WHAT IF Check report

This file was created 2011-12-16 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 pdb2ikq.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 M

All-atom RMS fit for the two chains : 0.648
CA-only RMS fit for the two chains : 0.498

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 M

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 M

All-atom RMS fit for the two chains : 0.260
CA-only RMS fit for the two chains : 0.068

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 M

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

 777 PO4   ( 101-)  A  -
 778 PO4   ( 102-)  B  -
 779 PO4   ( 103-)  M  -

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: M

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'.

 262 GLU   ( 633-)  A      CG
 262 GLU   ( 633-)  A      CD
 262 GLU   ( 633-)  A      OE1
 262 GLU   ( 633-)  A      OE2

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

  65 MET   ( 436-)  A    0.40
  68 ARG   ( 439-)  A    0.10
 219 MET   ( 590-)  A    0.10
 330 ARG   ( 439-)  B    0.60
 468 GLN   ( 577-)  B    0.80
 725 LEU   ( 579-)  M    0.80
 726 SER   ( 580-)  M    0.80
 727 PRO   ( 581-)  M    0.80
 728 GLN   ( 582-)  M    0.80
 729 ASN   ( 583-)  M    0.80
 730 SER   ( 584-)  M    0.80
 731 LYS   ( 585-)  M    0.80
 732 ASP   ( 586-)  M    0.80
 733 PHE   ( 587-)  M    0.80
 734 VAL   ( 588-)  M    0.80

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: M

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

  85 TYR   ( 456-)  A
 347 TYR   ( 456-)  B
 602 TYR   ( 456-)  M

Warning: Phenylalanine convention problem

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

 228 PHE   ( 599-)  A
 490 PHE   ( 599-)  B
 745 PHE   ( 599-)  M

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.

 244 ASP   ( 615-)  A
 506 ASP   ( 615-)  B
 761 ASP   ( 615-)  M

Geometric checks

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.998984  0.000554 -0.000173|
 |  0.000554  0.997380 -0.000169|
 | -0.000173 -0.000169  0.999870|
Proposed new scale matrix

 |  0.008559 -0.000004  0.001631|
 | -0.000007  0.013427  0.000002|
 |  0.000002  0.000002  0.010052|
With corresponding cell

    A    = 116.840  B   =  74.476  C    = 101.272
    Alpha=  90.031  Beta= 100.797  Gamma=  89.936

The CRYST1 cell dimensions

    A    = 116.960  B   =  74.671  C    = 101.279
    Alpha=  90.000  Beta= 100.790  Gamma=  90.000

Variance: 55.718
(Under-)estimated Z-score: 5.501

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.

   2 ARG   ( 373-)  A      CG   CD   NE   99.35   -6.6
  12 ARG   ( 383-)  A      N    CA   CB   99.89   -6.2
  12 ARG   ( 383-)  A      CB   CG   CD  103.01   -5.5
 264 ARG   ( 373-)  B      CG   CD   NE  101.26   -5.4
 274 ARG   ( 383-)  B      N    CA   CB  101.85   -5.1
 274 ARG   ( 383-)  B      CB   CG   CD  102.76   -5.7
 345 HIS   ( 454-)  B      CG   ND1  CE1 109.66    4.1
 529 ARG   ( 383-)  M      N    CA   CB  101.41   -5.3
 529 ARG   ( 383-)  M      CB   CG   CD  103.12   -5.5
 600 HIS   ( 454-)  M      CG   ND1  CE1 109.62    4.0

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.

 244 ASP   ( 615-)  A
 506 ASP   ( 615-)  B
 761 ASP   ( 615-)  M

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.

 475 SER   ( 584-)  B    4.22
 213 SER   ( 584-)  A    4.02
 730 SER   ( 584-)  M    4.02

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.

 243 THR   ( 614-)  A    -2.6
 760 THR   ( 614-)  M    -2.6
 505 THR   ( 614-)  B    -2.6
 771 PRO   ( 625-)  M    -2.5
 516 PRO   ( 625-)  B    -2.5
 135 PRO   ( 506-)  A    -2.4
 652 PRO   ( 506-)  M    -2.4
 397 PRO   ( 506-)  B    -2.4
 254 PRO   ( 625-)  A    -2.4
  58 PRO   ( 429-)  A    -2.4
 575 PRO   ( 429-)  M    -2.4
 247 ILE   ( 618-)  A    -2.4
 320 PRO   ( 429-)  B    -2.4
 764 ILE   ( 618-)  M    -2.3
 509 ILE   ( 618-)  B    -2.3
 423 SER   ( 532-)  B    -2.2
 161 SER   ( 532-)  A    -2.2
 678 SER   ( 532-)  M    -2.2
 203 CYS   ( 574-)  A    -2.2
 775 PHE   ( 629-)  M    -2.2
 572 LYS   ( 426-)  M    -2.2
 720 CYS   ( 574-)  M    -2.2
 498 GLU   ( 607-)  B    -2.1
 753 GLU   ( 607-)  M    -2.1
 317 LYS   ( 426-)  B    -2.1
  55 LYS   ( 426-)  A    -2.1
 236 GLU   ( 607-)  A    -2.1
 246 PRO   ( 617-)  A    -2.1
 465 CYS   ( 574-)  B    -2.1
 763 PRO   ( 617-)  M    -2.1
 508 PRO   ( 617-)  B    -2.1
 626 LEU   ( 480-)  M    -2.0
 371 LEU   ( 480-)  B    -2.0
 162 GLU   ( 533-)  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.

