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 pdb1inv.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.

 395 EQP   ( 500-)  A  -

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 GLU   (  77-)  A    0.67
   2 PRO   (  78-)  A    0.80
   3 GLU   (  79-)  A    0.91
   4 TRP   (  80-)  A    0.87
   5 THR   (  81-)  A    0.88
   6 TYR   (  82-)  A    0.96
   7 PRO   (  83-)  A    0.92
   8 ARG   (  84-)  A    0.97
   9 LEU   (  85-)  A    0.80
  10 SER   (  86-)  A    0.97
  11 CYS   (  87-)  A    0.92
  12 GLN   (  88-)  A    0.73
  13 GLY   (  89-)  A    0.91
  14 SER   (  90-)  A    0.96
  16 PHE   (  92-)  A    0.94
  17 GLN   (  93-)  A    0.93
  18 LYS   (  94-)  A    0.97
  21 LEU   (  97-)  A    0.92
  24 PRO   ( 100-)  A    0.95
  25 HIS   ( 101-)  A    0.90
  26 ARG   ( 102-)  A    0.94
  27 PHE   ( 103-)  A    0.92
  30 ILE   ( 106-)  A    0.82
  31 LYS   ( 107-)  A    0.76
  32 GLY   ( 108-)  A    0.93
And so on for a total of 260 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 : 34.62

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.

  25 HIS   ( 101-)  A      CG   ND1  CE1 109.61    4.0
 139 HIS   ( 215-)  A      CG   ND1  CE1 109.64    4.0
 149 GLN   ( 225-)  A      N    CA   C   126.28    5.4
 197 HIS   ( 273-)  A      CG   ND1  CE1 109.67    4.1
 217 ASP   ( 293-)  A      N    CA   C    97.83   -4.8
 219 SER   ( 295-)  A      N    CA   C   122.54    4.0
 280 ARG   ( 356-)  A      CG   CD   NE  103.61   -4.1
 355 HIS   ( 431-)  A      CG   ND1  CE1 109.74    4.1
 379 LEU   ( 455-)  A      N    CA   C   122.97    4.2

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.

 149 GLN   ( 225-)  A    5.85
  26 ARG   ( 102-)  A    4.86
 379 LEU   ( 455-)  A    4.74
 135 THR   ( 211-)  A    4.64
 217 ASP   ( 293-)  A    4.55
 365 ALA   ( 441-)  A    4.47
 219 SER   ( 295-)  A    4.17
 195 VAL   ( 271-)  A    4.07
 331 GLY   ( 407-)  A    4.07

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 : 1.661

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.

  59 TYR   ( 135-)  A    -3.1
 252 PRO   ( 328-)  A    -2.8
 298 ARG   ( 374-)  A    -2.6
  40 ARG   ( 116-)  A    -2.6
 291 ARG   ( 367-)  A    -2.4
 194 ARG   ( 270-)  A    -2.3
  71 ARG   ( 147-)  A    -2.3
 221 THR   ( 297-)  A    -2.3
 197 HIS   ( 273-)  A    -2.2
 331 GLY   ( 407-)  A    -2.2
 361 THR   ( 437-)  A    -2.2
 148 THR   ( 224-)  A    -2.1
 285 ILE   ( 361-)  A    -2.1
 150 GLU   ( 226-)  A    -2.1
 245 THR   ( 321-)  A    -2.1
 303 LEU   ( 379-)  A    -2.0
 277 VAL   ( 353-)  A    -2.0
  23 SER   (  99-)  A    -2.0
  15 THR   (  91-)  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.

  41 GLU   ( 117-)  A  Poor phi/psi
  50 GLU   ( 126-)  A  Poor phi/psi
  59 TYR   ( 135-)  A  Poor phi/psi
  62 GLN   ( 138-)  A  PRO omega poor
 110 ARG   ( 186-)  A  Poor phi/psi
 148 THR   ( 224-)  A  Poor phi/psi
 150 GLU   ( 226-)  A  Poor phi/psi
 182 GLU   ( 258-)  A  Poor phi/psi
 219 SER   ( 295-)  A  Poor phi/psi
 234 ASP   ( 310-)  A  Poor phi/psi
 249 THR   ( 325-)  A  PRO omega poor
 308 ASP   ( 384-)  A  Poor phi/psi
 332 TRP   ( 408-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.772

