WHAT IF Check report

This file was created 2012-01-31 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 pdb2zdh.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 D

All-atom RMS fit for the two chains : 0.959
CA-only RMS fit for the two chains : 0.605

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

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.

1271 ADP   ( 701-)  A  -
1272 DAL   ( 801-)  A  -
1275 ADP   ( 702-)  B  -
1278 ADP   ( 703-)  C  -
1282 DAL   ( 802-)  D  -
1283 ADP   ( 704-)  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: 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'.

 855 THR   ( 227-)  C      OG1
 855 THR   ( 227-)  C      CG2
 856 LYS   ( 228-)  C      CG
 856 LYS   ( 228-)  C      CD
 856 LYS   ( 228-)  C      CE
 856 LYS   ( 228-)  C      NZ
 858 THR   ( 230-)  C      OG1
 858 THR   ( 230-)  C      CG2

Warning: What type of B-factor?

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

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

Crystal temperature (K) :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.

   2 ARG   (   2-)  A
  26 ARG   (  26-)  A
  73 ARG   (  73-)  A
 121 ARG   ( 121-)  A
 168 ARG   ( 168-)  A
 217 ARG   ( 217-)  A
 264 ARG   ( 264-)  A
 268 ARG   ( 268-)  A
 297 ARG   ( 297-)  A
 345 ARG   (  26-)  B
 361 ARG   (  42-)  B
 392 ARG   (  73-)  B
 403 ARG   (  84-)  B
 484 ARG   ( 165-)  B
 500 ARG   ( 181-)  B
 576 ARG   ( 264-)  B
 633 ARG   (   2-)  C
 673 ARG   (  42-)  C
 812 ARG   ( 181-)  C
 848 ARG   ( 217-)  C
 892 ARG   ( 264-)  C
 949 ARG   (   2-)  D
1084 ARG   ( 137-)  D
1112 ARG   ( 165-)  D
1211 ARG   ( 264-)  D
1215 ARG   ( 268-)  D
1259 ARG   ( 312-)  D

Warning: Tyrosine convention problem

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

 229 TYR   ( 229-)  A
 421 TYR   ( 102-)  B
 501 TYR   ( 182-)  B
 854 TYR   ( 223-)  C
 857 TYR   ( 229-)  C
1170 TYR   ( 223-)  D

Warning: Phenylalanine convention problem

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

  85 PHE   (  85-)  A
  94 PHE   (  94-)  A
 146 PHE   ( 146-)  A
 150 PHE   ( 150-)  A
 289 PHE   ( 289-)  A
 384 PHE   (  65-)  B
 413 PHE   (  94-)  B
 465 PHE   ( 146-)  B
 601 PHE   ( 289-)  B
 716 PHE   (  85-)  C
 725 PHE   (  94-)  C
1025 PHE   (  78-)  D
1041 PHE   (  94-)  D
1093 PHE   ( 146-)  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.

  40 ASP   (  40-)  A
 183 ASP   ( 183-)  A
 224 ASP   ( 224-)  A
 359 ASP   (  40-)  B
 502 ASP   ( 183-)  B
 555 ASP   ( 243-)  B
 671 ASP   (  40-)  C
 871 ASP   ( 243-)  C
 987 ASP   (  40-)  D
1171 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.

  22 GLU   (  22-)  A
  96 GLU   (  96-)  A
 140 GLU   ( 140-)  A
 197 GLU   ( 197-)  A
 235 GLU   ( 235-)  A
 366 GLU   (  47-)  B
 373 GLU   (  54-)  B
 379 GLU   (  60-)  B
 415 GLU   (  96-)  B
 486 GLU   ( 167-)  B
 503 GLU   ( 184-)  B
 587 GLU   ( 275-)  B
 589 GLU   ( 277-)  B
 594 GLU   ( 282-)  B
 627 GLU   ( 315-)  B
 646 GLU   (  15-)  C
 653 GLU   (  22-)  C
 727 GLU   (  96-)  C
 771 GLU   ( 140-)  C
 804 GLU   ( 173-)  C
 828 GLU   ( 197-)  C
 863 GLU   ( 235-)  C
 876 GLU   ( 248-)  C
 905 GLU   ( 277-)  C
 910 GLU   ( 282-)  C
 943 GLU   ( 315-)  C
 969 GLU   (  22-)  D
1007 GLU   (  60-)  D
1043 GLU   (  96-)  D
1144 GLU   ( 197-)  D
1173 GLU   ( 226-)  D
1222 GLU   ( 275-)  D

