WHAT IF Check report

This file was created 2011-12-17 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 pdb2nzj.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.

 632 GDP   (1001-)  A  -
 635 GDP   (1002-)  B  -
 637 GDP   (1003-)  C  -
 639 GDP   (1004-)  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'.

  26 LYS   ( 103-)  A      CG
  26 LYS   ( 103-)  A      CD
  26 LYS   ( 103-)  A      CE
  26 LYS   ( 103-)  A      NZ
  29 GLN   ( 111-)  A      CG
  29 GLN   ( 111-)  A      CD
  29 GLN   ( 111-)  A      OE1
  29 GLN   ( 111-)  A      NE2
  32 GLU   ( 114-)  A      CG
  32 GLU   ( 114-)  A      CD
  32 GLU   ( 114-)  A      OE1
  32 GLU   ( 114-)  A      OE2
  36 GLU   ( 118-)  A      CG
  36 GLU   ( 118-)  A      CD
  36 GLU   ( 118-)  A      OE1
  36 GLU   ( 118-)  A      OE2
  59 GLU   ( 148-)  A      CD
  59 GLU   ( 148-)  A      OE1
  59 GLU   ( 148-)  A      OE2
  60 SER   ( 149-)  A      OG
  63 GLN   ( 152-)  A      CG
  63 GLN   ( 152-)  A      CD
  63 GLN   ( 152-)  A      OE1
  63 GLN   ( 152-)  A      NE2
  85 GLU   ( 174-)  A      CD
And so on for a total of 246 lines.

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: 12

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.

 110 ARG   ( 203-)  A
 160 ARG   (  82-)  B
 313 ARG   ( 246-)  B
 559 ARG   ( 176-)  D
 563 ARG   ( 180-)  D

Warning: Tyrosine convention problem

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

   4 TYR   (  81-)  A
  35 TYR   ( 117-)  A
  68 TYR   ( 157-)  A
 159 TYR   (  81-)  B
 195 TYR   ( 117-)  B
 229 TYR   ( 157-)  B
 233 TYR   ( 161-)  B
 319 TYR   (  81-)  C
 350 TYR   ( 117-)  C
 384 TYR   ( 157-)  C
 478 TYR   (  81-)  D
 540 TYR   ( 157-)  D

Warning: Phenylalanine convention problem

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

 600 PHE   ( 217-)  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.

  45 ASP   ( 127-)  A
 105 ASP   ( 198-)  A
 348 ASP   ( 115-)  C
 360 ASP   ( 127-)  C
 425 ASP   ( 198-)  C
 504 ASP   ( 115-)  D
 516 ASP   ( 127-)  D
 581 ASP   ( 198-)  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.

 359 GLU   ( 126-)  C
 591 GLU   ( 208-)  D
 592 GLU   ( 209-)  D

Geometric checks

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  0.998486 -0.000046  0.000325|
 | -0.000046  0.997929 -0.000158|
 |  0.000325 -0.000158  0.997574|
Proposed new scale matrix

 |  0.022950  0.000001 -0.000007|
 |  0.000000  0.009797  0.000002|
 | -0.000002  0.000000  0.006055|
With corresponding cell

    A    =  43.573  B   = 102.069  C    = 165.161
    Alpha=  90.010  Beta=  89.963  Gamma=  90.003

The CRYST1 cell dimensions

    A    =  43.640  B   = 102.284  C    = 165.565
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 78.335
(Under-)estimated Z-score: 6.523

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.

 269 CYS   ( 202-)  B      C    CA   CB  102.30   -4.1

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.

  45 ASP   ( 127-)  A
 105 ASP   ( 198-)  A
 110 ARG   ( 203-)  A
 160 ARG   (  82-)  B
 313 ARG   ( 246-)  B
 348 ASP   ( 115-)  C
 359 GLU   ( 126-)  C
 360 ASP   ( 127-)  C
 425 ASP   ( 198-)  C
 504 ASP   ( 115-)  D
 516 ASP   ( 127-)  D
 559 ARG   ( 176-)  D
 563 ARG   ( 180-)  D
 581 ASP   ( 198-)  D
 591 GLU   ( 208-)  D
 592 GLU   ( 209-)  D

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.

