WHAT IF Check report

This file was created 2011-12-15 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 pdb1ggy.ent

Administrative problems that can generate validation failures

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

 702 ARG   ( 727-)  A  -
1407 ARG   ( 727-)  B  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

 702 ARG   ( 727-)  A      O
1407 ARG   ( 727-)  B      O

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.

1197 ASN   ( 517-)  B    High
1224 HIS   ( 544-)  B    High
1296 ARG   ( 616-)  B    High

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) :293.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Geometric checks

Warning: 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.

  34 LEU   (  52-)  A      N    CA   C    97.64   -4.8
 152 LEU   ( 170-)  A      N    CA   C    99.91   -4.0
 251 LYS   ( 269-)  A      N    CA   C    96.20   -5.4
 493 VAL   ( 518-)  A      N    CA   C    97.00   -5.1
 641 HIS   ( 666-)  A      CG   ND1  CE1 109.66    4.1
 751 HIS   (  64-)  B      CG   ND1  CE1 109.76    4.2
 803 TYR   ( 116-)  B      N    CA   C    99.92   -4.0
 857 LEU   ( 170-)  B      N    CA   C    99.08   -4.3
 888 ARG   ( 201-)  B      CB   CG   CD  105.40   -4.4
1001 CYS   ( 314-)  B      N    CA   C   122.79    4.1
1029 HIS   ( 342-)  B      CG   ND1  CE1 109.79    4.2
1092 GLY   ( 405-)  B      N    CA   C   126.09    4.7
1188 GLY   ( 501-)  B      N    CA   C   124.40    4.1
1247 GLU   ( 567-)  B      N    CA   C    99.72   -4.1
1396 HIS   ( 716-)  B      CG   ND1  CE1 109.72    4.1

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.

1001 CYS   ( 314-)  B    6.71
 278 VAL   ( 296-)  A    6.19
1115 ALA   ( 428-)  B    6.19
 251 LYS   ( 269-)  A    5.82
 470 GLU   ( 488-)  A    5.56
1275 MET   ( 595-)  B    5.53
 410 ALA   ( 428-)  A    5.50
 493 VAL   ( 518-)  A    5.34
 885 GLU   ( 198-)  B    5.20
  34 LEU   (  52-)  A    5.09
 770 TYR   (  83-)  B    4.82
 982 SER   ( 295-)  B    4.69
 904 VAL   ( 217-)  B    4.64
1189 ALA   ( 502-)  B    4.52
1092 GLY   ( 405-)  B    4.49
 857 LEU   ( 170-)  B    4.46
 983 VAL   ( 296-)  B    4.33
 956 LYS   ( 269-)  B    4.28
 803 TYR   ( 116-)  B    4.24
 401 HIS   ( 419-)  A    4.23
1247 GLU   ( 567-)  B    4.19
 152 LEU   ( 170-)  A    4.10

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 : 1.646

Torsion-related checks

Warning: Ramachandran Z-score low

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

Ramachandran Z-score : -3.221

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.

 746 THR   (  59-)  B    -3.0
 100 PRO   ( 118-)  A    -2.9
 265 TYR   ( 283-)  A    -2.7
1377 PRO   ( 697-)  B    -2.7
  78 ARG   (  96-)  A    -2.6
 806 VAL   ( 119-)  B    -2.6
 910 ARG   ( 223-)  B    -2.6
 786 PHE   (  99-)  B    -2.5
 970 TYR   ( 283-)  B    -2.5
 691 HIS   ( 716-)  A    -2.5
1396 HIS   ( 716-)  B    -2.5
1353 THR   ( 673-)  B    -2.5
1256 THR   ( 576-)  B    -2.4
 730 GLU   (  43-)  B    -2.4
 785 LEU   (  98-)  B    -2.4
 445 LEU   ( 463-)  A    -2.4
 196 TYR   ( 214-)  A    -2.4
 732 LEU   (  45-)  B    -2.3
1150 LEU   ( 463-)  B    -2.3
1026 PHE   ( 339-)  B    -2.3
 859 THR   ( 172-)  B    -2.3
  27 LEU   (  45-)  A    -2.3
 388 MET   ( 406-)  A    -2.3
 815 GLY   ( 128-)  B    -2.3
 763 VAL   (  76-)  B    -2.3
And so on for a total of 77 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 GLY   (   9-)  A  Poor phi/psi
  27 LEU   (  45-)  A  Poor phi/psi
  36 LYS   (  54-)  A  Poor phi/psi
  37 GLU   (  55-)  A  Poor phi/psi
  38 ARG   (  56-)  A  Poor phi/psi
  47 HIS   (  65-)  A  Poor phi/psi
  76 PRO   (  94-)  A  Poor phi/psi
 118 MET   ( 136-)  A  Poor phi/psi
 120 GLU   ( 138-)  A  Poor phi/psi
 122 ARG   ( 140-)  A  Poor phi/psi
 196 TYR   ( 214-)  A  Poor phi/psi
 253 ASP   ( 271-)  A  Poor phi/psi
 255 GLY   ( 273-)  A  Poor phi/psi
 263 ASN   ( 281-)  A  Poor phi/psi
 265 TYR   ( 283-)  A  Poor phi/psi
 278 VAL   ( 296-)  A  Poor phi/psi
 288 GLU   ( 306-)  A  Poor phi/psi
 292 ARG   ( 310-)  A  omega poor
 321 PHE   ( 339-)  A  Poor phi/psi
 325 ASP   ( 343-)  A  Poor phi/psi
 328 ALA   ( 346-)  A  Poor phi/psi
 362 MET   ( 380-)  A  Poor phi/psi
 368 PRO   ( 386-)  A  Poor phi/psi
 388 MET   ( 406-)  A  Poor phi/psi
 392 GLY   ( 410-)  A  Poor phi/psi
And so on for a total of 69 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 : -4.308

