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 pdb1aa1.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    = 157.600  B   = 158.700  C    = 203.300
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    = 111.830  B   = 111.830  C    = 203.300
    Alpha=  90.000  Beta=  90.000  Gamma=  89.601

Dimensions of the conventional cell

    A    = 111.830  B   = 111.830  C    = 203.300
    Alpha=  90.000  Beta=  90.000  Gamma=  90.399

Transformation to conventional cell

 | -0.500000  0.500000  0.000000|
 | -0.500000 -0.500000  0.000000|
 |  0.000000  0.000000  1.000000|

Crystal class of the cell: ORTHORHOMBIC

Crystal class of the conventional CELL: TETRAGONAL

Space group name: C 2 2 21

Bravais type of conventional cell is: P

Warning: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

2250 3PG   ( 477-)  L  -
2251 3PG   ( 478-)  L  -
2253 3PG   ( 477-)  B  -
2254 3PG   ( 478-)  B  -
2256 3PG   ( 477-)  E  -
2257 3PG   ( 478-)  E  -
2259 3PG   ( 477-)  H  -
2260 3PG   ( 478-)  H  -

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: L

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

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

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) :283.000

Warning: More than 2 percent of buried atoms has low B-factor

For protein structures determined at room temperature, no more than about 1 percent of the B factors of buried atoms is below 5.0.

Percentage of buried atoms with B less than 5 : 3.70

Note: B-factor plot

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

Chain identifier: L

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Nomenclature related problems

Warning: Heavy atom naming convention problem

The atoms listed in the table below have nonstandard names in the input file. (Be aware that we sometimes consider an asterix and an apostrophe identical, and thus do not warn for the use of asterixes. Please be aware that the PDB wants us to deliberately make some nomenclature errors; especially in non-canonical amino acids.

 181 KCX   ( 201-)  L      CH     CX
 181 KCX   ( 201-)  L      OX1    OQ1
 181 KCX   ( 201-)  L      OX2    OQ2
 742 KCX   ( 201-)  B      CH     CX
 742 KCX   ( 201-)  B      OX1    OQ1
 742 KCX   ( 201-)  B      OX2    OQ2
1303 KCX   ( 201-)  E      CH     CX
1303 KCX   ( 201-)  E      OX1    OQ1
1303 KCX   ( 201-)  E      OX2    OQ2
1864 KCX   ( 201-)  H      CH     CX
1864 KCX   ( 201-)  H      OX1    OQ1
1864 KCX   ( 201-)  H      OX2    OQ2

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

 |  0.998667  0.000006 -0.000003|
 |  0.000006  0.998673  0.000009|
 | -0.000003  0.000009  0.999286|
Proposed new scale matrix

 |  0.006353  0.000000  0.000000|
 |  0.000000  0.006309  0.000000|
 |  0.000000  0.000000  0.004923|
With corresponding cell

    A    = 157.394  B   = 158.494  C    = 203.148
    Alpha=  90.002  Beta=  90.002  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 157.600  B   = 158.700  C    = 203.300
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 99.053
(Under-)estimated Z-score: 7.335

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.

  16 ILE   (  36-)  L      N    CA   C    98.88   -4.4
 133 HIS   ( 153-)  L      CG   ND1  CE1 109.65    4.1
 218 HIS   ( 238-)  L      CG   ND1  CE1 109.60    4.0
 243 PRO   ( 263-)  L      N    CA   C   123.76    4.8
 274 HIS   ( 294-)  L      CG   ND1  CE1 109.73    4.1
 437 TRP   ( 462-)  L      N    CA   C   126.02    5.3
 577 ILE   (  36-)  B      N    CA   C    98.91   -4.4
 694 HIS   ( 153-)  B      CG   ND1  CE1 109.67    4.1
 804 PRO   ( 263-)  B      N    CA   C   123.77    4.8
 835 HIS   ( 294-)  B      CG   ND1  CE1 109.77    4.2
 998 TRP   ( 462-)  B      N    CA   C   126.06    5.3
1138 ILE   (  36-)  E      N    CA   C    98.87   -4.4
1255 HIS   ( 153-)  E      CG   ND1  CE1 109.65    4.1
1365 PRO   ( 263-)  E      N    CA   C   123.75    4.8
1396 HIS   ( 294-)  E      CG   ND1  CE1 109.69    4.1
1559 TRP   ( 462-)  E      N    CA   C   126.01    5.3
1699 ILE   (  36-)  H      N    CA   C    98.88   -4.4
1816 HIS   ( 153-)  H      CG   ND1  CE1 109.65    4.1
1926 PRO   ( 263-)  H      N    CA   C   123.78    4.8
1957 HIS   ( 294-)  H      CG   ND1  CE1 109.71    4.1
2120 TRP   ( 462-)  H      N    CA   C   126.01    5.3

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.

