WHAT IF Check report

This file was created 2011-12-17 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 pdb3qbp.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    =  97.880  B   = 114.080  C    =  98.840
    Alpha=  90.000  Beta= 107.010  Gamma=  90.000

Dimensions of a reduced cell

    A    =  97.880  B   =  98.840  C    = 114.080
    Alpha=  90.000  Beta=  90.000  Gamma=  72.990

Dimensions of the conventional cell

    A    = 117.002  B   = 158.146  C    = 114.080
    Alpha=  90.000  Beta=  90.000  Gamma=  90.585

Transformation to conventional cell

 | -1.000000  0.000000 -1.000000|
 | -1.000000  0.000000  1.000000|
 |  0.000000  1.000000  0.000000|

Crystal class of the cell: MONOCLINIC

Crystal class of the conventional CELL: ORTHORHOMBIC

Space group name: P 1 21 1

Bravais type of conventional cell is: C

Warning: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

1406 THR   ( 107-)  D  -

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

1406 THR   ( 107-)  D  -

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

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'.

   1 ARG   (  26-)  A      CG
   1 ARG   (  26-)  A      CD
   1 ARG   (  26-)  A      NE
   1 ARG   (  26-)  A      CZ
   1 ARG   (  26-)  A      NH1
   1 ARG   (  26-)  A      NH2
   5 LYS   (  30-)  A      CG
   5 LYS   (  30-)  A      CD
   5 LYS   (  30-)  A      CE
   5 LYS   (  30-)  A      NZ
  14 ARG   (  39-)  A      CG
  14 ARG   (  39-)  A      CD
  14 ARG   (  39-)  A      NE
  14 ARG   (  39-)  A      CZ
  14 ARG   (  39-)  A      NH1
  14 ARG   (  39-)  A      NH2
  28 ARG   (  53-)  A      CG
  28 ARG   (  53-)  A      CD
  28 ARG   (  53-)  A      NE
  28 ARG   (  53-)  A      CZ
  28 ARG   (  53-)  A      NH1
  28 ARG   (  53-)  A      NH2
 404 LYS   ( 435-)  A      CG
 404 LYS   ( 435-)  A      CD
 404 LYS   ( 435-)  A      CE
And so on for a total of 203 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: 4

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

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.

 251 ARG   ( 276-)  A
 469 ARG   (  53-)  B
 692 ARG   ( 276-)  B
 911 ARG   (  53-)  C
1134 ARG   ( 276-)  C
1563 ARG   ( 264-)  D
1575 ARG   ( 276-)  D

Warning: Tyrosine convention problem

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

 839 TYR   ( 423-)  B
1713 TYR   ( 423-)  D

Warning: Phenylalanine convention problem

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

  75 PHE   ( 100-)  A
 180 PHE   ( 205-)  A
 245 PHE   ( 270-)  A
 516 PHE   ( 100-)  B
 621 PHE   ( 205-)  B
 958 PHE   ( 100-)  C
1063 PHE   ( 205-)  C
1128 PHE   ( 270-)  C
1399 PHE   ( 100-)  D
1504 PHE   ( 205-)  D
1569 PHE   ( 270-)  D

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.

  47 ASP   (  72-)  A
 415 ASP   ( 446-)  A
 488 ASP   (  72-)  B
 862 ASP   ( 446-)  B
 930 ASP   (  72-)  C
1299 ASP   ( 446-)  C
1371 ASP   (  72-)  D
1736 ASP   ( 446-)  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.

 495 GLU   (  79-)  B
 841 GLU   ( 425-)  B
1715 GLU   ( 425-)  D

Geometric checks

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.648
RMS-deviation in bond distances: 0.015

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.993937  0.000357  0.000307|
 |  0.000357  0.993619 -0.000059|
 |  0.000307 -0.000059  0.994247|
Proposed new scale matrix

 |  0.010278 -0.000004  0.003140|
 | -0.000003  0.008822  0.000000|
 | -0.000003  0.000000  0.010641|
With corresponding cell

    A    =  97.283  B   = 113.349  C    =  98.252
    Alpha=  90.013  Beta= 106.970  Gamma=  89.960

The CRYST1 cell dimensions

    A    =  97.880  B   = 114.080  C    =  98.840
    Alpha=  90.000  Beta= 107.010  Gamma=  90.000

Variance: 1934.437
(Under-)estimated Z-score: 32.415

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.

