WHAT IF Check report

This file was created 2012-01-05 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 pdb1nug.ent

Checks that need to be done early-on in validation

Warning: Chain identifier inconsistency

WHAT IF believes that certain residue(s) have the wrong chain identifier. It has corrected these chain identifiers as indicated in the table. In this table the residues (ligands, drugs, lipids, ions, sugars, etc) that got their chain identifier corrected are listed with the new chain identifier that is used throughout this validation report. WHAT IF does not care about the chain identifiers of water molecules.

1358  CL   ( 702-)  B  A
1363  CL   ( 702-)  A  B

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

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

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

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

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.

 553 ARG   ( 570-)  A
 570 ARG   ( 587-)  A
1232 ARG   ( 570-)  B
1249 ARG   ( 587-)  B

Warning: Tyrosine convention problem

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

 346 TYR   ( 346-)  A
 401 TYR   ( 401-)  A
 421 TYR   ( 421-)  A
 508 TYR   ( 525-)  A
 545 TYR   ( 562-)  A
 915 TYR   ( 240-)  B
 987 TYR   ( 312-)  B
1021 TYR   ( 346-)  B
1076 TYR   ( 401-)  B
1096 TYR   ( 421-)  B
1187 TYR   ( 525-)  B
1224 TYR   ( 562-)  B

Warning: Phenylalanine convention problem

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

  14 PHE   (  14-)  A
  24 PHE   (  24-)  A
 117 PHE   ( 117-)  A
 130 PHE   ( 130-)  A
 177 PHE   ( 177-)  A
 364 PHE   ( 364-)  A
 662 PHE   ( 679-)  A
 689 PHE   (  14-)  B
 699 PHE   (  24-)  B
 792 PHE   ( 117-)  B
 852 PHE   ( 177-)  B
 873 PHE   ( 198-)  B
1039 PHE   ( 364-)  B
1341 PHE   ( 679-)  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.

 141 ASP   ( 141-)  A
 183 ASP   ( 183-)  A
 245 ASP   ( 245-)  A
 301 ASP   ( 301-)  A
 303 ASP   ( 303-)  A
 324 ASP   ( 324-)  A
 493 ASP   ( 510-)  A
 549 ASP   ( 566-)  A
 627 ASP   ( 644-)  A
 642 ASP   ( 659-)  A
 816 ASP   ( 141-)  B
 858 ASP   ( 183-)  B
 902 ASP   ( 227-)  B
 920 ASP   ( 245-)  B
 976 ASP   ( 301-)  B
 978 ASP   ( 303-)  B
 995 ASP   ( 320-)  B
 999 ASP   ( 324-)  B
1172 ASP   ( 510-)  B
1241 ASP   ( 579-)  B
1306 ASP   ( 644-)  B
1321 ASP   ( 659-)  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.

  28 GLU   (  28-)  A
 152 GLU   ( 152-)  A
 153 GLU   ( 153-)  A
 157 GLU   ( 157-)  A
 254 GLU   ( 254-)  A
 391 GLU   ( 391-)  A
 515 GLU   ( 532-)  A
 529 GLU   ( 546-)  A
 825 GLU   ( 150-)  B
 827 GLU   ( 152-)  B
 828 GLU   ( 153-)  B
 832 GLU   ( 157-)  B
 856 GLU   ( 181-)  B
1066 GLU   ( 391-)  B
1136 GLU   ( 474-)  B
1159 GLU   ( 497-)  B
1194 GLU   ( 532-)  B
1208 GLU   ( 546-)  B
1209 GLU   ( 547-)  B
1261 GLU   ( 599-)  B
1284 GLU   ( 622-)  B
1314 GLU   ( 652-)  B

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.

 507 ILE   ( 524-)  A      N    CA   C    98.57   -4.5
1186 ILE   ( 524-)  B      N    CA   C    97.78   -4.8

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.

