WHAT IF Check report

This file was created 2013-12-09 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 pdb3rfy.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

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

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.

 117 ARG   ( 194-)  A    High
 221 THR   ( 298-)  A    High
 222 GLY   ( 299-)  A    High
 223 ASP   ( 300-)  A    High
 224 PRO   ( 301-)  A    High
 225 GLU   ( 302-)  A    High
 226 GLY   ( 303-)  A    High
 227 PRO   ( 304-)  A    High
 228 ALA   ( 305-)  A    High
 229 GLU   ( 306-)  A    High
 230 GLY   ( 307-)  A    High
 231 PHE   ( 308-)  A    High
 232 ILE   ( 309-)  A    High
 233 ASP   ( 310-)  A    High
 234 PRO   ( 311-)  A    High
 235 SER   ( 312-)  A    High
 236 THR   ( 313-)  A    High
 237 GLU   ( 314-)  A    High
 238 LYS   ( 315-)  A    High
 239 THR   ( 316-)  A    High
 240 ARG   ( 317-)  A    High
 241 THR   ( 318-)  A    High
 242 VAL   ( 319-)  A    High
 243 PRO   ( 320-)  A    High
 244 LEU   ( 321-)  A    High
And so on for a total of 59 lines.

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) :103.000

Note: B-factor plot

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

Chain identifier: A

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

  32 TYR   ( 109-)  A
 132 TYR   ( 209-)  A
 188 TYR   ( 265-)  A
 206 TYR   ( 283-)  A
 256 TYR   ( 333-)  A
 322 TYR   ( 399-)  A
 356 TYR   ( 433-)  A

Warning: Phenylalanine convention problem

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

 144 PHE   ( 221-)  A
 181 PHE   ( 258-)  A
 205 PHE   ( 282-)  A
 274 PHE   ( 351-)  A
 277 PHE   ( 354-)  A
 329 PHE   ( 406-)  A

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.

  25 ASP   ( 102-)  A
  64 ASP   ( 141-)  A
  94 ASP   ( 171-)  A
 178 ASP   ( 255-)  A
 223 ASP   ( 300-)  A
 233 ASP   ( 310-)  A
 325 ASP   ( 402-)  A

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.

  27 GLU   ( 104-)  A
  67 GLU   ( 144-)  A
 150 GLU   ( 227-)  A
 177 GLU   ( 254-)  A
 202 GLU   ( 279-)  A
 225 GLU   ( 302-)  A
 285 GLU   ( 362-)  A
 288 GLU   ( 365-)  A

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.

 252 LYS   ( 329-)  A      CA   C     1.62    4.4
 298 TRP   ( 375-)  A      NE1  CE2   1.49   11.3
 298 TRP   ( 375-)  A      CD2  CE3   1.46    4.1

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

 |  0.996887 -0.000419 -0.000607|
 | -0.000419  0.996857  0.000701|
 | -0.000607  0.000701  0.996953|
Proposed new scale matrix

 |  0.017388  0.000007  0.000011|
 |  0.000004  0.010372 -0.000007|
 |  0.000004 -0.000004  0.006012|
With corresponding cell

    A    =  57.510  B   =  96.417  C    = 166.325
    Alpha=  89.919  Beta=  90.070  Gamma=  90.048

The CRYST1 cell dimensions

    A    =  57.690  B   =  96.720  C    = 166.820
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 109.434
(Under-)estimated Z-score: 7.710

