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 pdb3it8.ent

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

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

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 ARG   (   6-)  A    High
   2 THR   (   7-)  A    High
   3 PRO   (   8-)  A    High
   4 SER   (   9-)  A    High
   5 ASP   (  10-)  A    High
  16 GLN   (  21-)  A    High
  18 GLU   (  23-)  A    High
  20 GLN   (  25-)  A    High
  28 ALA   (  33-)  A    High
  40 ASP   (  45-)  A    High
  48 GLU   (  53-)  A    High
  62 GLN   (  67-)  A    High
  63 GLY   (  68-)  A    High
  64 CYS   (  69-)  A    High
  65 PRO   (  70-)  A    High
  66 SER   (  71-)  A    High
  67 THR   (  72-)  A    High
  68 HIS   (  73-)  A    High
  69 VAL   (  74-)  A    High
  96 CYS   ( 101-)  A    High
  97 GLN   ( 102-)  A    High
  98 ARG   ( 103-)  A    High
  99 GLU   ( 104-)  A    High
 100 THR   ( 105-)  A    High
 101 PRO   ( 106-)  A    High
And so on for a total of 848 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:

Crystal temperature (K) :100.000

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 1.574 over 15390 bonds
Average difference in B over a bond : 3.37
RMS difference in B over a bond : 7.72

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

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.

  27 ARG   (  32-)  A
  77 ARG   (  82-)  A
  98 ARG   ( 103-)  A
 126 ARG   ( 131-)  A
 133 ARG   ( 138-)  A
 179 ARG   (  32-)  B
 229 ARG   (  82-)  B
 250 ARG   ( 103-)  B
 278 ARG   ( 131-)  B
 285 ARG   ( 138-)  B
 331 ARG   (  32-)  C
 381 ARG   (  82-)  C
 402 ARG   ( 103-)  C
 430 ARG   ( 131-)  C
 437 ARG   ( 138-)  C
1380 ARG   (  32-)  G
1430 ARG   (  82-)  G
1451 ARG   ( 103-)  G
1479 ARG   ( 131-)  G
1486 ARG   ( 138-)  G
1532 ARG   (  32-)  H
1582 ARG   (  82-)  H
1603 ARG   ( 103-)  H
1631 ARG   ( 131-)  H
1638 ARG   ( 138-)  H
1684 ARG   (  32-)  I
1734 ARG   (  82-)  I
1755 ARG   ( 103-)  I
1783 ARG   ( 131-)  I
1790 ARG   ( 138-)  I

Warning: Tyrosine convention problem

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

  82 TYR   (  87-)  A
 136 TYR   ( 141-)  A
 234 TYR   (  87-)  B
 288 TYR   ( 141-)  B
 386 TYR   (  87-)  C
 440 TYR   ( 141-)  C
 478 TYR   (  22-)  D
 610 TYR   ( 154-)  D
 682 TYR   ( 226-)  D
 690 TYR   ( 234-)  D
 699 TYR   ( 243-)  D
 749 TYR   ( 293-)  D
 777 TYR   (  22-)  E
 853 TYR   (  98-)  E
 909 TYR   ( 154-)  E
 981 TYR   ( 226-)  E
 989 TYR   ( 234-)  E
 998 TYR   ( 243-)  E
1048 TYR   ( 293-)  E
1076 TYR   (  22-)  F
1152 TYR   (  98-)  F
1208 TYR   ( 154-)  F
1280 TYR   ( 226-)  F
1288 TYR   ( 234-)  F
1297 TYR   ( 243-)  F
1347 TYR   ( 293-)  F
1435 TYR   (  87-)  G
1489 TYR   ( 141-)  G
1587 TYR   (  87-)  H
1641 TYR   ( 141-)  H
1739 TYR   (  87-)  I
1793 TYR   ( 141-)  I
1831 TYR   (  22-)  J
1963 TYR   ( 154-)  J
2035 TYR   ( 226-)  J
2043 TYR   ( 234-)  J
2052 TYR   ( 243-)  J
2130 TYR   (  22-)  K
2206 TYR   (  98-)  K
2262 TYR   ( 154-)  K
2334 TYR   ( 226-)  K
2342 TYR   ( 234-)  K
2351 TYR   ( 243-)  K
2429 TYR   (  22-)  L
2505 TYR   (  98-)  L
2561 TYR   ( 154-)  L
2633 TYR   ( 226-)  L
2641 TYR   ( 234-)  L
2650 TYR   ( 243-)  L
2700 TYR   ( 293-)  L

