WHAT IF Check report

This file was created 2012-07-04 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 pdb3scr.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 : 0.122
CA-only RMS fit for the two chains : 0.090

Warning: New symmetry found

Independent molecules in the asymmetric unit actually look like symmetry relatives. This fact needs manual checking.

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.

 946 MES   (1005-)  A  -
 951 MES   (1006-)  B  -

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

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) :105.000

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

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

 127 TYR   ( 131-)  A
 137 TYR   ( 141-)  A
 181 TYR   ( 185-)  A
 243 TYR   ( 247-)  A
 267 TYR   ( 271-)  A
 311 TYR   ( 315-)  A
 396 TYR   ( 400-)  A
 426 TYR   ( 430-)  A
 441 TYR   ( 445-)  A
 464 TYR   ( 468-)  A
 597 TYR   ( 129-)  B
 599 TYR   ( 131-)  B
 609 TYR   ( 141-)  B
 653 TYR   ( 185-)  B
 715 TYR   ( 247-)  B
 739 TYR   ( 271-)  B
 783 TYR   ( 315-)  B
 868 TYR   ( 400-)  B
 913 TYR   ( 445-)  B
 936 TYR   ( 468-)  B

Warning: Phenylalanine convention problem

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

  78 PHE   (  82-)  A
  83 PHE   (  87-)  A
  91 PHE   (  95-)  A
 168 PHE   ( 172-)  A
 170 PHE   ( 174-)  A
 211 PHE   ( 215-)  A
 405 PHE   ( 409-)  A
 550 PHE   (  82-)  B
 555 PHE   (  87-)  B
 563 PHE   (  95-)  B
 640 PHE   ( 172-)  B
 642 PHE   ( 174-)  B
 683 PHE   ( 215-)  B
 877 PHE   ( 409-)  B

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.

 147 ASP   ( 151-)  A
 286 ASP   ( 290-)  A
 468 ASP   ( 472-)  A
 619 ASP   ( 151-)  B
 758 ASP   ( 290-)  B
 940 ASP   ( 472-)  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.

  95 GLU   (  99-)  A
 101 GLU   ( 105-)  A
 567 GLU   (  99-)  B
 573 GLU   ( 105-)  B

Geometric checks

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.553
RMS-deviation in bond distances: 0.013

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

 |  0.995699  0.000049 -0.000306|
 |  0.000049  0.995282 -0.000203|
 | -0.000306 -0.000203  0.995841|
Proposed new scale matrix

 |  0.012595  0.000000  0.000004|
 |  0.000000  0.009951  0.000002|
 |  0.000002  0.000002  0.007877|
With corresponding cell

    A    =  79.395  B   = 100.493  C    = 126.956
    Alpha=  90.023  Beta=  90.035  Gamma=  90.001

The CRYST1 cell dimensions

    A    =  79.740  B   = 100.966  C    = 127.493
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 626.086
(Under-)estimated Z-score: 18.441

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 TRP   (   6-)  A      CA   CB   CG  121.24    4.0
 263 HIS   ( 267-)  A      CG   ND1  CE1 109.69    4.1
 687 HIS   ( 219-)  B      CG   ND1  CE1 109.66    4.1

Warning: Low bond angle variability

Bond angles were found to deviate less than normal from the standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond angles: 0.656
RMS-deviation in bond angles: 1.333

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.

  95 GLU   (  99-)  A
 101 GLU   ( 105-)  A
 147 ASP   ( 151-)  A
 286 ASP   ( 290-)  A
 468 ASP   ( 472-)  A
 567 GLU   (  99-)  B
 573 GLU   ( 105-)  B
 619 ASP   ( 151-)  B
 758 ASP   ( 290-)  B
 940 ASP   ( 472-)  B

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.

 498 VAL   (  30-)  B    5.19
  26 VAL   (  30-)  A    4.67

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.

 784 THR   ( 316-)  B    -2.9
 312 THR   ( 316-)  A    -2.8
 660 PRO   ( 192-)  B    -2.4
 319 GLN   ( 323-)  A    -2.3
 791 GLN   ( 323-)  B    -2.3
 188 PRO   ( 192-)  A    -2.3
 598 HIS   ( 130-)  B    -2.3
 777 TYR   ( 309-)  B    -2.2
 126 HIS   ( 130-)  A    -2.1
 599 TYR   ( 131-)  B    -2.1
 909 TRP   ( 441-)  B    -2.1
 437 TRP   ( 441-)  A    -2.0
 486 ARG   (  18-)  B    -2.0
 127 TYR   ( 131-)  A    -2.0
 264 ILE   ( 268-)  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.

