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.

Verification log for pdb1k2o.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.712
CA-only RMS fit for the two chains : 0.410

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

Note: No crystallographic symmetry between molecules

No extra crystallographic symmetry was observed between the independent molecules.

Note: Counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Z equals the number of matrices of the space group multiplied by the number of NCS relations. These numbers seem to be consistent.

Space group as read from CRYST card: P 1
Number of matrices in space group: 1
Highest polymer chain multiplicity in structure: 2
Highest polymer chain multiplicity according to SEQRES: 2
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 2
Z, spacegroup, and NCS seem to agree administratively

Note: Matthews coefficient OK

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Molecular weight of all polymer chains: 95001.094
Volume of the Unit Cell V= 246443.891
Space group multiplicity: 1
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z: Vm= 2.594
Vm by authors and this calculated Vm agree well
Matthews coefficient read from REMARK 280 Vm= 2.650

Note: Chain identifiers OK

WHAT IF has not detected any serious chain identifier problems. But be aware that WHAT IF doesn't care about the chain identifiers of waters.

Warning: Topology could not be determined for some ligands

Some ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

 815 CAC   ( 501-)  A  -         Atom types
 816 CAC   ( 503-)  A  -         Atom types
 817 RFB   ( 901-)  A  -         Atom types
 818 CAC   ( 500-)  B  -         Atom types
 819 CAC   ( 502-)  B  -         Atom types
 820 CAC   ( 504-)  B  -         Atom types
 821 HEM   ( 417-)  A  -         OK
 822 RFA   ( 902-)  B  -         Atom types
 823 HEM   ( 417-)  B  -         OK

Administrative problems that can generate validation failures

Note: No strange inter-chain connections detected

No covalent bonds have been detected between molecules with non-identical chain identifiers.

Note: No duplicate atom names in ligands

All atom names in ligands seem adequately unique.

Note: No mixed usage of alternate atom problems detected

Either this structure does not contain alternate atoms, or they have not been mixed up, or the errors have remained unnoticed.

Note: In all cases the primary alternate atom was used

WHAT IF saw no need to make any alternate atom corrections (which means they are all correct, or there are none).

Note: No residues detected inside ligands

Either this structure does not contain ligands with amino acid groups inside it, or their naming is proper (enough).

Note: No attached groups interfere with hydrogen bond calculations

It seems there are no sugars, lipids, etc., bound (very close) to atoms that otherwise could form hydrogen bonds.

Note: No probable side chain atoms with zero occupancy detected.

Either there are no side chain atoms with zero occupancy, or the side chain atoms with zero occupancy were not present in the input PDB file (in which case they are listed as missing atoms), or their positions are sufficiently improbable to warrant a zero occupancy.

Note: No probable backbone atoms with zero occupancy detected.

Either there are no backbone atoms with zero occupancy, or the backbone atoms with zero occupancy were not present in the input PDB file (in which case they are listed as missing atoms), or their positions are sufficiently improbable to warrant a zero occupancy.

Note: All residues have a complete backbone.

No residues have missing backbone atoms.

Note: No C-alpha only residues

There are no residues that consist of only an alpha carbon atom.

Note: Non-canonicals

WHAT IF has not detected any non-canonical residue that it does not understand (or there are no non-canonical residues in the PDB file).

Non-validating, descriptive output paragraph

Note: Content of the PDB file as interpreted by WHAT IF

Content of the PDB file as interpreted by WHAT IF. WHAT IF has read your PDB file, and stored it internally in what is called 'the soup'. The content of this soup is listed here. An extensive explanation of all frequently used WHAT IF output formats can be found at swift.cmbi.ru.nl. Look under output formats. A course on reading this 'Molecules' table is part of the WHAT CHECK web pages.

     1     1 (    9)   406 (  414) A Protein             pdb1k2o.ent
     2   407 (    9)   812 (  414) B Protein             pdb1k2o.ent
     3   813 (  414)   813 (  414) A V O2 <-   406       pdb1k2o.ent
     4   814 (  414)   814 (  414) B V O2 <-   812       pdb1k2o.ent
     5   815 (  501)   815 (  501) A CAC                 pdb1k2o.ent
     6   816 (  503)   816 (  503) A CAC                 pdb1k2o.ent
     7   817 (  901)   817 (  901) A RFB                 pdb1k2o.ent
     8   818 (  500)   818 (  500) B CAC                 pdb1k2o.ent
     9   819 (  502)   819 (  502) B CAC                 pdb1k2o.ent
    10   820 (  504)   820 (  504) B CAC                 pdb1k2o.ent
    11   821 (  417)   821 (  417) A HEM                 pdb1k2o.ent
    12   822 (  902)   822 (  902) B RFA                 pdb1k2o.ent
    13   823 (  417)   823 (  417) B HEM                 pdb1k2o.ent
    14   824 ( HOH )   824 ( HOH ) A water   (  391)     pdb1k2o.ent
    15   825 ( HOH )   825 ( HOH ) B water   (  303)     pdb1k2o.ent

Note: Some notes regarding the PDB file contents

The numbers and remarks listed below have no explicit validation purpose, they are merely meant for the crystallographer or NMR spectroscopists to perhaps pinpoint something unexpected. See the WHAT_CHECK course for an explanation of terms like 'poor', 'missing', etcetera (in case those words pop up in the lines underneath this message).

