WHAT IF Check report

This file was created 2012-01-13 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 pdb1t5w.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 D

All-atom RMS fit for the two chains : 0.243
CA-only RMS fit for the two chains : 0.198

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 D

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: B and E

All-atom RMS fit for the two chains : 0.245
CA-only RMS fit for the two chains : 0.216

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: B and E

Administrative problems that can generate validation failures

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

   1 LYS   (   2-)  A  -   CB
   1 LYS   (   2-)  A  -   CG
   1 LYS   (   2-)  A  -   CD
   1 LYS   (   2-)  A  -   CE
   1 LYS   (   2-)  A  -   NZ
 288 PRO   ( 108-)  B  -   CB
 288 PRO   ( 108-)  B  -   CG
 288 PRO   ( 108-)  B  -   CD
 289 LEU   ( 109-)  B  -   CB
 289 LEU   ( 109-)  B  -   CG
 289 LEU   ( 109-)  B  -   CD1
 289 LEU   ( 109-)  B  -   CD2
 290 GLN   ( 110-)  B  -   CB
 290 GLN   ( 110-)  B  -   CG
 290 GLN   ( 110-)  B  -   CD
 290 GLN   ( 110-)  B  -   OE1
 290 GLN   ( 110-)  B  -   NE2
 350 VAL   ( 170-)  B  -   CB
 350 VAL   ( 170-)  B  -   CG1
 350 VAL   ( 170-)  B  -   CG2
 369 ARG   ( 189-)  B  -   CB
 369 ARG   ( 189-)  B  -   CG
 369 ARG   ( 189-)  B  -   CD
 369 ARG   ( 189-)  B  -   NE
 369 ARG   ( 189-)  B  -   CZ
 369 ARG   ( 189-)  B  -   NH1
 369 ARG   ( 189-)  B  -   NH2

Warning: Plausible backbone atoms detected with zero occupancy

Plausible backbone atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. However, if a backbone atom is present in the PDB file, and its position seems 'logical' (i.e. normal bond lengths with all atoms it should be bound to, and those atoms exist normally) WHAT IF will set the occupancy to 1.0 if it believes that the full presence of this atom will be beneficial to the rest of the validation process. If you get weird errors at, or near, these atoms, please check by hand what is going on, and repair things intelligently before running this validation again.

   1 LYS   (   2-)  A  -   N
   1 LYS   (   2-)  A  -   CA
   1 LYS   (   2-)  A  -   C
   1 LYS   (   2-)  A  -   O

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

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

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

  45 GLU   (  46-)  A    High
  49 ARG   (  50-)  A    High
  54 GLU   (  55-)  A    High
  56 GLN   (  57-)  A    High
  74 LYS   (  75-)  A    High
 100 GLU   ( 101-)  A    High
 171 GLU   ( 172-)  A    High
 181 GLY   (   1-)  B    High
 182 ASP   (   2-)  B    High
 202 GLU   (  22-)  B    High
 239 GLU   (  59-)  B    High
 245 LYS   (  65-)  B    High
 308 GLU   ( 128-)  B    High
 316 GLN   ( 136-)  B    High
 378 THR   (   7-)  C    High
 383 SER   (  12-)  C    High
 419 LYS   (  38-)  D    High
 421 GLU   (  40-)  D    High
 427 GLU   (  46-)  D    High
 432 PHE   (  51-)  D    High
 436 GLU   (  55-)  D    High
 438 GLN   (  57-)  D    High
 479 GLU   (  98-)  D    High
 480 LEU   (  99-)  D    High
 481 ARG   ( 100-)  D    High
And so on for a total of 52 lines.

Warning: What type of B-factor?

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

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

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

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.

  49 ARG   (  50-)  A
 251 ARG   (  71-)  B
 260 ARG   (  80-)  B
 310 ARG   ( 130-)  B
 346 ARG   ( 166-)  B
 369 ARG   ( 189-)  B
 431 ARG   (  50-)  D
 633 ARG   (  71-)  E
 642 ARG   (  80-)  E
 692 ARG   ( 130-)  E

Warning: Tyrosine convention problem

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

 149 TYR   ( 150-)  A
 351 TYR   ( 171-)  B
 373 TYR   (   2-)  C
 755 TYR   (   2-)  F

Warning: Phenylalanine convention problem

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

 111 PHE   ( 112-)  A
 193 PHE   (  13-)  B
 493 PHE   ( 112-)  D
 575 PHE   (  13-)  E

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.

 170 ASP   ( 171-)  A
 552 ASP   ( 171-)  D

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.