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

   4 LEU   (  81-)  A      N    CA   C   128.27    6.1
  47 PRO   ( 124-)  A      N    CA   C   101.78   -4.0
  75 ARG   ( 152-)  A      CB   CG   CD  105.30   -4.4
  79 GLN   ( 156-)  A      N    CA   C    95.86   -5.5
  87 GLY   ( 164-)  A      N    CA   C   132.19    6.8
  88 PHE   ( 165-)  A      N    CA   C   128.49    6.2
  89 ALA   ( 166-)  A      N    CA   C   125.96    5.3
 113 ILE   ( 190-)  A      N    CA   C    96.09   -5.4
 114 VAL   ( 191-)  A      N    CA   C    93.78   -6.2
 117 ARG   ( 194-)  A      N    CA   C    90.52   -7.4
 118 LYS   ( 195-)  A      N    CA   C    97.66   -4.8
 124 PRO   ( 201-)  A     -C    N    CA  102.13   -4.1
 125 LYS   ( 202-)  A      N    CA   C    92.44   -6.7
 142 ASP   ( 219-)  A      N    CA   C    95.35   -5.7
 145 PRO   ( 222-)  A      N    CA   C   124.10    4.9
 150 GLU   ( 227-)  A      N    CA   C   126.11    5.3
 161 ARG   ( 238-)  A      CG   CD   NE  102.40   -4.8
 174 PRO   ( 251-)  A      N    CA   C    97.17   -5.9
 203 ARG   ( 280-)  A      CG   CD   NE  117.50    4.1
 212 GLN   ( 289-)  A      N    CA   C    99.40   -4.2
 220 GLN   ( 297-)  A      N    CA   C    87.71   -8.4
 221 THR   ( 298-)  A     -C    N    CA  130.78    5.0
 221 THR   ( 298-)  A      N    CA   C   128.63    6.2
 221 THR   ( 298-)  A      N    CA   CB  102.76   -4.6
 223 ASP   ( 300-)  A      N    CA   C   125.25    5.0
And so on for a total of 63 lines.

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.

  25 ASP   ( 102-)  A
  27 GLU   ( 104-)  A
  64 ASP   ( 141-)  A
  67 GLU   ( 144-)  A
  94 ASP   ( 171-)  A
 150 GLU   ( 227-)  A
 177 GLU   ( 254-)  A
 178 ASP   ( 255-)  A
 202 GLU   ( 279-)  A
 223 ASP   ( 300-)  A
 225 GLU   ( 302-)  A
 233 ASP   ( 310-)  A
 285 GLU   ( 362-)  A
 288 GLU   ( 365-)  A
 325 ASP   ( 402-)  A

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.

 113 ILE   ( 190-)  A      CB     6.6    40.92    32.31
 124 PRO   ( 201-)  A      N     -6.2   -22.88    -2.48
 145 PRO   ( 222-)  A      N      9.6    28.97    -2.48
 243 PRO   ( 320-)  A      N     -6.6   -24.14    -2.48
 254 PRO   ( 331-)  A      N      7.3    21.55    -2.48
The average deviation= 1.353

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.

 125 LYS   ( 202-)  A   12.25
 220 GLN   ( 297-)  A    9.29
   4 LEU   (  81-)  A    8.34
 295 GLN   ( 372-)  A    7.81
 117 ARG   ( 194-)  A    7.78
  47 PRO   ( 124-)  A    7.56
  87 GLY   ( 164-)  A    6.68
  88 PHE   ( 165-)  A    6.65
 314 ASP   ( 391-)  A    6.56
 114 VAL   ( 191-)  A    6.28
 174 PRO   ( 251-)  A    6.14
  79 GLN   ( 156-)  A    6.09
  89 ALA   ( 166-)  A    6.04
 242 VAL   ( 319-)  A    6.03
  90 GLU   ( 167-)  A    5.97
 297 PHE   ( 374-)  A    5.93
 221 THR   ( 298-)  A    5.93
 311 ASN   ( 388-)  A    5.87
 248 VAL   ( 325-)  A    5.79
 356 TYR   ( 433-)  A    5.69
 290 ASP   ( 367-)  A    5.68
 281 ALA   ( 358-)  A    5.67
  98 GLU   ( 175-)  A    5.66
 310 SER   ( 387-)  A    5.41
 142 ASP   ( 219-)  A    5.39
And so on for a total of 52 lines.

Warning: High tau angle deviations

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

Tau angle RMS Z-score : 2.769

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 : -4.384

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.

