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 pdb1nud.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.686
CA-only RMS fit for the two chains : 0.410

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

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.

1359  BR   ( 711-)  B  A
1371  BR   ( 712-)  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.

 551 ARG   ( 570-)  A
 568 ARG   ( 587-)  A
 606 ARG   ( 625-)  A
1224 ARG   ( 570-)  B
1241 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

 240 TYR   ( 240-)  A
 312 TYR   ( 312-)  A
 401 TYR   ( 401-)  A
 421 TYR   ( 421-)  A
 506 TYR   ( 525-)  A
 543 TYR   ( 562-)  A
 913 TYR   ( 240-)  B
1019 TYR   ( 346-)  B
1074 TYR   ( 401-)  B
1094 TYR   ( 421-)  B
1112 TYR   ( 439-)  B
1179 TYR   ( 525-)  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
 163 PHE   ( 163-)  A
 177 PHE   ( 177-)  A
 364 PHE   ( 364-)  A
 639 PHE   ( 658-)  A
 660 PHE   ( 679-)  A
 687 PHE   (  14-)  B
 697 PHE   (  24-)  B
 836 PHE   ( 163-)  B
 850 PHE   ( 177-)  B
 871 PHE   ( 198-)  B
 969 PHE   ( 296-)  B
1037 PHE   ( 364-)  B
1062 PHE   ( 389-)  B
1333 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
 491 ASP   ( 510-)  A
 547 ASP   ( 566-)  A
 625 ASP   ( 644-)  A
 640 ASP   ( 659-)  A
 814 ASP   ( 141-)  B
 856 ASP   ( 183-)  B
 918 ASP   ( 245-)  B
 974 ASP   ( 301-)  B
 976 ASP   ( 303-)  B
 997 ASP   ( 324-)  B
1068 ASP   ( 395-)  B
1164 ASP   ( 510-)  B
1233 ASP   ( 579-)  B
1298 ASP   ( 644-)  B
1313 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.

 152 GLU   ( 152-)  A
 153 GLU   ( 153-)  A
 157 GLU   ( 157-)  A
 181 GLU   ( 181-)  A
 478 GLU   ( 497-)  A
 513 GLU   ( 532-)  A
 527 GLU   ( 546-)  A
 528 GLU   ( 547-)  A
 580 GLU   ( 599-)  A
 603 GLU   ( 622-)  A
 633 GLU   ( 652-)  A
 825 GLU   ( 152-)  B
 826 GLU   ( 153-)  B
 830 GLU   ( 157-)  B
 854 GLU   ( 181-)  B
 855 GLU   ( 182-)  B
1064 GLU   ( 391-)  B
1121 GLU   ( 448-)  B
1151 GLU   ( 497-)  B
1186 GLU   ( 532-)  B
1200 GLU   ( 546-)  B
1240 GLU   ( 586-)  B
1253 GLU   ( 599-)  B
1257 GLU   ( 603-)  B
1276 GLU   ( 622-)  B
1306 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.

 505 ILE   ( 524-)  A      N    CA   C    97.61   -4.9
 663 ILE   ( 682-)  A      N    CA   C    99.77   -4.1

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.

