WHAT IF Check report

This file was created 2012-01-19 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 pdb2c3t.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 : 0.741
CA-only RMS fit for the two chains : 0.443

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 : 0.873
CA-only RMS fit for the two chains : 0.611

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: A and D

All-atom RMS fit for the two chains : 0.720
CA-only RMS fit for the two chains : 0.390

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 D

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 : 0.691
CA-only RMS fit for the two chains : 0.407

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: B and D

All-atom RMS fit for the two chains : 0.645
CA-only RMS fit for the two chains : 0.275

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 D

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

 111 ARG   ( 112-)  A
 350 ARG   ( 112-)  B
 589 ARG   ( 112-)  C
 828 ARG   ( 112-)  D
 950 ARG   ( 234-)  D

Warning: Tyrosine convention problem

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

  72 TYR   (  73-)  A
  77 TYR   (  78-)  A
 311 TYR   (  73-)  B
 316 TYR   (  78-)  B
 550 TYR   (  73-)  C
 789 TYR   (  73-)  D
 794 TYR   (  78-)  D

Warning: Phenylalanine convention problem

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

  27 PHE   (  28-)  A
 119 PHE   ( 120-)  A
 184 PHE   ( 185-)  A
 219 PHE   ( 220-)  A
 266 PHE   (  28-)  B
 358 PHE   ( 120-)  B
 423 PHE   ( 185-)  B
 445 PHE   ( 207-)  B
 458 PHE   ( 220-)  B
 505 PHE   (  28-)  C
 597 PHE   ( 120-)  C
 662 PHE   ( 185-)  C
 684 PHE   ( 207-)  C
 697 PHE   ( 220-)  C
 744 PHE   (  28-)  D
 836 PHE   ( 120-)  D
 901 PHE   ( 185-)  D
 936 PHE   ( 220-)  D

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.

  33 ASP   (  34-)  A
  42 ASP   (  43-)  A
  81 ASP   (  82-)  A
 166 ASP   ( 167-)  A
 272 ASP   (  34-)  B
 281 ASP   (  43-)  B
 405 ASP   ( 167-)  B
 511 ASP   (  34-)  C
 565 ASP   (  88-)  C
 750 ASP   (  34-)  D
 759 ASP   (  43-)  D
 883 ASP   ( 167-)  D
 940 ASP   ( 224-)  D

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.

   3 GLU   (   4-)  A
 138 GLU   ( 139-)  A
 147 GLU   ( 148-)  A
 208 GLU   ( 209-)  A
 386 GLU   ( 148-)  B
 481 GLU   (   4-)  C
 625 GLU   ( 148-)  C
 855 GLU   ( 139-)  D
 925 GLU   ( 209-)  D

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.

 183 VAL   ( 184-)  A      CA   CB    1.61    4.2
 195 GLN   ( 196-)  A      CB   CG    1.67    5.1
 274 ILE   (  36-)  B      CA   CB    1.62    4.3
 324 PRO   (  86-)  B      N    CA    1.53    4.4
 356 VAL   ( 118-)  B      CA   CB    1.62    4.7
 357 MET   ( 119-)  B      N    CA    1.54    4.1
 409 ILE   ( 171-)  B      CA   CB    1.61    4.0
 595 VAL   ( 118-)  C      CA   CB    1.62    4.4
 596 MET   ( 119-)  C      N    CA    1.54    4.4
 596 MET   ( 119-)  C      CA   C     1.61    4.0
 640 ILE   ( 163-)  C      CA   CB    1.62    4.5
 835 MET   ( 119-)  D      N    CA    1.54    4.2
 901 PHE   ( 185-)  D      CA   C     1.62    4.3

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

 |  0.996862 -0.000255 -0.000567|
 | -0.000255  0.994705 -0.000037|
 | -0.000567 -0.000037  0.995194|
Proposed new scale matrix

 |  0.006097  0.000002  0.000003|
 |  0.000002  0.008991  0.000000|
 |  0.000010  0.000000  0.017967|
With corresponding cell

    A    = 164.012  B   = 111.227  C    =  55.657
    Alpha=  90.001  Beta=  90.065  Gamma=  90.029

The CRYST1 cell dimensions

    A    = 164.524  B   = 111.822  C    =  55.924
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 619.111
(Under-)estimated Z-score: 18.338

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.