 255 PHE   ( 332-)  A    -3.6
 145 PRO   ( 222-)  A    -3.1
 246 ILE   ( 323-)  A    -3.0
 254 PRO   ( 331-)  A    -2.9
 248 VAL   ( 325-)  A    -2.7
 274 PHE   ( 351-)  A    -2.6
 245 GLU   ( 322-)  A    -2.6
 144 PHE   ( 221-)  A    -2.6
 240 ARG   ( 317-)  A    -2.6
  88 PHE   ( 165-)  A    -2.5
 148 VAL   ( 225-)  A    -2.5
  90 GLU   ( 167-)  A    -2.5
 253 THR   ( 330-)  A    -2.4
 275 ASN   ( 352-)  A    -2.4
 291 SER   ( 368-)  A    -2.4
 234 PRO   ( 311-)  A    -2.4
 280 MET   ( 357-)  A    -2.4
 158 LEU   ( 235-)  A    -2.3
 147 GLU   ( 224-)  A    -2.3
 241 THR   ( 318-)  A    -2.3
  79 GLN   ( 156-)  A    -2.3
  41 ILE   ( 118-)  A    -2.3
 297 PHE   ( 374-)  A    -2.3
 233 ASP   ( 310-)  A    -2.2
  36 ILE   ( 113-)  A    -2.2
 115 GLU   ( 192-)  A    -2.2
   4 LEU   (  81-)  A    -2.2
 308 SER   ( 385-)  A    -2.2
  35 PRO   ( 112-)  A    -2.2
 221 THR   ( 298-)  A    -2.2
 251 GLU   ( 328-)  A    -2.2
 252 LYS   ( 329-)  A    -2.1
 285 GLU   ( 362-)  A    -2.1
 231 PHE   ( 308-)  A    -2.1
 125 LYS   ( 202-)  A    -2.1
  92 LYS   ( 169-)  A    -2.1
 226 GLY   ( 303-)  A    -2.1
 293 SER   ( 370-)  A    -2.1
 334 LYS   ( 411-)  A    -2.1
 284 ARG   ( 361-)  A    -2.1
  21 PRO   (  98-)  A    -2.1
 223 ASP   ( 300-)  A    -2.0
 117 ARG   ( 194-)  A    -2.0
 314 ASP   ( 391-)  A    -2.0
 302 GLU   ( 379-)  A    -2.0
 239 THR   ( 316-)  A    -2.0
  60 VAL   ( 137-)  A    -2.0
  83 ILE   ( 160-)  A    -2.0
 286 GLU   ( 363-)  A    -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.

  10 VAL   (  87-)  A  Poor phi/psi
  13 ASP   (  90-)  A  Poor phi/psi
  35 PRO   ( 112-)  A  Poor phi/psi
  47 PRO   ( 124-)  A  Poor phi/psi
  48 LEU   ( 125-)  A  Poor phi/psi
  79 GLN   ( 156-)  A  Poor phi/psi
  85 VAL   ( 162-)  A  Poor phi/psi
  86 ALA   ( 163-)  A  Poor phi/psi
  89 ALA   ( 166-)  A  Poor phi/psi
  90 GLU   ( 167-)  A  Poor phi/psi
 113 ILE   ( 190-)  A  Poor phi/psi
 116 ASP   ( 193-)  A  Poor phi/psi
 117 ARG   ( 194-)  A  Poor phi/psi
 118 LYS   ( 195-)  A  Poor phi/psi
 121 ALA   ( 198-)  A  Poor phi/psi
 122 VAL   ( 199-)  A  Poor phi/psi
 124 PRO   ( 201-)  A  Poor phi/psi
 140 MET   ( 217-)  A  Poor phi/psi
 142 ASP   ( 219-)  A  Poor phi/psi
 144 PHE   ( 221-)  A  Poor phi/psi
 145 PRO   ( 222-)  A  Poor phi/psi
 147 GLU   ( 224-)  A  Poor phi/psi
 151 GLU   ( 228-)  A  Poor phi/psi
 159 LYS   ( 236-)  A  Poor phi/psi
 175 ASN   ( 252-)  A  Poor phi/psi
And so on for a total of 66 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 : -5.563

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.

  74 SER   ( 151-)  A    0.38

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!

