WHAT IF Check report

This file was created 2012-01-25 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 pdb2f5p.ent

Checks that need to be done early-on in validation

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: P 21 21 21
Number of matrices in space group: 4
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 2
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 4
Polymer chain multiplicity and SEQRES multiplicity disagree 1 2
Z and NCS seem to support the 3D multiplicity
There is strong evidence, though, for multiplicity and Z: 1 4

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: 36354.688
Volume of the Unit Cell V= 442883.813
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 6.091
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 2.710 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)
There is strong evidence, though, for multiplicity and Z: 1 4
which would result in the much more normal Vm= 3.046
and which also agrees with the number of NCS matrices (labeled `don't use')
that the user provided in the MTRIX records 1

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

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

 177 VAL   ( 153-)  A      CG1
 177 VAL   ( 153-)  A      CG2
 241 GLN   ( 236-)  A      CG
 241 GLN   ( 236-)  A      CD
 241 GLN   ( 236-)  A      OE1
 241 GLN   ( 236-)  A      NE2
 242 HIS   ( 237-)  A      CG
 242 HIS   ( 237-)  A      ND1
 242 HIS   ( 237-)  A      CD2
 242 HIS   ( 237-)  A      CE1
 242 HIS   ( 237-)  A      NE2

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) : 77.000

Note: B-factor plot

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

Chain identifier: A

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

  36 ARG   (  12-)  A
  62 ARG   (  38-)  A
  92 ARG   (  68-)  A
 104 ARG   (  80-)  A
 136 ARG   ( 112-)  A
 151 ARG   ( 127-)  A
 181 ARG   ( 157-)  A
 256 ARG   ( 251-)  A
 269 ARG   ( 264-)  A
 276 ARG   ( 271-)  A
 279 ARG   ( 274-)  A

Warning: Tyrosine convention problem

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

 105 TYR   (  81-)  A
 132 TYR   ( 108-)  A
 200 TYR   ( 176-)  A
 245 TYR   ( 240-)  A

Warning: Phenylalanine convention problem

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

  67 PHE   (  43-)  A
  85 PHE   (  61-)  A
  88 PHE   (  64-)  A
 167 PHE   ( 143-)  A

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.

  63 ASP   (  39-)  A
  93 ASP   (  69-)  A
 150 ASP   ( 126-)  A
 189 ASP   ( 165-)  A

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.

  27 GLU   (   3-)  A
  32 GLU   (   8-)  A
  65 GLU   (  41-)  A
  80 GLU   (  56-)  A
 112 GLU   (  88-)  A
 115 GLU   (  91-)  A
 148 GLU   ( 124-)  A
 161 GLU   ( 137-)  A
 174 GLU   ( 150-)  A
 203 GLU   ( 179-)  A
 223 GLU   ( 199-)  A
 230 GLU   ( 206-)  A
 237 GLU   ( 213-)  A

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.

   2 DGUA  (   3-)  C      N9   C8   N7  113.20    4.2
   3 DGUA  (   4-)  C      N9   C8   N7  113.13    4.1
  11 DGUA  (  12-)  C      N9   C8   N7  113.12    4.0
  21 DCYT  (  10-)  D      C3'  C4'  C5' 108.55   -4.1
 195 GLY   ( 171-)  A      N    CA   C   126.78    4.9

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.

  27 GLU   (   3-)  A
  32 GLU   (   8-)  A
  36 ARG   (  12-)  A
  62 ARG   (  38-)  A
  63 ASP   (  39-)  A
  65 GLU   (  41-)  A
  80 GLU   (  56-)  A
  92 ARG   (  68-)  A
  93 ASP   (  69-)  A
 104 ARG   (  80-)  A
 112 GLU   (  88-)  A
 115 GLU   (  91-)  A
 136 ARG   ( 112-)  A
 148 GLU   ( 124-)  A
 150 ASP   ( 126-)  A
 151 ARG   ( 127-)  A
 161 GLU   ( 137-)  A
 174 GLU   ( 150-)  A
 181 ARG   ( 157-)  A
 189 ASP   ( 165-)  A
 203 GLU   ( 179-)  A
 223 GLU   ( 199-)  A
 230 GLU   ( 206-)  A
 237 GLU   ( 213-)  A
 256 ARG   ( 251-)  A
 269 ARG   ( 264-)  A
 276 ARG   ( 271-)  A
 279 ARG   ( 274-)  A

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.