  28 GLU   (  28-)  A
 141 ASP   ( 141-)  A
 152 GLU   ( 152-)  A
 153 GLU   ( 153-)  A
 157 GLU   ( 157-)  A
 183 ASP   ( 183-)  A
 245 ASP   ( 245-)  A
 254 GLU   ( 254-)  A
 301 ASP   ( 301-)  A
 303 ASP   ( 303-)  A
 324 ASP   ( 324-)  A
 391 GLU   ( 391-)  A
 493 ASP   ( 510-)  A
 515 GLU   ( 532-)  A
 529 GLU   ( 546-)  A
 549 ASP   ( 566-)  A
 553 ARG   ( 570-)  A
 570 ARG   ( 587-)  A
 627 ASP   ( 644-)  A
 642 ASP   ( 659-)  A
 816 ASP   ( 141-)  B
 825 GLU   ( 150-)  B
 827 GLU   ( 152-)  B
 828 GLU   ( 153-)  B
 832 GLU   ( 157-)  B
 856 GLU   ( 181-)  B
 858 ASP   ( 183-)  B
 902 ASP   ( 227-)  B
 920 ASP   ( 245-)  B
 976 ASP   ( 301-)  B
 978 ASP   ( 303-)  B
 995 ASP   ( 320-)  B
 999 ASP   ( 324-)  B
1066 GLU   ( 391-)  B
1136 GLU   ( 474-)  B
1159 GLU   ( 497-)  B
1172 ASP   ( 510-)  B
1194 GLU   ( 532-)  B
1208 GLU   ( 546-)  B
1209 GLU   ( 547-)  B
1232 ARG   ( 570-)  B
1241 ASP   ( 579-)  B
1249 ARG   ( 587-)  B
1261 GLU   ( 599-)  B
1284 GLU   ( 622-)  B
1306 ASP   ( 644-)  B
1314 GLU   ( 652-)  B
1321 ASP   ( 659-)  B

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.

 947 CYS   ( 272-)  B    5.41
 272 CYS   ( 272-)  A    5.22
1343 ALA   ( 681-)  B    5.10
 897 MET   ( 222-)  B    4.86
 907 LEU   ( 232-)  B    4.55
 232 LEU   ( 232-)  A    4.49
 222 MET   ( 222-)  A    4.45
1186 ILE   ( 524-)  B    4.22

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.

 979 ARG   ( 304-)  B    -2.5
1299 LEU   ( 637-)  B    -2.5
1206 PRO   ( 544-)  B    -2.4
1207 GLU   ( 545-)  B    -2.4
 528 GLU   ( 545-)  A    -2.3
 169 ARG   ( 169-)  A    -2.2
 853 GLY   ( 178-)  B    -2.2
 620 LEU   ( 637-)  A    -2.2
1288 ASP   ( 626-)  B    -2.1
 386 PRO   ( 386-)  A    -2.1
 424 THR   ( 424-)  A    -2.1
 442 PRO   ( 442-)  A    -2.1
1096 TYR   ( 421-)  B    -2.1
 164 VAL   ( 164-)  A    -2.1
 616 GLY   ( 633-)  A    -2.1
1295 GLY   ( 633-)  B    -2.1
1033 GLU   ( 358-)  B    -2.1
 125 VAL   ( 125-)  A    -2.1
 836 ILE   ( 161-)  B    -2.1
1099 THR   ( 424-)  B    -2.1
 140 VAL   ( 140-)  A    -2.1
 939 LEU   ( 264-)  B    -2.1
 765 SER   (  90-)  B    -2.0
 815 VAL   ( 140-)  B    -2.0
1061 PRO   ( 386-)  B    -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.

