WHAT IF Check report

This file was created 2012-01-31 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 pdb2wkl.ent

Checks that need to be done early-on in validation

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

 998 SO4   (1501-)  A  -
 999 SO4   (1502-)  A  -
1000 SO4   (1503-)  A  -
1001 SO4   (1504-)  A  -
1002 SO4   (1505-)  A  -
1003 SO4   (1506-)  A  -
1004 SO4   (1507-)  A  -
1005 SO4   (1508-)  A  -
1006 SO4   (1509-)  A  -
1007 SO4   (1500-)  B  -
1008 SO4   (1501-)  B  -
1009 SO4   (1502-)  B  -
1010 SO4   (1503-)  B  -
1011 SO4   (1504-)  B  -
1012 SO4   (1505-)  B  -
1013 SO4   (1506-)  B  -
1014 SO4   (1507-)  B  -
1015 SO4   (1508-)  B  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 994 NAG   (1499-)  A  -   O4  bound to  995 NAG   (1500-)  A  -   C1
 996 NAG   (1498-)  B  -   O4  bound to  997 NAG   (1499-)  B  -   C1

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: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

  58 ASN   (  59-)  A      OD1
  58 ASN   (  59-)  A      ND2
 154 LYS   ( 155-)  A      CD
 154 LYS   ( 155-)  A      CE
 154 LYS   ( 155-)  A      NZ
 165 GLN   ( 166-)  A      CG
 165 GLN   ( 166-)  A      CD
 165 GLN   ( 166-)  A      OE1
 165 GLN   ( 166-)  A      NE2
 223 LYS   ( 224-)  A      CE
 223 LYS   ( 224-)  A      NZ
 299 GLU   ( 300-)  A      CD
 299 GLU   ( 300-)  A      OE1
 299 GLU   ( 300-)  A      OE2
 345 PHE   ( 347-)  A      CG
 345 PHE   ( 347-)  A      CD1
 345 PHE   ( 347-)  A      CD2
 345 PHE   ( 347-)  A      CE1
 345 PHE   ( 347-)  A      CE2
 345 PHE   ( 347-)  A      CZ
 348 GLN   ( 350-)  A      OE1
 348 GLN   ( 350-)  A      NE2
 439 LYS   ( 441-)  A      CG
 439 LYS   ( 441-)  A      CD
 439 LYS   ( 441-)  A      CE
And so on for a total of 63 lines.

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. 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: 0

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

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.

   2 ARG   (   2-)  A
 431 ARG   ( 433-)  A
 928 ARG   ( 433-)  B

Warning: Tyrosine convention problem

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

  11 TYR   (  11-)  A
  22 TYR   (  22-)  A
 107 TYR   ( 108-)  A
 115 TYR   ( 116-)  A
 134 TYR   ( 135-)  A
 204 TYR   ( 205-)  A
 211 TYR   ( 212-)  A
 303 TYR   ( 304-)  A
 371 TYR   ( 373-)  A
 410 TYR   ( 412-)  A
 416 TYR   ( 418-)  A
 485 TYR   ( 487-)  A
 490 TYR   ( 492-)  A
 506 TYR   (  11-)  B
 517 TYR   (  22-)  B
 603 TYR   ( 108-)  B
 611 TYR   ( 116-)  B
 630 TYR   ( 135-)  B
 700 TYR   ( 205-)  B
 707 TYR   ( 212-)  B
 799 TYR   ( 304-)  B
 868 TYR   ( 373-)  B
 907 TYR   ( 412-)  B
 982 TYR   ( 487-)  B

Warning: Phenylalanine convention problem

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

  26 PHE   (  26-)  A
  74 PHE   (  75-)  A
  80 PHE   (  81-)  A
 108 PHE   ( 109-)  A
 141 PHE   ( 142-)  A
 146 PHE   ( 147-)  A
 329 PHE   ( 331-)  A
 335 PHE   ( 337-)  A
 395 PHE   ( 397-)  A
 409 PHE   ( 411-)  A
 415 PHE   ( 417-)  A
 424 PHE   ( 426-)  A
 504 PHE   (   9-)  B
 521 PHE   (  26-)  B
 570 PHE   (  75-)  B
 637 PHE   ( 142-)  B
 642 PHE   ( 147-)  B
 741 PHE   ( 246-)  B
 811 PHE   ( 316-)  B
 826 PHE   ( 331-)  B
 832 PHE   ( 337-)  B
 842 PHE   ( 347-)  B
 912 PHE   ( 417-)  B
 921 PHE   ( 426-)  B
 974 PHE   ( 479-)  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.