 195 GLY   ( 171-)  A    4.74
 119 HIS   (  95-)  A    4.20
 130 LEU   ( 106-)  A    4.04

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.

 154 PRO   ( 130-)  A    -2.8
 264 THR   ( 259-)  A    -2.7
 243 HIS   ( 238-)  A    -2.4
  79 LEU   (  55-)  A    -2.4
 138 PHE   ( 114-)  A    -2.4
 136 ARG   ( 112-)  A    -2.4
 193 VAL   ( 169-)  A    -2.1
 157 GLU   ( 133-)  A    -2.1

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.

  42 ILE   (  18-)  A  Poor phi/psi
  60 HIS   (  36-)  A  PRO omega poor
  90 LEU   (  66-)  A  Poor phi/psi
 100 ARG   (  76-)  A  Poor phi/psi
 117 HIS   (  93-)  A  Poor phi/psi
 153 PRO   ( 129-)  A  PRO omega poor
 157 GLU   ( 133-)  A  Poor phi/psi
 178 LYS   ( 154-)  A  Poor phi/psi
 242 HIS   ( 237-)  A  Poor phi/psi
 243 HIS   ( 238-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.538

Warning: Unusual rotamers

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

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

 204 SER   ( 180-)  A    0.36

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 DGUA  (   4-)  C      0
   4 DTHY  (   5-)  C      0
   5 DADE  (   6-)  C      0
   6 DGUA  (   7-)  C      0
   7 DADE  (   8-)  C      0
   8 DCYT  (   9-)  C      0
   9 DTHY  (  10-)  C      0
  10 DTHY  (  11-)  C      0
  11 DGUA  (  12-)  C      0
  12 DGUA  (  13-)  C      0
  13 DADE  (  14-)  C      0
  14 DTHY  (   3-)  D      0
  15 DCYT  (   4-)  D      0
  16 DCYT  (   5-)  D      0
  17 DADE  (   6-)  D      0
  18 DADE  (   7-)  D      0
  19 DGUA  (   8-)  D      0
  20 DTHY  (   9-)  D      0
  21 DCYT  (  10-)  D      0
  22 DTHY  (  11-)  D      0
  23 DADE  (  12-)  D      0
  24 DCYT  (  13-)  D      0
  25 DCYT  (  14-)  D      0
  26 PRO   (   2-)  A      0
  27 GLU   (   3-)  A      0
And so on for a total of 121 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 : 1.688

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].

  26 PRO   (   2-)  A  -115.2 envelop C-gamma (-108 degrees)
 153 PRO   ( 129-)  A  -114.0 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.

