WHAT IF Check report

This file was created 2012-01-30 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 pdb3cmu.ent

Checks that need to be done early-on in validation

Warning: Topology could not be determined for some ligands

Some ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

1954 ALF   ( 501-)  A  -         Atom types
1956 ALF   (1501-)  A  -         Atom types
1958 ALF   (2501-)  A  -         Atom types
1960 ALF   (3501-)  A  -         Atom types
1962 ALF   (4501-)  A  -         Atom types
1964 ALF   (5501-)  A  -         Atom types
1965 ADP   (1502-)  A  -         OK
1966 ADP   (2502-)  A  -         OK
1967 ADP   (3502-)  A  -         OK
1968 ADP   (4502-)  A  -         OK
1969 ADP   (5502-)  A  -         OK
1970 ADP   ( 502-)  A  -         OK

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

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 DTHY  (1002-)  B    High
   2 DTHY  (1003-)  B    High
   3 DTHY  (1004-)  B    High
   4 DTHY  (1005-)  B    High
   5 DTHY  (1006-)  B    High
   6 DTHY  (1007-)  B    High
   7 DTHY  (1008-)  B    High
   8 DTHY  (1009-)  B    High
   9 DTHY  (1010-)  B    High
  10 DTHY  (1011-)  B    High
  11 DTHY  (1012-)  B    High
  12 DTHY  (1013-)  B    High
  13 DTHY  (1014-)  B    High
  14 DTHY  (1015-)  B    High
  15 DTHY  (1016-)  B    High
  16 VAL   (  37-)  A    High
  17 GLU   (  38-)  A    High
  18 THR   (  39-)  A    High
  19 ILE   (  40-)  A    High
  20 SER   (  41-)  A    High
  21 THR   (  42-)  A    High
  22 GLY   (  43-)  A    High
  23 SER   (  44-)  A    High
  24 LEU   (  45-)  A    High
  25 SER   (  46-)  A    High
And so on for a total of 1952 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

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Note: B-factor plot

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

Chain identifier: A

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

 197 TYR   ( 218-)  A
 250 TYR   ( 271-)  A
 525 TYR   (1218-)  A
 578 TYR   (1271-)  A
 858 TYR   (2218-)  A
 911 TYR   (2271-)  A
1191 TYR   (3218-)  A
1244 TYR   (3271-)  A
1524 TYR   (4218-)  A
1577 TYR   (4271-)  A
1842 TYR   (5218-)  A
1895 TYR   (5271-)  A

Warning: Phenylalanine convention problem

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

  71 PHE   (  92-)  A
 170 PHE   ( 191-)  A
 182 PHE   ( 203-)  A
 239 PHE   ( 260-)  A
 249 PHE   ( 270-)  A
 399 PHE   (1092-)  A
 498 PHE   (1191-)  A
 510 PHE   (1203-)  A
 567 PHE   (1260-)  A
 577 PHE   (1270-)  A
 732 PHE   (2092-)  A
 831 PHE   (2191-)  A
 843 PHE   (2203-)  A
 900 PHE   (2260-)  A
 910 PHE   (2270-)  A
1065 PHE   (3092-)  A
1164 PHE   (3191-)  A
1176 PHE   (3203-)  A
1233 PHE   (3260-)  A
1243 PHE   (3270-)  A
1398 PHE   (4092-)  A
1509 PHE   (4203-)  A
1566 PHE   (4260-)  A
1576 PHE   (4270-)  A
1731 PHE   (5092-)  A
1823 PHE   (5191-)  A
1884 PHE   (5260-)  A
1894 PHE   (5270-)  A

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.

  79 ASP   ( 100-)  A
  89 ASP   ( 110-)  A
 407 ASP   (1100-)  A
 417 ASP   (1110-)  A
 740 ASP   (2100-)  A
 750 ASP   (2110-)  A
1073 ASP   (3100-)  A
1083 ASP   (3110-)  A
1406 ASP   (4100-)  A
1416 ASP   (4110-)  A
1739 ASP   (5100-)  A
1749 ASP   (5110-)  A

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.