  11 GLU   ( 382-)  A  omega poor
 104 GLN   ( 475-)  A  Poor phi/psi
 105 GLN   ( 476-)  A  Poor phi/psi
 107 ASN   ( 478-)  A  omega poor
 142 ASN   ( 513-)  A  Poor phi/psi
 165 ASP   ( 536-)  A  omega poor
 184 SER   ( 555-)  A  omega poor
 187 ASN   ( 558-)  A  Poor phi/psi, omega poor
 193 ALA   ( 564-)  A  Poor phi/psi
 222 LYS   ( 593-)  A  omega poor
 227 GLY   ( 598-)  A  omega poor
 235 GLY   ( 606-)  A  omega poor
 258 PHE   ( 629-)  A  omega poor
 273 GLU   ( 382-)  B  omega poor
 324 PHE   ( 433-)  B  omega poor
 366 GLN   ( 475-)  B  Poor phi/psi
 367 GLN   ( 476-)  B  Poor phi/psi
 369 ASN   ( 478-)  B  omega poor
 404 ASN   ( 513-)  B  Poor phi/psi
 427 ASP   ( 536-)  B  omega poor
 446 SER   ( 555-)  B  omega poor
 449 ASN   ( 558-)  B  Poor phi/psi
 455 ALA   ( 564-)  B  Poor phi/psi
 484 LYS   ( 593-)  B  omega poor
 497 GLY   ( 606-)  B  omega poor
 528 GLU   ( 382-)  M  omega poor
 621 GLN   ( 475-)  M  Poor phi/psi
 622 GLN   ( 476-)  M  Poor phi/psi
 624 ASN   ( 478-)  M  omega poor
 659 ASN   ( 513-)  M  Poor phi/psi
 682 ASP   ( 536-)  M  omega poor
 701 SER   ( 555-)  M  omega poor
 704 ASN   ( 558-)  M  Poor phi/psi
 710 ALA   ( 564-)  M  Poor phi/psi
 729 ASN   ( 583-)  M  omega poor
 739 LYS   ( 593-)  M  omega poor
 744 GLY   ( 598-)  M  omega poor
 752 GLY   ( 606-)  M  omega poor
 772 THR   ( 626-)  M  omega poor
 chi-1/chi-2 correlation Z-score : -3.662

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 : -3.662

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.

 171 SER   ( 542-)  A    0.35
 433 SER   ( 542-)  B    0.35
 688 SER   ( 542-)  M    0.35

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!

   9 HIS   ( 380-)  A      0
  11 GLU   ( 382-)  A      0
  19 LYS   ( 390-)  A      0
  25 CYS   ( 396-)  A      0
  29 LYS   ( 400-)  A      0
  36 ASN   ( 407-)  A      0
  41 HIS   ( 412-)  A      0
  51 ARG   ( 422-)  A      0
  56 ASP   ( 427-)  A      0
  61 VAL   ( 432-)  A      0
  88 PRO   ( 459-)  A      0
 104 GLN   ( 475-)  A      0
 105 GLN   ( 476-)  A      0
 106 ASP   ( 477-)  A      0
 107 ASN   ( 478-)  A      0
 108 HIS   ( 479-)  A      0
 109 LEU   ( 480-)  A      0
 118 PHE   ( 489-)  A      0
 120 TRP   ( 491-)  A      0
 123 TRP   ( 494-)  A      0
 125 ALA   ( 496-)  A      0
 142 ASN   ( 513-)  A      0
 144 SER   ( 515-)  A      0
 152 HIS   ( 523-)  A      0
 160 ILE   ( 531-)  A      0
And so on for a total of 273 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!

 773 GLY   ( 627-)  M   1.65   11

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].

