WHAT IF Check report

This file was created 2011-12-28 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 pdb1i0e.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: C

Note: Ramachandran plot

Chain identifier: D

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'.

   3 PHE   (  10-)  A      CG
   3 PHE   (  10-)  A      CD1
   3 PHE   (  10-)  A      CD2
   3 PHE   (  10-)  A      CE1
   3 PHE   (  10-)  A      CE2
   3 PHE   (  10-)  A      CZ
  30 GLU   (  37-)  A      CG
  30 GLU   (  37-)  A      CD
  30 GLU   (  37-)  A      OE1
  30 GLU   (  37-)  A      OE2
  76 GLU   (  83-)  A      CG
  76 GLU   (  83-)  A      CD
  76 GLU   (  83-)  A      OE1
  76 GLU   (  83-)  A      OE2
  87 SER   (  94-)  A      OG
  93 TYR   ( 100-)  A      OH
 117 ASN   ( 124-)  A      CG
 117 ASN   ( 124-)  A      OD1
 117 ASN   ( 124-)  A      ND2
 175 LYS   ( 182-)  A      CG
 175 LYS   ( 182-)  A      CD
 175 LYS   ( 182-)  A      CE
 175 LYS   ( 182-)  A      NZ
 320 VAL   ( 336-)  A      CG1
 320 VAL   ( 336-)  A      CG2
And so on for a total of 100 lines.

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.

   1 ASN   (   8-)  A    High
  18 LYS   (  25-)  A    High
  20 ASN   (  27-)  A    High
  33 LYS   (  40-)  A    High
  59 HIS   (  66-)  A    High
  60 PRO   (  67-)  A    High
  61 PHE   (  68-)  A    High
 100 LYS   ( 107-)  A    High
 118 TYR   ( 125-)  A    High
 120 LEU   ( 127-)  A    High
 163 LYS   ( 170-)  A    High
 165 LYS   ( 172-)  A    High
 175 LYS   ( 182-)  A    High
 176 GLU   ( 183-)  A    High
 178 GLN   ( 185-)  A    High
 179 GLN   ( 186-)  A    High
 182 ASP   ( 189-)  A    High
 184 HIS   ( 191-)  A    High
 185 PHE   ( 192-)  A    High
 186 LEU   ( 193-)  A    High
 187 PHE   ( 194-)  A    High
 188 ASP   ( 195-)  A    High
 189 LYS   ( 196-)  A    High
 191 VAL   ( 198-)  A    High
 192 SER   ( 199-)  A    High
And so on for a total of 163 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) :291.000

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 12.72

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

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

 118 TYR   ( 125-)  A
 167 TYR   ( 174-)  A
 483 TYR   ( 125-)  B
 532 TYR   ( 174-)  B
 848 TYR   ( 125-)  C
 897 TYR   ( 174-)  C
1213 TYR   ( 125-)  D
1262 TYR   ( 174-)  D

Warning: Phenylalanine convention problem

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

 257 PHE   ( 264-)  A
 622 PHE   ( 264-)  B
 987 PHE   ( 264-)  C
1352 PHE   ( 264-)  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.

  37 ASP   (  44-)  A
  71 ASP   (  78-)  A
 188 ASP   ( 195-)  A
 319 ASP   ( 335-)  A
 402 ASP   (  44-)  B
 436 ASP   (  78-)  B
 553 ASP   ( 195-)  B
 684 ASP   ( 335-)  B
 767 ASP   (  44-)  C
 801 ASP   (  78-)  C
 918 ASP   ( 195-)  C
1049 ASP   ( 335-)  C
1132 ASP   (  44-)  D
1166 ASP   (  78-)  D
1283 ASP   ( 195-)  D
1414 ASP   ( 335-)  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.

  12 GLU   (  19-)  A
  80 GLU   (  87-)  A
 161 GLU   ( 168-)  A
 176 GLU   ( 183-)  A
 254 GLU   ( 261-)  A
 332 GLU   ( 348-)  A
 377 GLU   (  19-)  B
 445 GLU   (  87-)  B
 526 GLU   ( 168-)  B
 541 GLU   ( 183-)  B
 619 GLU   ( 261-)  B
 697 GLU   ( 348-)  B
 742 GLU   (  19-)  C
 810 GLU   (  87-)  C
 891 GLU   ( 168-)  C
 906 GLU   ( 183-)  C
 984 GLU   ( 261-)  C
1062 GLU   ( 348-)  C
1107 GLU   (  19-)  D
1175 GLU   (  87-)  D
1256 GLU   ( 168-)  D
1271 GLU   ( 183-)  D
1349 GLU   ( 261-)  D
1427 GLU   ( 348-)  D

Geometric checks

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.

