WHAT IF Check report

This file was created 2011-12-17 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 pdb3qxa.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 0.740
CA-only RMS fit for the two chains : 0.457

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: B and E

All-atom RMS fit for the two chains : 1.223
CA-only RMS fit for the two chains : 1.006

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: B and E

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: C and F

All-atom RMS fit for the two chains : 0.798
CA-only RMS fit for the two chains : 0.451

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: C and F

Administrative problems that can generate validation failures

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

  35 LYS   (  38-)  A  -   CD
  35 LYS   (  38-)  A  -   CE
  35 LYS   (  38-)  A  -   NZ
  36 LYS   (  39-)  A  -   CG
  36 LYS   (  39-)  A  -   CD
  36 LYS   (  39-)  A  -   CE
  36 LYS   (  39-)  A  -   NZ
  43 GLU   (  46-)  A  -   CD
  43 GLU   (  46-)  A  -   OE1
  43 GLU   (  46-)  A  -   OE2
  52 GLU   (  55-)  A  -   CD
  52 GLU   (  55-)  A  -   OE1
  52 GLU   (  55-)  A  -   OE2
  57 LEU   (  60-)  A  -   CD1
  57 LEU   (  60-)  A  -   CD2
  89 LEU   (  92-)  A  -   CD2
  98 GLU   ( 101-)  A  -   OE1
  98 GLU   ( 101-)  A  -   OE2
 115 ASN   ( 118-)  A  -   ND2
 120 ARG   ( 123-)  A  -   NH1
 120 ARG   ( 123-)  A  -   NH2
 125 VAL   ( 128-)  A  -   CG1
 127 THR   ( 130-)  A  -   CB
 127 THR   ( 130-)  A  -   OG1
 127 THR   ( 130-)  A  -   CG2
And so on for a total of 159 lines.

Warning: Plausible backbone atoms detected with zero occupancy

Plausible backbone atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. However, if a backbone atom is present in the PDB file, and its position seems 'logical' (i.e. normal bond lengths with all atoms it should be bound to, and those atoms exist normally) WHAT IF will set the occupancy to 1.0 if it believes that the full presence of this atom will be beneficial to the rest of the validation process. If you get weird errors at, or near, these atoms, please check by hand what is going on, and repair things intelligently before running this validation again.

 179 ALA   ( 182-)  A  -   N
 179 ALA   ( 182-)  A  -   CA
 179 ALA   ( 182-)  A  -   C
 179 ALA   ( 182-)  A  -   O
 548 ALA   ( 182-)  D  -   N
 548 ALA   ( 182-)  D  -   CA
 548 ALA   ( 182-)  D  -   C
 548 ALA   ( 182-)  D  -   O
 549 GLY   (   1-)  E  -   N
 549 GLY   (   1-)  E  -   CA
 549 GLY   (   1-)  E  -   C
 549 GLY   (   1-)  E  -   O
 729 THR   ( 181-)  E  -   CA
 751 GLN   ( 100-)  C  -   N
 752 ALA   ( 101-)  C  -   CA
 752 ALA   ( 101-)  C  -   C
 752 ALA   ( 101-)  C  -   O
 764 GLN   ( 100-)  F  -   N
 764 GLN   ( 100-)  F  -   CA
 764 GLN   ( 100-)  F  -   C
 764 GLN   ( 100-)  F  -   O
 766 ALA   ( 182-)  D  -   O''

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: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: F

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.

  79 ILE   (  82-)  A    Zero

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first.

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


Number of TLS groups mentione in PDB file header: 6

Crystal temperature (K) :100.000

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 1.573 over 5661 bonds
Average difference in B over a bond : 3.19
RMS difference in B over a bond : 5.12

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: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: F

Nomenclature related problems

Warning: Arginine nomenclature problem

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

  47 ARG   (  50-)  A
 250 ARG   (  71-)  B
 259 ARG   (  80-)  B
 309 ARG   ( 130-)  B
 416 ARG   (  50-)  D
 619 ARG   (  71-)  E
 628 ARG   (  80-)  E
 678 ARG   ( 130-)  E

Warning: Tyrosine convention problem

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

  76 TYR   (  79-)  A
 147 TYR   ( 150-)  A
 158 TYR   ( 161-)  A
 350 TYR   ( 171-)  B
 379 TYR   (  13-)  D
 445 TYR   (  79-)  D
 516 TYR   ( 150-)  D
 527 TYR   ( 161-)  D
 580 TYR   (  32-)  E
 595 TYR   (  47-)  E
 650 TYR   ( 102-)  E
 719 TYR   ( 171-)  E

Warning: Phenylalanine convention problem

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

 109 PHE   ( 112-)  A
 134 PHE   ( 137-)  A
 145 PHE   ( 148-)  A
 177 PHE   ( 180-)  A
 192 PHE   (  13-)  B
 478 PHE   ( 112-)  D
 561 PHE   (  13-)  E
 670 PHE   ( 122-)  E

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.