Warning: Phenylalanine convention problem

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

  59 PHE   (  64-)  A
 139 PHE   ( 144-)  A
 211 PHE   (  64-)  B
 291 PHE   ( 144-)  B
 363 PHE   (  64-)  C
 443 PHE   ( 144-)  C
 502 PHE   (  46-)  D
 560 PHE   ( 104-)  D
 583 PHE   ( 127-)  D
 801 PHE   (  46-)  E
 859 PHE   ( 104-)  E
 882 PHE   ( 127-)  E
1100 PHE   (  46-)  F
1158 PHE   ( 104-)  F
1181 PHE   ( 127-)  F
1412 PHE   (  64-)  G
1492 PHE   ( 144-)  G
1564 PHE   (  64-)  H
1644 PHE   ( 144-)  H
1716 PHE   (  64-)  I
1796 PHE   ( 144-)  I
1855 PHE   (  46-)  J
1913 PHE   ( 104-)  J
1936 PHE   ( 127-)  J
2154 PHE   (  46-)  K
2212 PHE   ( 104-)  K
2235 PHE   ( 127-)  K
2453 PHE   (  46-)  L
2511 PHE   ( 104-)  L
2534 PHE   ( 127-)  L

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.

   5 ASP   (  10-)  A
 157 ASP   (  10-)  B
 309 ASP   (  10-)  C
1358 ASP   (  10-)  G
1510 ASP   (  10-)  H
1662 ASP   (  10-)  I

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.

 130 GLU   ( 135-)  A
 141 GLU   ( 146-)  A
 282 GLU   ( 135-)  B
 293 GLU   ( 146-)  B
 434 GLU   ( 135-)  C
 445 GLU   ( 146-)  C
 681 GLU   ( 225-)  D
 980 GLU   ( 225-)  E
1279 GLU   ( 225-)  F
1483 GLU   ( 135-)  G
1494 GLU   ( 146-)  G
1635 GLU   ( 135-)  H
1646 GLU   ( 146-)  H
1787 GLU   ( 135-)  I
1798 GLU   ( 146-)  I
2034 GLU   ( 225-)  J
2333 GLU   ( 225-)  K
2632 GLU   ( 225-)  L

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.

  78 ILE   (  83-)  A      N    CA   C    99.55   -4.2
 230 ILE   (  83-)  B      N    CA   C    99.30   -4.2
 382 ILE   (  83-)  C      N    CA   C    99.14   -4.3
 497 HIS   (  41-)  D      CG   ND1  CE1 109.63    4.0
 691 PRO   ( 235-)  D      N    CA   C   101.43   -4.1
 692 GLU   ( 236-)  D      N    CA   C   126.73    5.5
 743 THR   ( 287-)  D      N    CA   C    99.56   -4.2
 744 LEU   ( 288-)  D      CA   CB   CG  135.80    5.6
 990 PRO   ( 235-)  E      N    CA   C   101.18   -4.2
 991 GLU   ( 236-)  E      N    CA   C   126.56    5.5
1042 THR   ( 287-)  E      N    CA   C    99.02   -4.4
1043 LEU   ( 288-)  E      CA   CB   CG  135.88    5.6
1289 PRO   ( 235-)  F      N    CA   C   101.33   -4.2
1290 GLU   ( 236-)  F      N    CA   C   126.72    5.5
1341 THR   ( 287-)  F      N    CA   C    99.62   -4.1
1342 LEU   ( 288-)  F      CA   CB   CG  134.98    5.3
1431 ILE   (  83-)  G      N    CA   C    98.87   -4.4
1583 ILE   (  83-)  H      N    CA   C    99.65   -4.1
1735 ILE   (  83-)  I      N    CA   C    99.83   -4.1
2044 PRO   ( 235-)  J      N    CA   C   101.19   -4.2
2045 GLU   ( 236-)  J      N    CA   C   126.82    5.6
2096 THR   ( 287-)  J      N    CA   C    99.82   -4.1
2097 LEU   ( 288-)  J      CA   CB   CG  135.97    5.6
2344 GLU   ( 236-)  K      N    CA   C   126.69    5.5
2395 THR   ( 287-)  K      N    CA   C    99.77   -4.1
2396 LEU   ( 288-)  K      CA   CB   CG  136.00    5.6
2642 PRO   ( 235-)  L      N    CA   C   101.00   -4.3
2643 GLU   ( 236-)  L      N    CA   C   126.82    5.6
2694 THR   ( 287-)  L      N    CA   C    99.22   -4.3
2695 LEU   ( 288-)  L      CA   CB   CG  135.43    5.5