  14 ARG   (  18-)  A  Poor phi/psi
  26 VAL   (  30-)  A  Poor phi/psi
  27 GLU   (  31-)  A  omega poor
  59 ALA   (  63-)  A  Poor phi/psi
  61 ASP   (  65-)  A  Poor phi/psi
  77 ASN   (  81-)  A  Poor phi/psi
  79 ASP   (  83-)  A  omega poor
 127 TYR   ( 131-)  A  Poor phi/psi, omega poor
 167 TRP   ( 171-)  A  omega poor
 181 TYR   ( 185-)  A  Poor phi/psi
 187 PRO   ( 191-)  A  PRO omega poor
 189 LYS   ( 193-)  A  Poor phi/psi
 193 LYS   ( 197-)  A  omega poor
 231 GLN   ( 235-)  A  Poor phi/psi
 285 LYS   ( 289-)  A  Poor phi/psi
 311 TYR   ( 315-)  A  omega poor
 350 ALA   ( 354-)  A  Poor phi/psi
 375 ASN   ( 379-)  A  Poor phi/psi
 389 ALA   ( 393-)  A  omega poor
 390 ASN   ( 394-)  A  Poor phi/psi
 429 TRP   ( 433-)  A  omega poor
 432 LEU   ( 436-)  A  omega poor
 437 TRP   ( 441-)  A  Poor phi/psi
 446 GLY   ( 450-)  A  omega poor
 455 LEU   ( 459-)  A  Poor phi/psi
 486 ARG   (  18-)  B  Poor phi/psi
 498 VAL   (  30-)  B  Poor phi/psi
 499 GLU   (  31-)  B  omega poor
 525 ASN   (  57-)  B  Poor phi/psi
 531 ALA   (  63-)  B  Poor phi/psi
 533 ASP   (  65-)  B  Poor phi/psi
 549 ASN   (  81-)  B  Poor phi/psi
 593 TYR   ( 125-)  B  omega poor
 599 TYR   ( 131-)  B  Poor phi/psi, omega poor
 639 TRP   ( 171-)  B  omega poor
 659 PRO   ( 191-)  B  PRO omega poor
 661 LYS   ( 193-)  B  Poor phi/psi
 663 CYS   ( 195-)  B  Poor phi/psi
 665 LYS   ( 197-)  B  omega poor
 703 GLN   ( 235-)  B  Poor phi/psi
 757 LYS   ( 289-)  B  Poor phi/psi
 786 SER   ( 318-)  B  omega poor
 794 MET   ( 326-)  B  omega poor
 822 ALA   ( 354-)  B  Poor phi/psi
 862 ASN   ( 394-)  B  Poor phi/psi
 901 TRP   ( 433-)  B  omega poor
 904 LEU   ( 436-)  B  omega poor
 909 TRP   ( 441-)  B  Poor phi/psi
 918 GLY   ( 450-)  B  omega poor
 927 LEU   ( 459-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.145

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.

 408 SER   ( 412-)  A    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!

   6 LEU   (  10-)  A      0
  10 ALA   (  14-)  A      0
  13 LYS   (  17-)  A      0
  14 ARG   (  18-)  A      0
  26 VAL   (  30-)  A      0
  27 GLU   (  31-)  A      0
  29 MET   (  33-)  A      0
  30 ALA   (  34-)  A      0
  31 ALA   (  35-)  A      0
  32 SER   (  36-)  A      0
  45 HIS   (  49-)  A      0
  47 PRO   (  51-)  A      0
  49 ASN   (  53-)  A      0
  51 ALA   (  55-)  A      0
  54 GLN   (  58-)  A      0
  57 ASP   (  61-)  A      0
  59 ALA   (  63-)  A      0
  60 THR   (  64-)  A      0
  61 ASP   (  65-)  A      0
  62 GLN   (  66-)  A      0
  65 ARG   (  69-)  A      0
  76 LEU   (  80-)  A      0
  77 ASN   (  81-)  A      0
  78 PHE   (  82-)  A      0
  87 TRP   (  91-)  A      0
And so on for a total of 364 lines.