 141 ASP   ( 141-)  A
 152 GLU   ( 152-)  A
 153 GLU   ( 153-)  A
 157 GLU   ( 157-)  A
 181 GLU   ( 181-)  A
 183 ASP   ( 183-)  A
 245 ASP   ( 245-)  A
 301 ASP   ( 301-)  A
 478 GLU   ( 497-)  A
 491 ASP   ( 510-)  A
 513 GLU   ( 532-)  A
 527 GLU   ( 546-)  A
 528 GLU   ( 547-)  A
 547 ASP   ( 566-)  A
 551 ARG   ( 570-)  A
 568 ARG   ( 587-)  A
 580 GLU   ( 599-)  A
 603 GLU   ( 622-)  A
 606 ARG   ( 625-)  A
 625 ASP   ( 644-)  A
 633 GLU   ( 652-)  A
 640 ASP   ( 659-)  A
 814 ASP   ( 141-)  B
 825 GLU   ( 152-)  B
 826 GLU   ( 153-)  B
 830 GLU   ( 157-)  B
 854 GLU   ( 181-)  B
 855 GLU   ( 182-)  B
 856 ASP   ( 183-)  B
 918 ASP   ( 245-)  B
 974 ASP   ( 301-)  B
 976 ASP   ( 303-)  B
 997 ASP   ( 324-)  B
1064 GLU   ( 391-)  B
1068 ASP   ( 395-)  B
1121 GLU   ( 448-)  B
1151 GLU   ( 497-)  B
1164 ASP   ( 510-)  B
1186 GLU   ( 532-)  B
1200 GLU   ( 546-)  B
1224 ARG   ( 570-)  B
1233 ASP   ( 579-)  B
1240 GLU   ( 586-)  B
1241 ARG   ( 587-)  B
1253 GLU   ( 599-)  B
1257 GLU   ( 603-)  B
1276 GLU   ( 622-)  B
1298 ASP   ( 644-)  B
1306 GLU   ( 652-)  B
1313 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.

 945 CYS   ( 272-)  B    5.95
 905 LEU   ( 232-)  B    5.34
 232 LEU   ( 232-)  A    5.09
 505 ILE   ( 524-)  A    4.28
 272 CYS   ( 272-)  A    4.14

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.

  63 PRO   (  63-)  A    -2.7
 842 ARG   ( 169-)  B    -2.6
 526 GLU   ( 545-)  A    -2.3
1059 PRO   ( 386-)  B    -2.3
 636 ARG   ( 655-)  A    -2.2
1167 THR   ( 513-)  B    -2.2
 837 VAL   ( 164-)  B    -2.2
 681 ILE   (   8-)  B    -2.2
 798 VAL   ( 125-)  B    -2.2
 589 LYS   ( 608-)  A    -2.2
 488 LEU   ( 507-)  A    -2.2
1287 GLY   ( 633-)  B    -2.1
1097 THR   ( 424-)  B    -2.1
 424 THR   ( 424-)  A    -2.1
  41 MET   (  41-)  A    -2.1
 606 ARG   ( 625-)  A    -2.1
 614 GLY   ( 633-)  A    -2.1
 583 ASN   ( 602-)  A    -2.1
1121 GLU   ( 448-)  B    -2.1
 643 PRO   ( 662-)  A    -2.1
 551 ARG   ( 570-)  A    -2.0
 642 LEU   ( 661-)  A    -2.0
 755 GLY   (  82-)  B    -2.0
  11 GLN   (  11-)  A    -2.0
 811 LEU   ( 138-)  B    -2.0
1199 GLU   ( 545-)  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
 119 GLN   ( 119-)  A  Poor phi/psi
 120 GLY   ( 120-)  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
 268 ARG   ( 268-)  A  omega poor
 297 ASN   ( 297-)  A  Poor phi/psi
 304 ARG   ( 304-)  A  Poor phi/psi
 306 LEU   ( 306-)  A  Poor phi/psi
 337 PHE   ( 337-)  A  Poor phi/psi
 361 GLN   ( 361-)  A  Poor phi/psi
 367 GLY   ( 367-)  A  PRO omega poor
 382 ASN   ( 382-)  A  omega poor
 416 HIS   ( 416-)  A  Poor phi/psi
 526 GLU   ( 545-)  A  Poor phi/psi
 546 SER   ( 565-)  A  Poor phi/psi
 560 ASP   ( 579-)  A  Poor phi/psi
 583 ASN   ( 602-)  A  Poor phi/psi
 588 ARG   ( 607-)  A  Poor phi/psi
 632 LYS   ( 651-)  A  Poor phi/psi
 686 ALA   (  13-)  B  Poor phi/psi
 741 MET   (  68-)  B  Poor phi/psi
 749 SER   (  76-)  B  Poor phi/psi
 755 GLY   (  82-)  B  Poor phi/psi
 837 VAL   ( 164-)  B  Poor phi/psi
 842 ARG   ( 169-)  B  Poor phi/psi
 856 ASP   ( 183-)  B  Poor phi/psi
 874 ASP   ( 201-)  B  Poor phi/psi
 900 ASP   ( 227-)  B  Poor phi/psi
 902 ASN   ( 229-)  B  Poor phi/psi
 908 ASN   ( 235-)  B  Poor phi/psi
 937 LEU   ( 264-)  B  Poor phi/psi
 941 ARG   ( 268-)  B  omega poor
 970 ASN   ( 297-)  B  Poor phi/psi
 977 ARG   ( 304-)  B  Poor phi/psi
 979 LEU   ( 306-)  B  Poor phi/psi
1029 PRO   ( 356-)  B  Poor phi/psi
1034 GLN   ( 361-)  B  Poor phi/psi
1040 GLY   ( 367-)  B  PRO omega poor
1055 ASN   ( 382-)  B  omega poor
1190 ASP   ( 536-)  B  Poor phi/psi
1192 ALA   ( 538-)  B  Poor phi/psi
1199 GLU   ( 545-)  B  Poor phi/psi
1221 ASN   ( 567-)  B  Poor phi/psi
1233 ASP   ( 579-)  B  Poor phi/psi
1261 ARG   ( 607-)  B  Poor phi/psi
1280 ASP   ( 626-)  B  Poor phi/psi
1305 LYS   ( 651-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.516