 605 ILE   ( 222-)  D    -2.4
 110 ARG   ( 203-)  A    -2.4
 184 ARG   ( 106-)  B    -2.2
 517 THR   ( 128-)  D    -2.2
 449 ILE   ( 222-)  C    -2.2
 443 VAL   ( 216-)  C    -2.1
 351 GLU   ( 118-)  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.

  15 GLY   (  92-)  A  Poor phi/psi
  31 GLY   ( 113-)  A  omega poor
 103 LYS   ( 196-)  A  Poor phi/psi
 106 LEU   ( 199-)  A  Poor phi/psi
 125 ASP   ( 218-)  A  Poor phi/psi
 131 THR   ( 224-)  A  omega poor
 138 ASN   ( 231-)  A  Poor phi/psi
 157 ALA   (  79-)  B  Poor phi/psi
 170 GLY   (  92-)  B  Poor phi/psi
 179 ALA   ( 101-)  B  omega poor
 180 GLY   ( 102-)  B  omega poor
 193 ASP   ( 115-)  B  Poor phi/psi, omega poor
 225 GLY   ( 153-)  B  omega poor
 263 LYS   ( 196-)  B  Poor phi/psi
 266 LEU   ( 199-)  B  Poor phi/psi
 298 ASN   ( 231-)  B  Poor phi/psi
 330 GLY   (  92-)  C  Poor phi/psi
 347 GLU   ( 114-)  C  omega poor
 348 ASP   ( 115-)  C  Poor phi/psi
 379 GLN   ( 152-)  C  omega poor
 423 LYS   ( 196-)  C  Poor phi/psi
 426 LEU   ( 199-)  C  Poor phi/psi
 458 ASN   ( 231-)  C  Poor phi/psi
 489 GLY   (  92-)  D  Poor phi/psi
 498 ALA   ( 101-)  D  omega poor
 501 LEU   ( 112-)  D  omega poor
 579 LYS   ( 196-)  D  Poor phi/psi
 582 LEU   ( 199-)  D  Poor phi/psi
 607 THR   ( 224-)  D  omega poor
 614 ASN   ( 231-)  D  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.384

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

 245 SER   ( 173-)  B    0.36
  84 SER   ( 173-)  A    0.36
 400 SER   ( 173-)  C    0.37

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!

  11 ASP   (  88-)  A      0
  12 PRO   (  89-)  A      0
  14 VAL   (  91-)  A      0
  25 GLY   ( 102-)  A      0
  26 LYS   ( 103-)  A      0
  27 HIS   ( 109-)  A      0
  28 GLU   ( 110-)  A      0
  30 LEU   ( 112-)  A      0
  32 GLU   ( 114-)  A      0
  33 ASP   ( 115-)  A      0
  37 ARG   ( 119-)  A      0
  41 VAL   ( 123-)  A      0
  52 ASP   ( 134-)  A      0
  53 THR   ( 135-)  A      0
  54 TRP   ( 136-)  A      0
  55 SER   ( 144-)  A      0
  56 TRP   ( 145-)  A      0
  92 ARG   ( 181-)  A      0
  93 THR   ( 182-)  A      0
  94 HIS   ( 187-)  A      0
  95 VAL   ( 188-)  A      0
 102 ASN   ( 195-)  A      0
 103 LYS   ( 196-)  A      0
 106 LEU   ( 199-)  A      0
 109 CYS   ( 202-)  A      0
And so on for a total of 215 lines.

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

  12 PRO   (  89-)  A    0.18 LOW
 572 PRO   ( 189-)  D    0.19 LOW

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.