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: 0.257
RMS-deviation in bond distances: 0.006

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

 |  0.998638  0.000265  0.000008|
 |  0.000265  0.998840 -0.000211|
 |  0.000008 -0.000211  0.998883|
Proposed new scale matrix

 |  0.014524 -0.000004  0.000000|
 | -0.000003  0.009499  0.000002|
 |  0.000000  0.000001  0.005012|
With corresponding cell

    A    =  68.853  B   = 105.274  C    = 199.537
    Alpha=  90.024  Beta=  90.002  Gamma=  89.970

The CRYST1 cell dimensions

    A    =  68.946  B   = 105.394  C    = 199.748
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 61.037
(Under-)estimated Z-score: 5.758

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.

 154 PRO   ( 154-)  A      N    CA   C    99.05   -5.1
 473 PRO   ( 154-)  B      N    CA   C    98.57   -5.3
 785 PRO   ( 154-)  C      N    CA   C    99.00   -5.1
1101 PRO   ( 154-)  D      N    CA   C   100.94   -4.3

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: 0.597
RMS-deviation in bond angles: 1.380

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.

   2 ARG   (   2-)  A
  22 GLU   (  22-)  A
  26 ARG   (  26-)  A
  40 ASP   (  40-)  A
  73 ARG   (  73-)  A
  96 GLU   (  96-)  A
 121 ARG   ( 121-)  A
 140 GLU   ( 140-)  A
 168 ARG   ( 168-)  A
 183 ASP   ( 183-)  A
 197 GLU   ( 197-)  A
 217 ARG   ( 217-)  A
 224 ASP   ( 224-)  A
 235 GLU   ( 235-)  A
 264 ARG   ( 264-)  A
 268 ARG   ( 268-)  A
 297 ARG   ( 297-)  A
 345 ARG   (  26-)  B
 359 ASP   (  40-)  B
 361 ARG   (  42-)  B
 366 GLU   (  47-)  B
 373 GLU   (  54-)  B
 379 GLU   (  60-)  B
 392 ARG   (  73-)  B
 403 ARG   (  84-)  B
And so on for a total of 69 lines.

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

 473 PRO   ( 154-)  B    5.91
 785 PRO   ( 154-)  C    5.71
 154 PRO   ( 154-)  A    5.69
1101 PRO   ( 154-)  D    4.84
 896 ARG   ( 268-)  C    4.26
 268 ARG   ( 268-)  A    4.23
 580 ARG   ( 268-)  B    4.23
 470 PHE   ( 151-)  B    4.12
 151 PHE   ( 151-)  A    4.09
 782 PHE   ( 151-)  C    4.04
1112 ARG   ( 165-)  D    4.03

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.

1104 THR   ( 157-)  D    -2.9
 157 THR   ( 157-)  A    -2.9
 788 THR   ( 157-)  C    -2.6
1237 THR   ( 290-)  D    -2.5
1179 GLY   ( 232-)  D    -2.4
 872 PRO   ( 244-)  C    -2.4
 348 PRO   (  29-)  B    -2.2
 223 TYR   ( 223-)  A    -2.2
1033 GLY   (  86-)  D    -2.1
 514 VAL   ( 195-)  B    -2.1
 387 PRO   (  68-)  B    -2.1
 134 VAL   ( 134-)  A    -2.1
1142 VAL   ( 195-)  D    -2.1
 772 PRO   ( 141-)  C    -2.1
 826 VAL   ( 195-)  C    -2.0
 729 LEU   (  98-)  C    -2.0
1170 TYR   ( 223-)  D    -2.0
 222 PHE   ( 222-)  A    -2.0
 397 PHE   (  78-)  B    -2.0
  78 PHE   (  78-)  A    -2.0
1224 GLU   ( 277-)  D    -2.0
 993 GLY   (  46-)  D    -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.

