WHAT IF Check report

This file was created 2011-12-21 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 pdb1cj1.ent

Checks that need to be done early-on in validation

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.

1153 C78   ( 155-)  A  -
1154 C78   ( 156-)  B  -
1155 C78   ( 157-)  C  -
1156 C78   ( 158-)  D  -
1157 C78   ( 159-)  E  -
1158 C78   ( 160-)  F  -
1159 C78   ( 161-)  G  -
1160 C78   ( 162-)  H  -
1161 C78   ( 163-)  I  -
1162 C78   ( 164-)  J  -
1163 C78   ( 165-)  K  -
1164 C78   ( 166-)  L  -

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

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

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

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

  13 LYS   (  69-)  A    High
  22 ARG   (  78-)  A    High
 109 LYS   (  69-)  B    High
 118 ARG   (  78-)  B    High
 205 LYS   (  69-)  C    High
 214 ARG   (  78-)  C    High
 301 LYS   (  69-)  D    High
 310 ARG   (  78-)  D    High
 397 LYS   (  69-)  E    High
 406 ARG   (  78-)  E    High
 493 LYS   (  69-)  F    High
 502 ARG   (  78-)  F    High
 589 LYS   (  69-)  G    High
 598 ARG   (  78-)  G    High
 685 LYS   (  69-)  H    High
 694 ARG   (  78-)  H    High
 781 LYS   (  69-)  I    High
 790 ARG   (  78-)  I    High
 877 LYS   (  69-)  J    High
 886 ARG   (  78-)  J    High
 973 LYS   (  69-)  K    High
 982 ARG   (  78-)  K    High
1069 LYS   (  69-)  L    High
1078 ARG   (  78-)  L    High

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

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 14.48

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

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

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.

   1 PRO   (  57-)  A      N    CA    1.54    4.8
   1 PRO   (  57-)  A      CG   CD    1.66    4.7
  17 MET   (  73-)  A      SD   CE    2.06    4.5
  67 VAL   ( 123-)  A      CA   CB    1.45   -4.0
  79 HIS   ( 135-)  A      CA   C     1.44   -4.1
  97 PRO   (  57-)  B      N    CA    1.54    4.8
  97 PRO   (  57-)  B      CG   CD    1.66    4.7
 113 MET   (  73-)  B      SD   CE    2.06    4.5
 175 HIS   ( 135-)  B      CA   C     1.44   -4.0
 193 PRO   (  57-)  C      N    CA    1.54    4.8
 193 PRO   (  57-)  C      CG   CD    1.66    4.7
 209 MET   (  73-)  C      SD   CE    2.06    4.5
 271 HIS   ( 135-)  C      CA   C     1.44   -4.1
 289 PRO   (  57-)  D      N    CA    1.54    4.8
 289 PRO   (  57-)  D      CG   CD    1.66    4.6
 305 MET   (  73-)  D      SD   CE    2.06    4.5
 367 HIS   ( 135-)  D      CA   C     1.44   -4.1
 385 PRO   (  57-)  E      N    CA    1.54    4.8
 385 PRO   (  57-)  E      CG   CD    1.66    4.7
 401 MET   (  73-)  E      SD   CE    2.06    4.5
 451 VAL   ( 123-)  E      CA   CB    1.45   -4.0
 463 HIS   ( 135-)  E      CA   C     1.44   -4.1
 481 PRO   (  57-)  F      N    CA    1.54    4.8
 481 PRO   (  57-)  F      CG   CD    1.66    4.7
 497 MET   (  73-)  F      SD   CE    2.06    4.5
And so on for a total of 54 lines.

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

 |  1.007916  0.000556  0.000533|
 |  0.000556  1.007115 -0.000142|
 |  0.000533 -0.000142  1.007027|
Proposed new scale matrix

 |  0.013444 -0.000007 -0.000007|
 | -0.000006  0.010642  0.000002|
 | -0.000002  0.000000  0.004265|
With corresponding cell

    A    =  74.385  B   =  93.965  C    = 234.465
    Alpha=  90.009  Beta=  89.939  Gamma=  89.937

The CRYST1 cell dimensions

    A    =  73.800  B   =  93.300  C    = 232.800
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 2186.267
(Under-)estimated Z-score: 34.460

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.