  68 MET   (  68-)  A  Poor phi/psi
  76 SER   (  76-)  A  Poor phi/psi
  82 GLY   (  82-)  A  Poor phi/psi
 164 VAL   ( 164-)  A  Poor phi/psi
 183 ASP   ( 183-)  A  Poor phi/psi
 227 ASP   ( 227-)  A  Poor phi/psi
 229 ASN   ( 229-)  A  Poor phi/psi
 264 LEU   ( 264-)  A  Poor phi/psi
 268 ARG   ( 268-)  A  omega poor
 297 ASN   ( 297-)  A  Poor phi/psi
 304 ARG   ( 304-)  A  Poor phi/psi
 361 GLN   ( 361-)  A  Poor phi/psi
 367 GLY   ( 367-)  A  PRO omega poor
 382 ASN   ( 382-)  A  omega poor
 519 ASP   ( 536-)  A  Poor phi/psi
 528 GLU   ( 545-)  A  Poor phi/psi
 550 ASN   ( 567-)  A  Poor phi/psi
 562 ASP   ( 579-)  A  Poor phi/psi
 590 ARG   ( 607-)  A  Poor phi/psi
 609 ASP   ( 626-)  A  Poor phi/psi
 634 LYS   ( 651-)  A  Poor phi/psi
 641 PHE   ( 658-)  A  Poor phi/psi
 664 ALA   ( 681-)  A  Poor phi/psi
 743 MET   (  68-)  B  Poor phi/psi
 751 SER   (  76-)  B  Poor phi/psi
 755 SER   (  80-)  B  Poor phi/psi
 758 TRP   (  83-)  B  Poor phi/psi
 853 GLY   ( 178-)  B  Poor phi/psi
 858 ASP   ( 183-)  B  Poor phi/psi
 902 ASP   ( 227-)  B  Poor phi/psi
 904 ASN   ( 229-)  B  Poor phi/psi
 939 LEU   ( 264-)  B  Poor phi/psi
 943 ARG   ( 268-)  B  omega poor
 972 ASN   ( 297-)  B  Poor phi/psi
 979 ARG   ( 304-)  B  Poor phi/psi
 981 LEU   ( 306-)  B  Poor phi/psi
1007 TRP   ( 332-)  B  Poor phi/psi
1036 GLN   ( 361-)  B  Poor phi/psi
1042 GLY   ( 367-)  B  PRO omega poor
1053 ASP   ( 378-)  B  Poor phi/psi
1057 ASN   ( 382-)  B  omega poor
1080 THR   ( 405-)  B  Poor phi/psi
1207 GLU   ( 545-)  B  Poor phi/psi
1229 ASN   ( 567-)  B  Poor phi/psi
1241 ASP   ( 579-)  B  Poor phi/psi
1269 ARG   ( 607-)  B  Poor phi/psi
1313 LYS   ( 651-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.746

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.

 484 VAL   ( 501-)  A    0.36
 741 SER   (  66-)  B    0.36
 186 SER   ( 186-)  A    0.37
 895 SER   ( 220-)  B    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 LEU   (   3-)  A      0
   6 GLN   (   6-)  A      0
  10 TRP   (  10-)  A      0
  20 HIS   (  20-)  A      0
  21 THR   (  21-)  A      0
  22 ASP   (  22-)  A      0
  24 PHE   (  24-)  A      0
  25 SER   (  25-)  A      0
  27 GLN   (  27-)  A      0
  33 ARG   (  33-)  A      0
  43 MET   (  43-)  A      0
  51 GLU   (  51-)  A      0
  59 THR   (  59-)  A      0
  63 PRO   (  63-)  A      0
  68 MET   (  68-)  A      0
  69 THR   (  69-)  A      0
  70 LYS   (  70-)  A      0
  76 SER   (  76-)  A      0
  77 ASN   (  77-)  A      0
  83 TRP   (  83-)  A      0
  88 GLN   (  88-)  A      0
  91 ASN   (  91-)  A      0
  93 ASN   (  93-)  A      0
 107 ILE   ( 107-)  A      0
 109 ARG   ( 109-)  A      0
And so on for a total of 562 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 : 1.328

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!

