WHAT IF Check report

This file was created 2013-12-10 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 pdb3wd5.ent

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.

 197 LYS   (  45-)  L  -   CE
 233 GLU   (  81-)  L  -   CG
 252 GLN   ( 100-)  L  -   CG
 278 LYS   ( 126-)  L  -   CE
 278 LYS   ( 126-)  L  -   NZ
 299 GLN   ( 147-)  L  -   CG
 306 LEU   ( 154-)  L  -   CD1
 306 LEU   ( 154-)  L  -   CD2
 321 LYS   ( 169-)  L  -   CG
 321 LYS   ( 169-)  L  -   CD
 321 LYS   ( 169-)  L  -   CE
 340 LYS   ( 188-)  L  -   NZ
 363 ARG   ( 211-)  L  -   NH2
 365 GLU   ( 213-)  L  -   CB
 365 GLU   ( 213-)  L  -   CG
 366 GLU   (   1-)  H  -   OE2
 454 GLU   (  89-)  H  -   CG
 500 SER   ( 135-)  H  -   CB
 501 SER   ( 136-)  H  -   CB
 569 LYS   ( 209-)  H  -   CD
 569 LYS   ( 209-)  H  -   CE
 569 LYS   ( 209-)  H  -   NZ

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.

 364 GLY   ( 212-)  L  -   CA
 365 GLU   ( 213-)  L  -   CA
 365 GLU   ( 213-)  L  -   O
 406 PRO   (  41-)  H  -   CA
 500 SER   ( 135-)  H  -   CA
 502 GLY   ( 142-)  H  -   CA
 556 SER   ( 196-)  H  -   N
 558 GLY   ( 198-)  H  -   CA

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: L

Note: Ramachandran plot

Chain identifier: H

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.

  81 SER   (  86-)  A    High
  82 TYR   (  87-)  A    High
  98 ARG   ( 103-)  A    High
  99 GLU   ( 104-)  A    High
 102 GLU   ( 107-)  A    High
 103 GLY   ( 108-)  A    High
 557 LEU   ( 197-)  H    High
 559 THR   ( 199-)  H    High
 560 GLN   ( 200-)  H    High
 561 THR   ( 201-)  H    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. 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: 0

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

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 : 1.776 over 3910 bonds
Average difference in B over a bond : 3.99
RMS difference in B over a bond : 7.11

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: L

Note: B-factor plot

Chain identifier: H

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.

 170 ARG   (  18-)  L
 213 ARG   (  61-)  L
 260 ARG   ( 108-)  L
 363 ARG   ( 211-)  L

Warning: Tyrosine convention problem

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

  51 TYR   (  56-)  A
  54 TYR   (  59-)  A
  82 TYR   (  87-)  A
 110 TYR   ( 115-)  A
 114 TYR   ( 119-)  A
 184 TYR   (  32-)  L
 201 TYR   (  49-)  L
 344 TYR   ( 192-)  L
 397 TYR   (  32-)  H
 425 TYR   (  60-)  H
 445 TYR   (  80-)  H
 460 TYR   (  95-)  H
 475 TYR   ( 110-)  H
 544 TYR   ( 184-)  H

Warning: Phenylalanine convention problem

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

 119 PHE   ( 124-)  A
 214 PHE   (  62-)  L
 291 PHE   ( 139-)  L
 361 PHE   ( 209-)  L
 392 PHE   (  27-)  H
 394 PHE   (  29-)  H
 495 PHE   ( 130-)  H
 534 PHE   ( 174-)  H

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

   5 ASP   (  10-)  A
 274 ASP   ( 122-)  L
 319 ASP   ( 167-)  L
 322 ASP   ( 170-)  L
 337 ASP   ( 185-)  L
 438 ASP   (  73-)  H

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

  18 GLU   (  23-)  A
  48 GLU   (  53-)  A
  99 GLU   ( 104-)  A
 102 GLU   ( 107-)  A
 111 GLU   ( 116-)  A
 122 GLU   ( 127-)  A
 141 GLU   ( 146-)  A
 275 GLU   ( 123-)  L
 317 GLU   ( 165-)  L
 411 GLU   (  46-)  H
 516 GLU   ( 156-)  H

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.

  10 HIS   (  15-)  A      CG   ND1  CE1 109.70    4.1
 244 ASN   (  92-)  L      N    CA   C   124.43    4.7
 245 ARG   (  93-)  L     -CA  -C    N   127.67    5.7
 245 ARG   (  93-)  L     -C    N    CA  136.64    8.3
 260 ARG   ( 108-)  L      CB   CG   CD  105.95   -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.