   3 GLU   (   4-)  A
  33 ASP   (  34-)  A
  42 ASP   (  43-)  A
  81 ASP   (  82-)  A
 111 ARG   ( 112-)  A
 138 GLU   ( 139-)  A
 147 GLU   ( 148-)  A
 166 ASP   ( 167-)  A
 208 GLU   ( 209-)  A
 272 ASP   (  34-)  B
 281 ASP   (  43-)  B
 350 ARG   ( 112-)  B
 386 GLU   ( 148-)  B
 405 ASP   ( 167-)  B
 481 GLU   (   4-)  C
 511 ASP   (  34-)  C
 565 ASP   (  88-)  C
 589 ARG   ( 112-)  C
 625 GLU   ( 148-)  C
 750 ASP   (  34-)  D
 759 ASP   (  43-)  D
 828 ARG   ( 112-)  D
 855 GLU   ( 139-)  D
 883 ASP   ( 167-)  D
 925 GLU   ( 209-)  D
 940 ASP   ( 224-)  D
 950 ARG   ( 234-)  D

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.

 101 GLN   ( 102-)  A    4.14

Error: Side chain planarity problems

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

 405 ASP   ( 167-)  B    7.83
 644 ASP   ( 167-)  C    6.79
  81 ASP   (  82-)  A    6.50
 832 HIS   ( 116-)  D    6.12
 653 HIS   ( 176-)  C    5.90
 593 HIS   ( 116-)  C    5.78
 804 ASP   (  88-)  D    5.72
  11 GLN   (  12-)  A    5.69
 892 HIS   ( 176-)  D    5.56
 115 HIS   ( 116-)  A    5.39
 883 ASP   ( 167-)  D    5.37
 889 GLU   ( 173-)  D    5.36
 354 HIS   ( 116-)  B    5.29
 326 ASP   (  88-)  B    5.26
 262 ASN   (  24-)  B    5.26
 489 GLN   (  12-)  C    5.19
 579 GLN   ( 102-)  C    5.13
 878 HIS   ( 162-)  D    5.13
 414 HIS   ( 176-)  B    5.04
 728 GLN   (  12-)  D    4.98
 740 ASN   (  24-)  D    4.95
 411 GLU   ( 173-)  B    4.88
  86 GLN   (  87-)  A    4.87
 172 GLU   ( 173-)  A    4.85
 377 GLU   ( 139-)  B    4.84
 166 ASP   ( 167-)  A    4.70
 250 GLN   (  12-)  B    4.65
 573 ASP   (  96-)  C    4.64
 340 GLN   ( 102-)  B    4.64
  95 ASP   (  96-)  A    4.61
 855 GLU   ( 139-)  D    4.57
  87 ASP   (  88-)  A    4.50
 812 ASP   (  96-)  D    4.48
 175 HIS   ( 176-)  A    4.47
 685 GLN   ( 208-)  C    4.39
 147 GLU   ( 148-)  A    4.33
 204 ASP   ( 205-)  A    4.32
 798 ASP   (  82-)  D    4.32
 818 GLN   ( 102-)  D    4.25
 650 GLU   ( 173-)  C    4.19
 777 ASP   (  61-)  D    4.18
 434 GLN   ( 196-)  B    4.16
 299 ASP   (  61-)  B    4.14
 228 GLN   ( 229-)  A    4.13
 208 GLU   ( 209-)  A    4.11

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.

