N1     0.42    2.58  INTRA BF
 401 ARG   ( 401-)  A      NH1 <->  450 LEU   ( 450-)  A      O      0.42    2.28  INTRA BL
2544 OGUA  (   7-)  I      N1  <-> 2620 OADE  (  66-)  I      N1     0.41    2.59  INTRA BF
2543 OADE  (   6-)  I      N1  <-> 2621 OURA  (  67-)  I      N3     0.40    2.60  INTRA BF
2451 OADE  (   6-)  H      N1  <-> 2529 OURA  (  67-)  H      N3     0.39    2.61  INTRA BF
2360 OGUA  (   7-)  G      N1  <-> 2436 OADE  (  66-)  G      N1     0.39    2.61  INTRA BF
 462 GLN   (  10-)  B      NE2 <-> 2279 OGUA  (  19-)  F      OP1    0.39    2.31  INTRA BF
2267 OADE  (   6-)  F      N1  <-> 2345 OURA  (  67-)  F      N3     0.39    2.61  INTRA BF
 484 ARG   (  32-)  B      NH1 <-> 2278 OGUA  (  18-)  F      OP1    0.38    2.32  INTRA BF
2268 OGUA  (   7-)  F      N1  <-> 2344 OADE  (  66-)  F      N1     0.38    2.62  INTRA BF
2635 OADE  (   6-)  J      N1  <-> 2713 OURA  (  67-)  J      N3     0.38    2.62  INTRA BF
1357 MET   (   1-)  D      CG  <-> 1358 LYS   (   2-)  D      N      0.38    2.62  INTRA BL
1189 LLP   ( 285-)  C      OP1 <-> 1668 ARG   ( 312-)  D      NH1    0.37    2.33  INTRA BL
1003 GLU   (  99-)  C      O   <-> 1427 ARG   (  71-)  D      NH2    0.37    2.33  INTRA BF
2452 OGUA  (   7-)  H      N1  <-> 2528 OADE  (  66-)  H      N1     0.36    2.64  INTRA BF
And so on for a total of 1176 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

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.

1912 TYR   ( 104-)  E      -8.94
1879 ARG   (  71-)  E      -7.16
 568 ARG   ( 116-)  B      -6.67
1757 ARG   ( 401-)  D      -6.55
 853 ARG   ( 401-)  B      -6.44
2209 ARG   ( 401-)  E      -6.39
1305 ARG   ( 401-)  C      -6.35
1472 ARG   ( 116-)  D      -6.25
 401 ARG   ( 401-)  A      -6.25
1924 ARG   ( 116-)  E      -6.21
 415 GLU   ( 415-)  A      -6.12
 867 GLU   ( 415-)  B      -6.11
1319 GLU   ( 415-)  C      -6.04
 116 ARG   ( 116-)  A      -5.99
1771 GLU   ( 415-)  D      -5.96
1020 ARG   ( 116-)  C      -5.92
2223 GLU   ( 415-)  E      -5.87
1877 ILE   (  69-)  E      -5.68
 875 ARG   ( 423-)  B      -5.64
1442 ARG   (  86-)  D      -5.57
1327 ARG   ( 423-)  C      -5.52
1910 ASN   ( 102-)  E      -5.51
2099 GLN   ( 291-)  E      -5.39
  86 ARG   (  86-)  A      -5.38
 221 MET   ( 221-)  A      -5.34
 222 GLU   ( 222-)  A      -5.34
 538 ARG   (  86-)  B      -5.33
 287 LEU   ( 287-)  A      -5.33
2231 ARG   ( 423-)  E      -5.29
1779 ARG   ( 423-)  D      -5.28
 739 LEU   ( 287-)  B      -5.27
1019 LYS   ( 115-)  C      -5.25
 990 ARG   (  86-)  C      -5.21
1471 LYS   ( 115-)  D      -5.19
1894 ARG   (  86-)  E      -5.18
 911 GLN   (   7-)  C      -5.16
 567 LYS   ( 115-)  B      -5.14
1815 GLN   (   7-)  E      -5.12
1458 ASN   ( 102-)  D      -5.09
1006 ASN   ( 102-)  C      -5.08
 554 ASN   ( 102-)  B      -5.08
 115 LYS   ( 115-)  A      -5.05
1930 HIS   ( 122-)  E      -5.04
 102 ASN   ( 102-)  A      -5.03
2095 LEU   ( 287-)  E      -5.00

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.

 220 TYR   ( 220-)  A       222 - GLU    222- ( A)         -5.15
 238 HIS   ( 238-)  A       240 - TYR    240- ( A)         -4.25
 690 HIS   ( 238-)  B       692 - TYR    240- ( B)         -4.45
1142 HIS   ( 238-)  C      1144 - TYR    240- ( C)         -4.44
1594 HIS   ( 238-)  D      1596 - TYR    240- ( D)         -4.34
2046 HIS   ( 238-)  E      2048 - TYR    240- ( E)         -4.30

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

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: E

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.