  47 GLU   (  68-)  A
 106 GLU   ( 127-)  A
 133 GLU   ( 154-)  A
 135 GLU   ( 156-)  A
 245 GLU   ( 266-)  A
 325 GLU   (1018-)  A
 375 GLU   (1068-)  A
 434 GLU   (1127-)  A
 461 GLU   (1154-)  A
 463 GLU   (1156-)  A
 465 GLU   (1158-)  A
 573 GLU   (1266-)  A
 658 GLU   (2018-)  A
 708 GLU   (2068-)  A
 767 GLU   (2127-)  A
 794 GLU   (2154-)  A
 796 GLU   (2156-)  A
 798 GLU   (2158-)  A
 906 GLU   (2266-)  A
 991 GLU   (3018-)  A
1041 GLU   (3068-)  A
1100 GLU   (3127-)  A
1127 GLU   (3154-)  A
1129 GLU   (3156-)  A
1131 GLU   (3158-)  A
1239 GLU   (3266-)  A
1324 GLU   (4018-)  A
1374 GLU   (4068-)  A
1433 GLU   (4127-)  A
1460 GLU   (4154-)  A
1462 GLU   (4156-)  A
1464 GLU   (4158-)  A
1572 GLU   (4266-)  A
1657 GLU   (5018-)  A
1707 GLU   (5068-)  A
1766 GLU   (5127-)  A
1793 GLU   (5154-)  A
1795 GLU   (5156-)  A
1890 GLU   (5266-)  A

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.

   1 DTHY  (1002-)  B      C3'  O3'   1.49    4.3
   1 DTHY  (1002-)  B      C1'  N1    1.57    7.0
   1 DTHY  (1002-)  B      N1   C6    1.42    5.7
   1 DTHY  (1002-)  B      N1   C2    1.42    5.6
   1 DTHY  (1002-)  B      N3   C2    1.41    4.9
   1 DTHY  (1002-)  B      C4   N3    1.44    6.6
   2 DTHY  (1003-)  B      C1'  N1    1.54    4.7
   5 DTHY  (1006-)  B      C1'  N1    1.54    4.5
   5 DTHY  (1006-)  B      N1   C6    1.41    4.3
   6 DTHY  (1007-)  B      C3'  O3'   1.38   -4.2
   7 DTHY  (1008-)  B      C5   C7    1.52    4.2
   8 DTHY  (1009-)  B      C1'  N1    1.54    4.7
   9 DTHY  (1010-)  B      O5'  C5'   1.37   -4.1
   9 DTHY  (1010-)  B      C1'  N1    1.53    4.2
  11 DTHY  (1012-)  B      C3'  O3'   1.37   -4.5
  11 DTHY  (1012-)  B      C1'  N1    1.54    4.8
  11 DTHY  (1012-)  B      N1   C6    1.41    4.5
  12 DTHY  (1013-)  B      C1'  N1    1.53    4.3
  12 DTHY  (1013-)  B      N1   C6    1.41    4.0
  14 DTHY  (1015-)  B      C1'  N1    1.54    4.6
  14 DTHY  (1015-)  B      N1   C2    1.41    4.0
  15 DTHY  (1016-)  B      C1'  N1    1.53    4.3
 248 ASN   ( 269-)  A      N   -C     1.43    5.0
1794 ILE   (5155-)  A      CA   CB    1.61    4.1

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.997406 -0.000327  0.000822|
 | -0.000327  0.997273 -0.000561|
 |  0.000822 -0.000561  0.998742|
Proposed new scale matrix

 |  0.006428  0.003713 -0.000003|
 |  0.000002  0.007422  0.000004|
 | -0.000004  0.000003  0.004745|
With corresponding cell

    A    = 155.602  B   = 155.624  C    = 210.750
    Alpha=  90.103  Beta=  89.906  Gamma= 120.033

The CRYST1 cell dimensions

    A    = 156.000  B   = 156.000  C    = 211.000
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 353.247
(Under-)estimated Z-score: 13.852

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.