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.

   5 ASP   (  10-)  A
  27 ARG   (  32-)  A
  77 ARG   (  82-)  A
  98 ARG   ( 103-)  A
 126 ARG   ( 131-)  A
 130 GLU   ( 135-)  A
 133 ARG   ( 138-)  A
 141 GLU   ( 146-)  A
 157 ASP   (  10-)  B
 179 ARG   (  32-)  B
 229 ARG   (  82-)  B
 250 ARG   ( 103-)  B
 278 ARG   ( 131-)  B
 282 GLU   ( 135-)  B
 285 ARG   ( 138-)  B
 293 GLU   ( 146-)  B
 309 ASP   (  10-)  C
 331 ARG   (  32-)  C
 381 ARG   (  82-)  C
 402 ARG   ( 103-)  C
 430 ARG   ( 131-)  C
 434 GLU   ( 135-)  C
 437 ARG   ( 138-)  C
 445 GLU   ( 146-)  C
 681 GLU   ( 225-)  D
And so on for a total of 54 lines.

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.

2643 GLU   ( 236-)  L    5.24
2045 GLU   ( 236-)  J    5.24
 692 GLU   ( 236-)  D    5.21
1290 GLU   ( 236-)  F    5.21
2344 GLU   ( 236-)  K    5.20
 991 GLU   ( 236-)  E    5.16
2642 PRO   ( 235-)  L    4.64
 990 PRO   ( 235-)  E    4.57
2044 PRO   ( 235-)  J    4.56
1289 PRO   ( 235-)  F    4.51
 691 PRO   ( 235-)  D    4.47
1431 ILE   (  83-)  G    4.35
2343 PRO   ( 235-)  K    4.32
 382 ILE   (  83-)  C    4.23
 230 ILE   (  83-)  B    4.16
 633 LYS   ( 177-)  D    4.10
1042 THR   ( 287-)  E    4.07
1231 LYS   ( 177-)  F    4.05
  78 ILE   (  83-)  A    4.05
 337 ALA   (  38-)  C    4.03
1986 LYS   ( 177-)  J    4.03
2694 THR   ( 287-)  L    4.01
1583 ILE   (  83-)  H    4.00

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.

 693 TRP   ( 237-)  D    -2.9
1291 TRP   ( 237-)  F    -2.9
2644 TRP   ( 237-)  L    -2.9
2345 TRP   ( 237-)  K    -2.9
 992 TRP   ( 237-)  E    -2.9
2046 TRP   ( 237-)  J    -2.9
1342 LEU   ( 288-)  F    -2.8
 744 LEU   ( 288-)  D    -2.8
1043 LEU   ( 288-)  E    -2.8
2396 LEU   ( 288-)  K    -2.8
2097 LEU   ( 288-)  J    -2.8
2695 LEU   ( 288-)  L    -2.8
1492 PHE   ( 144-)  G    -2.8
1644 PHE   ( 144-)  H    -2.8
1796 PHE   ( 144-)  I    -2.8
 443 PHE   ( 144-)  C    -2.8
 291 PHE   ( 144-)  B    -2.8
 139 PHE   ( 144-)  A    -2.8
  74 THR   (  79-)  A    -2.6
1758 PRO   ( 106-)  I    -2.6
 101 PRO   ( 106-)  A    -2.6
1454 PRO   ( 106-)  G    -2.6
 405 PRO   ( 106-)  C    -2.6
1606 PRO   ( 106-)  H    -2.6
 253 PRO   ( 106-)  B    -2.6
And so on for a total of 165 lines.

