WHAT IF Check report

This file was created 2013-12-09 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 pdb3v7a.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: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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 GLN   (   1-)  F    High
   2 VAL   (   2-)  F    High
   3 GLN   (   3-)  F    High
   5 GLN   (   5-)  F    High
  10 GLU   (  10-)  F    High
  12 VAL   (  12-)  F    High
  13 ARG   (  13-)  F    High
  16 THR   (  16-)  F    High
  17 SER   (  17-)  F    High
  22 CYS   (  22-)  F    High
  23 LYS   (  23-)  F    High
  27 TYR   (  27-)  F    High
  28 ALA   (  28-)  F    High
  29 PHE   (  29-)  F    High
  30 THR   (  30-)  F    High
  40 ARG   (  40-)  F    High
  43 GLN   (  43-)  F    High
  46 GLU   (  46-)  F    High
  48 ILE   (  48-)  F    High
  54 ARG   (  54-)  F    High
  57 ASP   (  57-)  F    High
  60 SER   (  60-)  F    High
  61 ASN   (  61-)  F    High
  62 GLU   (  62-)  F    High
  63 LYS   (  63-)  F    High
And so on for a total of 551 lines.

Warning: Occupancies atoms do not add up to 1.0.

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

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

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

 370 LYS   ( 150-)  G    0.63
 375 GLU   ( 155-)  G    0.80
 376 ARG   ( 156-)  G    0.77
 378 ASN   ( 158-)  G    0.90
 432 ARG   ( 212-)  G    0.21
 805 LYS   ( 150-)  H    0.63
 810 GLU   ( 155-)  H    0.80
 811 ARG   ( 156-)  H    0.77
 813 ASN   ( 158-)  H    0.90
 867 ARG   ( 212-)  H    0.21

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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 12

Crystal temperature (K) :298.000

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 : 1.700 over 8071 bonds
Average difference in B over a bond : 6.63
RMS difference in B over a bond : 8.64

Note: B-factor plot

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

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Warning: Tyrosine convention problem

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

  27 TYR   (  27-)  F
  32 TYR   (  32-)  F
  94 TYR   (  94-)  F
 104 TYR   ( 104-)  F
 109 TYR   ( 109-)  F
 152 TYR   ( 152-)  F
 256 TYR   (  36-)  G
 361 TYR   ( 141-)  G
 413 TYR   ( 193-)  G
 462 TYR   (  27-)  E
 467 TYR   (  32-)  E
 529 TYR   (  94-)  E
 539 TYR   ( 104-)  E
 544 TYR   ( 109-)  E
 587 TYR   ( 152-)  E
 691 TYR   (  36-)  H
 796 TYR   ( 141-)  H
 848 TYR   ( 193-)  H
1099 TYR   ( 452-)  A
1169 TYR   ( 522-)  A
1180 TYR   ( 533-)  A
1408 TYR   ( 452-)  B
1478 TYR   ( 522-)  B

Warning: Phenylalanine convention problem

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

 153 PHE   ( 153-)  F
 173 PHE   ( 173-)  F
 282 PHE   (  62-)  G
 291 PHE   (  71-)  G
 319 PHE   (  99-)  G
 360 PHE   ( 140-)  G
 588 PHE   ( 153-)  E
 608 PHE   ( 173-)  E
 726 PHE   (  71-)  H
 754 PHE   (  99-)  H
 795 PHE   ( 140-)  H
 874 PHE   ( 227-)  A
 977 PHE   ( 330-)  A
1089 PHE   ( 442-)  A
1092 PHE   ( 445-)  A
1151 PHE   ( 504-)  A
1188 PHE   ( 227-)  B
1291 PHE   ( 330-)  B
1350 PHE   ( 394-)  B
1398 PHE   ( 442-)  B
1401 PHE   ( 445-)  B
1460 PHE   ( 504-)  B

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.

  89 ASP   (  89-)  F
 221 ASP   (   1-)  G
 386 ASP   ( 166-)  G
 524 ASP   (  89-)  E
 656 ASP   (   1-)  H
 821 ASP   ( 166-)  H
 894 ASP   ( 247-)  A
 943 ASP   ( 296-)  A
 967 ASP   ( 320-)  A
1105 ASP   ( 458-)  A
1126 ASP   ( 479-)  A
1208 ASP   ( 247-)  B
1257 ASP   ( 296-)  B
1281 ASP   ( 320-)  B
1414 ASP   ( 458-)  B
1435 ASP   ( 479-)  B

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.