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]

 345 PRO   ( 349-)  A    0.17 LOW
 817 PRO   ( 349-)  B    0.04 LOW

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short 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.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

 526 GLN   (  58-)  B      NE2  <->   953 HOH   ( 772 )  B      O    0.41    2.29  INTRA
 290 LYS   ( 294-)  A      NZ   <->   952 HOH   ( 777 )  A      O    0.24    2.46  INTRA
 950 GOL   (1008-)  B      C1   <->   953 HOH   ( 867 )  B      O    0.20    2.60  INTRA
 948 GOL   (1007-)  A      C3   <->   952 HOH   ( 788 )  A      O    0.20    2.60  INTRA
  54 GLN   (  58-)  A      NE2  <->   952 HOH   ( 838 )  A      O    0.19    2.51  INTRA BL
 372 LYS   ( 376-)  A      NZ   <->   952 HOH   ( 660 )  A      O    0.16    2.54  INTRA
 260 ARG   ( 264-)  A      NH2  <->   952 HOH   ( 695 )  A      O    0.16    2.54  INTRA
   1 ASN   (   5-)  A      CG   <->     2 TRP   (   6-)  A      N    0.15    2.85  INTRA
 813 LYS   ( 345-)  B      NZ   <->   953 HOH   ( 803 )  B      O    0.14    2.56  INTRA
 191 CYS   ( 195-)  A      SG   <->   194 CYS   ( 198-)  A      N    0.13    3.17  INTRA
 115 GLN   ( 119-)  A      NE2  <->   952 HOH   ( 775 )  A      O    0.12    2.58  INTRA
 675 GLU   ( 207-)  B      N    <->   676 PRO   ( 208-)  B      CD   0.12    2.88  INTRA BL
 231 GLN   ( 235-)  A      CG   <->   952 HOH   ( 576 )  A      O    0.12    2.68  INTRA
 587 GLN   ( 119-)  B      NE2  <->   953 HOH   ( 731 )  B      O    0.11    2.59  INTRA
 811 PHE   ( 343-)  B      N    <->   953 HOH   ( 714 )  B      O    0.11    2.59  INTRA
 842 LYS   ( 374-)  B      NZ   <->   953 HOH   ( 815 )  B      O    0.10    2.60  INTRA
 203 GLU   ( 207-)  A      N    <->   204 PRO   ( 208-)  A      CD   0.10    2.90  INTRA BL
 732 ARG   ( 264-)  B      NH2  <->   953 HOH   ( 716 )  B      O    0.09    2.61  INTRA
 324 GLN   ( 328-)  A      OE1  <->   952 HOH   ( 746 )  A      O    0.08    2.32  INTRA
 186 ASN   ( 190-)  A      ND2  <->   952 HOH   ( 585 )  A      O    0.08    2.62  INTRA
 789 LYS   ( 321-)  B      NZ   <->   953 HOH   ( 487 )  B      O    0.08    2.62  INTRA
 663 CYS   ( 195-)  B      SG   <->   666 CYS   ( 198-)  B      N    0.07    3.23  INTRA
 700 ALA   ( 232-)  B      O    <->   703 GLN   ( 235-)  B      NE2  0.06    2.64  INTRA
 446 GLY   ( 450-)  A      O    <->   460 LYS   ( 464-)  A      NZ   0.06    2.64  INTRA BL
 715 TYR   ( 247-)  B      OH   <->   735 HIS   ( 267-)  B      ND1  0.06    2.64  INTRA BL
 762 LYS   ( 294-)  B      NZ   <->   953 HOH   ( 506 )  B      O    0.05    2.65  INTRA
   1 ASN   (   5-)  A      O    <->     4 GLY   (   8-)  A      N    0.04    2.66  INTRA
 681 HIS   ( 213-)  B      ND1  <->   748 TYR   ( 280-)  B      OH   0.04    2.66  INTRA BL
 587 GLN   ( 119-)  B      NE2  <->   953 HOH   ( 862 )  B      O    0.03    2.67  INTRA
 115 GLN   ( 119-)  A      NE2  <->   952 HOH   ( 817 )  A      O    0.03    2.67  INTRA
 310 GLN   ( 314-)  A      O    <->   383 ASN   ( 387-)  A      ND2  0.03    2.67  INTRA BL
 227 GLN   ( 231-)  A      O    <->   231 GLN   ( 235-)  A      NE2  0.03    2.67  INTRA
 468 ASP   ( 472-)  A      OD1  <->   952 HOH   ( 508 )  A      O    0.03    2.37  INTRA
 526 GLN   (  58-)  B      NE2  <->   953 HOH   ( 837 )  B      O    0.02    2.68  INTRA
 370 LYS   ( 374-)  A      NZ   <->   952 HOH   ( 850 )  A      O    0.02    2.68  INTRA
 844 LYS   ( 376-)  B      NZ   <->   953 HOH   ( 720 )  B      O    0.02    2.68  INTRA
 772 LYS   ( 304-)  B      NZ   <->   953 HOH   ( 764 )  B      O    0.02    2.68  INTRA
 919 ILE   ( 451-)  B      N    <->   920 VAL   ( 452-)  B      N    0.02    2.58  INTRA BL
 809 TYR   ( 341-)  B      N    <->   953 HOH   ( 492 )  B      O    0.02    2.68  INTRA
 871 ASP   ( 403-)  B      OD2  <->   874 ARG   ( 406-)  B      NH1  0.02    2.68  INTRA BL
 290 LYS   ( 294-)  A      NZ   <->   952 HOH   ( 684 )  A      O    0.01    2.69  INTRA
 169 THR   ( 173-)  A      OG1  <->   215 HIS   ( 219-)  A      ND1  0.01    2.69  INTRA BL
 923 ASP   ( 455-)  B      O    <->   927 LEU   ( 459-)  B      N    0.01    2.69  INTRA BL
 554 ARG   (  86-)  B      NH2  <->   643 ASN   ( 175-)  B      OD1  0.01    2.69  INTRA BL
 599 TYR   ( 131-)  B      CD2  <->   909 TRP   ( 441-)  B      CZ2  0.01    3.19  INTRA BL
 796 GLN   ( 328-)  B      OE1  <->   953 HOH   ( 685 )  B      O    0.01    2.39  INTRA
 664 THR   ( 196-)  B      O    <->   953 HOH   ( 822 )  B      O    0.01    2.39  INTRA
 433 ASP   ( 437-)  A      OD1  <->   460 LYS   ( 464-)  A      NZ   0.01    2.69  INTRA BL
 290 LYS   ( 294-)  A      N    <->   952 HOH   ( 763 )  A      O    0.01    2.69  INTRA
 766 GLU   ( 298-)  B      OE1  <->   953 HOH   ( 814 )  B      O    0.01    2.39  INTRA

