WHAT IF Check report

This file was created 2011-12-13 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 pdb1bxb.ent

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

  65 GLN   (  65-)  A      CG
  65 GLN   (  65-)  A      CD
  65 GLN   (  65-)  A      OE1
  65 GLN   (  65-)  A      NE2
 452 GLN   (  65-)  B      CG
 452 GLN   (  65-)  B      CD
 452 GLN   (  65-)  B      OE1
 452 GLN   (  65-)  B      NE2
 839 GLN   (  65-)  C      CG
 839 GLN   (  65-)  C      CD
 839 GLN   (  65-)  C      OE1
 839 GLN   (  65-)  C      NE2
1226 GLN   (  65-)  D      CG
1226 GLN   (  65-)  D      CD
1226 GLN   (  65-)  D      OE1
1226 GLN   (  65-)  D      NE2

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) :287.000

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 17.21

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

Geometric checks

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

 |  0.998967  0.000318  0.000063|
 |  0.000318  1.000355 -0.000089|
 |  0.000063 -0.000089  0.998858|
Proposed new scale matrix

 |  0.013649 -0.000004  0.000000|
 | -0.000002  0.006940  0.000000|
 |  0.000000  0.000000  0.006456|
With corresponding cell

    A    =  73.265  B   = 144.102  C    = 154.886
    Alpha=  90.002  Beta=  90.001  Gamma=  89.964

The CRYST1 cell dimensions

    A    =  73.340  B   = 144.050  C    = 155.070
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 30.439
(Under-)estimated Z-score: 4.066

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.

 203 HIS   ( 203-)  A      CG   ND1  CE1 109.65    4.0
 229 HIS   ( 229-)  A      CG   ND1  CE1 109.66    4.1
 590 HIS   ( 203-)  B      CG   ND1  CE1 109.67    4.1

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

 143 GLU   ( 143-)  A      C      7.6    11.01    -0.03
 530 GLU   ( 143-)  B      C      7.3    10.62    -0.03
1304 GLU   ( 143-)  D      C      7.3    10.60    -0.03
The average deviation= 1.513

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 574 ARG   ( 187-)  B    4.29
 246 ASN   ( 246-)  A    4.13
 143 GLU   ( 143-)  A    4.12
 961 ARG   ( 187-)  C    4.08
 258 ARG   ( 258-)  A    4.06
 139 ARG   ( 139-)  A    4.03

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

 381 TYR   ( 381-)  A      CB   4.46
1542 TYR   ( 381-)  D      CB   4.16
1155 TYR   ( 381-)  C      CB   4.02
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -0.591

