WHAT IF Check report

This file was created 2012-01-12 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 pdb1qz2.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 : 1.072
CA-only RMS fit for the two chains : 0.564

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: A and C

All-atom RMS fit for the two chains : 1.105
CA-only RMS fit for the two chains : 0.557

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 C

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 C

All-atom RMS fit for the two chains : 1.156
CA-only RMS fit for the two chains : 0.587

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 C

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: G and H

All-atom RMS fit for the two chains : 3.677
CA-only RMS fit for the two chains : 1.163

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: G and H

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

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

Warning: Missing atoms

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

 106 GLU   ( 246-)  A      CB
 106 GLU   ( 246-)  A      CG
 106 GLU   ( 246-)  A      CD
 106 GLU   ( 246-)  A      OE1
 106 GLU   ( 246-)  A      OE2
 135 GLU   ( 275-)  A      CB
 135 GLU   ( 275-)  A      CG
 135 GLU   ( 275-)  A      CD
 135 GLU   ( 275-)  A      OE1
 135 GLU   ( 275-)  A      OE2
 391 GLU   ( 246-)  B      CB
 391 GLU   ( 246-)  B      CG
 391 GLU   ( 246-)  B      CD
 391 GLU   ( 246-)  B      OE1
 391 GLU   ( 246-)  B      OE2
 420 GLU   ( 275-)  B      CB
 420 GLU   ( 275-)  B      CG
 420 GLU   ( 275-)  B      CD
 420 GLU   ( 275-)  B      OE1
 420 GLU   ( 275-)  B      OE2
 705 GLU   ( 275-)  C      CB
 705 GLU   ( 275-)  C      CG
 705 GLU   ( 275-)  C      CD
 705 GLU   ( 275-)  C      OE1
 705 GLU   ( 275-)  C      OE2

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.

  12 ARG   ( 152-)  A    High
  13 ARG   ( 153-)  A    High
  15 GLN   ( 155-)  A    High
  16 THR   ( 156-)  A    High
  17 ARG   ( 157-)  A    High
  18 GLY   ( 158-)  A    High
  19 GLU   ( 159-)  A    High
  20 GLY   ( 160-)  A    High
  21 TYR   ( 161-)  A    High
  35 GLU   ( 175-)  A    High
  38 TYR   ( 178-)  A    High
  39 LYS   ( 179-)  A    High
  40 ASP   ( 180-)  A    High
  45 GLN   ( 185-)  A    High
  47 GLU   ( 187-)  A    High
  62 TYR   ( 202-)  A    High
  72 GLU   ( 212-)  A    High
  80 TYR   ( 220-)  A    High
  88 GLY   ( 228-)  A    High
  93 GLU   ( 233-)  A    High
  96 GLN   ( 236-)  A    High
 100 ASN   ( 240-)  A    High
 101 ALA   ( 241-)  A    High
 102 GLU   ( 242-)  A    High
 163 GLU   ( 303-)  A    High
And so on for a total of 92 lines.

Warning: What type of B-factor?

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

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

Crystal temperature (K) : 90.000

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

Nomenclature related problems

Warning: Tyrosine convention problem

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

  62 TYR   ( 202-)  A
 105 TYR   ( 245-)  A
 140 TYR   ( 280-)  A
 146 TYR   ( 286-)  A
 153 TYR   ( 293-)  A
 271 TYR   ( 411-)  A
 347 TYR   ( 202-)  B
 365 TYR   ( 220-)  B
 370 TYR   ( 225-)  B
 390 TYR   ( 245-)  B
 425 TYR   ( 280-)  B
 431 TYR   ( 286-)  B
 438 TYR   ( 293-)  B
 528 TYR   ( 383-)  B
 607 TYR   ( 177-)  C
 650 TYR   ( 220-)  C
 675 TYR   ( 245-)  C
 710 TYR   ( 280-)  C
 716 TYR   ( 286-)  C
 723 TYR   ( 293-)  C

Warning: Phenylalanine convention problem

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

  50 PHE   ( 190-)  A
  87 PHE   ( 227-)  A
 112 PHE   ( 252-)  A
 195 PHE   ( 335-)  A
 217 PHE   ( 357-)  A
 229 PHE   ( 369-)  A
 236 PHE   ( 376-)  A
 335 PHE   ( 190-)  B
 372 PHE   ( 227-)  B
 451 PHE   ( 306-)  B
 480 PHE   ( 335-)  B
 502 PHE   ( 357-)  B
 514 PHE   ( 369-)  B
 521 PHE   ( 376-)  B
 620 PHE   ( 190-)  C
 657 PHE   ( 227-)  C
 665 PHE   ( 235-)  C
 682 PHE   ( 252-)  C
 736 PHE   ( 306-)  C
 765 PHE   ( 335-)  C
 787 PHE   ( 357-)  C
 799 PHE   ( 369-)  C
 806 PHE   ( 376-)  C

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.

