WHAT IF Check report

This file was created 2012-01-05 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 pdb1nuf.ent

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: What type of B-factor?

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

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

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

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.

 553 ARG   ( 570-)  A
 570 ARG   ( 587-)  A

Warning: Tyrosine convention problem

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

 312 TYR   ( 312-)  A
 346 TYR   ( 346-)  A
 401 TYR   ( 401-)  A
 421 TYR   ( 421-)  A
 508 TYR   ( 525-)  A
 545 TYR   ( 562-)  A

Warning: Phenylalanine convention problem

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

  14 PHE   (  14-)  A
  24 PHE   (  24-)  A
 163 PHE   ( 163-)  A
 177 PHE   ( 177-)  A
 198 PHE   ( 198-)  A
 364 PHE   ( 364-)  A
 389 PHE   ( 389-)  A
 662 PHE   ( 679-)  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.

 141 ASP   ( 141-)  A
 183 ASP   ( 183-)  A
 201 ASP   ( 201-)  A
 228 ASP   ( 228-)  A
 245 ASP   ( 245-)  A
 301 ASP   ( 301-)  A
 324 ASP   ( 324-)  A
 446 ASP   ( 446-)  A
 642 ASP   ( 659-)  A
 656 ASP   ( 673-)  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.

 152 GLU   ( 152-)  A
 153 GLU   ( 153-)  A
 157 GLU   ( 157-)  A
 391 GLU   ( 391-)  A
 462 GLU   ( 479-)  A
 515 GLU   ( 532-)  A
 529 GLU   ( 546-)  A
 569 GLU   ( 586-)  A
 586 GLU   ( 603-)  A

Geometric checks

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

 507 ILE   ( 524-)  A      N    CA   C    99.74   -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.

 141 ASP   ( 141-)  A
 152 GLU   ( 152-)  A
 153 GLU   ( 153-)  A
 157 GLU   ( 157-)  A
 183 ASP   ( 183-)  A
 201 ASP   ( 201-)  A
 228 ASP   ( 228-)  A
 245 ASP   ( 245-)  A
 301 ASP   ( 301-)  A
 324 ASP   ( 324-)  A
 391 GLU   ( 391-)  A
 446 ASP   ( 446-)  A
 462 GLU   ( 479-)  A
 515 GLU   ( 532-)  A
 529 GLU   ( 546-)  A
 553 ARG   ( 570-)  A
 569 GLU   ( 586-)  A
 570 ARG   ( 587-)  A
 586 GLU   ( 603-)  A
 642 ASP   ( 659-)  A
 656 ASP   ( 673-)  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.

 272 CYS   ( 272-)  A    6.08
 664 ALA   ( 681-)  A    4.95
 232 LEU   ( 232-)  A    4.29

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.

 561 PRO   ( 578-)  A    -2.6
   8 ILE   (   8-)  A    -2.5
 528 GLU   ( 545-)  A    -2.4
 424 THR   ( 424-)  A    -2.3
 266 PRO   ( 266-)  A    -2.2
 621 LEU   ( 638-)  A    -2.2
  12 THR   (  12-)  A    -2.2
 616 GLY   ( 633-)  A    -2.1
 138 LEU   ( 138-)  A    -2.1
 306 LEU   ( 306-)  A    -2.0
  11 GLN   (  11-)  A    -2.0
 384 ASP   ( 384-)  A    -2.0
 494 THR   ( 511-)  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.

  20 HIS   (  20-)  A  Poor phi/psi
  68 MET   (  68-)  A  Poor phi/psi
  80 SER   (  80-)  A  Poor phi/psi
 119 GLN   ( 119-)  A  Poor phi/psi
 183 ASP   ( 183-)  A  Poor phi/psi
 227 ASP   ( 227-)  A  Poor phi/psi
 264 LEU   ( 264-)  A  Poor phi/psi
 268 ARG   ( 268-)  A  omega poor
 297 ASN   ( 297-)  A  Poor phi/psi
 367 GLY   ( 367-)  A  PRO omega poor
 378 ASP   ( 378-)  A  Poor phi/psi
 382 ASN   ( 382-)  A  omega poor
 463 PRO   ( 480-)  A  Poor phi/psi
 464 SER   ( 481-)  A  Poor phi/psi
 493 ASP   ( 510-)  A  Poor phi/psi
 519 ASP   ( 536-)  A  Poor phi/psi
 528 GLU   ( 545-)  A  Poor phi/psi
 550 ASN   ( 567-)  A  Poor phi/psi
 590 ARG   ( 607-)  A  Poor phi/psi
 634 LYS   ( 651-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.672