  56 LYS   (  56-)  A  Poor phi/psi
  65 PHE   (  65-)  A  PRO omega poor
  68 PRO   (  68-)  A  Poor phi/psi
  85 PHE   (  85-)  A  Poor phi/psi
 148 PRO   ( 148-)  A  PRO omega poor
 160 SER   ( 160-)  A  Poor phi/psi
 193 SER   ( 193-)  A  PRO omega poor
 206 VAL   ( 206-)  A  Poor phi/psi
 238 ILE   ( 238-)  A  PRO omega poor
 267 ALA   ( 267-)  A  Poor phi/psi
 375 LYS   (  56-)  B  Poor phi/psi
 384 PHE   (  65-)  B  PRO omega poor
 404 PHE   (  85-)  B  Poor phi/psi
 467 PRO   ( 148-)  B  PRO omega poor
 478 SER   ( 159-)  B  Poor phi/psi
 479 SER   ( 160-)  B  Poor phi/psi
 512 SER   ( 193-)  B  PRO omega poor
 525 VAL   ( 206-)  B  Poor phi/psi
 550 ILE   ( 238-)  B  PRO omega poor
 688 ALA   (  57-)  C  Poor phi/psi
 696 PHE   (  65-)  C  PRO omega poor
 699 PRO   (  68-)  C  Poor phi/psi
 716 PHE   (  85-)  C  Poor phi/psi
 779 PRO   ( 148-)  C  PRO omega poor
 788 THR   ( 157-)  C  Poor phi/psi
 790 SER   ( 159-)  C  Poor phi/psi
 791 SER   ( 160-)  C  Poor phi/psi
 824 SER   ( 193-)  C  PRO omega poor
 837 VAL   ( 206-)  C  Poor phi/psi
 856 LYS   ( 228-)  C  Poor phi/psi
 857 TYR   ( 229-)  C  Poor phi/psi
 866 ILE   ( 238-)  C  PRO omega poor
 993 GLY   (  46-)  D  Poor phi/psi
1003 LYS   (  56-)  D  Poor phi/psi
1012 PHE   (  65-)  D  PRO omega poor
1032 PHE   (  85-)  D  Poor phi/psi
1086 GLY   ( 139-)  D  Poor phi/psi
1095 PRO   ( 148-)  D  PRO omega poor
1140 SER   ( 193-)  D  PRO omega poor
1153 VAL   ( 206-)  D  Poor phi/psi
1179 GLY   ( 232-)  D  Poor phi/psi
1180 ARG   ( 233-)  D  Poor phi/psi
1185 ILE   ( 238-)  D  PRO omega poor
1214 ALA   ( 267-)  D  Poor phi/psi
1237 THR   ( 290-)  D  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.375

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!

   7 ALA   (   7-)  A      0
  10 VAL   (  10-)  A      0
  29 PRO   (  29-)  A      0
  31 PRO   (  31-)  A      0
  45 LEU   (  45-)  A      0
  47 GLU   (  47-)  A      0
  55 ALA   (  55-)  A      0
  56 LYS   (  56-)  A      0
  63 HIS   (  63-)  A      0
  65 PHE   (  65-)  A      0
  67 PRO   (  67-)  A      0
  68 PRO   (  68-)  A      0
  70 SER   (  70-)  A      0
  79 PRO   (  79-)  A      0
  80 LEU   (  80-)  A      0
  82 HIS   (  82-)  A      0
  84 ARG   (  84-)  A      0
  85 PHE   (  85-)  A      0
  87 GLU   (  87-)  A      0
  90 THR   (  90-)  A      0
 103 VAL   ( 103-)  A      0
 105 ALA   ( 105-)  A      0
 114 MET   ( 114-)  A      0
 132 PRO   ( 132-)  A      0
 133 TRP   ( 133-)  A      0
And so on for a total of 446 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 : 1.310

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].