  10 GLU   (  10-)  F
  62 GLU   (  62-)  F
 198 GLU   ( 198-)  F
 326 GLU   ( 106-)  G
 344 GLU   ( 124-)  G
 375 GLU   ( 155-)  G
 445 GLU   (  10-)  E
 497 GLU   (  62-)  E
 633 GLU   ( 198-)  E
 761 GLU   ( 106-)  H
 779 GLU   ( 124-)  H
 810 GLU   ( 155-)  H
 918 GLU   ( 271-)  A
 996 GLU   ( 349-)  A
1119 GLU   ( 472-)  A
1232 GLU   ( 271-)  B
1428 GLU   ( 472-)  B

Geometric checks

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.

  10 GLU   (  10-)  F
  62 GLU   (  62-)  F
  89 ASP   (  89-)  F
 198 GLU   ( 198-)  F
 221 ASP   (   1-)  G
 326 GLU   ( 106-)  G
 344 GLU   ( 124-)  G
 375 GLU   ( 155-)  G
 386 ASP   ( 166-)  G
 445 GLU   (  10-)  E
 497 GLU   (  62-)  E
 524 ASP   (  89-)  E
 633 GLU   ( 198-)  E
 656 ASP   (   1-)  H
 761 GLU   ( 106-)  H
 779 GLU   ( 124-)  H
 810 GLU   ( 155-)  H
 821 ASP   ( 166-)  H
 894 ASP   ( 247-)  A
 918 GLU   ( 271-)  A
 943 ASP   ( 296-)  A
 967 ASP   ( 320-)  A
 996 GLU   ( 349-)  A
1105 ASP   ( 458-)  A
1119 GLU   ( 472-)  A
1126 ASP   ( 479-)  A
1208 ASP   ( 247-)  B
1232 GLU   ( 271-)  B
1257 ASP   ( 296-)  B
1281 ASP   ( 320-)  B
1414 ASP   ( 458-)  B
1428 GLU   ( 472-)  B
1435 ASP   ( 479-)  B

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.

 156 PRO   ( 156-)  F    -3.0
 591 PRO   ( 156-)  E    -2.9
 631 PRO   ( 196-)  E    -2.8
 196 PRO   ( 196-)  F    -2.8
 154 PRO   ( 154-)  F    -2.7
 589 PRO   ( 154-)  E    -2.6
  71 THR   (  71-)  F    -2.5
 735 PRO   (  80-)  H    -2.5
 506 THR   (  71-)  E    -2.5
  41 PRO   (  41-)  F    -2.5
 300 PRO   (  80-)  G    -2.5
 250 TYR   (  30-)  G    -2.4
 685 TYR   (  30-)  H    -2.4
 476 PRO   (  41-)  E    -2.4
1429 SER   ( 473-)  B    -2.4
 163 SER   ( 163-)  F    -2.4
 598 SER   ( 163-)  E    -2.4
 477 GLY   (  42-)  E    -2.3
1120 SER   ( 473-)  A    -2.3
 645 SER   ( 210-)  E    -2.3
  42 GLY   (  42-)  F    -2.3
 210 SER   ( 210-)  F    -2.3
 101 THR   ( 101-)  F    -2.3
 260 GLN   (  40-)  G    -2.3
 695 GLN   (  40-)  H    -2.3
And so on for a total of 60 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.

  42 GLY   (  42-)  F  Poor phi/psi
  66 GLY   (  66-)  F  omega poor
  76 SER   (  76-)  F  omega poor
  95 PHE   (  95-)  F  omega poor
 138 GLN   ( 138-)  F  Poor phi/psi
 153 PHE   ( 153-)  F  Poor phi/psi, PRO omega poor
 155 GLU   ( 155-)  F  PRO omega poor
 163 SER   ( 163-)  F  Poor phi/psi
 179 SER   ( 179-)  F  Poor phi/psi
 180 ASP   ( 180-)  F  Poor phi/psi
 194 THR   ( 194-)  F  Poor phi/psi
 195 TRP   ( 195-)  F  PRO omega poor
 227 SER   (   7-)  G  PRO omega poor
 250 TYR   (  30-)  G  Poor phi/psi
 251 SER   (  31-)  G  Poor phi/psi
 270 ASN   (  50-)  G  Poor phi/psi
 271 VAL   (  51-)  G  Poor phi/psi
 296 ASN   (  76-)  G  Poor phi/psi
 315 PRO   (  95-)  G  PRO omega poor
 361 TYR   ( 141-)  G  PRO omega poor
 372 ASP   ( 152-)  G  Poor phi/psi
 377 GLN   ( 157-)  G  Poor phi/psi
 477 GLY   (  42-)  E  Poor phi/psi
 501 GLY   (  66-)  E  omega poor
 511 SER   (  76-)  E  omega poor
And so on for a total of 64 lines.