 128 HIS   ( 153-)  A      CG   ND1  CE1 109.60    4.0
 815 ASN   ( 399-)  B      N    CA   CB  103.70   -4.0
1021 HIS   ( 163-)  C      CG   ND1  CE1 109.61    4.0
1050 HIS   ( 192-)  C      CG   ND1  CE1 109.65    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.

  47 ASP   (  72-)  A
 251 ARG   ( 276-)  A
 415 ASP   ( 446-)  A
 469 ARG   (  53-)  B
 488 ASP   (  72-)  B
 495 GLU   (  79-)  B
 692 ARG   ( 276-)  B
 841 GLU   ( 425-)  B
 862 ASP   ( 446-)  B
 911 ARG   (  53-)  C
 930 ASP   (  72-)  C
1134 ARG   ( 276-)  C
1299 ASP   ( 446-)  C
1371 ASP   (  72-)  D
1563 ARG   ( 264-)  D
1575 ARG   ( 276-)  D
1715 GLU   ( 425-)  D
1736 ASP   ( 446-)  D

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.

 816 ALA   ( 400-)  B    7.08
1334 ALA   (  35-)  D    4.57
  10 ALA   (  35-)  A    4.07

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.

 650 THR   ( 234-)  B    -2.3
1406 THR   ( 107-)  D    -2.3
 959 PRO   ( 101-)  C    -2.3
1323 LYS   ( 470-)  C    -2.2
1400 PRO   ( 101-)  D    -2.2
  76 PRO   ( 101-)  A    -2.2
1172 ILE   ( 314-)  C    -2.1
1089 ILE   ( 231-)  C    -2.1
1306 LYS   ( 453-)  C    -2.1
1741 GLY   ( 451-)  D    -2.1
1743 LYS   ( 453-)  D    -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.

   9 ARG   (  34-)  A  Poor phi/psi
  78 ASP   ( 103-)  A  omega poor
 116 SER   ( 141-)  A  Poor phi/psi
 167 HIS   ( 192-)  A  Poor phi/psi
 168 LEU   ( 193-)  A  Poor phi/psi
 209 THR   ( 234-)  A  Poor phi/psi, omega poor
 216 ASN   ( 241-)  A  Poor phi/psi, omega poor
 281 GLY   ( 306-)  A  PRO omega poor
 326 ALA   ( 357-)  A  omega poor
 330 PHE   ( 361-)  A  Poor phi/psi
 368 ASN   ( 399-)  A  omega poor
 406 ARG   ( 437-)  A  Poor phi/psi
 450 ARG   (  34-)  B  Poor phi/psi
 557 SER   ( 141-)  B  Poor phi/psi
 559 SER   ( 143-)  B  omega poor
 608 HIS   ( 192-)  B  Poor phi/psi
 609 LEU   ( 193-)  B  Poor phi/psi
 650 THR   ( 234-)  B  Poor phi/psi, omega poor
 657 ASN   ( 241-)  B  Poor phi/psi
 722 GLY   ( 306-)  B  PRO omega poor
 773 ALA   ( 357-)  B  omega poor
 777 PHE   ( 361-)  B  Poor phi/psi
 815 ASN   ( 399-)  B  omega poor
 892 ARG   (  34-)  C  Poor phi/psi
 961 ASP   ( 103-)  C  omega poor
 999 SER   ( 141-)  C  Poor phi/psi
1018 ALA   ( 160-)  C  omega poor
1050 HIS   ( 192-)  C  Poor phi/psi
1051 LEU   ( 193-)  C  Poor phi/psi
1092 THR   ( 234-)  C  Poor phi/psi
1099 ASN   ( 241-)  C  Poor phi/psi
1164 GLY   ( 306-)  C  PRO omega poor
1210 ALA   ( 357-)  C  omega poor
1214 PHE   ( 361-)  C  Poor phi/psi
1290 ARG   ( 437-)  C  Poor phi/psi
1323 LYS   ( 470-)  C  Poor phi/psi
1333 ARG   (  34-)  D  Poor phi/psi
1406 THR   ( 107-)  D  omega poor
1440 SER   ( 141-)  D  Poor phi/psi
1491 HIS   ( 192-)  D  Poor phi/psi
1492 LEU   ( 193-)  D  Poor phi/psi
1533 THR   ( 234-)  D  Poor phi/psi, omega poor
1540 ASN   ( 241-)  D  Poor phi/psi
1605 GLY   ( 306-)  D  PRO omega poor
1647 ALA   ( 357-)  D  omega poor
1651 PHE   ( 361-)  D  Poor phi/psi
1727 ARG   ( 437-)  D  Poor phi/psi
1760 LYS   ( 470-)  D  Poor phi/psi
 chi-1/chi-2 correlation Z-score : 0.045

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.