 142 PRO   ( 142-)  A    47.7 half-chair C-delta/C-gamma (54 degrees)
 221 PRO   ( 221-)  A  -115.3 envelop C-gamma (-108 degrees)
 231 PRO   ( 231-)  A  -113.6 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.

 528 GLU   ( 209-)  B      OE2 <->  624 ARG   ( 312-)  B      NH2    0.33    2.37  INTRA
 657 ARG   (  26-)  C      NH1 <->  658 HIS   (  27-)  C      CE1    0.25    2.85  INTRA BF
  27 HIS   (  27-)  A      ND1 <->  306 TYR   ( 306-)  A      CD2    0.25    2.85  INTRA
 292 THR   ( 292-)  A      O   <->  297 ARG   ( 297-)  A      NE     0.24    2.46  INTRA
 403 ARG   (  84-)  B      NH1 <->  404 PHE   (  85-)  B      CE2    0.22    2.88  INTRA
 974 HIS   (  27-)  D      ND1 <-> 1253 TYR   ( 306-)  D      CD2    0.20    2.90  INTRA BF
 165 ARG   ( 165-)  A      NE  <->  167 GLU   ( 167-)  A      OE2    0.19    2.51  INTRA
1173 GLU   ( 226-)  D      CD  <-> 1180 ARG   ( 233-)  D      NH1    0.18    2.92  INTRA BF
1173 GLU   ( 226-)  D      O   <-> 1177 THR   ( 230-)  D      N      0.17    2.53  INTRA BF
1036 GLY   (  89-)  D      CA  <-> 1039 GLN   (  92-)  D      NE2    0.17    2.93  INTRA BL
 557 GLY   ( 245-)  B      N   <-> 1285 HOH   ( 933 )  B      O      0.16    2.54  INTRA
1130 ASP   ( 183-)  D      OD1 <-> 1131 GLU   ( 184-)  D      N      0.15    2.45  INTRA
 578 MET   ( 266-)  B      SD  <->  601 PHE   ( 289-)  B      CE2    0.15    3.25  INTRA
 848 ARG   ( 217-)  C      NH1 <->  863 GLU   ( 235-)  C      OE1    0.15    2.55  INTRA
 264 ARG   ( 264-)  A      NH1 <-> 1284 HOH   ( 954 )  A      O      0.15    2.55  INTRA
 925 ARG   ( 297-)  C      NH1 <-> 1286 HOH   ( 907 )  C      O      0.14    2.56  INTRA
  22 GLU   (  22-)  A      CG  <->   26 ARG   (  26-)  A      NH1    0.14    2.96  INTRA BF
 985 ALA   (  38-)  D      CB  <-> 1008 GLY   (  61-)  D      N      0.14    2.96  INTRA
 796 ARG   ( 165-)  C      NH1 <->  798 GLU   ( 167-)  C      OE1    0.13    2.57  INTRA BF
 768 ARG   ( 137-)  C      NH2 <-> 1286 HOH   ( 822 )  C      O      0.13    2.57  INTRA
1178 PRO   ( 231-)  D      O   <-> 1180 ARG   ( 233-)  D      N      0.13    2.57  INTRA BF
  14 HIS   (  14-)  A      CE1 <->   58 ALA   (  58-)  A      N      0.13    2.97  INTRA BL
 408 GLY   (  89-)  B      CA  <->  411 GLN   (  92-)  B      NE2    0.13    2.97  INTRA BL
 514 VAL   ( 195-)  B      N   <->  850 GLU   ( 219-)  C      OE2    0.13    2.57  INTRA
 720 GLY   (  89-)  C      CA  <->  723 GLN   (  92-)  C      NE2    0.12    2.98  INTRA BL
And so on for a total of 123 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.