   9 PRO   (  86-)  A      0
  11 ILE   (  88-)  A      0
  12 PRO   (  89-)  A      0
  13 ASP   (  90-)  A      0
  19 SER   (  96-)  A      0
  22 PRO   (  99-)  A      0
  24 LYS   ( 101-)  A      0
  35 PRO   ( 112-)  A      0
  37 ASP   ( 114-)  A      0
  38 ASN   ( 115-)  A      0
  47 PRO   ( 124-)  A      0
  48 LEU   ( 125-)  A      0
  58 ALA   ( 135-)  A      0
  60 VAL   ( 137-)  A      0
  78 GLN   ( 155-)  A      0
  79 GLN   ( 156-)  A      0
  84 ILE   ( 161-)  A      0
  86 ALA   ( 163-)  A      0
  88 PHE   ( 165-)  A      0
  89 ALA   ( 166-)  A      0
  90 GLU   ( 167-)  A      0
  91 SER   ( 168-)  A      0
 112 LYS   ( 189-)  A      0
 113 ILE   ( 190-)  A      0
 114 VAL   ( 191-)  A      0
And so on for a total of 178 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 2.278

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!

 230 GLY   ( 307-)  A   2.89   11
 278 GLY   ( 355-)  A   1.64   40

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

  89 ALA   ( 166-)  A   2.66
  90 GLU   ( 167-)  A   1.84

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]

 145 PRO   ( 222-)  A    0.49 HIGH
 149 PRO   ( 226-)  A    0.50 HIGH
 191 PRO   ( 268-)  A    0.18 LOW
 254 PRO   ( 331-)  A    0.46 HIGH
 273 PRO   ( 350-)  A    0.47 HIGH
 307 PRO   ( 384-)  A    0.47 HIGH
 354 PRO   ( 431-)  A    0.45 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].

   9 PRO   (  86-)  A  -112.6 envelop C-gamma (-108 degrees)
  26 PRO   ( 103-)  A  -124.5 half-chair C-delta/C-gamma (-126 degrees)
  35 PRO   ( 112-)  A   -25.6 half-chair C-alpha/N (-18 degrees)
  47 PRO   ( 124-)  A  -128.4 half-chair C-delta/C-gamma (-126 degrees)
 124 PRO   ( 201-)  A   109.8 envelop C-beta (108 degrees)
 145 PRO   ( 222-)  A   102.5 envelop C-beta (108 degrees)
 156 PRO   ( 233-)  A   104.6 envelop C-beta (108 degrees)
 234 PRO   ( 311-)  A   -21.3 half-chair C-alpha/N (-18 degrees)
 243 PRO   ( 320-)  A   117.9 half-chair C-beta/C-alpha (126 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.

  48 LEU   ( 125-)  A      N   <->  357 HOH   ( 671 )  A      O      0.72    1.98  INTRA BL
  11 ILE   (  88-)  A      N   <->   12 PRO   (  89-)  A      CD     0.69    2.31  INTRA BF
 242 VAL   ( 319-)  A      N   <->  243 PRO   ( 320-)  A      CD     0.64    2.36  INTRA BF
 123 ALA   ( 200-)  A      O   <->  125 LYS   ( 202-)  A      N      0.59    2.11  INTRA BL
  77 LEU   ( 154-)  A      O   <->   79 GLN   ( 156-)  A      N      0.56    2.14  INTRA BL
  92 LYS   ( 169-)  A      CD  <->  142 ASP   ( 219-)  A      OD2    0.53    2.27  INTRA BF
  10 VAL   (  87-)  A      C   <->   12 PRO   (  89-)  A      CD     0.50    2.70  INTRA BF
 125 LYS   ( 202-)  A      N   <->  126 GLN   ( 203-)  A      N      0.48    2.12  INTRA BL
   3 ILE   (  80-)  A      CG2 <->  330 LEU   ( 407-)  A      CD1    0.48    2.72  INTRA BL
 301 LYS   ( 378-)  A      NZ  <->  357 HOH   ( 641 )  A      O      0.47    2.23  INTRA BL
 171 LYS   ( 248-)  A      O   <->  334 LYS   ( 411-)  A      NZ     0.47    2.23  INTRA BL
 274 PHE   ( 351-)  A      N   <->  357 HOH   ( 679 )  A      O      0.45    2.25  INTRA BF
 213 ARG   ( 290-)  A      NH2 <->  215 ASP   ( 292-)  A      OD1    0.45    2.25  INTRA BF
 114 VAL   ( 191-)  A      N   <->  115 GLU   ( 192-)  A      N      0.44    2.16  INTRA BF
  67 GLU   ( 144-)  A      OE2 <->   71 ARG   ( 148-)  A      NH1    0.43    2.27  INTRA BL
 113 ILE   ( 190-)  A      C   <->  115 GLU   ( 192-)  A      N      0.42    2.48  INTRA BF
  47 PRO   ( 124-)  A      O   <->   49 GLU   ( 126-)  A      N      0.41    2.29  INTRA BL
 301 LYS   ( 378-)  A      CE  <->  357 HOH   ( 641 )  A      O      0.40    2.40  INTRA BL
 349 GLU   ( 426-)  A      OE1 <->  357 HOH   ( 654 )  A      O      0.37    2.03  INTRA BL
 143 GLY   ( 220-)  A      N   <->  357 HOH   ( 707 )  A      O      0.37    2.33  INTRA BF
 303 SER   ( 380-)  A      OG  <->  357 HOH   ( 641 )  A      O      0.36    2.04  INTRA BL
 349 GLU   ( 426-)  A      OE1 <->  357 HOH   ( 605 )  A      O      0.36    2.04  INTRA BL
 203 ARG   ( 280-)  A      CD  <->  357 HOH   ( 683 )  A      O      0.35    2.45  INTRA BL
 315 GLY   ( 392-)  A      N   <->  357 HOH   ( 653 )  A      O      0.35    2.35  INTRA BF
  36 ILE   ( 113-)  A      CD1 <->  137 GLU   ( 214-)  A      O      0.34    2.46  INTRA BL
And so on for a total of 195 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