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

 639 ARG   ( 252-)  B    -2.8
1413 ARG   ( 252-)  D    -2.8
 252 ARG   ( 252-)  A    -2.7
1026 ARG   ( 252-)  C    -2.7
 863 THR   (  89-)  C    -2.6
1250 THR   (  89-)  D    -2.6
  89 THR   (  89-)  A    -2.6
 524 PRO   ( 137-)  B    -2.6
 476 THR   (  89-)  B    -2.5
  52 LEU   (  52-)  A    -2.5
 826 LEU   (  52-)  C    -2.5
1213 LEU   (  52-)  D    -2.5
 439 LEU   (  52-)  B    -2.4
 246 ASN   ( 246-)  A    -2.4
 911 PRO   ( 137-)  C    -2.4
 137 PRO   ( 137-)  A    -2.4
 633 ASN   ( 246-)  B    -2.4
 526 ARG   ( 139-)  B    -2.3
1020 ASN   ( 246-)  C    -2.3
1407 ASN   ( 246-)  D    -2.3
 913 ARG   ( 139-)  C    -2.2
1300 ARG   ( 139-)  D    -2.2
 139 ARG   ( 139-)  A    -2.2
1159 VAL   ( 385-)  C    -2.2
1546 VAL   ( 385-)  D    -2.2
 772 VAL   ( 385-)  B    -2.2
 385 VAL   ( 385-)  A    -2.2
1298 PRO   ( 137-)  D    -2.2
1508 SER   ( 347-)  D    -2.2
1121 SER   ( 347-)  C    -2.2
 734 SER   ( 347-)  B    -2.1
1306 GLU   ( 145-)  D    -2.1
 594 ARG   ( 207-)  B    -2.1
 532 GLU   ( 145-)  B    -2.1
 919 GLU   ( 145-)  C    -2.1
1368 ARG   ( 207-)  D    -2.1
 145 GLU   ( 145-)  A    -2.1
 347 SER   ( 347-)  A    -2.1
 981 ARG   ( 207-)  C    -2.1
  45 LEU   (  45-)  A    -2.1
1412 SER   ( 251-)  D    -2.0
 819 LEU   (  45-)  C    -2.0
 432 LEU   (  45-)  B    -2.0
 143 GLU   ( 143-)  A    -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 ARG   (   9-)  A  Poor phi/psi
  52 LEU   (  52-)  A  omega poor
  84 LYS   (  84-)  A  omega poor
  93 PHE   (  93-)  A  Poor phi/psi
 142 ALA   ( 142-)  A  omega poor
 175 TYR   ( 175-)  A  omega poor
 185 GLU   ( 185-)  A  Poor phi/psi, PRO omega poor
 192 PHE   ( 192-)  A  omega poor
 213 LEU   ( 213-)  A  omega poor
 247 ASP   ( 247-)  A  omega poor
 250 MET   ( 250-)  A  omega poor
 251 SER   ( 251-)  A  Poor phi/psi
 282 PRO   ( 282-)  A  omega poor
 347 SER   ( 347-)  A  omega poor
 348 ARG   ( 348-)  A  Poor phi/psi
 360 PRO   ( 360-)  A  Poor phi/psi
 386 ARG   ( 386-)  A  omega poor
 396 ARG   (   9-)  B  Poor phi/psi
 439 LEU   (  52-)  B  omega poor
 450 PRO   (  63-)  B  PRO omega poor
 480 PHE   (  93-)  B  Poor phi/psi
 489 ALA   ( 102-)  B  Poor phi/psi
 529 ALA   ( 142-)  B  omega poor
 562 TYR   ( 175-)  B  omega poor
 572 GLU   ( 185-)  B  Poor phi/psi, PRO omega poor
And so on for a total of 67 lines.

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

1358 SER   ( 197-)  D    0.35
 971 SER   ( 197-)  C    0.35
 584 SER   ( 197-)  B    0.35
 197 SER   ( 197-)  A    0.36

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   5 LYS   (   5-)  A      0
   8 HIS   (   8-)  A      0
  10 PHE   (  10-)  A      0
  16 THR   (  16-)  A      0
  23 ASP   (  23-)  A      0
  25 PHE   (  25-)  A      0
  45 LEU   (  45-)  A      0
  48 TYR   (  48-)  A      0
  60 ARG   (  60-)  A      0
  86 PRO   (  86-)  A      0
  92 LEU   (  92-)  A      0
  93 PHE   (  93-)  A      0
  94 SER   (  94-)  A      0
 100 ASP   ( 100-)  A      0
 102 ALA   ( 102-)  A      0
 103 PHE   ( 103-)  A      0
 105 SER   ( 105-)  A      0
 128 LEU   ( 128-)  A      0
 131 GLU   ( 131-)  A      0
 137 PRO   ( 137-)  A      0
 140 GLU   ( 140-)  A      0
 143 GLU   ( 143-)  A      0
 145 GLU   ( 145-)  A      0
 147 THR   ( 147-)  A      0
 153 VAL   ( 153-)  A      0
And so on for a total of 509 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].