The total number of amino acids found is 812.
Number of water molecules 694

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Secondary structure

This is the secondary structure according to DSSP. Only helix (H), overwound or 3/10-helix (3), strand (S), turn (T) and coil (blank) are shown [REF]. All DSSP related information can be found at the DSSP page This is not really a structure validation option, but a very scattered secondary structure (i.e. many strands of only a few residues length, many Ts inside helices, etc) tends to indicate a poor structure. A full explanation of the DSSP secondary structure determination program together with a series of examples can be found at the WHAT_CHECK website.
                     10        20        30        40        50        60
                      |         |         |         |         |         |
    1 -   60 ANLAPLPPHVPEHLVFDFDMYNPSNLSAGVQEAWAVLQESNVPDLVWTRCNGGHWIATRG
(   9)-(  68)       TTT 333     TTT TT333 HHHHH3333TTTT TSSSS 333 SSSS TH
                     70        80        90       100       110       120
                      |         |         |         |         |         |
   61 -  120 QLIREAYEDYRHFSSECPFIPREAGEAYDFIPTSMDPPEQRQFRALANQVVGMPVVDKLE
(  69)-( 128)HHHHHHHH TTTSS T   TT3333TT   TTTT  TTHHHHHHHHHHHHHTHHHHHHHH
                    130       140       150       160       170       180
                      |         |         |         |         |         |
  121 -  180 NRIQELACSLIESLRPQGQCNFTEDYAEPFPIRIFMLLAGLPEEDIPHLKYLTDQMTRPD
( 129)-( 188)HHHHHHHHHHHHHH333TSSSHHHHTTTHHHHHHHHHHHT  333HHHHHHHHHHHHT
                    190       200       210       220       230       240
                      |         |         |         |         |         |
  181 -  240 GSMTFAEAKEALYDYLIPIIEQRRQKPGTDAISIVANGQVNGRPITSDEAKRMCGLLLVG
( 189)-( 248)TTT HHHHHHHHHHHHHHHHHHHHHT  TTHHHHHHT SSTTSS  HHHHHHHHHHHHHT
                    250       260       270       280       290       300
                      |         |         |         |         |         |
  241 -  300 GLDTVVNFLSFSMEFLAKSPEHRQELIERPERIPAACEELLRRFSLVADGRILTSDYEFH
( 249)-( 308)TTHHHHHHHHHHHHHHHH HHHHHHHHH 333HHHHHHHHHHHT    SSSSSTT SSST
                    310       320       330       340       350       360
                      |         |         |         |         |         |
  301 -  360 GVQLKKGDQILLPQMLSGLDERENAAPMHVDFSRQKVSHTTFGHGSHLCLGQHLARREII
( 309)-( 368)TSSS TT SSSS HHHHHH TTTTTTTTT  TT T     TT  333  TTHHHHHHHHH
                    370       380       390       400
                      |         |         |         |
  361 -  406 VTLKEWLTRIPDFSIAPGAQIQHKSGIVSGVQALPLVWDPATTKAV
( 369)-( 414)HHHHHHHHH    SS TT    SS TT  SST  SSS  333
 
              410       420       430       440       450       460
                |         |         |         |         |         |
  407 -  466 ANLAPLPPHVPEHLVFDFDMYNPSNLSAGVQEAWAVLQESNVPDLVWTRCNGGHWIATRG
(   9)-(  68)       TTT 333     TTT TT333 HHHHH3333TTTT TSSSS TTT SSSS TH
              470       480       490       500       510       520
                |         |         |         |         |         |
  467 -  526 QLIREAYEDYRHFSSECPFIPREAGEAYDFIPTSMDPPEQRQFRALANQVVGMPVVDKLE
(  69)-( 128)HHHHHHHH TTTSS T   TT333TTT   TTTT  TTTTHHHHHHHHHHHTHHHHHHHH
              530       540       550       560       570       580
                |         |         |         |         |         |
  527 -  586 NRIQELACSLIESLRPQGQCNFTEDYAEPFPIRIFMLLAGLPEEDIPHLKYLTDQMTRPD
( 129)-( 188)HHHHHHHHHHHHHH333TSSSHHHHTTTHHHHHHHHHHHT  333HHHHHHHHHHHHT
              590       600       610       620       630       640
                |         |         |         |         |         |
  587 -  646 GSMTFAEAKEALYDYLIPIIEQRRQKPGTDAISIVANGQVNGRPITSDEAKRMCGLLLVG
( 189)-( 248)TTT HHHHHHHHHHHHHHHHHHHHHT  TTHHHHHHT SSTTSS  HHHHHHHHHHHHHT
              650       660       670       680       690       700
                |         |         |         |         |         |
  647 -  706 GLDTVVNFLSFSMEFLAKSPEHRQELIERPERIPAACEELLRRFSLVADGRILTSDYEFH
( 249)-( 308)TTHHHHHHHHHHHHHHHH HHHHHHHHH 333HHHHHHHHHHHT    SSSSSTT SSST
              710       720       730       740       750       760
                |         |         |         |         |         |
  707 -  766 GVQLKKGDQILLPQMLSGLDERENAAPMHVDFSRQKVSHTTFGHGSHLCLGQHLARREII
( 309)-( 368)TSSS TT SSSS HHHHHH TTTTTTTTT  TT TT    TT  333  TTHHHHHHHHH
              770       780       790       800       810
                |         |         |         |         |
  767 -  812 VTLKEWLTRIPDFSIAPGAQIQHKSGIVSGVQALPLVWDPATTKAV
( 369)-( 414)HHHHHHHHH    SS TT    SS TT  SST  SSS  333
 
 
 

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

Note: No rounded coordinates detected

No significant rounding of atom coordinates has been detected.