Warning: chi-1/chi-2 angle correlation Z-score low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is a bit low.

chi-1/chi-2 correlation Z-score : -3.377

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!

  14 PRO   (  14-)  F      0
  25 SER   (  25-)  F      0
  27 TYR   (  27-)  F      0
  28 ALA   (  28-)  F      0
  31 ASN   (  31-)  F      0
  41 PRO   (  41-)  F      0
  43 GLN   (  43-)  F      0
  47 TRP   (  47-)  F      0
  48 ILE   (  48-)  F      0
  55 SER   (  55-)  F      0
  57 ASP   (  57-)  F      0
  59 ASN   (  59-)  F      0
  61 ASN   (  61-)  F      0
  64 PHE   (  64-)  F      0
  68 ALA   (  68-)  F      0
  77 SER   (  77-)  F      0
  78 THR   (  78-)  F      0
  85 SER   (  85-)  F      0
  91 SER   (  91-)  F      0
 103 ALA   ( 103-)  F      0
 105 PHE   ( 105-)  F      0
 107 MET   ( 107-)  F      0
 119 SER   ( 119-)  F      0
 136 ALA   ( 136-)  F      0
 137 ALA   ( 137-)  F      0
And so on for a total of 667 lines.

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 723 GLY   (  68-)  H   1.79   19
 808 GLY   ( 153-)  H   1.71   80
 373 GLY   ( 153-)  G   1.68   80
 288 GLY   (  68-)  G   1.68   17

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].

  14 PRO   (  14-)  F  -121.2 half-chair C-delta/C-gamma (-126 degrees)
  41 PRO   (  41-)  F   105.9 envelop C-beta (108 degrees)
 130 PRO   ( 130-)  F    52.3 half-chair C-delta/C-gamma (54 degrees)
 156 PRO   ( 156-)  F   -62.4 half-chair C-beta/C-alpha (-54 degrees)
 196 PRO   ( 196-)  F   -62.9 half-chair C-beta/C-alpha (-54 degrees)
 300 PRO   (  80-)  G   110.4 envelop C-beta (108 degrees)
 449 PRO   (  14-)  E  -120.8 half-chair C-delta/C-gamma (-126 degrees)
 476 PRO   (  41-)  E   106.1 envelop C-beta (108 degrees)
 591 PRO   ( 156-)  E   -61.7 half-chair C-beta/C-alpha (-54 degrees)
 631 PRO   ( 196-)  E   -63.2 envelop C-beta (-72 degrees)
 735 PRO   (  80-)  H   111.4 envelop C-beta (108 degrees)
 969 PRO   ( 322-)  A  -115.3 envelop C-gamma (-108 degrees)
1000 PRO   ( 353-)  A    34.3 envelop C-delta (36 degrees)
1165 PRO   ( 518-)  A  -114.2 envelop C-gamma (-108 degrees)
1184 PRO   ( 537-)  A  -117.0 envelop C-gamma (-108 degrees)
1283 PRO   ( 322-)  B  -115.2 envelop C-gamma (-108 degrees)
1309 PRO   ( 353-)  B    34.6 envelop C-delta (36 degrees)
1474 PRO   ( 518-)  B  -113.6 envelop C-gamma (-108 degrees)
1493 PRO   ( 537-)  B  -118.0 half-chair C-delta/C-gamma (-126 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.