 256 ARG   ( 251-)  A      NH2 <->  283 HOH   ( 427 )  A      O      0.46    2.24  INTRA BF
  10 DTHY  (  11-)  C      N3  <->   17 DADE  (   6-)  D      N1     0.25    2.75  INTRA BL
  82 ARG   (  58-)  A      NE  <->  283 HOH   ( 360 )  A      O      0.24    2.46  INTRA
  51 ARG   (  27-)  A      NH2 <->  283 HOH   ( 371 )  A      O      0.19    2.51  INTRA
  18 DADE  (   7-)  D      N7  <->  282 HOH   (  25 )  D      O      0.18    2.52  INTRA
  12 DGUA  (  13-)  C      N1  <->   15 DCYT  (   4-)  D      N3     0.18    2.82  INTRA BF
   7 DADE  (   8-)  C      N7  <->  281 HOH   ( 137 )  C      O      0.17    2.53  INTRA BF
  98 HIS   (  74-)  A      ND1 <->  100 ARG   (  76-)  A      N      0.15    2.85  INTRA BL
 148 GLU   ( 124-)  A      OE2 <->  152 ARG   ( 128-)  A      NH2    0.15    2.55  INTRA BF
  11 DGUA  (  12-)  C      O4' <->  136 ARG   ( 112-)  A      NH2    0.14    2.56  INTRA
  12 DGUA  (  13-)  C      C2' <->   13 DADE  (  14-)  C      N7     0.14    2.96  INTRA BF
  12 DGUA  (  13-)  C      N2  <->   15 DCYT  (   4-)  D      O2     0.14    2.56  INTRA BF
 142 HIS   ( 118-)  A      ND1 <->  283 HOH   ( 317 )  A      O      0.13    2.57  INTRA BL
   3 DGUA  (   4-)  C      N2  <->   24 DCYT  (  13-)  D      O2     0.13    2.57  INTRA BF
 101 MET   (  77-)  A      N   <->  283 HOH   ( 332 )  A      O      0.13    2.57  INTRA BL
   6 DGUA  (   7-)  C      N1  <->   21 DCYT  (  10-)  D      N3     0.12    2.88  INTRA
   3 DGUA  (   4-)  C      N1  <->   24 DCYT  (  13-)  D      N3     0.12    2.88  INTRA BF
   9 DTHY  (  10-)  C      N3  <->   18 DADE  (   7-)  D      N1     0.11    2.89  INTRA BL
  84 LYS   (  60-)  A      NZ  <->  283 HOH   ( 308 )  A      O      0.10    2.60  INTRA BL
  28 LEU   (   4-)  A      N   <->   29 PRO   (   5-)  A      CD     0.08    2.92  INTRA BL
   5 DADE  (   6-)  C      N1  <->   22 DTHY  (  11-)  D      N3     0.08    2.92  INTRA BF
 152 ARG   ( 128-)  A      NH2 <->  283 HOH   ( 414 )  A      O      0.08    2.62  INTRA BF
 102 GLU   (  78-)  A      OE2 <->  136 ARG   ( 112-)  A      CD     0.07    2.73  INTRA BL
 148 GLU   ( 124-)  A      OE2 <->  152 ARG   ( 128-)  A      NE     0.07    2.63  INTRA BF
 183 VAL   ( 159-)  A      N   <->  214 ARG   ( 190-)  A      O      0.07    2.63  INTRA BL
 131 ARG   ( 107-)  A      NH2 <->  283 HOH   ( 388 )  A      O      0.07    2.63  INTRA BL
  24 DCYT  (  13-)  D      C2' <->   25 DCYT  (  14-)  D      C5     0.07    3.13  INTRA BF
  48 GLU   (  24-)  A      N   <->  123 CYS   (  99-)  A      O      0.06    2.64  INTRA BL
   8 DCYT  (   9-)  C      N3  <->   19 DGUA  (   8-)  D      N1     0.06    2.94  INTRA BL
  75 THR   (  51-)  A      N   <->   91 ASP   (  67-)  A      OD2    0.05    2.65  INTRA BL
 264 THR   ( 259-)  A      O   <->  271 THR   ( 266-)  A      N      0.05    2.65  INTRA
 242 HIS   ( 237-)  A      O   <->  243 HIS   ( 238-)  A      CG     0.05    2.65  INTRA BF
 169 PRO   ( 145-)  A      O   <->  173 ALA   ( 149-)  A      N      0.05    2.65  INTRA
 106 ALA   (  82-)  A      O   <->  131 ARG   ( 107-)  A      N      0.05    2.65  INTRA BL
  83 GLY   (  59-)  A      N   <->  161 GLU   ( 137-)  A      OE2    0.04    2.66  INTRA BL
  10 DTHY  (  11-)  C      OP1 <->  137 LYS   ( 113-)  A      NZ     0.04    2.66  INTRA BL
 115 GLU   (  91-)  A      OE1 <->  131 ARG   ( 107-)  A      NH2    0.04    2.66  INTRA
   7 DADE  (   8-)  C      N1  <->   20 DTHY  (   9-)  D      N3     0.03    2.97  INTRA BL
  13 DADE  (  14-)  C      N1  <->   14 DTHY  (   3-)  D      N3     0.02    2.98  INTRA BF
 156 ALA   ( 132-)  A      C   <->  157 GLU   ( 133-)  A      CG     0.02    3.08  INTRA
 144 TYR   ( 120-)  A      C   <->  145 ALA   ( 121-)  A      C      0.02    2.78  INTRA BL
  19 DGUA  (   8-)  D      N3  <->  100 ARG   (  76-)  A      NE     0.02    2.98  INTRA BL
  80 GLU   (  56-)  A      O   <->   87 LYS   (  63-)  A      N      0.01    2.69  INTRA BL
  96 ILE   (  72-)  A      N   <->  142 HIS   ( 118-)  A      O      0.01    2.69  INTRA BL
 196 PHE   ( 172-)  A      CZ  <->  235 ILE   ( 211-)  A      CG1    0.01    3.19  INTRA
 255 LYS   ( 250-)  A      N   <->  283 HOH   ( 346 )  A      O      0.01    2.69  INTRA BL
  60 HIS   (  36-)  A      CD2 <->  143 VAL   ( 119-)  A      O      0.01    2.79  INTRA BL
 117 HIS   (  93-)  A      ND1 <->  283 HOH   ( 337 )  A      O      0.01    2.69  INTRA BL
  90 LEU   (  66-)  A      O   <->  146 LYS   ( 122-)  A      NZ     0.01    2.69  INTRA BL
  29 PRO   (   5-)  A      CG  <->  238 ALA   ( 214-)  A      CB     0.01    3.19  INTRA BF