Note: No artificial side chains detected

No artificial side-chain positions characterized by chi-1=0.0 or chi-1=180.0 have been detected.

Note: No missing atoms detected in residues

All expected atoms are present in residues. This validation option has not looked at 'things' that can or should be attached to the elemantary building blocks (amino acids, nucleotides). Even the C-terminal oxygens are treated separately.

Note: All B-factors fall in the range 0.0 - 100.0

All B-factors are larger than zero, and none are observed above 100.0.

Note: No C-terminal nitrogen detected

The PDB indicates that a residue is not the true C-terminus by including only the backbone N of the next residue. This has not been observed in this PDB file.

Note: Test capping of (pseudo) C-termini

No extra capping groups were found on pseudo C-termini. This can imply that no pseudo C-termini are present.

Note: No OXT found in the middle of chains

No OXT groups were found in the middle of protein chains.

Note: Weights checked OK

All atomic occupancy factors ('weights') fall in the 0.0-1.0 range.

Note: Normal distribution of occupancy values

The distribution of the occupancy values in this file seems 'normal'.

Be aware that this evaluation is merely the result of comparing this file with about 500 well-refined high-resolution files in the PDB. If this file has much higher or much lower resolution than the PDB files used in WHAT IF's training set, non-normal values might very well be perfectly fine, or normal values might actually be not so normal. So, this check is actually more an indicator and certainly not a check in which I have great confidence.

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.

  12 GLU   (  20-)  A    0.75
 418 GLU   (  20-)  B    0.75
 507 ARG   ( 109-)  B    0.70

Warning: What type of B-factor?

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

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

Crystal temperature (K) :100.000

Note: Number of buried atoms with low B-factor is OK

For protein structures determined at room temperature, no more than about 1 percent of the B factors of buried atoms is below 5.0.

Percentage of buried atoms with B less than 5 : 0.00

Note: B-factor distribution normal

The distribution of B-factors within residues is within expected ranges. A value over 1.5 here would mean that the B-factors show signs of over- refinement.

RMS Z-score : 0.335 over 5770 bonds
Average difference in B over a bond : 0.33
RMS difference in B over a bond : 0.45

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Note: Introduction to the nomenclature section.

Nomenclature problems seem, at first, rather unimportant. After all who cares if we call the delta atoms in leucine delta2 and delta1 rather than the other way around. Chemically speaking that is correct. But structures have not been solved and deposited just for chemists to look at them. Most times a structure is used, it is by software in a bioinformatics lab. And if they compare structures in which the one used C delta1 and delta2 and the other uses C delta2 and delta1, then that comparison will fail. Also, we recalculate all structures every so many years to make sure that everybody always can get access to the best coordinates that can be obtained from the (your?) experimental data. These recalculations will be troublesome if there are nomenclature problems.

Several nomenclature problems actually are worse than that. At the WHAT_CHECK website you can get an overview of the importance of all nomenclature problems that we list.

Note: Valine nomenclature OK

No errors were detected in valine nomenclature.

Note: Threonine nomenclature OK

No errors were detected in threonine nomenclature.

Note: Isoleucine nomenclature OK

No errors were detected in isoleucine nomenclature.

Note: Leucine nomenclature OK

No errors were detected in leucine nomenclature.

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

  82 ARG   (  90-)  A
 122 ARG   ( 130-)  A
 334 ARG   ( 342-)  A
 356 ARG   ( 364-)  A
 528 ARG   ( 130-)  B
 740 ARG   ( 342-)  B
 762 ARG   ( 364-)  B

Warning: Tyrosine convention problem

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

  21 TYR   (  29-)  A
  70 TYR   (  78-)  A
 146 TYR   ( 154-)  A
 193 TYR   ( 201-)  A
 195 TYR   ( 203-)  A
 427 TYR   (  29-)  B
 552 TYR   ( 154-)  B
 599 TYR   ( 201-)  B
 601 TYR   ( 203-)  B

Warning: Phenylalanine convention problem

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

  16 PHE   (  24-)  A
  79 PHE   (  87-)  A
 103 PHE   ( 111-)  A
 248 PHE   ( 256-)  A
 255 PHE   ( 263-)  A
 284 PHE   ( 292-)  A
 373 PHE   ( 381-)  A
 422 PHE   (  24-)  B
 509 PHE   ( 111-)  B
 654 PHE   ( 256-)  B
 661 PHE   ( 263-)  B
 690 PHE   ( 292-)  B
 779 PHE   ( 381-)  B

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.

  17 ASP   (  25-)  A
  44 ASP   (  52-)  A
  89 ASP   (  97-)  A
 117 ASP   ( 125-)  A
 180 ASP   ( 188-)  A
 228 ASP   ( 236-)  A
 243 ASP   ( 251-)  A
 308 ASP   ( 316-)  A
 320 ASP   ( 328-)  A
 331 ASP   ( 339-)  A
 372 ASP   ( 380-)  A
 399 ASP   ( 407-)  A
 423 ASP   (  25-)  B
 450 ASP   (  52-)  B
 495 ASP   (  97-)  B
 523 ASP   ( 125-)  B
 586 ASP   ( 188-)  B
 634 ASP   ( 236-)  B
 649 ASP   ( 251-)  B
 714 ASP   ( 316-)  B
 726 ASP   ( 328-)  B
 737 ASP   ( 339-)  B
 778 ASP   ( 380-)  B
 805 ASP   ( 407-)  B

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.

