WHAT IF Check report

This file was created 2011-12-16 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 pdb1mz6.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.

 626 DAN   ( 700-)  A  -

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'.

  23 SER   (  23-)  A      OG
  28 ARG   (  28-)  A      CG
  28 ARG   (  28-)  A      CD
  28 ARG   (  28-)  A      NE
  28 ARG   (  28-)  A      CZ
  28 ARG   (  28-)  A      NH1
  28 ARG   (  28-)  A      NH2
  31 VAL   (  31-)  A      CG1
  31 VAL   (  31-)  A      CG2
 123 GLN   ( 123-)  A      CG
 123 GLN   ( 123-)  A      CD
 123 GLN   ( 123-)  A      OE1
 123 GLN   ( 123-)  A      NE2
 125 ARG   ( 125-)  A      CG
 125 ARG   ( 125-)  A      CD
 125 ARG   ( 125-)  A      NE
 125 ARG   ( 125-)  A      CZ
 125 ARG   ( 125-)  A      NH1
 125 ARG   ( 125-)  A      NH2
 156 LYS   ( 156-)  A      CG
 156 LYS   ( 156-)  A      CD
 156 LYS   ( 156-)  A      CE
 156 LYS   ( 156-)  A      NZ
 167 GLU   ( 167-)  A      CG
 167 GLU   ( 167-)  A      CD
 167 GLU   ( 167-)  A      OE1
 167 GLU   ( 167-)  A      OE2
 391 ASN   ( 391-)  A      CG
 391 ASN   ( 391-)  A      OD1
 391 ASN   ( 391-)  A      ND2
 534 GLU   ( 541-)  A      CG
 534 GLU   ( 541-)  A      CD
 534 GLU   ( 541-)  A      OE1
 534 GLU   ( 541-)  A      OE2
 538 LYS   ( 545-)  A      CG
 538 LYS   ( 545-)  A      CD
 538 LYS   ( 545-)  A      CE
 538 LYS   ( 545-)  A      NZ

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

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.

  36 ARG   (  36-)  A
  88 ARG   (  88-)  A
 251 ARG   ( 251-)  A
 252 ARG   ( 252-)  A
 384 ARG   ( 384-)  A
 431 ARG   ( 438-)  A
 468 ARG   ( 475-)  A
 548 ARG   ( 555-)  A

Warning: Tyrosine convention problem

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

  55 TYR   (  55-)  A
  70 TYR   (  70-)  A
 193 TYR   ( 193-)  A
 354 TYR   ( 354-)  A
 469 TYR   ( 476-)  A
 512 TYR   ( 519-)  A
 522 TYR   ( 529-)  A
 539 TYR   ( 546-)  A

Warning: Phenylalanine convention problem

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

  11 PHE   (  11-)  A
  35 PHE   (  35-)  A
 168 PHE   ( 168-)  A
 176 PHE   ( 176-)  A
 205 PHE   ( 205-)  A
 227 PHE   ( 227-)  A
 329 PHE   ( 329-)  A
 372 PHE   ( 372-)  A
 416 PHE   ( 423-)  A
 449 PHE   ( 456-)  A
 471 PHE   ( 478-)  A
 578 PHE   ( 585-)  A

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.

  60 ASP   (  60-)  A
  74 ASP   (  74-)  A
 169 ASP   ( 169-)  A
 213 ASP   ( 213-)  A
 214 ASP   ( 214-)  A
 248 ASP   ( 248-)  A
 259 ASP   ( 259-)  A
 316 ASP   ( 316-)  A
 324 ASP   ( 324-)  A
 351 ASP   ( 351-)  A
 504 ASP   ( 511-)  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.