 387 HIS   (  29-)  B      CG   ND1  CE1 109.66    4.1
 841 GLY   ( 118-)  C      N    CA   C   100.70   -4.1

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.

  12 GLU   (  19-)  A
  37 ASP   (  44-)  A
  71 ASP   (  78-)  A
  80 GLU   (  87-)  A
 161 GLU   ( 168-)  A
 176 GLU   ( 183-)  A
 188 ASP   ( 195-)  A
 254 GLU   ( 261-)  A
 319 ASP   ( 335-)  A
 332 GLU   ( 348-)  A
 377 GLU   (  19-)  B
 402 ASP   (  44-)  B
 436 ASP   (  78-)  B
 445 GLU   (  87-)  B
 526 GLU   ( 168-)  B
 541 GLU   ( 183-)  B
 553 ASP   ( 195-)  B
 619 GLU   ( 261-)  B
 684 ASP   ( 335-)  B
 697 GLU   ( 348-)  B
 742 GLU   (  19-)  C
 767 ASP   (  44-)  C
 801 ASP   (  78-)  C
 810 GLU   (  87-)  C
 891 GLU   ( 168-)  C
 906 GLU   ( 183-)  C
 918 ASP   ( 195-)  C
 984 GLU   ( 261-)  C
1049 ASP   ( 335-)  C
1062 GLU   ( 348-)  C
1107 GLU   (  19-)  D
1132 ASP   (  44-)  D
1166 ASP   (  78-)  D
1175 GLU   (  87-)  D
1256 GLU   ( 168-)  D
1271 GLU   ( 183-)  D
1283 ASP   ( 195-)  D
1349 GLU   ( 261-)  D
1414 ASP   ( 335-)  D
1427 GLU   ( 348-)  D

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.

 506 ARG   ( 148-)  B    5.08
 141 ARG   ( 148-)  A    4.83
 871 ARG   ( 148-)  C    4.82
1236 ARG   ( 148-)  D    4.80
 841 GLY   ( 118-)  C    4.62
  51 GLN   (  58-)  A    4.53
 111 GLY   ( 118-)  A    4.52
1183 ASP   (  95-)  D    4.36
 781 GLN   (  58-)  C    4.34
 909 GLN   ( 186-)  C    4.34
1206 GLY   ( 118-)  D    4.32
 476 GLY   ( 118-)  B    4.31
 544 GLN   ( 186-)  B    4.23
 179 GLN   ( 186-)  A    4.22
 416 GLN   (  58-)  B    4.17
 818 ASP   (  95-)  C    4.15
 756 VAL   (  33-)  C    4.11
 453 ASP   (  95-)  B    4.05
1146 GLN   (  58-)  D    4.05
1274 GLN   ( 186-)  D    4.04

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 : -5.073

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.

 570 PRO   ( 212-)  B    -3.0
 935 PRO   ( 212-)  C    -3.0
 205 PRO   ( 212-)  A    -3.0
1300 PRO   ( 212-)  D    -3.0
 666 PHE   ( 308-)  B    -2.9
1031 PHE   ( 308-)  C    -2.9
 301 PHE   ( 308-)  A    -2.9
1396 PHE   ( 308-)  D    -2.9
 173 THR   ( 180-)  A    -2.7
 903 THR   ( 180-)  C    -2.7
 538 THR   ( 180-)  B    -2.7
1268 THR   ( 180-)  D    -2.7
1155 PRO   (  67-)  D    -2.6
 425 PRO   (  67-)  B    -2.6
  60 PRO   (  67-)  A    -2.6
 790 PRO   (  67-)  C    -2.6
 136 PRO   ( 143-)  A    -2.5
1279 HIS   ( 191-)  D    -2.5
 914 HIS   ( 191-)  C    -2.5
 549 HIS   ( 191-)  B    -2.5
 501 PRO   ( 143-)  B    -2.4
 184 HIS   ( 191-)  A    -2.4
 866 PRO   ( 143-)  C    -2.4
 518 GLU   ( 160-)  B    -2.4
 153 GLU   ( 160-)  A    -2.4
And so on for a total of 91 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.