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.

 859 SER   ( 186-)  B    0.36
 739 SER   (  66-)  B    0.36
 220 SER   ( 220-)  A    0.36

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   3 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
  26 SER   (  26-)  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
  68 MET   (  68-)  A      0
  69 THR   (  69-)  A      0
  83 TRP   (  83-)  A      0
  88 GLN   (  88-)  A      0
  89 ALA   (  89-)  A      0
  91 ASN   (  91-)  A      0
  93 ASN   (  93-)  A      0
 107 ILE   ( 107-)  A      0
 109 ARG   ( 109-)  A      0
 118 SER   ( 118-)  A      0
 119 GLN   ( 119-)  A      0
 137 TRP   ( 137-)  A      0
And so on for a total of 550 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 : 1.244

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!

1287 GLY   ( 633-)  B   2.13   18
 614 GLY   ( 633-)  A   2.04   16
1117 GLY   ( 444-)  B   1.53   80

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]

 600 PRO   ( 619-)  A    0.46 HIGH

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.

 976 ASP   ( 303-)  B      CB  <-> 1362  CA   ( 703-)  B     CA      0.44    2.76  INTRA
 592 ASN   ( 611-)  A      CB  <->  638 ARG   ( 657-)  A      NH2    0.35    2.75  INTRA
 478 GLU   ( 497-)  A      N   <-> 1372 HOH   ( 860 )  A      O      0.34    2.36  INTRA BL
1197 ASP   ( 543-)  B      N   <-> 1200 GLU   ( 546-)  B      OE1    0.31    2.39  INTRA BF
 976 ASP   ( 303-)  B      CB  <->  978 ASN   ( 305-)  B      ND2    0.31    2.79  INTRA
 217 ARG   ( 217-)  A      NH2 <->  365 GLN   ( 365-)  A      NE2    0.30    2.55  INTRA BL
 169 ARG   ( 169-)  A      NH2 <->  573 ASP   ( 592-)  A      CG     0.29    2.81  INTRA
 361 GLN   ( 361-)  A      N   <-> 1372 HOH   ( 845 )  A      O      0.28    2.42  INTRA
 941 ARG   ( 268-)  B      NH1 <-> 1373 HOH   ( 753 )  B      O      0.28    2.42  INTRA BL
 291 ARG   ( 291-)  A      NH2 <-> 1355  CL   ( 707-)  A     CL      0.26    2.84  INTRA BL
 420 ARG   ( 420-)  A      NH1 <-> 1372 HOH   ( 737 )  A      O      0.25    2.45  INTRA
 986 ASP   ( 313-)  B      OD1 <->  988 MET   ( 315-)  B      N      0.25    2.45  INTRA
 890 ARG   ( 217-)  B      NH2 <-> 1038 GLN   ( 365-)  B      NE2    0.24    2.61  INTRA
1032 ARG   ( 359-)  B      NH1 <-> 1035 GLY   ( 362-)  B      O      0.24    2.46  INTRA
  23 LYS   (  23-)  A      NZ  <-> 1372 HOH   ( 738 )  A      O      0.24    2.46  INTRA BL
 361 GLN   ( 361-)  A      NE2 <-> 1372 HOH   ( 747 )  A      O      0.24    2.46  INTRA
1172 MET   ( 518-)  B      SD  <-> 1204 HIS   ( 550-)  B      CD2    0.24    3.16  INTRA
1008 GLY   ( 335-)  B      N   <-> 1023 GLN   ( 350-)  B      O      0.24    2.46  INTRA BL
1365  CL   ( 706-)  B     CL   <-> 1373 HOH   ( 824 )  B      O      0.23    2.57  INTRA
 448 GLU   ( 448-)  A      OE2 <->  449 ARG   ( 449-)  A      NE     0.23    2.47  INTRA
 964 ARG   ( 291-)  B      NH2 <-> 1366  CL   ( 707-)  B     CL      0.23    2.87  INTRA BL
 945 CYS   ( 272-)  B      SG  <-> 1179 TYR   ( 525-)  B      OH     0.23    2.77  INTRA BL
1018 SER   ( 345-)  B      N   <-> 1373 HOH   ( 729 )  B      O      0.22    2.48  INTRA
 654 ASP   ( 673-)  A      OD1 <->  664 LYS   ( 683-)  A      NZ     0.22    2.48  INTRA BL
1265 ASN   ( 611-)  B      ND2 <-> 1311 ARG   ( 657-)  B      NH2    0.22    2.63  INTRA
And so on for a total of 289 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.