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!

   4 ARG   (  11-)  A      0
   5 ARG   (  12-)  A      0
  10 ASN   (  17-)  A      0
  11 ASN   (  18-)  A      0
  15 ALA   (  22-)  A      0
  23 GLU   (  30-)  A      0
  24 LEU   (  31-)  A      0
  25 GLU   (  43-)  A      0
  26 PHE   (  44-)  A      0
  27 LEU   (  45-)  A      0
  30 THR   (  48-)  A      0
  35 PHE   (  53-)  A      0
  36 LYS   (  54-)  A      0
  37 GLU   (  55-)  A      0
  39 TRP   (  57-)  A      0
  47 HIS   (  65-)  A      0
  48 THR   (  66-)  A      0
  49 ASP   (  67-)  A      0
  51 TYR   (  69-)  A      0
  52 GLU   (  70-)  A      0
  53 ASN   (  71-)  A      0
  60 ARG   (  78-)  A      0
  71 SER   (  89-)  A      0
  72 ARG   (  90-)  A      0
  77 ARG   (  95-)  A      0
And so on for a total of 608 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 : 1.587

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!

 644 GLY   ( 669-)  A   2.14   17
1173 GLY   ( 486-)  B   2.02   80

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]

 805 PRO   ( 118-)  B    0.46 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].

  73 PRO   (  91-)  A  -115.3 envelop C-gamma (-108 degrees)
  76 PRO   (  94-)  A  -116.0 envelop C-gamma (-108 degrees)
 368 PRO   ( 386-)  A    99.2 envelop C-beta (108 degrees)
 539 PRO   ( 564-)  A    46.9 half-chair C-delta/C-gamma (54 degrees)
 778 PRO   (  91-)  B  -117.1 half-chair C-delta/C-gamma (-126 degrees)
1355 PRO   ( 675-)  B  -118.9 half-chair C-delta/C-gamma (-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.