  22 ASP   (  25-)  A
 168 ASP   ( 171-)  A
 178 ASP   ( 181-)  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   (  30-)  A
  68 GLU   (  71-)  A
 138 GLU   ( 141-)  A
 155 GLU   ( 158-)  A
 176 GLU   ( 179-)  A
 355 GLU   ( 176-)  B
 370 GLU   (   4-)  D
 396 GLU   (  30-)  D
 467 GLU   ( 101-)  D
 524 GLU   ( 158-)  D
 545 GLU   ( 179-)  D
 600 GLU   (  52-)  E
 710 GLU   ( 162-)  E

Geometric checks

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.

  22 ASP   (  25-)  A
  27 GLU   (  30-)  A
  47 ARG   (  50-)  A
  68 GLU   (  71-)  A
 138 GLU   ( 141-)  A
 155 GLU   ( 158-)  A
 168 ASP   ( 171-)  A
 176 GLU   ( 179-)  A
 178 ASP   ( 181-)  A
 250 ARG   (  71-)  B
 259 ARG   (  80-)  B
 309 ARG   ( 130-)  B
 355 GLU   ( 176-)  B
 370 GLU   (   4-)  D
 396 GLU   (  30-)  D
 416 ARG   (  50-)  D
 467 GLU   ( 101-)  D
 524 GLU   ( 158-)  D
 545 GLU   ( 179-)  D
 600 GLU   (  52-)  E
 619 ARG   (  71-)  E
 628 ARG   (  80-)  E
 678 ARG   ( 130-)  E
 710 GLU   ( 162-)  E

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

 110 THR   ( 113-)  A    -2.7
 654 THR   ( 106-)  E    -2.6
 479 THR   ( 113-)  D    -2.6
 336 THR   ( 157-)  B    -2.5
 551 THR   (   3-)  E    -2.4
 173 LYS   ( 176-)  A    -2.4
 729 THR   ( 181-)  E    -2.4
 705 THR   ( 157-)  E    -2.3
 458 LEU   (  92-)  D    -2.3
 285 THR   ( 106-)  B    -2.3
 754 LYS   (  90-)  F    -2.3
 382 PRO   (  16-)  D    -2.3
 737 ARG   ( 189-)  E    -2.3
 273 ARG   (  94-)  B    -2.3
 114 VAL   ( 117-)  A    -2.2
 519 PHE   ( 153-)  D    -2.2
 711 THR   ( 163-)  E    -2.2
 517 LEU   ( 151-)  D    -2.2
 213 GLN   (  34-)  B    -2.1
  97 ARG   ( 100-)  A    -2.1
 303 PRO   ( 124-)  B    -2.1
 112 PRO   ( 115-)  A    -2.1
 586 VAL   (  38-)  E    -2.1
 509 HIS   ( 143-)  D    -2.0
 150 PHE   ( 153-)  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.

  12 ASN   (  15-)  A  PRO omega poor
  15 GLN   (  18-)  A  Poor phi/psi
  36 LYS   (  39-)  A  Poor phi/psi
  75 ASN   (  78-)  A  Poor phi/psi
  76 TYR   (  79-)  A  Poor phi/psi
  92 SER   (  95-)  A  Poor phi/psi
  97 ARG   ( 100-)  A  Poor phi/psi
 106 ILE   ( 109-)  A  omega poor
 108 LYS   ( 111-)  A  Poor phi/psi
 110 THR   ( 113-)  A  PRO omega poor
 112 PRO   ( 115-)  A  Poor phi/psi
 126 THR   ( 129-)  A  Poor phi/psi
 140 HIS   ( 143-)  A  Poor phi/psi
 198 ASN   (  19-)  B  Poor phi/psi
 212 ASN   (  33-)  B  Poor phi/psi
 289 GLN   ( 110-)  B  Poor phi/psi
 302 TYR   ( 123-)  B  PRO omega poor
 313 ASN   ( 134-)  B  Poor phi/psi
 332 TRP   ( 153-)  B  Poor phi/psi
 381 ASN   (  15-)  D  PRO omega poor
 444 ASN   (  78-)  D  Poor phi/psi
 445 TYR   (  79-)  D  Poor phi/psi
 466 ARG   ( 100-)  D  Poor phi/psi
 477 LYS   ( 111-)  D  Poor phi/psi
 479 THR   ( 113-)  D  PRO omega poor
 481 PRO   ( 115-)  D  Poor phi/psi
 509 HIS   ( 143-)  D  Poor phi/psi
 581 ASN   (  33-)  E  Poor phi/psi
 658 GLN   ( 110-)  E  Poor phi/psi
 671 TYR   ( 123-)  E  PRO omega poor
 672 PRO   ( 124-)  E  Poor phi/psi
 682 ASN   ( 134-)  E  Poor phi/psi
 701 TRP   ( 153-)  E  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.830

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!