  35 ILE   (  36-)  A    -2.2
 160 PRO   ( 161-)  A    -2.1
 224 PRO   ( 225-)  A    -2.1
 463 PRO   ( 225-)  B    -2.0
 679 VAL   ( 202-)  C    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  24 ASP   (  25-)  A  Poor phi/psi
  51 LYS   (  52-)  A  Poor phi/psi
  53 VAL   (  54-)  A  PRO omega poor
  65 GLU   (  66-)  A  Poor phi/psi
  78 LYS   (  79-)  A  Poor phi/psi
 104 THR   ( 105-)  A  Poor phi/psi
 121 VAL   ( 122-)  A  Poor phi/psi
 152 GLN   ( 153-)  A  Poor phi/psi
 263 ASP   (  25-)  B  Poor phi/psi
 292 VAL   (  54-)  B  PRO omega poor
 304 GLU   (  66-)  B  Poor phi/psi
 343 THR   ( 105-)  B  Poor phi/psi
 391 GLN   ( 153-)  B  Poor phi/psi
 526 ASN   (  49-)  C  Poor phi/psi
 529 LYS   (  52-)  C  Poor phi/psi
 531 VAL   (  54-)  C  PRO omega poor
 543 GLU   (  66-)  C  Poor phi/psi
 582 THR   ( 105-)  C  Poor phi/psi
 630 GLN   ( 153-)  C  Poor phi/psi
 694 ALA   ( 217-)  C  Poor phi/psi
 702 PRO   ( 225-)  C  Poor phi/psi
 768 LYS   (  52-)  D  Poor phi/psi
 770 VAL   (  54-)  D  PRO omega poor
 782 GLU   (  66-)  D  Poor phi/psi
 795 LYS   (  79-)  D  Poor phi/psi
 821 THR   ( 105-)  D  Poor phi/psi
 869 GLN   ( 153-)  D  Poor phi/psi
 941 PRO   ( 225-)  D  Poor phi/psi
 chi-1/chi-2 correlation Z-score : 2.533

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   (   7-)  A      0
   9 LEU   (  10-)  A      0
  38 GLN   (  39-)  A      0
  47 VAL   (  48-)  A      0
  51 LYS   (  52-)  A      0
  52 LYS   (  53-)  A      0
  58 ASP   (  59-)  A      0
  60 ASP   (  61-)  A      0
  64 THR   (  65-)  A      0
  65 GLU   (  66-)  A      0
  78 LYS   (  79-)  A      0
  83 TRP   (  84-)  A      0
  85 PRO   (  86-)  A      0
 103 THR   ( 104-)  A      0
 104 THR   ( 105-)  A      0
 105 LEU   ( 106-)  A      0
 116 LYS   ( 117-)  A      0
 118 MET   ( 119-)  A      0
 120 PRO   ( 121-)  A      0
 122 PHE   ( 123-)  A      0
 151 LEU   ( 152-)  A      0
 152 GLN   ( 153-)  A      0
 153 ASN   ( 154-)  A      0
 155 ALA   ( 156-)  A      0
 156 PHE   ( 157-)  A      0
And so on for a total of 284 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 : 1.285

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].