 981 SER   ( 123-)  C    0.36
 668 SER   ( 252-)  B    0.36
 672 SER   ( 256-)  B    0.36
1110 SER   ( 252-)  C    0.36
1114 SER   ( 256-)  C    0.36
1555 SER   ( 256-)  D    0.36
 528 SER   ( 112-)  B    0.37
1551 SER   ( 252-)  D    0.37
 227 SER   ( 252-)  A    0.38
1411 SER   ( 112-)  D    0.38
 529 SER   ( 113-)  B    0.40
 970 SER   ( 112-)  C    0.40

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!

   7 LEU   (  32-)  A      0
   9 ARG   (  34-)  A      0
  19 PHE   (  44-)  A      0
  20 PRO   (  45-)  A      0
  21 ILE   (  46-)  A      0
  22 SER   (  47-)  A      0
  26 LEU   (  51-)  A      0
  50 LEU   (  75-)  A      0
  51 LEU   (  76-)  A      0
  72 ASP   (  97-)  A      0
  75 PHE   ( 100-)  A      0
  76 PRO   ( 101-)  A      0
  81 GLN   ( 106-)  A      0
  82 THR   ( 107-)  A      0
  84 SER   ( 109-)  A      0
 111 ASP   ( 136-)  A      0
 112 ASP   ( 137-)  A      0
 115 MET   ( 140-)  A      0
 116 SER   ( 141-)  A      0
 137 SER   ( 162-)  A      0
 138 HIS   ( 163-)  A      0
 157 TRP   ( 182-)  A      0
 166 THR   ( 191-)  A      0
 167 HIS   ( 192-)  A      0
 168 LEU   ( 193-)  A      0
And so on for a total of 491 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]

 218 PRO   ( 243-)  A    0.13 LOW
 550 PRO   ( 134-)  B    0.14 LOW
 832 PRO   ( 416-)  B    0.14 LOW
1007 PRO   ( 149-)  C    0.15 LOW
1706 PRO   ( 416-)  D    0.19 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].

   3 PRO   (  28-)  A  -161.6 half-chair N/C-delta (-162 degrees)
 124 PRO   ( 149-)  A  -115.0 envelop C-gamma (-108 degrees)
 444 PRO   (  28-)  B    99.5 envelop C-beta (108 degrees)
 751 PRO   ( 335-)  B   101.1 envelop C-beta (108 degrees)
1101 PRO   ( 243-)  C  -117.7 half-chair C-delta/C-gamma (-126 degrees)
1180 PRO   ( 327-)  C   115.1 envelop C-beta (108 degrees)
1377 PRO   (  78-)  D    99.3 envelop C-beta (108 degrees)
1433 PRO   ( 134-)  D  -127.7 half-chair C-delta/C-gamma (-126 degrees)
1448 PRO   ( 149-)  D  -119.4 half-chair C-delta/C-gamma (-126 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 673 GLN   ( 257-)  B      NE2 <-> 1764 HOH   (1214 )  B      O      0.57    2.13  INTRA
 807 ARG   ( 391-)  B    A NH1 <->  900 GLU   (  42-)  C      O      0.50    2.20  INTRA
 807 ARG   ( 391-)  B    A NE  <-> 1764 HOH   ( 630 )  B      O      0.46    2.24  INTRA
 371 HIS   ( 402-)  A      ND1 <-> 1763 HOH   (1408 )  A      O      0.43    2.27  INTRA
 807 ARG   ( 391-)  B    A NH2 <-> 1764 HOH   ( 959 )  B      O      0.40    2.30  INTRA
 523 THR   ( 107-)  B      CG2 <-> 1765 HOH   ( 879 )  C      O      0.33    2.47  INTRA BL
 216 ASN   ( 241-)  A      ND2 <-> 1763 HOH   (1211 )  A      O      0.31    2.39  INTRA
 874 GLU   ( 458-)  B      OE2 <->  877 ARG   ( 461-)  B    A NH2    0.29    2.41  INTRA
 820 ARG   ( 404-)  B      NH1 <-> 1764 HOH   ( 603 )  B      O      0.28    2.42  INTRA
 469 ARG   (  53-)  B    A NE  <->  513 ASP   (  97-)  B      OD2    0.28    2.42  INTRA
 401 GLN   ( 432-)  A      OE1 <->  416 ARG   ( 447-)  A      NH1    0.26    2.44  INTRA
1764 HOH   ( 960 )  B      O   <-> 1766 HOH   (1223 )  D      O      0.26    2.14  INTRA
 232 GLN   ( 257-)  A      OE1 <-> 1763 HOH   (1213 )  A      O      0.24    2.16  INTRA
1471 GLN   ( 172-)  D      CG  <-> 1766 HOH   (1061 )  D      O      0.23    2.57  INTRA
1115 GLN   ( 257-)  C      NE2 <-> 1765 HOH   (1533 )  C      O      0.23    2.47  INTRA
 400 LYS   ( 431-)  A      NZ  <-> 1763 HOH   (1187 )  A      O      0.22    2.48  INTRA
 400 LYS   ( 431-)  A      NZ  <-> 1763 HOH   ( 830 )  A      O      0.18    2.52  INTRA
 818 HIS   ( 402-)  B      ND1 <-> 1764 HOH   ( 491 )  B      O      0.17    2.53  INTRA
 360 ARG   ( 391-)  A    A NH1 <-> 1341 GLU   (  42-)  D      O      0.17    2.53  INTRA
 219 GLU   ( 244-)  A      OE2 <-> 1323 LYS   ( 470-)  C      NZ     0.17    2.53  INTRA
 108 HIS   ( 133-)  A    A ND1 <->  111 ASP   ( 136-)  A      N      0.16    2.84  INTRA BL
1694 ARG   ( 404-)  D      NH2 <-> 1766 HOH   ( 847 )  D      O      0.15    2.55  INTRA
1681 ARG   ( 391-)  D      NE  <-> 1766 HOH   (1056 )  D      O      0.14    2.56  INTRA
1311 GLU   ( 458-)  C      OE2 <-> 1315 ARG   ( 462-)  C      NE     0.14    2.56  INTRA
 162 LYS   ( 187-)  A      NZ  <->  179 GLU   ( 204-)  A    A OE1    0.13    2.57  INTRA BL
And so on for a total of 97 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