   8 GLU   (  11-)  A      0
  12 ASN   (  15-)  A      0
  14 ASP   (  17-)  A      0
  15 GLN   (  18-)  A      0
  23 PHE   (  26-)  A      0
  29 PHE   (  32-)  A      0
  30 HIS   (  33-)  A      0
  36 LYS   (  39-)  A      0
  48 PHE   (  51-)  A      0
  52 GLU   (  55-)  A      0
  75 ASN   (  78-)  A      0
  76 TYR   (  79-)  A      0
  91 ASN   (  94-)  A      0
  96 LEU   (  99-)  A      0
  97 ARG   ( 100-)  A      0
  99 PRO   ( 102-)  A      0
 100 ASN   ( 103-)  A      0
 107 ASP   ( 110-)  A      0
 108 LYS   ( 111-)  A      0
 109 PHE   ( 112-)  A      0
 110 THR   ( 113-)  A      0
 112 PRO   ( 115-)  A      0
 113 VAL   ( 116-)  A      0
 115 ASN   ( 118-)  A      0
 120 ARG   ( 123-)  A      0
And so on for a total of 299 lines.

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].

 112 PRO   ( 115-)  A    31.1 envelop C-delta (36 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.

 739 VAL   (  88-)  C      N   <->  772 HOH   ( 142 )  C      O      0.44    2.26  INTRA BF
 618 GLN   (  70-)  E      O   <->  771 HOH   ( 196 )  E      O      0.40    2.00  INTRA
 590 SER   (  42-)  E      O   <->  771 HOH   ( 201 )  E      O      0.35    2.05  INTRA BL
 770 HOH   ( 184 )  D      O   <->  770 HOH   ( 224 )  D      O      0.34    1.86  INTRA
 120 ARG   ( 123-)  A      NE  <->  158 TYR   ( 161-)  A      CE2    0.33    2.77  INTRA BF
 716 GLY   ( 168-)  E      N   <->  737 ARG   ( 189-)  E      NH1    0.32    2.53  INTRA
 460 ASN   (  94-)  D      O   <->  770 HOH   ( 207 )  D      O      0.31    2.09  INTRA BL
 770 HOH   ( 201 )  D      O   <->  771 HOH   ( 204 )  E      O      0.30    2.10  INTRA BL
 370 GLU   (   4-)  D      N   <->  770 HOH   ( 229 )  D      O      0.28    2.42  INTRA
 343 VAL   ( 164-)  B      O   <->  345 ARG   ( 166-)  B      NH1    0.27    2.43  INTRA
  27 GLU   (  30-)  A      OE1 <->  768 HOH   ( 204 )  A      O      0.27    2.13  INTRA BL
 413 GLU   (  47-)  D      OE2 <->  770 HOH   ( 214 )  D      O      0.25    2.15  INTRA BF
 716 GLY   ( 168-)  E      CA  <->  737 ARG   ( 189-)  E      NH2    0.24    2.86  INTRA
 644 GLU   (  96-)  E      N   <->  771 HOH   ( 199 )  E      O      0.23    2.47  INTRA BL
 737 ARG   ( 189-)  E      NE  <->  771 HOH   ( 224 )  E      O      0.21    2.49  INTRA
 394 GLY   (  28-)  D      O   <->  512 ARG   ( 146-)  D      NH2    0.21    2.49  INTRA
  52 GLU   (  55-)  A      CG  <->   54 GLN   (  57-)  A      NE2    0.17    2.93  INTRA BF
 618 GLN   (  70-)  E      NE2 <->  619 ARG   (  71-)  E      NH1    0.17    2.68  INTRA
 543 HIS   ( 177-)  D      NE2 <->  545 GLU   ( 179-)  D      OE1    0.16    2.54  INTRA BL
 234 ARG   (  55-)  B      N   <->  235 PRO   (  56-)  B      CD     0.16    2.84  INTRA BL
 771 HOH   ( 205 )  E      O   <->  771 HOH   ( 213 )  E      O      0.15    2.05  INTRA
 202 ARG   (  23-)  B      NH2 <->  222 ASP   (  43-)  B      OD1    0.15    2.55  INTRA
 603 ARG   (  55-)  E      N   <->  604 PRO   (  56-)  E      CD     0.13    2.87  INTRA BL
 178 ASP   ( 181-)  A      CB  <->  653 LYS   ( 105-)  E      NZ     0.13    2.97  INTRA BF
 581 ASN   (  33-)  E      ND2 <->  771 HOH   ( 226 )  E      O      0.13    2.57  INTRA
And so on for a total of 96 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: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Warning: Abnormal packing environment for some residues

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

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

 751 GLN   ( 100-)  C      -6.94
 466 ARG   ( 100-)  D      -6.19
 318 LYS   ( 139-)  B      -5.82
 737 ARG   ( 189-)  E      -5.80
 687 LYS   ( 139-)  E      -5.47
  97 ARG   ( 100-)  A      -5.28
 416 ARG   (  50-)  D      -5.25
  15 GLN   (  18-)  A      -5.23
 763 MET   (  99-)  F      -5.11
 384 GLN   (  18-)  D      -5.06
  76 TYR   (  79-)  A      -5.05

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: D

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: E

Note: Quality value plot

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

Chain identifier: C

Warning: Low packing Z-score for some residues

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

 418 ALA   (  52-)  D   -2.79

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: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: C

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.