 857 TYR   ( 229-)  C      -7.77
 403 ARG   (  84-)  B      -6.83
 715 ARG   (  84-)  C      -6.50
 658 HIS   (  27-)  C      -6.15
 346 HIS   (  27-)  B      -6.10
  27 HIS   (  27-)  A      -6.07
 541 PHE   ( 222-)  B      -6.01
 974 HIS   (  27-)  D      -6.00
1031 ARG   (  84-)  D      -5.83
 704 ARG   (  73-)  C      -5.60
1020 ARG   (  73-)  D      -5.58
  73 ARG   (  73-)  A      -5.57
 392 ARG   (  73-)  B      -5.56
1166 GLU   ( 219-)  D      -5.54
 219 GLU   ( 219-)  A      -5.37
 143 VAL   ( 143-)  A      -5.35
 774 VAL   ( 143-)  C      -5.33
 444 GLN   ( 125-)  B      -5.33
 125 GLN   ( 125-)  A      -5.32
1072 GLN   ( 125-)  D      -5.32
 756 GLN   ( 125-)  C      -5.32
 657 ARG   (  26-)  C      -5.30
 462 VAL   ( 143-)  B      -5.28
  84 ARG   (  84-)  A      -5.27
1090 VAL   ( 143-)  D      -5.27
1180 ARG   ( 233-)  D      -5.02
 233 ARG   ( 233-)  A      -5.01

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.

1167 ALA   ( 220-)  D   -2.84
 745 MET   ( 114-)  C   -2.75
 433 MET   ( 114-)  B   -2.71
 114 MET   ( 114-)  A   -2.59
1061 MET   ( 114-)  D   -2.59

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

1285 HOH   ( 978 )  B      O     54.39  -61.27  -67.25
1287 HOH   ( 949 )  D      O     20.13   -7.82  -33.99

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.

1286 HOH   ( 889 )  C      O

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

  14 HIS   (  14-)  A
  63 HIS   (  63-)  A
 156 ASN   ( 156-)  A
 333 HIS   (  14-)  B
 411 GLN   (  92-)  B
 559 GLN   ( 247-)  B
 645 HIS   (  14-)  C
 670 GLN   (  39-)  C
 723 GLN   (  92-)  C
 974 HIS   (  27-)  D
1039 GLN   (  92-)  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.

  57 ALA   (  57-)  A      N
  81 LEU   (  81-)  A      N
  82 HIS   (  82-)  A      N
 133 TRP   ( 133-)  A      N
 146 PHE   ( 146-)  A      N
 153 LYS   ( 153-)  A      NZ
 160 SER   ( 160-)  A      N
 168 ARG   ( 168-)  A      N
 192 LEU   ( 192-)  A      N
 222 PHE   ( 222-)  A      N
 223 TYR   ( 223-)  A      N
 264 ARG   ( 264-)  A      N
 288 GLY   ( 288-)  A      N
 349 PHE   (  30-)  B      N
 400 LEU   (  81-)  B      N
 407 ASP   (  88-)  B      N
 440 ARG   ( 121-)  B      NE
 465 PHE   ( 146-)  B      N
 479 SER   ( 160-)  B      N
 487 ARG   ( 168-)  B      N
 511 LEU   ( 192-)  B      N
 576 ARG   ( 264-)  B      N
 661 PHE   (  30-)  C      N
 712 LEU   (  81-)  C      N
 719 ASP   (  88-)  C      N
 784 LYS   ( 153-)  C      NZ
 791 SER   ( 160-)  C      N
 799 ARG   ( 168-)  C      N
 823 LEU   ( 192-)  C      N
 849 TYR   ( 218-)  C      N
 861 ARG   ( 233-)  C      NE
 892 ARG   ( 264-)  C      N
 977 PHE   (  30-)  D      N
1028 LEU   (  81-)  D      N
1029 HIS   (  82-)  D      N
1031 ARG   (  84-)  D      NE
1068 ARG   ( 121-)  D      NE
1093 PHE   ( 146-)  D      N
1107 SER   ( 160-)  D      N
1115 ARG   ( 168-)  D      N
1139 LEU   ( 192-)  D      N
1169 PHE   ( 222-)  D      N
1170 TYR   ( 223-)  D      N
1174 THR   ( 227-)  D      OG1
1180 ARG   ( 233-)  D      NH1
1211 ARG   ( 264-)  D      N
1235 GLY   ( 288-)  D      N
1253 TYR   ( 306-)  D      OH
Only metal coordination for  282 GLU  ( 282-) A      OE2
Only metal coordination for  594 GLU  ( 282-) B      OE1