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.

1179 MET   ( 326-)  C      -6.96
 736 GLN   ( 320-)  B      -6.23
1290 ARG   ( 437-)  C      -5.99
1743 LYS   ( 453-)  D      -5.62
 673 GLN   ( 257-)  B      -5.59
1556 GLN   ( 257-)  D      -5.59
 232 GLN   ( 257-)  A      -5.58
1115 GLN   ( 257-)  C      -5.55
 459 ASN   (  43-)  B      -5.34
  18 ASN   (  43-)  A      -5.32
1342 ASN   (  43-)  D      -5.31
 901 ASN   (  43-)  C      -5.27
 742 MET   ( 326-)  B      -5.27
 360 ARG   ( 391-)  A      -5.21
 807 ARG   ( 391-)  B      -5.14
1726 GLU   ( 436-)  D      -5.12
  70 GLN   (  95-)  A      -5.10
 405 GLU   ( 436-)  A      -5.10
1244 ARG   ( 391-)  C      -5.08
1681 ARG   ( 391-)  D      -5.08
1289 GLU   ( 436-)  C      -5.05
1306 LYS   ( 453-)  C      -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

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

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.

1348 ARG   (  49-)  D   -3.52
 907 ARG   (  49-)  C   -3.35
 465 ARG   (  49-)  B   -3.24
 869 LYS   ( 453-)  B   -3.17
1727 ARG   ( 437-)  D   -2.73
 441 GLU   ( 472-)  A   -2.69
 888 GLU   ( 472-)  B   -2.68
1088 ALA   ( 230-)  C   -2.66
1529 ALA   ( 230-)  D   -2.65
 205 ALA   ( 230-)  A   -2.64
 646 ALA   ( 230-)  B   -2.64
 422 LYS   ( 453-)  A   -2.60
 744 GLY   ( 328-)  B   -2.53

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

 742 MET   ( 326-)  B     -  746 VAL   ( 330-)  B        -2.09

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

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.

1763 HOH   (1231 )  A      O     -8.31   -4.52  -57.81
1766 HOH   (1320 )  D      O    -71.99  -35.38  -55.51

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.

 110 ASN   ( 135-)  A
 551 ASN   ( 135-)  B
 588 GLN   ( 172-)  B
 673 GLN   ( 257-)  B
 736 GLN   ( 320-)  B
 993 ASN   ( 135-)  C
1335 GLN   (  36-)  D
1434 ASN   ( 135-)  D
1614 GLN   ( 315-)  D

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.