  32 GLU   (  40-)  A
  39 GLU   (  47-)  A
  68 GLU   (  76-)  A
  99 GLU   ( 107-)  A
 125 GLU   ( 133-)  A
 132 GLU   ( 140-)  A
 144 GLU   ( 152-)  A
 148 GLU   ( 156-)  A
 163 GLU   ( 171-)  A
 164 GLU   ( 172-)  A
 201 GLU   ( 209-)  A
 229 GLU   ( 237-)  A
 254 GLU   ( 262-)  A
 261 GLU   ( 269-)  A
 265 GLU   ( 273-)  A
 268 GLU   ( 276-)  A
 271 GLU   ( 279-)  A
 278 GLU   ( 286-)  A
 365 GLU   ( 373-)  A
 438 GLU   (  40-)  B
 445 GLU   (  47-)  B
 474 GLU   (  76-)  B
 482 GLU   (  84-)  B
 492 GLU   (  94-)  B
 505 GLU   ( 107-)  B
 531 GLU   ( 133-)  B
 538 GLU   ( 140-)  B
 550 GLU   ( 152-)  B
 554 GLU   ( 156-)  B
 569 GLU   ( 171-)  B
 607 GLU   ( 209-)  B
 635 GLU   ( 237-)  B
 660 GLU   ( 262-)  B
 667 GLU   ( 269-)  B
 671 GLU   ( 273-)  B
 674 GLU   ( 276-)  B
 677 GLU   ( 279-)  B
 684 GLU   ( 286-)  B
 771 GLU   ( 373-)  B

Note: Phosphate group names OK

No errors were detected in phosphate group naming conventions.

Note: Heavy atom naming OK

No errors were detected in the atom names for non-hydrogen atoms. Please be aware that the PDB wants us to deliberately make some nomenclature errors; especially in non-canonical amino acids.

Note: Chain names are OK

All chain names assigned to polymer molecules are unique, and all residue numbers are strictly increasing within each chain.

Geometric checks

Note: All bond lengths OK

All bond lengths are in agreement with standard bond lengths using a tolerance of 4 sigma (both standard values and sigma for amino acids have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF])

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: 0.311
RMS-deviation in bond distances: 0.008

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

 |  0.998267  0.000416 -0.000007|
 |  0.000416  0.998211  0.000054|
 | -0.000007  0.000054  0.997973|
Proposed new scale matrix

 |  0.015688 -0.008238 -0.006015|
 | -0.000007  0.016873 -0.002723|
 |  0.000000  0.000000  0.015418|
With corresponding cell

    A    =  63.759  B   =  66.954  C    =  72.379
    Alpha=  71.139  Beta=  65.187  Gamma=  62.271

The CRYST1 cell dimensions

    A    =  63.870  B   =  67.050  C    =  72.520
    Alpha=  71.160  Beta=  65.200  Gamma=  62.310

Variance: 94.093
(Under-)estimated Z-score: 7.149

Note: All bond angles OK

All bond angles are in agreement with standard bond angles using a tolerance of 4 sigma (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al. [REF]). Please note that disulphide bridges are neglected.

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: 0.618
RMS-deviation in bond angles: 1.317

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.

  17 ASP   (  25-)  A
  32 GLU   (  40-)  A
  39 GLU   (  47-)  A
  44 ASP   (  52-)  A
  68 GLU   (  76-)  A
  82 ARG   (  90-)  A
  89 ASP   (  97-)  A
  99 GLU   ( 107-)  A
 117 ASP   ( 125-)  A
 122 ARG   ( 130-)  A
 125 GLU   ( 133-)  A
 132 GLU   ( 140-)  A
 144 GLU   ( 152-)  A
 148 GLU   ( 156-)  A
 163 GLU   ( 171-)  A
 164 GLU   ( 172-)  A
 180 ASP   ( 188-)  A
 201 GLU   ( 209-)  A
 228 ASP   ( 236-)  A
 229 GLU   ( 237-)  A
 243 ASP   ( 251-)  A
 254 GLU   ( 262-)  A
 261 GLU   ( 269-)  A
 265 GLU   ( 273-)  A
 268 GLU   ( 276-)  A
And so on for a total of 70 lines.

Note: Chirality OK

All protein atoms have proper chirality. But, look at the previous table to see a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

Note: Improper dihedral angle distribution OK

The RMS Z-score for all improper dihedrals in the structure is within normal ranges.

Improper dihedral RMS Z-score : 0.696

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.

 316 LEU   ( 324-)  A    6.04
 551 ASP   ( 153-)  B    5.12
 507 ARG   ( 109-)  B    4.98
 145 ASP   ( 153-)  A    4.76
 110 VAL   ( 118-)  A    4.71
 526 GLU   ( 128-)  B    4.69
 722 LEU   ( 324-)  B    4.65
 516 VAL   ( 118-)  B    4.47
 135 ARG   ( 143-)  A    4.38
 541 ARG   ( 143-)  B    4.34
 142 PHE   ( 150-)  A    4.18
 101 ARG   ( 109-)  A    4.14

Note: Normal tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure falls within the normal range that we guess to be 0.5 - 1.5. Be aware, 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 : 1.388

Note: Side chain planarity OK

All of the side chains of residues that have a planar group are planar within expected RMS deviations.