   9 GLU   (   9-)  A
  22 GLU   (  22-)  A
  29 GLU   (  29-)  A
 222 GLU   ( 222-)  A
 256 GLU   ( 256-)  A
 296 GLU   ( 296-)  A
 339 GLU   ( 339-)  A
 358 GLU   ( 358-)  A
 427 GLU   ( 434-)  A
 500 GLU   ( 507-)  A

Geometric checks

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

 |  1.001753 -0.000008  0.000015|
 | -0.000008  1.001486  0.000338|
 |  0.000015  0.000338  1.001018|
Proposed new scale matrix

 |  0.013100  0.000000  0.000000|
 |  0.000000  0.010645 -0.000004|
 |  0.000000 -0.000003  0.009487|
With corresponding cell

    A    =  76.336  B   =  93.939  C    = 105.404
    Alpha=  89.961  Beta=  90.001  Gamma=  90.001

The CRYST1 cell dimensions

    A    =  76.200  B   =  93.800  C    = 105.300
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 42.255
(Under-)estimated Z-score: 4.791

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.

  24 ASN   (  24-)  A      C    CA   CB  102.31   -4.1
  30 ARG   (  30-)  A      CG   CD   NE  118.98    5.0
  42 ASN   (  42-)  A      N    CA   CB  101.85   -5.1
  42 ASN   (  42-)  A      CA   CB   CG  117.64    5.0
  44 ASP   (  44-)  A      N    CA   CB  103.67   -4.0
  68 VAL   (  68-)  A      N    CA   CB  117.56    4.2
 100 VAL   ( 100-)  A      C    CA   CB  100.10   -5.3
 118 ARG   ( 118-)  A      CG   CD   NE  119.31    5.2
 129 ASP   ( 129-)  A     -C    N    CA  113.24   -4.7
 185 VAL   ( 185-)  A      C    CA   CB  101.90   -4.3
 194 PRO   ( 194-)  A      N    CA   C    99.97   -4.7
 197 ILE   ( 197-)  A      C    CA   CB  100.60   -5.0
 200 MET   ( 200-)  A      N    CA   C    99.89   -4.0
 206 THR   ( 206-)  A      N    CA   CB  101.91   -5.1
 242 ILE   ( 242-)  A      C    CA   CB  123.09    6.8
 242 ILE   ( 242-)  A      CA   CB   CG1 118.50    4.8
 242 ILE   ( 242-)  A      CB   CG1  CD1 102.30   -5.5
 246 ARG   ( 246-)  A      CG   CD   NE  103.63   -4.0
 294 THR   ( 294-)  A      CG2  CB   OG1  99.03   -5.1
 356 LEU   ( 356-)  A      N    CA   C    97.81   -4.8
 364 VAL   ( 364-)  A      N    CA   C    98.09   -4.7
 388 GLU   ( 388-)  A      CB   CG   CD  120.20    4.5
 426 TRP   ( 433-)  A      N    CA   C    98.97   -4.4
 436 ASN   ( 443-)  A      C    CA   CB  120.90    5.7
 482 VAL   ( 489-)  A      C    CA   CB  101.14   -4.7
 487 LEU   ( 494-)  A      CA   CB   CG  135.77    5.6
 500 GLU   ( 507-)  A      C    CA   CB  100.41   -5.1
 508 LEU   ( 515-)  A      N    CA   C    98.71   -4.5
 535 LEU   ( 542-)  A      C    CA   CB  101.58   -4.5
 535 LEU   ( 542-)  A      CA   CB   CG  132.00    4.5
 540 HIS   ( 547-)  A      CG   ND1  CE1 109.96    4.4
 577 HIS   ( 584-)  A      CG   ND1  CE1 109.60    4.0
 601 ARG   ( 611-)  A      CG   CD   NE  118.26    4.6

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.