 947 ARG   ( 260-)  B      NH1 <-> 1095 ARG   ( 408-)  B      CZ     0.36    2.74  INTRA BL
 262 ASP   ( 280-)  A      O   <->  264 ILE   ( 282-)  A      N      0.34    2.36  INTRA
  17 ASP   (  24-)  A      O   <->  140 ARG   ( 158-)  A      NH2    0.32    2.38  INTRA BF
1069 ARG   ( 382-)  B      NH2 <-> 1098 PRO   ( 411-)  B      O      0.31    2.39  INTRA BL
 910 ARG   ( 223-)  B      NH2 <-> 1417 HOH   (6078 )  B      O      0.28    2.42  INTRA BL
 739 LEU   (  52-)  B      O   <->  741 LYS   (  54-)  B      N      0.28    2.42  INTRA
 743 ARG   (  56-)  B      NH1 <->  754 ASP   (  67-)  B      O      0.27    2.43  INTRA BL
1029 HIS   ( 342-)  B      ND1 <-> 1121 GLU   ( 434-)  B      OE2    0.26    2.44  INTRA BL
1381 GLY   ( 701-)  B      N   <-> 1405 ILE   ( 725-)  B      O      0.23    2.47  INTRA BF
  60 ARG   (  78-)  A      NH1 <->  134 CYS   ( 152-)  A      O      0.23    2.47  INTRA BL
1105 LYS   ( 418-)  B      NZ  <-> 1166 ASP   ( 479-)  B      O      0.22    2.48  INTRA BL
 217 LEU   ( 235-)  A      CA  <->  309 CYS   ( 327-)  A      SG     0.22    3.18  INTRA BL
 961 VAL   ( 274-)  B      O   <->  996 VAL   ( 309-)  B      N      0.22    2.48  INTRA BL
 405 CYS   ( 423-)  A      SG  <-> 1416 HOH   (5033 )  A      O      0.21    2.79  INTRA
 120 GLU   ( 138-)  A      O   <->  122 ARG   ( 140-)  A      N      0.21    2.49  INTRA BF
  82 ARG   ( 100-)  A      CG  <->  146 TRP   ( 164-)  A      NE1    0.21    2.89  INTRA BF
 636 ARG   ( 661-)  A      NH2 <->  656 ARG   ( 681-)  A      O      0.21    2.49  INTRA BF
 861 ARG   ( 174-)  B      NH2 <->  866 ASP   ( 179-)  B      OD1    0.20    2.50  INTRA
 682 ALA   ( 707-)  A      N   <->  694 GLY   ( 719-)  A      O      0.19    2.51  INTRA BL
 448 THR   ( 466-)  A      O   <->  457 MET   ( 475-)  A      N      0.18    2.52  INTRA BL
 337 GLU   ( 355-)  A      N   <->  341 ASN   ( 359-)  A      O      0.18    2.52  INTRA
 813 GLN   ( 126-)  B      CG  <->  814 SER   ( 127-)  B      N      0.18    2.82  INTRA BF
 623 VAL   ( 648-)  A      CG2 <->  670 CYS   ( 695-)  A      SG     0.18    3.22  INTRA BF
   5 ARG   (  12-)  A      NH2 <-> 1093 MET   ( 406-)  B      CE     0.18    2.92  INTRA BF
1395 ARG   ( 715-)  B      CG  <-> 1396 HIS   ( 716-)  B      N      0.18    2.82  INTRA BL
And so on for a total of 260 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Warning: Abnormal packing environment for some residues

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

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

 972 TYR   ( 285-)  B      -8.32
 267 TYR   ( 285-)  A      -7.45
 727 GLN   (  32-)  B      -7.20
 156 ARG   ( 174-)  A      -7.08
 861 ARG   ( 174-)  B      -7.03
 149 TYR   ( 167-)  A      -7.00
  26 PHE   (  44-)  A      -6.81
  90 TYR   ( 108-)  A      -6.62
 706 ARG   (  11-)  B      -6.58
 782 ARG   (  95-)  B      -6.42
 795 TYR   ( 108-)  B      -6.32
1361 ARG   ( 681-)  B      -6.32
1317 ARG   ( 637-)  B      -6.29
   4 ARG   (  11-)  A      -6.23
  78 ARG   (  96-)  A      -6.11
1155 GLN   ( 468-)  B      -5.90
1224 HIS   ( 544-)  B      -5.88
 108 GLN   ( 126-)  A      -5.86
 519 HIS   ( 544-)  A      -5.84
1354 ARG   ( 674-)  B      -5.79
1093 MET   ( 406-)  B      -5.75
 612 ARG   ( 637-)  A      -5.72
1337 LYS   ( 657-)  B      -5.71
 813 GLN   ( 126-)  B      -5.68
 632 LYS   ( 657-)  A      -5.65
 388 MET   ( 406-)  A      -5.64
1133 LYS   ( 446-)  B      -5.61
1194 ASN   ( 507-)  B      -5.55
  89 ARG   ( 107-)  A      -5.53
  46 HIS   (  64-)  A      -5.37
  77 ARG   (  95-)  A      -5.37
 794 ARG   ( 107-)  B      -5.36
 450 GLN   ( 468-)  A      -5.35
 783 ARG   (  96-)  B      -5.35
  94 ASN   ( 112-)  A      -5.33
 489 ASN   ( 507-)  A      -5.32
 799 ASN   ( 112-)  B      -5.32
 466 GLN   ( 484-)  A      -5.21
 428 LYS   ( 446-)  A      -5.18
1277 GLN   ( 597-)  B      -5.18
 369 VAL   ( 387-)  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.

 388 MET   ( 406-)  A       390 - ARG    408- ( A)         -4.84
1093 MET   ( 406-)  B      1095 - ARG    408- ( B)         -5.10

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Warning: Low packing Z-score for some residues

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

 120 GLU   ( 138-)  A   -2.87
 617 VAL   ( 642-)  A   -2.68
1094 TYR   ( 407-)  B   -2.58
 273 ALA   ( 291-)  A   -2.54
 193 VAL   ( 211-)  A   -2.54
 389 TYR   ( 407-)  A   -2.54
 407 GLN   ( 425-)  A   -2.52

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.

