WHAT IF Check report

This file was created 2011-12-22 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 pdb1ex0.ent

Checks that need to be done early-on in validation

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: P 1 21 1
Number of matrices in space group: 2
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 2
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 4
Polymer chain multiplicity and SEQRES multiplicity disagree 1 2
Z and NCS seem to support the SEQRES multiplicity (so the matrix counting
problems seem not overly severe)

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.

1423 PGO   (1340-)  A  -
1424 PGO   (1341-)  A  -
1425 PGO   (1342-)  A  -
1429 PGO   (1343-)  B  -
1430 PGO   (1344-)  B  -
1432 PGO   (1345-)  B  -

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

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'.

 492 SER   ( 509-)  A      OG
 493 ARG   ( 510-)  A      CG
 493 ARG   ( 510-)  A      CD
 493 ARG   ( 510-)  A      NE
 493 ARG   ( 510-)  A      CZ
 493 ARG   ( 510-)  A      NH1
 493 ARG   ( 510-)  A      NH2
 735 VAL   (  34-)  B      CG1
 735 VAL   (  34-)  B      CG2
 736 ASN   (  35-)  B      CG
 736 ASN   (  35-)  B      OD1
 736 ASN   (  35-)  B      ND2
 737 LEU   (  36-)  B      CG
 737 LEU   (  36-)  B      CD1
 737 LEU   (  36-)  B      CD2
1205 SER   ( 509-)  B      OG
1206 ARG   ( 510-)  B      CG
1206 ARG   ( 510-)  B      CD
1206 ARG   ( 510-)  B      NE
1206 ARG   ( 510-)  B      CZ
1206 ARG   ( 510-)  B      NH1
1206 ARG   ( 510-)  B      NH2
1207 SER   ( 511-)  B      OG

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

1205 SER   ( 509-)  B    High
1206 ARG   ( 510-)  B    High
1207 SER   ( 511-)  B    High

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

 346 LYS   ( 363-)  A    0.50
 490 ASN   ( 507-)  A    0.80
 492 SER   ( 509-)  A    0.50
 493 ARG   ( 510-)  A    0.50
 898 GLU   ( 202-)  B    0.75
1419 ARG   ( 728-)  B    0.50
1420 PRO   ( 729-)  B    0.50

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) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

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

 |  0.996271 -0.000155  0.001273|
 | -0.000155  0.998696  0.001103|
 |  0.001273  0.001103  0.998232|
Proposed new scale matrix

 |  0.009980 -0.000002  0.002859|
 |  0.000002  0.014174 -0.000016|
 | -0.000010 -0.000009  0.007817|
With corresponding cell

    A    = 100.168  B   =  70.549  C    = 133.028
    Alpha=  89.873  Beta= 105.915  Gamma=  90.018

The CRYST1 cell dimensions

    A    = 100.540  B   =  70.640  C    = 133.380
    Alpha=  90.000  Beta= 106.080  Gamma=  90.000

Variance: 303.743
(Under-)estimated Z-score: 12.845

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.

  18 ASP   (  24-)  A      CA   CB   CG  117.01    4.4
  19 ASP   (  25-)  A      CA   CB   CG  118.27    5.7
  23 VAL   (  29-)  A      N    CA   CB  117.99    4.4
  29 ASN   (  46-)  A      N    CA   CB  117.67    4.2
  29 ASN   (  46-)  A      CB   CG   ND2 123.42    4.7
  34 HIS   (  51-)  A      CG   ND1  CE1 109.97    4.4
  39 ARG   (  56-)  A      CD   NE   CZ  129.04    4.1
  47 HIS   (  64-)  A      CA   CB   CG  109.14   -4.7
  47 HIS   (  64-)  A      CG   ND1  CE1 110.03    4.4
  48 HIS   (  65-)  A      CA   CB   CG  119.05    5.3
  48 HIS   (  65-)  A      CG   ND1  CE1 111.14    5.5
  50 ASP   (  67-)  A      CA   CB   CG  116.96    4.4
  76 ASP   (  93-)  A      CA   CB   CG  117.19    4.6
  78 ARG   (  95-)  A      CG   CD   NE  119.51    5.3
  78 ARG   (  95-)  A      CD   NE   CZ  153.65   17.7
  79 ARG   (  96-)  A      CB   CG   CD  105.64   -4.2
  83 ARG   ( 100-)  A      CG   CD   NE  124.99    8.5
  83 ARG   ( 100-)  A      CD   NE   CZ  132.16    5.8
 121 GLU   ( 138-)  A      N    CA   CB  119.18    5.1
 124 SER   ( 141-)  A      CA   CB   OG  103.07   -4.0
 126 ARG   ( 143-)  A      CD   NE   CZ  129.17    4.1
 144 VAL   ( 161-)  A     -C    N    CA  114.33   -4.1
 154 ARG   ( 171-)  A      CD   NE   CZ  130.06    4.6
 176 VAL   ( 193-)  A     -O   -C    N   116.59   -4.0
 176 VAL   ( 193-)  A      N    CA   CB   96.49   -8.2
And so on for a total of 208 lines.