 215 PRO   ( 215-)  A    51.9 half-chair C-delta/C-gamma (54 degrees)
 323 PRO   ( 323-)  A  -116.6 envelop C-gamma (-108 degrees)
 568 PRO   ( 181-)  B   -64.8 envelop C-beta (-72 degrees)
 602 PRO   ( 215-)  B    47.7 half-chair C-delta/C-gamma (54 degrees)
 710 PRO   ( 323-)  B  -121.7 half-chair C-delta/C-gamma (-126 degrees)
 955 PRO   ( 181-)  C   -62.8 half-chair C-beta/C-alpha (-54 degrees)
 989 PRO   ( 215-)  C    45.8 half-chair C-delta/C-gamma (54 degrees)
1097 PRO   ( 323-)  C  -119.4 half-chair C-delta/C-gamma (-126 degrees)
1342 PRO   ( 181-)  D   -57.0 half-chair C-beta/C-alpha (-54 degrees)
1376 PRO   ( 215-)  D    47.3 half-chair C-delta/C-gamma (54 degrees)
1484 PRO   ( 323-)  D  -121.6 half-chair C-delta/C-gamma (-126 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 383 LEU   ( 383-)  A      O   <-> 1476 ARG   ( 315-)  D      NH2    0.36    2.34  INTRA
1312 ARG   ( 151-)  D      NH1 <-> 1552 HOH   ( 524 )  D      O      0.35    2.35  INTRA BF
 619 ALA   ( 232-)  B      O   <-> 1312 ARG   ( 151-)  D      NH2    0.34    2.36  INTRA
 538 ARG   ( 151-)  B      NH2 <-> 1393 ALA   ( 232-)  D      O      0.33    2.37  INTRA
 770 LEU   ( 383-)  B      O   <-> 1089 ARG   ( 315-)  C      NH2    0.32    2.38  INTRA
 232 ALA   ( 232-)  A      O   <->  925 ARG   ( 151-)  C      NH2    0.32    2.38  INTRA
 151 ARG   ( 151-)  A      NH2 <-> 1006 ALA   ( 232-)  C      O      0.32    2.38  INTRA
 315 ARG   ( 315-)  A      NH2 <-> 1544 LEU   ( 383-)  D      O      0.31    2.39  INTRA
 925 ARG   ( 151-)  C      NH1 <-> 1551 HOH   ( 650 )  C      O      0.31    2.39  INTRA BF
 538 ARG   ( 151-)  B      NH1 <-> 1550 HOH   ( 423 )  B      O      0.30    2.40  INTRA BF
 392 LYS   (   5-)  B      N   <->  395 HIS   (   8-)  B      ND1    0.30    2.70  INTRA
 151 ARG   ( 151-)  A      NH1 <-> 1549 HOH   ( 552 )  A      O      0.29    2.41  INTRA BF
1166 LYS   (   5-)  D      N   <-> 1169 HIS   (   8-)  D      ND1    0.29    2.71  INTRA
 702 ARG   ( 315-)  B      NH2 <-> 1157 LEU   ( 383-)  C      O      0.28    2.42  INTRA
 779 LYS   (   5-)  C      N   <->  782 HIS   (   8-)  C      ND1    0.28    2.72  INTRA
   5 LYS   (   5-)  A      N   <->    8 HIS   (   8-)  A      ND1    0.27    2.73  INTRA