  58 PRO   ( 429-)  A   -64.0 envelop C-beta (-72 degrees)
 224 PRO   ( 595-)  A    41.2 envelop C-delta (36 degrees)
 254 PRO   ( 625-)  A   -23.9 half-chair C-alpha/N (-18 degrees)
 320 PRO   ( 429-)  B   -63.7 envelop C-beta (-72 degrees)
 486 PRO   ( 595-)  B    39.4 envelop C-delta (36 degrees)
 516 PRO   ( 625-)  B   -27.1 envelop C-alpha (-36 degrees)
 575 PRO   ( 429-)  M   -64.0 envelop C-beta (-72 degrees)
 741 PRO   ( 595-)  M    39.8 envelop C-delta (36 degrees)
 771 PRO   ( 625-)  M   -28.0 envelop C-alpha (-36 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 473 GLN   ( 582-)  B      NE2 <->  481 MET   ( 590-)  B      SD     0.54    2.76  INTRA BF
 345 HIS   ( 454-)  B      ND1 <->  444 CYS   ( 553-)  B      SG     0.53    2.77  INTRA BF
 600 HIS   ( 454-)  M      ND1 <->  699 CYS   ( 553-)  M      SG     0.52    2.78  INTRA BF
  83 HIS   ( 454-)  A      ND1 <->  182 CYS   ( 553-)  A      SG     0.52    2.78  INTRA BF
 728 GLN   ( 582-)  M      NE2 <->  736 MET   ( 590-)  M      SD     0.49    2.81  INTRA BF
 258 PHE   ( 629-)  A      CE1 <->  484 LYS   ( 593-)  B      CG     0.34    2.86  INTRA BF
  82 ASP   ( 453-)  A      C   <->   83 HIS   ( 454-)  A      CD2    0.33    2.77  INTRA BF
 261 ARG   ( 632-)  A      NH2 <->  486 PRO   ( 595-)  B      CD     0.32    2.78  INTRA BF
 344 ASP   ( 453-)  B      C   <->  345 HIS   ( 454-)  B      CD2    0.32    2.78  INTRA BF
 599 ASP   ( 453-)  M      C   <->  600 HIS   ( 454-)  M      CD2    0.31    2.79  INTRA BF
  91 ARG   ( 462-)  A      NH2 <->  777 PO4   ( 101-)  A      O2     0.30    2.40  INTRA BL
   9 HIS   ( 380-)  A      NE2 <->  777 PO4   ( 101-)  A      P      0.24    3.06  INTRA BL
   1 LYS   ( 372-)  A      O   <->    2 ARG   ( 373-)  A      CG     0.22    2.48  INTRA BF
 258 PHE   ( 629-)  A      CZ  <->  484 LYS   ( 593-)  B      CG     0.22    2.98  INTRA BF
 255 THR   ( 626-)  A      CG2 <->  514 HIS   ( 623-)  B      CD2    0.21    2.99  INTRA BL
 263 LYS   ( 372-)  B      O   <->  264 ARG   ( 373-)  B      CG     0.20    2.50  INTRA BF
 217 VAL   ( 588-)  A      CG1 <->  221 ARG   ( 592-)  A      NH2    0.20    2.90  INTRA BF
   1 LYS   ( 372-)  A      CG  <->  187 ASN   ( 558-)  A      ND2    0.20    2.90  INTRA BF
  65 MET   ( 436-)  A      SD  <->  327 MET   ( 436-)  B      SD     0.19    3.26  INTRA BL
 263 LYS   ( 372-)  B      CG  <->  449 ASN   ( 558-)  B      ND2    0.19    2.91  INTRA BF
 252 HIS   ( 623-)  A      CB  <->  300 ASN   ( 409-)  B      ND2    0.19    2.91  INTRA BL
   1 LYS   ( 372-)  A      C   <->    2 ARG   ( 373-)  A      CG     0.18    2.92  INTRA BF
 526 HIS   ( 380-)  M      NE2 <->  779 PO4   ( 103-)  M      P      0.17    3.13  INTRA BL
 263 LYS   ( 372-)  B      C   <->  264 ARG   ( 373-)  B      CG     0.16    2.94  INTRA BF
 734 VAL   ( 588-)  M      CG1 <->  738 ARG   ( 592-)  M      NH2    0.16    2.94  INTRA BF
And so on for a total of 127 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: M

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.