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.

  30 VAL   (  47-)  A      CB     6.1   -24.91   -32.96
 176 VAL   ( 193-)  A      CB     7.4   -23.25   -32.96
 391 ARG   ( 408-)  A      C      6.7    10.37     0.13
 568 GLN   ( 590-)  A      C      6.2     9.85     0.15
 889 VAL   ( 193-)  B      CB     9.9   -19.95   -32.96
 913 VAL   ( 217-)  B      CB    10.9   -18.74   -32.96
 931 LEU   ( 235-)  B      CG     6.8   -20.96   -33.01
 984 PRO   ( 288-)  B      C      6.5    10.69     0.42
1161 VAL   ( 465-)  B      CB     9.3   -20.72   -32.96
The average deviation= 1.738

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.

1296 HIS   ( 605-)  B    4.91
1003 ASN   ( 307-)  B    4.34
 326 ASP   ( 343-)  A    4.15

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.

 707 THR   (   6-)  B    -3.6
1420 PRO   ( 729-)  B    -2.6
 633 PRO   ( 655-)  A    -2.6
 979 TYR   ( 283-)  B    -2.5
1419 ARG   ( 728-)  B    -2.5
 453 GLY   ( 470-)  A    -2.4
1412 LEU   ( 721-)  B    -2.4
1395 LYS   ( 704-)  B    -2.3
 446 LEU   ( 463-)  A    -2.3
  36 PHE   (  53-)  A    -2.3
 437 ASN   ( 454-)  A    -2.3
1204 THR   ( 508-)  B    -2.3
 176 VAL   ( 193-)  A    -2.3
 651 THR   ( 673-)  A    -2.3
 919 ARG   ( 223-)  B    -2.3
1261 LYS   ( 570-)  B    -2.2
 266 TYR   ( 283-)  A    -2.2
 889 VAL   ( 193-)  B    -2.2
 694 HIS   ( 716-)  A    -2.2
 206 ARG   ( 223-)  A    -2.2
1407 HIS   ( 716-)  B    -2.2
1360 GLY   ( 669-)  B    -2.2
 178 LEU   ( 195-)  A    -2.2
1295 LEU   ( 604-)  B    -2.2
1250 PHE   ( 559-)  B    -2.1
 337 LEU   ( 354-)  A    -2.1
 699 LEU   ( 721-)  A    -2.1
 647 GLY   ( 669-)  A    -2.1
 123 ARG   ( 140-)  A    -2.1
 832 MET   ( 136-)  B    -2.1
 197 TYR   ( 214-)  A    -2.1
1150 ASN   ( 454-)  B    -2.0
 449 THR   ( 466-)  A    -2.0
1307 ARG   ( 616-)  B    -2.0
1364 THR   ( 673-)  B    -2.0
 912 GLU   ( 216-)  B    -2.0
1376 PRO   ( 685-)  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.