 203 HIS   ( 203-)  A      ND1 <->  977 HIS   ( 203-)  C      ND1    0.25    2.75  INTRA
1141 ARG   ( 367-)  C      NH2 <-> 1551 HOH   ( 592 )  C      O      0.22    2.48  INTRA
 636 ARG   ( 249-)  B      NH2 <-> 1550 HOH   ( 420 )  B      O      0.21    2.49  INTRA
1130 ARG   ( 356-)  C      NH1 <-> 1551 HOH   ( 434 )  C      O      0.21    2.49  INTRA BF
 116 ARG   ( 116-)  A      NH2 <-> 1131 ALA   ( 357-)  C      O      0.19    2.51  INTRA
1410 ARG   ( 249-)  D      NH2 <-> 1552 HOH   ( 521 )  D      O      0.19    2.51  INTRA
1183 ARG   (  22-)  D      NH2 <-> 1552 HOH   ( 553 )  D      O      0.19    2.51  INTRA BF
1528 ARG   ( 367-)  D      NH2 <-> 1552 HOH   ( 635 )  D      O      0.19    2.51  INTRA BL
  99 LYS   (  99-)  A      NZ  <-> 1141 ARG   ( 367-)  C      O      0.18    2.52  INTRA BL
And so on for a total of 154 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 667 GLN   ( 280-)  B      -6.92
 280 GLN   ( 280-)  A      -6.89
1441 GLN   ( 280-)  D      -6.86
1054 GLN   ( 280-)  C      -6.82
  60 ARG   (  60-)  A      -6.46
 834 ARG   (  60-)  C      -6.43
 447 ARG   (  60-)  B      -6.42
1221 ARG   (  60-)  D      -6.41
1183 ARG   (  22-)  D      -6.34
  22 ARG   (  22-)  A      -6.34
 409 ARG   (  22-)  B      -6.33
 796 ARG   (  22-)  C      -6.32
1193 ARG   (  32-)  D      -6.20
 806 ARG   (  32-)  C      -6.20
  32 ARG   (  32-)  A      -6.14
 773 ARG   ( 386-)  B      -6.10
 386 ARG   ( 386-)  A      -6.05
1547 ARG   ( 386-)  D      -6.05
1160 ARG   ( 386-)  C      -6.05
 419 ARG   (  32-)  B      -6.01
 753 ARG   ( 366-)  B      -5.88
 782 HIS   (   8-)  C      -5.77
   8 HIS   (   8-)  A      -5.76
 395 HIS   (   8-)  B      -5.76
1169 HIS   (   8-)  D      -5.73
1140 ARG   ( 366-)  C      -5.70
1527 ARG   ( 366-)  D      -5.68
 366 ARG   ( 366-)  A      -5.68
1300 ARG   ( 139-)  D      -5.60
 139 ARG   ( 139-)  A      -5.59
 526 ARG   ( 139-)  B      -5.56
 913 ARG   ( 139-)  C      -5.52
 356 ARG   ( 356-)  A      -5.49
1130 ARG   ( 356-)  C      -5.49
 945 GLN   ( 171-)  C      -5.47
 171 GLN   ( 171-)  A      -5.47
 558 GLN   ( 171-)  B      -5.46
1332 GLN   ( 171-)  D      -5.46
1517 ARG   ( 356-)  D      -5.45
1410 ARG   ( 249-)  D      -5.07
1132 GLU   ( 358-)  C      -5.04
1519 GLU   ( 358-)  D      -5.01