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   4 TRP   (  80-)  A      0
   8 ARG   (  84-)  A      0
  12 GLN   (  88-)  A      0
  14 SER   (  90-)  A      0
  17 GLN   (  93-)  A      0
  18 LYS   (  94-)  A      0
  19 ALA   (  95-)  A      0
  20 LEU   (  96-)  A      0
  25 HIS   ( 101-)  A      0
  27 PHE   ( 103-)  A      0
  30 ILE   ( 106-)  A      0
  39 ILE   ( 115-)  A      0
  40 ARG   ( 116-)  A      0
  41 GLU   ( 117-)  A      0
  49 LYS   ( 125-)  A      0
  50 GLU   ( 126-)  A      0
  58 HIS   ( 134-)  A      0
  62 GLN   ( 138-)  A      0
  63 PRO   ( 139-)  A      0
  66 TYR   ( 142-)  A      0
  67 TYR   ( 143-)  A      0
  68 ASN   ( 144-)  A      0
  70 THR   ( 146-)  A      0
  74 ARG   ( 150-)  A      0
  78 ARG   ( 154-)  A      0
And so on for a total of 203 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 : 2.021

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!

 270 GLY   ( 346-)  A   1.70   15

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.

  40 ARG   ( 116-)  A      NH2 <->  395 EQP   ( 500-)  A      O3P    0.26    2.44  INTRA
 298 ARG   ( 374-)  A      NH2 <->  395 EQP   ( 500-)  A      O3P    0.22    2.48  INTRA
 106 CYS   ( 182-)  A      SG  <->  155 CYS   ( 231-)  A      SG     0.15    3.30  INTRA
 192 THR   ( 268-)  A      O   <->  238 ILE   ( 314-)  A      N      0.13    2.57  INTRA BL
  15 THR   (  91-)  A      O   <->  373 MET   ( 449-)  A      N      0.12    2.58  INTRA BL
  25 HIS   ( 101-)  A      NE2 <->  364 SER   ( 440-)  A      OG     0.11    2.59  INTRA BL
  11 CYS   (  87-)  A      SG  <->  344 CYS   ( 420-)  A      C      0.10    3.30  INTRA BL
  26 ARG   ( 102-)  A      N   <->   27 PHE   ( 103-)  A      N      0.09    2.51  INTRA BL
 205 PHE   ( 281-)  A      N   <->  396 HOH   ( 575 )  A      O      0.09    2.61  INTRA BL
 200 GLU   ( 276-)  A      N   <->  396 HOH   ( 554 )  A      O      0.09    2.61  INTRA BL
   2 PRO   (  78-)  A      O   <->  110 ARG   ( 186-)  A      NH1    0.09    2.61  INTRA BF
 192 THR   ( 268-)  A      CG2 <->  193 GLY   ( 269-)  A      N      0.07    2.93  INTRA
  41 GLU   ( 117-)  A      N   <->   42 PRO   ( 118-)  A      CD     0.07    2.93  INTRA
   2 PRO   (  78-)  A      O   <->  110 ARG   ( 186-)  A      CD     0.07    2.73  INTRA
 206 ALA   ( 282-)  A      N   <->  207 SER   ( 283-)  A      N      0.06    2.54  INTRA BL
  25 HIS   ( 101-)  A      NE2 <->  364 SER   ( 440-)  A      CB     0.06    3.04  INTRA BL
 223 LYS   ( 299-)  A      NZ  <->  261 CYS   ( 337-)  A      O      0.05    2.65  INTRA
   8 ARG   (  84-)  A      NH2 <->  342 LYS   ( 418-)  A      O      0.05    2.65  INTRA
  82 SER   ( 158-)  A      OG  <->   97 HIS   ( 173-)  A      NE2    0.05    2.65  INTRA BL
 294 SER   ( 370-)  A      OG  <->  297 ASN   ( 373-)  A      N      0.05    2.65  INTRA BL
 230 ASN   ( 306-)  A      OD1 <->  232 GLU   ( 308-)  A      N      0.05    2.65  INTRA
 171 GLY   ( 247-)  A      O   <->  197 HIS   ( 273-)  A      ND1    0.04    2.66  INTRA BL
 230 ASN   ( 306-)  A      OD1 <->  233 THR   ( 309-)  A      N      0.04    2.66  INTRA
 200 GLU   ( 276-)  A      OE1 <->  216 ARG   ( 292-)  A      NH2    0.04    2.66  INTRA BL
 118 ASP   ( 194-)  A      O   <->  125 LEU   ( 201-)  A      N      0.04    2.66  INTRA
 280 ARG   ( 356-)  A      NH2 <->  338 GLU   ( 414-)  A      OE2    0.03    2.67  INTRA
 107 HIS   ( 183-)  A      ND1 <->  109 GLY   ( 185-)  A      N      0.03    2.97  INTRA
 305 VAL   ( 381-)  A      CG2 <->  306 ARG   ( 382-)  A      N      0.03    2.97  INTRA BL
  11 CYS   (  87-)  A      N   <->  345 ASP   ( 421-)  A      O      0.02    2.68  INTRA
 142 ALA   ( 218-)  A      N   <->  143 HIS   ( 219-)  A      N      0.02    2.58  INTRA B3
 118 ASP   ( 194-)  A      CG  <->  127 LYS   ( 203-)  A      NZ     0.02    3.08  INTRA BL
 222 ALA   ( 298-)  A      N   <->  223 LYS   ( 299-)  A      N      0.02    2.58  INTRA B3
 122 ASN   ( 198-)  A      N   <->  396 HOH   ( 543 )  A      O      0.02    2.68  INTRA BL
 148 THR   ( 224-)  A      OG1 <->  149 GLN   ( 225-)  A      N      0.01    2.59  INTRA BL
  97 HIS   ( 173-)  A      ND1 <->  396 HOH   ( 536 )  A      O      0.01    2.69  INTRA BL
 163 MET   ( 239-)  A      SD  <->  201 CYS   ( 277-)  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.