  12 PRO   (  13-)  A  -112.2 envelop C-gamma (-108 degrees)
  54 PRO   (  55-)  A   -65.7 envelop C-beta (-72 degrees)
  80 PRO   (  81-)  A   127.2 half-chair C-beta/C-alpha (126 degrees)
 120 PRO   ( 121-)  A  -118.0 half-chair C-delta/C-gamma (-126 degrees)
 176 PRO   ( 177-)  A  -118.3 half-chair C-delta/C-gamma (-126 degrees)
 224 PRO   ( 225-)  A   160.1 half-chair C-alpha/N (162 degrees)
 232 PRO   ( 233-)  A  -116.9 envelop C-gamma (-108 degrees)
 319 PRO   (  81-)  B   106.4 envelop C-beta (108 degrees)
 399 PRO   ( 161-)  B   -63.3 envelop C-beta (-72 degrees)
 415 PRO   ( 177-)  B  -114.1 envelop C-gamma (-108 degrees)
 427 PRO   ( 189-)  B  -127.7 half-chair C-delta/C-gamma (-126 degrees)
 463 PRO   ( 225-)  B   139.5 envelop C-alpha (144 degrees)
 527 PRO   (  50-)  C  -126.2 half-chair C-delta/C-gamma (-126 degrees)
 598 PRO   ( 121-)  C  -121.8 half-chair C-delta/C-gamma (-126 degrees)
 638 PRO   ( 161-)  C    38.3 envelop C-delta (36 degrees)
 743 PRO   (  27-)  D   -55.0 half-chair C-beta/C-alpha (-54 degrees)
 905 PRO   ( 189-)  D  -112.6 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 192 THR   ( 193-)  A      CG2 <->  196 ARG   ( 197-)  A      NH1    0.51    2.59  INTRA BL
 601 LEU   ( 124-)  C      O   <->  705 LYS   ( 228-)  C      NZ     0.49    2.21  INTRA BF
 431 THR   ( 193-)  B      CG2 <->  435 ARG   ( 197-)  B      NH1    0.48    2.62  INTRA BL
 701 ASP   ( 224-)  C      C   <->  703 THR   ( 226-)  C      N      0.37    2.53  INTRA BF
 824 ARG   ( 108-)  D      NE  <->  960 ARG   ( 240-)  D      O''    0.34    2.36  INTRA
 866 LYS   ( 150-)  D      NZ  <->  964 HOH   (2044 )  D      O      0.33    2.37  INTRA
 833 LYS   ( 117-)  D      NZ  <->  964 HOH   (2038 )  D      O      0.33    2.37  INTRA BF
  14 ARG   (  15-)  A      NH2 <->  175 HIS   ( 176-)  A      ND1    0.32    2.68  INTRA BL
 774 LYS   (  58-)  D      NZ  <->  776 GLY   (  60-)  D      O      0.30    2.40  INTRA
 701 ASP   ( 224-)  C      O   <->  703 THR   ( 226-)  C      N      0.29    2.41  INTRA BF
 535 LYS   (  58-)  C      NZ  <->  537 GLY   (  60-)  C      O      0.28    2.42  INTRA
  50 LEU   (  51-)  A      O   <->  233 ARG   ( 234-)  A      NH2    0.28    2.42  INTRA BF
  10 SER   (  11-)  A      OG  <->   13 CYS   (  14-)  A      SG     0.27    2.73  INTRA BL
 731 ARG   (  15-)  D      NH2 <->  888 THR   ( 172-)  D      O      0.24    2.46  INTRA BL
 253 ARG   (  15-)  B      NH2 <->  414 HIS   ( 176-)  B      ND1    0.24    2.76  INTRA BL
 585 ARG   ( 108-)  C      NE  <->  959 ARG   ( 240-)  C      O''    0.23    2.47  INTRA
 628 PHE   ( 151-)  C      O   <->  632 LYS   ( 155-)  C      NZ     0.18    2.52  INTRA BL
 828 ARG   ( 112-)  D      NH1 <->  955 ILE   ( 239-)  D      O      0.17    2.53  INTRA
 559 ASP   (  82-)  C      OD2 <->  564 GLN   (  87-)  C      NE2    0.17    2.53  INTRA BL
 941 PRO   ( 225-)  D      O   <->  945 GLN   ( 229-)  D      NE2    0.17    2.53  INTRA BF
 389 PHE   ( 151-)  B      O   <->  393 LYS   ( 155-)  B      NZ     0.16    2.54  INTRA BL
 559 ASP   (  82-)  C      N   <->  963 HOH   (2025 )  C      O      0.16    2.54  INTRA BL
 196 ARG   ( 197-)  A      NH2 <->  961 HOH   (2040 )  A      O      0.15    2.55  INTRA BL
 867 PHE   ( 151-)  D      O   <->  871 LYS   ( 155-)  D      NZ     0.15    2.55  INTRA BL
 492 ARG   (  15-)  C      NH2 <->  653 HIS   ( 176-)  C      ND1    0.14    2.86  INTRA BL
And so on for a total of 78 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Warning: Abnormal packing environment for some residues

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

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

 182 GLN   ( 183-)  A      -5.93
 769 LYS   (  53-)  D      -5.73
  78 LYS   (  79-)  A      -5.38
 530 LYS   (  53-)  C      -5.33
  52 LYS   (  53-)  A      -5.25
 561 TRP   (  84-)  C      -5.11
 322 TRP   (  84-)  B      -5.06

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Warning: Low packing Z-score for some residues

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

 289 LEU   (  51-)  B   -2.87
 599 VAL   ( 122-)  C   -2.74
 954 MET   ( 238-)  D   -2.51

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

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.

