WHAT IF Check report

This file was created 2012-01-04 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 pdb1m9e.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 B

All-atom RMS fit for the two chains : 0.850
CA-only RMS fit for the two chains : 0.381

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 B

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 D

All-atom RMS fit for the two chains : 1.312
CA-only RMS fit for the two chains : 0.870

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 D

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: 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

Crystal temperature (K) :100.000

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

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Nomenclature related problems

Warning: Phenylalanine convention problem

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

  36 PHE   (  36-)  A
 169 PHE   (   7-)  B
 198 PHE   (  36-)  B
 274 PHE   ( 112-)  B

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.

 282 GLU   ( 120-)  B
 305 GLU   ( 143-)  B
 355 GLU   (  29-)  C
 361 GLU   (  35-)  C
 371 GLU   (  45-)  C

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 500 MET   (  39-)  D      SD   CE    1.49   -5.1

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.

   1 MET   (   1-)  A      CG   SD   CE   91.17   -4.4
   6 VAL   (   6-)  A      CA   CB   CG2 100.47   -5.9
   6 VAL   (   6-)  A      CG1  CB   CG2 119.98    4.2
  19 ARG   (  19-)  A      NE   CZ   NH2 112.17   -4.1
  69 ARG   (  69-)  A      CG   CD   NE  101.68   -5.2
  73 THR   (  73-)  A     -C    N    CA  114.45   -4.0
  76 LYS   (  76-)  A      CA   CB   CG  123.49    4.7
 102 ASN   ( 102-)  A      N    CA   C   123.88    4.5
 115 CYS   ( 115-)  A      C    CA   CB  101.39   -4.6
 131 LYS   ( 131-)  A      N    CA   CB  102.11   -4.9
 131 LYS   ( 131-)  A      CD   CE   NZ   96.44   -4.8
 133 LYS   ( 133-)  A      N    CA   C    99.94   -4.0
 136 MET   ( 136-)  A      CB   CG   SD  100.49   -4.1
 138 ILE   ( 138-)  A      CG2  CB   CG1 123.26    4.2
 143 GLU   ( 143-)  A      N    CA   CB  103.20   -4.3
 144 ARG   ( 144-)  A      CA   CB   CG  105.97   -4.1
 144 ARG   ( 144-)  A      CB   CG   CD  125.18    5.5
 149 ASN   ( 149-)  A      CA   CB   CG  116.81    4.2
 151 LYS   ( 151-)  A      CD   CE   NZ  125.43    4.2
 168 VAL   (   6-)  B      CA   CB   CG2 102.90   -4.5
 174 VAL   (  12-)  B     -C    N    CA  129.10    4.1
 177 GLU   (  15-)  B      C    CA   CB  102.08   -4.2
 182 VAL   (  20-)  B      C    CA   CB  101.67   -4.4
 186 LEU   (  24-)  B      CB   CG   CD1  98.38   -4.1
 189 ASP   (  27-)  B      OD2  CG   OD1 112.27   -4.4
And so on for a total of 97 lines.

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

 282 GLU   ( 120-)  B
 305 GLU   ( 143-)  B
 355 GLU   (  29-)  C
 361 GLU   (  35-)  C
 371 GLU   (  45-)  C

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.

  34 GLU   (  34-)  A      C      6.2     8.92    -0.03
  75 GLY   (  75-)  A      C     -6.2    -8.18     0.06
  86 GLU   (  86-)  A      C     -6.9   -10.07    -0.03
 254 HIS   (  92-)  B      C     -7.3   -10.82     0.15
 313 LYS   ( 151-)  B      C     -6.9   -10.36     0.11
 414 ALA   (  88-)  C      C      7.8    12.06     0.08
 450 ILE   ( 124-)  C      CB     6.4    40.63    32.31
 473 HIS   (  12-)  D      CA   -13.2     9.78    34.11
 493 PHE   (  32-)  D      C      6.3    10.48     0.23
 571 THR   ( 110-)  D      C     -7.1   -10.39     0.30
The average deviation= 2.514

Warning: High improper dihedral angle deviations

The RMS Z-score for the improper dihedrals in the structure is high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 2.0 worries us a bit. However, we determined the improper normal distribution from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Improper dihedral RMS Z-score : 2.132

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.