   9 GLU   (   9-)  A
  22 GLU   (  22-)  A
  29 GLU   (  29-)  A
  36 ARG   (  36-)  A
  60 ASP   (  60-)  A
  74 ASP   (  74-)  A
  88 ARG   (  88-)  A
 169 ASP   ( 169-)  A
 213 ASP   ( 213-)  A
 214 ASP   ( 214-)  A
 222 GLU   ( 222-)  A
 248 ASP   ( 248-)  A
 251 ARG   ( 251-)  A
 252 ARG   ( 252-)  A
 256 GLU   ( 256-)  A
 259 ASP   ( 259-)  A
 296 GLU   ( 296-)  A
 316 ASP   ( 316-)  A
 324 ASP   ( 324-)  A
 339 GLU   ( 339-)  A
 351 ASP   ( 351-)  A
 358 GLU   ( 358-)  A
 384 ARG   ( 384-)  A
 427 GLU   ( 434-)  A
 431 ARG   ( 438-)  A
 468 ARG   ( 475-)  A
 500 GLU   ( 507-)  A
 504 ASP   ( 511-)  A
 548 ARG   ( 555-)  A

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.

 194 PRO   ( 194-)  A    5.28
 356 LEU   ( 356-)  A    5.02
 121 TRP   ( 121-)  A    4.99
 499 LEU   ( 506-)  A    4.87
 364 VAL   ( 364-)  A    4.85
 161 LYS   ( 161-)  A    4.73
 614 SER   ( 624-)  A    4.68
 508 LEU   ( 515-)  A    4.63
 426 TRP   ( 433-)  A    4.56
 373 ILE   ( 373-)  A    4.55
 419 HIS   ( 426-)  A    4.51
 365 TYR   ( 365-)  A    4.51
 184 ILE   ( 184-)  A    4.36
 291 VAL   ( 291-)  A    4.27
  64 ILE   (  64-)  A    4.19
 496 GLY   ( 503-)  A    4.05

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.752

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.

 270 THR   ( 270-)  A    -3.2
 276 THR   ( 276-)  A    -3.0
  37 ILE   (  37-)  A    -2.8
 149 THR   ( 149-)  A    -2.7
 147 LYS   ( 147-)  A    -2.7
 334 ILE   ( 334-)  A    -2.5
 235 LEU   ( 235-)  A    -2.5
 356 LEU   ( 356-)  A    -2.5
 281 SER   ( 281-)  A    -2.5
 273 HIS   ( 273-)  A    -2.4
 145 ASN   ( 145-)  A    -2.4
 140 THR   ( 140-)  A    -2.4
 296 GLU   ( 296-)  A    -2.4
 448 LYS   ( 455-)  A    -2.4
  90 SER   (  90-)  A    -2.4
 250 ASN   ( 250-)  A    -2.4
 132 PRO   ( 132-)  A    -2.3
  57 THR   (  57-)  A    -2.3
 336 ILE   ( 336-)  A    -2.3
 174 LYS   ( 174-)  A    -2.3
 535 LEU   ( 542-)  A    -2.3
  82 ILE   (  82-)  A    -2.3
  85 LYS   (  85-)  A    -2.3
 530 THR   ( 537-)  A    -2.2
 226 LYS   ( 226-)  A    -2.2
And so on for a total of 51 lines.

