WHAT IF Check report

This file was created 2012-01-25 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 pdb2iam.ent

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:


Number of TLS groups mentione in PDB file header: 0

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

Note: B-factor plot

Chain identifier: P

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Nomenclature related problems

Warning: Tyrosine convention problem

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

  11 TYR   (  13-)  A
  77 TYR   (  79-)  A
 262 TYR   (  83-)  B
 342 TYR   ( 171-)  B
 460 TYR   (  84-)  C
 608 TYR   (  35-)  D
 620 TYR   (  47-)  D
 637 TYR   (  64-)  D
 673 TYR   ( 100-)  D
 757 TYR   ( 184-)  D

Warning: Phenylalanine convention problem

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

  24 PHE   (  26-)  A
 135 PHE   ( 137-)  A
 143 PHE   ( 145-)  A
 196 PHE   (  17-)  B
 219 PHE   (  40-)  B
 293 PHE   ( 122-)  B
 410 PHE   (  34-)  C
 674 PHE   ( 101-)  D
 769 PHE   ( 196-)  D

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

 157 ASP   ( 159-)  A
 160 ASP   ( 162-)  A
 179 ASP   ( 181-)  A
 376 ASP   (  37-)  P
 611 ASP   (  38-)  D
 646 ASP   (  73-)  D
 685 ASP   ( 112-)  D
 754 ASP   ( 181-)  D

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

   2 GLU   (   4-)  A
  19 GLU   (  21-)  A
  44 GLU   (  46-)  A
  45 GLU   (  47-)  A
 164 GLU   ( 166-)  A
 170 GLU   ( 172-)  A
 177 GLU   ( 179-)  A
 201 GLU   (  22-)  B
 214 GLU   (  35-)  B
 231 GLU   (  52-)  B
 275 GLU   (  96-)  B
 299 GLU   ( 128-)  B
 308 GLU   ( 137-)  B
 333 GLU   ( 162-)  B
 340 GLU   ( 169-)  B
 358 GLU   ( 187-)  B
 390 GLU   (  14-)  C
 568 GLU   ( 192-)  C
 791 GLU   ( 218-)  D

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.

 178 PHE   ( 180-)  A      N   -C     1.42    4.3
 340 GLU   ( 169-)  B      CD   OE1   1.65   21.3
 340 GLU   ( 169-)  B      CD   OE2   1.36    5.7
 361 ALA   ( 190-)  B      C    O     1.36    6.7
 566 ILE   ( 190-)  C      CA   CB    1.62    4.3
 599 ASP   (  26-)  D      CB   CG    1.63    4.7
 684 GLU   ( 111-)  D      CG   CD    1.63    4.5

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

 |  0.999040  0.000055  0.000027|
 |  0.000055  0.997140 -0.000306|
 |  0.000027 -0.000306  0.998841|
Proposed new scale matrix

 |  0.011586  0.000000  0.000000|
 |  0.000000  0.003707  0.000001|
 |  0.000000  0.000003  0.010279|
With corresponding cell

    A    =  86.310  B   = 269.789  C    =  97.287
    Alpha=  90.035  Beta=  90.001  Gamma=  90.002

The CRYST1 cell dimensions

    A    =  86.391  B   = 270.542  C    =  97.396
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 86.903
(Under-)estimated Z-score: 6.870

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.