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.

   4 SER   (   9-)  A  Poor phi/psi
   5 ASP   (  10-)  A  Poor phi/psi
  28 ALA   (  33-)  A  Poor phi/psi
  41 ASN   (  46-)  A  Poor phi/psi
  63 GLY   (  68-)  A  Poor phi/psi
  65 PRO   (  70-)  A  Poor phi/psi
  67 THR   (  72-)  A  Poor phi/psi
  83 GLN   (  88-)  A  Poor phi/psi
  95 PRO   ( 100-)  A  Poor phi/psi
  98 ARG   ( 103-)  A  Poor phi/psi
 100 THR   ( 105-)  A  Poor phi/psi
 103 GLY   ( 108-)  A  Poor phi/psi
 105 GLU   ( 110-)  A  Poor phi/psi
 106 ALA   ( 111-)  A  Poor phi/psi
 141 GLU   ( 146-)  A  Poor phi/psi
 142 SER   ( 147-)  A  Poor phi/psi
 156 SER   (   9-)  B  Poor phi/psi
 157 ASP   (  10-)  B  Poor phi/psi
 180 ALA   (  33-)  B  Poor phi/psi
 193 ASN   (  46-)  B  Poor phi/psi
 215 GLY   (  68-)  B  Poor phi/psi
 217 PRO   (  70-)  B  Poor phi/psi
 219 THR   (  72-)  B  Poor phi/psi
 235 GLN   (  88-)  B  Poor phi/psi
 247 PRO   ( 100-)  B  Poor phi/psi
And so on for a total of 263 lines.

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.

 826 SER   (  71-)  E    0.33
2179 SER   (  71-)  K    0.35
1973 SER   ( 164-)  J    0.35
2571 SER   ( 164-)  L    0.35
 527 SER   (  71-)  D    0.35
1880 SER   (  71-)  J    0.35
 620 SER   ( 164-)  D    0.36
2272 SER   ( 164-)  K    0.36
1218 SER   ( 164-)  F    0.36
 919 SER   ( 164-)  E    0.36
2478 SER   (  71-)  L    0.37
1125 SER   (  71-)  F    0.37

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 PRO   (   8-)  A      0
   4 SER   (   9-)  A      0
   5 ASP   (  10-)  A      0
  17 ALA   (  22-)  A      0
  18 GLU   (  23-)  A      0
  25 ASN   (  30-)  A      0
  26 ARG   (  31-)  A      0
  27 ARG   (  32-)  A      0
  29 ASN   (  34-)  A      0
  31 LEU   (  36-)  A      0
  32 LEU   (  37-)  A      0
  33 ALA   (  38-)  A      0
  34 ASN   (  39-)  A      0
  39 ARG   (  44-)  A      0
  41 ASN   (  46-)  A      0
  48 GLU   (  53-)  A      0
  50 LEU   (  55-)  A      0
  54 TYR   (  59-)  A      0
  62 GLN   (  67-)  A      0
  66 SER   (  71-)  A      0
  67 THR   (  72-)  A      0
  68 HIS   (  73-)  A      0
  79 ALA   (  84-)  A      0
  81 SER   (  86-)  A      0
  82 TYR   (  87-)  A      0
And so on for a total of 1264 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 : 1.414

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

 661 ASN   ( 205-)  D   1.75
 750 THR   ( 294-)  D   2.45
 960 ASN   ( 205-)  E   1.95
1049 THR   ( 294-)  E   2.55
1259 ASN   ( 205-)  F   1.79
1348 THR   ( 294-)  F   2.56
2014 ASN   ( 205-)  J   1.77
2103 THR   ( 294-)  J   2.50
2313 ASN   ( 205-)  K   1.79
2402 THR   ( 294-)  K   2.56
2612 ASN   ( 205-)  L   1.84
2701 THR   ( 294-)  L   2.60

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

1238 PRO   ( 184-)  F    0.45 HIGH

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].