Note: Atoms connected to aromatic rings OK

All of the atoms that are connected to planar aromatic rings in side chains of amino-acid residues are in the plane within expected RMS deviations.

Torsion-related checks

Note: Ramachandran Z-score OK

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is within expected ranges for well-refined structures.

Ramachandran Z-score : -1.129

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.

 498 PRO   ( 100-)  B    -3.0
  92 PRO   ( 100-)  A    -3.0

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.

   2 ASN   (  10-)  A  Poor phi/psi
  80 ILE   (  88-)  A  PRO omega poor
  86 GLU   (  94-)  A  Poor phi/psi
  91 ILE   (  99-)  A  PRO omega poor
  97 PRO   ( 105-)  A  PRO omega poor
 140 CYS   ( 148-)  A  Poor phi/psi
 221 ASN   ( 229-)  A  Poor phi/psi
 242 LEU   ( 250-)  A  Poor phi/psi
 408 ASN   (  10-)  B  Poor phi/psi
 431 ASN   (  33-)  B  Poor phi/psi
 486 ILE   (  88-)  B  PRO omega poor
 492 GLU   (  94-)  B  Poor phi/psi
 497 ILE   (  99-)  B  PRO omega poor
 503 PRO   ( 105-)  B  PRO omega poor
 546 CYS   ( 148-)  B  Poor phi/psi
 586 ASP   ( 188-)  B  Poor phi/psi
 648 LEU   ( 250-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.588

Note: chi-1/chi-2 angle correlation Z-score OK

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is within expected ranges for well-refined structures.

chi-1/chi-2 correlation Z-score : -0.588

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.

 133 SER   ( 141-)  A    0.36
 213 SER   ( 221-)  A    0.36
 252 SER   ( 260-)  A    0.36
 539 SER   ( 141-)  B    0.36
 658 SER   ( 260-)  B    0.36
 619 SER   ( 221-)  B    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!

   9 HIS   (  17-)  A      0
  24 SER   (  32-)  A      0
  28 ALA   (  36-)  A      0
  44 ASP   (  52-)  A      0
  45 LEU   (  53-)  A      0
  49 ARG   (  57-)  A      0
  50 CYS   (  58-)  A      0
  51 ASN   (  59-)  A      0
  54 HIS   (  62-)  A      0
  70 TYR   (  78-)  A      0
  72 HIS   (  80-)  A      0
  75 SER   (  83-)  A      0
  76 GLU   (  84-)  A      0
  77 CYS   (  85-)  A      0
  78 PRO   (  86-)  A      0
  79 PHE   (  87-)  A      0
  80 ILE   (  88-)  A      0
  81 PRO   (  89-)  A      0
  82 ARG   (  90-)  A      0
  86 GLU   (  94-)  A      0
  87 ALA   (  95-)  A      0
  88 TYR   (  96-)  A      0
  90 PHE   (  98-)  A      0
  91 ILE   (  99-)  A      0
  92 PRO   ( 100-)  A      0
And so on for a total of 271 lines.

Note: Backbone conformation Z-score OK

The backbone conformation analysis gives a score that is normal for well refined protein structures.

Backbone conformation Z-score : -1.275

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 : 1.420

Note: Backbone oxygen evaluation OK

All residues for which the local backbone conformation could be found in the WHAT IF database have a normal backbone oxygen position.

Note: Peptide bond conformations

We could not find any peptide bonds that are likely to actually be a cis bond. This check has not yet fully matured...

Note: PRO puckering amplitude OK

Puckering amplitudes for all PRO residues are within normal ranges.

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].

   5 PRO   (  13-)  A  -113.7 envelop C-gamma (-108 degrees)
 411 PRO   (  13-)  B  -118.0 half-chair C-delta/C-gamma (-126 degrees)
 498 PRO   ( 100-)  B   -64.8 envelop C-beta (-72 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.

 124 GLN   ( 132-)  A      NE2 <->  128 CYS   ( 136-)  A      SG     0.69    2.61  INTRA
  77 CYS   (  85-)  A      SG  <->  815 CAC   ( 501-)  A      C1     0.47    2.93  INTRA
 456 CYS   (  58-)  B      SG  <->  819 CAC   ( 502-)  B      C1     0.40    3.00  INTRA
 298 GLU   ( 306-)  A      CG  <->  303 GLN   ( 311-)  A      NE2    0.40    2.70  INTRA
 349 CYS   ( 357-)  A      SG  <->  821 HEM   ( 417-)  A      NC     0.39    2.91  INTRA BL
 755 CYS   ( 357-)  B      SG  <->  823 HEM   ( 417-)  B      NC     0.37    2.93  INTRA BL
 298 GLU   ( 306-)  A      CD  <->  303 GLN   ( 311-)  A      NE2    0.33    2.77  INTRA
 755 CYS   ( 357-)  B      SG  <->  823 HEM   ( 417-)  B      NB     0.31    2.99  INTRA BL
  50 CYS   (  58-)  A      SG  <->  816 CAC   ( 503-)  A      C1     0.29    3.11  INTRA
 128 CYS   ( 136-)  A      SG  <->  369 ARG   ( 377-)  A      NH2    0.29    3.01  INTRA
  22 ASN   (  30-)  A    A ND2 <->  824 HOH   (1520 )  A      O      0.28    2.42  INTRA
 534 CYS   ( 136-)  B    A SG  <->  825 HOH   (1421 )  B      O      0.27    2.73  INTRA
  51 ASN   (  59-)  A      ND2 <->  824 HOH   (1407 )  A      O      0.26    2.44  INTRA
 349 CYS   ( 357-)  A      SG  <->  821 HEM   ( 417-)  A      NB     0.26    3.04  INTRA BL
  85 GLY   (  93-)  A      C   <->  817 RFB   ( 901-)  A    B F46    0.25    2.95  INTRA
 128 CYS   ( 136-)  A      SG  <->  824 HOH   (1017 )  A      O      0.24    2.76  INTRA
 534 CYS   ( 136-)  B    A CB  <->  820 CAC   ( 504-)  B     AS      0.22    2.98  INTRA BF
 583 THR   ( 185-)  B      CA  <->  822 RFA   ( 902-)  B    A F48    0.21    2.99  INTRA
  76 GLU   (  84-)  A      CD  <->   82 ARG   (  90-)  A      NH2    0.19    2.91  INTRA
 559 ARG   ( 161-)  B      NE  <->  825 HOH   (1199 )  B      O      0.18    2.52  INTRA
 133 SER   ( 141-)  A      O   <->  137 GLN   ( 145-)  A      NE2    0.17    2.53  INTRA
 122 ARG   ( 130-)  A      NH1 <->  157 LEU   ( 165-)  A      CD1    0.17    2.93  INTRA
 102 GLN   ( 110-)  A      OE1 <->  221 ASN   ( 229-)  A      N      0.15    2.55  INTRA
 269 ARG   ( 277-)  A      NH2 <->  824 HOH   (1418 )  A      O      0.15    2.55  INTRA
  76 GLU   (  84-)  A      OE2 <->   82 ARG   (  90-)  A      NH2    0.15    2.55  INTRA
And so on for a total of 84 lines.