 152 ASP   ( 153-)  A
 356 ASP   ( 358-)  A

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

 221 GLU   ( 222-)  A
 324 GLU   ( 326-)  A
 347 GLU   ( 349-)  A
 730 GLU   ( 235-)  B
 844 GLU   ( 349-)  B
 883 GLU   ( 388-)  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.

 341 VAL   ( 343-)  A      C    CA   CB  100.23   -5.2
 363 HIS   ( 365-)  A      CG   ND1  CE1 109.67    4.1
 780 ARG   ( 285-)  B      CB   CG   CD  105.41   -4.3
 845 GLN   ( 350-)  B      N    CA   CB  102.29   -4.8
 848 ARG   ( 353-)  B     -C    N    CA  114.34   -4.1
 848 ARG   ( 353-)  B      CB   CG   CD  105.56   -4.3

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.

   2 ARG   (   2-)  A
 152 ASP   ( 153-)  A
 221 GLU   ( 222-)  A
 324 GLU   ( 326-)  A
 347 GLU   ( 349-)  A
 356 ASP   ( 358-)  A
 431 ARG   ( 433-)  A
 730 GLU   ( 235-)  B
 844 GLU   ( 349-)  B
 883 GLU   ( 388-)  B
 928 ARG   ( 433-)  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.

 901 ILE   ( 406-)  B    4.94
 838 VAL   ( 343-)  B    4.19

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.

 846 SER   ( 351-)  B    -2.7
 808 TYR   ( 313-)  B    -2.7
 480 THR   ( 482-)  A    -2.6
 288 PRO   ( 289-)  A    -2.6
 965 LEU   ( 470-)  B    -2.5
 977 THR   ( 482-)  B    -2.5
   2 ARG   (   2-)  A    -2.5
 625 ILE   ( 130-)  B    -2.5
 481 ILE   ( 483-)  A    -2.5
 784 PRO   ( 289-)  B    -2.4
 129 ILE   ( 130-)  A    -2.3
 468 LEU   ( 470-)  A    -2.3
 848 ARG   ( 353-)  B    -2.3
 447 LEU   ( 449-)  A    -2.2
 396 VAL   ( 398-)  A    -2.2
 744 LEU   ( 249-)  B    -2.2
  33 LEU   (  34-)  A    -2.2
 199 GLN   ( 200-)  A    -2.2
 736 LEU   ( 241-)  B    -2.1
 839 GLY   ( 344-)  B    -2.1
 234 GLU   ( 235-)  A    -2.1
 942 VAL   ( 447-)  B    -2.1
  69 GLN   (  70-)  A    -2.1
 413 PRO   ( 415-)  A    -2.1
 776 LEU   ( 281-)  B    -2.0
 958 ARG   ( 463-)  B    -2.0
 845 GLN   ( 350-)  B    -2.0
 874 THR   ( 379-)  B    -2.0
 113 ILE   ( 114-)  A    -2.0
 525 THR   (  30-)  B    -2.0
 280 LEU   ( 281-)  A    -2.0
 485 TYR   ( 487-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  11 TYR   (  11-)  A  omega poor
  19 ASN   (  19-)  A  Poor phi/psi
  26 PHE   (  26-)  A  omega poor
  74 PHE   (  75-)  A  Poor phi/psi
 107 TYR   ( 108-)  A  omega poor
 123 ALA   ( 124-)  A  Poor phi/psi
 125 CYS   ( 126-)  A  Poor phi/psi
 132 TYR   ( 133-)  A  Poor phi/psi
 139 ASP   ( 140-)  A  Poor phi/psi
 140 ASP   ( 141-)  A  Poor phi/psi
 223 LYS   ( 224-)  A  Poor phi/psi
 232 GLU   ( 233-)  A  Poor phi/psi
 234 GLU   ( 235-)  A  Poor phi/psi
 245 PHE   ( 246-)  A  omega poor
 280 LEU   ( 281-)  A  Poor phi/psi
 287 LEU   ( 288-)  A  PRO omega poor
 311 TRP   ( 312-)  A  omega poor
 315 PHE   ( 316-)  A  Poor phi/psi
 318 ALA   ( 320-)  A  Poor phi/psi
 321 THR   ( 323-)  A  Poor phi/psi
 340 CYS   ( 342-)  A  Poor phi/psi
 342 GLY   ( 344-)  A  Poor phi/psi
 372 HIS   ( 374-)  A  Poor phi/psi
 379 TRP   ( 381-)  A  Poor phi/psi
 388 GLY   ( 390-)  A  PRO omega poor
And so on for a total of 60 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 : -3.299

