WHAT IF Check report

This file was created 2012-01-13 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb1tnf.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 1.768
CA-only RMS fit for the two chains : 1.309

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 1.496
CA-only RMS fit for the two chains : 0.929

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and C

All-atom RMS fit for the two chains : 1.704
CA-only RMS fit for the two chains : 1.311

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and C

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

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'.

   1 ARG   (   6-)  A      CG
   1 ARG   (   6-)  A      CD
   1 ARG   (   6-)  A      NE
   1 ARG   (   6-)  A      CZ
   1 ARG   (   6-)  A      NH1
   1 ARG   (   6-)  A      NH2
 153 ARG   (   6-)  B      CG
 153 ARG   (   6-)  B      CD
 153 ARG   (   6-)  B      NE
 153 ARG   (   6-)  B      CZ
 153 ARG   (   6-)  B      NH1
 153 ARG   (   6-)  B      NH2
 305 ARG   (   6-)  C      CG
 305 ARG   (   6-)  C      CD
 305 ARG   (   6-)  C      NE
 305 ARG   (   6-)  C      CZ
 305 ARG   (   6-)  C      NH1
 305 ARG   (   6-)  C      NH2

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:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

  26 ARG   (  31-)  A
  27 ARG   (  32-)  A
  39 ARG   (  44-)  A
  77 ARG   (  82-)  A
  98 ARG   ( 103-)  A
 126 ARG   ( 131-)  A
 133 ARG   ( 138-)  A
 178 ARG   (  31-)  B
 179 ARG   (  32-)  B
 191 ARG   (  44-)  B
 229 ARG   (  82-)  B
 250 ARG   ( 103-)  B
 278 ARG   ( 131-)  B
 285 ARG   ( 138-)  B
 330 ARG   (  31-)  C
 331 ARG   (  32-)  C
 343 ARG   (  44-)  C
 381 ARG   (  82-)  C
 402 ARG   ( 103-)  C
 430 ARG   ( 131-)  C
 437 ARG   ( 138-)  C

Warning: Tyrosine convention problem

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

  82 TYR   (  87-)  A
 110 TYR   ( 115-)  A
 136 TYR   ( 141-)  A
 206 TYR   (  59-)  B
 266 TYR   ( 119-)  B
 288 TYR   ( 141-)  B
 418 TYR   ( 119-)  C
 440 TYR   ( 141-)  C
 450 TYR   ( 151-)  C

Warning: Phenylalanine convention problem

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

  59 PHE   (  64-)  A
 119 PHE   ( 124-)  A
 147 PHE   ( 152-)  A
 211 PHE   (  64-)  B
 363 PHE   (  64-)  C
 423 PHE   ( 124-)  C
 451 PHE   ( 152-)  C

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.

   5 ASP   (  10-)  A
 157 ASP   (  10-)  B
 287 ASP   ( 140-)  B
 309 ASP   (  10-)  C
 429 ASP   ( 130-)  C

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.

  18 GLU   (  23-)  A
  37 GLU   (  42-)  A
  48 GLU   (  53-)  A
  99 GLU   ( 104-)  A
 111 GLU   ( 116-)  A
 122 GLU   ( 127-)  A
 130 GLU   ( 135-)  A
 189 GLU   (  42-)  B
 254 GLU   ( 107-)  B
 263 GLU   ( 116-)  B
 274 GLU   ( 127-)  B
 282 GLU   ( 135-)  B
 341 GLU   (  42-)  C
 409 GLU   ( 110-)  C
 415 GLU   ( 116-)  C
 426 GLU   ( 127-)  C
 434 GLU   ( 135-)  C

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.