1093 ILE   ( 446-)  A      O   <-> 1302 ARG   ( 341-)  B      NH2    0.60    2.10  INTRA BF
 988 ARG   ( 341-)  A      NH1 <-> 1410 ASN   ( 454-)  B      OD1    0.57    2.13  INTRA BL
 988 ARG   ( 341-)  A      NH2 <-> 1402 ILE   ( 446-)  B      O      0.53    2.17  INTRA BF
 567 ALA   ( 132-)  E      O   <->  655 ARG   ( 220-)  E      NH1    0.52    2.18  INTRA BF
 132 ALA   ( 132-)  F      O   <->  220 ARG   ( 220-)  F      NH1    0.52    2.18  INTRA BF
1101 ASN   ( 454-)  A      OD1 <-> 1302 ARG   ( 341-)  B      NH1    0.52    2.18  INTRA BL
  67 LYS   (  67-)  F      NZ  <->   90 ASP   (  90-)  F      OD2    0.43    2.27  INTRA BF
   6 GLN   (   6-)  F      N   <->  112 GLN   ( 112-)  F      OE1    0.41    2.29  INTRA BF
 502 LYS   (  67-)  E      NZ  <->  525 ASP   (  90-)  E      OD2    0.41    2.29  INTRA BF
 441 GLN   (   6-)  E      N   <->  547 GLN   ( 112-)  E      OE1    0.39    2.31  INTRA BF
 914 THR   ( 267-)  A      OG1 <->  916 ASP   ( 269-)  A      OD1    0.32    2.08  INTRA BF
1228 THR   ( 267-)  B      OG1 <-> 1230 ASP   ( 269-)  B      OD1    0.32    2.08  INTRA BF
 490 SER   (  55-)  E      OG  <->  492 ASP   (  57-)  E      OD2    0.28    2.12  INTRA BF
  55 SER   (  55-)  F      OG  <->   57 ASP   (  57-)  F      OD2    0.28    2.12  INTRA BF
 971 PRO   ( 324-)  A      O   <->  974 THR   ( 327-)  A      OG1    0.27    2.13  INTRA BL
1203 PHE   ( 242-)  B      O   <-> 1205 LEU   ( 244-)  B      N      0.26    2.44  INTRA BL
1285 PRO   ( 324-)  B      O   <-> 1288 THR   ( 327-)  B      OG1    0.26    2.14  INTRA BL
 941 VAL   ( 294-)  A      N   <->  949 HIS   ( 302-)  A      O      0.25    2.45  INTRA BF
 889 PHE   ( 242-)  A      O   <->  891 LEU   ( 244-)  A      N      0.23    2.47  INTRA BF
 252 TYR   (  32-)  G      OH  <-> 1491 LEU   ( 535-)  B      O      0.23    2.17  INTRA BL
1255 VAL   ( 294-)  B      N   <-> 1263 HIS   ( 302-)  B      O      0.23    2.47  INTRA BF
 896 LEU   ( 249-)  A      O   <-> 1162 VAL   ( 515-)  A      N      0.22    2.48  INTRA BL
1210 LEU   ( 249-)  B      O   <-> 1471 VAL   ( 515-)  B      N      0.22    2.48  INTRA BL
 574 THR   ( 139-)  E      CG2 <->  575 ASN   ( 140-)  E      N      0.22    2.78  INTRA BF
 474 GLN   (  39-)  E      OE1 <->  693 GLN   (  38-)  H      NE2    0.21    2.49  INTRA BF
And so on for a total of 183 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: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

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.

