WHAT IF Check report

This file was created 2011-12-15 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 pdb3gvl.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.

 671 SLB   ( 911-)  A  -
 672 SIA   (   1-)  A  -
 673 SLB   (   2-)  A  -

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

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

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

 170 LYS   ( 410-)  A    0.50
 509 CYS   ( 749-)  A    0.50
 541 ASN   ( 781-)  A    0.50

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

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.

  48 ARG   ( 288-)  A
 166 ARG   ( 406-)  A
 273 ARG   ( 513-)  A
 328 ARG   ( 568-)  A
 329 ARG   ( 569-)  A
 359 ARG   ( 599-)  A
 362 ARG   ( 602-)  A
 381 ARG   ( 621-)  A
 420 ARG   ( 660-)  A
 432 ARG   ( 672-)  A
 519 ARG   ( 759-)  A
 544 ARG   ( 784-)  A
 572 ARG   ( 812-)  A
 625 ARG   ( 865-)  A

Warning: Tyrosine convention problem

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

  38 TYR   ( 278-)  A
  56 TYR   ( 296-)  A
  66 TYR   ( 306-)  A
  84 TYR   ( 324-)  A
  85 TYR   ( 325-)  A
 104 TYR   ( 344-)  A
 326 TYR   ( 566-)  A
 347 TYR   ( 587-)  A
 421 TYR   ( 661-)  A
 425 TYR   ( 665-)  A
 453 TYR   ( 693-)  A
 475 TYR   ( 715-)  A
 489 TYR   ( 729-)  A
 526 TYR   ( 766-)  A
 617 TYR   ( 857-)  A
 629 TYR   ( 869-)  A
 644 TYR   ( 884-)  A

Warning: Phenylalanine convention problem

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

  77 PHE   ( 317-)  A
 160 PHE   ( 400-)  A
 216 PHE   ( 456-)  A
 267 PHE   ( 507-)  A
 289 PHE   ( 529-)  A
 316 PHE   ( 556-)  A
 382 PHE   ( 622-)  A
 393 PHE   ( 633-)  A
 429 PHE   ( 669-)  A
 478 PHE   ( 718-)  A
 524 PHE   ( 764-)  A
 537 PHE   ( 777-)  A
 552 PHE   ( 792-)  A
 583 PHE   ( 823-)  A
 600 PHE   ( 840-)  A
 658 PHE   ( 898-)  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.

 378 GLU   ( 618-)  A

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: 0.395
RMS-deviation in bond distances: 0.009

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

 |  0.997205  0.000009 -0.000160|
 |  0.000009  0.997857 -0.000323|
 | -0.000160 -0.000323  0.997552|
Proposed new scale matrix

 |  0.008420  0.004858  0.000003|
 |  0.000000  0.009717  0.000003|
 |  0.000000  0.000002  0.005696|
With corresponding cell

    A    = 118.759  B   = 118.816  C    = 175.564
    Alpha=  90.027  Beta=  90.010  Gamma= 119.984

The CRYST1 cell dimensions

    A    = 119.092  B   = 119.092  C    = 175.981
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 138.074
(Under-)estimated Z-score: 8.660

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.

 264 GLY   ( 504-)  A      N    CA   C   131.69    6.6

Warning: Low bond angle variability

Bond angles were found to deviate less than normal from the standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). 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 angles: 0.643
RMS-deviation in bond angles: 1.332

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.

  48 ARG   ( 288-)  A
 166 ARG   ( 406-)  A
 273 ARG   ( 513-)  A
 328 ARG   ( 568-)  A
 329 ARG   ( 569-)  A
 359 ARG   ( 599-)  A
 362 ARG   ( 602-)  A
 378 GLU   ( 618-)  A
 381 ARG   ( 621-)  A
 420 ARG   ( 660-)  A
 432 ARG   ( 672-)  A
 519 ARG   ( 759-)  A
 544 ARG   ( 784-)  A
 572 ARG   ( 812-)  A
 625 ARG   ( 865-)  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.