 998 TRP   ( 462-)  B    7.81
 437 TRP   ( 462-)  L    7.80
1559 TRP   ( 462-)  E    7.79
2120 TRP   ( 462-)  H    7.79
 104 VAL   ( 124-)  L    6.62
 665 VAL   ( 124-)  B    6.60
1787 VAL   ( 124-)  H    6.60
1226 VAL   ( 124-)  E    6.59
1537 GLU   ( 440-)  E    6.22
 415 GLU   ( 440-)  L    6.20
 976 GLU   ( 440-)  B    6.20
2098 GLU   ( 440-)  H    6.17
1965 ASP   ( 302-)  H    4.86
1404 ASP   ( 302-)  E    4.85
 282 ASP   ( 302-)  L    4.85
 843 ASP   ( 302-)  B    4.83
1932 TYR   ( 269-)  H    4.66
 810 TYR   ( 269-)  B    4.66
 249 TYR   ( 269-)  L    4.66
1371 TYR   ( 269-)  E    4.64
 696 ILE   ( 155-)  B    4.60
 135 ILE   ( 155-)  L    4.59
1447 ARG   ( 350-)  E    4.57
 325 ARG   ( 350-)  L    4.56
 886 ARG   ( 350-)  B    4.56
And so on for a total of 52 lines.

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.607

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.

 905 VAL   ( 369-)  B    -2.7
 344 VAL   ( 369-)  L    -2.7
2027 VAL   ( 369-)  H    -2.7
1466 VAL   ( 369-)  E    -2.7
1312 PRO   ( 210-)  E    -2.6
 190 PRO   ( 210-)  L    -2.6
1873 PRO   ( 210-)  H    -2.6
 751 PRO   ( 210-)  B    -2.6
 872 VAL   ( 331-)  B    -2.4
1994 VAL   ( 331-)  H    -2.4
 311 VAL   ( 331-)  L    -2.4
1433 VAL   ( 331-)  E    -2.4
2130 LEU   (   9-)  I    -2.4
1569 LEU   (   9-)  F    -2.4
1008 LEU   (   9-)  C    -2.4
 447 LEU   (   9-)  S    -2.4
1574 THR   (  14-)  F    -2.2
 452 THR   (  14-)  S    -2.2
1013 THR   (  14-)  C    -2.2
2135 THR   (  14-)  I    -2.2
1055 HIS   (  56-)  C    -2.2
2177 HIS   (  56-)  I    -2.2
1616 HIS   (  56-)  F    -2.2
 494 HIS   (  56-)  S    -2.2
 976 GLU   ( 440-)  B    -2.2
1537 GLU   ( 440-)  E    -2.2
 415 GLU   ( 440-)  L    -2.2
2098 GLU   ( 440-)  H    -2.2
2235 SER   ( 114-)  I    -2.2
1113 SER   ( 114-)  C    -2.1
 552 SER   ( 114-)  S    -2.1
1674 SER   ( 114-)  F    -2.1
1479 ILE   ( 382-)  E    -2.0
2040 ILE   ( 382-)  H    -2.0
 357 ILE   ( 382-)  L    -2.0
 918 ILE   ( 382-)  B    -2.0
1223 VAL   ( 121-)  E    -2.0
1784 VAL   ( 121-)  H    -2.0
 101 VAL   ( 121-)  L    -2.0
 662 VAL   ( 121-)  B    -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.