   7 ASP   ( 147-)  A
  40 ASP   ( 180-)  A
  44 ASP   ( 184-)  A
 329 ASP   ( 184-)  B
 614 ASP   ( 184-)  C

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.

 207 GLU   ( 347-)  A
 230 GLU   ( 370-)  A
 281 GLU   ( 421-)  A
 339 GLU   ( 194-)  B
 360 GLU   ( 215-)  B
 448 GLU   ( 303-)  B
 492 GLU   ( 347-)  B
 506 GLU   ( 361-)  B
 515 GLU   ( 370-)  B
 565 GLU   ( 420-)  B
 683 GLU   ( 253-)  C
 694 GLU   ( 264-)  C
 713 GLU   ( 283-)  C
 850 GLU   ( 420-)  C
 851 GLU   ( 421-)  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.

   4 MET   (   4-)  A      SD   CE    2.07    4.7

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.

 288 HIS   (   3-)  B      CG   ND1  CE1 109.66    4.1
 573 HIS   (   3-)  C     -C    N    CA  114.31   -4.1
 573 HIS   (   3-)  C      N    CA   C   127.78    5.9
 863 GLU   (   3-)  H      N    CA   C   124.07    4.6

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.

   7 ASP   ( 147-)  A
  40 ASP   ( 180-)  A
  44 ASP   ( 184-)  A
 207 GLU   ( 347-)  A
 230 GLU   ( 370-)  A
 281 GLU   ( 421-)  A
 329 ASP   ( 184-)  B
 339 GLU   ( 194-)  B
 360 GLU   ( 215-)  B
 448 GLU   ( 303-)  B
 492 GLU   ( 347-)  B
 506 GLU   ( 361-)  B
 515 GLU   ( 370-)  B
 565 GLU   ( 420-)  B
 614 ASP   ( 184-)  C
 683 GLU   ( 253-)  C
 694 GLU   ( 264-)  C
 713 GLU   ( 283-)  C
 850 GLU   ( 420-)  C
 851 GLU   ( 421-)  C

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.

 743 LYS   ( 313-)  C    6.82
 573 HIS   (   3-)  C    5.36
 207 GLU   ( 347-)  A    5.18
 173 LYS   ( 313-)  A    5.10
 454 GLU   ( 309-)  B    4.80
 765 PHE   ( 335-)  C    4.68
 191 LYS   ( 331-)  A    4.67
 195 PHE   ( 335-)  A    4.63
 716 TYR   ( 286-)  C    4.54
 863 GLU   (   3-)  H    4.31
 486 SER   ( 341-)  B    4.13
 823 LEU   ( 393-)  C    4.13
 373 GLY   ( 228-)  B    4.12

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 : 1.602

Torsion-related checks

Error: Ramachandran Z-score very low

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

Ramachandran Z-score : -4.601

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.

 591 TYR   ( 161-)  C    -3.4
  95 PHE   ( 235-)  A    -3.2
 669 PRO   ( 239-)  C    -3.0
  19 GLU   ( 159-)  A    -2.5
 306 TYR   ( 161-)  B    -2.5
   2 SER   (   2-)  A    -2.4
  83 PRO   ( 223-)  A    -2.4
 304 GLU   ( 159-)  B    -2.4
 398 GLU   ( 253-)  B    -2.3
 403 SER   ( 258-)  B    -2.3
 315 VAL   ( 170-)  B    -2.2
  32 VAL   ( 172-)  A    -2.2
 334 ARG   ( 189-)  B    -2.2
 368 PRO   ( 223-)  B    -2.2
 577 ASP   ( 147-)  C    -2.2
  21 TYR   ( 161-)  A    -2.2
 864 VAL   (   4-)  H    -2.2
 108 HIS   ( 248-)  A    -2.2
  18 GLY   ( 158-)  A    -2.2
 538 LEU   ( 393-)  B    -2.1
 857 GLU   (   2-)  G    -2.1
 575 GLU   ( 145-)  C    -2.1
  87 PHE   ( 227-)  A    -2.1
 659 SER   ( 229-)  C    -2.1
 797 ASN   ( 367-)  C    -2.1
  88 GLY   ( 228-)  A    -2.1
 730 LEU   ( 300-)  C    -2.1
   6 GLU   ( 146-)  A    -2.1
 478 GLN   ( 333-)  B    -2.1
 657 PHE   ( 227-)  C    -2.1
 604 LEU   ( 174-)  C    -2.1
 678 HIS   ( 248-)  C    -2.1
  50 PHE   ( 190-)  A    -2.1
 296 ILE   ( 151-)  B    -2.0
 373 GLY   ( 228-)  B    -2.0
 383 PRO   ( 238-)  B    -2.0
 858 GLU   (   3-)  G    -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.