 473 HIS   (  12-)  D    6.49
 575 GLN   ( 114-)  D    6.19
 303 ALA   ( 141-)  B    5.11
 305 GLU   ( 143-)  B    5.07
 345 THR   (  19-)  C    5.06
 595 ILE   ( 134-)  D    4.68
 492 ALA   (  31-)  D    4.54
 133 LYS   ( 133-)  A    4.38
 390 ALA   (  64-)  C    4.32
 415 GLY   (  89-)  C    4.28
 282 GLU   ( 120-)  B    4.25
  18 GLY   (  18-)  A    4.19
 344 ARG   (  18-)  C    4.13
 356 LYS   (  30-)  C    4.03
 579 MET   ( 118-)  D    4.01
 571 THR   ( 110-)  D    4.01
 503 ALA   (  42-)  D    4.00

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 : 1.736

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

  43 GLU   (  43-)  A    9.24
 439 GLU   ( 113-)  C    8.44
 232 HIS   (  70-)  B    8.01
 347 ASN   (  21-)  C    7.73
  92 HIS   (  92-)  A    7.29
 376 GLN   (  50-)  C    7.22
 270 ASN   ( 108-)  B    7.08
 216 HIS   (  54-)  B    6.49
 454 GLU   ( 128-)  C    6.10
 288 HIS   ( 126-)  B    6.07
 163 GLN   ( 163-)  A    5.96
 523 HIS   (  62-)  D    5.46
  88 PHE   (  88-)  A    5.39
 296 GLU   ( 134-)  B    5.37
 254 HIS   (  92-)  B    5.06
  34 GLU   (  34-)  A    5.05
 388 HIS   (  62-)  C    4.94
 518 ASN   (  57-)  D    4.89
 400 ASN   (  74-)  C    4.85
 383 ASN   (  57-)  C    4.78
 247 ASP   (  85-)  B    4.74
 429 ASP   ( 103-)  C    4.74
 401 GLU   (  75-)  C    4.71
 246 GLU   (  84-)  B    4.69
   7 PHE   (   7-)  A    4.59
 210 TYR   (  48-)  B    4.39
 123 ASP   ( 123-)  A    4.37
 205 GLU   (  43-)  B    4.35
 185 GLU   (  23-)  B    4.22
  46 PHE   (  46-)  A    4.13
  83 PHE   (  83-)  A    4.08
 545 HIS   (  84-)  D    4.00

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.

 586 PRO   ( 125-)  D    -2.8
 493 PHE   (  32-)  D    -2.7
 584 PRO   ( 123-)  D    -2.5
 572 LEU   ( 111-)  D    -2.3
 476 ILE   (  15-)  D    -2.3
 222 PHE   (  60-)  B    -2.2
 191 VAL   (  29-)  B    -2.2
  61 MET   (  61-)  A    -2.2
 360 PRO   (  34-)  C    -2.2
 223 MET   (  61-)  B    -2.2
  29 VAL   (  29-)  A    -2.1
 271 GLY   ( 109-)  B    -2.1
 491 LYS   (  30-)  D    -2.1
 109 GLY   ( 109-)  A    -2.1
 208 PHE   (  46-)  B    -2.0
 557 MET   (  96-)  D    -2.0
 329 VAL   (   3-)  C    -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.

  47 GLY   (  47-)  A  omega poor
  60 PHE   (  60-)  A  Poor phi/psi
  61 MET   (  61-)  A  omega poor
  70 HIS   (  70-)  A  Poor phi/psi
 102 ASN   ( 102-)  A  Poor phi/psi
 125 LYS   ( 125-)  A  Poor phi/psi
 209 GLY   (  47-)  B  omega poor
 231 ARG   (  69-)  B  Poor phi/psi
 232 HIS   (  70-)  B  Poor phi/psi
 241 TYR   (  79-)  B  omega poor
 254 HIS   (  92-)  B  omega poor
 315 SER   ( 153-)  B  omega poor
 318 ILE   ( 156-)  B  omega poor
 357 ALA   (  31-)  C  Poor phi/psi
 414 ALA   (  88-)  C  omega poor
 447 ASN   ( 121-)  C  PRO omega poor
 492 ALA   (  31-)  D  omega poor
 493 PHE   (  32-)  D  Poor phi/psi, omega poor
 562 GLY   ( 101-)  D  Poor phi/psi
 582 ASN   ( 121-)  D  PRO omega poor
 chi-1/chi-2 correlation Z-score : -1.970

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!

  12 VAL   (  12-)  A      0
  16 PRO   (  16-)  A      0
  25 PHE   (  25-)  A      0
  26 ALA   (  26-)  A      0
  28 LYS   (  28-)  A      0
  29 VAL   (  29-)  A      0
  43 GLU   (  43-)  A      0
  44 LYS   (  44-)  A      0
  46 PHE   (  46-)  A      0
  48 TYR   (  48-)  A      0
  49 LYS   (  49-)  A      0
  53 PHE   (  53-)  A      0
  54 HIS   (  54-)  A      0
  55 ARG   (  55-)  A      0
  58 PRO   (  58-)  A      0
  60 PHE   (  60-)  A      0
  61 MET   (  61-)  A      0
  68 THR   (  68-)  A      0
  69 ARG   (  69-)  A      0
  70 HIS   (  70-)  A      0
  71 ASN   (  71-)  A      0
  73 THR   (  73-)  A      0
  79 TYR   (  79-)  A      0
  82 LYS   (  82-)  A      0
  86 GLU   (  86-)  A      0
And so on for a total of 230 lines.

