WHAT IF Check report

This file was created 2011-12-28 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 pdb1fsr.ent

Checks that need to be done early-on in validation

Warning: Unconventional cell on CRYST1

The derived `conventional cell' is different from the cell given on the CRYST1 card.

The CRYST1 cell dimensions

    A    =  42.300  B   =  43.800  C    =  67.600
    Alpha=  86.700  Beta=  90.000  Gamma=  75.600

Dimensions of a reduced cell

    A    =  42.300  B   =  43.800  C    =  67.600
    Alpha=  93.300  Beta=  90.000  Gamma= 104.400

Dimensions of the conventional cell

    A    =  42.300  B   =  43.800  C    =  67.600
    Alpha=  93.300  Beta=  90.000  Gamma= 104.400

Transformation to conventional cell

 | -1.000000  0.000000  0.000000|
 |  0.000000  1.000000  0.000000|
 |  0.000000  0.000000 -1.000000|

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. 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) :130.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Warning: Tyrosine convention problem

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

 112 TYR   ( 114-)  A
 370 TYR   ( 114-)  B

Warning: Phenylalanine convention problem

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

  64 PHE   (  66-)  A
 173 PHE   ( 176-)  A
 223 PHE   ( 226-)  A
 257 PHE   ( 260-)  A
 322 PHE   (  66-)  B
 431 PHE   ( 176-)  B
 481 PHE   ( 226-)  B
 515 PHE   ( 260-)  B

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

  32 ASP   (  34-)  A
  39 ASP   (  41-)  A
  50 ASP   (  52-)  A
  83 ASP   (  85-)  A
 162 ASP   ( 165-)  A
 172 ASP   ( 175-)  A
 290 ASP   (  34-)  B
 297 ASP   (  41-)  B
 308 ASP   (  52-)  B
 341 ASP   (  85-)  B
 420 ASP   ( 165-)  B
 430 ASP   ( 175-)  B

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

 184 GLU   ( 187-)  A
 233 GLU   ( 236-)  A
 235 GLU   ( 238-)  A
 236 GLU   ( 239-)  A
 442 GLU   ( 187-)  B
 491 GLU   ( 236-)  B
 493 GLU   ( 238-)  B
 494 GLU   ( 239-)  B

Geometric checks

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.

  57 ILE   (  59-)  A      N    CA   C    99.82   -4.1
 205 THR   ( 208-)  A      N    CA   C    99.61   -4.1
 315 ILE   (  59-)  B      N    CA   C    99.81   -4.1
 463 THR   ( 208-)  B      N    CA   C    99.64   -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.

  32 ASP   (  34-)  A
  39 ASP   (  41-)  A
  50 ASP   (  52-)  A
  83 ASP   (  85-)  A
 162 ASP   ( 165-)  A
 172 ASP   ( 175-)  A
 184 GLU   ( 187-)  A
 233 GLU   ( 236-)  A
 235 GLU   ( 238-)  A
 236 GLU   ( 239-)  A
 290 ASP   (  34-)  B
 297 ASP   (  41-)  B
 308 ASP   (  52-)  B
 341 ASP   (  85-)  B
 420 ASP   ( 165-)  B
 430 ASP   ( 175-)  B
 442 GLU   ( 187-)  B
 491 GLU   ( 236-)  B
 493 GLU   ( 238-)  B
 494 GLU   ( 239-)  B

Error: Tau angle problems

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

 462 VAL   ( 207-)  B    5.33
 204 VAL   ( 207-)  A    5.32
 249 LYS   ( 252-)  A    4.24
 507 LYS   ( 252-)  B    4.22
 205 THR   ( 208-)  A    4.15
 463 THR   ( 208-)  B    4.14
 316 LEU   (  60-)  B    4.09
  58 LEU   (  60-)  A    4.09

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.