  28 LEU   (  45-)  A  omega poor
  48 HIS   (  65-)  A  Poor phi/psi
  98 THR   ( 115-)  A  omega poor
 122 ASP   ( 139-)  A  Poor phi/psi
 134 LYS   ( 151-)  A  omega poor
 197 TYR   ( 214-)  A  Poor phi/psi
 209 SER   ( 226-)  A  omega poor
 229 GLN   ( 246-)  A  Poor phi/psi
 251 ALA   ( 268-)  A  omega poor
 254 ASP   ( 271-)  A  Poor phi/psi
 256 GLY   ( 273-)  A  omega poor
 264 ASN   ( 281-)  A  Poor phi/psi
 266 TYR   ( 283-)  A  Poor phi/psi
 289 GLU   ( 306-)  A  Poor phi/psi
 293 ARG   ( 310-)  A  omega poor
 295 GLY   ( 312-)  A  omega poor
 296 GLN   ( 313-)  A  omega poor
 322 PHE   ( 339-)  A  Poor phi/psi
 326 ASP   ( 343-)  A  Poor phi/psi
 328 ASP   ( 345-)  A  Poor phi/psi
 329 ALA   ( 346-)  A  Poor phi/psi
 385 ASN   ( 402-)  A  Poor phi/psi
 393 GLY   ( 410-)  A  PRO omega poor
 404 HIS   ( 421-)  A  omega poor
 405 VAL   ( 422-)  A  omega poor
And so on for a total of 98 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 ARG   (  11-)  A      0
   6 ARG   (  12-)  A      0
   7 ALA   (  13-)  A      0
  11 ASN   (  17-)  A      0
  12 ASN   (  18-)  A      0
  16 ALA   (  22-)  A      0
  23 VAL   (  29-)  A      0
  24 GLU   (  30-)  A      0
  25 GLN   (  42-)  A      0
  26 GLU   (  43-)  A      0
  28 LEU   (  45-)  A      0
  36 PHE   (  53-)  A      0
  37 LYS   (  54-)  A      0
  40 TRP   (  57-)  A      0
  48 HIS   (  65-)  A      0
  49 THR   (  66-)  A      0
  50 ASP   (  67-)  A      0
  52 TYR   (  69-)  A      0
  53 GLU   (  70-)  A      0
  54 ASN   (  71-)  A      0
  61 ARG   (  78-)  A      0
  72 SER   (  89-)  A      0
  73 ARG   (  90-)  A      0
  75 TYR   (  92-)  A      0
  79 ARG   (  96-)  A      0
And so on for a total of 620 lines.

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!

1360 GLY   ( 669-)  B   2.33   15
 647 GLY   ( 669-)  A   1.97   21
 911 GLY   ( 215-)  B   1.55   10

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

  10 PRO   (  16-)  A    0.16 LOW
  21 PRO   (  27-)  A    0.17 LOW
  74 PRO   (  91-)  A    0.08 LOW
  77 PRO   (  94-)  A    0.18 LOW
 101 PRO   ( 118-)  A    0.17 LOW
 133 PRO   ( 150-)  A    0.46 HIGH
 159 PRO   ( 176-)  A    0.08 LOW
 314 PRO   ( 331-)  A    0.47 HIGH
 382 PRO   ( 399-)  A    0.50 HIGH
 675 PRO   ( 697-)  A    0.13 LOW
 787 PRO   (  91-)  B    0.17 LOW
1255 PRO   ( 564-)  B    0.46 HIGH
1388 PRO   ( 697-)  B    0.09 LOW

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].

  92 PRO   ( 109-)  A   -65.0 envelop C-beta (-72 degrees)
 149 PRO   ( 166-)  A   106.8 envelop C-beta (108 degrees)
 238 PRO   ( 255-)  A   -65.7 envelop C-beta (-72 degrees)
 272 PRO   ( 289-)  A   120.5 half-chair C-beta/C-alpha (126 degrees)
 557 PRO   ( 579-)  A   103.8 envelop C-beta (108 degrees)
 633 PRO   ( 655-)  A   -40.0 envelop C-alpha (-36 degrees)
 663 PRO   ( 685-)  A   162.9 half-chair C-alpha/N (162 degrees)
 814 PRO   ( 118-)  B   -44.9 envelop C-alpha (-36 degrees)
 985 PRO   ( 289-)  B    99.5 envelop C-beta (108 degrees)
1079 PRO   ( 383-)  B   -61.3 half-chair C-beta/C-alpha (-54 degrees)
1346 PRO   ( 655-)  B   -42.2 envelop C-alpha (-36 degrees)
1376 PRO   ( 685-)  B   100.3 envelop C-beta (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.