1295 GLY   ( 633-)  B   2.08   23
 616 GLY   ( 633-)  A   2.07   20
1094 GLY   ( 419-)  B   1.53   16

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.

 594 ASN   ( 611-)  A      CB  <->  640 ARG   ( 657-)  A      NH2    0.39    2.71  INTRA
 169 ARG   ( 169-)  A      NH2 <->  575 ASP   ( 592-)  A      OD1    0.32    2.38  INTRA
 676 ALA   (   1-)  B      C   <->  794 GLN   ( 119-)  B      NE2    0.32    2.78  INTRA
1267 ARG   ( 605-)  B      N   <-> 1368 HOH   ( 935 )  B      O      0.32    2.38  INTRA
 169 ARG   ( 169-)  A      NH1 <-> 1367 HOH   ( 982 )  A      O      0.31    2.39  INTRA
 234 GLY   ( 234-)  A      N   <-> 1367 HOH   ( 948 )  A      O      0.30    2.40  INTRA
1274 VAL   ( 612-)  B      O   <-> 1319 ARG   ( 657-)  B      NH1    0.30    2.40  INTRA
 559 LYS   ( 576-)  A      NZ  <->  563 GLU   ( 580-)  A      O      0.28    2.42  INTRA BL
 604 ASP   ( 621-)  A      OD1 <->  634 LYS   ( 651-)  A      NZ     0.27    2.43  INTRA
 872 ASN   ( 197-)  B      ND2 <-> 1368 HOH   ( 729 )  B      O      0.27    2.43  INTRA BL
 768 ASN   (  93-)  B      ND2 <-> 1368 HOH   (1078 )  B      O      0.25    2.45  INTRA
 885 ASN   ( 210-)  B      ND2 <-> 1368 HOH   (1026 )  B      O      0.23    2.47  INTRA
 362 GLY   ( 362-)  A      N   <-> 1367 HOH   ( 962 )  A      O      0.22    2.48  INTRA
 480 GLU   ( 497-)  A      CG  <->  482 ASN   ( 499-)  A      ND2    0.21    2.89  INTRA BL
  48 GLY   (  48-)  A      N   <->   51 GLU   (  51-)  A      OE1    0.21    2.49  INTRA
 359 ARG   ( 359-)  A      CZ  <->  364 PHE   ( 364-)  A      CE2    0.21    2.99  INTRA
1339 ASN   ( 677-)  B      ND2 <-> 1340 LYS   ( 678-)  B      N      0.20    2.55  INTRA BL
 844 ARG   ( 169-)  B      NH1 <-> 1368 HOH   ( 954 )  B      O      0.19    2.51  INTRA
 320 ASP   ( 320-)  A      O   <->  322 GLY   ( 322-)  A      N      0.19    2.51  INTRA
 892 ARG   ( 217-)  B      NH2 <-> 1036 GLN   ( 361-)  B      OE1    0.18    2.52  INTRA
  41 MET   (  41-)  A      CE  <->   43 MET   (  43-)  A      SD     0.18    3.22  INTRA
 910 ASN   ( 235-)  B      ND2 <->  912 SER   ( 237-)  B      N      0.17    2.68  INTRA BL
 685 TRP   (  10-)  B      O   <->  690 ASN   (  15-)  B      ND2    0.17    2.53  INTRA BL
 814 ASN   ( 139-)  B      N   <-> 1368 HOH   ( 906 )  B      O      0.17    2.53  INTRA
 504 TRP   ( 521-)  A      O   <->  553 ARG   ( 570-)  A      N      0.16    2.54  INTRA BL
And so on for a total of 221 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

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.