  29 GLU   (  30-)  A
  46 GLU   (  47-)  A
  54 GLU   (  55-)  A
  97 GLU   (  98-)  A
 100 GLU   ( 101-)  A
 171 GLU   ( 172-)  A
 202 GLU   (  22-)  B
 239 GLU   (  59-)  B
 318 GLU   ( 138-)  B
 356 GLU   ( 176-)  B
 411 GLU   (  30-)  D
 428 GLU   (  47-)  D
 436 GLU   (  55-)  D
 479 GLU   (  98-)  D
 482 GLU   ( 101-)  D
 553 GLU   ( 172-)  D
 560 GLU   ( 179-)  D
 584 GLU   (  22-)  E
 621 GLU   (  59-)  E
 700 GLU   ( 138-)  E
 738 GLU   ( 176-)  E

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.

  87 GLU   (  88-)  A      N    CA   C    98.87   -4.4

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.

  29 GLU   (  30-)  A
  46 GLU   (  47-)  A
  49 ARG   (  50-)  A
  54 GLU   (  55-)  A
  97 GLU   (  98-)  A
 100 GLU   ( 101-)  A
 170 ASP   ( 171-)  A
 171 GLU   ( 172-)  A
 202 GLU   (  22-)  B
 239 GLU   (  59-)  B
 251 ARG   (  71-)  B
 260 ARG   (  80-)  B
 310 ARG   ( 130-)  B
 318 GLU   ( 138-)  B
 346 ARG   ( 166-)  B
 356 GLU   ( 176-)  B
 369 ARG   ( 189-)  B
 411 GLU   (  30-)  D
 428 GLU   (  47-)  D
 431 ARG   (  50-)  D
 436 GLU   (  55-)  D
 479 GLU   (  98-)  D
 482 GLU   ( 101-)  D
 552 ASP   ( 171-)  D
 553 GLU   ( 172-)  D
 560 GLU   ( 179-)  D
 584 GLU   (  22-)  E
 621 GLU   (  59-)  E
 633 ARG   (  71-)  E
 642 ARG   (  80-)  E
 692 ARG   ( 130-)  E
 700 GLU   ( 138-)  E
 738 GLU   ( 176-)  E

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.

  87 GLU   (  88-)  A    4.55

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.

  99 ARG   ( 100-)  A    -3.0
 481 ARG   ( 100-)  D    -3.0
 112 THR   ( 113-)  A    -2.7
 494 THR   ( 113-)  D    -2.7
 337 THR   ( 157-)  B    -2.4
 719 THR   ( 157-)  E    -2.4
 334 THR   ( 154-)  B    -2.4
 152 PHE   ( 153-)  A    -2.3
 716 THR   ( 154-)  E    -2.3
 534 PHE   ( 153-)  D    -2.3
 591 ARG   (  29-)  E    -2.2
 209 ARG   (  29-)  B    -2.2
 517 VAL   ( 136-)  D    -2.1
 218 VAL   (  38-)  B    -2.1
 600 VAL   (  38-)  E    -2.1
  15 PRO   (  16-)  A    -2.1
 397 PRO   (  16-)  D    -2.1
 135 VAL   ( 136-)  A    -2.1

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.

  14 ASN   (  15-)  A  PRO omega poor
  17 GLN   (  18-)  A  Poor phi/psi
  77 ASN   (  78-)  A  Poor phi/psi
  78 TYR   (  79-)  A  Poor phi/psi
  99 ARG   ( 100-)  A  Poor phi/psi
 112 THR   ( 113-)  A  PRO omega poor
 114 PRO   ( 115-)  A  Poor phi/psi
 142 HIS   ( 143-)  A  Poor phi/psi
 212 TYR   (  32-)  B  Poor phi/psi
 213 ASN   (  33-)  B  Poor phi/psi
 285 LYS   ( 105-)  B  Poor phi/psi
 290 GLN   ( 110-)  B  Poor phi/psi
 303 TYR   ( 123-)  B  PRO omega poor
 333 TRP   ( 153-)  B  Poor phi/psi
 396 ASN   (  15-)  D  PRO omega poor
 399 GLN   (  18-)  D  Poor phi/psi
 459 ASN   (  78-)  D  Poor phi/psi
 460 TYR   (  79-)  D  Poor phi/psi
 481 ARG   ( 100-)  D  Poor phi/psi
 494 THR   ( 113-)  D  PRO omega poor
 524 HIS   ( 143-)  D  Poor phi/psi
 594 TYR   (  32-)  E  Poor phi/psi
 595 ASN   (  33-)  E  Poor phi/psi
 667 LYS   ( 105-)  E  Poor phi/psi
 672 GLN   ( 110-)  E  Poor phi/psi
 685 TYR   ( 123-)  E  PRO omega poor
 715 TRP   ( 153-)  E  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.079

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!