   1 PRO   (  57-)  A      N    CA   CB  112.15    8.3
   1 PRO   (  57-)  A      CD   N    CA  103.49   -6.1
  17 MET   (  73-)  A      C    CA   CB  102.42   -4.0
  17 MET   (  73-)  A      CB   CG   SD   98.05   -4.9
  43 VAL   (  99-)  A      C    CA   CB  100.09   -5.3
  66 VAL   ( 122-)  A     -C    N    CA  112.65   -5.0
  70 ASN   ( 126-)  A      N    CA   CB  117.78    4.3
  80 ARG   ( 136-)  A     -C    N    CA  113.40   -4.6
  80 ARG   ( 136-)  A      CB   CG   CD  100.50   -6.8
  84 VAL   ( 140-)  A      N    CA   CB  103.41   -4.2
  95 ILE   ( 151-)  A      N    CA   CB  102.99   -4.4
  97 PRO   (  57-)  B      N    CA   CB  112.17    8.3
  97 PRO   (  57-)  B      CD   N    CA  103.48   -6.1
 113 MET   (  73-)  B      C    CA   CB  102.40   -4.1
 113 MET   (  73-)  B      CB   CG   SD   98.03   -4.9
 139 VAL   (  99-)  B      C    CA   CB  100.06   -5.3
 162 VAL   ( 122-)  B     -C    N    CA  112.68   -5.0
 166 ASN   ( 126-)  B      N    CA   CB  117.80    4.3
 176 ARG   ( 136-)  B     -C    N    CA  113.40   -4.6
 176 ARG   ( 136-)  B      CB   CG   CD  100.50   -6.8
 180 VAL   ( 140-)  B      N    CA   CB  103.42   -4.2
 191 ILE   ( 151-)  B      N    CA   CB  103.00   -4.4
 193 PRO   (  57-)  C      N    CA   CB  112.13    8.3
 193 PRO   (  57-)  C      CD   N    CA  103.53   -6.0
 209 MET   (  73-)  C      C    CA   CB  102.44   -4.0
And so on for a total of 132 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.

 961 PRO   (  57-)  K    4.14
 385 PRO   (  57-)  E    4.13
 865 PRO   (  57-)  J    4.13
 673 PRO   (  57-)  H    4.12
 481 PRO   (  57-)  F    4.12
 577 PRO   (  57-)  G    4.12
   1 PRO   (  57-)  A    4.12
 769 PRO   (  57-)  I    4.12
 289 PRO   (  57-)  D    4.12
  97 PRO   (  57-)  B    4.12
1057 PRO   (  57-)  L    4.11
 193 PRO   (  57-)  C    4.10

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.586

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.

1084 LEU   (  84-)  L    -2.4
 124 LEU   (  84-)  B    -2.4
 988 LEU   (  84-)  K    -2.4
 412 LEU   (  84-)  E    -2.4
  28 LEU   (  84-)  A    -2.4
 316 LEU   (  84-)  D    -2.4
 604 LEU   (  84-)  G    -2.4
 220 LEU   (  84-)  C    -2.4
 700 LEU   (  84-)  H    -2.4
 796 LEU   (  84-)  I    -2.4
 508 LEU   (  84-)  F    -2.4
 892 LEU   (  84-)  J    -2.4
 201 ILE   (  65-)  C    -2.2
 969 ILE   (  65-)  K    -2.2
 873 ILE   (  65-)  J    -2.2
 105 ILE   (  65-)  B    -2.2
 681 ILE   (  65-)  H    -2.2
 777 ILE   (  65-)  I    -2.2
1065 ILE   (  65-)  L    -2.2
 585 ILE   (  65-)  G    -2.2
 297 ILE   (  65-)  D    -2.2
 489 ILE   (  65-)  F    -2.2
 393 ILE   (  65-)  E    -2.2
   9 ILE   (  65-)  A    -2.2
 372 VAL   ( 140-)  D    -2.2
And so on for a total of 60 lines.

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.