 770 HOH   ( 209 )  D      O     -1.31   31.30   30.32

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.

 770 HOH   ( 224 )  D      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.

 189 GLN   (  10-)  B
 315 GLN   ( 136-)  B
 558 GLN   (  10-)  E
 618 GLN   (  70-)  E
 658 GLN   ( 110-)  E
 722 GLN   ( 174-)  E
 764 GLN   ( 100-)  F

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.

  14 ASP   (  17-)  A      N
  42 LEU   (  45-)  A      N
  54 GLN   (  57-)  A      N
  92 SER   (  95-)  A      N
 127 THR   ( 130-)  A      N
 177 PHE   ( 180-)  A      N
 178 ASP   ( 181-)  A      N
 208 ARG   (  29-)  B      NE
 216 SER   (  37-)  B      OG
 225 GLU   (  46-)  B      N
 226 TYR   (  47-)  B      OH
 236 ASP   (  57-)  B      N
 272 ARG   (  93-)  B      N
 290 HIS   ( 111-)  B      N
 321 VAL   ( 142-)  B      N
 410 ARG   (  44-)  D      NE
 411 LEU   (  45-)  D      N
 442 ARG   (  76-)  D      NH1
 557 TRP   (   9-)  E      NE1
 558 GLN   (  10-)  E      NE2
 577 ARG   (  29-)  E      NE
 585 SER   (  37-)  E      OG
 594 GLU   (  46-)  E      N
 605 ASP   (  57-)  E      N
 618 GLN   (  70-)  E      N
 623 VAL   (  75-)  E      N
 658 GLN   ( 110-)  E      NE2
 681 ARG   ( 133-)  E      NE
 716 GLY   ( 168-)  E      N
 737 ARG   ( 189-)  E      NH1
 754 LYS   (  90-)  F      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.

   8 GLU   (  11-)  A      OE1
  63 ASP   (  66-)  A      OD2
 377 GLU   (  11-)  D      OE1
 432 ASP   (  66-)  D      OD1
 432 ASP   (  66-)  D      OD2
 605 ASP   (  57-)  E      OD2
 655 GLN   ( 107-)  E      OE1
 724 GLU   ( 176-)  E      OE1

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.

  18 GLU   (  21-)  A   H-bonding suggests Gln
  43 GLU   (  46-)  A   H-bonding suggests Gln
 156 ASP   ( 159-)  A   H-bonding suggests Asn; but Alt-Rotamer
 387 GLU   (  21-)  D   H-bonding suggests Gln
 432 ASP   (  66-)  D   H-bonding suggests Asn
 524 GLU   ( 158-)  D   H-bonding suggests Gln
 525 ASP   ( 159-)  D   H-bonding suggests Asn; but Alt-Rotamer
 528 ASP   ( 162-)  D   H-bonding suggests Asn; but Alt-Rotamer
 547 ASP   ( 181-)  D   H-bonding suggests Asn
 617 GLU   (  69-)  E   H-bonding suggests Gln
 686 GLU   ( 138-)  E   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 :   0.169
  2nd generation packing quality :  -0.904
  Ramachandran plot appearance   :  -0.766
  chi-1/chi-2 rotamer normality  :  -0.830
  Backbone conformation          :   0.066

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.161 (tight)
  Bond angles                    :   0.423 (tight)
  Omega angle restraints         :   0.788
  Side chain planarity           :   0.151 (tight)
  Improper dihedral distribution :   0.354
  B-factor distribution          :   1.573 (loose)
  Inside/Outside distribution    :   1.038

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 : 2.71


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.4
  2nd generation packing quality :   0.7
  Ramachandran plot appearance   :   1.6
  chi-1/chi-2 rotamer normality  :   1.3
  Backbone conformation          :   0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.161 (tight)
  Bond angles                    :   0.423 (tight)
  Omega angle restraints         :   0.788
  Side chain planarity           :   0.151 (tight)
  Improper dihedral distribution :   0.354
  B-factor distribution          :   1.573 (loose)
  Inside/Outside distribution    :   1.038
==============

WHAT IF
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    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
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      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
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      refinement,
    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,
      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.