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.

 125 GLN   ( 125-)  A      OE1
 197 GLU   ( 197-)  A      OE2
 960 GLU   (  13-)  D      OE2
1171 ASP   ( 224-)  D      OD1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

1273  MG   ( 811-)  A   -.-  -.-  Part of ionic cluster
1273  MG   ( 811-)  A     0.52   1.04 Is perhaps NA
1274  MG   ( 812-)  A   -.-  -.-  Part of ionic cluster
1274  MG   ( 812-)  A     0.74   1.24 Scores about as good as CA
1277  MG   ( 814-)  B     0.72   1.20 Scores about as good as CA
1279  MG   ( 815-)  C     0.76   1.28 Scores about as good as CA
1280  MG   ( 816-)  C     0.67   1.10 Scores about as good as CA
1281  MG   ( 817-)  D     0.53   1.07 Is perhaps NA

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.

1284 HOH   ( 865 )  A      O  1.10  K  4
1284 HOH   ( 904 )  A      O  0.88  K  4
1285 HOH   ( 851 )  B      O  0.90  K  5 NCS 1/1
1286 HOH   ( 863 )  C      O  1.11  K  5 Ion-B NCS 1/1
1286 HOH   ( 949 )  C      O  0.98  K  4 ION-B
1287 HOH   ( 858 )  D      O  0.87  K  7 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.

  13 GLU   (  13-)  A   H-bonding suggests Gln; Ligand-contact
  54 GLU   (  54-)  A   H-bonding suggests Gln
 703 GLU   (  72-)  C   H-bonding suggests Gln
 814 ASP   ( 183-)  C   H-bonding suggests Asn; but Alt-Rotamer
 960 GLU   (  13-)  D   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
1001 GLU   (  54-)  D   H-bonding suggests Gln
1019 GLU   (  72-)  D   H-bonding suggests Gln; but Alt-Rotamer
1171 ASP   ( 224-)  D   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 :   0.226
  2nd generation packing quality :  -0.619
  Ramachandran plot appearance   :  -0.259
  chi-1/chi-2 rotamer normality  :  -0.375
  Backbone conformation          :   0.771

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.257 (tight)
  Bond angles                    :   0.597 (tight)
  Omega angle restraints         :   0.238 (tight)
  Side chain planarity           :   0.218 (tight)
  Improper dihedral distribution :   0.598
  B-factor distribution          :   0.529
  Inside/Outside distribution    :   0.985

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 : 1.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.7
  2nd generation packing quality :  -0.7
  Ramachandran plot appearance   :   0.1
  chi-1/chi-2 rotamer normality  :   0.2
  Backbone conformation          :   0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.257 (tight)
  Bond angles                    :   0.597 (tight)
  Omega angle restraints         :   0.238 (tight)
  Side chain planarity           :   0.218 (tight)
  Improper dihedral distribution :   0.598
  B-factor distribution          :   0.529
  Inside/Outside distribution    :   0.985
==============

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.