   7 PRO   (  12-)  A  -118.0 half-chair C-delta/C-gamma (-126 degrees)
  15 PRO   (  20-)  A    52.0 half-chair C-delta/C-gamma (54 degrees)
 159 PRO   (  12-)  B  -116.4 envelop C-gamma (-108 degrees)
 167 PRO   (  20-)  B    51.5 half-chair C-delta/C-gamma (54 degrees)
 311 PRO   (  12-)  C  -118.2 half-chair C-delta/C-gamma (-126 degrees)
 704 PRO   ( 248-)  D  -113.0 envelop C-gamma (-108 degrees)
1360 PRO   (  12-)  G  -118.3 half-chair C-delta/C-gamma (-126 degrees)
1368 PRO   (  20-)  G    53.0 half-chair C-delta/C-gamma (54 degrees)
1512 PRO   (  12-)  H  -117.8 half-chair C-delta/C-gamma (-126 degrees)
1520 PRO   (  20-)  H    52.1 half-chair C-delta/C-gamma (54 degrees)
1664 PRO   (  12-)  I  -115.9 envelop C-gamma (-108 degrees)
1672 PRO   (  20-)  I    52.6 half-chair C-delta/C-gamma (54 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.

1392 ARG   (  44-)  G      NH1 <-> 2041 ARG   ( 232-)  J      NH2    0.57    2.28  INTRA BF
2438 THR   (  31-)  L      OG1 <-> 2454 ARG   (  47-)  L      NH1    0.43    2.27  INTRA BF
 487 THR   (  31-)  D      OG1 <->  503 ARG   (  47-)  D      NH1    0.42    2.28  INTRA BL
1840 THR   (  31-)  J      OG1 <-> 1856 ARG   (  47-)  J      NH1    0.42    2.28  INTRA BL
 786 THR   (  31-)  E      OG1 <->  802 ARG   (  47-)  E      NH1    0.40    2.30  INTRA BL
1085 THR   (  31-)  F      OG1 <-> 1101 ARG   (  47-)  F      NH1    0.40    2.30  INTRA BF
2296 VAL   ( 188-)  K      O   <-> 2407 CYS   ( 299-)  K      SG     0.40    2.45  INTRA BF
1997 VAL   ( 188-)  J      O   <-> 2108 CYS   ( 299-)  J      SG     0.38    2.47  INTRA BF
2595 VAL   ( 188-)  L      O   <-> 2706 CYS   ( 299-)  L      SG     0.38    2.47  INTRA BF
 644 VAL   ( 188-)  D      O   <->  755 CYS   ( 299-)  D      SG     0.37    2.48  INTRA BF
 943 VAL   ( 188-)  E      O   <-> 1054 CYS   ( 299-)  E      SG     0.37    2.48  INTRA BF
2139 THR   (  31-)  K      OG1 <-> 2155 ARG   (  47-)  K      NH1    0.37    2.33  INTRA BL
1242 VAL   ( 188-)  F      O   <-> 1353 CYS   ( 299-)  F      SG     0.36    2.49  INTRA BF
1906 CYS   (  97-)  J      SG  <-> 1972 CYS   ( 163-)  J      SG     0.35    3.10  INTRA BL
2017 TYR   ( 208-)  J      O   <-> 2019 PRO   ( 210-)  J      N      0.34    2.36  INTRA BF
1262 TYR   ( 208-)  F      O   <-> 1264 PRO   ( 210-)  F      N      0.34    2.36  INTRA BF
2205 CYS   (  97-)  K      SG  <-> 2271 CYS   ( 163-)  K      SG     0.34    3.11  INTRA BL
1921 THR   ( 112-)  J      CG2 <-> 1923 ASN   ( 114-)  J      N      0.34    2.76  INTRA BL
 963 TYR   ( 208-)  E      O   <->  965 PRO   ( 210-)  E      N      0.33    2.37  INTRA BF
2519 THR   ( 112-)  L      CG2 <-> 2521 ASN   ( 114-)  L      N      0.33    2.77  INTRA BF
2316 TYR   ( 208-)  K      O   <-> 2318 PRO   ( 210-)  K      N      0.32    2.38  INTRA BF
1166 THR   ( 112-)  F      CG2 <-> 1168 ASN   ( 114-)  F      N      0.32    2.78  INTRA BF
2615 TYR   ( 208-)  L      O   <-> 2617 PRO   ( 210-)  L      N      0.32    2.38  INTRA BF
 867 THR   ( 112-)  E      CG2 <->  869 ASN   ( 114-)  E      N      0.32    2.78  INTRA BF
2105 SER   ( 296-)  J      C   <-> 2107 GLY   ( 298-)  J      N      0.32    2.58  INTRA BF
And so on for a total of 635 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