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!

   6 PRO   (   6-)  A      0
   9 PHE   (   9-)  A      0
  11 TYR   (  11-)  A      0
  18 CYS   (  18-)  A      0
  22 TYR   (  22-)  A      0
  23 CYS   (  23-)  A      0
  24 ASP   (  24-)  A      0
  26 PHE   (  26-)  A      0
  29 PRO   (  29-)  A      0
  30 THR   (  30-)  A      0
  31 PRO   (  32-)  A      0
  32 ALA   (  33-)  A      0
  33 LEU   (  34-)  A      0
  44 SER   (  45-)  A      0
  47 ARG   (  48-)  A      0
  48 MET   (  49-)  A      0
  56 GLN   (  57-)  A      0
  58 ASN   (  59-)  A      0
  60 THR   (  61-)  A      0
  64 LEU   (  65-)  A      0
  74 PHE   (  75-)  A      0
  78 LYS   (  79-)  A      0
  80 PHE   (  81-)  A      0
  84 MET   (  85-)  A      0
 113 ILE   ( 114-)  A      0
And so on for a total of 433 lines.

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]

 252 PRO   ( 253-)  A    0.04 LOW
 523 PRO   (  28-)  B    0.20 LOW
 964 PRO   ( 469-)  B    0.11 LOW

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].

  28 PRO   (  28-)  A    47.6 half-chair C-delta/C-gamma (54 degrees)
  31 PRO   (  32-)  A   -22.9 half-chair C-alpha/N (-18 degrees)
  54 PRO   (  55-)  A   -64.4 envelop C-beta (-72 degrees)
 170 PRO   ( 171-)  A  -135.1 envelop C-delta (-144 degrees)
 181 PRO   ( 182-)  A   109.1 envelop C-beta (108 degrees)
 200 PRO   ( 201-)  A   105.4 envelop C-beta (108 degrees)
 298 PRO   ( 299-)  A  -118.4 half-chair C-delta/C-gamma (-126 degrees)
 330 PRO   ( 332-)  A  -118.6 half-chair C-delta/C-gamma (-126 degrees)
 413 PRO   ( 415-)  A   101.1 envelop C-beta (108 degrees)
 467 PRO   ( 469-)  A    30.5 envelop C-delta (36 degrees)
 566 PRO   (  71-)  B    45.8 half-chair C-delta/C-gamma (54 degrees)
 654 PRO   ( 159-)  B   102.2 envelop C-beta (108 degrees)
 666 PRO   ( 171-)  B    99.2 envelop C-beta (108 degrees)
 677 PRO   ( 182-)  B   103.9 envelop C-beta (108 degrees)
 696 PRO   ( 201-)  B   104.6 envelop C-beta (108 degrees)
 731 PRO   ( 236-)  B  -119.6 half-chair C-delta/C-gamma (-126 degrees)
 740 PRO   ( 245-)  B   -50.2 half-chair C-beta/C-alpha (-54 degrees)
 794 PRO   ( 299-)  B  -117.6 half-chair C-delta/C-gamma (-126 degrees)
 814 PRO   ( 319-)  B  -135.9 envelop C-delta (-144 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.