   3 PHE   (  10-)  A  Poor phi/psi
  61 PHE   (  68-)  A  Poor phi/psi
  66 GLY   (  73-)  A  Poor phi/psi
  88 ASP   (  95-)  A  Poor phi/psi
  98 LYS   ( 105-)  A  Poor phi/psi
 112 ASP   ( 119-)  A  Poor phi/psi
 118 TYR   ( 125-)  A  Poor phi/psi
 138 HIS   ( 145-)  A  Poor phi/psi
 159 THR   ( 166-)  A  Poor phi/psi
 160 GLY   ( 167-)  A  Poor phi/psi
 173 THR   ( 180-)  A  Poor phi/psi
 174 GLU   ( 181-)  A  Poor phi/psi
 177 GLN   ( 184-)  A  Poor phi/psi
 184 HIS   ( 191-)  A  Poor phi/psi
 185 PHE   ( 192-)  A  Poor phi/psi
 190 PRO   ( 197-)  A  Poor phi/psi
 191 VAL   ( 198-)  A  Poor phi/psi
 203 ASP   ( 210-)  A  Poor phi/psi
 204 TRP   ( 211-)  A  PRO omega poor
 224 GLU   ( 231-)  A  Poor phi/psi
 283 GLY   ( 290-)  A  Poor phi/psi
 309 ARG   ( 316-)  A  Poor phi/psi
 312 LYS   ( 319-)  A  Poor phi/psi
 354 GLY   ( 370-)  A  Poor phi/psi
 359 ASP   ( 375-)  A  Poor phi/psi
And so on for a total of 108 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 : -4.768

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!

   6 ASN   (  13-)  A      0
   7 TYR   (  14-)  A      0
  13 TYR   (  20-)  A      0
  16 LEU   (  23-)  A      0
  18 LYS   (  25-)  A      0
  20 ASN   (  27-)  A      0
  22 HIS   (  29-)  A      0
  35 LEU   (  42-)  A      0
  36 ARG   (  43-)  A      0
  37 ASP   (  44-)  A      0
  39 GLU   (  46-)  A      0
  42 SER   (  49-)  A      0
  57 PRO   (  64-)  A      0
  59 HIS   (  66-)  A      0
  62 ILE   (  69-)  A      0
  65 VAL   (  72-)  A      0
  67 CYS   (  74-)  A      0
  87 SER   (  94-)  A      0
  88 ASP   (  95-)  A      0
  90 HIS   (  97-)  A      0
  94 LYS   ( 101-)  A      0
  98 LYS   ( 105-)  A      0
 103 LEU   ( 110-)  A      0
 105 HIS   ( 112-)  A      0
 109 LYS   ( 116-)  A      0
And so on for a total of 647 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 : 1.057

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]

 136 PRO   ( 143-)  A    0.45 HIGH
 501 PRO   ( 143-)  B    0.46 HIGH
 664 PRO   ( 306-)  B    0.46 HIGH
 866 PRO   ( 143-)  C    0.45 HIGH
1029 PRO   ( 306-)  C    0.45 HIGH
1231 PRO   ( 143-)  D    0.46 HIGH
1394 PRO   ( 306-)  D    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   (  16-)  A  -115.3 envelop C-gamma (-108 degrees)
 374 PRO   (  16-)  B  -115.0 envelop C-gamma (-108 degrees)
 739 PRO   (  16-)  C  -115.6 envelop C-gamma (-108 degrees)
1104 PRO   (  16-)  D  -115.3 envelop C-gamma (-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.