 946 ARG   ( 299-)  A      -8.55
1260 ARG   ( 299-)  B      -8.54
 573 GLN   ( 138-)  E      -6.81
 138 GLN   ( 138-)  F      -6.79
 942 GLN   ( 295-)  A      -6.38
1256 GLN   ( 295-)  B      -6.38
1071 MET   ( 424-)  A      -6.36
 377 GLN   ( 157-)  G      -6.35
 812 GLN   ( 157-)  H      -6.32
1380 MET   ( 424-)  B      -6.28
 489 ARG   (  54-)  E      -6.04
  54 ARG   (  54-)  F      -6.00
 695 GLN   (  40-)  H      -5.99
 260 GLN   (  40-)  G      -5.97
1376 LEU   ( 420-)  B      -5.89
1124 LEU   ( 477-)  A      -5.88
 112 GLN   ( 112-)  F      -5.85
 547 GLN   ( 112-)  E      -5.82
1433 LEU   ( 477-)  B      -5.82
1067 LEU   ( 420-)  A      -5.81
 763 LYS   ( 108-)  H      -5.48
 328 LYS   ( 108-)  G      -5.47
1163 VAL   ( 516-)  A      -5.42
1472 VAL   ( 516-)  B      -5.36
 466 ASN   (  31-)  E      -5.31
 155 GLU   ( 155-)  F      -5.31
 844 ARG   ( 189-)  H      -5.31
  31 ASN   (  31-)  F      -5.31
 590 GLU   ( 155-)  E      -5.28
 409 ARG   ( 189-)  G      -5.24
 685 TYR   (  30-)  H      -5.20
 945 HIS   ( 298-)  A      -5.17
 250 TYR   (  30-)  G      -5.16
1259 HIS   ( 298-)  B      -5.14
1099 TYR   ( 452-)  A      -5.12
 597 ASN   ( 162-)  E      -5.10
1012 TYR   ( 365-)  A      -5.10
 162 ASN   ( 162-)  F      -5.09
1119 GLU   ( 472-)  A      -5.02
1428 GLU   ( 472-)  B      -5.02

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.

 944 GLU   ( 297-)  A       946 - ARG    299- ( A)         -5.98
1069 LEU   ( 422-)  A      1071 - MET    424- ( A)         -4.98
1258 GLU   ( 297-)  B      1260 - ARG    299- ( B)         -5.97
1378 LEU   ( 422-)  B      1380 - MET    424- ( B)         -4.89

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: 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: 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: 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: 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: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

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.

 171 HIS   ( 171-)  F
 258 GLN   (  38-)  G
 299 GLN   (  79-)  G
 606 HIS   ( 171-)  E
 693 GLN   (  38-)  H
 734 GLN   (  79-)  H
 951 ASN   ( 304-)  A
1265 ASN   ( 304-)  B

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.

   2 VAL   (   2-)  F      N
   7 SER   (   7-)  F      OG
  27 TYR   (  27-)  F      OH
  36 TRP   (  36-)  F      NE1
  45 LEU   (  45-)  F      N
  74 LYS   (  74-)  F      N
  82 GLN   (  82-)  F      NE2
 101 THR   ( 101-)  F      N
 102 THR   ( 102-)  F      N
 135 SER   ( 135-)  F      N
 142 MET   ( 142-)  F      N
 180 ASP   ( 180-)  F      N
 195 TRP   ( 195-)  F      N
 200 VAL   ( 200-)  F      N
 209 SER   ( 209-)  F      N
 214 ASP   ( 214-)  F      N
 223 GLN   (   3-)  G      N
 247 GLU   (  27-)  G      N
 249 ILE   (  29-)  G      N
 255 TRP   (  35-)  G      NE1
 309 GLN   (  89-)  G      NE2
 310 HIS   (  90-)  G      NE2
 317 TRP   (  97-)  G      N
 318 THR   (  98-)  G      N
 328 LYS   ( 108-)  G      N
And so on for a total of 149 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.

 382 ASN   ( 162-)  G      OD1
 924 GLN   ( 277-)  A      OE1
1084 GLU   ( 437-)  A      OE2
1105 ASP   ( 458-)  A      OD2
1143 GLU   ( 496-)  A      OE1
1238 GLN   ( 277-)  B      OE1
1414 ASP   ( 458-)  B      OD2
1424 HIS   ( 468-)  B      NE2
1452 GLU   ( 496-)  B      OE1

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 :  -1.191
  2nd generation packing quality :  -0.885
  Ramachandran plot appearance   :  -2.588
  chi-1/chi-2 rotamer normality  :  -3.377 (poor)
  Backbone conformation          :  -0.109

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.213 (tight)
  Bond angles                    :   0.433 (tight)
  Omega angle restraints         :   0.876
  Side chain planarity           :   0.185 (tight)
  Improper dihedral distribution :   0.441
  B-factor distribution          :   1.700 (loose)
  Inside/Outside distribution    :   0.989

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 : 3.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.1
  2nd generation packing quality :   1.1
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :   0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.213 (tight)
  Bond angles                    :   0.433 (tight)
  Omega angle restraints         :   0.876
  Side chain planarity           :   0.185 (tight)
  Improper dihedral distribution :   0.441
  B-factor distribution          :   1.700 (loose)
  Inside/Outside distribution    :   0.989
==============

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.