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.

 689 TYR   ( 233-)  D      -8.38
2640 TYR   ( 233-)  L      -8.35
2341 TYR   ( 233-)  K      -8.35
1287 TYR   ( 233-)  F      -8.35
 988 TYR   ( 233-)  E      -8.34
2042 TYR   ( 233-)  J      -8.33
2348 LYS   ( 240-)  K      -6.51
2049 LYS   ( 240-)  J      -6.51
 995 LYS   ( 240-)  E      -6.50
 696 LYS   ( 240-)  D      -6.50
2647 LYS   ( 240-)  L      -6.49
1294 LYS   ( 240-)  F      -6.48
1719 GLN   (  67-)  I      -6.46
1567 GLN   (  67-)  H      -6.45
  62 GLN   (  67-)  A      -6.43
 214 GLN   (  67-)  B      -6.41
1415 GLN   (  67-)  G      -6.40
 366 GLN   (  67-)  C      -6.39
 406 GLU   ( 107-)  C      -5.92
 102 GLU   ( 107-)  A      -5.92
1455 GLU   ( 107-)  G      -5.92
1607 GLU   ( 107-)  H      -5.92
1759 GLU   ( 107-)  I      -5.92
 254 GLU   ( 107-)  B      -5.92
2240 HIS   ( 132-)  K      -5.76
And so on for a total of 108 lines.

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: 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: C

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: D

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: E

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: F

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: G

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: H

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: I

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: J

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: K

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: L

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.

2383 MET   ( 275-)  K   -2.65
2682 MET   ( 275-)  L   -2.65
1329 MET   ( 275-)  F   -2.65
 731 MET   ( 275-)  D   -2.65
2084 MET   ( 275-)  J   -2.63
 652 GLY   ( 196-)  D   -2.61
2603 GLY   ( 196-)  L   -2.60
2042 TYR   ( 233-)  J   -2.59
2029 GLU   ( 220-)  J   -2.59
2304 GLY   ( 196-)  K   -2.59
2005 GLY   ( 196-)  J   -2.55
1573 HIS   (  73-)  H   -2.51
1030 MET   ( 275-)  E   -2.51

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

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.

  14 ASN   (  19-)  A
  25 ASN   (  30-)  A
  56 GLN   (  61-)  A
  73 HIS   (  78-)  A
 166 ASN   (  19-)  B
 177 ASN   (  30-)  B
 208 GLN   (  61-)  B
 225 HIS   (  78-)  B
 249 GLN   ( 102-)  B
 318 ASN   (  19-)  C
 360 GLN   (  61-)  C
 377 HIS   (  78-)  C
 401 GLN   ( 102-)  C
 484 GLN   (  28-)  D
 499 ASN   (  43-)  D
 577 HIS   ( 121-)  D
 741 HIS   ( 285-)  D
 783 GLN   (  28-)  E
 798 ASN   (  43-)  E
 876 HIS   ( 121-)  E
1040 HIS   ( 285-)  E
1082 GLN   (  28-)  F
1097 ASN   (  43-)  F
1175 HIS   ( 121-)  F
1339 HIS   ( 285-)  F
1367 ASN   (  19-)  G
1378 ASN   (  30-)  G
1409 GLN   (  61-)  G
1519 ASN   (  19-)  H
1530 ASN   (  30-)  H
1561 GLN   (  61-)  H
1602 GLN   ( 102-)  H
1671 ASN   (  19-)  I
1682 ASN   (  30-)  I
1713 GLN   (  61-)  I
1754 GLN   ( 102-)  I
1837 GLN   (  28-)  J
1852 ASN   (  43-)  J
1930 HIS   ( 121-)  J
2094 HIS   ( 285-)  J
2136 GLN   (  28-)  K
2151 ASN   (  43-)  K
2229 HIS   ( 121-)  K
2393 HIS   ( 285-)  K
2435 GLN   (  28-)  L
2450 ASN   (  43-)  L
2528 HIS   ( 121-)  L
2692 HIS   ( 285-)  L