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: B

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: C

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: D

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

1031 LEU   ( 257-)  C   -2.76
 644 LEU   ( 257-)  B   -2.75
 257 LEU   ( 257-)  A   -2.75
1418 LEU   ( 257-)  D   -2.74
 642 GLN   ( 255-)  B   -2.61
 255 GLN   ( 255-)  A   -2.58
1416 GLN   ( 255-)  D   -2.57
1133 LEU   ( 359-)  C   -2.57
1029 GLN   ( 255-)  C   -2.56
1383 MET   ( 222-)  D   -2.55
1520 LEU   ( 359-)  D   -2.52
 359 LEU   ( 359-)  A   -2.50

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

Error: Water clusters without contacts with non-water atoms

The water molecules listed in the table below are part of water molecule clusters that do not make contacts with non-waters. These water molecules are part of clusters that have a distance at least 1 Angstrom larger than the sum of the Van der Waals radii to the nearest non-solvent atom. Because these kinds of water clusters usually are not observed with X-ray diffraction their presence could indicate a refinement artifact. The number in brackets is the identifier of the water molecule in the input file.

1549 HOH   ( 452 )  A      O
1550 HOH   ( 494 )  B      O
1550 HOH   ( 529 )  B      O
1550 HOH   ( 545 )  B      O
1551 HOH   ( 552 )  C      O
1551 HOH   ( 570 )  C      O
1552 HOH   ( 549 )  D      O
1552 HOH   ( 581 )  D      O
1552 HOH   ( 586 )  D      O
1552 HOH   ( 594 )  D      O
1552 HOH   ( 600 )  D      O
1552 HOH   ( 658 )  D      O

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

1549 HOH   ( 407 )  A      O    -38.80 -119.56   90.61
1549 HOH   ( 413 )  A      O    -21.24 -129.32  121.87
1549 HOH   ( 415 )  A      O    -34.71 -133.84  125.58
1549 HOH   ( 420 )  A      O    -20.79 -136.46  124.44
1549 HOH   ( 422 )  A      O    -31.68 -117.99  116.96
1549 HOH   ( 428 )  A      O    -31.73 -132.37  115.09
1549 HOH   ( 432 )  A      O    -31.32 -116.64  128.87
1549 HOH   ( 435 )  A      O    -49.76 -173.31  103.12
1549 HOH   ( 436 )  A      O    -27.67 -114.26  105.93
1549 HOH   ( 439 )  A      O    -19.51 -170.45  106.33
1549 HOH   ( 443 )  A      O    -39.06 -157.58  136.72
1549 HOH   ( 444 )  A      O    -20.19 -141.63  111.11
1549 HOH   ( 447 )  A      O    -38.95 -135.16  127.35
1549 HOH   ( 449 )  A      O    -41.86 -129.56   85.26
1549 HOH   ( 452 )  A      O      5.72 -199.09  125.24
1549 HOH   ( 454 )  A      O    -27.61 -153.06  132.05
1549 HOH   ( 456 )  A      O    -37.68 -175.43  106.81
1549 HOH   ( 458 )  A      O    -39.20 -119.82   95.60
1549 HOH   ( 461 )  A      O    -42.55 -129.15  127.06
1549 HOH   ( 462 )  A      O    -20.50 -191.31  109.86
1549 HOH   ( 464 )  A      O    -37.07 -160.81  132.99
1549 HOH   ( 466 )  A      O    -37.00 -141.91  119.10
1549 HOH   ( 471 )  A      O     15.13 -155.18  134.23
1549 HOH   ( 477 )  A      O    -38.62 -140.85  114.45
1549 HOH   ( 480 )  A      O    -41.85 -149.30   98.96
And so on for a total of 245 lines.

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

1549 HOH   ( 407 )  A      O
1549 HOH   ( 425 )  A      O
1549 HOH   ( 443 )  A      O
1549 HOH   ( 452 )  A      O
1549 HOH   ( 458 )  A      O
1549 HOH   ( 468 )  A      O
1549 HOH   ( 505 )  A      O
1549 HOH   ( 516 )  A      O
1549 HOH   ( 517 )  A      O
1549 HOH   ( 528 )  A      O
1549 HOH   ( 579 )  A      O
1549 HOH   ( 598 )  A      O
1549 HOH   ( 603 )  A      O
1549 HOH   ( 631 )  A      O
1549 HOH   ( 643 )  A      O
1549 HOH   ( 652 )  A      O
1549 HOH   ( 653 )  A      O
1549 HOH   ( 667 )  A      O
1549 HOH   ( 668 )  A      O
1550 HOH   ( 449 )  B      O
1550 HOH   ( 467 )  B      O
1550 HOH   ( 474 )  B      O
1550 HOH   ( 478 )  B      O
1550 HOH   ( 486 )  B      O
1550 HOH   ( 494 )  B      O
And so on for a total of 82 lines.

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.

  40 HIS   (  40-)  A
 229 HIS   ( 229-)  A
 233 GLN   ( 233-)  A
 246 ASN   ( 246-)  A
 248 GLN   ( 248-)  A
 376 GLN   ( 376-)  A
 395 HIS   (   8-)  B
 406 ASN   (  19-)  B
 571 ASN   ( 184-)  B
 616 HIS   ( 229-)  B
 620 GLN   ( 233-)  B
 633 ASN   ( 246-)  B
 635 GLN   ( 248-)  B
 763 GLN   ( 376-)  B
 793 ASN   (  19-)  C
 988 ASN   ( 214-)  C
1003 HIS   ( 229-)  C
1007 GLN   ( 233-)  C
1020 ASN   ( 246-)  C
1022 GLN   ( 248-)  C
1150 GLN   ( 376-)  C
1180 ASN   (  19-)  D
1212 ASN   (  51-)  D
1345 ASN   ( 184-)  D
1390 HIS   ( 229-)  D
1407 ASN   ( 246-)  D
1409 GLN   ( 248-)  D
1537 GLN   ( 376-)  D