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 GLU   (   9-)  A  Poor phi/psi
  37 ILE   (  37-)  A  Poor phi/psi
  45 GLY   (  45-)  A  Poor phi/psi
  88 ARG   (  88-)  A  Poor phi/psi
  97 ASP   (  97-)  A  Poor phi/psi
 116 LYS   ( 116-)  A  Poor phi/psi
 126 ASP   ( 126-)  A  Poor phi/psi
 143 ALA   ( 143-)  A  Poor phi/psi
 144 ALA   ( 144-)  A  Poor phi/psi
 147 LYS   ( 147-)  A  Poor phi/psi
 180 VAL   ( 180-)  A  Poor phi/psi
 183 ALA   ( 183-)  A  Poor phi/psi
 238 GLU   ( 238-)  A  Poor phi/psi
 267 ALA   ( 267-)  A  Poor phi/psi
 270 THR   ( 270-)  A  Poor phi/psi
 273 HIS   ( 273-)  A  Poor phi/psi
 278 SER   ( 278-)  A  Poor phi/psi
 281 SER   ( 281-)  A  Poor phi/psi
 308 ASN   ( 308-)  A  Poor phi/psi
 312 ARG   ( 312-)  A  Poor phi/psi
 315 ARG   ( 315-)  A  Poor phi/psi
 325 ASN   ( 325-)  A  Poor phi/psi
 337 GLY   ( 337-)  A  Poor phi/psi
 341 SER   ( 341-)  A  Poor phi/psi
 350 ASP   ( 350-)  A  Poor phi/psi
 351 ASP   ( 351-)  A  Poor phi/psi
 358 GLU   ( 358-)  A  omega poor
 363 ASP   ( 363-)  A  Poor phi/psi
 418 SER   ( 425-)  A  Poor phi/psi
 421 ALA   ( 428-)  A  Poor phi/psi
 439 ASN   ( 446-)  A  Poor phi/psi
 445 ASN   ( 452-)  A  Poor phi/psi
 460 VAL   ( 467-)  A  Poor phi/psi
 516 ARG   ( 523-)  A  Poor phi/psi
 535 LEU   ( 542-)  A  Poor phi/psi
 536 HIS   ( 543-)  A  Poor phi/psi
 547 ASP   ( 554-)  A  Poor phi/psi
 548 ARG   ( 555-)  A  Poor phi/psi
 586 PRO   ( 596-)  A  Poor phi/psi
 617 MET   ( 627-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -4.599

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -4.599

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.

 381 SER   ( 381-)  A    0.37

Warning: Unusual backbone conformations

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

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

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

   3 PRO   (   3-)  A      0
   5 SER   (   5-)  A      0
   6 SER   (   6-)  A      0
  10 LEU   (  10-)  A      0
  11 PHE   (  11-)  A      0
  13 ARG   (  13-)  A      0
  14 LYS   (  14-)  A      0
  15 ASN   (  15-)  A      0
  16 SER   (  16-)  A      0
  29 GLU   (  29-)  A      0
  33 HIS   (  33-)  A      0
  36 ARG   (  36-)  A      0
  37 ILE   (  37-)  A      0
  38 PRO   (  38-)  A      0
  42 ASN   (  42-)  A      0
  43 VAL   (  43-)  A      0
  44 ASP   (  44-)  A      0
  55 TYR   (  55-)  A      0
  56 GLU   (  56-)  A      0
  57 THR   (  57-)  A      0
  62 SER   (  62-)  A      0
  63 PHE   (  63-)  A      0
  72 VAL   (  72-)  A      0
  74 ASP   (  74-)  A      0
  76 ALA   (  76-)  A      0
And so on for a total of 312 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]

   3 PRO   (   3-)  A    0.19 LOW
  38 PRO   (  38-)  A    0.48 HIGH
 194 PRO   ( 194-)  A    0.13 LOW
 279 PRO   ( 279-)  A    0.19 LOW
 459 PRO   ( 466-)  A    0.06 LOW
 573 PRO   ( 580-)  A    0.18 LOW
 583 PRO   ( 590-)  A    0.12 LOW
 586 PRO   ( 596-)  A    0.07 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].

 157 PRO   ( 157-)  A    41.6 envelop C-delta (36 degrees)
 399 PRO   ( 399-)  A    44.4 envelop C-delta (36 degrees)
 402 PRO   ( 402-)  A  -112.0 envelop C-gamma (-108 degrees)
 409 PRO   ( 416-)  A    50.9 half-chair C-delta/C-gamma (54 degrees)
 493 PRO   ( 500-)  A    50.5 half-chair C-delta/C-gamma (54 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.