 729 GLN   ( 380-)  B      CD  <->  730 LYS   ( 381-)  B      N      0.44    2.56  INTRA BF
1459 GLN   ( 380-)  D      CD  <-> 1460 LYS   ( 381-)  D      N      0.43    2.57  INTRA BF
 542 GLN   ( 184-)  B      NE2 <->  546 ILE   ( 188-)  B      CD1    0.43    2.67  INTRA BF
1272 GLN   ( 184-)  D      NE2 <-> 1276 ILE   ( 188-)  D      CD1    0.42    2.68  INTRA BL
1094 GLN   ( 380-)  C      CD  <-> 1095 LYS   ( 381-)  C      N      0.40    2.60  INTRA BF
 907 GLN   ( 184-)  C      O   <->  911 ILE   ( 188-)  C      N      0.40    2.30  INTRA BF
 907 GLN   ( 184-)  C      NE2 <->  911 ILE   ( 188-)  C      CD1    0.40    2.70  INTRA BF
 364 GLN   ( 380-)  A      CD  <->  365 LYS   ( 381-)  A      N      0.40    2.60  INTRA BF
 177 GLN   ( 184-)  A      NE2 <->  181 ILE   ( 188-)  A      CD1    0.40    2.70  INTRA BF
1272 GLN   ( 184-)  D      O   <-> 1276 ILE   ( 188-)  D      N      0.39    2.31  INTRA BF
 174 GLU   ( 181-)  A      N   <->  177 GLN   ( 184-)  A      CB     0.39    2.71  INTRA BF
 542 GLN   ( 184-)  B      O   <->  546 ILE   ( 188-)  B      N      0.39    2.31  INTRA BF
 176 GLU   ( 183-)  A      O   <->  180 LEU   ( 187-)  A      N      0.38    2.32  INTRA BF
 127 GLY   ( 134-)  A      O   <->  128 ARG   ( 135-)  A      NH1    0.38    2.22  INTRA BL
 177 GLN   ( 184-)  A      O   <->  181 ILE   ( 188-)  A      N      0.38    2.32  INTRA BF
 338 VAL   ( 354-)  A      CG2 <->  339 ASP   ( 355-)  A      N      0.38    2.62  INTRA
 541 GLU   ( 183-)  B      O   <->  545 LEU   ( 187-)  B      N      0.38    2.32  INTRA BF
 906 GLU   ( 183-)  C      O   <->  910 LEU   ( 187-)  C      N      0.37    2.33  INTRA BF
 703 VAL   ( 354-)  B      CG2 <->  704 ASP   ( 355-)  B      N      0.37    2.63  INTRA BL
1271 GLU   ( 183-)  D      O   <-> 1275 LEU   ( 187-)  D      N      0.37    2.33  INTRA BF
1269 GLU   ( 181-)  D      N   <-> 1272 GLN   ( 184-)  D      CB     0.36    2.74  INTRA BF
 545 LEU   ( 187-)  B      O   <->  550 PHE   ( 192-)  B      N      0.36    2.34  INTRA BF
 180 LEU   ( 187-)  A      O   <->  185 PHE   ( 192-)  A      N      0.35    2.35  INTRA BF
 539 GLU   ( 181-)  B      N   <->  542 GLN   ( 184-)  B      CB     0.35    2.75  INTRA BF
1275 LEU   ( 187-)  D      O   <-> 1280 PHE   ( 192-)  D      N      0.35    2.35  INTRA BF
And so on for a total of 748 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

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.

 474 LYS   ( 116-)  B      -6.41
1204 LYS   ( 116-)  D      -6.40
 109 LYS   ( 116-)  A      -6.39
 839 LYS   ( 116-)  C      -6.36
1330 LYS   ( 242-)  D      -6.18
 235 LYS   ( 242-)  A      -6.18
 965 LYS   ( 242-)  C      -6.17
 600 LYS   ( 242-)  B      -6.14
 367 LYS   (   9-)  B      -5.85
   2 LYS   (   9-)  A      -5.85
 732 LYS   (   9-)  C      -5.82
1097 LYS   (   9-)  D      -5.80
1297 ARG   ( 209-)  D      -5.58
 567 ARG   ( 209-)  B      -5.55
 932 ARG   ( 209-)  C      -5.55
1295 MET   ( 207-)  D      -5.55
 202 ARG   ( 209-)  A      -5.53
 565 MET   ( 207-)  B      -5.50
 360 MET   ( 376-)  A      -5.50
 930 MET   ( 207-)  C      -5.47
 819 ARG   (  96-)  C      -5.46
 200 MET   ( 207-)  A      -5.45
1090 MET   ( 376-)  C      -5.45
 454 ARG   (  96-)  B      -5.44
1193 LYS   ( 105-)  D      -5.44
1184 ARG   (  96-)  D      -5.44
 463 LYS   ( 105-)  B      -5.42
1455 MET   ( 376-)  D      -5.41
  98 LYS   ( 105-)  A      -5.37
 828 LYS   ( 105-)  C      -5.37
 725 MET   ( 376-)  B      -5.37
1156 PHE   (  68-)  D      -5.25
  89 ARG   (  96-)  A      -5.24
 791 PHE   (  68-)  C      -5.24
  61 PHE   (  68-)  A      -5.23
 426 PHE   (  68-)  B      -5.23
 676 GLN   ( 318-)  B      -5.17
1041 GLN   ( 318-)  C      -5.14
1406 GLN   ( 318-)  D      -5.13
 311 GLN   ( 318-)  A      -5.12

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.

