WHAT IF Check report

This file was created 2012-01-12 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 pdb1r2z.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: 37692.375
Volume of the Unit Cell V= 429299.563
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 5.695
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 2.800 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= 2.847
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'.

 111 GLU   (  88-)  A      CD
 111 GLU   (  88-)  A      OE1
 111 GLU   (  88-)  A      OE2
 156 GLU   ( 133-)  A      CG
 156 GLU   ( 133-)  A      CD
 156 GLU   ( 133-)  A      OE1
 156 GLU   ( 133-)  A      OE2
 173 GLU   ( 150-)  A      CG
 173 GLU   ( 150-)  A      CD
 173 GLU   ( 150-)  A      OE1
 173 GLU   ( 150-)  A      OE2
 177 LYS   ( 154-)  A      CD
 177 LYS   ( 154-)  A      CE
 177 LYS   ( 154-)  A      NZ
 179 LYS   ( 156-)  A      CD
 179 LYS   ( 156-)  A      CE
 179 LYS   ( 156-)  A      NZ
 220 SER   ( 197-)  A      OG
 221 LYS   ( 198-)  A      CD
 221 LYS   ( 198-)  A      CE
 221 LYS   ( 198-)  A      NZ
 224 GLU   ( 201-)  A      CG
 224 GLU   ( 201-)  A      CD
 224 GLU   ( 201-)  A      OE1
 224 GLU   ( 201-)  A      OE2
 228 GLU   ( 205-)  A      CD
 228 GLU   ( 205-)  A      OE1
 228 GLU   ( 205-)  A      OE2
 240 LYS   ( 217-)  A      CD
 240 LYS   ( 217-)  A      CE
 240 LYS   ( 217-)  A      NZ
 246 ARG   ( 223-)  A      CD
 246 ARG   ( 223-)  A      NE
 246 ARG   ( 223-)  A      CZ
 246 ARG   ( 223-)  A      NH1
 246 ARG   ( 223-)  A      NH2
 247 THR   ( 224-)  A      CB
 247 THR   ( 224-)  A      OG1
 247 THR   ( 224-)  A      CG2
 274 ARG   ( 251-)  A      CD
 274 ARG   ( 251-)  A      NE
 274 ARG   ( 251-)  A      CZ
 274 ARG   ( 251-)  A      NH1
 274 ARG   ( 251-)  A      NH2

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 DGUA  (   1-)  B    High
   2 DTHY  (   2-)  B    High
  23 DADE  (  23-)  C    High
  24 DCYT  (  24-)  C    High

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) :100.000

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.

  80 ARG   (  57-)  A
 135 ARG   ( 112-)  A
 150 ARG   ( 127-)  A
 180 ARG   ( 157-)  A
 294 ARG   ( 271-)  A

Warning: Tyrosine convention problem

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

 104 TYR   (  81-)  A
 131 TYR   ( 108-)  A
 199 TYR   ( 176-)  A
 248 TYR   ( 225-)  A
 291 TYR   ( 268-)  A

Warning: Phenylalanine convention problem

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

  66 PHE   (  43-)  A
  87 PHE   (  64-)  A
 137 PHE   ( 114-)  A
 166 PHE   ( 143-)  A
 258 PHE   ( 235-)  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.

  62 ASP   (  39-)  A
 133 ASP   ( 110-)  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.

  29 GLU   (   6-)  A
  79 GLU   (  56-)  A
 160 GLU   ( 137-)  A
 202 GLU   ( 179-)  A
 222 GLU   ( 199-)  A
 236 GLU   ( 213-)  A
 254 GLU   ( 231-)  A
 280 GLU   ( 257-)  A

Geometric checks

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.254
RMS-deviation in bond distances: 0.006

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.

   1 DGUA  (   1-)  B      N9   C8   N7  113.16    4.1
  10 DGUA  (  10-)  B      N9   C8   N7  113.13    4.1
  17 DADE  (  17-)  C      C2'  C1'  N9  107.23   -4.4

Warning: Low bond angle variability

Bond angles were found to deviate less than normal from the standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond angles: 0.636
RMS-deviation in bond angles: 1.293

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.

  29 GLU   (   6-)  A
  62 ASP   (  39-)  A
  79 GLU   (  56-)  A
  80 ARG   (  57-)  A
 133 ASP   ( 110-)  A
 135 ARG   ( 112-)  A
 150 ARG   ( 127-)  A
 160 GLU   ( 137-)  A
 180 ARG   ( 157-)  A
 202 GLU   ( 179-)  A
 222 GLU   ( 199-)  A
 236 GLU   ( 213-)  A
 254 GLU   ( 231-)  A
 280 GLU   ( 257-)  A
 294 ARG   ( 271-)  A

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.

