WHAT IF Check report

This file was created 2011-12-17 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 pdb1rxo.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   = 158.500  C    = 202.600
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    = 111.759  B   = 111.759  C    = 202.600
    Alpha=  90.000  Beta=  90.000  Gamma=  90.326

Dimensions of the conventional cell

    A    = 111.759  B   = 111.759  C    = 202.600
    Alpha=  90.000  Beta=  90.000  Gamma=  89.674

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.

2317 RUB   ( 476-)  L  -
2319 RUB   ( 476-)  B  -
2321 RUB   ( 476-)  E  -
2324 RUB   ( 476-)  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: Artificial side chains detected

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

 347 GLU   ( 355-)  L
 925 GLU   ( 355-)  B
2081 GLU   ( 355-)  H

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) :279.000

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 : 4.26

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.

 193 KCX   ( 201-)  L      CH     CX
 193 KCX   ( 201-)  L      OX1    OQ1
 193 KCX   ( 201-)  L      OX2    OQ2
 771 KCX   ( 201-)  B      CH     CX
 771 KCX   ( 201-)  B      OX1    OQ1
 771 KCX   ( 201-)  B      OX2    OQ2
1349 KCX   ( 201-)  E      CH     CX
1349 KCX   ( 201-)  E      OX1    OQ1
1349 KCX   ( 201-)  E      OX2    OQ2
1927 KCX   ( 201-)  H      CH     CX
1927 KCX   ( 201-)  H      OX1    OQ1
1927 KCX   ( 201-)  H      OX2    OQ2

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.

   3 VAL   (  11-)  L      CA   CB    1.63    4.8
 581 VAL   (  11-)  B      CA   CB    1.63    4.8
1159 VAL   (  11-)  E      CA   CB    1.63    4.8
1737 VAL   (  11-)  H      CA   CB    1.63    4.8

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

 |  0.998373  0.000008  0.000004|
 |  0.000008  0.998367  0.000002|
 |  0.000004  0.000002  0.999346|
Proposed new scale matrix

 |  0.006355  0.000000  0.000000|
 |  0.000000  0.006319  0.000000|
 |  0.000000  0.000000  0.004939|
With corresponding cell

    A    = 157.348  B   = 158.245  C    = 202.461
    Alpha=  90.002  Beta=  90.002  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 157.600  B   = 158.500  C    = 202.600
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 139.435
(Under-)estimated Z-score: 8.703

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.

   4 GLY   (  12-)  L     -C    N    CA  128.73    4.8
   4 GLY   (  12-)  L      N    CA   C    87.91   -8.5
   5 PHE   (  13-)  L      N    CA   C   123.42    4.4
  67 THR   (  75-)  L      C    CA   CB   99.90   -5.4
  71 ARG   (  79-)  L      CB   CG   CD  105.15   -4.5
  71 ARG   (  79-)  L      CG   CD   NE  117.47    4.1
 113 VAL   ( 121-)  L      N    CA   CB  103.45   -4.1
 255 PRO   ( 263-)  L      N    CA   C   124.47    5.1
 259 HIS   ( 267-)  L      CG   ND1  CE1 109.84    4.2
 286 HIS   ( 294-)  L      CG   ND1  CE1 109.83    4.2
 299 HIS   ( 307-)  L      CG   ND1  CE1 109.92    4.3
 317 HIS   ( 325-)  L      C    CA   CB  101.08   -4.7
 401 HIS   ( 409-)  L      CG   ND1  CE1 109.77    4.2
 582 GLY   (  12-)  B     -C    N    CA  128.71    4.8
 582 GLY   (  12-)  B      N    CA   C    87.91   -8.5
 583 PHE   (  13-)  B      N    CA   C   123.41    4.4
 645 THR   (  75-)  B      C    CA   CB   99.92   -5.4
 649 ARG   (  79-)  B      CB   CG   CD  105.12   -4.5
 649 ARG   (  79-)  B      CG   CD   NE  117.47    4.1
 691 VAL   ( 121-)  B      N    CA   CB  103.47   -4.1
 833 PRO   ( 263-)  B      N    CA   C   124.47    5.1
 837 HIS   ( 267-)  B      CG   ND1  CE1 109.86    4.3
 864 HIS   ( 294-)  B      CG   ND1  CE1 109.85    4.3
 877 HIS   ( 307-)  B      CG   ND1  CE1 109.95    4.3
 895 HIS   ( 325-)  B      C    CA   CB  101.08   -4.7
And so on for a total of 56 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.