Packing, accessibility and threading

Note: Inside/Outside residue distribution normal

The distribution of residue types over the inside and the outside of the protein is normal.

inside/outside RMS Z-score : 0.971

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

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.

 584 ARG   ( 186-)  B      -5.94
 392 GLN   ( 400-)  A      -5.92
 798 GLN   ( 400-)  B      -5.73
 611 GLN   ( 213-)  B      -5.60
 178 ARG   ( 186-)  A      -5.57
 205 GLN   ( 213-)  A      -5.55
 542 PRO   ( 144-)  B      -5.53
 543 GLN   ( 145-)  B      -5.50
 136 PRO   ( 144-)  A      -5.50
 137 GLN   ( 145-)  A      -5.48
 206 LYS   ( 214-)  A      -5.37
 322 ARG   ( 330-)  A      -5.32
  51 ASN   (  59-)  A      -5.27
 728 ARG   ( 330-)  B      -5.26
 415 HIS   (  17-)  B      -5.08
 347 HIS   ( 355-)  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.

 204 ARG   ( 212-)  A       206 - LYS    214- ( A)         -5.09
 610 ARG   ( 212-)  B       612 - LYS    214- ( B)         -4.90

Note: Structural average packing environment OK

The structural average packing score is within normal ranges.

Average for range 1 - 812 : -0.560

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

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.

 434 ALA   (  36-)  B   -2.96
  71 ARG   (  79-)  A   -2.83
 490 ALA   (  92-)  B   -2.60
  84 ALA   (  92-)  A   -2.59

Note: No series of residues with abnormal new packing environment

There are no stretches of four or more residues each having a packing Z-score worse than -1.75.

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

Note: Water contacts OK

All water clusters make at least one contact with a non-water atom.

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.

 824 HOH   (1274 )  A      O     29.31   -9.36    0.83
 824 HOH   (1305 )  A      O    -30.63   -6.81  -48.32
 824 HOH   (1468 )  A      O     -5.20   26.13  -47.60
 824 HOH   (1586 )  A      O    -13.45    7.90  -50.00
 824 HOH   (1587 )  A      O    -14.59   10.30  -49.37
 824 HOH   (1588 )  A      O    -16.99    8.71  -49.60
 824 HOH   (1611 )  A      O    -11.43   26.70  -51.15
 825 HOH   (1510 )  B      O    -14.98  -22.21   -0.15

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.

 824 HOH   (1002 )  A      O
 824 HOH   (1444 )  A      O
 824 HOH   (1466 )  A      O
 824 HOH   (1525 )  A      O
 824 HOH   (1618 )  A      O
 825 HOH   (1226 )  B      O
 825 HOH   (1262 )  B      O
 825 HOH   (1661 )  B      O
Marked this atom as acceptor  817 RFB  ( 901-) A    B F46
Marked this atom as acceptor  817 RFB  ( 901-) A    B F47
Marked this atom as acceptor  817 RFB  ( 901-) A    B F48
Marked this atom as acceptor  817 RFB  ( 901-) A    B F49
Marked this atom as acceptor  817 RFB  ( 901-) A    B F56
Marked this atom as acceptor  817 RFB  ( 901-) A    B F57
Marked this atom as acceptor  817 RFB  ( 901-) A    B F58
Marked this atom as acceptor  817 RFB  ( 901-) A    B F59
Marked this atom as acceptor  822 RFA  ( 902-) B    A F46
Marked this atom as acceptor  822 RFA  ( 902-) B    A F47
Marked this atom as acceptor  822 RFA  ( 902-) B    A F48
Marked this atom as acceptor  822 RFA  ( 902-) B    A F49
Marked this atom as acceptor  822 RFA  ( 902-) B    A F56
Marked this atom as acceptor  822 RFA  ( 902-) B    A F57
Marked this atom as acceptor  822 RFA  ( 902-) B    A F58
Marked this atom as acceptor  822 RFA  ( 902-) B    A F59

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.