 264 GLY   ( 504-)  A    8.84

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.

 660 THR   ( 900-)  A    -2.9
 143 PRO   ( 383-)  A    -2.9
  88 TRP   ( 328-)  A    -2.5
 313 LEU   ( 553-)  A    -2.5
 464 VAL   ( 704-)  A    -2.4
 345 LYS   ( 585-)  A    -2.4
 514 ILE   ( 754-)  A    -2.4
 449 THR   ( 689-)  A    -2.3
 568 SER   ( 808-)  A    -2.3
 438 TRP   ( 678-)  A    -2.2
 487 TRP   ( 727-)  A    -2.1
 547 PRO   ( 787-)  A    -2.1
 247 PRO   ( 487-)  A    -2.1
 261 TRP   ( 501-)  A    -2.0
  44 PRO   ( 284-)  A    -2.0
 478 PHE   ( 718-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

  34 ASN   ( 274-)  A  Poor phi/psi
  49 PHE   ( 289-)  A  omega poor
  51 ASN   ( 291-)  A  Poor phi/psi
  70 GLU   ( 310-)  A  Poor phi/psi
  79 ILE   ( 319-)  A  omega poor
  90 GLN   ( 330-)  A  omega poor
  91 ASP   ( 331-)  A  omega poor
  98 ASN   ( 338-)  A  Poor phi/psi
 107 SER   ( 347-)  A  Poor phi/psi
 114 ARG   ( 354-)  A  Poor phi/psi
 115 LEU   ( 355-)  A  omega poor
 116 HIS   ( 356-)  A  omega poor
 118 SER   ( 358-)  A  omega poor
 119 TRP   ( 359-)  A  omega poor
 125 ASP   ( 365-)  A  Poor phi/psi
 142 TYR   ( 382-)  A  PRO omega poor
 157 ASN   ( 397-)  A  Poor phi/psi
 171 ASN   ( 411-)  A  Poor phi/psi
 188 HIS   ( 428-)  A  omega poor
 198 ASN   ( 438-)  A  Poor phi/psi
 199 GLN   ( 439-)  A  omega poor
 221 ASN   ( 461-)  A  Poor phi/psi
 223 ALA   ( 463-)  A  Poor phi/psi
 227 VAL   ( 467-)  A  omega poor
 263 MET   ( 503-)  A  omega poor
And so on for a total of 60 lines.

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 LYS   ( 247-)  A      0
  11 VAL   ( 251-)  A      0
  14 ASP   ( 254-)  A      0
  34 ASN   ( 274-)  A      0
  44 PRO   ( 284-)  A      0
  45 ASP   ( 285-)  A      0
  58 ARG   ( 298-)  A      0
  59 ILE   ( 299-)  A      0
  60 PRO   ( 300-)  A      0
  62 GLN   ( 302-)  A      0
  69 GLU   ( 309-)  A      0
  70 GLU   ( 310-)  A      0
  71 PHE   ( 311-)  A      0
  73 GLN   ( 313-)  A      0
  80 THR   ( 320-)  A      0
  81 ASP   ( 321-)  A      0
  84 TYR   ( 324-)  A      0
  85 TYR   ( 325-)  A      0
  86 ASN   ( 326-)  A      0
  87 ALA   ( 327-)  A      0
  88 TRP   ( 328-)  A      0
  89 PRO   ( 329-)  A      0
  90 GLN   ( 330-)  A      0
  91 ASP   ( 331-)  A      0
  92 LYS   ( 332-)  A      0
And so on for a total of 338 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 7.193

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].

 143 PRO   ( 383-)  A   -60.0 half-chair C-beta/C-alpha (-54 degrees)
 247 PRO   ( 487-)  A    41.4 envelop C-delta (36 degrees)
 547 PRO   ( 787-)  A    50.7 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.