  92 GLN   ( 110-)  A     -   95 LYS   ( 113-)  A        -1.57
 780 ASP   (  93-)  B     -  783 ARG   (  96-)  B        -1.23

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

1417 HOH   (3117 )  B      O     28.95    9.49   62.45

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.

1416 HOH   (5030 )  A      O
1417 HOH   (3120 )  B      O
1417 HOH   (5019 )  B      O

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

  54 ASN   (  72-)  A
1197 ASN   ( 517-)  B
1270 GLN   ( 590-)  B

Warning: Buried unsatisfied hydrogen bond donors

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

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

Waters are not listed by this option.

   3 GLY   (  10-)  A      N
   7 VAL   (  14-)  A      N
  35 PHE   (  53-)  A      N
  39 TRP   (  57-)  A      N
  42 ASN   (  60-)  A      N
  42 ASN   (  60-)  A      ND2
  43 LYS   (  61-)  A      N
  50 LYS   (  68-)  A      N
  56 LEU   (  74-)  A      N
  57 ILE   (  75-)  A      N
  62 GLN   (  80-)  A      N
  72 ARG   (  90-)  A      N
  72 ARG   (  90-)  A      NE
  78 ARG   (  96-)  A      N
  81 PHE   (  99-)  A      N
  82 ARG   ( 100-)  A      NE
  85 TYR   ( 103-)  A      OH
  98 TYR   ( 116-)  A      N
 130 SER   ( 148-)  A      N
 131 SER   ( 149-)  A      N
 136 VAL   ( 154-)  A      N
 156 ARG   ( 174-)  A      NE
 179 ASN   ( 197-)  A      N
 195 PHE   ( 213-)  A      N
 205 ARG   ( 223-)  A      NH2
And so on for a total of 142 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.

  92 GLN   ( 110-)  A      OE1
 201 ASP   ( 219-)  A      OD2
 319 ASN   ( 337-)  A      OD1
 420 ASP   ( 438-)  A      OD1
 432 HIS   ( 450-)  A      ND1
 580 HIS   ( 605-)  A      ND1
 758 ASN   (  71-)  B      OD1
1029 HIS   ( 342-)  B      ND1
1060 HIS   ( 373-)  B      ND1
1121 GLU   ( 434-)  B      OE2
1137 HIS   ( 450-)  B      ND1
1325 ASP   ( 645-)  B      OD1
1372 GLU   ( 692-)  B      OE2
1402 ASP   ( 722-)  B      OD1

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

  45 ASP   (  63-)  A   H-bonding suggests Asn
  69 ASP   (  87-)  A   H-bonding suggests Asn; but Alt-Rotamer
 198 GLU   ( 216-)  A   H-bonding suggests Gln
 230 ASP   ( 248-)  A   H-bonding suggests Asn
 420 ASP   ( 438-)  A   H-bonding suggests Asn; but Alt-Rotamer
 549 ASP   ( 574-)  A   H-bonding suggests Asn; but Alt-Rotamer
 903 GLU   ( 216-)  B   H-bonding suggests Gln
 935 ASP   ( 248-)  B   H-bonding suggests Asn; but Alt-Rotamer
 958 ASP   ( 271-)  B   H-bonding suggests Asn; but Alt-Rotamer
1251 GLU   ( 571-)  B   H-bonding suggests Gln
1294 GLU   ( 614-)  B   H-bonding suggests Gln; but Alt-Rotamer
1311 GLU   ( 631-)  B   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.976
  2nd generation packing quality :  -2.017
  Ramachandran plot appearance   :  -3.221 (poor)
  chi-1/chi-2 rotamer normality  :  -4.308 (bad)
  Backbone conformation          :  -0.514

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.493 (tight)
  Bond angles                    :   0.789
  Omega angle restraints         :   0.289 (tight)
  Side chain planarity           :   0.524 (tight)
  Improper dihedral distribution :   1.064
  B-factor distribution          :   1.014
  Inside/Outside distribution    :   1.051

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 : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.0
  2nd generation packing quality :  -0.7
  Ramachandran plot appearance   :  -1.0
  chi-1/chi-2 rotamer normality  :  -2.3
  Backbone conformation          :  -0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.493 (tight)
  Bond angles                    :   0.789
  Omega angle restraints         :   0.289 (tight)
  Side chain planarity           :   0.524 (tight)
  Improper dihedral distribution :   1.064
  B-factor distribution          :   1.014
  Inside/Outside distribution    :   1.051
==============

WHAT IF
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      WHAT IF: a molecular modelling and drug design program,
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WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
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    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
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      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.