 316 LEU   (  60-)  B    -2.6
  58 LEU   (  60-)  A    -2.6
 404 LYS   ( 149-)  B    -2.4
 146 LYS   ( 149-)  A    -2.4
 283 ARG   (  27-)  B    -2.4
  25 ARG   (  27-)  A    -2.4
 280 LYS   (  24-)  B    -2.4
  22 LYS   (  24-)  A    -2.4
  90 GLN   (  92-)  A    -2.3
 348 GLN   (  92-)  B    -2.3
 483 LYS   ( 228-)  B    -2.3
 225 LYS   ( 228-)  A    -2.3
 196 THR   ( 199-)  A    -2.2
 454 THR   ( 199-)  B    -2.2
 269 PRO   (  13-)  B    -2.2
  11 PRO   (  13-)  A    -2.2
  28 PRO   (  30-)  A    -2.2
 512 LYS   ( 257-)  B    -2.2
 254 LYS   ( 257-)  A    -2.2
 330 GLN   (  74-)  B    -2.1
  72 GLN   (  74-)  A    -2.1
 286 PRO   (  30-)  B    -2.1
 278 ILE   (  22-)  B    -2.1
  20 ILE   (  22-)  A    -2.1
 174 THR   ( 177-)  A    -2.1
 432 THR   ( 177-)  B    -2.1
 406 GLY   ( 151-)  B    -2.1
 148 GLY   ( 151-)  A    -2.1
  67 GLU   (  69-)  A    -2.0
 325 GLU   (  69-)  B    -2.0
 154 LEU   ( 157-)  A    -2.0
 412 LEU   ( 157-)  B    -2.0
 315 ILE   (  59-)  B    -2.0
  57 ILE   (  59-)  A    -2.0
 431 PHE   ( 176-)  B    -2.0
 173 PHE   ( 176-)  A    -2.0
 507 LYS   ( 252-)  B    -2.0
 249 LYS   ( 252-)  A    -2.0
 414 LYS   ( 159-)  B    -2.0
 156 LYS   ( 159-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

  27 SER   (  29-)  A  PRO omega poor
  50 ASP   (  52-)  A  Poor phi/psi
  61 GLY   (  63-)  A  Poor phi/psi
 108 ASP   ( 110-)  A  Poor phi/psi
 109 LYS   ( 111-)  A  Poor phi/psi
 198 PRO   ( 201-)  A  PRO omega poor
 200 LEU   ( 203-)  A  Poor phi/psi
 240 ASP   ( 243-)  A  Poor phi/psi
 249 LYS   ( 252-)  A  Poor phi/psi
 285 SER   (  29-)  B  PRO omega poor
 308 ASP   (  52-)  B  Poor phi/psi
 319 GLY   (  63-)  B  Poor phi/psi
 366 ASP   ( 110-)  B  Poor phi/psi
 367 LYS   ( 111-)  B  Poor phi/psi
 456 PRO   ( 201-)  B  PRO omega poor
 458 LEU   ( 203-)  B  Poor phi/psi
 498 ASP   ( 243-)  B  Poor phi/psi
 507 LYS   ( 252-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.782

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.782

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!

   3 TRP   (   5-)  A      0
   5 TYR   (   7-)  A      0
   8 HIS   (  10-)  A      0
  17 ASP   (  19-)  A      0
  18 PHE   (  20-)  A      0
  20 ILE   (  22-)  A      0
  22 LYS   (  24-)  A      0
  25 ARG   (  27-)  A      0
  26 GLN   (  28-)  A      0
  27 SER   (  29-)  A      0
  35 THR   (  37-)  A      0
  36 ALA   (  38-)  A      0
  50 ASP   (  52-)  A      0
  51 GLN   (  53-)  A      0
  53 THR   (  55-)  A      0
  54 SER   (  56-)  A      0
  57 ILE   (  59-)  A      0
  60 ASN   (  62-)  A      0
  62 HIS   (  64-)  A      0
  63 ALA   (  65-)  A      0
  64 PHE   (  66-)  A      0
  70 ASP   (  72-)  A      0
  71 SER   (  73-)  A      0
  73 ASP   (  75-)  A      0
  74 LYS   (  76-)  A      0
And so on for a total of 256 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 : 1.296

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 490 GLY   ( 235-)  B   1.88   80
 232 GLY   ( 235-)  A   1.88   80
   4 GLY   (   6-)  A   1.56   12
 262 GLY   (   6-)  B   1.56   12

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]

 192 PRO   ( 195-)  A    0.19 LOW
 244 PRO   ( 247-)  A    0.14 LOW
 450 PRO   ( 195-)  B    0.19 LOW
 502 PRO   ( 247-)  B    0.14 LOW

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].