  89 ARG   (  96-)  A        91 - GLY     98- ( A)         -4.65
 311 GLN   ( 318-)  A       315 - THR    322- ( A)         -4.70
 358 ASP   ( 374-)  A       361 - ILE    377- ( A)         -4.80
 454 ARG   (  96-)  B       456 - GLY     98- ( B)         -4.72
 676 GLN   ( 318-)  B       680 - THR    322- ( B)         -4.68
 723 ASP   ( 374-)  B       726 - ILE    377- ( B)         -4.75
 819 ARG   (  96-)  C       821 - GLY     98- ( C)         -4.73
1041 GLN   ( 318-)  C      1045 - THR    322- ( C)         -4.69
1088 ASP   ( 374-)  C      1091 - ILE    377- ( C)         -4.77
1184 ARG   (  96-)  D      1186 - GLY     98- ( D)         -4.70
1406 GLN   ( 318-)  D      1410 - THR    322- ( D)         -4.68
1453 ASP   ( 374-)  D      1456 - ILE    377- ( D)         -4.75

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

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.

 175 LYS   ( 182-)  A   -3.65
1270 LYS   ( 182-)  D   -3.59
 368 PHE   (  10-)  B   -2.96
 733 PHE   (  10-)  C   -2.87
1212 ASN   ( 124-)  D   -2.58

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

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.

 104 ASN   ( 111-)  A
 105 HIS   ( 112-)  A
 107 ASN   ( 114-)  A
 138 HIS   ( 145-)  A
 262 HIS   ( 269-)  A
 268 GLN   ( 275-)  A
 311 GLN   ( 318-)  A
 322 ASN   ( 338-)  A
 335 GLN   ( 351-)  A
 384 HIS   (  26-)  B
 469 ASN   ( 111-)  B
 470 HIS   ( 112-)  B
 472 ASN   ( 114-)  B
 503 HIS   ( 145-)  B
 676 GLN   ( 318-)  B
 687 ASN   ( 338-)  B
 700 GLN   ( 351-)  B
 834 ASN   ( 111-)  C
 837 ASN   ( 114-)  C
 868 HIS   ( 145-)  C
 998 GLN   ( 275-)  C
1041 GLN   ( 318-)  C
1052 ASN   ( 338-)  C
1065 GLN   ( 351-)  C
1199 ASN   ( 111-)  D
1200 HIS   ( 112-)  D
1202 ASN   ( 114-)  D
1233 HIS   ( 145-)  D
1363 GLN   ( 275-)  D
1406 GLN   ( 318-)  D
1417 ASN   ( 338-)  D
1430 GLN   ( 351-)  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.

   2 LYS   (   9-)  A      N
   6 ASN   (  13-)  A      N
  10 GLU   (  17-)  A      N
  21 ASN   (  28-)  A      N
  21 ASN   (  28-)  A      ND2
  28 THR   (  35-)  A      N
  37 ASP   (  44-)  A      N
  42 SER   (  49-)  A      N
  46 VAL   (  53-)  A      N
  59 HIS   (  66-)  A      N
  61 PHE   (  68-)  A      N
  73 GLU   (  80-)  A      N
  80 GLU   (  87-)  A      N
  99 HIS   ( 106-)  A      N
  99 HIS   ( 106-)  A      NE2
 101 THR   ( 108-)  A      OG1
 102 ASP   ( 109-)  A      N
 113 ASP   ( 120-)  A      N
 114 LEU   ( 121-)  A      N
 121 SER   ( 128-)  A      N
 123 ARG   ( 130-)  A      NE
 123 ARG   ( 130-)  A      NH2
 133 TYR   ( 140-)  A      N
 144 ARG   ( 151-)  A      NE
 170 LYS   ( 177-)  A      N
And so on for a total of 215 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.