  42 SER   (  62-)  L  Poor phi/psi
  43 THR   (  63-)  L  Poor phi/psi
  44 GLY   (  64-)  L  Poor phi/psi
 143 ASN   ( 163-)  L  Poor phi/psi
 155 LYS   ( 175-)  L  PRO omega poor
 187 ASN   ( 207-)  L  Poor phi/psi
 277 MET   ( 297-)  L  Poor phi/psi
 311 VAL   ( 331-)  L  Poor phi/psi
 345 SER   ( 370-)  L  Poor phi/psi
 451 GLU   (  13-)  S  Poor phi/psi
 453 LEU   (  15-)  S  Poor phi/psi
 475 LYS   (  37-)  S  Poor phi/psi
 509 LYS   (  71-)  S  Poor phi/psi
 547 GLU   ( 109-)  S  Poor phi/psi
 552 SER   ( 114-)  S  Poor phi/psi
 603 SER   (  62-)  B  Poor phi/psi
 604 THR   (  63-)  B  Poor phi/psi
 605 GLY   (  64-)  B  Poor phi/psi
 704 ASN   ( 163-)  B  Poor phi/psi
 716 LYS   ( 175-)  B  PRO omega poor
 748 ASN   ( 207-)  B  Poor phi/psi
 838 MET   ( 297-)  B  Poor phi/psi
 872 VAL   ( 331-)  B  Poor phi/psi
 906 SER   ( 370-)  B  Poor phi/psi
1012 GLU   (  13-)  C  Poor phi/psi
And so on for a total of 60 lines.

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 TYR   (  25-)  L      0
   6 THR   (  26-)  L      0
  26 PRO   (  46-)  L      0
  41 SER   (  61-)  L      0
  42 SER   (  62-)  L      0
  43 THR   (  63-)  L      0
  46 TRP   (  66-)  L      0
  50 TRP   (  70-)  L      0
  54 LEU   (  74-)  L      0
  56 ASN   (  76-)  L      0
  57 LEU   (  77-)  L      0
  65 TYR   (  85-)  L      0
  71 ALA   (  91-)  L      0
  74 GLU   (  94-)  L      0
  87 LEU   ( 107-)  L      0
  90 GLU   ( 110-)  L      0
 101 VAL   ( 121-)  L      0
 107 PHE   ( 127-)  L      0
 111 ARG   ( 131-)  L      0
 112 ALA   ( 132-)  L      0
 117 ASP   ( 137-)  L      0
 131 PRO   ( 151-)  L      0
 132 PRO   ( 152-)  L      0
 133 HIS   ( 153-)  L      0
 135 ILE   ( 155-)  L      0
And so on for a total of 826 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 : 1.694

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

  30 PRO   (  50-)  L   1.89   18
 591 PRO   (  50-)  B   1.89   18
1152 PRO   (  50-)  E   1.89   18
1713 PRO   (  50-)  H   1.89   18

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].

  24 PRO   (  44-)  L    49.6 half-chair C-delta/C-gamma (54 degrees)
  26 PRO   (  46-)  L  -112.5 envelop C-gamma (-108 degrees)
 585 PRO   (  44-)  B    49.7 half-chair C-delta/C-gamma (54 degrees)
 587 PRO   (  46-)  B  -112.5 envelop C-gamma (-108 degrees)
1146 PRO   (  44-)  E    49.7 half-chair C-delta/C-gamma (54 degrees)
1148 PRO   (  46-)  E  -112.6 envelop C-gamma (-108 degrees)
1707 PRO   (  44-)  H    49.7 half-chair C-delta/C-gamma (54 degrees)
1709 PRO   (  46-)  H  -112.5 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.