   3 HIS   (   5-)  A      CG   ND1  CE1 109.61    4.0
  13 ASN   (  15-)  A      N    CA   C   122.87    4.2
 112 PRO   ( 114-)  A     -C    N    CA  144.44    4.4
 112 PRO   ( 114-)  A     -C    N    CD  104.34   -5.0
 112 PRO   ( 114-)  A      CD   N    CA  105.83   -4.4
 115 VAL   ( 117-)  A      C    CA   CB  102.49   -4.0
 147 HIS   ( 149-)  A      CG   ND1  CE1 109.91    4.3
 177 GLU   ( 179-)  A      CB   CG   CD  105.10   -4.4
 256 THR   (  77-)  B      C    CA   CB  102.36   -4.1
 295 PRO   ( 124-)  B      N    CA   C   100.70   -4.4
 340 GLU   ( 169-)  B      CG   CD   OE1 107.16   -4.9
 361 ALA   ( 190-)  B      CA   C    O   110.18   -6.2
 378 GLN   (   2-)  C      N    CA   C   123.14    4.3
 382 SER   (   6-)  C      C    CA   CB  117.87    4.1
 423 TYR   (  47-)  C      N    CA   C    98.54   -4.5
 456 ASP   (  80-)  C     -C    N    CA  114.32   -4.1
 462 CYS   (  86-)  C      N    CA   CB  118.48    4.7
 470 GLN   (  94-)  C     -C    N    CA  106.20   -8.6
 471 LYS   (  95-)  C      CA   CB   CG  124.20    5.0
 532 CYS   ( 156-)  C      CA   CB   SG  123.62    4.0
 581 PRO   (   8-)  D      CD   N    CA  104.96   -5.0
 667 THR   (  94-)  D      C    CA   CB   99.99   -5.3
 721 PRO   ( 148-)  D     -C    N    CD  108.56   -4.0

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

   2 GLU   (   4-)  A
  19 GLU   (  21-)  A
  44 GLU   (  46-)  A
  45 GLU   (  47-)  A
 157 ASP   ( 159-)  A
 160 ASP   ( 162-)  A
 164 GLU   ( 166-)  A
 170 GLU   ( 172-)  A
 177 GLU   ( 179-)  A
 179 ASP   ( 181-)  A
 201 GLU   (  22-)  B
 214 GLU   (  35-)  B
 231 GLU   (  52-)  B
 275 GLU   (  96-)  B
 299 GLU   ( 128-)  B
 308 GLU   ( 137-)  B
 333 GLU   ( 162-)  B
 340 GLU   ( 169-)  B
 358 GLU   ( 187-)  B
 376 ASP   (  37-)  P
 390 GLU   (  14-)  C
 568 GLU   ( 192-)  C
 611 ASP   (  38-)  D
 646 ASP   (  73-)  D
 685 ASP   ( 112-)  D
 754 ASP   ( 181-)  D
 791 GLU   ( 218-)  D

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.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 112 PRO   ( 114-)  A      N      8.3    24.72    -2.48
 720 PHE   ( 147-)  D      C      6.4    10.62     0.23
 721 PRO   ( 148-)  D      N      7.7    22.76    -2.48
The average deviation= 1.199

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.

 423 TYR   (  47-)  C    4.84
 295 PRO   ( 124-)  B    4.76
 378 GLN   (   2-)  C    4.62
 623 VAL   (  50-)  D    4.40
 382 SER   (   6-)  C    4.09
 701 GLU   ( 128-)  D    4.07

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.

 340 GLU   ( 169-)  B   11.49

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.

 182 THR   (   3-)  B    -3.5
 581 PRO   (   8-)  D    -3.1
 647 PHE   (  74-)  D    -2.9
 424 ILE   (  48-)  C    -2.8
  90 LEU   (  92-)  A    -2.7
 295 PRO   ( 124-)  B    -2.7
 112 PRO   ( 114-)  A    -2.6
 573 PRO   ( 197-)  C    -2.5
 501 SER   ( 125-)  C    -2.5
 266 GLU   (  87-)  B    -2.5
 451 SER   (  75-)  C    -2.5
 633 VAL   (  60-)  D    -2.4
 667 THR   (  94-)  D    -2.4
 128 THR   ( 130-)  A    -2.4
 752 LEU   ( 179-)  D    -2.3
 100 PRO   ( 102-)  A    -2.3
 279 THR   ( 100-)  B    -2.3
 639 VAL   (  66-)  D    -2.3
 586 LEU   (  13-)  D    -2.3
 334 THR   ( 163-)  B    -2.3
 592 MET   (  19-)  D    -2.3
 368 LEU   (  29-)  P    -2.2
 144 ARG   ( 146-)  A    -2.2
 132 GLU   ( 134-)  A    -2.2
  79 PRO   (  81-)  A    -2.2
And so on for a total of 53 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.