 492 ARG   ( 509-)  A      -7.25
1171 ARG   ( 509-)  B      -7.08
1140 GLN   ( 478-)  B      -7.07
 621 LEU   ( 638-)  A      -6.96
1300 LEU   ( 638-)  B      -6.88
 737 TYR   (  62-)  B      -6.63
1326 ARG   ( 664-)  B      -6.49
 647 ARG   ( 664-)  A      -6.33
 590 ARG   ( 607-)  A      -6.31
1269 ARG   ( 607-)  B      -6.22
 794 GLN   ( 119-)  B      -6.22
 844 ARG   ( 169-)  B      -5.74
 460 LYS   ( 460-)  A      -5.71
 200 ARG   ( 200-)  A      -5.68
 875 ARG   ( 200-)  B      -5.68
 119 GLN   ( 119-)  A      -5.57
 383 PHE   ( 383-)  A      -5.43
1058 PHE   ( 383-)  B      -5.35
 169 ARG   ( 169-)  A      -5.35
 702 GLN   (  27-)  B      -5.30
 304 ARG   ( 304-)  A      -5.28
 979 ARG   ( 304-)  B      -5.27
  27 GLN   (  27-)  A      -5.23
 885 ASN   ( 210-)  B      -5.23
 361 GLN   ( 361-)  A      -5.19
 943 ARG   ( 268-)  B      -5.06
 375 ARG   ( 375-)  A      -5.05
 268 ARG   ( 268-)  A      -5.03

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

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.

1268 VAL   ( 606-)  B   -3.02
 589 VAL   ( 606-)  A   -2.90
 621 LEU   ( 638-)  A   -2.68

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

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.

1367 HOH   ( 877 )  A      O    -30.19   -2.26   -0.92
1367 HOH   (1081 )  A      O     22.07   27.20   83.69

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.

1367 HOH   ( 774 )  A      O
1367 HOH   (1050 )  A      O
1368 HOH   ( 800 )  B      O
1368 HOH   ( 970 )  B      O
Marked this atom as acceptor 1357  CL  ( 701-) A     CL
Marked this atom as acceptor 1358  CL  ( 702-) B     CL
Marked this atom as acceptor 1362  CL  ( 701-) B     CL
Marked this atom as acceptor 1363  CL  ( 702-) A     CL

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.

  20 HIS   (  20-)  A
 210 ASN   ( 210-)  A
 226 ASN   ( 226-)  A
 235 ASN   ( 235-)  A
 509 ASN   ( 526-)  A
 533 HIS   ( 550-)  A
 550 ASN   ( 567-)  A
 594 ASN   ( 611-)  A
 623 ASN   ( 640-)  A
 885 ASN   ( 210-)  B
 975 HIS   ( 300-)  B
1003 ASN   ( 328-)  B
1105 ASN   ( 430-)  B
1179 ASN   ( 517-)  B
1188 ASN   ( 526-)  B
1302 ASN   ( 640-)  B
1331 GLN   ( 669-)  B
1339 ASN   ( 677-)  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.

  30 ILE   (  30-)  A      N
  65 GLU   (  65-)  A      N
  80 SER   (  80-)  A      N
 101 SER   ( 101-)  A      N
 228 ASP   ( 228-)  A      N
 255 ILE   ( 255-)  A      N
 271 GLN   ( 271-)  A      N
 280 ASN   ( 280-)  A      ND2
 290 SER   ( 290-)  A      OG
 329 PHE   ( 329-)  A      N
 333 ASN   ( 333-)  A      ND2
 350 GLN   ( 350-)  A      NE2
 379 VAL   ( 379-)  A      N
 444 GLY   ( 444-)  A      N
 447 GLN   ( 447-)  A      N
 530 GLU   ( 547-)  A      N
 544 ARG   ( 561-)  A      N
 585 ASN   ( 602-)  A      N
 585 ASN   ( 602-)  A      ND2
 594 ASN   ( 611-)  A      N
 705 ILE   (  30-)  B      N
 776 SER   ( 101-)  B      N
 924 TRP   ( 249-)  B      N
 930 ILE   ( 255-)  B      N
 943 ARG   ( 268-)  B      NH2
 946 GLN   ( 271-)  B      N
 948 TRP   ( 273-)  B      N
 955 ASN   ( 280-)  B      ND2
 970 ASN   ( 295-)  B      ND2
 982 SER   ( 307-)  B      N
1004 PHE   ( 329-)  B      N
1008 ASN   ( 333-)  B      ND2
1122 GLN   ( 447-)  B      N
1124 ARG   ( 449-)  B      NH1
1168 ASN   ( 506-)  B      ND2
1191 LEU   ( 529-)  B      N
1228 ASP   ( 566-)  B      N
1264 ASN   ( 602-)  B      N
1275 GLN   ( 613-)  B      NE2
1284 GLU   ( 622-)  B      N
1319 ARG   ( 657-)  B      NH1
Only metal coordination for  303 ASP  ( 303-) A      OD1
Only metal coordination for  393 ASN  ( 393-) A      OD1
Only metal coordination for 1068 ASN  ( 393-) B      OD1