 283 VAL   ( 523-)  A      CG2 <->  674 HOH   (1388 )  A      O      0.55    2.25  INTRA BF
  85 TYR   ( 325-)  A      OH  <->  110 HIS   ( 350-)  A    A CE1    0.37    2.43  INTRA
 328 ARG   ( 568-)  A    A NH1 <->  674 HOH   (1388 )  A      O      0.35    2.35  INTRA BF
 128 THR   ( 368-)  A    A CG2 <->  674 HOH   (1350 )  A      O      0.27    2.53  INTRA BL
 188 HIS   ( 428-)  A      ND1 <->  262 HIS   ( 502-)  A      CD2    0.22    2.88  INTRA BL
 209 HIS   ( 449-)  A      CD2 <->  211 LEU   ( 451-)  A      N      0.20    2.90  INTRA BL
 328 ARG   ( 568-)  A    A NH2 <->  674 HOH   (1388 )  A      O      0.19    2.51  INTRA BF
 329 ARG   ( 569-)  A      NE  <->  674 HOH   (1870 )  A      O      0.14    2.56  INTRA
 139 HIS   ( 379-)  A      ND1 <->  141 ASP   ( 381-)  A      N      0.14    2.86  INTRA BL
  82 THR   ( 322-)  A      CB  <->   86 ASN   ( 326-)  A      ND2    0.12    2.98  INTRA BL
 203 THR   ( 443-)  A    A CG2 <->  674 HOH   (2020 )  A      O      0.12    2.68  INTRA
 517 ASP   ( 757-)  A      O   <->  674 HOH   (1117 )  A      O      0.12    2.28  INTRA
   1 VAL   ( 241-)  A      O   <->    3 ARG   ( 243-)  A      NH1    0.11    2.59  INTRA
 336 GLU   ( 576-)  A      N   <->  337 PRO   ( 577-)  A      CD     0.10    2.90  INTRA BL
 328 ARG   ( 568-)  A    A CZ  <->  674 HOH   (1388 )  A      O      0.10    2.70  INTRA BF
 100 ILE   ( 340-)  A      CG2 <->  477 MET   ( 717-)  A    A CE     0.10    3.10  INTRA BL
 410 ASN   ( 650-)  A      ND2 <->  674 HOH   (1984 )  A      O      0.10    2.60  INTRA
 359 ARG   ( 599-)  A      NH1 <->  674 HOH   ( 920 )  A      O      0.08    2.62  INTRA
 499 LYS   ( 739-)  A    A NZ  <->  674 HOH   (1932 )  A      O      0.08    2.62  INTRA
  82 THR   ( 322-)  A      O   <->  674 HOH   (1305 )  A      O      0.08    2.32  INTRA BL
  82 THR   ( 322-)  A      CG2 <->   86 ASN   ( 326-)  A      ND2    0.03    3.07  INTRA BL
  23 ASN   ( 263-)  A      ND2 <->  674 HOH   (1504 )  A      O      0.03    2.67  INTRA
  90 GLN   ( 330-)  A      NE2 <->  287 HIS   ( 527-)  A      CE1    0.03    3.07  INTRA BL
 503 HIS   ( 743-)  A      O   <->  674 HOH   (1305 )  A      O      0.03    2.37  INTRA BL
  30 LYS   ( 270-)  A      NZ  <->  674 HOH   (1745 )  A      O      0.02    2.68  INTRA
  65 TYR   ( 305-)  A      O   <->  447 ASN   ( 687-)  A      N      0.02    2.68  INTRA BL
 133 GLU   ( 373-)  A      OE2 <->  268 HIS   ( 508-)  A    A CE1    0.02    2.78  INTRA BL
  88 TRP   ( 328-)  A      O   <->   92 LYS   ( 332-)  A      NZ     0.02    2.68  INTRA BL
 411 GLU   ( 651-)  A      OE2 <->  419 ASP   ( 659-)  A      N      0.01    2.69  INTRA BL
 282 SER   ( 522-)  A      N   <->  674 HOH   (1497 )  A      O      0.01    2.69  INTRA

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

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.