 118 LEU   ( 138-)  L      O   <->  296 LYS   ( 316-)  L      NZ     0.24    2.46  INTRA BL
 679 LEU   ( 138-)  B      O   <->  857 LYS   ( 316-)  B      NZ     0.24    2.46  INTRA BL
1801 LEU   ( 138-)  H      O   <-> 1979 LYS   ( 316-)  H      NZ     0.24    2.46  INTRA BL
1240 LEU   ( 138-)  E      O   <-> 1418 LYS   ( 316-)  E      NZ     0.24    2.46  INTRA BL
1961 HIS   ( 298-)  H      NE2 <-> 2260 3PG   ( 478-)  H      C3     0.19    2.91  INTRA
 278 HIS   ( 298-)  L      NE2 <-> 2251 3PG   ( 478-)  L      C3     0.19    2.91  INTRA
 839 HIS   ( 298-)  B      NE2 <-> 2254 3PG   ( 478-)  B      C3     0.19    2.91  INTRA
1400 HIS   ( 298-)  E      NE2 <-> 2257 3PG   ( 478-)  E      C3     0.19    2.91  INTRA
 716 LYS   ( 175-)  B      NZ  <-> 2253 3PG   ( 477-)  B      C2     0.17    2.93  INTRA BF
1277 LYS   ( 175-)  E      NZ  <-> 2256 3PG   ( 477-)  E      C2     0.17    2.93  INTRA BF
 155 LYS   ( 175-)  L      NZ  <-> 2250 3PG   ( 477-)  L      C2     0.17    2.93  INTRA BF
1838 LYS   ( 175-)  H      NZ  <-> 2259 3PG   ( 477-)  H      C2     0.16    2.94  INTRA BF
1847 ASN   ( 184-)  H      ND2 <-> 2267 HOH   ( 522 )  H      O      0.16    2.54  INTRA
1286 ASN   ( 184-)  E      ND2 <-> 2265 HOH   ( 518 )  E      O      0.16    2.54  INTRA
 164 ASN   ( 184-)  L      ND2 <-> 2261 HOH   ( 511 )  L      O      0.16    2.54  INTRA
 725 ASN   ( 184-)  B      ND2 <-> 2263 HOH   ( 519 )  B      O      0.16    2.54  INTRA
1435 GLU   ( 338-)  E      N   <-> 2265 HOH   ( 672 )  E      O      0.16    2.54  INTRA BF
 874 GLU   ( 338-)  B      N   <-> 2263 HOH   ( 673 )  B      O      0.16    2.54  INTRA BF
1996 GLU   ( 338-)  H      N   <-> 2267 HOH   ( 675 )  H      O      0.16    2.54  INTRA BF
 313 GLU   ( 338-)  L      N   <-> 2261 HOH   ( 664 )  L      O      0.16    2.54  INTRA BF
 627 HIS   (  86-)  B      CE1 <-> 2263 HOH   ( 657 )  B      O      0.15    2.65  INTRA
1188 HIS   (  86-)  E      CE1 <-> 2265 HOH   ( 656 )  E      O      0.15    2.65  INTRA
  66 HIS   (  86-)  L      CE1 <-> 2261 HOH   ( 648 )  L      O      0.15    2.65  INTRA
1749 HIS   (  86-)  H      CE1 <-> 2267 HOH   ( 659 )  H      O      0.15    2.65  INTRA
2093 ARG   ( 435-)  H      NH2 <-> 2105 GLU   ( 447-)  H      OE1    0.14    2.56  INTRA
And so on for a total of 175 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: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

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: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

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.

1841 LEU   ( 178-)  H      -6.31
 158 LEU   ( 178-)  L      -6.31
 719 LEU   ( 178-)  B      -6.31
1280 LEU   ( 178-)  E      -6.31
1074 PHE   (  75-)  C      -6.11
1635 PHE   (  75-)  F      -6.10
 513 PHE   (  75-)  S      -6.10
2196 PHE   (  75-)  I      -6.07
1251 GLN   ( 149-)  E      -6.00
1812 GLN   ( 149-)  H      -5.96
 690 GLN   ( 149-)  B      -5.96
 129 GLN   ( 149-)  L      -5.96
 414 ARG   ( 439-)  L      -5.79
2097 ARG   ( 439-)  H      -5.79
1536 ARG   ( 439-)  E      -5.79
 975 ARG   ( 439-)  B      -5.79
 672 ARG   ( 131-)  B      -5.61
 111 ARG   ( 131-)  L      -5.61
1794 ARG   ( 131-)  H      -5.60
1233 ARG   ( 131-)  E      -5.60
1168 TRP   (  66-)  E      -5.35
 607 TRP   (  66-)  B      -5.34
1729 TRP   (  66-)  H      -5.34
  46 TRP   (  66-)  L      -5.34
1277 LYS   ( 175-)  E      -5.23
1838 LYS   ( 175-)  H      -5.23
 155 LYS   ( 175-)  L      -5.23
 716 LYS   ( 175-)  B      -5.23
2008 ARG   ( 350-)  H      -5.22
 325 ARG   ( 350-)  L      -5.22
1447 ARG   ( 350-)  E      -5.22
 886 ARG   ( 350-)  B      -5.22
2120 TRP   ( 462-)  H      -5.11
 998 TRP   ( 462-)  B      -5.11
1559 TRP   ( 462-)  E      -5.11
 437 TRP   ( 462-)  L      -5.11
 504 TYR   (  66-)  S      -5.10
 267 ASN   ( 287-)  L      -5.10
1389 ASN   ( 287-)  E      -5.09
 828 ASN   ( 287-)  B      -5.09
2018 ARG   ( 360-)  H      -5.09
1457 ARG   ( 360-)  E      -5.09
1950 ASN   ( 287-)  H      -5.09
 335 ARG   ( 360-)  L      -5.09
 896 ARG   ( 360-)  B      -5.09
 968 ASN   ( 432-)  B      -5.02
1529 ASN   ( 432-)  E      -5.02
2090 ASN   ( 432-)  H      -5.02
 407 ASN   ( 432-)  L      -5.02

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: L

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: S

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: E

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: F

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: H

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: I

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.