  12 GLN   (  88-)  A      -7.46
  49 LYS   ( 125-)  A      -6.78
  66 TYR   ( 142-)  A      -6.71
 110 ARG   ( 186-)  A      -5.95
  62 GLN   ( 138-)  A      -5.91
  26 ARG   ( 102-)  A      -5.53
 298 ARG   ( 374-)  A      -5.50
  33 ASN   ( 109-)  A      -5.47
 379 LEU   ( 455-)  A      -5.42
 181 ARG   ( 257-)  A      -5.34
  59 TYR   ( 135-)  A      -5.31
  71 ARG   ( 147-)  A      -5.30
  30 ILE   ( 106-)  A      -5.18
  67 TYR   ( 143-)  A      -5.12
  74 ARG   ( 150-)  A      -5.12
 343 LYS   ( 419-)  A      -5.11

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.

  66 TYR   ( 142-)  A        68 - ASN    144- ( A)         -5.43

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.

  17 GLN   (  93-)  A
  58 HIS   ( 134-)  A
  93 ASN   ( 169-)  A
 264 ASN   ( 340-)  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.

  40 ARG   ( 116-)  A      NH1
  44 VAL   ( 120-)  A      N
  60 ALA   ( 136-)  A      N
  71 ARG   ( 147-)  A      NE
  75 ASN   ( 151-)  A      N
  78 ARG   ( 154-)  A      NE
 102 SER   ( 178-)  A      N
 119 GLY   ( 195-)  A      N
 127 LYS   ( 203-)  A      NZ
 134 TYR   ( 210-)  A      N
 137 THR   ( 213-)  A      OG1
 138 TYR   ( 214-)  A      OH
 139 HIS   ( 215-)  A      N
 151 SER   ( 227-)  A      N
 198 THR   ( 274-)  A      OG1
 218 ASN   ( 294-)  A      N
 221 THR   ( 297-)  A      N
 273 LYS   ( 349-)  A      N
 276 PHE   ( 352-)  A      N
 316 ASP   ( 392-)  A      N
 317 ALA   ( 393-)  A      N
 327 ILE   ( 403-)  A      N
 336 GLY   ( 412-)  A      N
 354 VAL   ( 430-)  A      N
 360 ASP   ( 436-)  A      N
 361 THR   ( 437-)  A      N
 362 TRP   ( 438-)  A      NE1
 363 HIS   ( 439-)  A      N
 380 TRP   ( 456-)  A      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.

 197 HIS   ( 273-)  A      NE2
 199 GLU   ( 275-)  A      OE2
 208 ASN   ( 284-)  A      OD1

Warning: Unusual ion packing

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

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

 393  CA   ( 468-)  A     0.78   1.01 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.

  29 GLU   ( 105-)  A   H-bonding suggests Gln; but Alt-Rotamer
 108 ASP   ( 184-)  A   H-bonding suggests Asn; but Alt-Rotamer
 166 ASP   ( 242-)  A   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.343
  2nd generation packing quality :  -1.368
  Ramachandran plot appearance   :  -1.995
  chi-1/chi-2 rotamer normality  :  -2.772
  Backbone conformation          :  -0.757

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.540 (tight)
  Bond angles                    :   0.812
  Omega angle restraints         :   0.367 (tight)
  Side chain planarity           :   0.468 (tight)
  Improper dihedral distribution :   1.071
  Inside/Outside distribution    :   1.081

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 :  -0.6
  2nd generation packing quality :  -0.2
  Ramachandran plot appearance   :  -0.2
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :  -0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.540 (tight)
  Bond angles                    :   0.812
  Omega angle restraints         :   0.367 (tight)
  Side chain planarity           :   0.468 (tight)
  Improper dihedral distribution :   1.071
  Inside/Outside distribution    :   1.081
==============

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.