 619 LEU   ( 638-)  A      -7.11
1163 ARG   ( 509-)  B      -7.00
 792 GLN   ( 119-)  B      -6.98
1292 LEU   ( 638-)  B      -6.91
 735 TYR   (  62-)  B      -6.79
 490 ARG   ( 509-)  A      -6.79
 119 GLN   ( 119-)  A      -6.64
 588 ARG   ( 607-)  A      -6.57
1318 ARG   ( 664-)  B      -6.53
 645 ARG   ( 664-)  A      -6.38
 842 ARG   ( 169-)  B      -6.30
  62 TYR   (  62-)  A      -6.27
1261 ARG   ( 607-)  B      -6.27
 873 ARG   ( 200-)  B      -5.71
 169 ARG   ( 169-)  A      -5.60
 200 ARG   ( 200-)  A      -5.60
 361 GLN   ( 361-)  A      -5.38
  27 GLN   (  27-)  A      -5.37
1056 PHE   ( 383-)  B      -5.35
 383 PHE   ( 383-)  A      -5.30
 913 TYR   ( 240-)  B      -5.23
1034 GLN   ( 361-)  B      -5.20
 472 MET   ( 491-)  A      -5.07
1048 ARG   ( 375-)  B      -5.07
 375 ARG   ( 375-)  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.

1260 VAL   ( 606-)  B   -3.05
1180 ASN   ( 526-)  B   -2.90
 587 VAL   ( 606-)  A   -2.88
 507 ASN   ( 526-)  A   -2.80
 380 GLN   ( 380-)  A   -2.52

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.

1373 HOH   ( 845 )  B      O     38.45  -25.16   60.19
1373 HOH   ( 902 )  B      O     98.34   16.64   82.30

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.

1372 HOH   ( 775 )  A      O
1372 HOH   ( 789 )  A      O
1372 HOH   ( 795 )  A      O
1372 HOH   ( 837 )  A      O
1373 HOH   ( 755 )  B      O
1373 HOH   ( 764 )  B      O
1373 HOH   ( 768 )  B      O
1373 HOH   ( 778 )  B      O
1373 HOH   ( 781 )  B      O
1373 HOH   ( 799 )  B      O
1373 HOH   ( 861 )  B      O
1373 HOH   ( 897 )  B      O
1373 HOH   ( 908 )  B      O
Marked this atom as acceptor 1352  CL  ( 704-) A     CL
Marked this atom as acceptor 1353  CL  ( 705-) A     CL
Marked this atom as acceptor 1354  CL  ( 706-) A     CL
Marked this atom as acceptor 1355  CL  ( 707-) A     CL
Marked this atom as acceptor 1363  CL  ( 704-) B     CL
Marked this atom as acceptor 1364  CL  ( 705-) B     CL
Marked this atom as acceptor 1365  CL  ( 706-) B     CL
Marked this atom as acceptor 1366  CL  ( 707-) B     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.