 644 TYR   ( 884-)  A      -8.32
 489 TYR   ( 729-)  A      -7.97
 662 TYR   ( 902-)  A      -7.61
 581 TYR   ( 821-)  A      -7.57
 525 ARG   ( 765-)  A      -7.41
 526 TYR   ( 766-)  A      -7.08
 583 PHE   ( 823-)  A      -6.99
 651 LEU   ( 891-)  A      -6.98
 577 MET   ( 817-)  A      -6.97
 637 GLN   ( 877-)  A      -6.30
  58 ARG   ( 298-)  A      -6.22
 552 PHE   ( 792-)  A      -6.11
 604 GLU   ( 844-)  A      -5.97
 484 PHE   ( 724-)  A      -5.95
 522 ARG   ( 762-)  A      -5.90
 580 GLU   ( 820-)  A      -5.89
   3 ARG   ( 243-)  A      -5.77
 421 TYR   ( 661-)  A      -5.70
 669 VAL   ( 909-)  A      -5.47
 363 LEU   ( 603-)  A      -5.32
 584 ILE   ( 824-)  A      -5.31
 578 GLU   ( 818-)  A      -5.26
 109 ARG   ( 349-)  A      -5.24
 249 GLN   ( 489-)  A      -5.07
 110 HIS   ( 350-)  A      -5.06
 560 HIS   ( 800-)  A      -5.03
 498 PHE   ( 738-)  A      -5.00

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.

 518 ASN   ( 758-)  A       520 - VAL    760- ( A)         -4.45
 576 LEU   ( 816-)  A       578 - GLU    818- ( A)         -5.43
 649 THR   ( 889-)  A       651 - LEU    891- ( A)         -5.07
 657 ARG   ( 897-)  A       659 - THR    899- ( A)         -4.38
 668 ILE   ( 908-)  A       670 - THR    910- ( A)         -4.79

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

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.

 515 GLY   ( 755-)  A   -2.61
 471 ASP   ( 711-)  A   -2.60
 485 ASN   ( 725-)  A   -2.54

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.

 415 GLY   ( 655-)  A     -  418 ASP   ( 658-)  A        -2.01
 483 HIS   ( 723-)  A     -  487 TRP   ( 727-)  A        -1.61

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

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.