  31 GLN   (  39-)  A
  38 GLN   (  46-)  A
  51 ASN   (  59-)  A
  61 GLN   (  69-)  A
  72 HIS   (  80-)  A
 124 GLN   ( 132-)  A
 141 ASN   ( 149-)  A
 202 GLN   ( 210-)  A
 264 GLN   ( 272-)  A
 415 HIS   (  17-)  B
 428 ASN   (  30-)  B
 437 GLN   (  39-)  B
 444 GLN   (  46-)  B
 457 ASN   (  59-)  B
 506 GLN   ( 108-)  B
 508 GLN   ( 110-)  B
 514 ASN   ( 116-)  B
 543 GLN   ( 145-)  B
 608 GLN   ( 210-)  B
 623 ASN   ( 225-)  B
 715 GLN   ( 317-)  B
 735 HIS   ( 337-)  B

Note: Histidine type assignments

For all complete HIS residues in the structure a tentative assignment to HIS-D (protonated on ND1), HIS-E (protonated on NE2), or HIS-H (protonated on both ND1 and NE2, positively charged) is made based on the hydrogen bond network. A second assignment is made based on which of the Engh and Huber [REF] histidine geometries fits best to the structure.

In the table below all normal histidine residues are listed. The assignment based on the geometry of the residue is listed first, together with the RMS Z-score for the fit to the Engh and Huber parameters. For all residues where the H-bond assignment is different, the assignment is listed in the last columns, together with its RMS Z-score to the Engh and Huber parameters.

As always, the RMS Z-scores should be close to 1.0 if the residues were restrained to the Engh and Huber parameters during refinement.

Please note that because the differences between the geometries of the different types are small it is possible that the geometric assignment given here does not correspond to the type used in refinement. This is especially true if the RMS Z-scores are much higher than 1.0.

If the two assignments differ, or the `geometry' RMS Z-score is high, it is advisable to verify the hydrogen bond assignment, check the HIS type used during the refinement and possibly adjust it.

   9 HIS   (  17-)  A     HIS-H   0.12 HIS-E   0.59
  13 HIS   (  21-)  A     HIS-H   0.08 HIS-D   0.53
  54 HIS   (  62-)  A     HIS-H   0.13 HIS-D   0.56
  72 HIS   (  80-)  A     HIS-H   0.27 HIS-D   0.50
 168 HIS   ( 176-)  A     HIS-H   0.12
 262 HIS   ( 270-)  A     HIS-H   0.13
 300 HIS   ( 308-)  A     HIS-H   0.09 HIS-E   0.58
 329 HIS   ( 337-)  A     HIS-H   0.11 HIS-D   0.51
 339 HIS   ( 347-)  A     HIS-H   0.15 HIS-E   0.59
 344 HIS   ( 352-)  A     HIS-H   0.26 HIS-E   0.59
 347 HIS   ( 355-)  A     HIS-H   0.11 HIS-E   0.56
 353 HIS   ( 361-)  A     HIS-H   0.04
 383 HIS   ( 391-)  A     HIS-H   0.16 HIS-E   0.59
 415 HIS   (  17-)  B     HIS-H   0.14 HIS-E   0.56
 419 HIS   (  21-)  B     HIS-H   0.07 HIS-E   0.58
 460 HIS   (  62-)  B     HIS-D   0.44
 478 HIS   (  80-)  B     HIS-H   0.13 HIS-D   0.50
 574 HIS   ( 176-)  B     HIS-H   0.09
 668 HIS   ( 270-)  B     HIS-H   0.10
 706 HIS   ( 308-)  B     HIS-H   0.05 HIS-E   0.60
 735 HIS   ( 337-)  B     HIS-H   0.05 HIS-D   0.57
 745 HIS   ( 347-)  B     HIS-H   0.13 HIS-E   0.57
 750 HIS   ( 352-)  B     HIS-H   0.09 HIS-E   0.62
 753 HIS   ( 355-)  B     HIS-H   0.13 HIS-E   0.59
 759 HIS   ( 361-)  B     HIS-H   0.06 HIS-E   0.60
 789 HIS   ( 391-)  B     HIS-H   0.09 HIS-E   0.61

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.

   3 LEU   (  11-)  A      N
  31 GLN   (  39-)  A      NE2
  59 ARG   (  67-)  A      N
  80 ILE   (  88-)  A      N
  83 GLU   (  91-)  A      N
  88 TYR   (  96-)  A      OH
  90 PHE   (  98-)  A      N
 102 GLN   ( 110-)  A      N
 104 ARG   ( 112-)  A      NH1
 139 GLN   ( 147-)  A      N
 164 GLU   ( 172-)  A      N
 204 ARG   ( 212-)  A      NH2
 272 ARG   ( 280-)  A      NH1
 291 ARG   ( 299-)  A      NH1
 303 GLN   ( 311-)  A      NE2
 350 LEU   ( 358-)  A      N
 366 TRP   ( 374-)  A      NE1
 373 PHE   ( 381-)  A      N
 406 VAL   ( 414-)  A      N
 437 GLN   (  39-)  B      NE2
 447 ASN   (  49-)  B      N
 465 ARG   (  67-)  B      N
 476 TYR   (  78-)  B      N
 486 ILE   (  88-)  B      N
 496 PHE   (  98-)  B      N
 506 GLN   ( 108-)  B      NE2
 507 ARG   ( 109-)  B      NE
 510 ARG   ( 112-)  B      NH1
 541 ARG   ( 143-)  B      NE
 545 GLN   ( 147-)  B      N
 558 ILE   ( 160-)  B      N
 697 ARG   ( 299-)  B      NH1
 701 SER   ( 303-)  B      N
 756 LEU   ( 358-)  B      N
 772 TRP   ( 374-)  B      NE1
 779 PHE   ( 381-)  B      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.