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 LEU   (   3-)  A      0
   6 GLN   (   6-)  A      0
  10 TRP   (  10-)  A      0
  20 HIS   (  20-)  A      0
  21 THR   (  21-)  A      0
  22 ASP   (  22-)  A      0
  24 PHE   (  24-)  A      0
  25 SER   (  25-)  A      0
  27 GLN   (  27-)  A      0
  33 ARG   (  33-)  A      0
  43 MET   (  43-)  A      0
  51 GLU   (  51-)  A      0
  59 THR   (  59-)  A      0
  68 MET   (  68-)  A      0
  69 THR   (  69-)  A      0
  70 LYS   (  70-)  A      0
  77 ASN   (  77-)  A      0
  80 SER   (  80-)  A      0
  83 TRP   (  83-)  A      0
  88 GLN   (  88-)  A      0
  91 ASN   (  91-)  A      0
  93 ASN   (  93-)  A      0
 104 SER   ( 104-)  A      0
 107 ILE   ( 107-)  A      0
 109 ARG   ( 109-)  A      0
And so on for a total of 270 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.204

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 444 GLY   ( 444-)  A   2.16   80
 616 GLY   ( 633-)  A   1.98   23

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].

  74 PRO   (  74-)  A    49.1 half-chair C-delta/C-gamma (54 degrees)
 561 PRO   ( 578-)  A   104.4 envelop C-beta (108 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.

 300 HIS   ( 300-)  A      ND1 <->  686 HOH   ( 848 )  A      O      0.42    2.28  INTRA
 462 GLU   ( 479-)  A      N   <->  463 PRO   ( 480-)  A      CD     0.38    2.62  INTRA BF
 268 ARG   ( 268-)  A      NH1 <->  686 HOH   ( 762 )  A      O      0.36    2.34  INTRA BL
 656 ASP   ( 673-)  A      OD2 <->  666 LYS   ( 683-)  A      NZ     0.28    2.42  INTRA BL
 396 ARG   ( 396-)  A      NH2 <->  569 GLU   ( 586-)  A      CD     0.28    2.82  INTRA BF
 363 VAL   ( 363-)  A      CG1 <->  364 PHE   ( 364-)  A      N      0.24    2.76  INTRA BF
 320 ASP   ( 320-)  A      O   <->  322 GLY   ( 322-)  A      N      0.23    2.47  INTRA BF
  16 ARG   (  16-)  A      NH1 <->   26 SER   (  26-)  A      O      0.23    2.47  INTRA BL
 169 ARG   ( 169-)  A      NH2 <->  575 ASP   ( 592-)  A      OD1    0.22    2.48  INTRA BL
 489 ASN   ( 506-)  A      ND2 <->  490 LEU   ( 507-)  A      N      0.22    2.53  INTRA BF
 395 ASP   ( 395-)  A      OD1 <->  415 SER   ( 415-)  A      CB     0.22    2.58  INTRA BF
 357 GLN   ( 357-)  A      NE2 <->  686 HOH   ( 848 )  A      O      0.22    2.48  INTRA
 360 SER   ( 360-)  A      N   <->  363 VAL   ( 363-)  A      O      0.22    2.48  INTRA BF
 378 ASP   ( 378-)  A      OD1 <->  454 LYS   ( 454-)  A      NZ     0.21    2.49  INTRA BF
  52 ARG   (  52-)  A      NH1 <->   54 GLU   (  54-)  A      OE2    0.21    2.49  INTRA BF
 588 ARG   ( 605-)  A      NH1 <->  591 LYS   ( 608-)  A      NZ     0.21    2.64  INTRA BF
 211 ASP   ( 211-)  A      CG  <->  213 LYS   ( 213-)  A      NZ     0.21    2.89  INTRA BL
 380 GLN   ( 380-)  A      CG  <->  458 LYS   ( 458-)  A      CD     0.20    3.00  INTRA BF
 378 ASP   ( 378-)  A      C   <->  380 GLN   ( 380-)  A      NE2    0.20    2.90  INTRA
  44 ASN   (  44-)  A      ND2 <->   45 LYS   (  45-)  A      CG     0.20    2.90  INTRA
 420 ARG   ( 420-)  A      NH1 <->  686 HOH   ( 746 )  A      O      0.18    2.52  INTRA
 300 HIS   ( 300-)  A      N   <->  325 SER   ( 325-)  A      O      0.17    2.53  INTRA BF
 613 MET   ( 630-)  A      CG  <->  623 ASN   ( 640-)  A      ND2    0.17    2.93  INTRA BL
  19 HIS   (  19-)  A      ND1 <->   32 ARG   (  32-)  A      N      0.16    2.84  INTRA BL
 396 ARG   ( 396-)  A      NH2 <->  569 GLU   ( 586-)  A      OE2    0.16    2.54  INTRA BF
And so on for a total of 152 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

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.