   6 ILE   (   8-)  A  omega poor
   9 GLU   (  11-)  A  omega poor
  10 PHE   (  12-)  A  omega poor
  12 LEU   (  14-)  A  omega poor
  28 GLU   (  30-)  A  omega poor
  30 PHE   (  32-)  A  omega poor
  37 LYS   (  39-)  A  Poor phi/psi
  50 ALA   (  52-)  A  omega poor
  53 GLU   (  55-)  A  omega poor
  76 ASN   (  78-)  A  Poor phi/psi
  87 VAL   (  89-)  A  omega poor
  98 ARG   ( 100-)  A  Poor phi/psi
 108 ASP   ( 110-)  A  omega poor
 109 LYS   ( 111-)  A  Poor phi/psi
 111 THR   ( 113-)  A  PRO omega poor
 112 PRO   ( 114-)  A  Poor phi/psi
 113 PRO   ( 115-)  A  Poor phi/psi
 122 ASN   ( 124-)  A  Poor phi/psi
 130 VAL   ( 132-)  A  omega poor
 134 VAL   ( 136-)  A  Poor phi/psi
 141 HIS   ( 143-)  A  Poor phi/psi
 148 TYR   ( 150-)  A  omega poor
 156 GLU   ( 158-)  A  omega poor
 157 ASP   ( 159-)  A  omega poor
 175 HIS   ( 177-)  A  omega poor
And so on for a total of 91 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -4.567

Warning: Unusual rotamers

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

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

 538 SER   ( 162-)  C    0.39

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 HIS   (   5-)  A      0
   9 GLU   (  11-)  A      0
  13 ASN   (  15-)  A      0
  17 SER   (  19-)  A      0
  20 PHE   (  22-)  A      0
  24 PHE   (  26-)  A      0
  29 ILE   (  31-)  A      0
  30 PHE   (  32-)  A      0
  34 MET   (  36-)  A      0
  37 LYS   (  39-)  A      0
  49 PHE   (  51-)  A      0
  54 ALA   (  56-)  A      0
  75 SER   (  77-)  A      0
  76 ASN   (  78-)  A      0
  77 TYR   (  79-)  A      0
  90 LEU   (  92-)  A      0
  97 LEU   (  99-)  A      0
  98 ARG   ( 100-)  A      0
 100 PRO   ( 102-)  A      0
 101 ASN   ( 103-)  A      0
 108 ASP   ( 110-)  A      0
 109 LYS   ( 111-)  A      0
 111 THR   ( 113-)  A      0
 112 PRO   ( 114-)  A      0
 113 PRO   ( 115-)  A      0
And so on for a total of 353 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 9.601

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!

 339 GLY   ( 168-)  B   2.46   75
 468 GLY   (  92-)  C   2.11   17
 296 GLY   ( 125-)  B   1.79   45

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]

 581 PRO   (   8-)  D    0.47 HIGH
 648 PRO   (  75-)  D    0.10 LOW
 743 PRO   ( 170-)  D    0.18 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].

  79 PRO   (  81-)  A    33.4 envelop C-delta (36 degrees)
  94 PRO   (  96-)  A  -130.5 half-chair C-delta/C-gamma (-126 degrees)
 100 PRO   ( 102-)  A   109.4 envelop C-beta (108 degrees)
 112 PRO   ( 114-)  A   168.1 half-chair C-alpha/N (162 degrees)
 150 PRO   ( 152-)  A    46.2 half-chair C-delta/C-gamma (54 degrees)
 171 PRO   ( 173-)  A  -143.2 envelop C-delta (-144 degrees)
 184 PRO   (   5-)  B  -126.2 half-chair C-delta/C-gamma (-126 degrees)
 282 PRO   ( 103-)  B   -60.6 half-chair C-beta/C-alpha (-54 degrees)
 295 PRO   ( 124-)  B    34.9 envelop C-delta (36 degrees)
 384 PRO   (   8-)  C    34.4 envelop C-delta (36 degrees)
 425 PRO   (  49-)  C  -114.2 envelop C-gamma (-108 degrees)
 489 PRO   ( 113-)  C   109.8 envelop C-beta (108 degrees)
 567 PRO   ( 191-)  C   101.7 envelop C-beta (108 degrees)
 573 PRO   ( 197-)  C   131.2 half-chair C-beta/C-alpha (126 degrees)
 581 PRO   (   8-)  D   174.8 envelop N (180 degrees)
 721 PRO   ( 148-)  D  -142.2 envelop C-delta (-144 degrees)
 799 PRO   ( 226-)  D   -29.7 envelop C-alpha (-36 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short 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.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