   2 SER   (   2-)  A  Poor phi/psi
   3 HIS   (   3-)  A  Poor phi/psi
   4 MET   (   4-)  A  Poor phi/psi
  14 ILE   ( 154-)  A  Poor phi/psi
  17 ARG   ( 157-)  A  Poor phi/psi
  19 GLU   ( 159-)  A  Poor phi/psi
  20 GLY   ( 160-)  A  Poor phi/psi
  21 TYR   ( 161-)  A  Poor phi/psi
  39 LYS   ( 179-)  A  Poor phi/psi
  40 ASP   ( 180-)  A  Poor phi/psi
  46 ARG   ( 186-)  A  Poor phi/psi
  73 LYS   ( 213-)  A  Poor phi/psi
  74 GLY   ( 214-)  A  Poor phi/psi
  77 SER   ( 217-)  A  Poor phi/psi
  86 ALA   ( 226-)  A  Poor phi/psi
  87 PHE   ( 227-)  A  Poor phi/psi
  88 GLY   ( 228-)  A  Poor phi/psi
  92 LYS   ( 232-)  A  Poor phi/psi
  93 GLU   ( 233-)  A  Poor phi/psi
  94 LYS   ( 234-)  A  Poor phi/psi
  95 PHE   ( 235-)  A  Poor phi/psi
  96 GLN   ( 236-)  A  Poor phi/psi
 100 ASN   ( 240-)  A  Poor phi/psi
 110 LYS   ( 250-)  A  Poor phi/psi
 111 SER   ( 251-)  A  Poor phi/psi
And so on for a total of 82 lines.

Warning: chi-1/chi-2 angle correlation Z-score low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is a bit low.

chi-1/chi-2 correlation Z-score : -3.526

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

 466 SER   ( 321-)  B    0.34
 341 GLU   ( 196-)  B    0.36
 766 SER   ( 336-)  C    0.36
 130 SER   ( 270-)  A    0.38
 481 SER   ( 336-)  B    0.38

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 HIS   (   3-)  A      0
   4 MET   (   4-)  A      0
   5 GLU   ( 145-)  A      0
   6 GLU   ( 146-)  A      0
   7 ASP   ( 147-)  A      0
  15 GLN   ( 155-)  A      0
  17 ARG   ( 157-)  A      0
  19 GLU   ( 159-)  A      0
  21 TYR   ( 161-)  A      0
  24 PRO   ( 164-)  A      0
  25 ASN   ( 165-)  A      0
  26 GLU   ( 166-)  A      0
  35 GLU   ( 175-)  A      0
  38 TYR   ( 178-)  A      0
  39 LYS   ( 179-)  A      0
  40 ASP   ( 180-)  A      0
  43 PHE   ( 183-)  A      0
  44 ASP   ( 184-)  A      0
  45 GLN   ( 185-)  A      0
  46 ARG   ( 186-)  A      0
  52 ILE   ( 192-)  A      0
  54 GLU   ( 194-)  A      0
  70 ARG   ( 210-)  A      0
  72 GLU   ( 212-)  A      0
  73 LYS   ( 213-)  A      0
And so on for a total of 278 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.141

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!

 658 GLY   ( 228-)  C   3.22   26
  18 GLY   ( 158-)  A   1.90   26
 303 GLY   ( 158-)  B   1.52   24

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...

 573 HIS   (   3-)  C   2.63
 863 GLU   (   3-)  H   2.43

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.