1184 GLU   ( 488-)  B      OE2 <-> 1187 ARG   ( 491-)  B      NH1    0.33    2.37  INTRA BF
 832 MET   ( 136-)  B    A CG  <->  839 ARG   ( 143-)  B      CB     0.30    2.90  INTRA BF
1038 HIS   ( 342-)  B      ND1 <-> 1130 GLU   ( 434-)  B      OE1    0.29    2.41  INTRA BL
 999 ARG   ( 303-)  B      NE  <-> 1434 HOH   (1754 )  B      O      0.26    2.44  INTRA
 325 HIS   ( 342-)  A      ND1 <->  417 GLU   ( 434-)  A      OE1    0.25    2.45  INTRA BL
 455 ASP   ( 472-)  A      OD2 <->  682 LYS   ( 704-)  A      NZ     0.25    2.45  INTRA BF
 206 ARG   ( 223-)  A    A NH2 <->  694 HIS   ( 716-)  A      CE1    0.24    2.86  INTRA
 445 LYS   ( 462-)  A      NZ  <-> 1427 PO4   (1330-)  A      O3     0.24    2.46  INTRA
 611 ILE   ( 633-)  A      O   <->  629 GLN   ( 651-)  A      N      0.23    2.47  INTRA BF
 680 HIS   ( 702-)  A      ND1 <->  681 ARG   ( 703-)  A      N      0.19    2.71  INTRA BF
 326 ASP   ( 343-)  A      OD2 <->  712 ARG   (  11-)  B      NH1    0.19    2.51  INTRA
 534 ASN   ( 556-)  A      ND2 <-> 1433 HOH   (1768 )  A      O      0.19    2.51  INTRA BF
 354 ASN   ( 371-)  A      ND2 <-> 1433 HOH   (1399 )  A      O      0.18    2.52  INTRA BL
1187 ARG   ( 491-)  B      NH2 <-> 1191 GLU   ( 495-)  B      OE1    0.17    2.53  INTRA BF
 411 ALA   ( 428-)  A      N   <->  412 PRO   ( 429-)  A      CD     0.17    2.83  INTRA BL
 781 GLN   (  85-)  B      NE2 <->  783 ASP   (  87-)  B      OD1    0.17    2.53  INTRA
1208 ASN   ( 517-)  B      N   <-> 1434 HOH   (1709 )  B      O      0.17    2.53  INTRA
1124 ALA   ( 428-)  B      N   <-> 1125 PRO   ( 429-)  B      CD     0.16    2.84  INTRA BL
 206 ARG   ( 223-)  A    A NH2 <->  696 TYR   ( 718-)  A      OH     0.15    2.55  INTRA
 181 GLU   ( 198-)  A      OE1 <->  184 ARG   ( 201-)  A      NH2    0.15    2.55  INTRA
 332 GLN   ( 349-)  A      NE2 <->  489 LEU   ( 506-)  A      O      0.15    2.55  INTRA BF
  37 LYS   (  54-)  A      NZ  <->   55 ASN   (  72-)  A      O      0.15    2.55  INTRA
1342 GLN   ( 651-)  B      NE2 <-> 1381 GLN   ( 690-)  B      NE2    0.15    2.70  INTRA BL
1247 ASN   ( 556-)  B      ND2 <-> 1434 HOH   (2038 )  B      O      0.15    2.55  INTRA BF
1352 ARG   ( 661-)  B      NH1 <-> 1373 GLU   ( 682-)  B      OE1    0.15    2.55  INTRA BF
And so on for a total of 156 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

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.