 742 ASP   ( 169-)  D      OD1  <->   762 ARG   ( 189-)  D      NH2  0.50    2.20  INTRA BF
  33 ASP   (  35-)  A      O    <->    37 LYS   (  39-)  A      N    0.42    2.28  INTRA BF
 778 ARG   ( 205-)  D      NH1  <->   780 GLN   ( 207-)  D      OE1  0.42    2.28  INTRA BF
 337 ARG   ( 166-)  B      N    <->   340 GLU   ( 169-)  B      OE1  0.38    2.32  INTRA BL
 405 ASN   (  29-)  C      OD1  <->   406 ASN   (  30-)  C      N    0.30    2.30  INTRA BL
 295 PRO   ( 124-)  B      CD   <->   348 HIS   ( 177-)  B      CE1  0.28    2.92  INTRA BF
 181 ASP   (   2-)  B      O    <->   182 THR   (   3-)  B      CB   0.28    2.32  INTRA BF
 541 PHE   ( 165-)  C      CZ   <->   709 LYS   ( 136-)  D      NZ   0.26    2.84  INTRA BF
 301 ARG   ( 130-)  B      NH1  <->   308 GLU   ( 137-)  B      CD   0.26    2.84  INTRA BF
 165 HIS   ( 167-)  A      ND1  <->   167 GLY   ( 169-)  A      N    0.25    2.75  INTRA BF
 165 HIS   ( 167-)  A      ND1  <->   166 TRP   ( 168-)  A      N    0.25    2.65  INTRA BF
 626 GLY   (  53-)  D      N    <->   641 ARG   (  68-)  D      O    0.24    2.46  INTRA BL
 622 SER   (  49-)  D      OG   <->   641 ARG   (  68-)  D      NH1  0.24    2.46  INTRA BL
 134 VAL   ( 136-)  A      N    <->   815 HOH   ( 185 )  A      O    0.24    2.46  INTRA BF
 272 ARG   (  93-)  B      NH2  <->   324 TRP   ( 153-)  B      O    0.23    2.47  INTRA BF
 107 ILE   ( 109-)  A      O    <->   145 LYS   ( 147-)  A      N    0.23    2.47  INTRA BF
 700 SER   ( 127-)  D      OG   <->   703 GLU   ( 130-)  D      N    0.23    2.47  INTRA BF
  73 LYS   (  75-)  A      NZ   <->   376 ASP   (  37-)  P      OD2  0.23    2.47  INTRA BF
 379 VAL   (   3-)  C      CG1  <->   462 CYS   (  86-)  C      SG   0.23    3.17  INTRA BL
 811 ARG   ( 238-)  D      NH1  <->   813 ASP   ( 240-)  D      OD1  0.23    2.47  INTRA BF
 561 PHE   ( 185-)  C      O    <->   564 SER   ( 188-)  C      N    0.23    2.47  INTRA BF
 198 ASN   (  19-)  B      ND2  <->   201 GLU   (  22-)  B      CG   0.23    2.87  INTRA BF
  15 ASP   (  17-)  A      OD2  <->   185 ARG   (   6-)  B      NH2  0.21    2.49  INTRA BL
  37 LYS   (  39-)  A      NZ   <->   815 HOH   ( 199 )  A      O    0.21    2.49  INTRA BF
 722 ASP   ( 149-)  D      OD1  <->   745 PRO   ( 172-)  D      CG   0.20    2.60  INTRA BF
And so on for a total of 179 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Warning: Abnormal packing environment for some residues

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

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

 183 ARG   (   4-)  B      -7.31
  98 ARG   ( 100-)  A      -6.87
 487 GLN   ( 111-)  C      -6.48
 476 GLN   ( 100-)  C      -6.06
 500 LYS   ( 124-)  C      -5.82
 774 ARG   ( 201-)  D      -5.62
  16 GLN   (  18-)  A      -5.52
 614 MET   (  41-)  D      -5.52
 310 LYS   ( 139-)  B      -5.30
 771 GLN   ( 198-)  D      -5.19
 178 PHE   ( 180-)  A      -5.15
 565 ILE   ( 189-)  C      -5.13
 442 GLU   (  66-)  C      -5.04

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.