 737 SER   ( 307-)  C      O   <->  739 GLU   ( 309-)  C      N      0.53    2.17  INTRA BF
 209 ASP   ( 349-)  A      O   <->  211 ASN   ( 351-)  A      N      0.53    2.17  INTRA BL
 311 GLU   ( 166-)  B      O   <->  313 ALA   ( 168-)  B      N      0.51    2.19  INTRA BL
 445 LEU   ( 300-)  B      O   <->  463 ARG   ( 318-)  B      NH1    0.37    2.33  INTRA BL
  93 GLU   ( 233-)  A      O   <->   95 PHE   ( 235-)  A      N      0.37    2.33  INTRA BF
 574 MET   (   4-)  C      SD  <->  640 ARG   ( 210-)  C      CZ     0.37    3.03  INTRA BL
 377 LYS   ( 232-)  B      O   <->  380 PHE   ( 235-)  B      N      0.33    2.37  INTRA BF
 263 GLN   ( 403-)  A      NE2 <->  573 HIS   (   3-)  C      NE2    0.33    2.67  INTRA BF
  93 GLU   ( 233-)  A      C   <->   95 PHE   ( 235-)  A      N      0.32    2.58  INTRA BF
 289 MET   (   4-)  B      CE  <->  355 ARG   ( 210-)  B      CZ     0.32    2.88  INTRA BF
   4 MET   (   4-)  A      CG  <->   70 ARG   ( 210-)  A      NH1    0.31    2.79  INTRA BF
 524 VAL   ( 379-)  B      O   <->  528 TYR   ( 383-)  B      N      0.30    2.40  INTRA BL
 734 SER   ( 304-)  C      O   <->  736 PHE   ( 306-)  C      N      0.30    2.40  INTRA BF
 193 GLN   ( 333-)  A      NE2 <->  581 ILE   ( 151-)  C      CD1    0.30    2.80  INTRA BF
  35 GLU   ( 175-)  A      O   <->  106 GLU   ( 246-)  A      N      0.29    2.41  INTRA BF
 289 MET   (   4-)  B      CE  <->  355 ARG   ( 210-)  B      NH2    0.28    2.82  INTRA BF
 323 TYR   ( 178-)  B      CG  <->  324 LYS   ( 179-)  B      N      0.27    2.73  INTRA BF
 449 SER   ( 304-)  B      O   <->  803 ARG   ( 373-)  C      NH1    0.27    2.43  INTRA BF
  38 TYR   ( 178-)  A      O   <->   40 ASP   ( 180-)  A      N      0.26    2.44  INTRA BF
 653 PRO   ( 223-)  C      CG  <->  671 ALA   ( 241-)  C      C      0.25    2.95  INTRA BF
 512 ASN   ( 367-)  B      ND2 <->  514 PHE   ( 369-)  B      CZ     0.25    2.85  INTRA BF
 301 THR   ( 156-)  B      O   <->  303 GLY   ( 158-)  B      N      0.24    2.46  INTRA BF
 316 GLU   ( 171-)  B      CD  <->  334 ARG   ( 189-)  B      NE     0.23    2.87  INTRA BF
 209 ASP   ( 349-)  A      C   <->  211 ASN   ( 351-)  A      N      0.23    2.67  INTRA BL
  86 ALA   ( 226-)  A      C   <->   88 GLY   ( 228-)  A      N      0.23    2.67  INTRA BF
And so on for a total of 301 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

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.

  21 TYR   ( 161-)  A      -8.61
 306 TYR   ( 161-)  B      -8.42
 591 TYR   ( 161-)  C      -7.70
 162 TYR   ( 302-)  A      -7.31
  17 ARG   ( 157-)  A      -6.57
 302 ARG   ( 157-)  B      -6.37
 587 ARG   ( 157-)  C      -6.02
 324 LYS   ( 179-)  B      -5.85
 609 LYS   ( 179-)  C      -5.69
 569 LYS   ( 424-)  B      -5.63
   3 HIS   (   3-)  A      -5.58
 864 VAL   (   4-)  H      -5.47
   4 MET   (   4-)  A      -5.37
 284 LYS   ( 424-)  A      -5.35
  39 LYS   ( 179-)  A      -5.31
 854 LYS   ( 424-)  C      -5.29
 666 GLN   ( 236-)  C      -5.27
 330 GLN   ( 185-)  B      -5.26
 857 GLU   (   2-)  G      -5.21
 385 ASN   ( 240-)  B      -5.14
 732 TYR   ( 302-)  C      -5.06
  49 ARG   ( 189-)  A      -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.

 287 SER   (   2-)  B       289 - MET      4- ( B)         -4.50
 857 GLU   (   2-)  G       860 - ASP      5- ( G)         -4.63

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

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.

  90 VAL   ( 230-)  A   -2.97
 420 GLU   ( 275-)  B   -2.61
 856 MET   (   1-)  G   -2.55

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

Water, ion, and hydrogenbond related checks

Error: Water clusters without contacts with non-water atoms

The water molecules listed in the table below are part of water molecule clusters that do not make contacts with non-waters. These water molecules are part of clusters that have a distance at least 1 Angstrom larger than the sum of the Van der Waals radii to the nearest non-solvent atom. Because these kinds of water clusters usually are not observed with X-ray diffraction their presence could indicate a refinement artifact. The number in brackets is the identifier of the water molecule in the input file.