 775 PHE   ( 629-)  M      -8.00
 261 ARG   ( 632-)  A      -7.47
 667 ARG   ( 521-)  M      -7.00
 412 ARG   ( 521-)  B      -6.75
 150 ARG   ( 521-)  A      -6.73
 769 HIS   ( 623-)  M      -6.62
  41 HIS   ( 412-)  A      -5.80
 308 ARG   ( 417-)  B      -5.68
  46 ARG   ( 417-)  A      -5.68
 563 ARG   ( 417-)  M      -5.65
 558 HIS   ( 412-)  M      -5.65
 303 HIS   ( 412-)  B      -5.56
 504 LEU   ( 613-)  B      -5.55
 759 LEU   ( 613-)  M      -5.55
 242 LEU   ( 613-)  A      -5.48
 702 LYS   ( 556-)  M      -5.40
 185 LYS   ( 556-)  A      -5.39
 447 LYS   ( 556-)  B      -5.36
 498 GLU   ( 607-)  B      -5.27
 236 GLU   ( 607-)  A      -5.26
 259 ASN   ( 630-)  A      -5.23
 753 GLU   ( 607-)  M      -5.23
 723 GLN   ( 577-)  M      -5.19
 468 GLN   ( 577-)  B      -5.19
 206 GLN   ( 577-)  A      -5.18
 765 LEU   ( 619-)  M      -5.18
 742 TYR   ( 596-)  M      -5.17
 260 TRP   ( 631-)  A      -5.16
 551 ARG   ( 405-)  M      -5.12
  34 ARG   ( 405-)  A      -5.08
 286 GLN   ( 395-)  B      -5.07
 541 GLN   ( 395-)  M      -5.05
 772 THR   ( 626-)  M      -5.00

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.

  45 GLN   ( 416-)  A        47 - SER    418- ( A)         -4.77
 258 PHE   ( 629-)  A       261 - ARG    632- ( A)         -5.71
 307 GLN   ( 416-)  B       309 - SER    418- ( B)         -4.71
 562 GLN   ( 416-)  M       564 - SER    418- ( M)         -4.73
 767 LEU   ( 621-)  M       769 - HIS    623- ( M)         -5.26

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: M

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.

 205 LEU   ( 576-)  A   -2.59
 235 GLY   ( 606-)  A   -2.58

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: M

Water, ion, and hydrogenbond related checks

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.

 782 HOH   (  10 )  M      O

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.

   2 ARG   ( 373-)  A      N
   2 ARG   ( 373-)  A      NH2
   3 CYS   ( 374-)  A      N
   8 ARG   ( 379-)  A      NE
  18 GLY   ( 389-)  A      N
  20 TYR   ( 391-)  A      N
  22 LEU   ( 393-)  A      N
  36 ASN   ( 407-)  A      N
  46 ARG   ( 417-)  A      NH1
  51 ARG   ( 422-)  A      N
  66 GLN   ( 437-)  A      NE2
  84 VAL   ( 455-)  A      N
  91 ARG   ( 462-)  A      N
 119 GLU   ( 490-)  A      N
 120 TRP   ( 491-)  A      N
 122 LYS   ( 493-)  A      N
 124 VAL   ( 495-)  A      N
 128 THR   ( 499-)  A      N
 132 TRP   ( 503-)  A      NE1
 144 SER   ( 515-)  A      N
 149 TYR   ( 520-)  A      N
 194 HIS   ( 565-)  A      ND1
 195 ALA   ( 566-)  A      N
 196 SER   ( 567-)  A      OG
 199 GLU   ( 570-)  A      N
And so on for a total of 82 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.

 119 GLU   ( 490-)  A      OE1
 236 GLU   ( 607-)  A      OE2
 271 HIS   ( 380-)  B      NE2
 466 GLN   ( 575-)  B      OE1
 636 GLU   ( 490-)  M      OE1

Warning: Possible wrong residue type

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

 114 GLU   ( 485-)  A   H-bonding suggests Gln
 376 GLU   ( 485-)  B   H-bonding suggests Gln
 381 GLU   ( 490-)  B   H-bonding suggests Gln; Ligand-contact
 631 GLU   ( 485-)  M   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 :  -1.515
  2nd generation packing quality :  -2.025
  Ramachandran plot appearance   :  -1.835
  chi-1/chi-2 rotamer normality  :  -3.662 (poor)
  Backbone conformation          :  -0.858

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.500 (tight)
  Bond angles                    :   0.730
  Omega angle restraints         :   1.153
  Side chain planarity           :   0.385 (tight)
  Improper dihedral distribution :   0.741
  B-factor distribution          :   0.342
  Inside/Outside distribution    :   1.016

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.61


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.9
  2nd generation packing quality :  -0.6
  Ramachandran plot appearance   :   0.4
  chi-1/chi-2 rotamer normality  :  -1.3
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.500 (tight)
  Bond angles                    :   0.730
  Omega angle restraints         :   1.153
  Side chain planarity           :   0.385 (tight)
  Improper dihedral distribution :   0.741
  B-factor distribution          :   0.342
  Inside/Outside distribution    :   1.016
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.