 540 HIS   ( 547-)  A      CD2 <->  627 HOH   ( 735 )  A      O      0.48    2.32  INTRA BL
 277 ASN   ( 277-)  A      ND2 <->  278 SER   ( 278-)  A      OG     0.48    2.22  INTRA BL
 196 GLN   ( 196-)  A      NE2 <->  231 GLU   ( 231-)  A      N      0.48    2.37  INTRA BL
  26 THR   (  26-)  A      CG2 <->  625 NAG   ( 655-)  A      C1     0.44    2.76  INTRA
 336 ILE   ( 336-)  A      N   <->  339 GLU   ( 339-)  A      OE2    0.44    2.26  INTRA BL
 396 ILE   ( 396-)  A      CG2 <->  617 MET   ( 627-)  A      CE     0.43    2.77  INTRA
  17 THR   (  17-)  A      CG2 <->   29 GLU   (  29-)  A      OE1    0.42    2.38  INTRA
 480 ALA   ( 487-)  A      CB  <->  596 ILE   ( 606-)  A      CD1    0.42    2.78  INTRA BL
 226 LYS   ( 226-)  A      CD  <->  255 TYR   ( 255-)  A      OH     0.40    2.40  INTRA
 237 TRP   ( 237-)  A      O   <->  240 LYS   ( 240-)  A      N      0.37    2.33  INTRA
 327 ARG   ( 327-)  A      NH2 <->  430 TYR   ( 437-)  A      CE2    0.35    2.75  INTRA BL
 513 ASP   ( 520-)  A      OD2 <->  519 ARG   ( 526-)  A      NE     0.35    2.35  INTRA
 251 ARG   ( 251-)  A      NH2 <->  465 GLN   ( 472-)  A      O      0.33    2.37  INTRA BL
 548 ARG   ( 555-)  A      O   <->  566 VAL   ( 573-)  A      N      0.32    2.38  INTRA
 471 PHE   ( 478-)  A      O   <->  473 ASN   ( 480-)  A      N      0.32    2.38  INTRA BL
 550 GLY   ( 557-)  A      O   <->  563 GLY   ( 570-)  A      N      0.31    2.39  INTRA
  36 ARG   (  36-)  A      NE  <->  358 GLU   ( 358-)  A      OE2    0.31    2.39  INTRA BL
 190 ASN   ( 190-)  A      ND2 <->  260 MET   ( 260-)  A      SD     0.31    2.99  INTRA
 246 ARG   ( 246-)  A      NH2 <->  248 ASP   ( 248-)  A      OD1    0.30    2.40  INTRA BL
 168 PHE   ( 168-)  A      O   <->  171 ILE   ( 171-)  A      N      0.30    2.40  INTRA
 576 SER   ( 583-)  A      OG  <->  577 HIS   ( 584-)  A      ND1    0.29    2.41  INTRA BL
 546 ALA   ( 553-)  A      O   <->  549 GLN   ( 556-)  A      N      0.28    2.42  INTRA BL
 310 LYS   ( 310-)  A      NZ  <->  340 ASN   ( 340-)  A      OD1    0.28    2.42  INTRA
 305 HIS   ( 305-)  A      CD2 <->  306 PRO   ( 306-)  A      CD     0.27    2.93  INTRA BL
 103 LYS   ( 103-)  A      NZ  <->  214 ASP   ( 214-)  A      OD1    0.26    2.44  INTRA
And so on for a total of 191 lines.

Packing, accessibility and threading

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.

 568 ARG   ( 575-)  A      -8.05
 442 ARG   ( 449-)  A      -6.41
 489 LYS   ( 496-)  A      -6.16
 200 MET   ( 200-)  A      -6.07
 118 ARG   ( 118-)  A      -5.80
 462 ARG   ( 469-)  A      -5.62
 463 GLN   ( 470-)  A      -5.34
 400 VAL   ( 400-)  A      -5.24

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.

 500 GLU   ( 507-)  A       502 - PRO    509- ( A)         -4.30

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.

 156 LYS   ( 156-)  A   -2.51

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.