   1 DTHY  (1002-)  B      C2'  C1'  N1  123.80    6.0
   1 DTHY  (1002-)  B      C1'  N1   C6  113.19   -4.8
   1 DTHY  (1002-)  B      C1'  N1   C2  126.94    5.5
   1 DTHY  (1002-)  B      N1   C6   C5  127.44    6.2
   1 DTHY  (1002-)  B      N1   C2   N3  112.08   -4.2
   1 DTHY  (1002-)  B      C5   C4   O4  120.04   -6.9
   1 DTHY  (1002-)  B      C4   N3   C2  129.71    4.2
   1 DTHY  (1002-)  B      O4   C4   N3  125.33    9.1
   2 DTHY  (1003-)  B      O4'  C1'  N1  111.97    5.2
   2 DTHY  (1003-)  B      C5   C4   O4  120.09   -6.9
   2 DTHY  (1003-)  B      O4   C4   N3  124.33    7.4
   3 DTHY  (1004-)  B      OP2  P   -O3*  94.77   -4.2
   3 DTHY  (1004-)  B      P   -C3* -O3* 128.80    7.6
   3 DTHY  (1004-)  B      O5'  C5'  C4' 104.41   -4.1
   3 DTHY  (1004-)  B      O4   C4   N3  122.71    4.7
   4 DTHY  (1005-)  B      C4'  C3'  C2'  97.78   -5.4
   4 DTHY  (1005-)  B      O4'  C1'  N1  114.69    8.6
   4 DTHY  (1005-)  B      O4   C4   N3  122.44    4.2
   5 DTHY  (1006-)  B      P   -C3* -O3* 127.40    6.4
   5 DTHY  (1006-)  B      O4'  C1'  N1  111.51    4.6
   5 DTHY  (1006-)  B      C5   C4   O4  119.59   -7.6
   5 DTHY  (1006-)  B      O4   C4   N3  123.71    6.3
   6 DTHY  (1007-)  B      O5*  P   -O3*  93.76   -5.4
   6 DTHY  (1007-)  B      O5'  C5'  C4' 104.57   -4.0
   6 DTHY  (1007-)  B      O4   C4   N3  123.04    5.2
And so on for a total of 57 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.

  47 GLU   (  68-)  A
  79 ASP   ( 100-)  A
  89 ASP   ( 110-)  A
 106 GLU   ( 127-)  A
 133 GLU   ( 154-)  A
 135 GLU   ( 156-)  A
 245 GLU   ( 266-)  A
 325 GLU   (1018-)  A
 375 GLU   (1068-)  A
 407 ASP   (1100-)  A
 417 ASP   (1110-)  A
 434 GLU   (1127-)  A
 461 GLU   (1154-)  A
 463 GLU   (1156-)  A
 465 GLU   (1158-)  A
 573 GLU   (1266-)  A
 658 GLU   (2018-)  A
 708 GLU   (2068-)  A
 740 ASP   (2100-)  A
 750 ASP   (2110-)  A
 767 GLU   (2127-)  A
 794 GLU   (2154-)  A
 796 GLU   (2156-)  A
 798 GLU   (2158-)  A
 906 GLU   (2266-)  A
And so on for a total of 51 lines.

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.

1798 LEU   (5166-)  A    5.48
1139 LEU   (3166-)  A    5.29
1472 LEU   (4166-)  A    5.04
 806 LEU   (2166-)  A    5.01
 145 LEU   ( 166-)  A    4.82
 473 LEU   (1166-)  A    4.77

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 : -3.522

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.

1049 THR   (3076-)  A    -3.2
 716 THR   (2076-)  A    -3.2
1382 THR   (4076-)  A    -3.2
1715 THR   (5076-)  A    -3.2
  55 THR   (  76-)  A    -3.1
 383 THR   (1076-)  A    -3.1
1636 ASN   (4330-)  A    -2.5
 637 ASN   (1330-)  A    -2.5
1303 ASN   (3330-)  A    -2.5
 970 ASN   (2330-)  A    -2.5
 654 LEU   (2014-)  A    -2.5
1653 LEU   (5014-)  A    -2.4
 187 THR   ( 208-)  A    -2.4
 515 THR   (1208-)  A    -2.4
1514 THR   (4208-)  A    -2.4
1832 THR   (5208-)  A    -2.4
 178 ILE   ( 199-)  A    -2.4
1320 LEU   (4014-)  A    -2.4
1181 THR   (3208-)  A    -2.4
 321 LEU   (1014-)  A    -2.4
 848 THR   (2208-)  A    -2.4
 987 LEU   (3014-)  A    -2.4
1510 GLY   (4204-)  A    -2.4
 511 GLY   (1204-)  A    -2.4
1177 GLY   (3204-)  A    -2.4
And so on for a total of 71 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.