1738 GLY   (  12-)  H    9.22
 582 GLY   (  12-)  B    9.21
   4 GLY   (  12-)  L    9.21
1160 GLY   (  12-)  E    9.21
1850 VAL   ( 124-)  H    7.24
1272 VAL   ( 124-)  E    7.24
 116 VAL   ( 124-)  L    7.24
 694 VAL   ( 124-)  B    7.23
 872 ASP   ( 302-)  B    5.94
 294 ASP   ( 302-)  L    5.93
2028 ASP   ( 302-)  H    5.91
1450 ASP   ( 302-)  E    5.90
 954 VAL   ( 384-)  B    5.22
2110 VAL   ( 384-)  H    5.21
 376 VAL   ( 384-)  L    5.21
1532 VAL   ( 384-)  E    5.21
1498 ARG   ( 350-)  E    4.82
1417 TYR   ( 269-)  E    4.82
 725 ILE   ( 155-)  B    4.81
1881 ILE   ( 155-)  H    4.81
1995 TYR   ( 269-)  H    4.81
 839 TYR   ( 269-)  B    4.81
 147 ILE   ( 155-)  L    4.81
 342 ARG   ( 350-)  L    4.80
1303 ILE   ( 155-)  E    4.80
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 : 1.677

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.

 723 HIS   ( 153-)  B      CB   4.10
1301 HIS   ( 153-)  E      CB   4.09
 145 HIS   ( 153-)  L      CB   4.09
1879 HIS   ( 153-)  H      CB   4.07
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -0.812

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.

1161 PHE   (  13-)  E    -3.5
1739 PHE   (  13-)  H    -3.5
   5 PHE   (  13-)  L    -3.5
 583 PHE   (  13-)  B    -3.5
 581 VAL   (  11-)  B    -2.7
1737 VAL   (  11-)  H    -2.7
1159 VAL   (  11-)  E    -2.7
   3 VAL   (  11-)  L    -2.7
 939 VAL   ( 369-)  B    -2.6
1517 VAL   ( 369-)  E    -2.6
 361 VAL   ( 369-)  L    -2.6
2095 VAL   ( 369-)  H    -2.6
2302 ILE   ( 113-)  I    -2.6
  67 THR   (  75-)  L    -2.6
 645 THR   (  75-)  B    -2.6
1801 THR   (  75-)  H    -2.6
1223 THR   (  75-)  E    -2.6
 568 ILE   ( 113-)  S    -2.6
1724 ILE   ( 113-)  F    -2.6
1146 ILE   ( 113-)  C    -2.6
1743 VAL   (  17-)  H    -2.5
 587 VAL   (  17-)  B    -2.5
1165 VAL   (  17-)  E    -2.5
   9 VAL   (  17-)  L    -2.5
 464 LEU   (   9-)  S    -2.5
And so on for a total of 64 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.

   2 SER   (  10-)  L  Poor phi/psi
   3 VAL   (  11-)  L  Poor phi/psi
   5 PHE   (  13-)  L  Poor phi/psi
   6 LYS   (  14-)  L  Poor phi/psi
   9 VAL   (  17-)  L  Poor phi/psi
  10 LYS   (  18-)  L  Poor phi/psi
  12 TYR   (  20-)  L  Poor phi/psi
  13 LYS   (  21-)  L  Poor phi/psi
  15 THR   (  23-)  L  Poor phi/psi
  54 SER   (  62-)  L  Poor phi/psi
 155 ASN   ( 163-)  L  Poor phi/psi
 167 LYS   ( 175-)  L  PRO omega poor
 199 ASN   ( 207-)  L  Poor phi/psi
 289 MET   ( 297-)  L  Poor phi/psi
 362 SER   ( 370-)  L  Poor phi/psi
 468 GLU   (  13-)  S  Poor phi/psi
 470 LEU   (  15-)  S  Poor phi/psi
 492 LYS   (  37-)  S  Poor phi/psi
 502 ASP   (  47-)  S  Poor phi/psi
 526 LYS   (  71-)  S  Poor phi/psi
 580 SER   (  10-)  B  Poor phi/psi
 581 VAL   (  11-)  B  Poor phi/psi
 583 PHE   (  13-)  B  Poor phi/psi
 584 LYS   (  14-)  B  Poor phi/psi
 587 VAL   (  17-)  B  Poor phi/psi
And so on for a total of 80 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!