 284 ARG   ( 285-)  A      NH1 <->  317 PRO   ( 319-)  A      O      1.08    1.62  INTRA
 359 MET   ( 361-)  A      CE  <->  461 ARG   ( 463-)  A      CB     0.57    2.63  INTRA
 284 ARG   ( 285-)  A      NE  <->  311 TRP   ( 312-)  A      CZ3    0.55    2.55  INTRA
 359 MET   ( 361-)  A      CE  <->  461 ARG   ( 463-)  A      CA     0.51    2.69  INTRA
 205 HIS   ( 206-)  A      NE2 <->  254 HIS   ( 255-)  A      NE2    0.46    2.54  INTRA BL
 284 ARG   ( 285-)  A      NH1 <->  317 PRO   ( 319-)  A      C      0.39    2.71  INTRA
 284 ARG   ( 285-)  A      CZ  <->  317 PRO   ( 319-)  A      O      0.38    2.42  INTRA
 702 GLN   ( 207-)  B      NE2 <->  758 ASP   ( 263-)  B      OD1    0.35    2.35  INTRA
 284 ARG   ( 285-)  A      NH2 <->  311 TRP   ( 312-)  A      CZ3    0.33    2.77  INTRA
 449 HIS   ( 451-)  A      ND1 <->  451 ASP   ( 453-)  A      N      0.32    2.68  INTRA
 281 ASP   ( 282-)  A      OD1 <->  310 HIS   ( 311-)  A      NE2    0.31    2.39  INTRA BL
   1 ALA   (   1-)  A      N   <->   27 ASP   (  27-)  A      OD1    0.31    2.39  INTRA
 938 ASP   ( 443-)  B      N   <-> 1017 HOH   (2158 )  B      O      0.31    2.39  INTRA BL
 443 ASP   ( 445-)  A      OD2 <->  461 ARG   ( 463-)  A      NH1    0.30    2.40  INTRA
 109 SER   ( 110-)  A      OG  <->  111 GLU   ( 112-)  A      N      0.30    2.40  INTRA BL
 284 ARG   ( 285-)  A      NE  <->  311 TRP   ( 312-)  A      CH2    0.30    2.80  INTRA
 351 ARG   ( 353-)  A      NH1 <-> 1016 HOH   (2110 )  A      O      0.30    2.40  INTRA
 872 GLY   ( 377-)  B      C   <->  873 TRP   ( 378-)  B      CE3    0.29    2.81  INTRA
 757 ARG   ( 262-)  B      NH1 <-> 1017 HOH   (2098 )  B      O      0.28    2.42  INTRA
 284 ARG   ( 285-)  A      CZ  <->  311 TRP   ( 312-)  A      CZ3    0.27    2.93  INTRA
 539 ARG   (  44-)  B      NE  <-> 1010 SO4   (1503-)  B      O4     0.26    2.44  INTRA
 506 TYR   (  11-)  B      OH  <->  845 GLN   ( 350-)  B      NE2    0.25    2.45  INTRA
 752 ARG   ( 257-)  B      NH1 <-> 1013 SO4   (1506-)  B      O3     0.25    2.45  INTRA BF
 327 ARG   ( 329-)  A      NH2 <-> 1000 SO4   (1503-)  A      O3     0.24    2.46  INTRA
  41 SER   (  42-)  A      OG  <->  420 HIS   ( 422-)  A      NE2    0.24    2.46  INTRA BL
And so on for a total of 172 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.

 890 ARG   ( 395-)  B      -7.87
 168 GLN   ( 169-)  A      -6.52
 526 PHE   (  31-)  B      -6.32
 199 GLN   ( 200-)  A      -6.13
 842 PHE   ( 347-)  B      -6.11
 664 GLN   ( 169-)  B      -6.10
 695 GLN   ( 200-)  B      -6.00
 494 ARG   ( 496-)  A      -5.94
 261 ARG   ( 262-)  A      -5.72
 757 ARG   ( 262-)  B      -5.62
 991 ARG   ( 496-)  B      -5.57
 552 GLN   (  57-)  B      -5.37
 689 LYS   ( 194-)  B      -5.09
 221 GLU   ( 222-)  A      -5.09
 717 GLU   ( 222-)  B      -5.08
 193 LYS   ( 194-)  A      -5.06
 958 ARG   ( 463-)  B      -5.06
 625 ILE   ( 130-)  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.