 868 HOH   ( 534 )  A      O
ERROR. No atoms within 50 A?

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.

 868 HOH   ( 533 )  A      O
 868 HOH   ( 534 )  A      O
 869 HOH   ( 496 )  B      O
 869 HOH   ( 510 )  B      O
 869 HOH   ( 511 )  B      O
 870 HOH   ( 488 )  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.

 189 HIS   ( 329-)  A
 203 ASN   ( 343-)  A
 467 HIS   ( 322-)  B
 474 HIS   ( 329-)  B
 558 ASN   ( 413-)  B
 738 ASN   ( 308-)  C
 745 GLN   ( 315-)  C
 752 HIS   ( 322-)  C
 759 HIS   ( 329-)  C
 773 ASN   ( 343-)  C
 811 GLN   ( 381-)  C
 822 GLN   ( 392-)  C
 827 GLN   ( 397-)  C

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.

   7 ASP   ( 147-)  A      N
  10 ILE   ( 150-)  A      N
  20 GLY   ( 160-)  A      N
  48 LEU   ( 188-)  A      N
  72 GLU   ( 212-)  A      N
  73 LYS   ( 213-)  A      N
  74 GLY   ( 214-)  A      N
  96 GLN   ( 236-)  A      N
 148 GLN   ( 288-)  A      N
 178 ARG   ( 318-)  A      NE
 195 PHE   ( 335-)  A      N
 218 ARG   ( 358-)  A      NH1
 229 PHE   ( 369-)  A      N
 248 ALA   ( 388-)  A      N
 277 ARG   ( 417-)  A      NH2
 290 GLU   ( 145-)  B      N
 302 ARG   ( 157-)  B      N
 303 GLY   ( 158-)  B      N
 308 LYS   ( 163-)  B      N
 313 ALA   ( 168-)  B      N
 320 GLU   ( 175-)  B      N
 324 LYS   ( 179-)  B      N
 326 LYS   ( 181-)  B      N
 331 ARG   ( 186-)  B      N
 334 ARG   ( 189-)  B      NE
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.

  35 GLU   ( 175-)  A      OE1
 152 GLN   ( 292-)  A      OE1
 182 HIS   ( 322-)  A      ND1
 223 HIS   ( 363-)  A      ND1
 405 GLU   ( 260-)  B      OE2
 437 GLN   ( 292-)  B      OE1
 645 GLU   ( 215-)  C      OE1
 713 GLU   ( 283-)  C      OE1
 807 GLN   ( 377-)  C      OE1
 852 GLU   ( 422-)  C      OE2

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.

  35 GLU   ( 175-)  A   H-bonding suggests Gln
  72 GLU   ( 212-)  A   H-bonding suggests Gln
 291 GLU   ( 146-)  B   H-bonding suggests Gln
 485 GLU   ( 340-)  B   H-bonding suggests Gln
 610 ASP   ( 180-)  C   H-bonding suggests Asn
 683 GLU   ( 253-)  C   H-bonding suggests Gln; but Alt-Rotamer
 731 GLU   ( 301-)  C   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 :  -0.433
  2nd generation packing quality :  -1.313
  Ramachandran plot appearance   :  -4.601 (bad)
  chi-1/chi-2 rotamer normality  :  -3.526 (poor)
  Backbone conformation          :   0.173

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.327 (tight)
  Bond angles                    :   0.647 (tight)
  Omega angle restraints         :   0.207 (tight)
  Side chain planarity           :   0.217 (tight)
  Improper dihedral distribution :   0.562
  B-factor distribution          :   1.124
  Inside/Outside distribution    :   1.071

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 : 3.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.6
  2nd generation packing quality :   0.5
  Ramachandran plot appearance   :  -1.9
  chi-1/chi-2 rotamer normality  :  -1.2
  Backbone conformation          :   0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.327 (tight)
  Bond angles                    :   0.647 (tight)
  Omega angle restraints         :   0.207 (tight)
  Side chain planarity           :   0.217 (tight)
  Improper dihedral distribution :   0.562
  B-factor distribution          :   1.124
  Inside/Outside distribution    :   1.071
==============

WHAT IF
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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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Matthews' Coefficient
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Protein side chain planarity
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Puckering parameters
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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.