  11 PRO   (  13-)  A   105.5 envelop C-beta (108 degrees)
 198 PRO   ( 201-)  A   100.3 envelop C-beta (108 degrees)
 269 PRO   (  13-)  B   105.5 envelop C-beta (108 degrees)
 456 PRO   ( 201-)  B   100.2 envelop C-beta (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.

  13 HIS   (  15-)  A      ND1 <->   16 LYS   (  18-)  A      NZ     0.48    2.52  INTRA BL
 271 HIS   (  15-)  B      ND1 <->  274 LYS   (  18-)  B      NZ     0.48    2.52  INTRA BL
 352 HIS   (  96-)  B      NE2 <->  375 HIS   ( 119-)  B      ND1    0.22    2.78  INTRA BL
  94 HIS   (  96-)  A      NE2 <->  117 HIS   ( 119-)  A      ND1    0.22    2.78  INTRA BL
 327 ASP   (  71-)  B      OD2 <->  332 LYS   (  76-)  B      NZ     0.19    2.51  INTRA
  69 ASP   (  71-)  A      OD2 <->   74 LYS   (  76-)  A      NZ     0.19    2.51  INTRA
 348 GLN   (  92-)  B      OE1 <->  350 HIS   (  94-)  B      ND1    0.16    2.54  INTRA
 363 HIS   ( 107-)  B      NE2 <->  449 TYR   ( 194-)  B      OH     0.16    2.54  INTRA BL
  90 GLN   (  92-)  A      OE1 <->   92 HIS   (  94-)  A      ND1    0.16    2.54  INTRA
 105 HIS   ( 107-)  A      NE2 <->  191 TYR   ( 194-)  A      OH     0.16    2.54  INTRA BL
 286 PRO   (  30-)  B      O   <->  504 GLN   ( 249-)  B      N      0.15    2.55  INTRA BL
  28 PRO   (  30-)  A      O   <->  246 GLN   ( 249-)  A      N      0.15    2.55  INTRA BL
 451 GLY   ( 196-)  B      N   <->  462 VAL   ( 207-)  B      O      0.13    2.57  INTRA BL
 193 GLY   ( 196-)  A      N   <->  204 VAL   ( 207-)  A      O      0.13    2.57  INTRA BL
 120 HIS   ( 122-)  A      ND1 <->  139 ALA   ( 142-)  A      O      0.11    2.59  INTRA BL
 378 HIS   ( 122-)  B      ND1 <->  397 ALA   ( 142-)  B      O      0.11    2.59  INTRA BL
 104 GLU   ( 106-)  A      N   <->  115 GLU   ( 117-)  A      OE1    0.11    2.59  INTRA BL
 362 GLU   ( 106-)  B      N   <->  373 GLU   ( 117-)  B      OE1    0.11    2.59  INTRA BL
  53 THR   (  55-)  A      CG2 <->   74 LYS   (  76-)  A      NZ     0.11    2.99  INTRA
 311 THR   (  55-)  B      CG2 <->  332 LYS   (  76-)  B      NZ     0.11    2.99  INTRA
 458 LEU   ( 203-)  B      CD2 <->  501 ARG   ( 246-)  B      NH1    0.10    3.00  INTRA BL
 200 LEU   ( 203-)  A      CD2 <->  243 ARG   ( 246-)  A      NH1    0.10    3.00  INTRA BL
  54 SER   (  56-)  A      OG  <->  173 PHE   ( 176-)  A      O      0.09    2.31  INTRA
 312 SER   (  56-)  B      OG  <->  431 PHE   ( 176-)  B      O      0.09    2.31  INTRA
 220 VAL   ( 223-)  A      O   <->  223 PHE   ( 226-)  A      N      0.09    2.61  INTRA
And so on for a total of 86 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

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.

   8 HIS   (  10-)  A      -6.20
 266 HIS   (  10-)  B      -6.20
   2 HIS   (   4-)  A      -5.67
 260 HIS   (   4-)  B      -5.67
  34 HIS   (  36-)  A      -5.41
 292 HIS   (  36-)  B      -5.40
 391 GLN   ( 136-)  B      -5.02
 133 GLN   ( 136-)  A      -5.02

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

Error: 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.