  31 GLY   (  52-)  A  Poor phi/psi
  48 SER   (  69-)  A  Poor phi/psi
  50 GLY   (  71-)  A  Poor phi/psi
  73 ASP   (  94-)  A  Poor phi/psi
 124 SER   ( 145-)  A  Poor phi/psi
 142 HIS   ( 163-)  A  omega poor
 226 VAL   ( 247-)  A  omega poor
 231 ALA   ( 252-)  A  Poor phi/psi
 234 PHE   ( 255-)  A  Poor phi/psi
 261 LYS   ( 282-)  A  Poor phi/psi
 327 GLN   (1020-)  A  omega poor
 330 LYS   (1023-)  A  Poor phi/psi
 359 GLY   (1052-)  A  Poor phi/psi
 376 SER   (1069-)  A  Poor phi/psi
 378 GLY   (1071-)  A  Poor phi/psi
 401 ASP   (1094-)  A  Poor phi/psi
 452 SER   (1145-)  A  Poor phi/psi
 510 PHE   (1203-)  A  omega poor
 511 GLY   (1204-)  A  Poor phi/psi
 538 VAL   (1231-)  A  omega poor
 554 VAL   (1247-)  A  omega poor
 559 ALA   (1252-)  A  Poor phi/psi
 562 PHE   (1255-)  A  Poor phi/psi
 579 GLY   (1272-)  A  Poor phi/psi
 589 LYS   (1282-)  A  Poor phi/psi
And so on for a total of 88 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 : -4.463

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.

 353 SER   (1046-)  A    0.35
1019 SER   (3046-)  A    0.36
1685 SER   (5046-)  A    0.36
  25 SER   (  46-)  A    0.37
 686 SER   (2046-)  A    0.37
1352 SER   (4046-)  A    0.37

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!

   3 DTHY  (1004-)  B      0
   4 DTHY  (1005-)  B      0
   5 DTHY  (1006-)  B      0
   6 DTHY  (1007-)  B      0
   7 DTHY  (1008-)  B      0
   8 DTHY  (1009-)  B      0
   9 DTHY  (1010-)  B      0
  10 DTHY  (1011-)  B      0
  11 DTHY  (1012-)  B      0
  12 DTHY  (1013-)  B      0
  13 DTHY  (1014-)  B      0
  14 DTHY  (1015-)  B      0
  15 DTHY  (1016-)  B      0
  16 VAL   (  37-)  A      0
  17 GLU   (  38-)  A      0
  21 THR   (  42-)  A      0
  35 LEU   (  56-)  A      0
  37 MET   (  58-)  A      0
  44 TYR   (  65-)  A      0
  47 GLU   (  68-)  A      0
  48 SER   (  69-)  A      0
  49 SER   (  70-)  A      0
  65 GLU   (  86-)  A      0
  73 ASP   (  94-)  A      0
  74 ALA   (  95-)  A      0
And so on for a total of 649 lines.

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].

  80 PRO   ( 101-)  A  -124.7 half-chair C-delta/C-gamma (-126 degrees)
 408 PRO   (1101-)  A  -124.4 half-chair C-delta/C-gamma (-126 degrees)
 741 PRO   (2101-)  A  -124.2 half-chair C-delta/C-gamma (-126 degrees)
1074 PRO   (3101-)  A  -124.5 half-chair C-delta/C-gamma (-126 degrees)
1407 PRO   (4101-)  A  -124.9 half-chair C-delta/C-gamma (-126 degrees)
1740 PRO   (5101-)  A  -124.5 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.