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 SER   (   9-)  A      N
   4 SER   (   9-)  A      OG
   5 ASP   (  10-)  A      N
  22 GLN   (  27-)  A      N
  26 ARG   (  31-)  A      N
  27 ARG   (  32-)  A      N
  34 ASN   (  39-)  A      ND2
  38 LEU   (  43-)  A      N
  47 SER   (  52-)  A      N
  58 LEU   (  63-)  A      N
  68 HIS   (  73-)  A      N
  79 ALA   (  84-)  A      N
  92 ILE   (  97-)  A      N
  96 CYS   ( 101-)  A      N
  98 ARG   ( 103-)  A      N
 100 THR   ( 105-)  A      N
 103 GLY   ( 108-)  A      N
 104 ALA   ( 109-)  A      N
 128 SER   ( 133-)  A      OG
 135 ASP   ( 140-)  A      N
 139 PHE   ( 144-)  A      N
 140 ALA   ( 145-)  A      N
 144 GLN   ( 149-)  A      N
 146 TYR   ( 151-)  A      OH
 156 SER   (   9-)  B      N
And so on for a total of 300 lines.

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.

  62 GLN   (  67-)  A      OE1
  68 HIS   (  73-)  A      NE2
 214 GLN   (  67-)  B      OE1
 220 HIS   (  73-)  B      NE2
 366 GLN   (  67-)  C      OE1
 372 HIS   (  73-)  C      NE2
 403 GLU   ( 104-)  C      OE2
 479 ASP   (  23-)  D      OD1
 615 GLU   ( 159-)  D      OE1
 713 ASP   ( 257-)  D      OD1
 778 ASP   (  23-)  E      OD1
 914 GLU   ( 159-)  E      OE1
1012 ASP   ( 257-)  E      OD1
1077 ASP   (  23-)  F      OD1
1213 GLU   ( 159-)  F      OE1
1311 ASP   ( 257-)  F      OD1
1415 GLN   (  67-)  G      OE1
1421 HIS   (  73-)  G      NE2
1426 HIS   (  78-)  G      ND1
1567 GLN   (  67-)  H      OE1
1573 HIS   (  73-)  H      NE2
1578 HIS   (  78-)  H      ND1
1604 GLU   ( 104-)  H      OE2
1719 GLN   (  67-)  I      OE1
1725 HIS   (  73-)  I      NE2
1730 HIS   (  78-)  I      ND1
1832 ASP   (  23-)  J      OD1
1871 ASN   (  62-)  J      OD1
1968 GLU   ( 159-)  J      OE1
2029 GLU   ( 220-)  J      OE1
2066 ASP   ( 257-)  J      OD1
2131 ASP   (  23-)  K      OD1
2267 GLU   ( 159-)  K      OE1
2365 ASP   ( 257-)  K      OD1
2430 ASP   (  23-)  L      OD1
2566 GLU   ( 159-)  L      OE1
2664 ASP   ( 257-)  L      OD1

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.