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

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.

 324 GLN   ( 328-)  A      -6.89
 796 GLN   ( 328-)  B      -6.78
 795 GLN   ( 327-)  B      -6.65
 323 GLN   ( 327-)  A      -6.48
 587 GLN   ( 119-)  B      -5.58
 115 GLN   ( 119-)  A      -5.55
 193 LYS   ( 197-)  A      -5.48
 702 GLN   ( 234-)  B      -5.40
 230 GLN   ( 234-)  A      -5.38
 322 MET   ( 326-)  A      -5.26
 665 LYS   ( 197-)  B      -5.22
 745 ASN   ( 277-)  B      -5.20
 273 ASN   ( 277-)  A      -5.20
 525 ASN   (  57-)  B      -5.17
  53 ASN   (  57-)  A      -5.16
 486 ARG   (  18-)  B      -5.11
 735 HIS   ( 267-)  B      -5.11
 805 TRP   ( 337-)  B      -5.05
 263 HIS   ( 267-)  A      -5.03
  14 ARG   (  18-)  A      -5.02
 759 ARG   ( 291-)  B      -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.

  52 GLY   (  56-)  A        54 - GLN     58- ( A)         -4.57
 320 GLN   ( 324-)  A       324 - GLN    328- ( A)         -5.54
 524 GLY   (  56-)  B       526 - GLN     58- ( B)         -4.52
 792 GLN   ( 324-)  B       796 - GLN    328- ( B)         -5.45

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: 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

Water, ion, and hydrogenbond related checks

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.