  67 THR   (  72-)  A      CA   CB    1.65    6.2
  82 TYR   (  87-)  A      CA   CB    1.62    4.3
 188 VAL   (  41-)  B      CA   CB    1.65    5.9
 230 ILE   (  83-)  B      CA   CB    1.63    5.1
 327 TRP   (  28-)  C      NE1  CE2   1.32   -4.8
 340 VAL   (  41-)  C      CA   CB    1.61    4.2
 376 THR   (  77-)  C      CA   CB    1.63    4.9

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 PRO   (   8-)  A     -O   -C    N   115.43   -4.7
   3 PRO   (   8-)  A     -CA  -C    N   127.02    6.7
   4 SER   (   9-)  A     -CA  -C    N   107.59   -4.3
   4 SER   (   9-)  A      N    CA   CB  103.51   -4.1
   5 ASP   (  10-)  A      CA   CB   CG  116.91    4.3
   7 PRO   (  12-)  A     -CA  -C    N   125.22    5.5
   8 VAL   (  13-)  A      N    CA   CB  119.97    5.6
   8 VAL   (  13-)  A      C    CA   CB  101.87   -4.3
  14 ASN   (  19-)  A      CB   CG   ND2 122.91    4.3
  14 ASN   (  19-)  A      ND2  CG   OD1 116.90   -5.7
  16 GLN   (  21-)  A      NE2  CD   OE1 117.59   -5.0
  17 ALA   (  22-)  A      CA   C    O   130.61    5.8
  18 GLU   (  23-)  A     -CA  -C    N   106.95   -4.6
  20 GLN   (  25-)  A      CB   CG   CD  120.36    4.6
  20 GLN   (  25-)  A      NE2  CD   OE1 117.71   -4.9
  22 GLN   (  27-)  A      CB   CG   CD  105.66   -4.1
  23 TRP   (  28-)  A      CB   CG   CD1 119.45   -5.0
  23 TRP   (  28-)  A      CD1  CG   CD2 113.90    4.8
  23 TRP   (  28-)  A      CG   CD1  NE1 104.60   -4.3
  23 TRP   (  28-)  A      CE3  CD2  CG  138.71    4.8
  23 TRP   (  28-)  A      CG   CD2  CE2 100.50   -5.6
  25 ASN   (  30-)  A      CA   C    O   113.47   -4.3
  26 ARG   (  31-)  A     -CA  -C    N   129.43    6.6
  29 ASN   (  34-)  A      N    CA   C    98.52   -4.5
  32 LEU   (  37-)  A      N    CA   C    92.54   -6.7
And so on for a total of 287 lines.

Warning: High bond angle deviations

Bond angles were found to deviate more than normal from the mean standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set, and this is indeed observed for very high resolution X-ray structures. The fact that it is higher than 2.0 in this structure might indicate that the restraints used in the refinement were not strong enough. This will also occur if a different bond angle dictionary is used.

RMS Z-score for bond angles: 2.028
RMS-deviation in bond angles: 3.869

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.

   5 ASP   (  10-)  A
  18 GLU   (  23-)  A
  26 ARG   (  31-)  A
  27 ARG   (  32-)  A
  37 GLU   (  42-)  A
  39 ARG   (  44-)  A
  48 GLU   (  53-)  A
  77 ARG   (  82-)  A
  98 ARG   ( 103-)  A
  99 GLU   ( 104-)  A
 111 GLU   ( 116-)  A
 122 GLU   ( 127-)  A
 126 ARG   ( 131-)  A
 130 GLU   ( 135-)  A
 133 ARG   ( 138-)  A
 157 ASP   (  10-)  B
 178 ARG   (  31-)  B
 179 ARG   (  32-)  B
 189 GLU   (  42-)  B
 191 ARG   (  44-)  B
 229 ARG   (  82-)  B
 250 ARG   ( 103-)  B
 254 GLU   ( 107-)  B
 263 GLU   ( 116-)  B
 274 GLU   ( 127-)  B
 278 ARG   ( 131-)  B
 282 GLU   ( 135-)  B
 285 ARG   ( 138-)  B
 287 ASP   ( 140-)  B
 309 ASP   (  10-)  C
 330 ARG   (  31-)  C
 331 ARG   (  32-)  C
 341 GLU   (  42-)  C
 343 ARG   (  44-)  C
 381 ARG   (  82-)  C
 402 ARG   ( 103-)  C
 409 GLU   ( 110-)  C
 415 GLU   ( 116-)  C
 426 GLU   ( 127-)  C
 429 ASP   ( 130-)  C
 430 ARG   ( 131-)  C
 434 GLU   ( 135-)  C
 437 ARG   ( 138-)  C

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.