 492 ARG   ( 509-)  A      -8.08
 621 LEU   ( 638-)  A      -6.94
 647 ARG   ( 664-)  A      -6.83
  62 TYR   (  62-)  A      -6.79
 590 ARG   ( 607-)  A      -6.60
 119 GLN   ( 119-)  A      -6.46
 169 ARG   ( 169-)  A      -6.23
 304 ARG   ( 304-)  A      -5.90
 200 ARG   ( 200-)  A      -5.62
  27 GLN   (  27-)  A      -5.44
 474 MET   ( 491-)  A      -5.27
 383 PHE   ( 383-)  A      -5.20
 460 LYS   ( 460-)  A      -5.08

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.

 589 VAL   ( 606-)  A   -3.06
 563 GLU   ( 580-)  A   -2.50

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

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.

 686 HOH   ( 786 )  A      O
 686 HOH   ( 802 )  A      O
 686 HOH   ( 804 )  A      O
 686 HOH   ( 830 )  A      O
 686 HOH   ( 846 )  A      O
 686 HOH   ( 888 )  A      O
 686 HOH   ( 902 )  A      O
Marked this atom as acceptor  677  CL  ( 701-) A     CL
Marked this atom as acceptor  679  CL  ( 703-) A     CL
Marked this atom as acceptor  680  CL  ( 704-) A     CL
Marked this atom as acceptor  681  CL  ( 705-) A     CL

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.

  35 GLN   (  35-)  A
  44 ASN   (  44-)  A
 210 ASN   ( 210-)  A
 235 ASN   ( 235-)  A
 280 ASN   ( 280-)  A
 357 GLN   ( 357-)  A
 380 GLN   ( 380-)  A
 414 ASN   ( 414-)  A
 489 ASN   ( 506-)  A
 500 ASN   ( 517-)  A
 509 ASN   ( 526-)  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.

   4 GLY   (   4-)  A      N
  35 GLN   (  35-)  A      N
  45 LYS   (  45-)  A      N
  70 LYS   (  70-)  A      N
  80 SER   (  80-)  A      N
 101 SER   ( 101-)  A      N
 115 GLN   ( 115-)  A      NE2
 140 VAL   ( 140-)  A      N
 148 HIS   ( 148-)  A      N
 163 PHE   ( 163-)  A      N
 166 SER   ( 166-)  A      OG
 225 SER   ( 225-)  A      OG
 227 ASP   ( 227-)  A      N
 229 ASN   ( 229-)  A      ND2
 236 TRP   ( 236-)  A      N
 255 ILE   ( 255-)  A      N
 271 GLN   ( 271-)  A      N
 273 TRP   ( 273-)  A      N
 280 ASN   ( 280-)  A      ND2
 329 PHE   ( 329-)  A      N
 346 TYR   ( 346-)  A      N
 357 GLN   ( 357-)  A      NE2
 379 VAL   ( 379-)  A      N
 380 GLN   ( 380-)  A      N
 385 MET   ( 385-)  A      N
 417 THR   ( 417-)  A      OG1
 465 ILE   ( 482-)  A      N
 489 ASN   ( 506-)  A      ND2
 544 ARG   ( 561-)  A      N
 548 SER   ( 565-)  A      N
 549 ASP   ( 566-)  A      N
 573 ILE   ( 590-)  A      N
 585 ASN   ( 602-)  A      N
 621 LEU   ( 638-)  A      N
 661 LYS   ( 678-)  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.

  44 ASN   (  44-)  A      OD1
 224 ASN   ( 224-)  A      OD1
 254 GLU   ( 254-)  A      OE1
 295 ASN   ( 295-)  A      OD1
 533 HIS   ( 550-)  A      ND1
 594 ASN   ( 611-)  A      OD1
 596 GLN   ( 613-)  A      OE1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

 682  CA   ( 706-)  A     0.46   1.50 Is perhaps  K

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.

 301 ASP   ( 301-)  A   H-bonding suggests Asn; but Alt-Rotamer
 528 GLU   ( 545-)  A   H-bonding suggests Gln
 563 GLU   ( 580-)  A   H-bonding suggests Gln

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 :  -0.344
  2nd generation packing quality :  -1.697
  Ramachandran plot appearance   :  -2.349
  chi-1/chi-2 rotamer normality  :  -2.672
  Backbone conformation          :   0.174

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.296 (tight)
  Bond angles                    :   0.595 (tight)
  Omega angle restraints         :   0.219 (tight)
  Side chain planarity           :   0.261 (tight)
  Improper dihedral distribution :   0.590
  B-factor distribution          :   0.368
  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 : 2.70


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.8
  2nd generation packing quality :  -0.0
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :  -0.4
  Backbone conformation          :   0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.296 (tight)
  Bond angles                    :   0.595 (tight)
  Omega angle restraints         :   0.219 (tight)
  Side chain planarity           :   0.261 (tight)
  Improper dihedral distribution :   0.590
  B-factor distribution          :   0.368
  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.