  71 SER   ( 127-)  A  Poor phi/psi
 167 SER   ( 127-)  B  Poor phi/psi
 263 SER   ( 127-)  C  Poor phi/psi
 359 SER   ( 127-)  D  Poor phi/psi
 455 SER   ( 127-)  E  Poor phi/psi
 551 SER   ( 127-)  F  Poor phi/psi
 647 SER   ( 127-)  G  Poor phi/psi
 743 SER   ( 127-)  H  Poor phi/psi
 839 SER   ( 127-)  I  Poor phi/psi
 935 SER   ( 127-)  J  Poor phi/psi
1031 SER   ( 127-)  K  Poor phi/psi
1127 SER   ( 127-)  L  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -4.171

Error: chi-1/chi-2 angle correlation Z-score very low

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

chi-1/chi-2 correlation Z-score : -4.171

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!

   4 TRP   (  60-)  A      0
   5 PHE   (  61-)  A      0
   8 LYS   (  64-)  A      0
  24 ASP   (  80-)  A      0
  26 ALA   (  82-)  A      0
  27 PHE   (  83-)  A      0
  35 ALA   (  91-)  A      0
  36 PRO   (  92-)  A      0
  45 PHE   ( 101-)  A      0
  47 ASN   ( 103-)  A      0
  63 PHE   ( 119-)  A      0
  64 LEU   ( 120-)  A      0
  65 TRP   ( 121-)  A      0
  66 VAL   ( 122-)  A      0
  67 VAL   ( 123-)  A      0
  70 ASN   ( 126-)  A      0
  79 HIS   ( 135-)  A      0
  81 SER   ( 137-)  A      0
  84 VAL   ( 140-)  A      0
  87 ASN   ( 143-)  A      0
  88 GLN   ( 144-)  A      0
  95 ILE   ( 151-)  A      0
  96 GLU   ( 152-)  A      0
  97 PRO   (  57-)  B      0
  98 HIS   (  58-)  B      0
And so on for a total of 464 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 : 2.386

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]

   3 PRO   (  59-)  A    0.46 HIGH
  10 PRO   (  66-)  A    0.45 HIGH
  36 PRO   (  92-)  A    0.52 HIGH
  99 PRO   (  59-)  B    0.46 HIGH
 106 PRO   (  66-)  B    0.45 HIGH
 132 PRO   (  92-)  B    0.52 HIGH
 195 PRO   (  59-)  C    0.46 HIGH
 202 PRO   (  66-)  C    0.45 HIGH
 228 PRO   (  92-)  C    0.52 HIGH
 291 PRO   (  59-)  D    0.46 HIGH
 298 PRO   (  66-)  D    0.45 HIGH
 324 PRO   (  92-)  D    0.52 HIGH
 387 PRO   (  59-)  E    0.46 HIGH
 394 PRO   (  66-)  E    0.45 HIGH
 420 PRO   (  92-)  E    0.52 HIGH
 483 PRO   (  59-)  F    0.46 HIGH
 490 PRO   (  66-)  F    0.45 HIGH
 516 PRO   (  92-)  F    0.52 HIGH
 579 PRO   (  59-)  G    0.46 HIGH
 586 PRO   (  66-)  G    0.45 HIGH
 612 PRO   (  92-)  G    0.52 HIGH
 675 PRO   (  59-)  H    0.46 HIGH
 682 PRO   (  66-)  H    0.45 HIGH
 708 PRO   (  92-)  H    0.52 HIGH
 771 PRO   (  59-)  I    0.46 HIGH
 778 PRO   (  66-)  I    0.45 HIGH
 804 PRO   (  92-)  I    0.52 HIGH
 867 PRO   (  59-)  J    0.46 HIGH
 874 PRO   (  66-)  J    0.45 HIGH
 900 PRO   (  92-)  J    0.52 HIGH
 963 PRO   (  59-)  K    0.46 HIGH
 970 PRO   (  66-)  K    0.45 HIGH
 996 PRO   (  92-)  K    0.52 HIGH
1059 PRO   (  59-)  L    0.46 HIGH
1066 PRO   (  66-)  L    0.45 HIGH
1092 PRO   (  92-)  L    0.52 HIGH

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.