  19 HIS   (  26-)  A      ND1
 212 HIS   ( 219-)  A      ND1
 302 GLU   ( 309-)  A      OE1
 330 GLU   ( 346-)  A      OE1
 330 GLU   ( 346-)  A      OE2
 352 GLU   ( 368-)  A      OE2
 384 HIS   (  26-)  B      ND1
 421 ASN   (  63-)  B      OD1
 541 GLU   ( 183-)  B      OE1
 543 GLN   ( 185-)  B      OE1
 547 ASP   ( 189-)  B      OD1
 577 HIS   ( 219-)  B      ND1
 633 GLN   ( 275-)  B      OE1
 667 GLU   ( 309-)  B      OE1
 695 GLU   ( 346-)  B      OE2
 749 HIS   (  26-)  C      ND1
 786 ASN   (  63-)  C      OD1
 908 GLN   ( 185-)  C      OE1
 942 HIS   ( 219-)  C      ND1
1060 GLU   ( 346-)  C      OE2
1082 GLU   ( 368-)  C      OE2
1114 HIS   (  26-)  D      ND1
1151 ASN   (  63-)  D      OD1
1307 HIS   ( 219-)  D      ND1
1425 GLU   ( 346-)  D      OE2
1447 GLU   ( 368-)  D      OE2
   -0.5000   -0.8660   -0.0000     0.0000 ROT=  120.0034
    0.8660   -0.5000    0.0000     0.0000 DET=    0.9998
    0.0000    0.0000    0.9998   134.3003
ISYM out of range in SYMNEG 30 24
    0.5000   -0.8660   -0.0000     0.0000 ROT=  179.3782
   -0.8660   -0.5000   -0.0000     0.0000 DET=    0.9998
    0.0000    0.0000   -0.9998   268.6006
ISYM out of range in SYMNEG 26 25
ISYM out of range in SYMNEG 26 25

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.

  48 ASP   (  55-)  A   H-bonding suggests Asn; but Alt-Rotamer
  83 ASP   (  90-)  A   H-bonding suggests Asn; but Alt-Rotamer
 112 ASP   ( 119-)  A   H-bonding suggests Asn
 113 ASP   ( 120-)  A   H-bonding suggests Asn; but Alt-Rotamer
 176 GLU   ( 183-)  A   H-bonding suggests Gln
 182 ASP   ( 189-)  A   H-bonding suggests Asn
 183 ASP   ( 190-)  A   H-bonding suggests Asn
 358 ASP   ( 374-)  A   H-bonding suggests Asn; but Alt-Rotamer
 413 ASP   (  55-)  B   H-bonding suggests Asn; but Alt-Rotamer
 448 ASP   (  90-)  B   H-bonding suggests Asn; but Alt-Rotamer
 477 ASP   ( 119-)  B   H-bonding suggests Asn
 478 ASP   ( 120-)  B   H-bonding suggests Asn; but Alt-Rotamer
 541 GLU   ( 183-)  B   H-bonding suggests Gln
 547 ASP   ( 189-)  B   H-bonding suggests Asn
 548 ASP   ( 190-)  B   H-bonding suggests Asn
 723 ASP   ( 374-)  B   H-bonding suggests Asn
 778 ASP   (  55-)  C   H-bonding suggests Asn; but Alt-Rotamer
 813 ASP   (  90-)  C   H-bonding suggests Asn; but Alt-Rotamer
 842 ASP   ( 119-)  C   H-bonding suggests Asn
 843 ASP   ( 120-)  C   H-bonding suggests Asn; but Alt-Rotamer
 906 GLU   ( 183-)  C   H-bonding suggests Gln
 912 ASP   ( 189-)  C   H-bonding suggests Asn
 913 ASP   ( 190-)  C   H-bonding suggests Asn
1088 ASP   ( 374-)  C   H-bonding suggests Asn; but Alt-Rotamer
1143 ASP   (  55-)  D   H-bonding suggests Asn; but Alt-Rotamer
1178 ASP   (  90-)  D   H-bonding suggests Asn; but Alt-Rotamer
1207 ASP   ( 119-)  D   H-bonding suggests Asn
1208 ASP   ( 120-)  D   H-bonding suggests Asn; but Alt-Rotamer
1271 GLU   ( 183-)  D   H-bonding suggests Gln
1277 ASP   ( 189-)  D   H-bonding suggests Asn
1278 ASP   ( 190-)  D   H-bonding suggests Asn
1453 ASP   ( 374-)  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 :  -1.975
  2nd generation packing quality :  -2.052
  Ramachandran plot appearance   :  -5.073 (bad)
  chi-1/chi-2 rotamer normality  :  -4.768 (bad)
  Backbone conformation          :  -0.567

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.382 (tight)
  Bond angles                    :   0.673
  Omega angle restraints         :   0.192 (tight)
  Side chain planarity           :   0.237 (tight)
  Improper dihedral distribution :   0.590
  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 : 3.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.6
  2nd generation packing quality :   0.1
  Ramachandran plot appearance   :  -2.0
  chi-1/chi-2 rotamer normality  :  -2.2
  Backbone conformation          :   0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.382 (tight)
  Bond angles                    :   0.673
  Omega angle restraints         :   0.192 (tight)
  Side chain planarity           :   0.237 (tight)
  Improper dihedral distribution :   0.590
  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

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    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
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      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,
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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
    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.