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!

 521 GLY   (  60-)  D   2.58   10

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]

 192 PRO   (  30-)  B    0.15 LOW
 257 PRO   (  95-)  B    0.16 LOW
 451 PRO   ( 125-)  C    0.15 LOW
 584 PRO   ( 123-)  D    0.50 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].

 178 PRO   (  16-)  B    99.2 envelop C-beta (108 degrees)
 343 PRO   (  17-)  C  -118.1 half-chair C-delta/C-gamma (-126 degrees)
 360 PRO   (  34-)  C   128.8 half-chair C-beta/C-alpha (126 degrees)
 425 PRO   (  99-)  C  -113.9 envelop C-gamma (-108 degrees)
 448 PRO   ( 122-)  C   -61.4 half-chair C-beta/C-alpha (-54 degrees)
 478 PRO   (  17-)  D   106.4 envelop C-beta (108 degrees)
 546 PRO   (  85-)  D  -129.6 half-chair C-delta/C-gamma (-126 degrees)
 586 PRO   ( 125-)  D    -5.7 envelop N (0 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.

 331 ASN   (   5-)  C      ND2 <->  333 GLN   (   7-)  C      OE1    0.77    1.93  INTRA BF
 331 ASN   (   5-)  C      ND2 <->  333 GLN   (   7-)  C      CD     0.56    2.54  INTRA BF
 125 LYS   ( 125-)  A      NZ  <->  612 HOH   ( 240 )  A      O      0.52    2.18  INTRA
 337 VAL   (  11-)  C      CG2 <->  338 HIS   (  12-)  C      N      0.42    2.58  INTRA
 468 VAL   ( 142-)  C      CG2 <->  604 ARG   ( 143-)  D      CD     0.38    2.82  INTRA
 193 LYS   (  31-)  B      NZ  <->  246 GLU   (  84-)  B      OE2    0.32    2.38  INTRA
 331 ASN   (   5-)  C      OD1 <->  335 GLN   (   9-)  C      N      0.31    2.39  INTRA BF
 331 ASN   (   5-)  C      ND2 <->  333 GLN   (   7-)  C      N      0.29    2.56  INTRA BF
 577 GLY   ( 116-)  D      O   <->  581 HIS   ( 120-)  D      ND1    0.28    2.42  INTRA BF
 131 LYS   ( 131-)  A      NZ  <->  612 HOH   ( 175 )  A      O      0.27    2.43  INTRA
 337 VAL   (  11-)  C      CG2 <->  614 HOH   ( 169 )  C      O      0.26    2.54  INTRA
 491 LYS   (  30-)  D      O   <->  493 PHE   (  32-)  D      N      0.25    2.45  INTRA BF
 571 THR   ( 110-)  D      O   <->  575 GLN   ( 114-)  D      N      0.23    2.47  INTRA
 492 ALA   (  31-)  D      C   <->  493 PHE   (  32-)  D      CB     0.19    2.61  INTRA BF
 581 HIS   ( 120-)  D      O   <->  584 PRO   ( 123-)  D      N      0.18    2.52  INTRA BF
 211 LYS   (  49-)  B      NZ  <->  613 HOH   ( 245 )  B      O      0.18    2.52  INTRA
 572 LEU   ( 111-)  D      O   <->  576 ILE   ( 115-)  D      N      0.17    2.53  INTRA
 581 HIS   ( 120-)  D      O   <->  584 PRO   ( 123-)  D      CA     0.16    2.64  INTRA BF
 593 ARG   ( 132-)  D      NH2 <->  615 HOH   ( 175 )  D      O      0.16    2.54  INTRA BF
 332 LEU   (   6-)  C      CB  <->  614 HOH   ( 246 )  C      O      0.16    2.64  INTRA BF
 332 LEU   (   6-)  C      N   <->  614 HOH   ( 246 )  C      O      0.15    2.55  INTRA
 576 ILE   ( 115-)  D      CA  <->  579 MET   ( 118-)  D      CE     0.15    3.05  INTRA BF
 334 GLY   (   8-)  C      N   <->  335 GLN   (   9-)  C      N      0.13    2.47  INTRA BF
 492 ALA   (  31-)  D      C   <->  493 PHE   (  32-)  D      CG     0.13    2.97  INTRA BF
 580 THR   ( 119-)  D      O   <->  581 HIS   ( 120-)  D      C      0.13    2.47  INTRA BF
And so on for a total of 99 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Warning: Abnormal packing environment for some residues