   8 TRP   (  33-)  A      N
  77 ILE   ( 102-)  A      N
  91 ASN   ( 116-)  A      ND2
 118 SER   ( 143-)  A      OG
 294 LEU   ( 319-)  A      N
 371 HIS   ( 402-)  A      N
 449 TRP   (  33-)  B      N
 469 ARG   (  53-)  B    A NE
 516 PHE   ( 100-)  B      N
 532 ASN   ( 116-)  B      ND2
 606 ARG   ( 190-)  B      NH1
 891 TRP   (  33-)  C      N
 897 ARG   (  39-)  C    A NE
 974 ASN   ( 116-)  C      ND2
1048 ARG   ( 190-)  C      NH1
1244 ARG   ( 391-)  C    A NE
1332 TRP   (  33-)  D      N
1406 THR   ( 107-)  D      N
1411 SER   ( 112-)  D      N
1415 ASN   ( 116-)  D      ND2
1744 LEU   ( 454-)  D      N

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.

 179 GLU   ( 204-)  A    A OE2
 620 GLU   ( 204-)  B      OE2
1062 GLU   ( 204-)  C      OE2
1503 GLU   ( 204-)  D      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.

1763 HOH   ( 516 )  A      O  0.98  K  4
1763 HOH   ( 577 )  A      O  1.08  K  4 Ion-B
1763 HOH   ( 604 )  A      O  1.12  K  4
1763 HOH   (1117 )  A      O  0.96  K  4 Ion-B
1763 HOH   (1131 )  A      O  0.99  K  4 Ion-B
1764 HOH   ( 574 )  B      O  1.02  K  4 H2O-B
1764 HOH   (1375 )  B      O  0.96  K  4 Ion-B
1764 HOH   (1380 )  B      O  0.85  K  4 Ion-B
1765 HOH   ( 501 )  C      O  0.88  K  4
1765 HOH   ( 521 )  C      O  0.94  K  4
1765 HOH   ( 918 )  C      O  1.00  K  6 ION-B
1766 HOH   ( 552 )  D      O  1.12  K  4
1766 HOH   (1610 )  D      O  1.08  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.

  78 ASP   ( 103-)  A   H-bonding suggests Asn
 121 ASP   ( 146-)  A   H-bonding suggests Asn
 170 ASP   ( 195-)  A   H-bonding suggests Asn
 415 ASP   ( 446-)  A   H-bonding suggests Asn
 488 ASP   (  72-)  B   H-bonding suggests Asn; but Alt-Rotamer
 519 ASP   ( 103-)  B   H-bonding suggests Asn
 562 ASP   ( 146-)  B   H-bonding suggests Asn
 589 ASP   ( 173-)  B   H-bonding suggests Asn
 611 ASP   ( 195-)  B   H-bonding suggests Asn
 862 ASP   ( 446-)  B   H-bonding suggests Asn
 961 ASP   ( 103-)  C   H-bonding suggests Asn
1004 ASP   ( 146-)  C   H-bonding suggests Asn
1053 ASP   ( 195-)  C   H-bonding suggests Asn
1299 ASP   ( 446-)  C   H-bonding suggests Asn
1371 ASP   (  72-)  D   H-bonding suggests Asn
1402 ASP   ( 103-)  D   H-bonding suggests Asn
1445 ASP   ( 146-)  D   H-bonding suggests Asn
1494 ASP   ( 195-)  D   H-bonding suggests Asn
1736 ASP   ( 446-)  D   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.105
  2nd generation packing quality :  -0.369
  Ramachandran plot appearance   :   0.386
  chi-1/chi-2 rotamer normality  :   0.045
  Backbone conformation          :   0.766

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.648 (tight)
  Bond angles                    :   0.667
  Omega angle restraints         :   0.926
  Side chain planarity           :   0.655 (tight)
  Improper dihedral distribution :   0.741
  B-factor distribution          :   0.493
  Inside/Outside distribution    :   1.012

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 : 1.85


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.7
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :   1.2
  chi-1/chi-2 rotamer normality  :   0.2
  Backbone conformation          :   0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.648 (tight)
  Bond angles                    :   0.667
  Omega angle restraints         :   0.926
  Side chain planarity           :   0.655 (tight)
  Improper dihedral distribution :   0.741
  B-factor distribution          :   0.493
  Inside/Outside distribution    :   1.012
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.