   3 PRO   (   8-)  A      N     -6.0   -22.18    -2.48
  86 VAL   (  91-)  A      CB    -6.8   -41.86   -32.96
 382 ILE   (  83-)  C      C     -6.4    -8.32     0.03
 382 ILE   (  83-)  C      CB     6.3    40.47    32.31
 386 TYR   (  87-)  C      C     -7.1   -10.70     0.33
The average deviation= 1.728

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.

  97 GLN   ( 102-)  A    7.60
 405 PRO   ( 106-)  C    7.39
  32 LEU   (  37-)  A    7.33
 386 TYR   (  87-)  C    7.25
 445 GLU   ( 146-)  C    7.00
 258 ALA   ( 111-)  B    6.90
 412 PRO   ( 113-)  C    6.58
 324 GLN   (  25-)  C    6.05
 310 LYS   (  11-)  C    5.97
  88 LEU   (  93-)  A    5.64
 336 LEU   (  37-)  C    5.63
 314 HIS   (  15-)  C    5.32
 410 ALA   ( 111-)  C    5.29
 104 ALA   ( 109-)  A    5.28
 294 SER   ( 147-)  B    5.15
 352 GLU   (  53-)  C    5.05
 249 GLN   ( 102-)  B    4.98
 342 LEU   (  43-)  C    4.85
 102 GLU   ( 107-)  A    4.82
 230 ILE   (  83-)  B    4.72
 305 ARG   (   6-)  C    4.65
  52 LEU   (  57-)  A    4.64
 446 SER   ( 147-)  C    4.57
  69 VAL   (  74-)  A    4.53
  21 LEU   (  26-)  A    4.49
 231 ALA   (  84-)  B    4.46
  94 SER   (  99-)  A    4.43
 172 GLN   (  25-)  B    4.33
  29 ASN   (  34-)  A    4.32
 348 VAL   (  49-)  C    4.26
 153 ARG   (   6-)  B    4.23
 202 LEU   (  55-)  B    4.22
  16 GLN   (  21-)  A    4.22
 229 ARG   (  82-)  B    4.19
  48 GLU   (  53-)  A    4.16
  68 HIS   (  73-)  A    4.15
 180 ALA   (  33-)  B    4.10
  61 GLY   (  66-)  A    4.10
  79 ALA   (  84-)  A    4.10
  89 LEU   (  94-)  A    4.02
 184 LEU   (  37-)  B    4.02

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 : 2.319

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.

 338 ASN   (  39-)  C    5.57

Torsion-related checks

Error: Ramachandran Z-score very low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is very low.

Ramachandran Z-score : -4.275

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.

 100 THR   ( 105-)  A    -3.6
 252 THR   ( 105-)  B    -3.6
 404 THR   ( 105-)  C    -3.5
  67 THR   (  72-)  A    -3.2
  82 TYR   (  87-)  A    -3.1
 405 PRO   ( 106-)  C    -3.1
 219 THR   (  72-)  B    -2.9
 371 THR   (  72-)  C    -2.8
 388 THR   (  89-)  C    -2.7
 178 ARG   (  31-)  B    -2.7
 325 LEU   (  26-)  C    -2.6
  65 PRO   (  70-)  A    -2.5
 330 ARG   (  31-)  C    -2.5
  78 ILE   (  83-)  A    -2.5
 112 PRO   ( 117-)  A    -2.5
 407 GLY   ( 108-)  C    -2.5
 171 GLY   (  24-)  B    -2.4
 263 GLU   ( 116-)  B    -2.4
 229 ARG   (  82-)  B    -2.4
  84 THR   (  89-)  A    -2.4
 220 HIS   (  73-)  B    -2.4
 291 PHE   ( 144-)  B    -2.4
  68 HIS   (  73-)  A    -2.4
 415 GLU   ( 116-)  C    -2.4
 176 LEU   (  29-)  B    -2.4
And so on for a total of 67 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 THR   (   7-)  A  PRO omega poor
   4 SER   (   9-)  A  Poor phi/psi
   6 LYS   (  11-)  A  PRO omega poor
  25 ASN   (  30-)  A  Poor phi/psi
  26 ARG   (  31-)  A  Poor phi/psi
  27 ARG   (  32-)  A  Poor phi/psi
  33 ALA   (  38-)  A  Poor phi/psi, omega poor
  39 ARG   (  44-)  A  Poor phi/psi
  41 ASN   (  46-)  A  Poor phi/psi
  65 PRO   (  70-)  A  Poor phi/psi
  67 THR   (  72-)  A  Poor phi/psi
  70 LEU   (  75-)  A  Poor phi/psi
  86 VAL   (  91-)  A  omega poor
  95 PRO   ( 100-)  A  Poor phi/psi
  98 ARG   ( 103-)  A  Poor phi/psi
  99 GLU   ( 104-)  A  Poor phi/psi
 100 THR   ( 105-)  A  PRO omega poor
 102 GLU   ( 107-)  A  Poor phi/psi
 105 GLU   ( 110-)  A  Poor phi/psi, omega poor
 154 THR   (   7-)  B  PRO omega poor
 155 PRO   (   8-)  B  Poor phi/psi
 156 SER   (   9-)  B  Poor phi/psi
 168 GLN   (  21-)  B  Poor phi/psi
 171 GLY   (  24-)  B  Poor phi/psi
 178 ARG   (  31-)  B  Poor phi/psi
And so on for a total of 72 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 : -6.294