 674 HOH   ( 119 )  A      O     46.76   32.01  -23.24
 674 HOH   ( 912 )  A      O     69.90   52.24  -55.22
 674 HOH   ( 943 )  A      O     57.45   33.83   22.25
 674 HOH   ( 960 )  A      O     44.94   39.02  -23.61
 674 HOH   ( 969 )  A      O     73.51   53.47  -38.53
 674 HOH   ( 982 )  A      O     71.96   52.31  -34.06
 674 HOH   ( 996 )  A      O     57.53   34.98   18.32
 674 HOH   (1015 )  A      O     46.58   11.80  -19.17
 674 HOH   (1055 )  A      O     44.97   40.33  -53.50
 674 HOH   (1069 )  A      O     50.38    4.91  -16.30
 674 HOH   (1084 )  A      O     72.54   45.86  -73.59
 674 HOH   (1104 )  A      O     31.34   64.21   30.67
 674 HOH   (1203 )  A      O     47.43   39.52  -25.72
 674 HOH   (1256 )  A      O     33.76    6.61  -24.57
 674 HOH   (1278 )  A      O     57.64   38.01   34.07
 674 HOH   (1284 )  A      O     55.56   36.78   35.28
 674 HOH   (1294 )  A      O     64.83   14.31  -25.76
 674 HOH   (1296 )  A      O     67.75   14.74  -26.16
 674 HOH   (1300 )  A      O     65.61   52.44   25.49
 674 HOH   (1303 )  A      O     18.35    5.67   -9.16
 674 HOH   (1358 )  A      O     53.23   45.48    0.32
 674 HOH   (1434 )  A      O     45.09   17.59   25.51
 674 HOH   (1458 )  A      O     54.08   43.58   -2.47
 674 HOH   (1498 )  A      O     48.79   43.91  -27.33
 674 HOH   (1501 )  A      O     71.62   30.91  -69.49
 674 HOH   (1512 )  A      O     65.37   56.43  -45.49
 674 HOH   (1515 )  A      O     70.80   28.22  -69.75
 674 HOH   (1684 )  A      O     45.01   63.81    6.57
 674 HOH   (1740 )  A      O     43.91   27.18  -32.54
 674 HOH   (1762 )  A      O     46.14   14.48  -19.44
 674 HOH   (1764 )  A      O     45.44   61.72    2.23
 674 HOH   (1802 )  A      O     53.81    2.91  -15.66
 674 HOH   (1823 )  A      O     64.81   51.83  -30.38
 674 HOH   (1854 )  A      O     58.99   31.97    7.17
 674 HOH   (1856 )  A      O     40.38   26.79  -12.72
 674 HOH   (1865 )  A      O     47.24   59.40    3.28
 674 HOH   (1872 )  A      O     41.95   32.19  -22.27
 674 HOH   (1875 )  A      O     56.76   35.72   31.58
 674 HOH   (1876 )  A      O     44.45   35.81  -23.31
 674 HOH   (1879 )  A      O     59.85   31.55  -79.82
 674 HOH   (1883 )  A      O     43.48   14.39    3.40
 674 HOH   (1909 )  A      O     51.38   16.79  -36.73
 674 HOH   (1917 )  A      O     57.86   35.17   15.03
 674 HOH   (2001 )  A      O     76.32   30.98  -55.67
 674 HOH   (2045 )  A      O     73.99   29.14  -23.71
 674 HOH   (2053 )  A      O     73.74   26.55  -69.60
 674 HOH   (2070 )  A      O     41.57   34.77  -23.48
 674 HOH   (2075 )  A      O     39.96   36.83  -22.12

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.

 674 HOH   ( 913 )  A      O
 674 HOH   ( 949 )  A      O
 674 HOH   ( 975 )  A      O
 674 HOH   ( 977 )  A      O
 674 HOH   ( 985 )  A      O
 674 HOH   (1083 )  A      O
 674 HOH   (1102 )  A      O
 674 HOH   (1109 )  A      O
 674 HOH   (1111 )  A      O
 674 HOH   (1224 )  A      O
 674 HOH   (1243 )  A      O
 674 HOH   (1281 )  A      O
 674 HOH   (1630 )  A      O
 674 HOH   (1755 )  A      O
 674 HOH   (1927 )  A      O
 674 HOH   (2018 )  A      O
 674 HOH   (2069 )  A      O
ERROR. No convergence in HB2STD
Old,New value: 2044.928 2046.415

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.

  34 ASN   ( 274-)  A
 127 GLN   ( 367-)  A
 157 ASN   ( 397-)  A
 209 HIS   ( 449-)  A
 287 HIS   ( 527-)  A
 302 HIS   ( 542-)  A
 330 GLN   ( 570-)  A
 385 ASN   ( 625-)  A
 613 GLN   ( 853-)  A
 637 GLN   ( 877-)  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.

  16 ALA   ( 256-)  A      N
  42 SER   ( 282-)  A      N
  84 TYR   ( 324-)  A      N
  86 ASN   ( 326-)  A      ND2
 131 THR   ( 371-)  A      OG1
 147 TYR   ( 387-)  A      N
 152 MET   ( 392-)  A      N
 185 ARG   ( 425-)  A      NE
 199 GLN   ( 439-)  A      N
 220 SER   ( 460-)  A    A OG
 221 ASN   ( 461-)  A      N
 223 ALA   ( 463-)  A      N
 226 GLY   ( 466-)  A      N
 252 SER   ( 492-)  A      N
 256 ASN   ( 496-)  A      ND2
 408 ALA   ( 648-)  A      N
 422 LYS   ( 662-)  A      N
 438 TRP   ( 678-)  A      NE1
 442 ASP   ( 682-)  A      N
 459 ASN   ( 699-)  A      N
 472 ASN   ( 712-)  A    A ND2
 482 ASP   ( 722-)  A      N
 485 ASN   ( 725-)  A      N
 528 ALA   ( 768-)  A      N
 548 ALA   ( 788-)  A      N
 566 SER   ( 806-)  A      OG
 596 GLN   ( 836-)  A      NE2
 604 GLU   ( 844-)  A      N
 608 SER   ( 848-)  A      N
 639 ALA   ( 879-)  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.