1953  MG   ( 500-)  A     MG   <-> 1954 ALF   ( 501-)  A      F2     1.05    1.95  INTRA BL
1955  MG   (1500-)  A     MG   <-> 1956 ALF   (1501-)  A      F2     1.05    1.95  INTRA BL
1957  MG   (2500-)  A     MG   <-> 1958 ALF   (2501-)  A      F2     1.03    1.97  INTRA BL
1959  MG   (3500-)  A     MG   <-> 1960 ALF   (3501-)  A      F2     1.03    1.97  INTRA BL
1961  MG   (4500-)  A     MG   <-> 1962 ALF   (4501-)  A      F2     1.02    1.98  INTRA BL
 555 LYS   (1248-)  A      NZ  <-> 1954 ALF   ( 501-)  A      F1     0.93    2.17  INTRA BL
1956 ALF   (1501-)  A      F2  <-> 1965 ADP   (1502-)  A      O1B    0.92    1.88  INTRA BL
1954 ALF   ( 501-)  A      F3  <-> 1970 ADP   ( 502-)  A      O3B    0.90    1.90  INTRA BL
1958 ALF   (2501-)  A      F3  <-> 1966 ADP   (2502-)  A      O3B    0.89    1.91  INTRA BL
1221 LYS   (3248-)  A      NZ  <-> 1958 ALF   (2501-)  A      F1     0.89    2.21  INTRA BL
1958 ALF   (2501-)  A      F2  <-> 1966 ADP   (2502-)  A      O1B    0.85    1.95  INTRA BL
1962 ALF   (4501-)  A      F2  <-> 1968 ADP   (4502-)  A      O1B    0.84    1.96  INTRA BL
1960 ALF   (3501-)  A      F2  <-> 1967 ADP   (3502-)  A      O1B    0.82    1.98  INTRA BL
  75 GLU   (  96-)  A      OE2 <-> 1954 ALF   ( 501-)  A      F4     0.81    1.99  INTRA BL
1554 LYS   (4248-)  A      NZ  <-> 1960 ALF   (3501-)  A      F1     0.80    2.30  INTRA BL
1956 ALF   (1501-)  A      F3  <-> 1965 ADP   (1502-)  A      O3B    0.79    2.01  INTRA BF
1960 ALF   (3501-)  A      F3  <-> 1967 ADP   (3502-)  A      O3B    0.79    2.01  INTRA BL
1954 ALF   ( 501-)  A      F2  <-> 1970 ADP   ( 502-)  A      O1B    0.78    2.02  INTRA BL
 888 LYS   (2248-)  A      NZ  <-> 1956 ALF   (1501-)  A      F1     0.78    2.32  INTRA BF
1963  MG   (5500-)  A     MG   <-> 1964 ALF   (5501-)  A      F2     0.77    2.23  INTRA BL
1958 ALF   (2501-)  A      F3  <-> 1966 ADP   (2502-)  A      PB     0.76    2.64  INTRA BL
1962 ALF   (4501-)  A      F3  <-> 1968 ADP   (4502-)  A      O3B    0.75    2.05  INTRA BL
1954 ALF   ( 501-)  A      F3  <-> 1970 ADP   ( 502-)  A      PB     0.73    2.67  INTRA BL
1962 ALF   (4501-)  A      F3  <-> 1968 ADP   (4502-)  A      PB     0.69    2.71  INTRA BL
1707 GLU   (5068-)  A      CA  <-> 1964 ALF   (5501-)  A      F1     0.68    2.52  INTRA BL
And so on for a total of 486 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

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.