 180 GLY   (   1-)  B       183 - ARG      4- ( B)         -5.11

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: P

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Warning: Low packing Z-score for some residues

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

 800 VAL   ( 227-)  D   -2.61
 432 GLY   (  56-)  C   -2.61

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.

 577 VAL   (   4-)  D     -  580 THR   (   7-)  D        -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

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

Error: 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.

  13 ASN   (  15-)  A
 147 HIS   ( 149-)  A
 189 GLN   (  10-)  B
 212 ASN   (  33-)  B
 321 ASN   ( 150-)  B
 327 GLN   ( 156-)  B
 369 ASN   (  30-)  P
 381 GLN   (   5-)  C
 411 HIS   (  35-)  C
 453 GLN   (  77-)  C
 544 ASN   ( 168-)  C
 579 GLN   (   6-)  D
 638 ASN   (  65-)  D
 669 HIS   (  96-)  D
 776 HIS   ( 203-)  D
 782 GLN   ( 209-)  D

Warning: Buried unsatisfied hydrogen bond donors

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

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

Waters are not listed by this option.

  11 TYR   (  13-)  A      OH
  20 PHE   (  22-)  A      N
  28 GLU   (  30-)  A      N
  30 PHE   (  32-)  A      N
  43 LEU   (  45-)  A      N
  53 GLU   (  55-)  A      N
 119 TRP   ( 121-)  A      NE1
 128 THR   ( 130-)  A      N
 130 VAL   ( 132-)  A      N
 166 TRP   ( 168-)  A      N
 186 PHE   (   7-)  B      N
 188 TRP   (   9-)  B      NE1
 208 ARG   (  29-)  B      NE
 216 SER   (  37-)  B      OG
 217 VAL   (  38-)  B      N
 225 GLU   (  46-)  B      N
 254 VAL   (  75-)  B      N
 261 ASN   (  82-)  B      ND2
 302 TRP   ( 131-)  B      NE1
 334 THR   ( 163-)  B      OG1
 337 ARG   ( 166-)  B      NH2
 342 TYR   ( 171-)  B      OH
 358 GLU   ( 187-)  B      N
 370 ALA   (  31-)  P      N
 381 GLN   (   5-)  C      NE2
And so on for a total of 56 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.

   9 GLU   (  11-)  A      OE1
  64 ASP   (  66-)  A      OD1
  64 ASP   (  66-)  A      OD2
 544 ASN   ( 168-)  C      OD1

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.

  19 GLU   (  21-)  A   H-bonding suggests Gln
  64 ASP   (  66-)  A   H-bonding suggests Asn
  96 GLU   (  98-)  A   H-bonding suggests Gln
 160 ASP   ( 162-)  A   H-bonding suggests Asn; but Alt-Rotamer
 179 ASP   ( 181-)  A   H-bonding suggests Asn
 340 GLU   ( 169-)  B   H-bonding suggests Gln; but Alt-Rotamer
 385 ASP   (   9-)  C   H-bonding suggests Asn
 498 ASP   ( 122-)  C   H-bonding suggests Asn; but Alt-Rotamer
 503 ASP   ( 127-)  C   H-bonding suggests Asn
 629 ASP   (  56-)  D   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.448
  2nd generation packing quality :  -1.512
  Ramachandran plot appearance   :  -1.820
  chi-1/chi-2 rotamer normality  :  -4.567 (bad)
  Backbone conformation          :  -0.452

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.822
  Bond angles                    :   0.947
  Omega angle restraints         :   1.746 (loose)
  Side chain planarity           :   0.924
  Improper dihedral distribution :   1.021
  B-factor distribution          :   0.396
  Inside/Outside distribution    :   1.030

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 : 2.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.8
  2nd generation packing quality :   0.1
  Ramachandran plot appearance   :   0.6
  chi-1/chi-2 rotamer normality  :  -2.2
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.822
  Bond angles                    :   0.947
  Omega angle restraints         :   1.746 (loose)
  Side chain planarity           :   0.924
  Improper dihedral distribution :   1.021
  B-factor distribution          :   0.396
  Inside/Outside distribution    :   1.030
==============

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.