   5 ASP   (  10-)  A
  18 GLU   (  23-)  A
  48 GLU   (  53-)  A
  99 GLU   ( 104-)  A
 102 GLU   ( 107-)  A
 111 GLU   ( 116-)  A
 122 GLU   ( 127-)  A
 141 GLU   ( 146-)  A
 170 ARG   (  18-)  L
 213 ARG   (  61-)  L
 260 ARG   ( 108-)  L
 274 ASP   ( 122-)  L
 275 GLU   ( 123-)  L
 317 GLU   ( 165-)  L
 319 ASP   ( 167-)  L
 322 ASP   ( 170-)  L
 337 ASP   ( 185-)  L
 363 ARG   ( 211-)  L
 411 GLU   (  46-)  H
 438 ASP   (  73-)  H
 516 GLU   ( 156-)  H

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 244 ASN   (  92-)  L      CA    -7.0    20.38    33.59
 245 ARG   (  93-)  L      CA    -9.3    18.64    33.91
The average deviation= 0.890

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.

 142 SER   ( 147-)  A    5.04
 244 ASN   (  92-)  L    4.17
 245 ARG   (  93-)  L    4.06

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.

  65 PRO   (  70-)  A    -3.1
 515 PRO   ( 155-)  H    -2.9
 467 LEU   ( 102-)  H    -2.8
  32 LEU   (  37-)  A    -2.7
 182 ARG   (  30-)  L    -2.7
 506 LEU   ( 146-)  H    -2.7
 524 SER   ( 164-)  H    -2.6
 100 THR   ( 105-)  A    -2.6
 420 SER   (  55-)  H    -2.6
 224 THR   (  72-)  L    -2.6
 332 THR   ( 180-)  L    -2.5
 260 ARG   ( 108-)  L    -2.5
 323 SER   ( 171-)  L    -2.5
 150 ILE   ( 155-)  A    -2.5
 181 ILE   (  29-)  L    -2.5
 517 PRO   ( 157-)  H    -2.5
 149 ILE   ( 154-)  A    -2.5
  77 ARG   (  82-)  A    -2.4
 131 ILE   ( 136-)  A    -2.4
 434 THR   (  69-)  H    -2.4
 258 ILE   ( 106-)  L    -2.4
  68 HIS   (  73-)  A    -2.4
 546 LEU   ( 186-)  H    -2.4
 333 LEU   ( 181-)  L    -2.3
 430 GLU   (  65-)  H    -2.3
 480 THR   ( 115-)  H    -2.3
 157 THR   (   5-)  L    -2.3
  58 LEU   (  63-)  A    -2.3
  84 THR   (  89-)  A    -2.3
  27 ARG   (  32-)  A    -2.3
 163 LEU   (  11-)  L    -2.3
 154 ILE   (   2-)  L    -2.2
  95 PRO   ( 100-)  A    -2.2
   8 VAL   (  13-)  A    -2.2
  39 ARG   (  44-)  A    -2.2
 483 THR   ( 118-)  H    -2.2
 527 LEU   ( 167-)  H    -2.1
 297 LYS   ( 145-)  L    -2.1
 283 SER   ( 131-)  L    -2.1
  67 THR   (  72-)  A    -2.1
  98 ARG   ( 103-)  A    -2.1
 428 SER   (  63-)  H    -2.1
   2 THR   (   7-)  A    -2.0
  96 CYS   ( 101-)  A    -2.0
 160 PRO   (   8-)  L    -2.0
 383 LEU   (  18-)  H    -2.0
  37 GLU   (  42-)  A    -2.0
  93 LYS   (  98-)  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.

   4 SER   (   9-)  A  Poor phi/psi
   9 ALA   (  14-)  A  omega poor
  11 VAL   (  16-)  A  omega poor
  26 ASP   (  31-)  A  Poor phi/psi
  27 ARG   (  32-)  A  omega poor
  28 ALA   (  33-)  A  Poor phi/psi, omega poor
  32 LEU   (  37-)  A  Poor phi/psi
  34 ASN   (  39-)  A  Poor phi/psi, omega poor
  41 ASN   (  46-)  A  Poor phi/psi
  65 PRO   (  70-)  A  Poor phi/psi
  67 THR   (  72-)  A  Poor phi/psi
  68 HIS   (  73-)  A  omega poor
  91 ALA   (  96-)  A  Poor phi/psi
  96 CYS   ( 101-)  A  Poor phi/psi
  97 GLN   ( 102-)  A  omega poor
  98 ARG   ( 103-)  A  Poor phi/psi, omega poor
  99 GLU   ( 104-)  A  Poor phi/psi
 101 PRO   ( 106-)  A  Poor phi/psi
 102 GLU   ( 107-)  A  omega poor
 105 GLU   ( 110-)  A  Poor phi/psi
 139 PHE   ( 144-)  A  omega poor
 141 GLU   ( 146-)  A  omega poor
 142 SER   ( 147-)  A  Poor phi/psi, omega poor
 143 GLY   ( 148-)  A  omega poor
 154 ILE   (   2-)  L  Poor phi/psi
And so on for a total of 67 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 : -4.169