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 PRO   (   8-)  A      0
   5 ASP   (  10-)  A      0
  18 GLU   (  23-)  A      0
  20 GLN   (  25-)  A      0
  25 ASN   (  30-)  A      0
  26 ARG   (  31-)  A      0
  27 ARG   (  32-)  A      0
  28 ALA   (  33-)  A      0
  29 ASN   (  34-)  A      0
  30 ALA   (  35-)  A      0
  31 LEU   (  36-)  A      0
  33 ALA   (  38-)  A      0
  34 ASN   (  39-)  A      0
  39 ARG   (  44-)  A      0
  40 ASP   (  45-)  A      0
  41 ASN   (  46-)  A      0
  42 GLN   (  47-)  A      0
  46 PRO   (  51-)  A      0
  48 GLU   (  53-)  A      0
  50 LEU   (  55-)  A      0
  60 LYS   (  65-)  A      0
  62 GLN   (  67-)  A      0
  65 PRO   (  70-)  A      0
  66 SER   (  71-)  A      0
  67 THR   (  72-)  A      0
And so on for a total of 259 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 : 9.052

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!

 295 GLY   ( 148-)  B   2.27   17
 143 GLY   ( 148-)  A   1.99   14

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]

 101 PRO   ( 106-)  A    0.46 HIGH
 134 PRO   ( 139-)  A    0.47 HIGH
 159 PRO   (  12-)  B    0.19 LOW
 167 PRO   (  20-)  B    0.47 HIGH
 247 PRO   ( 100-)  B    0.46 HIGH
 253 PRO   ( 106-)  B    0.46 HIGH
 286 PRO   ( 139-)  B    0.45 HIGH
 399 PRO   ( 100-)  C    0.45 HIGH
 405 PRO   ( 106-)  C    0.52 HIGH
 412 PRO   ( 113-)  C    0.51 HIGH

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].

   3 PRO   (   8-)  A  -121.7 half-chair C-delta/C-gamma (-126 degrees)
 101 PRO   ( 106-)  A    51.2 half-chair C-delta/C-gamma (54 degrees)
 108 PRO   ( 113-)  A   -64.4 envelop C-beta (-72 degrees)
 134 PRO   ( 139-)  A  -119.8 half-chair C-delta/C-gamma (-126 degrees)
 155 PRO   (   8-)  B   102.6 envelop C-beta (108 degrees)
 311 PRO   (  12-)  C   109.9 envelop C-beta (108 degrees)
 405 PRO   ( 106-)  C   106.5 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.