 627 HOH   ( 718 )  A      O
 627 HOH   ( 725 )  A      O
 627 HOH   ( 727 )  A      O
 627 HOH   ( 738 )  A      O
Bound group on Asn; dont flip   15 ASN  (  15-) A
Bound to:  624 NAG  ( 654-) A
Bound group on Asn; dont flip   24 ASN  (  24-) A
Bound to:  625 NAG  ( 655-) A
Bound group on Asn; dont flip  115 ASN  ( 115-) A
Bound to:  623 NAG  ( 653-) A
Bound group on Asn; dont flip  422 ASN  ( 429-) A
Bound to:  622 NAG  ( 652-) A
Bound group on Asn; dont flip  604 ASN  ( 614-) A
Bound to:  621 NAG  ( 651-) A

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.

  86 ASN   (  86-)  A
 124 HIS   ( 124-)  A
 196 GLN   ( 196-)  A
 250 ASN   ( 250-)  A
 305 HIS   ( 305-)  A
 357 HIS   ( 357-)  A
 360 ASN   ( 360-)  A
 615 GLN   ( 625-)  A

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.

   7 ARG   (   7-)  A      NH1
  24 ASN   (  24-)  A      N
  36 ARG   (  36-)  A      NH2
  54 ARG   (  54-)  A      NH2
  56 GLU   (  56-)  A      N
  57 THR   (  57-)  A      N
  61 ASN   (  61-)  A      N
  63 PHE   (  63-)  A      N
  72 VAL   (  72-)  A      N
  75 GLY   (  75-)  A      N
  86 ASN   (  86-)  A      ND2
 122 THR   ( 122-)  A      OG1
 176 PHE   ( 176-)  A      N
 178 GLY   ( 178-)  A      N
 208 ILE   ( 208-)  A      N
 234 VAL   ( 234-)  A      N
 244 ASN   ( 244-)  A      ND2
 246 ARG   ( 246-)  A      NH1
 246 ARG   ( 246-)  A      NH2
 253 LEU   ( 253-)  A      N
 255 TYR   ( 255-)  A      OH
 275 TRP   ( 275-)  A      NE1
 277 ASN   ( 277-)  A      ND2
 278 SER   ( 278-)  A      N
 283 GLN   ( 283-)  A      N
 284 GLN   ( 284-)  A      N
 287 GLN   ( 287-)  A      N
 313 TRP   ( 313-)  A      N
 315 ARG   ( 315-)  A      NH2
 316 ASP   ( 316-)  A      N
 325 ASN   ( 325-)  A      ND2
 408 VAL   ( 415-)  A      N
 463 GLN   ( 470-)  A      NE2
 517 GLN   ( 524-)  A      NE2
 579 TYR   ( 586-)  A      OH
 589 SER   ( 599-)  A      N
 590 ARG   ( 600-)  A      NE
 601 ARG   ( 611-)  A      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.

  97 ASP   (  97-)  A      OD1
 175 GLU   ( 175-)  A      OE1
 277 ASN   ( 277-)  A      OD1
 389 GLU   ( 389-)  A      OE2
 540 HIS   ( 547-)  A      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.

  73 ASP   (  73-)  A   H-bonding suggests Asn
 199 ASP   ( 199-)  A   H-bonding suggests Asn; but Alt-Rotamer
 485 ASP   ( 492-)  A   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 :  -0.412
  2nd generation packing quality :  -1.370
  Ramachandran plot appearance   :  -2.275
  chi-1/chi-2 rotamer normality  :  -4.599 (bad)
  Backbone conformation          :  -0.458

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.736
  Bond angles                    :   1.163
  Omega angle restraints         :   0.825
  Side chain planarity           :   0.774
  Improper dihedral distribution :   1.233
  B-factor distribution          :   0.498
  Inside/Outside distribution    :   0.991

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 : 2.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.4
  2nd generation packing quality :   0.3
  Ramachandran plot appearance   :   0.1
  chi-1/chi-2 rotamer normality  :  -2.3
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.736
  Bond angles                    :   1.163
  Omega angle restraints         :   0.825
  Side chain planarity           :   0.774
  Improper dihedral distribution :   1.233
  B-factor distribution          :   0.498
  Inside/Outside distribution    :   0.991
==============

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.