 150 TYR   ( 167-)  A      -8.09
 268 TYR   ( 285-)  A      -8.01
 981 TYR   ( 285-)  B      -8.01
1419 ARG   ( 728-)  B      -7.68
 870 ARG   ( 174-)  B      -7.18
 157 ARG   ( 174-)  A      -7.06
 733 GLN   (  32-)  B      -6.96
  78 ARG   (  95-)  A      -6.82
1418 ARG   ( 727-)  B      -6.80
 791 ARG   (  95-)  B      -6.56
 712 ARG   (  11-)  B      -6.36
 659 ARG   ( 681-)  A      -6.25
   5 ARG   (  11-)  A      -6.24
  79 ARG   (  96-)  A      -5.99
1372 ARG   ( 681-)  B      -5.96
 635 LYS   ( 657-)  A      -5.93
 863 TYR   ( 167-)  B      -5.90
1164 GLN   ( 468-)  B      -5.79
1142 LYS   ( 446-)  B      -5.78
 804 TYR   ( 108-)  B      -5.74
1203 ASN   ( 507-)  B      -5.70
 429 LYS   ( 446-)  A      -5.61
 522 HIS   ( 544-)  A      -5.59
  91 TYR   ( 108-)  A      -5.54
 451 GLN   ( 468-)  A      -5.54
 490 ASN   ( 507-)  A      -5.54
 615 ARG   ( 637-)  A      -5.51
 760 HIS   (  64-)  B      -5.46
  90 ARG   ( 107-)  A      -5.45
  47 HIS   (  64-)  A      -5.43
 788 TYR   (  92-)  B      -5.42
1365 ARG   ( 674-)  B      -5.35
 674 ARG   ( 696-)  A      -5.32
 803 ARG   ( 107-)  B      -5.31
  75 TYR   (  92-)  A      -5.29
 808 ASN   ( 112-)  B      -5.24
  95 ASN   ( 112-)  A      -5.24
1102 MET   ( 406-)  B      -5.23
1328 ARG   ( 637-)  B      -5.23
 822 GLN   ( 126-)  B      -5.15
 467 GLN   ( 484-)  A      -5.14
 109 GLN   ( 126-)  A      -5.14
1348 LYS   ( 657-)  B      -5.11
 792 ARG   (  96-)  B      -5.11
1180 GLN   ( 484-)  B      -5.08
 652 ARG   ( 674-)  A      -5.08
1132 ASN   ( 436-)  B      -5.04
1115 HIS   ( 419-)  B      -5.01
 419 ASN   ( 436-)  A      -5.01

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.

 389 MET   ( 406-)  A       391 - ARG    408- ( A)         -4.75
 732 LEU   (  31-)  B       734 - GLY     33- ( B)         -5.35
1102 MET   ( 406-)  B      1104 - ARG    408- ( B)         -4.86

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

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.

1206 ARG   ( 510-)  B   -2.88
 390 TYR   ( 407-)  A   -2.87
1365 ARG   ( 674-)  B   -2.61
 493 ARG   ( 510-)  A   -2.57
1103 TYR   ( 407-)  B   -2.53

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

 734 GLY   (  33-)  B     -  737 LEU   (  36-)  B        -1.66

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

Water, ion, and hydrogenbond related checks

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.

1433 HOH   (1697 )  A      O
1433 HOH   (1707 )  A      O
1433 HOH   (1749 )  A      O
1433 HOH   (1760 )  A      O
1433 HOH   (1765 )  A      O
1433 HOH   (1766 )  A      O
1433 HOH   (1843 )  A      O
1433 HOH   (1851 )  A      O
1433 HOH   (1856 )  A      O
1433 HOH   (1864 )  A      O
1433 HOH   (1868 )  A      O
1433 HOH   (1870 )  A      O
1433 HOH   (1876 )  A      O
1433 HOH   (1882 )  A      O
1433 HOH   (1883 )  A      O
1433 HOH   (1885 )  A      O
1433 HOH   (1888 )  A      O
1433 HOH   (1889 )  A      O
1433 HOH   (1891 )  A      O
1434 HOH   (1961 )  B      O
1434 HOH   (2000 )  B      O
1434 HOH   (2025 )  B      O
1434 HOH   (2039 )  B      O
1434 HOH   (2054 )  B      O
1434 HOH   (2062 )  B      O
1434 HOH   (2065 )  B      O
1434 HOH   (2072 )  B      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.

  93 GLN   ( 110-)  A
 354 ASN   ( 371-)  A
 568 GLN   ( 590-)  A
 579 GLN   ( 601-)  A
 914 ASN   ( 218-)  B
1043 ASN   ( 347-)  B
1281 GLN   ( 590-)  B
1292 GLN   ( 601-)  B
1381 GLN   ( 690-)  B

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.