  10 GLU   (  11-)  A      0
  14 ASN   (  15-)  A      0
  17 GLN   (  18-)  A      0
  20 GLU   (  21-)  A      0
  25 PHE   (  26-)  A      0
  31 PHE   (  32-)  A      0
  43 ARG   (  44-)  A      0
  50 PHE   (  51-)  A      0
  52 SER   (  53-)  A      0
  76 SER   (  77-)  A      0
  77 ASN   (  78-)  A      0
  78 TYR   (  79-)  A      0
  98 LEU   (  99-)  A      0
  99 ARG   ( 100-)  A      0
 109 ASP   ( 110-)  A      0
 110 LYS   ( 111-)  A      0
 111 PHE   ( 112-)  A      0
 112 THR   ( 113-)  A      0
 113 PRO   ( 114-)  A      0
 114 PRO   ( 115-)  A      0
 115 VAL   ( 116-)  A      0
 122 ARG   ( 123-)  A      0
 128 THR   ( 129-)  A      0
 129 THR   ( 130-)  A      0
 132 SER   ( 133-)  A      0
And so on for a total of 305 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 : 1.439

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!

 305 GLY   ( 125-)  B   1.54   46
 687 GLY   ( 125-)  E   1.53   50

Warning: Unusual peptide bond conformations

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

 491 ASP   ( 110-)  D   1.51

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]

  86 PRO   (  87-)  A    0.45 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.

 330 ASN   ( 150-)  B      ND2 <->  334 THR   ( 154-)  B      CG2    0.38    2.72  INTRA BL
 712 ASN   ( 150-)  E      ND2 <->  716 THR   ( 154-)  E      CG2    0.34    2.76  INTRA BF
 457 ARG   (  76-)  D      NH2 <->  619 ASP   (  57-)  E      OD2    0.32    2.38  INTRA BF
  75 ARG   (  76-)  A      NH2 <->  237 ASP   (  57-)  B      OD2    0.31    2.39  INTRA BL
 564 ASP   (   2-)  E      OD1 <->  568 ARG   (   6-)  E      NH2    0.29    2.41  INTRA BF
 622 TYR   (  60-)  E      CE1 <->  626 GLN   (  64-)  E      NE2    0.29    2.81  INTRA BF
 285 LYS   ( 105-)  B      NZ  <->  287 GLN   ( 107-)  B      NE2    0.26    2.59  INTRA BF
 667 LYS   ( 105-)  E      NZ  <->  669 GLN   ( 107-)  E      NE2    0.25    2.60  INTRA BF
 182 ASP   (   2-)  B      CG  <->  186 ARG   (   6-)  B      NH2    0.24    2.86  INTRA BF
 666 SER   ( 104-)  E      O   <->  675 ASN   ( 113-)  E      ND2    0.23    2.47  INTRA BF
 564 ASP   (   2-)  E      CG  <->  568 ARG   (   6-)  E      NH2    0.21    2.89  INTRA BF
 182 ASP   (   2-)  B      OD1 <->  186 ARG   (   6-)  B      NH2    0.21    2.49  INTRA BF
 558 HIS   ( 177-)  D      NE2 <->  560 GLU   ( 179-)  D      OE1    0.17    2.53  INTRA BF
 273 ARG   (  93-)  B      NH2 <->  771 HOH   ( 210 )  B      O      0.17    2.53  INTRA
 284 SER   ( 104-)  B      O   <->  293 ASN   ( 113-)  B      ND2    0.17    2.53  INTRA BF
 188 LEU   (   8-)  B      O   <->  212 TYR   (  32-)  B      O      0.17    2.08  INTRA
   1 LYS   (   2-)  A      O   <->  198 PHE   (  18-)  B      CD2    0.16    2.64  INTRA BL
   2 GLU   (   3-)  A      OE2 <->    5 VAL   (   6-)  A      CG2    0.15    2.65  INTRA BF
 166 HIS   ( 167-)  A      ND1 <->  168 GLY   ( 169-)  A      N      0.15    2.85  INTRA BL
 548 HIS   ( 167-)  D      ND1 <->  550 GLY   ( 169-)  D      N      0.15    2.85  INTRA BF
 690 GLU   ( 128-)  E      CD  <->  692 ARG   ( 130-)  E      NH2    0.14    2.96  INTRA BF
 308 GLU   ( 128-)  B      CD  <->  310 ARG   ( 130-)  B      NH2    0.14    2.96  INTRA BF
 176 HIS   ( 177-)  A      NE2 <->  178 GLU   ( 179-)  A      OE2    0.14    2.56  INTRA BL
 570 LEU   (   8-)  E      O   <->  594 TYR   (  32-)  E      O      0.14    2.11  INTRA BF
 273 ARG   (  93-)  B      CG  <->  303 TYR   ( 123-)  B      CD1    0.14    3.06  INTRA BL
And so on for a total of 114 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

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.