  59 HIS   (  60-)  A        62 - THR     63- ( A)         -4.53

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.

 892 PHE   ( 397-)  B   -2.79
 557 GLY   (  62-)  B   -2.74
 345 PHE   ( 347-)  A   -2.73
 495 GLN   ( 497-)  A   -2.59
 621 CYS   ( 126-)  B   -2.59
 665 ARG   ( 170-)  B   -2.56

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

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.

1017 HOH   (2178 )  B      O
Bound group on Asn; dont flip   19 ASN  (  19-) A
Bound to:  994 NAG  (1499-) A
Bound group on Asn; dont flip  145 ASN  ( 146-) A
Bound to:  993 NAG  (1498-) A
Bound group on Asn; dont flip  514 ASN  (  19-) B
Bound to:  996 NAG  (1498-) B

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.

 438 GLN   ( 440-)  A
 769 HIS   ( 274-)  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.

 128 SER   ( 129-)  A      N
 130 ARG   ( 131-)  A      N
 139 ASP   ( 140-)  A      N
 168 GLN   ( 169-)  A      N
 183 TRP   ( 184-)  A      N
 189 ALA   ( 190-)  A      N
 193 LYS   ( 194-)  A      N
 227 TRP   ( 228-)  A      NE1
 242 GLY   ( 243-)  A      N
 245 PHE   ( 246-)  A      N
 284 ARG   ( 285-)  A      NE
 306 GLY   ( 307-)  A      N
 314 ASP   ( 315-)  A      N
 339 ALA   ( 341-)  A      N
 341 VAL   ( 343-)  A      N
 344 LYS   ( 346-)  A      N
 346 TRP   ( 348-)  A      N
 354 SER   ( 356-)  A      OG
 355 TRP   ( 357-)  A      NE1
 376 TRP   ( 378-)  A      NE1
 380 ASN   ( 382-)  A      ND2
 382 ALA   ( 384-)  A      N
 390 ASN   ( 392-)  A      ND2
 412 GLN   ( 414-)  A      NE2
 526 PHE   (  31-)  B      N
And so on for a total of 54 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.

 150 GLU   ( 151-)  A      OE1
 150 GLU   ( 151-)  A      OE2
 324 GLU   ( 326-)  A      OE1
 360 GLN   ( 362-)  A      OE1
 363 HIS   ( 365-)  A      ND1
 417 HIS   ( 419-)  A      NE2
 914 HIS   ( 419-)  B      NE2

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.

 136 ASP   ( 137-)  A   H-bonding suggests Asn
 202 ASP   ( 203-)  A   H-bonding suggests Asn
 232 GLU   ( 233-)  A   H-bonding suggests Gln; but Alt-Rotamer
 324 GLU   ( 326-)  A   H-bonding suggests Gln
 698 ASP   ( 203-)  B   H-bonding suggests Asn
 713 ASP   ( 218-)  B   H-bonding suggests Asn
 728 GLU   ( 233-)  B   H-bonding suggests Gln
 875 ASP   ( 380-)  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 :  -0.504
  2nd generation packing quality :  -1.676
  Ramachandran plot appearance   :  -1.675
  chi-1/chi-2 rotamer normality  :  -3.299 (poor)
  Backbone conformation          :  -0.445

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.516 (tight)
  Bond angles                    :   0.756
  Omega angle restraints         :   1.171
  Side chain planarity           :   0.471 (tight)
  Improper dihedral distribution :   0.774
  B-factor distribution          :   0.420
  Inside/Outside distribution    :   1.033

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 :   0.6
  2nd generation packing quality :  -0.0
  Ramachandran plot appearance   :   0.9
  chi-1/chi-2 rotamer normality  :  -0.9
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.516 (tight)
  Bond angles                    :   0.756
  Omega angle restraints         :   1.171
  Side chain planarity           :   0.471 (tight)
  Improper dihedral distribution :   0.774
  B-factor distribution          :   0.420
  Inside/Outside distribution    :   1.033
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
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Bond lengths and angles, DNA/RNA
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      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,
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      protein structures
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Matthews' Coefficient
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      Solvent content of Protein Crystals
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Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
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    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
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      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.