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   3 PRO   (   8-)  A      0
   4 SER   (   9-)  A      0
  17 ALA   (  22-)  A      0
  18 GLU   (  23-)  A      0
  26 ASP   (  31-)  A      0
  27 ARG   (  32-)  A      0
  28 ALA   (  33-)  A      0
  29 ASN   (  34-)  A      0
  31 LEU   (  36-)  A      0
  32 LEU   (  37-)  A      0
  33 ALA   (  38-)  A      0
  34 ASN   (  39-)  A      0
  39 ARG   (  44-)  A      0
  40 ASP   (  45-)  A      0
  41 ASN   (  46-)  A      0
  46 PRO   (  51-)  A      0
  48 GLU   (  53-)  A      0
  50 LEU   (  55-)  A      0
  60 LYS   (  65-)  A      0
  62 GLN   (  67-)  A      0
  64 CYS   (  69-)  A      0
  65 PRO   (  70-)  A      0
  66 SER   (  71-)  A      0
  67 THR   (  72-)  A      0
  68 HIS   (  73-)  A      0
And so on for a total of 251 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 7.084

Warning: Unusual peptide bond conformations

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

 258 ILE   ( 106-)  L   1.82

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].

   7 PRO   (  12-)  A  -123.5 half-chair C-delta/C-gamma (-126 degrees)
  65 PRO   (  70-)  A    12.9 half-chair N/C-delta (18 degrees)
 211 PRO   (  59-)  L   100.1 envelop C-beta (108 degrees)
 272 PRO   ( 120-)  L  -112.8 envelop C-gamma (-108 degrees)
 356 PRO   ( 204-)  L   103.7 envelop C-beta (108 degrees)
 499 PRO   ( 134-)  H  -112.1 envelop C-gamma (-108 degrees)
 515 PRO   ( 155-)  H   -30.1 envelop C-alpha (-36 degrees)
 517 PRO   ( 157-)  H   -57.6 half-chair C-beta/C-alpha (-54 degrees)
 570 PRO   ( 210-)  H    99.3 envelop C-beta (108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

  64 CYS   (  69-)  A      SG  <->   96 CYS   ( 101-)  A      CB     0.75    1.75  INTRA BF
 426 ALA   (  61-)  H      O   <->  428 SER   (  63-)  H      N      0.53    2.17  INTRA BF
 429 VAL   (  64-)  H      O   <->  431 GLY   (  66-)  H      N      0.52    2.18  INTRA BL
  66 SER   (  71-)  A      O   <->   68 HIS   (  73-)  A      N      0.46    2.24  INTRA BF
 100 THR   ( 105-)  A      O   <->  102 GLU   ( 107-)  A      N      0.45    2.25  INTRA BF
 522 TRP   ( 162-)  H      N   <->  583 HOH   ( 315 )  H      O      0.43    2.27  INTRA BF
 555 SER   ( 195-)  H      O   <->  557 LEU   ( 197-)  H      N      0.41    2.29  INTRA BF
  98 ARG   ( 103-)  A      O   <->  100 THR   ( 105-)  A      N      0.40    2.30  INTRA BF
  97 GLN   ( 102-)  A      O   <->   99 GLU   ( 104-)  A      N      0.38    2.32  INTRA BF
  60 LYS   (  65-)  A      O   <->  182 ARG   (  30-)  L      NH2    0.36    2.34  INTRA BL
  80 VAL   (  85-)  A      O   <->   83 GLN   (  88-)  A      NE2    0.35    2.35  INTRA BF
 397 TYR   (  32-)  H      O   <->  437 ARG   (  72-)  H      NH2    0.34    2.36  INTRA BL
 424 ASP   (  59-)  H      OD2 <->  583 HOH   ( 303 )  H      O      0.34    2.06  INTRA BL
  42 GLN   (  47-)  A      CD  <->  126 ARG   ( 131-)  A      NH1    0.33    2.77  INTRA BF
 140 ALA   ( 145-)  A      O   <->  583 HOH   ( 303 )  H      O      0.33    2.07  INTRA
   6 LYS   (  11-)  A      O   <->   34 ASN   (  39-)  A      ND2    0.32    2.38  INTRA BL
  42 GLN   (  47-)  A      OE1 <->  126 ARG   ( 131-)  A      NH1    0.31    2.39  INTRA BF
  12 VAL   (  17-)  A      O   <->   24 LEU   (  29-)  A      N      0.28    2.42  INTRA BL
 523 ASN   ( 163-)  H      ND2 <->  583 HOH   ( 312 )  H      O      0.27    2.43  INTRA BF
  10 HIS   (  15-)  A      ND1 <->   54 TYR   (  59-)  A      OH     0.26    2.44  INTRA BL
 395 ASP   (  30-)  H      OD1 <->  583 HOH   ( 305 )  H      O      0.25    2.15  INTRA
 259 LYS   ( 107-)  L      CG  <->  260 ARG   ( 108-)  L      N      0.24    2.76  INTRA BF
 300 TRP   ( 148-)  L      NE1 <->  329 SER   ( 177-)  L      OG     0.24    2.46  INTRA BF
 497 LEU   ( 132-)  H      N   <->  507 GLY   ( 147-)  H      O      0.24    2.46  INTRA BF
  60 LYS   (  65-)  A      NZ  <->  244 ASN   (  92-)  L      O      0.22    2.48  INTRA BL
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: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