  56 ARG   ( 112-)  A      NH2 <->  152 ARG   ( 112-)  B      NH2    0.37    2.48  INTRA BF
 536 ARG   ( 112-)  F      NH1 <->  542 TYR   ( 118-)  F      CE2    0.31    2.79  INTRA BF
 248 ARG   ( 112-)  C      NH1 <->  254 TYR   ( 118-)  C      CE2    0.31    2.79  INTRA BF
1112 ARG   ( 112-)  L      NH1 <-> 1118 TYR   ( 118-)  L      CE2    0.31    2.79  INTRA BF
1016 ARG   ( 112-)  K      NH1 <-> 1022 TYR   ( 118-)  K      CE2    0.31    2.79  INTRA BF
 632 ARG   ( 112-)  G      NH1 <->  638 TYR   ( 118-)  G      CE2    0.31    2.79  INTRA BF
 440 ARG   ( 112-)  E      NH1 <->  446 TYR   ( 118-)  E      CE2    0.31    2.79  INTRA BF
  56 ARG   ( 112-)  A      NH1 <->   62 TYR   ( 118-)  A      CE2    0.31    2.79  INTRA BF
 728 ARG   ( 112-)  H      NH1 <->  734 TYR   ( 118-)  H      CE2    0.31    2.79  INTRA BF
 824 ARG   ( 112-)  I      NH1 <->  830 TYR   ( 118-)  I      CE2    0.31    2.79  INTRA BF
 152 ARG   ( 112-)  B      NH1 <->  158 TYR   ( 118-)  B      CE2    0.31    2.79  INTRA BF
 344 ARG   ( 112-)  D      NH1 <->  350 TYR   ( 118-)  D      CE2    0.31    2.79  INTRA BF
 920 ARG   ( 112-)  J      NH1 <->  926 TYR   ( 118-)  J      CE2    0.31    2.79  INTRA BF
 386 HIS   (  58-)  E      CD2 <->  487 GLY   (  63-)  F      CA     0.29    2.91  INTRA BL
 961 PRO   (  57-)  K      CB  <-> 1062 PHE   (  62-)  L      CZ     0.24    2.96  INTRA BL
 966 PHE   (  62-)  K      CZ  <-> 1057 PRO   (  57-)  L      CB     0.23    2.97  INTRA BL
 632 ARG   ( 112-)  G      NH2 <->  728 ARG   ( 112-)  H      NH2    0.21    2.64  INTRA BF
 632 ARG   ( 112-)  G      NH1 <->  638 TYR   ( 118-)  G      CZ     0.20    2.90  INTRA BF
 536 ARG   ( 112-)  F      NH1 <->  542 TYR   ( 118-)  F      CZ     0.20    2.90  INTRA BF
 248 ARG   ( 112-)  C      NH1 <->  254 TYR   ( 118-)  C      CZ     0.20    2.90  INTRA BF
 920 ARG   ( 112-)  J      NH1 <->  926 TYR   ( 118-)  J      CZ     0.20    2.90  INTRA BF
 152 ARG   ( 112-)  B      NH1 <->  158 TYR   ( 118-)  B      CZ     0.20    2.90  INTRA BF
1016 ARG   ( 112-)  K      NH1 <-> 1022 TYR   ( 118-)  K      CZ     0.20    2.90  INTRA BF
  56 ARG   ( 112-)  A      NH1 <->   62 TYR   ( 118-)  A      CZ     0.20    2.90  INTRA BF
1112 ARG   ( 112-)  L      NH1 <-> 1118 TYR   ( 118-)  L      CZ     0.20    2.90  INTRA BF
And so on for a total of 358 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

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.

 118 ARG   (  78-)  B      -6.28
 214 ARG   (  78-)  C      -6.27
 886 ARG   (  78-)  J      -6.27
 310 ARG   (  78-)  D      -6.23
 694 ARG   (  78-)  H      -6.23
1078 ARG   (  78-)  L      -6.23
 982 ARG   (  78-)  K      -6.23
  22 ARG   (  78-)  A      -6.23
 502 ARG   (  78-)  F      -6.23
 790 ARG   (  78-)  I      -6.23
 598 ARG   (  78-)  G      -6.23
 406 ARG   (  78-)  E      -6.23
 662 ARG   ( 142-)  G      -6.12
 950 ARG   ( 142-)  J      -6.12
1142 ARG   ( 142-)  L      -6.12
 278 ARG   ( 142-)  C      -6.12
  86 ARG   ( 142-)  A      -6.12
 182 ARG   ( 142-)  B      -6.12
1046 ARG   ( 142-)  K      -6.12
 854 ARG   ( 142-)  I      -6.11
 758 ARG   ( 142-)  H      -6.11
 566 ARG   ( 142-)  F      -6.11
 470 ARG   ( 142-)  E      -6.11
 374 ARG   ( 142-)  D      -6.11

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

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: E

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: F

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: G

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: H

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: I

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: J

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: K

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: L

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.