 481 ARG   ( 100-)  D      -6.16
  99 ARG   ( 100-)  A      -6.13
 319 LYS   ( 139-)  B      -5.66
 701 LYS   ( 139-)  E      -5.61
 764 LEU   (  11-)  F      -5.46
 399 GLN   (  18-)  D      -5.39
 382 LEU   (  11-)  C      -5.34
  17 GLN   (  18-)  A      -5.20
 656 ARG   (  94-)  E      -5.01

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.

 671 LEU   ( 109-)  E       673 - HIS    111- ( E)         -4.34

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

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.

 771 HOH   ( 229 )  B      O

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.

  17 GLN   (  18-)  A
 142 HIS   ( 143-)  A
 190 GLN   (  10-)  B
 287 GLN   ( 107-)  B
 314 ASN   ( 134-)  B
 376 GLN   (   5-)  C
 399 GLN   (  18-)  D
 524 HIS   ( 143-)  D
 572 GLN   (  10-)  E
 669 GLN   ( 107-)  E
 696 ASN   ( 134-)  E
 758 GLN   (   5-)  F

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.

  44 LEU   (  45-)  A      N
  56 GLN   (  57-)  A      N
  75 ARG   (  76-)  A      NH1
  94 SER   (  95-)  A      N
 120 TRP   ( 121-)  A      NE1
 139 ARG   ( 140-)  A      NE
 215 GLU   (  35-)  B      N
 217 SER   (  37-)  B      OG
 226 GLU   (  46-)  B      N
 237 ASP   (  57-)  B      N
 244 GLN   (  64-)  B      NE2
 246 ASP   (  66-)  B      N
 255 VAL   (  75-)  B      N
 293 ASN   ( 113-)  B      ND2
 294 LEU   ( 114-)  B      N
 330 ASN   ( 150-)  B      ND2
 338 LEU   ( 158-)  B      N
 378 THR   (   7-)  C      OG1
 380 LEU   (   9-)  C      N
 426 LEU   (  45-)  D      N
 438 GLN   (  57-)  D      N
 457 ARG   (  76-)  D      NH1
 476 SER   (  95-)  D      N
 502 TRP   ( 121-)  D      NE1
 521 ARG   ( 140-)  D      NE
 561 PHE   ( 180-)  D      N
 568 ARG   (   6-)  E      NH2
 571 TRP   (   9-)  E      NE1
 595 ASN   (  33-)  E      N
 599 SER   (  37-)  E      OG
 608 GLU   (  46-)  E      N
 619 ASP   (  57-)  E      N
 628 ASP   (  66-)  E      N
 637 VAL   (  75-)  E      N
 675 ASN   ( 113-)  E      ND2
 676 LEU   ( 114-)  E      N
 712 ASN   ( 150-)  E      ND2
 713 GLY   ( 151-)  E      N
 720 LEU   ( 158-)  E      N
 760 THR   (   7-)  F      OG1

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.

  10 GLU   (  11-)  A      OE1
  65 ASP   (  66-)  A      OD2
 148 HIS   ( 149-)  A      ND1
 392 GLU   (  11-)  D      OE1
 447 ASP   (  66-)  D      OD1
 447 ASP   (  66-)  D      OD2
 530 HIS   ( 149-)  D      ND1
 560 GLU   ( 179-)  D      OE2
 578 HIS   (  16-)  E      ND1
 614 GLU   (  52-)  E      OE2

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.

 774 HOH   ( 214 )  E      O  0.99  K  4 Ion-B

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.

  20 GLU   (  21-)  A   H-bonding suggests Gln
  65 ASP   (  66-)  A   H-bonding suggests Asn; but Alt-Rotamer
 161 ASP   ( 162-)  A   H-bonding suggests Asn; but Alt-Rotamer
 402 GLU   (  21-)  D   H-bonding suggests Gln
 447 ASP   (  66-)  D   H-bonding suggests Asn
 543 ASP   ( 162-)  D   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 :   0.423
  2nd generation packing quality :  -0.845
  Ramachandran plot appearance   :  -0.601
  chi-1/chi-2 rotamer normality  :  -1.079
  Backbone conformation          :   0.200

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.316 (tight)
  Bond angles                    :   0.643 (tight)
  Omega angle restraints         :   0.262 (tight)
  Side chain planarity           :   0.230 (tight)
  Improper dihedral distribution :   0.620
  B-factor distribution          :   1.303
  Inside/Outside distribution    :   1.043

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 :   1.4
  2nd generation packing quality :   0.2
  Ramachandran plot appearance   :   0.9
  chi-1/chi-2 rotamer normality  :   0.5
  Backbone conformation          :   0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.316 (tight)
  Bond angles                    :   0.643 (tight)
  Omega angle restraints         :   0.262 (tight)
  Side chain planarity           :   0.230 (tight)
  Improper dihedral distribution :   0.620
  B-factor distribution          :   1.303
  Inside/Outside distribution    :   1.043
==============

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Quality Control
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Checking checks
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