WHAT IF Check report

This file was created 2011-12-16 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 pdb1inx.ent

Checks that need to be done early-on in validation

Warning: Matthews Coefficient (Vm) high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 43915.145
Volume of the Unit Cell V= 2358564.8
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 6.713
Vm by authors and this calculated Vm do not agree very well

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.

 395 MAN   ( 475-)  A  -
 397 EQP   ( 500-)  A  -
 398 MAN   ( 476-)  A  -
 399 BMA   ( 474-)  A  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 391 NAG   ( 472A)  A  -   O4  bound to  392 NAG   ( 473B)  A  -   C1
 392 NAG   ( 473B)  A  -   O4  bound to  399 BMA   ( 474-)  A  -   C1

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

Warning: Very strange distribution of occupancy values

The distribution of the occupancy values in this file differs very much from distributions commonly observed in well-refined PDB files. This does not need to mean anything, but please look at it. This file should not be used in training sets that need to hold 'good' PDB files.

Be aware that this evaluation is merely the result of comparing this file with about 500 well-refined high-resolution files in the PDB. If this file has much higher or much lower resolution than the PDB files used in WHAT IF's training set, non-normal values might very well be perfectly fine, or normal values might actually be not so normal...

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

   1 VAL   (  82-)  A    0.72
   2 GLU   (  83-)  A    0.89
   3 TYR   (  84-)  A    0.80
   4 ARG   (  85-)  A    0.92
   5 ASN   (  86-)  A    0.94
   6 TRP   (  87-)  A    0.90
   7 SER   (  88-)  A    0.96
   8 LYS   (  89-)  A    0.77
   9 PRO   (  90-)  A    0.96
  10 GLN   (  91-)  A    0.90
  11 CYS   (  92-)  A    0.91
  12 GLN   (  93-)  A    0.85
  13 ILE   (  94-)  A    0.93
  14 THR   (  95-)  A    0.93
  16 PHE   (  97-)  A    0.96
  18 PRO   (  99-)  A    0.97
  19 PHE   ( 100-)  A    0.92
  20 SER   ( 101-)  A    0.97
  22 ASP   ( 103-)  A    0.95
  23 ASN   ( 104-)  A    0.91
  24 SER   ( 105-)  A    0.83
  26 ARG   ( 107-)  A    0.93
  27 LEU   ( 108-)  A    0.96
  28 SER   ( 109-)  A    0.93
  29 ALA   ( 110-)  A    0.77
And so on for a total of 316 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. 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:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

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 : 34.37

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.

 103 HIS   ( 184-)  A      CG   ND1  CE1 109.65    4.0
 110 HIS   ( 191-)  A      CG   ND1  CE1 109.77    4.2
 145 GLN   ( 226-)  A      N    CA   C   124.97    4.9
 157 THR   ( 238-)  A      C    CA   CB  100.96   -4.8
 242 GLY   ( 323-)  A      N    CA   C   124.90    4.3
 248 ASP   ( 329-)  A      N    CA   C    99.36   -4.2
 350 LYS   ( 431-)  A      N    CA   C    92.22   -6.8
 363 VAL   ( 444-)  A      N    CA   C    99.97   -4.0

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.

 350 LYS   ( 431-)  A    7.35
 145 GLN   ( 226-)  A    5.34
 242 GLY   ( 323-)  A    4.06
 248 ASP   ( 329-)  A    4.03

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 : 1.657

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.

 204 PRO   ( 285-)  A    -2.8
 350 LYS   ( 431-)  A    -2.7
  37 ARG   ( 118-)  A    -2.7
 290 ARG   ( 371-)  A    -2.7
 229 TYR   ( 310-)  A    -2.6
 246 ARG   ( 327-)  A    -2.5
  67 THR   ( 148-)  A    -2.4
 114 THR   ( 195-)  A    -2.4
 266 GLN   ( 347-)  A    -2.3
 383 ILE   ( 464-)  A    -2.3
 234 SER   ( 315-)  A    -2.3
  57 THR   ( 138-)  A    -2.3
 378 PRO   ( 459-)  A    -2.3
 289 LEU   ( 370-)  A    -2.2
 161 THR   ( 242-)  A    -2.2
  13 ILE   (  94-)  A    -2.2
 144 THR   ( 225-)  A    -2.2
 339 ARG   ( 420-)  A    -2.2
 268 VAL   ( 349-)  A    -2.1
  53 LEU   ( 134-)  A    -2.1
  30 GLY   ( 111-)  A    -2.1
 368 THR   ( 449-)  A    -2.1
 146 GLU   ( 227-)  A    -2.0
 202 ARG   ( 283-)  A    -2.0
 121 THR   ( 202-)  A    -2.0
 251 SER   ( 332-)  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.