 133 ARG   ( 138-)  A      NH1 <->  136 TYR   ( 141-)  A      CE2    0.36    2.74  INTRA
 329 ASN   (  30-)  C      ND2 <->  330 ARG   (  31-)  C      NH1    0.24    2.61  INTRA BF
 321 ALA   (  22-)  C      O   <->  323 GLY   (  24-)  C      N      0.23    2.47  INTRA BF
 272 GLN   ( 125-)  B      OE1 <->  305 ARG   (   6-)  C      N      0.22    2.48  INTRA
  90 SER   (  95-)  A      N   <->  295 GLY   ( 148-)  B      O      0.19    2.51  INTRA
 381 ARG   (  82-)  C      NH1 <->  429 ASP   ( 130-)  C      OD2    0.18    2.52  INTRA
 331 ARG   (  32-)  C      O   <->  333 ASN   (  34-)  C      N      0.16    2.54  INTRA BF
 331 ARG   (  32-)  C      NH2 <->  445 GLU   ( 146-)  C      CB     0.16    2.94  INTRA BF
  56 GLN   (  61-)  A      NE2 <->   58 LEU   (  63-)  A      CD2    0.15    2.95  INTRA BL
  64 CYS   (  69-)  A      SG  <->  109 TRP   ( 114-)  A      CD1    0.14    3.26  INTRA
 144 GLN   ( 149-)  A      CG  <->  145 VAL   ( 150-)  A      N      0.13    2.87  INTRA
 101 PRO   ( 106-)  A      O   <->  103 GLY   ( 108-)  A      N      0.11    2.59  INTRA BF
 220 HIS   (  73-)  B      CE1 <->  248 CYS   ( 101-)  B      O      0.11    2.69  INTRA
 291 PHE   ( 144-)  B      C   <->  293 GLU   ( 146-)  B      N      0.10    2.80  INTRA BL
 242 SER   (  95-)  B      N   <->  447 GLY   ( 148-)  C      O      0.10    2.60  INTRA
  66 SER   (  71-)  A      O   <->   68 HIS   (  73-)  A      N      0.10    2.60  INTRA BF
 343 ARG   (  44-)  C      O   <->  345 ASN   (  46-)  C      N      0.10    2.60  INTRA
 381 ARG   (  82-)  C      NH1 <->  429 ASP   ( 130-)  C      CG     0.10    3.00  INTRA
 316 VAL   (  17-)  C      O   <->  328 LEU   (  29-)  C      N      0.09    2.61  INTRA
  33 ALA   (  38-)  A      O   <->   35 GLY   (  40-)  A      N      0.09    2.61  INTRA
 308 SER   (   9-)  C      O   <->  310 LYS   (  11-)  C      N      0.09    2.61  INTRA
  63 GLY   (  68-)  A      N   <->  107 LYS   ( 112-)  A      O      0.08    2.62  INTRA
 292 ALA   ( 145-)  B      N   <->  293 GLU   ( 146-)  B      N      0.08    2.52  INTRA BL
 232 VAL   (  85-)  B      O   <->  235 GLN   (  88-)  B      NE2    0.08    2.62  INTRA BF
 224 THR   (  77-)  B      N   <->  284 ASN   ( 137-)  B      OD1    0.07    2.63  INTRA BL
And so on for a total of 52 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

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.

 178 ARG   (  31-)  B      -7.41
 386 TYR   (  87-)  C      -7.38
 402 ARG   ( 103-)  C      -7.35
 250 ARG   ( 103-)  B      -7.27
  16 GLN   (  21-)  A      -7.06
 249 GLN   ( 102-)  B      -6.45
 366 GLN   (  67-)  C      -6.34
  98 ARG   ( 103-)  A      -6.30
  97 GLN   ( 102-)  A      -6.19
 330 ARG   (  31-)  C      -6.10
  26 ARG   (  31-)  A      -5.96
 411 LYS   ( 112-)  C      -5.96
 324 GLN   (  25-)  C      -5.87
 443 PHE   ( 144-)  C      -5.82
 234 TYR   (  87-)  B      -5.38
 214 GLN   (  67-)  B      -5.37
 170 GLU   (  23-)  B      -5.36
 257 GLU   ( 110-)  B      -5.25
 322 GLU   (  23-)  C      -5.13
  83 GLN   (  88-)  A      -5.12
  62 GLN   (  67-)  A      -5.12
 387 GLN   (  88-)  C      -5.11
 320 GLN   (  21-)  C      -5.03
  18 GLU   (  23-)  A      -5.03

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.