1102 GLY   ( 102-)  L   -2.73

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

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

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.

1165 HOH   (   3 )  A      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.

  79 HIS   ( 135-)  A
  87 ASN   ( 143-)  A
 175 HIS   ( 135-)  B
 271 HIS   ( 135-)  C
 367 HIS   ( 135-)  D
 463 HIS   ( 135-)  E
 471 ASN   ( 143-)  E
 559 HIS   ( 135-)  F
 655 HIS   ( 135-)  G
 751 HIS   ( 135-)  H
 847 HIS   ( 135-)  I
 943 HIS   ( 135-)  J
1039 HIS   ( 135-)  K
1135 HIS   ( 135-)  L

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.

   4 TRP   (  60-)  A      N
   7 GLY   (  63-)  A      N
  11 ARG   (  67-)  A      NE
  11 ARG   (  67-)  A      NH2
  22 ARG   (  78-)  A      N
  23 HIS   (  79-)  A      N
  30 ARG   (  86-)  A      NH2
  32 SER   (  88-)  A      OG
  34 SER   (  90-)  A      N
  40 SER   (  96-)  A      OG
  53 LYS   ( 109-)  A      N
  53 LYS   ( 109-)  A      NZ
  70 ASN   ( 126-)  A      N
  71 SER   ( 127-)  A      N
  82 THR   ( 138-)  A      N
  86 ARG   ( 142-)  A      NE
  95 ILE   ( 151-)  A      N
 100 TRP   (  60-)  B      N
 103 GLY   (  63-)  B      N
 107 ARG   (  67-)  B      NE
 107 ARG   (  67-)  B      NH2
 118 ARG   (  78-)  B      N
 119 HIS   (  79-)  B      N
 126 ARG   (  86-)  B      NH2
 128 SER   (  88-)  B      OG
And so on for a total of 198 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.

 624 ASP   ( 104-)  G      OD1

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.

  48 ASP   ( 104-)  A   H-bonding suggests Asn; but Alt-Rotamer
 144 ASP   ( 104-)  B   H-bonding suggests Asn; but Alt-Rotamer
 240 ASP   ( 104-)  C   H-bonding suggests Asn; but Alt-Rotamer
 336 ASP   ( 104-)  D   H-bonding suggests Asn; but Alt-Rotamer
 432 ASP   ( 104-)  E   H-bonding suggests Asn; but Alt-Rotamer
 528 ASP   ( 104-)  F   H-bonding suggests Asn; but Alt-Rotamer
 624 ASP   ( 104-)  G   H-bonding suggests Asn; but Alt-Rotamer
 720 ASP   ( 104-)  H   H-bonding suggests Asn; but Alt-Rotamer
 816 ASP   ( 104-)  I   H-bonding suggests Asn; but Alt-Rotamer
 912 ASP   ( 104-)  J   H-bonding suggests Asn; but Alt-Rotamer
1008 ASP   ( 104-)  K   H-bonding suggests Asn; but Alt-Rotamer
1104 ASP   ( 104-)  L   H-bonding suggests Asn; but Alt-Rotamer

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 :  -0.610
  2nd generation packing quality :  -0.262
  Ramachandran plot appearance   :  -1.829
  chi-1/chi-2 rotamer normality  :  -4.171 (bad)
  Backbone conformation          :   0.669

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.189
  Bond angles                    :   1.317
  Omega angle restraints         :   0.434 (tight)
  Side chain planarity           :   0.987
  Improper dihedral distribution :   1.816 (loose)
  Inside/Outside distribution    :   0.990

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 3.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.4
  2nd generation packing quality :   1.3
  Ramachandran plot appearance   :   0.7
  chi-1/chi-2 rotamer normality  :  -1.8
  Backbone conformation          :   1.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.189
  Bond angles                    :   1.317
  Omega angle restraints         :   0.434 (tight)
  Side chain planarity           :   0.987
  Improper dihedral distribution :   1.816 (loose)
  Inside/Outside distribution    :   0.990
==============

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.