 961 HOH   (2047 )  A      O
 962 HOH   (2015 )  B      O
 964 HOH   (2046 )  D      O
 964 HOH   (2057 )  D      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.

  39 HIS   (  40-)  A
 102 HIS   ( 103-)  A
 278 HIS   (  40-)  B
 517 HIS   (  40-)  C
 608 GLN   ( 131-)  C
 756 HIS   (  40-)  D
 899 GLN   ( 183-)  D
 945 GLN   ( 229-)  D

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.

  14 ARG   (  15-)  A      NE
  23 ASN   (  24-)  A      ND2
  39 HIS   (  40-)  A      N
  46 GLN   (  47-)  A      N
  52 LYS   (  53-)  A      N
  78 LYS   (  79-)  A      N
  82 TYR   (  83-)  A      N
 107 ARG   ( 108-)  A      N
 130 GLN   ( 131-)  A      N
 159 GLY   ( 160-)  A      N
 189 LYS   ( 190-)  A      N
 217 LYS   ( 218-)  A      N
 253 ARG   (  15-)  B      NE
 262 ASN   (  24-)  B      ND2
 276 GLY   (  38-)  B      N
 278 HIS   (  40-)  B      N
 280 SER   (  42-)  B      N
 285 GLN   (  47-)  B      N
 291 LYS   (  53-)  B      N
 341 HIS   ( 103-)  B      N
 346 ARG   ( 108-)  B      N
 350 ARG   ( 112-)  B      NE
 388 LYS   ( 150-)  B      NZ
 398 GLY   ( 160-)  B      N
 400 HIS   ( 162-)  B      N
And so on for a total of 56 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.

 172 GLU   ( 173-)  A      OE2
 210 HIS   ( 211-)  A      NE2
 411 GLU   ( 173-)  B      OE2
 449 HIS   ( 211-)  B      NE2
 650 GLU   ( 173-)  C      OE2
 688 HIS   ( 211-)  C      NE2
 927 HIS   ( 211-)  D      NE2

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.

 963 HOH   (2023 )  C      O  0.98  K  4

Warning: Possible wrong residue type

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

   7 ASP   (   8-)  A   H-bonding suggests Asn; but Alt-Rotamer
 218 ASP   ( 219-)  A   H-bonding suggests Asn; but Alt-Rotamer
 457 ASP   ( 219-)  B   H-bonding suggests Asn; but Alt-Rotamer
 485 ASP   (   8-)  C   H-bonding suggests Asn
 502 ASP   (  25-)  C   H-bonding suggests Asn
 696 ASP   ( 219-)  C   H-bonding suggests Asn

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 :  -0.012
  2nd generation packing quality :  -0.810
  Ramachandran plot appearance   :  -2.239
  chi-1/chi-2 rotamer normality  :   2.533
  Backbone conformation          :  -0.868

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.917
  Bond angles                    :   0.613 (tight)
  Omega angle restraints         :   0.234 (tight)
  Side chain planarity           :   2.462 (loose)
  Improper dihedral distribution :   1.148
  B-factor distribution          :   0.454
  Inside/Outside distribution    :   0.938

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 : 2.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.9
  2nd generation packing quality :   0.2
  Ramachandran plot appearance   :  -0.4
  chi-1/chi-2 rotamer normality  :   3.9
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.917
  Bond angles                    :   0.613 (tight)
  Omega angle restraints         :   0.234 (tight)
  Side chain planarity           :   2.462 (loose)
  Improper dihedral distribution :   1.148
  B-factor distribution          :   0.454
  Inside/Outside distribution    :   0.938
==============

WHAT IF
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Bond lengths and angles, DNA/RNA
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DSSP
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      Dictionary of protein secondary structure: pattern
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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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    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
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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
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      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.