  54 GLN   (  58-)  A
 319 GLN   ( 323-)  A
 349 GLN   ( 353-)  A
 395 GLN   ( 399-)  A
 526 GLN   (  58-)  B
 821 GLN   ( 353-)  B
 867 GLN   ( 399-)  B
 930 HIS   ( 462-)  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.

   7 SER   (  11-)  A      N
   8 ARG   (  12-)  A      NH2
  22 SER   (  26-)  A      N
  35 ARG   (  39-)  A      NH1
  95 GLU   (  99-)  A      N
 123 ASN   ( 127-)  A      ND2
 231 GLN   ( 235-)  A      NE2
 241 ASN   ( 245-)  A      N
 243 TYR   ( 247-)  A      N
 247 SER   ( 251-)  A      N
 267 TYR   ( 271-)  A      OH
 276 TYR   ( 280-)  A      N
 291 PHE   ( 295-)  A      N
 305 TYR   ( 309-)  A      N
 333 TRP   ( 337-)  A      NE1
 340 ALA   ( 344-)  A      N
 347 GLY   ( 351-)  A      N
 383 ASN   ( 387-)  A      ND2
 384 GLY   ( 388-)  A      N
 425 GLY   ( 429-)  A      N
 434 ASN   ( 438-)  A      ND2
 443 SER   ( 447-)  A      N
 458 HIS   ( 462-)  A      ND1
 479 SER   (  11-)  B      N
 480 ARG   (  12-)  B      NH2
 485 LYS   (  17-)  B      N
 491 THR   (  23-)  B      OG1
 494 SER   (  26-)  B      N
 554 ARG   (  86-)  B      NH2
 567 GLU   (  99-)  B      N
 595 ASN   ( 127-)  B      ND2
 643 ASN   ( 175-)  B      ND2
 703 GLN   ( 235-)  B      NE2
 715 TYR   ( 247-)  B      N
 719 SER   ( 251-)  B      N
 735 HIS   ( 267-)  B      ND1
 739 TYR   ( 271-)  B      OH
 748 TYR   ( 280-)  B      N
 763 PHE   ( 295-)  B      N
 777 TYR   ( 309-)  B      N
 805 TRP   ( 337-)  B      NE1
 812 ALA   ( 344-)  B      N
 819 GLY   ( 351-)  B      N
 855 ASN   ( 387-)  B      ND2
 856 GLY   ( 388-)  B      N
 897 GLY   ( 429-)  B      N
 915 SER   ( 447-)  B      N
Only metal coordination for   64 HIS  (  68-) A      ND1
Only metal coordination for  536 HIS  (  68-) B      ND1

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.

 543 ASN   (  75-)  B      OD1

Warning: Unusual water packing

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

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

 952 HOH   ( 561 )  A      O  1.10  K  4
 953 HOH   ( 483 )  B      O  0.86  K  4 Ion-B
 953 HOH   ( 587 )  B      O  1.13  K  4 ION-B H2O-B
 953 HOH   ( 853 )  B      O  1.11  K  4 ION-B
 953 HOH   ( 858 )  B      O  0.92  K  4 ION-B

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.

 436 GLU   ( 440-)  A   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
 908 GLU   ( 440-)  B   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact

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 :  -0.332
  2nd generation packing quality :  -0.603
  Ramachandran plot appearance   :  -0.489
  chi-1/chi-2 rotamer normality  :  -0.145
  Backbone conformation          :  -1.011

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.553 (tight)
  Bond angles                    :   0.656 (tight)
  Omega angle restraints         :   1.084
  Side chain planarity           :   0.642 (tight)
  Improper dihedral distribution :   0.730
  B-factor distribution          :   0.532
  Inside/Outside distribution    :   0.972

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 : 1.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.0
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :  -0.4
  chi-1/chi-2 rotamer normality  :   0.1
  Backbone conformation          :  -1.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.553 (tight)
  Bond angles                    :   0.656 (tight)
  Omega angle restraints         :   1.084
  Side chain planarity           :   0.642 (tight)
  Improper dihedral distribution :   0.730
  B-factor distribution          :   0.532
  Inside/Outside distribution    :   0.972
==============

WHAT IF
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      WHAT IF: a molecular modelling and drug design program,
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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.