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.

 146 TYR   ( 223-)  A      -8.52
 284 ARG   ( 361-)  A      -8.06
 255 PHE   ( 332-)  A      -7.55
 256 TYR   ( 333-)  A      -7.30
 231 PHE   ( 308-)  A      -7.16
 277 PHE   ( 354-)  A      -6.98
 282 MET   ( 359-)  A      -6.92
 244 LEU   ( 321-)  A      -6.83
 225 GLU   ( 302-)  A      -6.64
 280 MET   ( 357-)  A      -6.49
 274 PHE   ( 351-)  A      -6.47
 297 PHE   ( 374-)  A      -6.40
 287 PHE   ( 364-)  A      -6.24
 144 PHE   ( 221-)  A      -6.21
 229 GLU   ( 306-)  A      -6.11
 252 LYS   ( 329-)  A      -6.04
 295 GLN   ( 372-)  A      -6.04
 313 LEU   ( 390-)  A      -5.97
 237 GLU   ( 314-)  A      -5.95
 232 ILE   ( 309-)  A      -5.88
 153 ARG   ( 230-)  A      -5.76
 188 TYR   ( 265-)  A      -5.75
 147 GLU   ( 224-)  A      -5.68
 289 ASN   ( 366-)  A      -5.61
 220 GLN   ( 297-)  A      -5.59
  24 LYS   ( 101-)  A      -5.57
 312 ILE   ( 389-)  A      -5.47
 117 ARG   ( 194-)  A      -5.36
 275 ASN   ( 352-)  A      -5.30
 175 ASN   ( 252-)  A      -5.22
 247 MET   ( 324-)  A      -5.12
 311 ASN   ( 388-)  A      -5.11
 148 VAL   ( 225-)  A      -5.10

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.

 146 TYR   ( 223-)  A       148 - VAL    225- ( A)         -6.43
 220 GLN   ( 297-)  A       225 - GLU    302- ( A)         -4.97
 231 PHE   ( 308-)  A       233 - ASP    310- ( A)         -5.82
 235 SER   ( 312-)  A       237 - GLU    314- ( A)         -5.04
 244 LEU   ( 321-)  A       248 - VAL    325- ( A)         -5.15
 274 PHE   ( 351-)  A       277 - PHE    354- ( A)         -5.74
 279 THR   ( 356-)  A       282 - MET    359- ( A)         -5.51
 287 PHE   ( 364-)  A       291 - SER    368- ( A)         -5.05
 293 SER   ( 370-)  A       299 - LEU    376- ( A)         -4.96
 308 SER   ( 385-)  A       316 - ARG    393- ( A)         -4.79

Warning: Structural average packing environment a bit worrysome

The structural average packing score is a bit low.

The protein is probably threaded correctly, but either poorly refined, or it is just a protein with an unusual (but correct) structure. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].