 521 HOH   ( 323 )  A      O
 522 HOH   ( 375 )  B      O
Metal-coordinating Histidine residue  92 fixed to   1
Metal-coordinating Histidine residue  94 fixed to   1
Metal-coordinating Histidine residue 117 fixed to   1
Metal-coordinating Histidine residue 350 fixed to   1
Metal-coordinating Histidine residue 352 fixed to   1
Metal-coordinating Histidine residue 375 fixed to   1

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.

  15 HIS   (  17-)  A
 134 GLN   ( 137-)  A
 155 GLN   ( 158-)  A
 250 ASN   ( 253-)  A
 273 HIS   (  17-)  B
 413 GLN   ( 158-)  B
 508 ASN   ( 253-)  B

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

   5 TYR   (   7-)  A      OH
  15 HIS   (  17-)  A      N
  29 VAL   (  31-)  A      N
  62 HIS   (  64-)  A      NE2
  65 ASN   (  67-)  A      ND2
  98 LEU   ( 100-)  A      N
 102 GLY   ( 104-)  A      N
 133 GLN   ( 136-)  A      N
 144 PHE   ( 147-)  A      N
 156 LYS   ( 159-)  A      NZ
 175 ASN   ( 178-)  A      N
 181 LEU   ( 184-)  A      N
 188 TYR   ( 191-)  A      OH
 197 THR   ( 200-)  A      N
 201 LEU   ( 204-)  A      N
 211 GLU   ( 214-)  A      N
 224 ARG   ( 227-)  A      NH2
 225 LYS   ( 228-)  A      N
 227 ASN   ( 230-)  A      ND2
 230 GLY   ( 233-)  A      N
 242 TRP   ( 245-)  A      N
 257 PHE   ( 260-)  A      N
 259 HIS   (   3-)  B      ND1
 263 TYR   (   7-)  B      OH
 287 VAL   (  31-)  B      N
 320 HIS   (  64-)  B      NE2
 356 LEU   ( 100-)  B      N
 360 GLY   ( 104-)  B      N
 391 GLN   ( 136-)  B      N
 402 PHE   ( 147-)  B      N
 414 LYS   ( 159-)  B      NZ
 433 ASN   ( 178-)  B      N
 439 LEU   ( 184-)  B      N
 446 TYR   ( 191-)  B      OH
 455 THR   ( 200-)  B      N
 459 LEU   ( 204-)  B      N
 469 GLU   ( 214-)  B      N
 482 ARG   ( 227-)  B      NH2
 483 LYS   ( 228-)  B      N
 485 ASN   ( 230-)  B      ND2
 488 GLY   ( 233-)  B      N
 500 TRP   ( 245-)  B      N
 515 PHE   ( 260-)  B      N
Only metal coordination for   94 HIS  (  96-) A      NE2
Only metal coordination for  117 HIS  ( 119-) A      ND1
Only metal coordination for  352 HIS  (  96-) B      NE2
Only metal coordination for  375 HIS  ( 119-) B      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.

  12 GLU   (  14-)  A   H-bonding suggests Gln
  50 ASP   (  52-)  A   H-bonding suggests Asn; but Alt-Rotamer
 270 GLU   (  14-)  B   H-bonding suggests Gln
 308 ASP   (  52-)  B   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 :  -0.538
  2nd generation packing quality :   0.059
  Ramachandran plot appearance   :  -2.410
  chi-1/chi-2 rotamer normality  :  -3.782 (poor)
  Backbone conformation          :  -1.210

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.322 (tight)
  Bond angles                    :   0.663 (tight)
  Omega angle restraints         :   0.236 (tight)
  Side chain planarity           :   0.134 (tight)
  Improper dihedral distribution :   0.583
  B-factor distribution          :   1.153
  Inside/Outside distribution    :   0.969

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 : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.2
  2nd generation packing quality :  -0.0
  Ramachandran plot appearance   :  -1.7
  chi-1/chi-2 rotamer normality  :  -2.6
  Backbone conformation          :  -1.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.322 (tight)
  Bond angles                    :   0.663 (tight)
  Omega angle restraints         :   0.236 (tight)
  Side chain planarity           :   0.134 (tight)
  Improper dihedral distribution :   0.583
  B-factor distribution          :   1.153
  Inside/Outside distribution    :   0.969
==============

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.