  99 ARG   (  76-)  A    -2.9
 282 THR   ( 259-)  A    -2.6
 153 PRO   ( 130-)  A    -2.4
 192 VAL   ( 169-)  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 ILE   (  18-)  A  Poor phi/psi
  59 HIS   (  36-)  A  PRO omega poor
  89 LEU   (  66-)  A  Poor phi/psi
  99 ARG   (  76-)  A  Poor phi/psi
 116 HIS   (  93-)  A  Poor phi/psi
 136 LYS   ( 113-)  A  Poor phi/psi
 152 PRO   ( 129-)  A  PRO omega poor
 177 LYS   ( 154-)  A  Poor phi/psi
 247 THR   ( 224-)  A  Poor phi/psi
 264 VAL   ( 241-)  A  Poor phi/psi
 285 ALA   ( 262-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : 0.385

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 DADE  (   3-)  B      0
   4 DGUA  (   4-)  B      0
   5 DADE  (   5-)  B      0
   6 DCYT  (   6-)  B      0
   7 DCYT  (   7-)  B      0
   8 DTHY  (   8-)  B      0
   9 DGUA  (   9-)  B      0
  10 DGUA  (  10-)  B      0
  11 DADE  (  11-)  B      0
  12 DCYT  (  12-)  B      0
  13 DGUA  (  13-)  C      0
  14 DTHY  (  14-)  C      0
  15 DCYT  (  15-)  C      0
  16 DCYT  (  16-)  C      0
  17 DADE  (  17-)  C      0
  18 UMP   (  18-)  C      0
  19 DGUA  (  19-)  C      0
  20 DTHY  (  20-)  C      0
  21 DCYT  (  21-)  C      0
  22 DTHY  (  22-)  C      0
  23 DADE  (  23-)  C      0
  24 DCYT  (  24-)  C      0
  25 PRO   (   2-)  A      0
  26 GLN   (   3-)  A      0
  42 VAL   (  19-)  A      0
And so on for a total of 117 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 : 1.385

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.

 250 ASN   ( 227-)  A      ND2 <->  254 GLU   ( 231-)  A      CB     0.22    2.88  INTRA BF
   6 DCYT  (   6-)  B      C2' <->    7 DCYT  (   7-)  B      C5'    0.20    3.00  INTRA
   8 DTHY  (   8-)  B      N3  <->   17 DADE  (  17-)  C      N1     0.18    2.82  INTRA BL
 147 GLU   ( 124-)  A      OE2 <->  150 ARG   ( 127-)  A      NH2    0.18    2.52  INTRA BF
   9 DGUA  (   9-)  B      N1  <->   16 DCYT  (  16-)  C      N3     0.16    2.84  INTRA
   2 DTHY  (   2-)  B      N3  <->   23 DADE  (  23-)  C      N1     0.16    2.84  INTRA BF
  20 DTHY  (  20-)  C      C4' <->   99 ARG   (  76-)  A      NH1    0.13    2.97  INTRA
   9 DGUA  (   9-)  B      O6  <->   16 DCYT  (  16-)  C      N4     0.11    2.59  INTRA
 108 SER   (  85-)  A      O   <->  130 ARG   ( 107-)  A      NH2    0.10    2.60  INTRA BL
 128 GLU   ( 105-)  A      OE2 <->  130 ARG   ( 107-)  A      NE     0.10    2.60  INTRA BL
 180 ARG   ( 157-)  A      NH2 <->  188 ASP   ( 165-)  A      OD2    0.09    2.61  INTRA
   6 DCYT  (   6-)  B      N3  <->   19 DGUA  (  19-)  C      N1     0.08    2.92  INTRA
  12 DCYT  (  12-)  B      N3  <->   13 DGUA  (  13-)  C      N1     0.06    2.94  INTRA BF
 234 ILE   ( 211-)  A      CG2 <->  235 GLY   ( 212-)  A      N      0.06    2.94  INTRA BL
 122 CYS   (  99-)  A      SG  <->  301 HOH   ( 413 )  A      O      0.06    2.94  INTRA
  97 HIS   (  74-)  A      CD2 <->   99 ARG   (  76-)  A      NH1    0.05    3.05  INTRA
  47 GLU   (  24-)  A      N   <->  122 CYS   (  99-)  A      O      0.05    2.65  INTRA BL
 250 ASN   ( 227-)  A      OD1 <->  252 GLN   ( 229-)  A      N      0.04    2.66  INTRA BF
 183 LYS   ( 160-)  A      NZ  <->  201 ASP   ( 178-)  A      OD1    0.04    2.66  INTRA BL
  91 ARG   (  68-)  A      NH1 <->   92 ASP   (  69-)  A      OD1    0.04    2.66  INTRA
 261 HIS   ( 238-)  A      NE2 <->  301 HOH   ( 472 )  A      O      0.04    2.66  INTRA BF
  91 ARG   (  68-)  A      NH2 <->  301 HOH   ( 369 )  A      O      0.03    2.67  INTRA
 213 ARG   ( 190-)  A      NH1 <->  222 GLU   ( 199-)  A      OE2    0.02    2.68  INTRA
  95 ILE   (  72-)  A      N   <->  141 HIS   ( 118-)  A      O      0.02    2.68  INTRA BL
  59 HIS   (  36-)  A      CA  <->   60 PRO   (  37-)  A      C      0.02    2.98  INTRA BL
 180 ARG   ( 157-)  A      NH2 <->  301 HOH   ( 405 )  A      O      0.02    2.68  INTRA
 141 HIS   ( 118-)  A      ND1 <->  301 HOH   ( 338 )  A      O      0.02    2.68  INTRA BL
 287 ARG   ( 264-)  A      NH1 <->  301 HOH   ( 594 )  A      O      0.01    2.69  INTRA BL
 113 LEU   (  90-)  A      N   <->  301 HOH   ( 546 )  A      O      0.01    2.69  INTRA
  12 DCYT  (  12-)  B      O2  <->   13 DGUA  (  13-)  C      N2     0.01    2.69  INTRA BF
  66 PHE   (  43-)  A      CE1 <->   70 MET   (  47-)  A      CE     0.01    3.19  INTRA BL