  97 GLN   ( 102-)  A        99 - GLU    104- ( A)         -5.81
 401 GLN   ( 102-)  C       403 - GLU    104- ( C)         -5.65

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

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.

 220 HIS   (  73-)  B   -3.02
 305 ARG   (   6-)  C   -2.93
  68 HIS   (  73-)  A   -2.90
 405 PRO   ( 106-)  C   -2.73

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.

  26 ARG   (  31-)  A     -   29 ASN   (  34-)  A        -1.92

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

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.

  14 ASN   (  19-)  A
  73 HIS   (  78-)  A
  97 GLN   ( 102-)  A
 172 GLN   (  25-)  B
 174 GLN   (  27-)  B
 186 ASN   (  39-)  B
 329 ASN   (  30-)  C
 333 ASN   (  34-)  C
 360 GLN   (  61-)  C
 377 HIS   (  78-)  C

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.

   6 LYS   (  11-)  A      N
   8 VAL   (  13-)  A      N
  25 ASN   (  30-)  A      N
  27 ARG   (  32-)  A      NE
  28 ALA   (  33-)  A      N
  42 GLN   (  47-)  A      N
  51 TYR   (  56-)  A      OH
  56 GLN   (  61-)  A      NE2
  58 LEU   (  63-)  A      N
  64 CYS   (  69-)  A      N
  70 LEU   (  75-)  A      N
  77 ARG   (  82-)  A      NE
  87 ASN   (  92-)  A      N
  92 ILE   (  97-)  A      N
 131 ILE   ( 136-)  A      N
 138 LEU   ( 143-)  A      N
 140 ALA   ( 145-)  A      N
 144 GLN   ( 149-)  A      NE2
 145 VAL   ( 150-)  A      N
 158 LYS   (  11-)  B      N
 168 GLN   (  21-)  B      N
 169 ALA   (  22-)  B      N
 172 GLN   (  25-)  B      N
 175 TRP   (  28-)  B      NE1
 177 ASN   (  30-)  B      N
And so on for a total of 62 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.

  42 GLN   (  47-)  A      OE1
  73 HIS   (  78-)  A      ND1
 125 ASP   ( 130-)  A      OD1
 144 GLN   ( 149-)  A      OE1
 208 GLN   (  61-)  B      OE1
 225 HIS   (  78-)  B      ND1
 277 ASP   ( 130-)  B      OD1
 293 GLU   ( 146-)  B      OE2
 296 GLN   ( 149-)  B      OE1
 338 ASN   (  39-)  C      OD1
 346 GLN   (  47-)  C      OE1
 445 GLU   ( 146-)  C      OE1
 448 GLN   ( 149-)  C      OE1

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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.

 111 GLU   ( 116-)  A   H-bonding suggests Gln
 293 GLU   ( 146-)  B   H-bonding suggests Gln
 341 GLU   (  42-)  C   H-bonding suggests Gln
 403 GLU   ( 104-)  C   H-bonding suggests Gln
 415 GLU   ( 116-)  C   H-bonding suggests Gln; but Alt-Rotamer
 445 GLU   ( 146-)  C   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 :  -1.541
  2nd generation packing quality :  -2.854
  Ramachandran plot appearance   :  -4.275 (bad)
  chi-1/chi-2 rotamer normality  :  -6.294 (bad)
  Backbone conformation          :  -1.149

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.933
  Bond angles                    :   2.028 (loose)
  Omega angle restraints         :   1.646 (loose)
  Side chain planarity           :   0.961
  Improper dihedral distribution :   1.490
  B-factor distribution          :   1.004
  Inside/Outside distribution    :   0.971

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 : 2.60


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.9
  2nd generation packing quality :  -1.4
  Ramachandran plot appearance   :  -1.6
  chi-1/chi-2 rotamer normality  :  -3.6 (poor)
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.933
  Bond angles                    :   2.028 (loose)
  Omega angle restraints         :   1.646 (loose)
  Side chain planarity           :   0.961
  Improper dihedral distribution :   1.490
  B-factor distribution          :   1.004
  Inside/Outside distribution    :   0.971
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
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    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
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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,
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      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,
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    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
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      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.