   3 VAL   (  11-)  L      0
   4 GLY   (  12-)  L      0
   5 PHE   (  13-)  L      0
   6 LYS   (  14-)  L      0
   7 ALA   (  15-)  L      0
   9 VAL   (  17-)  L      0
  10 LYS   (  18-)  L      0
  12 TYR   (  20-)  L      0
  15 THR   (  23-)  L      0
  16 TYR   (  24-)  L      0
  18 THR   (  26-)  L      0
  38 PRO   (  46-)  L      0
  53 SER   (  61-)  L      0
  54 SER   (  62-)  L      0
  55 THR   (  63-)  L      0
  58 TRP   (  66-)  L      0
  62 TRP   (  70-)  L      0
  66 LEU   (  74-)  L      0
  68 ASN   (  76-)  L      0
  77 TYR   (  85-)  L      0
  83 ALA   (  91-)  L      0
  86 GLU   (  94-)  L      0
  99 LEU   ( 107-)  L      0
 102 GLU   ( 110-)  L      0
 113 VAL   ( 121-)  L      0
And so on for a total of 887 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 : 2.061

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].

  36 PRO   (  44-)  L    46.8 half-chair C-delta/C-gamma (54 degrees)
  42 PRO   (  50-)  L  -112.5 envelop C-gamma (-108 degrees)
 255 PRO   ( 263-)  L   -64.6 envelop C-beta (-72 degrees)
 614 PRO   (  44-)  B    46.8 half-chair C-delta/C-gamma (54 degrees)
 620 PRO   (  50-)  B  -112.5 envelop C-gamma (-108 degrees)
 833 PRO   ( 263-)  B   -64.5 envelop C-beta (-72 degrees)
1192 PRO   (  44-)  E    46.8 half-chair C-delta/C-gamma (54 degrees)
1198 PRO   (  50-)  E  -112.5 envelop C-gamma (-108 degrees)
1411 PRO   ( 263-)  E   -64.6 envelop C-beta (-72 degrees)
1770 PRO   (  44-)  H    46.9 half-chair C-delta/C-gamma (54 degrees)
1776 PRO   (  50-)  H  -112.5 envelop C-gamma (-108 degrees)
1989 PRO   ( 263-)  H   -64.6 envelop C-beta (-72 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.

 638 THR   (  68-)  B      N   <-> 2327 HOH   ( 677 )  B      O      0.41    2.29  INTRA BF
1794 THR   (  68-)  H      N   <-> 2331 HOH   ( 679 )  H      O      0.41    2.29  INTRA BF
  60 THR   (  68-)  L      N   <-> 2325 HOH   ( 676 )  L      O      0.41    2.29  INTRA BF
1216 THR   (  68-)  E      N   <-> 2329 HOH   ( 725 )  E      O      0.41    2.29  INTRA BF
2026 VAL   ( 300-)  H      N   <-> 2331 HOH   ( 672 )  H      O      0.41    2.29  INTRA BF
 292 VAL   ( 300-)  L      N   <-> 2325 HOH   ( 669 )  L      O      0.41    2.29  INTRA BF
1448 VAL   ( 300-)  E      N   <-> 2329 HOH   ( 718 )  E      O      0.41    2.29  INTRA BF
 870 VAL   ( 300-)  B      N   <-> 2327 HOH   ( 670 )  B      O      0.41    2.29  INTRA BF
1329 SER   ( 181-)  E      N   <-> 2329 HOH   ( 597 )  E      O      0.38    2.32  INTRA
 751 SER   ( 181-)  B      N   <-> 2327 HOH   ( 554 )  B      O      0.38    2.32  INTRA
 173 SER   ( 181-)  L      N   <-> 2325 HOH   ( 553 )  L      O      0.38    2.32  INTRA
1907 SER   ( 181-)  H      N   <-> 2331 HOH   ( 556 )  H      O      0.38    2.32  INTRA
 844 PHE   ( 274-)  B      CD2 <-> 2327 HOH   ( 571 )  B      O      0.31    2.49  INTRA
 266 PHE   ( 274-)  L      CD2 <-> 2325 HOH   ( 570 )  L      O      0.30    2.50  INTRA
1422 PHE   ( 274-)  E      CD2 <-> 2329 HOH   ( 615 )  E      O      0.30    2.50  INTRA
2000 PHE   ( 274-)  H      CD2 <-> 2331 HOH   ( 573 )  H      O      0.30    2.50  INTRA
 683 VAL   ( 113-)  B      N   <-> 2327 HOH   ( 490 )  B      O      0.30    2.40  INTRA
 105 VAL   ( 113-)  L      N   <-> 2325 HOH   ( 489 )  L      O      0.30    2.40  INTRA
1839 VAL   ( 113-)  H      N   <-> 2331 HOH   ( 492 )  H      O      0.30    2.40  INTRA
1261 VAL   ( 113-)  E      N   <-> 2329 HOH   ( 527 )  E      O      0.30    2.40  INTRA
 176 ASN   ( 184-)  L      ND2 <-> 2325 HOH   ( 599 )  L      O      0.30    2.40  INTRA BL
1332 ASN   ( 184-)  E      ND2 <-> 2329 HOH   ( 644 )  E      O      0.30    2.40  INTRA BL
 754 ASN   ( 184-)  B      ND2 <-> 2327 HOH   ( 600 )  B      O      0.30    2.40  INTRA BL
1910 ASN   ( 184-)  H      ND2 <-> 2331 HOH   ( 602 )  H      O      0.30    2.40  INTRA BL
 582 GLY   (  12-)  B      N   <->  583 PHE   (  13-)  B      N      0.27    2.33  INTRA BF
And so on for a total of 295 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.