  19 ALA   (  19-)  A   -2.71
 471 ALA   (  19-)  B   -2.70
1375 ALA   (  19-)  D   -2.70
 923 ALA   (  19-)  C   -2.70
1827 ALA   (  19-)  E   -2.70

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

Note: Second generation quality Z-score plot

Chain identifier: E

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.

 122 HIS   ( 122-)  A
 574 HIS   ( 122-)  B
 799 GLN   ( 347-)  B
1026 HIS   ( 122-)  C
1478 HIS   ( 122-)  D
2155 GLN   ( 347-)  E

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.

   3 SER   (   3-)  A      N
   5 LEU   (   5-)  A      N
   6 ARG   (   6-)  A      N
   7 GLN   (   7-)  A      N
   8 ILE   (   8-)  A      N
  10 GLN   (  10-)  A      N
  10 GLN   (  10-)  A      NE2
  12 SER   (  12-)  A      OG
  22 TYR   (  22-)  A      N
  45 GLY   (  45-)  A      N
  54 LEU   (  54-)  A      N
  74 ASN   (  74-)  A      ND2
  80 ILE   (  80-)  A      N
  90 SER   (  90-)  A      OG
 103 GLY   ( 103-)  A      N
 107 LEU   ( 107-)  A      N
 113 GLU   ( 113-)  A      N
 115 LYS   ( 115-)  A      N
 120 ILE   ( 120-)  A      N
 123 ILE   ( 123-)  A      N
 125 LYS   ( 125-)  A      N
 138 VAL   ( 138-)  A      N
 141 ASN   ( 141-)  A      N
 141 ASN   ( 141-)  A      ND2
 142 ASN   ( 142-)  A      N
And so on for a total of 319 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.

 128 ASN   ( 128-)  A      OD1
 247 ASP   ( 247-)  A      OD2
 699 ASP   ( 247-)  B      OD2
1032 ASN   ( 128-)  C      OD1
1151 ASP   ( 247-)  C      OD1
1151 ASP   ( 247-)  C      OD2
1366 GLN   (  10-)  D      OE1
1380 GLU   (  24-)  D      OE2
1484 ASN   ( 128-)  D      OD1
1603 ASP   ( 247-)  D      OD2
1818 GLN   (  10-)  E      OE1
1900 ASP   (  92-)  E      OD2
1950 ASN   ( 142-)  E      OD1
2055 ASP   ( 247-)  E      OD2
2146 ASP   ( 338-)  E      OD2

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.

  16 GLU   (  16-)  A   H-bonding suggests Gln
  56 ASP   (  56-)  A   H-bonding suggests Asn; but Alt-Rotamer
 108 GLU   ( 108-)  A   H-bonding suggests Gln; but Alt-Rotamer
 438 ASP   ( 438-)  A   H-bonding suggests Asn
 508 ASP   (  56-)  B   H-bonding suggests Asn; but Alt-Rotamer
 717 GLU   ( 265-)  B   H-bonding suggests Gln
 960 ASP   (  56-)  C   H-bonding suggests Asn; but Alt-Rotamer
1412 ASP   (  56-)  D   H-bonding suggests Asn; but Alt-Rotamer
1521 GLU   ( 165-)  D   H-bonding suggests Gln; but Alt-Rotamer
1555 ASP   ( 199-)  D   H-bonding suggests Asn; but Alt-Rotamer
1621 GLU   ( 265-)  D   H-bonding suggests Gln
1864 ASP   (  56-)  E   H-bonding suggests Asn; but Alt-Rotamer
1973 GLU   ( 165-)  E   H-bonding suggests Gln; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.595
  2nd generation packing quality :  -1.452
  Ramachandran plot appearance   :  -3.280 (poor)
  chi-1/chi-2 rotamer normality  :  -2.454
  Backbone conformation          :  -0.231

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.409 (tight)
  Bond angles                    :   0.647 (tight)
  Omega angle restraints         :   0.263 (tight)
  Side chain planarity           :   0.279 (tight)
  Improper dihedral distribution :   0.664
  Inside/Outside distribution    :   0.979

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 : 7.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.3
  2nd generation packing quality :  -0.7
  Ramachandran plot appearance   :  -1.6
  chi-1/chi-2 rotamer normality  :  -1.2
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.409 (tight)
  Bond angles                    :   0.647 (tight)
  Omega angle restraints         :   0.263 (tight)
  Side chain planarity           :   0.279 (tight)
  Improper dihedral distribution :   0.664
  Inside/Outside distribution    :   0.979
==============

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.