 100 GLN   ( 108-)  A      OE1
 132 GLU   ( 140-)  A      OE1
 289 ASP   ( 297-)  A      OD2
 358 GLU   ( 366-)  A      OE1
 695 ASP   ( 297-)  B      OD2
 764 GLU   ( 366-)  B      OE1
 798 GLN   ( 400-)  B      OE1

Note: Crystallisation conditions from REMARK 280

Crystallisation conditions as found in the PDB file header.

CRYSTAL
SOLVENT CONTENT, VS   (%): 53.50
MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65
CRYSTALLIZATION CONDITIONS: HEPES, PEG, KCL, DTT, PH 7.5, SLOW
       COOLING, TEMPERATURE 277K

Note: No ions (of a type we can validate) in structure

Since there are no ions in the structure of a type we can validate, this check will not be executed.

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.

 824 HOH   (1016 )  A      O  0.86  K  4 *2
 824 HOH   (1038 )  A      O  0.90  K  4 *2
 824 HOH   (1158 )  A      O  0.94  K  4 *2
 824 HOH   (1168 )  A      O  0.89  K  6 *2
 824 HOH   (1216 )  A      O  0.80  K  5 *2 Ion-B
 824 HOH   (1403 )  A      O  1.01  K  4 *2
 824 HOH   (1426 )  A      O  0.89  K  4 *2
 824 HOH   (1526 )  A      O  0.81  K  4 *2
 825 HOH   (1091 )  B      O  0.79  K  4 *2
 825 HOH   (1174 )  B      O  0.84  K  4 *2 ION-B
 825 HOH   (1197 )  B      O  0.94  K  4 *2
 825 HOH   (1396 )  B      O  0.93  K  4 *2

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.

  19 ASP   (  27-)  A   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
  96 ASP   ( 104-)  A   H-bonding suggests Asn; but Alt-Rotamer
 600 ASP   ( 202-)  B   H-bonding suggests Asn; but Alt-Rotamer

Note: Content of the PDB file as interpreted by WHAT IF

Content of the PDB file as interpreted by WHAT IF. WHAT IF has read your PDB file, and stored it internally in what is called 'the soup'. The content of this soup is listed here. An extensive explanation of all frequently used WHAT IF output formats can be found at swift.cmbi.ru.nl. Look under output formats. A course on reading this 'Molecules' table is part of the WHAT CHECK web pages.

     1     1 (    9)   406 (  414) A Protein             pdb1k2o.ent
     2   407 (    9)   812 (  414) B Protein             pdb1k2o.ent
     3   813 (  414)   813 (  414) A V O2 <-   406       pdb1k2o.ent
     4   814 (  414)   814 (  414) B V O2 <-   812       pdb1k2o.ent
     5   815 (  501)   815 (  501) A CAC                 pdb1k2o.ent
     6   816 (  503)   816 (  503) A CAC                 pdb1k2o.ent
     7   817 (  901)   817 (  901) A RFB                 pdb1k2o.ent
     8   818 (  500)   818 (  500) B CAC                 pdb1k2o.ent
     9   819 (  502)   819 (  502) B CAC                 pdb1k2o.ent
    10   820 (  504)   820 (  504) B CAC                 pdb1k2o.ent
    11   821 (  417)   821 (  417) A HEM                 pdb1k2o.ent
    12   822 (  902)   822 (  902) B RFA                 pdb1k2o.ent
    13   823 (  417)   823 (  417) B HEM                 pdb1k2o.ent
    14   824 ( HOH )   824 ( HOH ) A water   (  391)     pdb1k2o.ent
    15   825 ( HOH )   825 ( HOH ) B water   (  303)     pdb1k2o.ent

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 :  -0.151
  2nd generation packing quality :  -1.386
  Ramachandran plot appearance   :  -1.129
  chi-1/chi-2 rotamer normality  :  -0.588
  Backbone conformation          :  -1.275

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.311 (tight)
  Bond angles                    :   0.618 (tight)
  Omega angle restraints         :   0.258 (tight)
  Side chain planarity           :   0.394 (tight)
  Improper dihedral distribution :   0.696
  B-factor distribution          :   0.335
  Inside/Outside distribution    :   0.971

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 : 1.65


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.1
  2nd generation packing quality :  -1.4
  Ramachandran plot appearance   :  -1.1
  chi-1/chi-2 rotamer normality  :  -0.8
  Backbone conformation          :  -1.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.311 (tight)
  Bond angles                    :   0.618 (tight)
  Omega angle restraints         :   0.258 (tight)
  Side chain planarity           :   0.394 (tight)
  Improper dihedral distribution :   0.696
  B-factor distribution          :   0.335
  Inside/Outside distribution    :   0.971
==============

WHAT IF
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Bond lengths and angles, DNA/RNA
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DSSP
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Hydrogen bond networks
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      protein structures
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Matthews' Coefficient
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Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
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Puckering parameters
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Quality Control
    G.Vriend and C.Sander,
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      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.