Average for range 1 - 356 : -1.649

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: 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

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.

 357 HOH   ( 615 )  A      O
 357 HOH   ( 620 )  A      O
 357 HOH   ( 626 )  A      O
 357 HOH   ( 637 )  A      O
 357 HOH   ( 643 )  A      O
 357 HOH   ( 659 )  A      O
 357 HOH   ( 677 )  A      O
 357 HOH   ( 678 )  A      O
 357 HOH   ( 680 )  A      O
 357 HOH   ( 682 )  A      O
 357 HOH   ( 695 )  A      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.

  38 ASN   ( 115-)  A
  45 GLN   ( 122-)  A
  79 GLN   ( 156-)  A
 173 ASN   ( 250-)  A
 175 ASN   ( 252-)  A
 309 ASN   ( 386-)  A
 311 ASN   ( 388-)  A
 326 ASN   ( 403-)  A

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.

   3 ILE   (  80-)  A      N
  14 VAL   (  91-)  A      N
  27 GLU   ( 104-)  A      N
  45 GLN   ( 122-)  A      NE2
  48 LEU   ( 125-)  A      N
  60 VAL   ( 137-)  A      N
  68 ARG   ( 145-)  A      N
  97 ASN   ( 174-)  A      N
 114 VAL   ( 191-)  A      N
 115 GLU   ( 192-)  A      N
 117 ARG   ( 194-)  A      N
 119 ARG   ( 196-)  A      NH1
 123 ALA   ( 200-)  A      N
 127 LYS   ( 204-)  A      N
 141 VAL   ( 218-)  A      N
 151 GLU   ( 228-)  A      N
 152 TYR   ( 229-)  A      N
 154 ASN   ( 231-)  A      N
 160 GLY   ( 237-)  A      N
 161 ARG   ( 238-)  A      NH1
 213 ARG   ( 290-)  A      N
 242 VAL   ( 319-)  A      N
 247 MET   ( 324-)  A      N
 258 SER   ( 335-)  A      N
 287 PHE   ( 364-)  A      N
 295 GLN   ( 372-)  A      N
 330 LEU   ( 407-)  A      N

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.

  97 ASN   ( 174-)  A      OD1
 137 GLU   ( 214-)  A      OE1
 137 GLU   ( 214-)  A      OE2
 220 GLN   ( 297-)  A      OE1
 262 GLU   ( 339-)  A      OE1
 304 GLU   ( 381-)  A      OE2

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.

 357 HOH   ( 711 )  A      O  1.05  K  4

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.

  13 ASP   (  90-)  A   H-bonding suggests Asn; but Alt-Rotamer
 101 GLU   ( 178-)  A   H-bonding suggests Gln
 109 ASP   ( 186-)  A   H-bonding suggests Asn
 223 ASP   ( 300-)  A   H-bonding suggests Asn
 233 ASP   ( 310-)  A   H-bonding suggests Asn
 245 GLU   ( 322-)  A   H-bonding suggests Gln; but Alt-Rotamer
 285 GLU   ( 362-)  A   H-bonding suggests Gln; but Alt-Rotamer
 337 ASP   ( 414-)  A   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -2.872
  2nd generation packing quality :  -2.548
  Ramachandran plot appearance   :  -4.384 (bad)
  chi-1/chi-2 rotamer normality  :  -5.563 (bad)
  Backbone conformation          :  -1.748

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.699
  Bond angles                    :   1.238
  Omega angle restraints         :   0.414 (tight)
  Side chain planarity           :   0.545 (tight)
  Improper dihedral distribution :   1.193
  B-factor distribution          :   0.731
  Inside/Outside distribution    :   1.088

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 : 2.39


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -2.6
  2nd generation packing quality :  -1.2
  Ramachandran plot appearance   :  -2.0
  chi-1/chi-2 rotamer normality  :  -3.6 (poor)
  Backbone conformation          :  -1.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.699
  Bond angles                    :   1.238
  Omega angle restraints         :   0.414 (tight)
  Side chain planarity           :   0.545 (tight)
  Improper dihedral distribution :   1.193
  B-factor distribution          :   0.731
  Inside/Outside distribution    :   1.088
==============

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.