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

   3 GLU   (   3-)  A      N
  15 TRP   (  15-)  A      N
  21 GLY   (  21-)  A      N
  65 GLN   (  65-)  A      N
  73 ARG   (  73-)  A      NH1
  87 MET   (  87-)  A      N
 111 ARG   ( 111-)  A      NE
 136 TRP   ( 136-)  A      NE1
 151 ARG   ( 151-)  A      NE
 151 ARG   ( 151-)  A      NH2
 154 TRP   ( 154-)  A      N
 184 ASN   ( 184-)  A      N
 184 ASN   ( 184-)  A      ND2
 187 ARG   ( 187-)  A      N
 192 PHE   ( 192-)  A      N
 194 THR   ( 194-)  A      N
 243 ILE   ( 243-)  A      N
 246 ASN   ( 246-)  A      N
 249 ARG   ( 249-)  A      NH1
 252 ARG   ( 252-)  A      N
 344 GLY   ( 344-)  A      N
 347 SER   ( 347-)  A      N
 348 ARG   ( 348-)  A      N
 348 ARG   ( 348-)  A      NE
 349 GLU   ( 349-)  A      N
And so on for a total of 110 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.

 219 HIS   ( 219-)  A      ND1
 229 HIS   ( 229-)  A      NE2
 993 HIS   ( 219-)  C      ND1
1380 HIS   ( 219-)  D      ND1

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

1549 HOH   ( 419 )  A      O  1.12  K  4
1549 HOH   ( 457 )  A      O  0.97  K  4
1549 HOH   ( 557 )  A      O  0.99  K  4
1550 HOH   ( 461 )  B      O  1.13  K  4
1551 HOH   ( 492 )  C      O  0.91  K  4
1551 HOH   ( 518 )  C      O  1.13  K  4
1551 HOH   ( 557 )  C      O  0.91  K  4
1551 HOH   ( 655 )  C      O  0.90  K  5
1552 HOH   ( 529 )  D      O  0.97  K  4
1552 HOH   ( 561 )  D      O  1.06  K  4
1552 HOH   ( 599 )  D      O  0.87  K  4

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.

  68 ASP   (  68-)  A   H-bonding suggests Asn
  79 ASP   (  79-)  A   H-bonding suggests Asn
 455 ASP   (  68-)  B   H-bonding suggests Asn
 466 ASP   (  79-)  B   H-bonding suggests Asn
 842 ASP   (  68-)  C   H-bonding suggests Asn
 853 ASP   (  79-)  C   H-bonding suggests Asn
1030 ASP   ( 256-)  C   H-bonding suggests Asn
1229 ASP   (  68-)  D   H-bonding suggests Asn
1240 ASP   (  79-)  D   H-bonding suggests Asn
1417 ASP   ( 256-)  D   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.385
  2nd generation packing quality :  -0.728
  Ramachandran plot appearance   :  -0.591
  chi-1/chi-2 rotamer normality  :  -2.455
  Backbone conformation          :   0.228

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.440 (tight)
  Bond angles                    :   0.584 (tight)
  Omega angle restraints         :   1.107
  Side chain planarity           :   1.262
  Improper dihedral distribution :   1.425
  Inside/Outside distribution    :   0.996

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.2
  2nd generation packing quality :  -0.2
  Ramachandran plot appearance   :   0.6
  chi-1/chi-2 rotamer normality  :  -1.1
  Backbone conformation          :   0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.440 (tight)
  Bond angles                    :   0.584 (tight)
  Omega angle restraints         :   1.107
  Side chain planarity           :   1.262
  Improper dihedral distribution :   1.425
  Inside/Outside distribution    :   0.996
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    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,
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      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
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      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.