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

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

 148 ARG   ( 148-)  A      -7.73
 310 ARG   ( 148-)  B      -7.49
 332 LEU   (   6-)  C      -6.73
 423 ARG   (  97-)  C      -6.64
 558 ARG   (  97-)  D      -6.58
 582 ASN   ( 121-)  D      -5.78
 447 ASN   ( 121-)  C      -5.78
 556 GLN   (  95-)  D      -5.75
 421 GLN   (  95-)  C      -5.60
 144 ARG   ( 144-)  A      -5.55
 306 ARG   ( 144-)  B      -5.54
 241 TYR   (  79-)  B      -5.09
 581 HIS   ( 120-)  D      -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.

 556 GLN   (  95-)  D       558 - ARG     97- ( D)         -5.48

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Warning: Low packing Z-score for some residues

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

  87 ASN   (  87-)  A   -3.03
 249 ASN   (  87-)  B   -2.81
  81 GLU   (  81-)  A   -2.71
 282 GLU   ( 120-)  B   -2.66

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.

 468 VAL   ( 142-)  C     -  471 TYR   ( 145-)  C        -1.91

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

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.

 612 HOH   ( 177 )  A      O     31.14   17.53   17.41
 612 HOH   ( 193 )  A      O     41.82   23.08   17.64
 612 HOH   ( 229 )  A      O     43.24   22.42   19.86
 612 HOH   ( 258 )  A      O     28.74   18.35   17.84
 612 HOH   ( 272 )  A      O     37.67   63.75   47.51
 612 HOH   ( 293 )  A      O     16.25   17.70   14.10
 613 HOH   ( 186 )  B      O     24.58   44.95   19.38
 613 HOH   ( 258 )  B      O     19.50   53.08   35.36
 614 HOH   ( 236 )  C      O     39.57   30.98   11.49
 615 HOH   ( 179 )  D      O     39.51   -3.66   39.27

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.

 613 HOH   ( 247 )  B      O
 613 HOH   ( 252 )  B      O
 614 HOH   ( 234 )  C      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.

 232 HIS   (  70-)  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.

  87 ASN   (  87-)  A      N
 117 ALA   ( 117-)  A      N
 121 TRP   ( 121-)  A      N
 154 LYS   ( 154-)  A      N
 208 PHE   (  46-)  B      N
 249 ASN   (  87-)  B      N
 264 ASN   ( 102-)  B      N
 279 ALA   ( 117-)  B      N
 283 TRP   ( 121-)  B      N
 316 LYS   ( 154-)  B      N
 330 GLN   (   4-)  C      N
 333 GLN   (   7-)  C      N
 358 PHE   (  32-)  C      N
 359 SER   (  33-)  C      OG
 389 GLN   (  63-)  C      NE2
 492 ALA   (  31-)  D      N
 494 SER   (  33-)  D      OG
 509 THR   (  48-)  D      OG1
 558 ARG   (  97-)  D      NE
 570 SER   ( 109-)  D      N
 571 THR   ( 110-)  D      OG1

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.

  15 GLU   (  15-)  A      OE1

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.

 612 HOH   ( 200 )  A      O  0.93  K  4

Warning: Possible wrong residue type

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

  15 GLU   (  15-)  A   H-bonding suggests Gln
  86 GLU   (  86-)  A   H-bonding suggests Gln; but Alt-Rotamer
 123 ASP   ( 123-)  A   H-bonding suggests Asn
 189 ASP   (  27-)  B   H-bonding suggests Asn
 248 GLU   (  86-)  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 :  -0.670
  2nd generation packing quality :  -0.823
  Ramachandran plot appearance   :  -0.685
  chi-1/chi-2 rotamer normality  :  -1.970
  Backbone conformation          :   0.325

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.680
  Bond angles                    :   1.534
  Omega angle restraints         :   1.097
  Side chain planarity           :   2.938 (loose)
  Improper dihedral distribution :   2.132 (loose)
  B-factor distribution          :   1.050
  Inside/Outside distribution    :   0.957

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 : 1.72


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.5
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :  -1.1
  chi-1/chi-2 rotamer normality  :  -2.2
  Backbone conformation          :  -0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.680
  Bond angles                    :   1.534
  Omega angle restraints         :   1.097
  Side chain planarity           :   2.938 (loose)
  Improper dihedral distribution :   2.132 (loose)
  B-factor distribution          :   1.050
  Inside/Outside distribution    :   0.957
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
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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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      Solvent content of Protein Crystals
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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,
      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.