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.

 466 TYR   ( 101-)  H      -6.26
 363 ARG   ( 211-)  L      -6.09
 478 GLN   ( 113-)  H      -5.55
 252 GLN   ( 100-)  L      -5.55
 408 LYS   (  43-)  H      -5.40
  97 GLN   ( 102-)  A      -5.36
 194 LYS   (  42-)  L      -5.35
 523 ASN   ( 163-)  H      -5.19
 114 TYR   ( 119-)  A      -5.16
 144 GLN   ( 149-)  A      -5.13
  98 ARG   ( 103-)  A      -5.01
 259 LYS   ( 107-)  L      -5.01

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.

  97 GLN   ( 102-)  A        99 - GLU    104- ( A)         -4.99

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: L

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: H

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: L

Note: Second generation quality Z-score plot

Chain identifier: H

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.

 583 HOH   ( 309 )  H      O      9.03   20.59   -1.65

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.

 581 HOH   ( 204 )  A      O

Error: HIS, ASN, GLN side chain flips

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

 304 ASN   ( 152-)  L
 307 GLN   ( 155-)  L
 567 ASN   ( 207-)  H

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.

  18 GLU   (  23-)  A      N
  20 GLN   (  25-)  A      N
  22 GLN   (  27-)  A      N
  38 LEU   (  43-)  A      N
  40 ASP   (  45-)  A      N
  42 GLN   (  47-)  A      N
  47 SER   (  52-)  A      N
  50 LEU   (  55-)  A      N
  58 LEU   (  63-)  A      N
  60 LYS   (  65-)  A      NZ
  67 THR   (  72-)  A      OG1
  69 VAL   (  74-)  A      N
  74 THR   (  79-)  A      OG1
  82 TYR   (  87-)  A      N
  90 SER   (  95-)  A      OG
  92 ILE   (  97-)  A      N
  99 GLU   ( 104-)  A      N
 107 LYS   ( 112-)  A      N
 110 TYR   ( 115-)  A      N
 126 ARG   ( 131-)  A      NH2
 142 SER   ( 147-)  A      N
 143 GLY   ( 148-)  A      N
 167 VAL   (  15-)  L      N
 178 SER   (  26-)  L      OG
 179 GLN   (  27-)  L      N
And so on for a total of 63 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.

 138 ASP   ( 143-)  A      OD2
 289 ASN   ( 137-)  L      OD1
 454 GLU   (  89-)  H      OE2
 565 ASN   ( 205-)  H      OD1

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

 583 HOH   ( 305 )  H      O  0.99 NA  4 *2

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.

 371 GLU   (   6-)  H   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 :  -0.624
  2nd generation packing quality :  -0.965
  Ramachandran plot appearance   :  -2.459
  chi-1/chi-2 rotamer normality  :  -4.169 (bad)
  Backbone conformation          :  -0.223

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.434 (tight)
  Bond angles                    :   0.701
  Omega angle restraints         :   1.288 (loose)
  Side chain planarity           :   0.452 (tight)
  Improper dihedral distribution :   0.789
  B-factor distribution          :   1.776 (loose)
  Inside/Outside distribution    :   0.958

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 : 3.10


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.6
  2nd generation packing quality :   0.9
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :  -1.7
  Backbone conformation          :   0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.434 (tight)
  Bond angles                    :   0.701
  Omega angle restraints         :   1.288 (loose)
  Side chain planarity           :   0.452 (tight)
  Improper dihedral distribution :   0.789
  B-factor distribution          :   1.776 (loose)
  Inside/Outside distribution    :   0.958
==============

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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Bond lengths and angles, DNA/RNA
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DSSP
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Hydrogen bond networks
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      protein structures
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Matthews' Coefficient
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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,
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      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.