 188 HIS   ( 428-)  A      ND1
 447 ASN   ( 687-)  A      OD1
 451 GLN   ( 691-)  A      OE1

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.

 674 HOH   ( 119 )  A      O  1.13  K  4
 674 HOH   ( 141 )  A      O  0.98  K  4
 674 HOH   ( 212 )  A      O  0.91  K  5
 674 HOH   ( 216 )  A      O  0.85  K  5
 674 HOH   ( 936 )  A      O  0.91  K  5 ION-B
 674 HOH   ( 951 )  A      O  1.04  K  4
 674 HOH   ( 972 )  A      O  0.93  K  4 ION-B H2O-B
 674 HOH   (1011 )  A      O  0.88  K  4 Ion-B
 674 HOH   (1015 )  A      O  1.10  K  6 ION-B
 674 HOH   (1110 )  A      O  0.96  K  4 Ion-B
 674 HOH   (1146 )  A      O  0.88  K  4
 674 HOH   (1161 )  A      O  0.95  K  8 ION-B
 674 HOH   (1166 )  A      O  1.11  K  4
 674 HOH   (1192 )  A      O  1.06  K  5
 674 HOH   (1207 )  A      O  0.96  K  5
 674 HOH   (1246 )  A      O  0.91  K  5
 674 HOH   (1274 )  A      O  0.87  K  4 Ion-B
 674 HOH   (1319 )  A      O  1.08  K  5
 674 HOH   (1334 )  A      O  0.89  K  4
 674 HOH   (1408 )  A      O  1.13  K  4
 674 HOH   (1425 )  A      O  0.86  K  4
 674 HOH   (1498 )  A      O  1.03  K  5
 674 HOH   (1518 )  A      O  0.86  K  4
 674 HOH   (1581 )  A      O  0.87  K  4 Ion-B H2O-B
 674 HOH   (1644 )  A      O  0.94  K  5
 674 HOH   (1856 )  A      O  0.97  K  4
 674 HOH   (1929 )  A      O  1.04  K  5

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

 124 ASP   ( 364-)  A   H-bonding suggests Asn
 450 ASP   ( 690-)  A   H-bonding suggests Asn; but Alt-Rotamer
 506 ASP   ( 746-)  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 :  -1.657
  2nd generation packing quality :  -1.206
  Ramachandran plot appearance   :  -0.572
  chi-1/chi-2 rotamer normality  :  -0.146
  Backbone conformation          :  -0.676

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.395 (tight)
  Bond angles                    :   0.643 (tight)
  Omega angle restraints         :   1.308 (loose)
  Side chain planarity           :   0.509 (tight)
  Improper dihedral distribution :   0.673
  B-factor distribution          :   0.394
  Inside/Outside distribution    :   1.095

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 : 1.41


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.1
  2nd generation packing quality :  -1.3
  Ramachandran plot appearance   :  -1.0
  chi-1/chi-2 rotamer normality  :  -0.7
  Backbone conformation          :  -1.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.395 (tight)
  Bond angles                    :   0.643 (tight)
  Omega angle restraints         :   1.308 (loose)
  Side chain planarity           :   0.509 (tight)
  Improper dihedral distribution :   0.673
  B-factor distribution          :   0.394
  Inside/Outside distribution    :   1.095
==============

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.