  37 ARG   ( 118-)  A  Poor phi/psi
  52 ALA   ( 133-)  A  Poor phi/psi
  66 ASP   ( 147-)  A  Poor phi/psi
  94 CYS   ( 175-)  A  Poor phi/psi
 141 ILE   ( 222-)  A  Poor phi/psi
 144 THR   ( 225-)  A  Poor phi/psi
 146 GLU   ( 227-)  A  Poor phi/psi
 153 ASN   ( 234-)  A  Poor phi/psi
 203 TYR   ( 284-)  A  PRO omega poor
 210 CYS   ( 291-)  A  Poor phi/psi
 229 TYR   ( 310-)  A  Poor phi/psi
 234 SER   ( 315-)  A  Poor phi/psi
 241 VAL   ( 322-)  A  Poor phi/psi
 244 THR   ( 325-)  A  PRO omega poor
 247 ASN   ( 328-)  A  Poor phi/psi
 248 ASP   ( 329-)  A  Poor phi/psi
 256 CYS   ( 337-)  A  Poor phi/psi
 261 ASN   ( 342-)  A  Poor phi/psi
 266 GLN   ( 347-)  A  Poor phi/psi
 272 ALA   ( 353-)  A  Poor phi/psi
 306 ASN   ( 387-)  A  Poor phi/psi
 312 ASN   ( 393-)  A  Poor phi/psi
 323 SER   ( 404-)  A  Poor phi/psi
 350 LYS   ( 431-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.427

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 : -3.427

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 ARG   (  85-)  A      0
   5 ASN   (  86-)  A      0
   6 TRP   (  87-)  A      0
   7 SER   (  88-)  A      0
  14 THR   (  95-)  A      0
  19 PHE   ( 100-)  A      0
  20 SER   ( 101-)  A      0
  22 ASP   ( 103-)  A      0
  24 SER   ( 105-)  A      0
  32 ASP   ( 113-)  A      0
  37 ARG   ( 118-)  A      0
  38 GLU   ( 119-)  A      0
  39 PRO   ( 120-)  A      0
  46 VAL   ( 127-)  A      0
  55 GLN   ( 136-)  A      0
  61 ASN   ( 142-)  A      0
  63 HIS   ( 144-)  A      0
  65 ASN   ( 146-)  A      0
  66 ASP   ( 147-)  A      0
  67 THR   ( 148-)  A      0
  68 VAL   ( 149-)  A      0
  70 ASP   ( 151-)  A      0
  71 ARG   ( 152-)  A      0
  72 ILE   ( 153-)  A      0
  75 ARG   ( 156-)  A      0
And so on for a total of 222 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 : 2.111

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].