  27 PHE   (  44-)  A      N
  58 ILE   (  75-)  A      N
  78 ARG   (  95-)  A      NH1
  84 VAL   ( 101-)  A      N
 123 ARG   ( 140-)  A      NE
 126 ARG   ( 143-)  A      NE
 131 SER   ( 148-)  A      N
 132 SER   ( 149-)  A      N
 154 ARG   ( 171-)  A      NH1
 180 ASN   ( 197-)  A      N
 184 ARG   ( 201-)  A      NH1
 206 ARG   ( 223-)  A    A NH1
 273 SER   ( 290-)  A      N
 296 GLN   ( 313-)  A      N
 298 TRP   ( 315-)  A      N
 305 ASN   ( 322-)  A      ND2
 326 ASP   ( 343-)  A      N
 327 ASN   ( 344-)  A      N
 332 GLN   ( 349-)  A      N
 355 TYR   ( 372-)  A      N
 380 SER   ( 397-)  A      OG
 446 LEU   ( 463-)  A      N
 512 LYS   ( 534-)  A      NZ
 556 GLU   ( 578-)  A      N
 579 GLN   ( 601-)  A      NE2
And so on for a total of 65 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.

  95 ASN   ( 112-)  A      OD1
 320 ASN   ( 337-)  A      OD1
 700 ASP   ( 722-)  A      OD1
1033 ASN   ( 337-)  B      OD1
1146 HIS   ( 450-)  B      ND1
1208 ASN   ( 517-)  B      OD1

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+.

1422  CA   (1320-)  A     0.31   0.67 Is perhaps  K
1426  CA   (1321-)  B     0.34   0.77 Is perhaps  K

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.

1433 HOH   (1360 )  A      O  0.94  K  4 NCS 1/1
1433 HOH   (1421 )  A      O  1.08  K  4 NCS 1/1
1433 HOH   (1439 )  A      O  1.01  K  4 NCS 1/1
1433 HOH   (1572 )  A      O  1.13  K  4
1433 HOH   (1613 )  A      O  0.97  K  4 Ion-B NCS 1/1
1433 HOH   (1690 )  A      O  1.01  K  4 Ion-B
1433 HOH   (1695 )  A      O  0.95  K  4 Ion-B
1433 HOH   (1745 )  A      O  0.91  K  4 Ion-B
1433 HOH   (1767 )  A      O  1.07  K  5 ION-B
1434 HOH   (1386 )  B      O  1.13  K  4 NCS 1/1
1434 HOH   (1412 )  B      O  1.06  K  4 NCS 1/1
1434 HOH   (1472 )  B      O  0.94  K  5 NCS 1/1
1434 HOH   (1490 )  B      O  0.91  K  6 NCS 1/1
1434 HOH   (1493 )  B      O  0.89  K  5
1434 HOH   (1539 )  B      O  0.92  K  5
1434 HOH   (1595 )  B      O  1.02  K  4 NCS 1/1
1434 HOH   (1676 )  B      O  0.88  K  4
1434 HOH   (1788 )  B      O  0.91  K  4 Ion-B NCS 1/1
1434 HOH   (2047 )  B      O  0.98  K  4 ION-B

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.

 107 GLU   ( 124-)  A   H-bonding suggests Gln
 199 GLU   ( 216-)  A   H-bonding suggests Gln
 499 ASP   ( 521-)  A   H-bonding suggests Asn; but Alt-Rotamer
 739 GLU   (  43-)  B   H-bonding suggests Gln
 912 GLU   ( 216-)  B   H-bonding suggests Gln
1322 GLU   ( 631-)  B   H-bonding suggests Gln

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 :  -0.509
  2nd generation packing quality :  -1.998
  Ramachandran plot appearance   :  -0.615
  chi-1/chi-2 rotamer normality  :  -2.257
  Backbone conformation          :  -0.441

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.613 (tight)
  Bond angles                    :   1.384
  Omega angle restraints         :   1.268
  Side chain planarity           :   1.010
  Improper dihedral distribution :   1.496
  B-factor distribution          :   0.657
  Inside/Outside distribution    :   1.042

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 : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.2
  2nd generation packing quality :  -1.3
  Ramachandran plot appearance   :  -0.0
  chi-1/chi-2 rotamer normality  :  -1.3
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.613 (tight)
  Bond angles                    :   1.384
  Omega angle restraints         :   1.268
  Side chain planarity           :   1.010
  Improper dihedral distribution :   1.496
  B-factor distribution          :   0.657
  Inside/Outside distribution    :   1.042
==============

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.