 509 MET   (1202-)  A      -7.40
 842 MET   (2202-)  A      -7.37
1175 MET   (3202-)  A      -7.35
1508 MET   (4202-)  A      -7.31
 181 MET   ( 202-)  A      -6.87
 143 MET   ( 164-)  A      -6.66
 182 PHE   ( 203-)  A      -6.07
1851 ARG   (5227-)  A      -6.05
 206 ARG   ( 227-)  A      -5.84
1533 ARG   (4227-)  A      -5.82
 534 ARG   (1227-)  A      -5.81
 471 MET   (1164-)  A      -5.78
1200 ARG   (3227-)  A      -5.76
 867 ARG   (2227-)  A      -5.71
1505 ILE   (4199-)  A      -5.71
 804 MET   (2164-)  A      -5.68
 838 LYS   (2198-)  A      -5.64
1504 LYS   (4198-)  A      -5.63
 972 ASN   (2332-)  A      -5.61
 113 ARG   ( 134-)  A      -5.60
1107 ARG   (3134-)  A      -5.60
1440 ARG   (4134-)  A      -5.60
 774 ARG   (2134-)  A      -5.59
 505 LYS   (1198-)  A      -5.59
 441 ARG   (1134-)  A      -5.59
And so on for a total of 55 lines.

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

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.

 874 GLY   (2234-)  A   -2.81
 541 GLY   (1234-)  A   -2.73
1207 GLY   (3234-)  A   -2.66
1170 MET   (3197-)  A   -2.56
1454 ALA   (4148-)  A   -2.54
 127 ALA   ( 148-)  A   -2.53
 455 ALA   (1148-)  A   -2.52
1121 ALA   (3148-)  A   -2.52
 788 ALA   (2148-)  A   -2.50

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.

1502 ARG   (4196-)  A     - 1505 ILE   (4199-)  A        -1.98

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

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.

 160 ASN   ( 181-)  A
 172 ASN   ( 193-)  A
 173 GLN   ( 194-)  A
 192 ASN   ( 213-)  A
 470 HIS   (1163-)  A
 480 GLN   (1173-)  A
 488 ASN   (1181-)  A
 500 ASN   (1193-)  A
 501 GLN   (1194-)  A
 803 HIS   (2163-)  A
 813 GLN   (2173-)  A
 821 ASN   (2181-)  A
 833 ASN   (2193-)  A
 834 GLN   (2194-)  A
 944 ASN   (2304-)  A
1136 HIS   (3163-)  A
1146 GLN   (3173-)  A
1154 ASN   (3181-)  A
1166 ASN   (3193-)  A
1167 GLN   (3194-)  A
1479 GLN   (4173-)  A
1487 ASN   (4181-)  A
1499 ASN   (4193-)  A
1500 GLN   (4194-)  A
1610 ASN   (4304-)  A
1805 GLN   (5173-)  A
1813 ASN   (5181-)  A
1825 ASN   (5193-)  A
1826 GLN   (5194-)  A
1928 ASN   (5304-)  A

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.

  11 DTHY  (1012-)  B      N3
  14 DTHY  (1015-)  B      N3
  32 ALA   (  53-)  A      N
  34 GLY   (  55-)  A      N
  38 GLY   (  59-)  A      N
  40 ILE   (  61-)  A      N
  47 GLU   (  68-)  A      N
  49 SER   (  70-)  A      OG
  51 LYS   (  72-)  A      NZ
  52 THR   (  73-)  A      N
  55 THR   (  76-)  A      OG1
  69 CYS   (  90-)  A      N
  77 ALA   (  98-)  A      N
  82 TYR   ( 103-)  A      OH
  97 GLN   ( 118-)  A      NE2
 100 THR   ( 121-)  A      N
 124 SER   ( 145-)  A      OG
 126 ALA   ( 147-)  A      N
 131 LYS   ( 152-)  A      N
 138 ILE   ( 159-)  A      N
 142 HIS   ( 163-)  A      N
 147 ALA   ( 168-)  A      N
 164 SER   ( 185-)  A      N
 173 GLN   ( 194-)  A      NE2
 174 ILE   ( 195-)  A      N
And so on for a total of 256 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.