  99 GLU   ( 104-)  A   H-bonding suggests Gln
 111 GLU   ( 116-)  A   H-bonding suggests Gln; but Alt-Rotamer
 251 GLU   ( 104-)  B   H-bonding suggests Gln
 263 GLU   ( 116-)  B   H-bonding suggests Gln; but Alt-Rotamer
 403 GLU   ( 104-)  C   H-bonding suggests Gln
 415 GLU   ( 116-)  C   H-bonding suggests Gln; but Alt-Rotamer
 469 ASP   (  13-)  D   H-bonding suggests Asn; but Alt-Rotamer
 615 GLU   ( 159-)  D   H-bonding suggests Gln; but Alt-Rotamer
 648 GLU   ( 192-)  D   H-bonding suggests Gln
 713 ASP   ( 257-)  D   H-bonding suggests Asn; but Alt-Rotamer
 742 ASP   ( 286-)  D   H-bonding suggests Asn; but Alt-Rotamer
 768 ASP   (  13-)  E   H-bonding suggests Asn; but Alt-Rotamer
 914 GLU   ( 159-)  E   H-bonding suggests Gln; but Alt-Rotamer
 947 GLU   ( 192-)  E   H-bonding suggests Gln
1012 ASP   ( 257-)  E   H-bonding suggests Asn; but Alt-Rotamer
1041 ASP   ( 286-)  E   H-bonding suggests Asn; but Alt-Rotamer
1067 ASP   (  13-)  F   H-bonding suggests Asn; but Alt-Rotamer
1213 GLU   ( 159-)  F   H-bonding suggests Gln; but Alt-Rotamer
1246 GLU   ( 192-)  F   H-bonding suggests Gln
1311 ASP   ( 257-)  F   H-bonding suggests Asn; but Alt-Rotamer
1340 ASP   ( 286-)  F   H-bonding suggests Asn; but Alt-Rotamer
1452 GLU   ( 104-)  G   H-bonding suggests Gln
1464 GLU   ( 116-)  G   H-bonding suggests Gln; but Alt-Rotamer
1604 GLU   ( 104-)  H   H-bonding suggests Gln
1616 GLU   ( 116-)  H   H-bonding suggests Gln; but Alt-Rotamer
1756 GLU   ( 104-)  I   H-bonding suggests Gln
1768 GLU   ( 116-)  I   H-bonding suggests Gln; but Alt-Rotamer
1822 ASP   (  13-)  J   H-bonding suggests Asn; but Alt-Rotamer
1968 GLU   ( 159-)  J   H-bonding suggests Gln; but Alt-Rotamer
2001 GLU   ( 192-)  J   H-bonding suggests Gln; but Alt-Rotamer
2066 ASP   ( 257-)  J   H-bonding suggests Asn; but Alt-Rotamer
2095 ASP   ( 286-)  J   H-bonding suggests Asn; but Alt-Rotamer
2121 ASP   (  13-)  K   H-bonding suggests Asn; but Alt-Rotamer
2267 GLU   ( 159-)  K   H-bonding suggests Gln; but Alt-Rotamer
2300 GLU   ( 192-)  K   H-bonding suggests Gln
2365 ASP   ( 257-)  K   H-bonding suggests Asn; but Alt-Rotamer
2394 ASP   ( 286-)  K   H-bonding suggests Asn; but Alt-Rotamer
2420 ASP   (  13-)  L   H-bonding suggests Asn; but Alt-Rotamer
2566 GLU   ( 159-)  L   H-bonding suggests Gln; but Alt-Rotamer
2599 GLU   ( 192-)  L   H-bonding suggests Gln
2664 ASP   ( 257-)  L   H-bonding suggests Asn; but Alt-Rotamer
2693 ASP   ( 286-)  L   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.109
  2nd generation packing quality :  -1.894
  Ramachandran plot appearance   :  -2.774
  chi-1/chi-2 rotamer normality  :  -2.221
  Backbone conformation          :  -0.798

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.338 (tight)
  Bond angles                    :   0.688
  Omega angle restraints         :   0.257 (tight)
  Side chain planarity           :   0.228 (tight)
  Improper dihedral distribution :   0.655
  B-factor distribution          :   1.574 (loose)
  Inside/Outside distribution    :   0.962

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 : 2.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -0.3
  Ramachandran plot appearance   :  -0.3
  chi-1/chi-2 rotamer normality  :  -0.2
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.338 (tight)
  Bond angles                    :   0.688
  Omega angle restraints         :   0.257 (tight)
  Side chain planarity           :   0.228 (tight)
  Improper dihedral distribution :   0.655
  B-factor distribution          :   1.574 (loose)
  Inside/Outside distribution    :   0.962
==============

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.