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

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.

 256 ARG   ( 251-)  A      -6.99
 101 MET   (  77-)  A      -6.92
 111 LEU   (  87-)  A      -6.02
 151 ARG   ( 127-)  A      -5.42
 163 LEU   ( 139-)  A      -5.26
 138 PHE   ( 114-)  A      -5.24
 243 HIS   ( 238-)  A      -5.23
 207 ARG   ( 183-)  A      -5.20
 180 LYS   ( 156-)  A      -5.03

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.

 136 ARG   ( 112-)  A       138 - PHE    114- ( A)         -4.84

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

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

 242 HIS   ( 237-)  A   -3.37
  99 LEU   (  75-)  A   -2.85

Warning: Abnormal packing Z-score for sequential residues

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

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

  98 HIS   (  74-)  A     -  101 MET   (  77-)  A        -2.01

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

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.

 252 ASN   ( 247-)  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.

  51 ARG   (  27-)  A      NH1
 168 SER   ( 144-)  A      N
 248 GLY   ( 243-)  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.

 119 HIS   (  95-)  A      ND1

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 :  -0.706
  2nd generation packing quality :  -0.787
  Ramachandran plot appearance   :  -0.282
  chi-1/chi-2 rotamer normality  :  -1.538
  Backbone conformation          :  -0.047

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.391 (tight)
  Bond angles                    :   0.706
  Omega angle restraints         :   0.307 (tight)
  Side chain planarity           :   0.229 (tight)
  Improper dihedral distribution :   0.664
  B-factor distribution          :   0.770
  Inside/Outside distribution    :   1.038

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 :  -0.4
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :  -0.7
  Backbone conformation          :  -0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.391 (tight)
  Bond angles                    :   0.706
  Omega angle restraints         :   0.307 (tight)
  Side chain planarity           :   0.229 (tight)
  Improper dihedral distribution :   0.664
  B-factor distribution          :   0.770
  Inside/Outside distribution    :   1.038
==============

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.