 220 PRO   ( 301-)  A  -113.6 envelop C-gamma (-108 degrees)
 259 PRO   ( 340-)  A  -112.8 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 392 NAG   ( 473-)  A      O4  <->  399 BMA   ( 474-)  A      C1     1.00    1.40  INTRA B3
 392 NAG   ( 473-)  A      C4  <->  399 BMA   ( 474-)  A      C1     0.83    2.37  INTRA
 356 TRP   ( 437-)  A      N   <->  388 ILE   ( 469-)  A      CG2    0.27    2.83  INTRA
 207 ARG   ( 288-)  A      NH1 <->  302 TRP   ( 383-)  A      CZ2    0.20    2.90  INTRA BL
 349 ARG   ( 430-)  A      NH2 <->  356 TRP   ( 437-)  A      CZ3    0.19    2.91  INTRA
 246 ARG   ( 327-)  A      NH2 <->  284 THR   ( 365-)  A      O      0.15    2.55  INTRA
  37 ARG   ( 118-)  A      NH2 <->  397 EQP   ( 500-)  A      O2P    0.14    2.56  INTRA
 103 HIS   ( 184-)  A      CD2 <->  105 GLY   ( 186-)  A      N      0.14    2.96  INTRA BL
 371 THR   ( 452-)  A      CG2 <->  372 TYR   ( 453-)  A      N      0.13    2.87  INTRA BL
 349 ARG   ( 430-)  A      NH1 <->  353 THR   ( 434-)  A      O      0.13    2.57  INTRA
 225 ASN   ( 306-)  A      OD1 <->  228 ASP   ( 309-)  A      N      0.11    2.59  INTRA
  61 ASN   ( 142-)  A      ND2 <->   63 HIS   ( 144-)  A      ND1    0.11    2.89  INTRA BL
 263 ARG   ( 344-)  A      NH2 <->  288 ASP   ( 369-)  A      OD1    0.11    2.59  INTRA BL
 249 ASP   ( 330-)  A      O   <->  308 LYS   ( 389-)  A      NZ     0.09    2.61  INTRA BL
 217 SER   ( 298-)  A      N   <->  218 ASN   ( 299-)  A      N      0.09    2.51  INTRA BL
 225 ASN   ( 306-)  A      OD1 <->  227 GLU   ( 308-)  A      N      0.09    2.61  INTRA
 239 GLY   ( 320-)  A      CA  <->  306 ASN   ( 387-)  A      ND2    0.09    3.01  INTRA BL
 337 ILE   ( 418-)  A      CD1 <->  339 ARG   ( 420-)  A      NH2    0.08    3.02  INTRA BL
 231 ILE   ( 312-)  A      CG2 <->  232 ASP   ( 313-)  A      N      0.08    2.92  INTRA BL
 211 ARG   ( 292-)  A      NH1 <->  213 ASN   ( 294-)  A      OD1    0.07    2.63  INTRA BL
 290 ARG   ( 371-)  A      NH2 <->  397 EQP   ( 500-)  A      O2P    0.06    2.64  INTRA
  14 THR   (  95-)  A      N   <->  368 THR   ( 449-)  A      O      0.06    2.64  INTRA BL
 354 ARG   ( 435-)  A      NH1 <->  383 ILE   ( 464-)  A      O      0.06    2.64  INTRA BL
 369 SER   ( 450-)  A      N   <->  370 GLY   ( 451-)  A      N      0.06    2.54  INTRA BL
 253 ASN   ( 334-)  A      CA  <->  306 ASN   ( 387-)  A      ND2    0.06    3.04  INTRA BL
 248 ASP   ( 329-)  A      C   <->  250 ARG   ( 331-)  A      N      0.05    2.85  INTRA
  80 ASN   ( 161-)  A      ND2 <->  400 HOH   ( 503 )  A      O      0.05    2.65  INTRA BL
 202 ARG   ( 283-)  A      O   <->  203 TYR   ( 284-)  A      C      0.05    2.55  INTRA BL
 101 SER   ( 182-)  A      C   <->  149 CYS   ( 230-)  A      SG     0.05    3.35  INTRA BL
 356 TRP   ( 437-)  A      CD1 <->  388 ILE   ( 469-)  A      CG2    0.04    3.16  INTRA
 246 ARG   ( 327-)  A      NH2 <->  283 ARG   ( 364-)  A      CD     0.04    3.06  INTRA
  97 TRP   ( 178-)  A      N   <->   98 SER   ( 179-)  A      N      0.04    2.56  INTRA BL
 164 SER   ( 245-)  A      O   <->  193 HIS   ( 274-)  A      CE1    0.03    2.77  INTRA BL
 221 VAL   ( 302-)  A      N   <->  234 SER   ( 315-)  A      O      0.03    2.67  INTRA BL
 247 ASN   ( 328-)  A      ND2 <->  251 SER   ( 332-)  A      O      0.03    2.67  INTRA BL
  44 ASP   ( 125-)  A      OD1 <->   46 VAL   ( 127-)  A      N      0.02    2.68  INTRA BL
 299 ILE   ( 380-)  A      N   <->  309 SER   ( 390-)  A      O      0.01    2.69  INTRA BL
 277 ASN   ( 358-)  A      N   <->  278 ASP   ( 359-)  A      N      0.01    2.59  INTRA BL
 102 CYS   ( 183-)  A      SG  <->  151 CYS   ( 232-)  A      SG     0.01    3.44  INTRA BL

Packing, accessibility and threading

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.

 168 ARG   ( 249-)  A      -7.24
 372 TYR   ( 453-)  A      -7.09
 203 TYR   ( 284-)  A      -6.75
 202 ARG   ( 283-)  A      -6.55
 266 GLN   ( 347-)  A      -6.49
 257 ARG   ( 338-)  A      -5.76
 354 ARG   ( 435-)  A      -5.57
 334 LYS   ( 415-)  A      -5.41
  71 ARG   ( 152-)  A      -5.33

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

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

 371 THR   ( 452-)  A       374 - THR    455- ( A)         -5.27

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.