 559 ARG   ( 176-)  D      NH1 <->  596 CYS   ( 213-)  D      O      0.39    2.31  INTRA
 110 ARG   ( 203-)  A      NH2 <->  130 GLU   ( 223-)  A      OE2    0.31    2.39  INTRA
 606 GLU   ( 223-)  D      O   <->  614 ASN   ( 231-)  D      ND2    0.28    2.42  INTRA
 549 ARG   ( 166-)  D      N   <->  587 GLU   ( 204-)  D      OE1    0.22    2.48  INTRA
 194 VAL   ( 116-)  B      CG1 <->  209 VAL   ( 131-)  B      CG1    0.20    3.00  INTRA BL
 200 THR   ( 122-)  B      OG1 <->  205 ASP   ( 127-)  B      OD1    0.16    2.24  INTRA BL
 171 LYS   (  93-)  B      NZ  <->  635 GDP   (1002-)  B      O1B    0.16    2.54  INTRA
 297 HIS   ( 230-)  B      ND1 <->  320 ARG   (  82-)  C      NH1    0.14    2.86  INTRA
 559 ARG   ( 176-)  D      CZ  <->  596 CYS   ( 213-)  D      SG     0.13    3.27  INTRA
 487 GLY   (  90-)  D      O   <->  579 LYS   ( 196-)  D      NZ     0.12    2.58  INTRA
 288 PHE   ( 221-)  B      N   <->  343 GLU   ( 110-)  C      O      0.10    2.60  INTRA
 137 HIS   ( 230-)  A      NE2 <->  520 VAL   ( 131-)  D      CG1    0.09    3.01  INTRA
 549 ARG   ( 166-)  D      NH2 <->  592 GLU   ( 209-)  D      OE1    0.09    2.61  INTRA
 403 ARG   ( 176-)  C      NH1 <->  440 CYS   ( 213-)  C      O      0.08    2.62  INTRA
  40 THR   ( 122-)  A      OG1 <->   45 ASP   ( 127-)  A      OD1    0.07    2.33  INTRA BL
 328 GLY   (  90-)  C      O   <->  423 LYS   ( 196-)  C      NZ     0.07    2.63  INTRA
 506 TYR   ( 117-)  D      O   <->  521 VAL   ( 132-)  D      N      0.07    2.63  INTRA BL
 262 ASN   ( 195-)  B      CG  <->  263 LYS   ( 196-)  B      N      0.07    2.93  INTRA
 328 GLY   (  90-)  C      N   <->  637 GDP   (1003-)  C      O3B    0.06    2.64  INTRA
 262 ASN   ( 195-)  B      ND2 <->  635 GDP   (1002-)  B      N7     0.06    2.94  INTRA
 422 ASN   ( 195-)  C      CG  <->  423 LYS   ( 196-)  C      N      0.06    2.94  INTRA
 546 ILE   ( 163-)  D      O   <->  587 GLU   ( 204-)  D      N      0.06    2.64  INTRA
 350 TYR   ( 117-)  C      O   <->  365 VAL   ( 132-)  C      N      0.05    2.65  INTRA BL
 578 ASN   ( 195-)  D      CG  <->  579 LYS   ( 196-)  D      N      0.04    2.96  INTRA
 102 ASN   ( 195-)  A      CG  <->  103 LYS   ( 196-)  A      N      0.04    2.96  INTRA
 214 TRP   ( 136-)  B      CZ2 <->  247 LEU   ( 175-)  B      CD2    0.04    3.16  INTRA
 378 LEU   ( 151-)  C      O   <->  410 HIS   ( 183-)  C      NE2    0.03    2.67  INTRA
  10 GLY   (  87-)  A      O   <->   16 LYS   (  93-)  A      NZ     0.03    2.67  INTRA BL
 442 VAL   ( 215-)  C      CG1 <->  443 VAL   ( 216-)  C      N      0.02    2.98  INTRA
  55 SER   ( 144-)  A      CB  <->   58 GLN   ( 147-)  A      CD     0.02    3.18  INTRA
 121 ALA   ( 214-)  A      O   <->  125 ASP   ( 218-)  A      N      0.02    2.68  INTRA
 331 LYS   (  93-)  C      N   <->  637 GDP   (1003-)  C      O1B    0.02    2.68  INTRA
  35 TYR   ( 117-)  A      O   <->   50 VAL   ( 132-)  A      N      0.02    2.68  INTRA BL
 491 THR   (  94-)  D      OG1 <->  523 ASP   ( 134-)  D      OD2    0.02    2.38  INTRA BL
 544 TYR   ( 161-)  D      O   <->  578 ASN   ( 195-)  D      N      0.02    2.68  INTRA
 195 TYR   ( 117-)  B      O   <->  210 VAL   ( 132-)  B      N      0.02    2.68  INTRA BL
 269 CYS   ( 202-)  B      O   <->  270 ARG   ( 203-)  B      C      0.01    2.59  INTRA
 490 LYS   (  93-)  D      NZ  <->  639 GDP   (1004-)  D      O1B    0.01    2.69  INTRA BL

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: 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.