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.

 115 GLN   ( 115-)  A      OE1
 280 ASN   ( 280-)  A      OD1
 295 ASN   ( 295-)  A      OD1
 357 GLN   ( 357-)  A      OE1
 443 GLU   ( 443-)  A      OE1
 955 ASN   ( 280-)  B      OD1
1033 GLU   ( 358-)  B      OE1

Warning: Unusual ion packing

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

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

1359  CA   ( 703-)  A     0.80   1.03 Scores about as good as NA *2
1360  CA   ( 704-)  A     0.58   0.80 Is perhaps NA *2
1361  MG   ( 705-)  A     0.52   1.05 Is perhaps NA *2
1364  CA   ( 703-)  B     0.73   0.97 Scores about as good as NA *2
1365  CA   ( 704-)  B     0.75   0.97 Scores about as good as NA *2
1366  MG   ( 705-)  B     0.48   0.95 Is perhaps NA *2

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.

1367 HOH   ( 745 )  A      O  0.89  K  4
1367 HOH   ( 805 )  A      O  0.87  K  4
1367 HOH   ( 822 )  A      O  1.02  K  5
1368 HOH   ( 717 )  B      O  1.06  K  4 NCS 1/1
1368 HOH   ( 752 )  B      O  1.12  K  4 NCS 1/1
1368 HOH   ( 789 )  B      O  0.98  K  4 NCS 1/1
1368 HOH   ( 831 )  B      O  1.13  K  4 NCS 1/1
1368 HOH   (1064 )  B      O  1.14  K  4 Ion-B NCS 1/1
1368 HOH   (1090 )  B      O  0.86  K  5 Ion-B NCS 1/1

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.

 181 GLU   ( 181-)  A   H-bonding suggests Gln
 227 ASP   ( 227-)  A   H-bonding suggests Asn
 857 GLU   ( 182-)  B   H-bonding suggests Gln
1033 GLU   ( 358-)  B   H-bonding suggests Gln
1172 ASP   ( 510-)  B   H-bonding suggests Asn
1198 ASP   ( 536-)  B   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.051
  2nd generation packing quality :  -1.548
  Ramachandran plot appearance   :  -1.369
  chi-1/chi-2 rotamer normality  :  -1.746
  Backbone conformation          :   0.042

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.285 (tight)
  Bond angles                    :   0.595 (tight)
  Omega angle restraints         :   0.242 (tight)
  Side chain planarity           :   0.262 (tight)
  Improper dihedral distribution :   0.588
  B-factor distribution          :   0.343
  Inside/Outside distribution    :   0.997

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.0
  2nd generation packing quality :  -0.4
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :  -0.1
  Backbone conformation          :   0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.285 (tight)
  Bond angles                    :   0.595 (tight)
  Omega angle restraints         :   0.242 (tight)
  Side chain planarity           :   0.262 (tight)
  Improper dihedral distribution :   0.588
  B-factor distribution          :   0.343
  Inside/Outside distribution    :   0.997
==============

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.