  73 ASP   (  94-)  A      OD1
  75 GLU   (  96-)  A      OE1
  75 GLU   (  96-)  A      OE2
  76 HIS   (  97-)  A      ND1
 123 ASP   ( 144-)  A      OD1
 123 ASP   ( 144-)  A      OD2
 401 ASP   (1094-)  A      OD1
 403 GLU   (1096-)  A      OE1
 404 HIS   (1097-)  A      ND1
 407 ASP   (1100-)  A      OD2
 451 ASP   (1144-)  A      OD1
 451 ASP   (1144-)  A      OD2
 734 ASP   (2094-)  A      OD1
 736 GLU   (2096-)  A      OE1
 736 GLU   (2096-)  A      OE2
 737 HIS   (2097-)  A      ND1
 784 ASP   (2144-)  A      OD1
 784 ASP   (2144-)  A      OD2
1067 ASP   (3094-)  A      OD1
1069 GLU   (3096-)  A      OE1
1070 HIS   (3097-)  A      ND1
1073 ASP   (3100-)  A      OD2
1117 ASP   (3144-)  A      OD1
1117 ASP   (3144-)  A      OD2
1400 ASP   (4094-)  A      OD1
1402 GLU   (4096-)  A      OE1
1402 GLU   (4096-)  A      OE2
1403 HIS   (4097-)  A      ND1
1433 GLU   (4127-)  A      OE1
1450 ASP   (4144-)  A      OD1
1450 ASP   (4144-)  A      OD2
1659 GLN   (5020-)  A      OE1
1733 ASP   (5094-)  A      OD1
1735 GLU   (5096-)  A      OE1
1752 ASN   (5113-)  A      OD1
1783 ASP   (5144-)  A      OD1
1783 ASP   (5144-)  A      OD2

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

1953  MG   ( 500-)  A   -.-  -.-  Low probability ion. B=162.4
1955  MG   (1500-)  A   -.-  -.-  Low probability ion. B=186.2
1957  MG   (2500-)  A   -.-  -.-  Low probability ion. B=177.4
1959  MG   (3500-)  A   -.-  -.-  Low probability ion. B=180.4
1961  MG   (4500-)  A   -.-  -.-  Low probability ion. B=162.1
1963  MG   (5500-)  A   -.-  -.-  Part of ionic cluster
1963  MG   (5500-)  A     0.52   1.03 Is perhaps NA (Few ligands (4) ) *2
Since there are no waters, the water check has been skipped.

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

  27 ASP   (  48-)  A   H-bonding suggests Asn; but Alt-Rotamer
 355 ASP   (1048-)  A   H-bonding suggests Asn; but Alt-Rotamer
 407 ASP   (1100-)  A   H-bonding suggests Asn; Ligand-contact
 580 GLU   (1273-)  A   H-bonding suggests Gln; but Alt-Rotamer
 740 ASP   (2100-)  A   H-bonding suggests Asn; Ligand-contact
 913 GLU   (2273-)  A   H-bonding suggests Gln; but Alt-Rotamer
1021 ASP   (3048-)  A   H-bonding suggests Asn
1073 ASP   (3100-)  A   H-bonding suggests Asn; Ligand-contact
1246 GLU   (3273-)  A   H-bonding suggests Gln; but Alt-Rotamer
1354 ASP   (4048-)  A   H-bonding suggests Asn; but Alt-Rotamer
1579 GLU   (4273-)  A   H-bonding suggests Gln; but Alt-Rotamer
1687 ASP   (5048-)  A   H-bonding suggests Asn; 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 :  -0.486
  2nd generation packing quality :  -1.516
  Ramachandran plot appearance   :  -3.522 (poor)
  chi-1/chi-2 rotamer normality  :  -4.463 (bad)
  Backbone conformation          :   0.158

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.623 (tight)
  Bond angles                    :   0.759
  Omega angle restraints         :   1.024
  Side chain planarity           :   0.373 (tight)
  Improper dihedral distribution :   0.633
  Inside/Outside distribution    :   0.993

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 : 4.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.8
  2nd generation packing quality :   0.5
  Ramachandran plot appearance   :  -0.6
  chi-1/chi-2 rotamer normality  :  -2.0
  Backbone conformation          :   1.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.623 (tight)
  Bond angles                    :   0.759
  Omega angle restraints         :   1.024
  Side chain planarity           :   0.373 (tight)
  Improper dihedral distribution :   0.633
  Inside/Outside distribution    :   0.993
==============

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.