 279 ALA   ( 299-)  L   -2.77
1401 ALA   ( 299-)  E   -2.77
1962 ALA   ( 299-)  H   -2.75
 840 ALA   ( 299-)  B   -2.70
 548 VAL   ( 110-)  S   -2.69
2231 VAL   ( 110-)  I   -2.68
1109 VAL   ( 110-)  C   -2.67
1670 VAL   ( 110-)  F   -2.67
1209 LEU   ( 107-)  E   -2.62
  87 LEU   ( 107-)  L   -2.62
 648 LEU   ( 107-)  B   -2.61
1770 LEU   ( 107-)  H   -2.60

Note: Second generation quality Z-score plot

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

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: S

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: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

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

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

2261 HOH   ( 574 )  L      O     29.42   67.46   50.17
2261 HOH   ( 592 )  L      O     20.23   23.17   57.22
2263 HOH   ( 582 )  B      O    -29.77   67.07   50.10
2263 HOH   ( 600 )  B      O     14.51   57.84   57.16
2263 HOH   ( 659 )  B      O      2.17   80.97    2.88
2265 HOH   ( 582 )  E      O    -29.46    7.84   50.20
2265 HOH   ( 600 )  E      O    -20.26   52.13   57.29
2265 HOH   ( 658 )  E      O    -38.94   44.02    3.09
2267 HOH   ( 585 )  H      O     29.82    8.22   50.10
2267 HOH   ( 603 )  H      O    -14.44   17.50   57.28
2267 HOH   ( 661 )  H      O     -2.34    2.46    2.94

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.

2261 HOH   ( 662 )  L      O
2263 HOH   ( 671 )  B      O
2265 HOH   ( 670 )  E      O
2267 HOH   ( 673 )  H      O

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.

  66 HIS   (  86-)  L
 164 ASN   ( 184-)  L
 209 GLN   ( 229-)  L
 218 HIS   ( 238-)  L
 221 ASN   ( 241-)  L
 247 HIS   ( 267-)  L
 257 ASN   ( 277-)  L
 284 GLN   ( 304-)  L
 361 HIS   ( 386-)  L
 395 ASN   ( 420-)  L
 407 ASN   ( 432-)  L
 467 GLN   (  29-)  S
 493 HIS   (  55-)  S
 495 ASN   (  57-)  S
 627 HIS   (  86-)  B
 770 GLN   ( 229-)  B
 779 HIS   ( 238-)  B
 782 ASN   ( 241-)  B
 808 HIS   ( 267-)  B
 818 ASN   ( 277-)  B
 845 GLN   ( 304-)  B
 922 HIS   ( 386-)  B
 956 ASN   ( 420-)  B
 968 ASN   ( 432-)  B
1028 GLN   (  29-)  C
And so on for a total of 53 lines.

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.

   4 TYR   (  24-)  L      N
  31 GLU   (  51-)  L      N
  55 THR   (  75-)  L      OG1
  56 ASN   (  76-)  L      N
 147 ARG   ( 167-)  L      N
 155 LYS   ( 175-)  L      N
 187 ASN   ( 207-)  L      ND2
 188 SER   ( 208-)  L      N
 196 ASP   ( 216-)  L      N
 219 TYR   ( 239-)  L      OH
 226 THR   ( 246-)  L      N
 256 ALA   ( 276-)  L      N
 262 HIS   ( 282-)  L      ND1
 275 ARG   ( 295-)  L      NE
 303 GLY   ( 323-)  L      N
 354 SER   ( 379-)  L      N
 376 GLN   ( 401-)  L      NE2
 379 GLY   ( 404-)  L      N
 388 ASN   ( 413-)  L      ND2
 414 ARG   ( 439-)  L      N
 429 GLU   ( 454-)  L      N
 440 GLN   (   2-)  S      N
 453 LEU   (  15-)  S      N
 488 PHE   (  50-)  S      N
 494 HIS   (  56-)  S      N
And so on for a total of 103 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.