 748 LEU   ( 178-)  B      -6.26
1904 LEU   ( 178-)  H      -6.26
 170 LEU   ( 178-)  L      -6.26
1326 LEU   ( 178-)  E      -6.26
1297 GLN   ( 149-)  E      -6.10
1875 GLN   ( 149-)  H      -6.10
 719 GLN   ( 149-)  B      -6.10
  14 LEU   (  22-)  L      -6.10
1170 LEU   (  22-)  E      -6.10
 592 LEU   (  22-)  B      -6.10
1748 LEU   (  22-)  H      -6.10
1686 PHE   (  75-)  F      -6.09
1108 PHE   (  75-)  C      -6.09
 530 PHE   (  75-)  S      -6.09
2264 PHE   (  75-)  I      -6.09
   6 LYS   (  14-)  L      -6.08
1740 LYS   (  14-)  H      -6.08
 584 LYS   (  14-)  B      -6.08
1162 LYS   (  14-)  E      -6.08
 141 GLN   ( 149-)  L      -6.07
1279 ARG   ( 131-)  E      -6.06
1857 ARG   ( 131-)  H      -6.06
 123 ARG   ( 131-)  L      -6.05
 701 ARG   ( 131-)  B      -6.05
 431 ARG   ( 439-)  L      -5.78
And so on for a total of 59 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: 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.

2198 LEU   (   9-)  I   -3.08
 464 LEU   (   9-)  S   -3.08
1447 ALA   ( 299-)  E   -2.84
 291 ALA   ( 299-)  L   -2.83
2025 ALA   ( 299-)  H   -2.79
 869 ALA   ( 299-)  B   -2.76
 565 VAL   ( 110-)  S   -2.73
1721 VAL   ( 110-)  F   -2.73
2299 VAL   ( 110-)  I   -2.72
1143 VAL   ( 110-)  C   -2.72
1255 LEU   ( 107-)  E   -2.57
  99 LEU   ( 107-)  L   -2.56
1833 LEU   ( 107-)  H   -2.56
  97 LEU   ( 105-)  L   -2.55
1253 LEU   ( 105-)  E   -2.55
1831 LEU   ( 105-)  H   -2.54
 675 LEU   ( 105-)  B   -2.54
 677 LEU   ( 107-)  B   -2.54

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

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.

 155 ASN   ( 163-)  L
 176 ASN   ( 184-)  L
 221 GLN   ( 229-)  L
 230 HIS   ( 238-)  L
 233 ASN   ( 241-)  L
 259 HIS   ( 267-)  L
 269 ASN   ( 277-)  L
 290 HIS   ( 298-)  L
 296 GLN   ( 304-)  L
 378 HIS   ( 386-)  L
 393 GLN   ( 401-)  L
 412 ASN   ( 420-)  L
 424 ASN   ( 432-)  L
 480 GLN   (  25-)  S
 484 GLN   (  29-)  S
 723 HIS   ( 153-)  B
 799 GLN   ( 229-)  B
 808 HIS   ( 238-)  B
 811 ASN   ( 241-)  B
 837 HIS   ( 267-)  B
 847 ASN   ( 277-)  B
 852 HIS   ( 282-)  B
 874 GLN   ( 304-)  B
 956 HIS   ( 386-)  B
 971 GLN   ( 401-)  B
And so on for a total of 58 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.