 400 HOH   ( 521 )  A      O
 400 HOH   ( 556 )  A      O
Bound group on Asn; dont flip    5 ASN  (  86-) A
Bound to:  389 NAG  ( 470-) A
Bound group on Asn; dont flip   65 ASN  ( 146-) A
Bound to:  390 NAG  ( 471-) A
Bound group on Asn; dont flip  119 ASN  ( 200-) A
Bound to:  391 NAG  ( 472-) A
Bound group on Asn; dont flip  153 ASN  ( 234-) A
Bound to:  393 NAG  ( 477-) A

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.

  12 GLN   (  93-)  A
  23 ASN   ( 104-)  A
  50 GLN   ( 131-)  A
  61 ASN   ( 142-)  A
 145 GLN   ( 226-)  A
 193 HIS   ( 274-)  A
 338 ASN   ( 419-)  A

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.

  26 ARG   ( 107-)  A      N
  37 ARG   ( 118-)  A      NH1
  41 VAL   ( 122-)  A      N
  56 GLY   ( 137-)  A      N
  57 THR   ( 138-)  A      N
  72 ILE   ( 153-)  A      N
  74 HIS   ( 155-)  A      N
  76 THR   ( 157-)  A      N
  94 CYS   ( 175-)  A      N
  98 SER   ( 179-)  A      N
 101 SER   ( 182-)  A      N
 105 GLY   ( 186-)  A      N
 108 TRP   ( 189-)  A      NE1
 120 ALA   ( 201-)  A      N
 142 LEU   ( 223-)  A      N
 145 GLN   ( 226-)  A      NE2
 147 SER   ( 228-)  A      N
 154 GLY   ( 235-)  A      N
 161 THR   ( 242-)  A      OG1
 167 GLY   ( 248-)  A      N
 188 ALA   ( 269-)  A      N
 193 HIS   ( 274-)  A      N
 211 ARG   ( 292-)  A      NH2
 212 ASP   ( 293-)  A      N
 226 MET   ( 307-)  A      N
 238 SER   ( 319-)  A      OG
 246 ARG   ( 327-)  A      NH2
 248 ASP   ( 329-)  A      N
 269 LYS   ( 350-)  A      N
 306 ASN   ( 387-)  A      ND2
 328 ILE   ( 409-)  A      N
 336 CYS   ( 417-)  A      N
 350 LYS   ( 431-)  A      N
 355 VAL   ( 436-)  A      N
 356 TRP   ( 437-)  A      N
 357 TRP   ( 438-)  A      N
 376 SER   ( 457-)  A      N
 390 NAG   ( 471-)  A      N2

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.

 103 HIS   ( 184-)  A      ND1
 195 GLU   ( 276-)  A      OE1
 243 ASP   ( 324-)  A      OD2

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

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

 396  CA   ( 478-)  A     0.83   1.02 Scores about as good as NA

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.

  44 ASP   ( 125-)  A   H-bonding suggests Asn; but Alt-Rotamer
 104 ASP   ( 185-)  A   H-bonding suggests Asn; but Alt-Rotamer
 162 ASP   ( 243-)  A   H-bonding suggests Asn; but Alt-Rotamer
 258 ASP   ( 339-)  A   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 :  -0.919
  2nd generation packing quality :  -1.567
  Ramachandran plot appearance   :  -2.548
  chi-1/chi-2 rotamer normality  :  -3.427 (poor)
  Backbone conformation          :  -1.041

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.571 (tight)
  Bond angles                    :   0.862
  Omega angle restraints         :   0.384 (tight)
  Side chain planarity           :   0.555 (tight)
  Improper dihedral distribution :   1.231
  Inside/Outside distribution    :   1.057

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -0.4
  Ramachandran plot appearance   :  -0.6
  chi-1/chi-2 rotamer normality  :  -1.6
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.571 (tight)
  Bond angles                    :   0.862
  Omega angle restraints         :   0.384 (tight)
  Side chain planarity           :   0.555 (tight)
  Improper dihedral distribution :   1.231
  Inside/Outside distribution    :   1.057
==============

WHAT IF
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    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

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      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
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      New parameters for the refinement of nucleic acid-containing structures
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DSSP
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      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
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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
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      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,
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Puckering parameters
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      A general definition of ring puckering coordinates
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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.