 473 ARG   ( 246-)  C   -3.34
 501 LEU   ( 112-)  D   -3.08
 268 ARG   ( 201-)  B   -3.01
 189 GLN   ( 111-)  B   -2.99
 108 ARG   ( 201-)  A   -2.79
 629 ARG   ( 246-)  D   -2.78
 284 PHE   ( 217-)  B   -2.62
 219 GLN   ( 147-)  B   -2.57
 153 ARG   ( 246-)  A   -2.56
 181 LYS   ( 103-)  B   -2.52
 474 ARG   ( 247-)  C   -2.52
 378 LEU   ( 151-)  C   -2.51

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

 152 LEU   ( 245-)  A     -  155 ARG   ( 248-)  A        -1.60
 180 GLY   ( 102-)  B     -  184 ARG   ( 106-)  B        -2.10

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: 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.

 137 HIS   ( 230-)  A
 342 HIS   ( 109-)  C
 457 HIS   ( 230-)  C
 613 HIS   ( 230-)  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.

   2 ALA   (  79-)  A      N
  10 GLY   (  87-)  A      N
  15 GLY   (  92-)  A      N
  16 LYS   (  93-)  A      N
  17 THR   (  94-)  A      N
  29 GLN   ( 111-)  A      N
  62 LEU   ( 151-)  A      N
 102 ASN   ( 195-)  A      ND2
 107 ALA   ( 200-)  A      N
 128 PHE   ( 221-)  A      N
 157 ALA   (  79-)  B      N
 160 ARG   (  82-)  B      NE
 165 GLY   (  87-)  B      N
 170 GLY   (  92-)  B      N
 171 LYS   (  93-)  B      N
 172 THR   (  94-)  B      N
 188 GLU   ( 110-)  B      N
 223 LEU   ( 151-)  B      N
 233 TYR   ( 161-)  B      OH
 248 ARG   ( 176-)  B      NE
 262 ASN   ( 195-)  B      ND2
 320 ARG   (  82-)  C      NH1
 325 GLY   (  87-)  C      N
 326 ASP   (  88-)  C      N
 330 GLY   (  92-)  C      N
 331 LYS   (  93-)  C      N
 332 THR   (  94-)  C      N
 388 TYR   ( 161-)  C      OH
 422 ASN   ( 195-)  C      ND2
 484 GLY   (  87-)  D      N
 489 GLY   (  92-)  D      N
 490 LYS   (  93-)  D      N
 491 THR   (  94-)  D      N
 501 LEU   ( 112-)  D      N
 523 ASP   ( 134-)  D      N
 540 TYR   ( 157-)  D      OH
 559 ARG   ( 176-)  D      NH1
 578 ASN   ( 195-)  D      ND2
 614 ASN   ( 231-)  D      N

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.

 367 ASP   ( 134-)  C      OD2
 566 HIS   ( 183-)  D      ND1

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.

 271 GLU   ( 204-)  B   H-bonding suggests Gln
 581 ASP   ( 198-)  D   H-bonding suggests Asn; Ligand-contact
 587 GLU   ( 204-)  D   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  2nd generation packing quality :  -0.810
  Ramachandran plot appearance   :  -0.760
  chi-1/chi-2 rotamer normality  :  -1.384
  Backbone conformation          :   1.248

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.550 (tight)
  Bond angles                    :   0.677
  Omega angle restraints         :   1.197
  Side chain planarity           :   0.402 (tight)
  Improper dihedral distribution :   0.659
  B-factor distribution          :   0.362
  Inside/Outside distribution    :   1.026

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 : 2.50


Structure Z-scores, positive is better than average:

  2nd generation packing quality :   0.2
  Ramachandran plot appearance   :   0.9
  chi-1/chi-2 rotamer normality  :   0.3
  Backbone conformation          :   1.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.550 (tight)
  Bond angles                    :   0.677
  Omega angle restraints         :   1.197
  Side chain planarity           :   0.402 (tight)
  Improper dihedral distribution :   0.659
  B-factor distribution          :   0.362
  Inside/Outside distribution    :   1.026
==============

WHAT IF
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Bond lengths and angles, DNA/RNA
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DSSP
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Hydrogen bond networks
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      protein structures
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Matthews' Coefficient
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Protein side chain planarity
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Puckering parameters
    D.Cremer and J.A.Pople,
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Quality Control
    G.Vriend and C.Sander,
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      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.