 248 ASP   ( 268-)  L      OD1
 248 ASP   ( 268-)  L      OD2
 376 GLN   ( 401-)  L      OE1
 809 ASP   ( 268-)  B      OD1
 809 ASP   ( 268-)  B      OD2
 937 GLN   ( 401-)  B      OE1
1370 ASP   ( 268-)  E      OD1
1370 ASP   ( 268-)  E      OD2
1384 HIS   ( 282-)  E      ND1
1498 GLN   ( 401-)  E      OE1
1931 ASP   ( 268-)  H      OD1
1931 ASP   ( 268-)  H      OD2
1945 HIS   ( 282-)  H      ND1
2059 GLN   ( 401-)  H      OE1

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+.

2249  MG   ( 476-)  L     0.46   0.91 Is perhaps NA *2
2252  MG   ( 476-)  B     0.46   0.91 Is perhaps NA *2
2255  MG   ( 476-)  E     0.46   0.91 Is perhaps NA *2
2258  MG   ( 476-)  H     0.46   0.91 Is perhaps NA *2

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.

2261 HOH   ( 514 )  L      O  1.01  K  4 NCS 3/3
2261 HOH   ( 581 )  L      O  0.99  K  4 NCS 3/3
2261 HOH   ( 608 )  L      O  1.15  K  4 ION-B NCS 3/3
2261 HOH   ( 673 )  L      O  1.00  K  4 NCS 3/3
2263 HOH   ( 480 )  B      O  1.11  K  4 NCS 3/3
2263 HOH   ( 589 )  B      O  0.99  K  4 NCS 3/3
2263 HOH   ( 616 )  B      O  1.15  K  4 ION-B NCS 3/3
2265 HOH   ( 480 )  E      O  0.90  K  4 NCS 3/3
2265 HOH   ( 521 )  E      O  0.96  K  4 NCS 3/3
2265 HOH   ( 589 )  E      O  0.99  K  4 NCS 3/3
2265 HOH   ( 616 )  E      O  1.15  K  4 ION-B NCS 3/3
2267 HOH   ( 485 )  H      O  0.94  K  4 NCS 3/3
2267 HOH   ( 525 )  H      O  1.11  K  4 NCS 3/3
2267 HOH   ( 592 )  H      O  0.99  K  4 NCS 3/3
2267 HOH   ( 619 )  H      O  1.15  K  4 ION-B NCS 3/3

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.

 171 GLU   ( 191-)  L   H-bonding suggests Gln; but Alt-Rotamer
 248 ASP   ( 268-)  L   H-bonding suggests Asn; but Alt-Rotamer
 282 ASP   ( 302-)  L   H-bonding suggests Asn
 547 GLU   ( 109-)  S   H-bonding suggests Gln; but Alt-Rotamer
 809 ASP   ( 268-)  B   H-bonding suggests Asn; but Alt-Rotamer
 843 ASP   ( 302-)  B   H-bonding suggests Asn
1370 ASP   ( 268-)  E   H-bonding suggests Asn; but Alt-Rotamer
1404 ASP   ( 302-)  E   H-bonding suggests Asn
1931 ASP   ( 268-)  H   H-bonding suggests Asn; but Alt-Rotamer
1965 ASP   ( 302-)  H   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 :  -0.885
  2nd generation packing quality :  -0.397
  Ramachandran plot appearance   :  -0.621
  chi-1/chi-2 rotamer normality  :  -1.731
  Backbone conformation          :  -0.546

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.368 (tight)
  Bond angles                    :   0.707
  Omega angle restraints         :   0.308 (tight)
  Side chain planarity           :   0.466 (tight)
  Improper dihedral distribution :   0.835
  B-factor distribution          :   0.876
  Inside/Outside distribution    :   1.072

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 :   0.0
  Ramachandran plot appearance   :   0.6
  chi-1/chi-2 rotamer normality  :  -0.4
  Backbone conformation          :  -0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.368 (tight)
  Bond angles                    :   0.707
  Omega angle restraints         :   0.308 (tight)
  Side chain planarity           :   0.466 (tight)
  Improper dihedral distribution :   0.835
  B-factor distribution          :   0.876
  Inside/Outside distribution    :   1.072
==============

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.