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

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.

 100 MET   (  77-)  A      -6.49
 110 LEU   (  87-)  A      -6.04
 261 HIS   ( 238-)  A      -5.72
 206 ARG   ( 183-)  A      -5.14
 137 PHE   ( 114-)  A      -5.13
 162 LEU   ( 139-)  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.

 135 ARG   ( 112-)  A       137 - PHE    114- ( A)         -4.62

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.

 135 ARG   ( 112-)  A   -2.68
 274 ARG   ( 251-)  A   -2.63
  98 LEU   (  75-)  A   -2.63

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.

  97 HIS   (  74-)  A     -  100 MET   (  77-)  A        -1.70

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

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

 301 HOH   ( 570 )  A      O    -18.09   77.58   14.80

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.

 300 HOH   (  31 )  C      O
ERROR. Strange cone in HB2INI
Affected atom   18 UMP  (  18-) C      P
Expected ambiguity-2 in FILL1HARR 0 21 453

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.

 227 HIS   ( 204-)  A
 252 GLN   ( 229-)  A
 260 HIS   ( 237-)  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.

   4 DGUA  (   4-)  B      N1
  22 DTHY  (  22-)  C      N3
  25 PRO   (   2-)  A      N
  26 GLN   (   3-)  A      NE2
  99 ARG   (  76-)  A      NE
 130 ARG   ( 107-)  A      NH2
 137 PHE   ( 114-)  A      N
 167 SER   ( 144-)  A      N
 210 LEU   ( 187-)  A      N
 216 ALA   ( 193-)  A      N
 245 VAL   ( 222-)  A      N
 246 ARG   ( 223-)  A      N
 266 GLY   ( 243-)  A      N
 287 ARG   ( 264-)  A      NH2

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.

  97 HIS   (  74-)  A      ND1

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and 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 nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple 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 method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

 301 HOH   ( 325 )  A      O  1.06  K  4
 301 HOH   ( 507 )  A      O  0.90  K  4 Ion-B

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 :  -0.877
  2nd generation packing quality :  -0.866
  Ramachandran plot appearance   :  -0.396
  chi-1/chi-2 rotamer normality  :   0.385
  Backbone conformation          :   0.120

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.254 (tight)
  Bond angles                    :   0.636 (tight)
  Omega angle restraints         :   0.252 (tight)
  Side chain planarity           :   0.198 (tight)
  Improper dihedral distribution :   0.573
  B-factor distribution          :   0.529
  Inside/Outside distribution    :   1.017

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 : 1.63


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.7
  2nd generation packing quality :  -1.2
  Ramachandran plot appearance   :  -0.8
  chi-1/chi-2 rotamer normality  :   0.1
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.254 (tight)
  Bond angles                    :   0.636 (tight)
  Omega angle restraints         :   0.252 (tight)
  Side chain planarity           :   0.198 (tight)
  Improper dihedral distribution :   0.573
  B-factor distribution          :   0.529
  Inside/Outside distribution    :   1.017
==============

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.