  14 LEU   (  22-)  L      N
  43 GLU   (  51-)  L      N
  59 THR   (  67-)  L      N
  61 VAL   (  69-)  L      N
  67 THR   (  75-)  L      OG1
  68 ASN   (  76-)  L      N
  69 LEU   (  77-)  L      N
 104 SER   ( 112-)  L      OG
 159 ARG   ( 167-)  L      N
 167 LYS   ( 175-)  L      N
 199 ASN   ( 207-)  L      ND2
 238 THR   ( 246-)  L      N
 287 ARG   ( 295-)  L      NE
 315 GLY   ( 323-)  L      N
 323 VAL   ( 331-)  L      N
 324 VAL   ( 332-)  L      N
 332 ASP   ( 340-)  L      N
 371 SER   ( 379-)  L      N
 393 GLN   ( 401-)  L      NE2
 395 GLY   ( 403-)  L      N
 396 GLY   ( 404-)  L      N
 405 ASN   ( 413-)  L      ND2
 446 GLU   ( 454-)  L      N
 457 GLN   (   2-)  S      N
 461 ILE   (   6-)  S      N
And so on for a total of 132 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.

 145 HIS   ( 153-)  L      ND1
 260 ASP   ( 268-)  L      OD1
 274 HIS   ( 282-)  L      ND1
 284 HIS   ( 292-)  L      NE2
 294 ASP   ( 302-)  L      OD2
 319 HIS   ( 327-)  L      NE2
 564 GLU   ( 109-)  S      OE2
 838 ASP   ( 268-)  B      OD1
 862 HIS   ( 292-)  B      NE2
1142 GLU   ( 109-)  C      OE2
1416 ASP   ( 268-)  E      OD1
1440 HIS   ( 292-)  E      NE2
1475 HIS   ( 327-)  E      NE2
1720 GLU   ( 109-)  F      OE2
1994 ASP   ( 268-)  H      OD1
2018 HIS   ( 292-)  H      NE2
2028 ASP   ( 302-)  H      OD2
2053 HIS   ( 327-)  H      NE2
2298 GLU   ( 109-)  I      OE2

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+.

2318  CA   ( 477-)  L     0.78   1.00 Scores about as good as NA
2320  CA   ( 477-)  B     0.78   1.00 Scores about as good as NA
2322  CA   ( 477-)  E     0.78   1.00 Scores about as good as NA
2323  CA   ( 477-)  H     0.78   1.00 Scores about as good as NA

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.

2325 HOH   ( 502 )  L      O  0.87 NA  4 ION-B NCS 3/3
2331 HOH   ( 597 )  H      O  1.01  K  4 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.

  85 GLU   (  93-)  L   H-bonding suggests Gln
 260 ASP   ( 268-)  L   H-bonding suggests Asn; but Alt-Rotamer
 294 ASP   ( 302-)  L   H-bonding suggests Asn
 663 GLU   (  93-)  B   H-bonding suggests Gln
 838 ASP   ( 268-)  B   H-bonding suggests Asn; but Alt-Rotamer
 872 ASP   ( 302-)  B   H-bonding suggests Asn
1241 GLU   (  93-)  E   H-bonding suggests Gln
1416 ASP   ( 268-)  E   H-bonding suggests Asn; but Alt-Rotamer
1450 ASP   ( 302-)  E   H-bonding suggests Asn
1819 GLU   (  93-)  H   H-bonding suggests Gln
1994 ASP   ( 268-)  H   H-bonding suggests Asn; but Alt-Rotamer
2028 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 :  -1.032
  2nd generation packing quality :  -0.478
  Ramachandran plot appearance   :  -0.812
  chi-1/chi-2 rotamer normality  :  -2.093
  Backbone conformation          :  -0.424

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.507 (tight)
  Bond angles                    :   0.808
  Omega angle restraints         :   0.375 (tight)
  Side chain planarity           :   0.557 (tight)
  Improper dihedral distribution :   1.031
  B-factor distribution          :   0.877
  Inside/Outside distribution    :   1.069

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 :  -0.3
  2nd generation packing quality :  -0.0
  Ramachandran plot appearance   :   0.4
  chi-1/chi-2 rotamer normality  :  -0.8
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.507 (tight)
  Bond angles                    :   0.808
  Omega angle restraints         :   0.375 (tight)
  Side chain planarity           :   0.557 (tight)
  Improper dihedral distribution :   1.031
  B-factor distribution          :   0.877
  Inside/Outside distribution    :   1.069
==============

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.