 271 GLN   ( 271-)  A
 280 ASN   ( 280-)  A
 357 GLN   ( 357-)  A
 361 GLN   ( 361-)  A
 487 ASN   ( 506-)  A
 498 ASN   ( 517-)  A
 539 GLN   ( 558-)  A
 583 ASN   ( 602-)  A
 684 GLN   (  11-)  B
 750 ASN   (  77-)  B
 812 ASN   ( 139-)  B
 908 ASN   ( 235-)  B
1034 GLN   ( 361-)  B
1180 ASN   ( 526-)  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.

  26 SER   (  26-)  A      N
  30 ILE   (  30-)  A      N
  35 GLN   (  35-)  A      N
 115 GLN   ( 115-)  A      NE2
 135 ASN   ( 135-)  A      N
 140 VAL   ( 140-)  A      N
 147 ASN   ( 147-)  A      N
 151 ARG   ( 151-)  A      NH1
 151 ARG   ( 151-)  A      NH2
 166 SER   ( 166-)  A      OG
 180 PHE   ( 180-)  A      N
 210 ASN   ( 210-)  A      N
 249 TRP   ( 249-)  A      N
 253 VAL   ( 253-)  A      N
 254 GLU   ( 254-)  A      N
 255 ILE   ( 255-)  A      N
 271 GLN   ( 271-)  A      N
 280 ASN   ( 280-)  A      ND2
 304 ARG   ( 304-)  A      N
 309 ASP   ( 309-)  A      N
 321 LYS   ( 321-)  A      N
 324 ASP   ( 324-)  A      N
 329 PHE   ( 329-)  A      N
 370 SER   ( 370-)  A      OG
 379 VAL   ( 379-)  A      N
And so on for a total of 75 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.

  77 ASN   (  77-)  A      OD1
 158 ASP   ( 158-)  A      OD2
 295 ASN   ( 295-)  A      OD1
 333 ASN   ( 333-)  A      OD1
 395 ASP   ( 395-)  A      OD1
 411 ASN   ( 411-)  A      OD1
 953 ASN   ( 280-)  B      OD1
 968 ASN   ( 295-)  B      OD1
1001 ASN   ( 328-)  B      OD1
1116 GLU   ( 443-)  B      OE2
1242 ASP   ( 588-)  B      OD1
1256 ASN   ( 602-)  B      OD1

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+.

1350  CA   ( 702-)  A     0.86   1.09 Scores about as good as NA
1362  CA   ( 703-)  B     0.48   1.53 Is perhaps  K

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.

1372 HOH   ( 759 )  A      O  1.05  K  4
1373 HOH   ( 762 )  B      O  1.00  K  4 NCS 1/1
1373 HOH   ( 846 )  B      O  0.91  K  5

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.

 855 GLU   ( 182-)  B   H-bonding suggests Gln
1164 ASP   ( 510-)  B   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 :  -0.117
  2nd generation packing quality :  -1.505
  Ramachandran plot appearance   :  -2.268
  chi-1/chi-2 rotamer normality  :  -2.516
  Backbone conformation          :   0.121

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.295 (tight)
  Bond angles                    :   0.600 (tight)
  Omega angle restraints         :   0.226 (tight)
  Side chain planarity           :   0.249 (tight)
  Improper dihedral distribution :   0.586
  B-factor distribution          :   0.357
  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 : 2.70


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.1
  2nd generation packing quality :   0.1
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :  -0.2
  Backbone conformation          :   0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.295 (tight)
  Bond angles                    :   0.600 (tight)
  Omega angle restraints         :   0.226 (tight)
  Side chain planarity           :   0.249 (tight)
  Improper dihedral distribution :   0.586
  B-factor distribution          :   0.357
  Inside/Outside distribution    :   0.997
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    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,
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      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.