WHAT IF Check report

This file was created 2011-12-18 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 pdb1v54.ent

Checks that need to be done early-on in validation

Warning: Unconventional orthorhombic cell

The primitive P 2 2 2 or P 21 21 21 cell specified does not conform to the convention that the axes should be given in order of increasing length.

The CRYST1 cell dimensions

    A    = 182.590  B   = 205.140  C    = 178.250
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Warning: Conventional cell

The conventional cell as mentioned earlier has been derived.

The CRYST1 cell dimensions

    A    = 182.590  B   = 205.140  C    = 178.250
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    = 178.250  B   = 182.590  C    = 205.140
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    = 178.250  B   = 182.590  C    = 205.140
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

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

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 N

All-atom RMS fit for the two chains : 0.114
CA-only RMS fit for the two chains : 0.036

Note: Low non-crystallographic symmetry phi and psi differences

All comparable residues in the two chains mentioned below have comparable backbone torsion angles

Chain identifiers of the two chains: A and N

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: B and O

All-atom RMS fit for the two chains : 0.310
CA-only RMS fit for the two chains : 0.062

Note: Low non-crystallographic symmetry phi and psi differences

All comparable residues in the two chains mentioned below have comparable backbone torsion angles

Chain identifiers of the two chains: B and O

Note: Low non-crystallographic symmetry RMS

All comparable residues in the two chains mentioned below have comparable locations.

Chain identifiers of the two chains: C and P

All-atom RMS fit for the two chains : 0.126
CA-only RMS fit for the two chains : 0.031

Note: Low non-crystallographic symmetry phi and psi differences

All comparable residues in the two chains mentioned below have comparable backbone torsion angles

Chain identifiers of the two chains: C and P

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: D and Q

All-atom RMS fit for the two chains : 0.411
CA-only RMS fit for the two chains : 0.063

Note: Low non-crystallographic symmetry phi and psi differences

All comparable residues in the two chains mentioned below have comparable backbone torsion angles

Chain identifiers of the two chains: D and Q

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: E and R

All-atom RMS fit for the two chains : 0.443
CA-only RMS fit for the two chains : 0.068

Note: Low non-crystallographic symmetry phi and psi differences

All comparable residues in the two chains mentioned below have comparable backbone torsion angles

Chain identifiers of the two chains: E and R

Note: NCS statistics suppressed

There are more pairs of NCS equivalent molecules, but the statistics will not be shown.

Note: No crystallographic symmetry between molecules

No extra crystallographic symmetry was observed between the independent molecules.

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: P 21 21 21
Number of matrices in space group: 4
Highest polymer chain multiplicity in structure: 2
Highest polymer chain multiplicity according to SEQRES: 4
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
There is also strong SEQRES evidence for a multiplicity of: 2
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 8
Polymer chain multiplicity and SEQRES multiplicity disagree 2 4
Z and NCS seem to support the 3D multiplicity
There is strong evidence, though, for multiplicity and Z: 2 8

Error: Matthews Coefficient (Vm) very high

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.

Numbers this high are almost always caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all).

Molecular weight of all polymer chains: 433439.906
Volume of the Unit Cell V= 6676053.5
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 7.701
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 4.070 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)
There is strong evidence, though, for multiplicity and Z: 2 8
which would result in the much more normal Vm= 3.851
and which also agrees with the number of NCS matrices (labeled `don't use')
that the user provided in the MTRIX records 1

Note: No atoms with high occupancy detected at special positions

Either there were no atoms at special positions, or all atoms at special positions have adequately reduced occupancies. An atom is considered to be located at a special position if it is within 0.3 Angstrom from one of its own symmetry copies. See also the next check...

Note: All atoms are sufficiently far away from symmetry axes

None of the atoms in the structure is closer than 0.77 Angstrom to a proper symmetry axis.

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.

3553 FME   (   1-)  A  -         OK
3555 FME   (   1-)  B  -         OK
3562 SAC   (   1-)  I  -         OK
3565 FME   (   1-)  N  -         OK
3578 HEA   ( 515-)  A  -         Atom types
3579 HEA   ( 516-)  A  -         Atom types
3580 TGL   (3521-)  A  -
3581 PGV   (3266-)  C  -         OK
3582 PGV   (3524-)  A  -         OK
3583 CUA   ( 228-)  B  -         Atom types
3584 CHD   (4085-)  T  -         OK
3585 CHD   (3525-)  A  -         OK
3586 CHD   (3271-)  C  -         OK
3587 CDL   (3270-)  C  -
3588 PEK   (3264-)  C  -         OK
3589 PEK   (3265-)  C  -         OK
3590 PGV   (3267-)  C  -         OK
3591 PGV   (3268-)  C  -         OK
3593 TGL   (3523-)  A  -
3594 PSC   (3230-)  B  -         OK
3596 CDL   (3269-)  G  -
3597 PEK   (4263-)  P  -         OK
3598 CHD   (3060-)  J  -         OK
3599 TGL   (3522-)  L  -
3600 DMU   (3526-)  M  -         OK
3604 HEA   ( 515-)  N  -         Atom types
3605 HEA   ( 516-)  N  -         Atom types
3606 TGL   (4521-)  N  -
3607 TGL   (4522-)  Y  -
3608 PGV   (4266-)  P  -         OK
3609 PGV   (4524-)  N  -         OK
3610 CHD   (3085-)  G  -         OK
3611 CUA   ( 228-)  O  -         Atom types
3612 CHD   (4525-)  N  -         OK
3613 CHD   (4271-)  P  -         OK
3614 CDL   (4270-)  P  -
3615 PEK   (4264-)  P  -         OK
3616 PEK   (4265-)  T  -         OK
3617 PGV   (4267-)  P  -         OK
3619 TGL   (4523-)  N  -
3621 CDL   (4269-)  T  -
3622 DMU   (4526-)  Z  -         OK
3623 CHD   (4060-)  W  -         OK
3624 PEK   (3263-)  C  -         OK
3625 PGV   (4268-)  P  -         OK
3626 PSC   (4230-)  O  -         OK
3627 SAC   (   1-)  V  -         OK
3628 FME   (   1-)  O  -         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).

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

   1 PHE   (   2-)  A  -   N   bound to 3553 FME   (   1-)  A  -   C
 514 ALA   (   2-)  B  -   N   bound to 3555 FME   (   1-)  B  -   C
1509 THR   (   2-)  I  -   N   bound to 3562 SAC   (   1-)  I  -   C
1777 PHE   (   2-)  N  -   N   bound to 3565 FME   (   1-)  N  -   C
2290 ALA   (   2-)  O  -   N   bound to 3628 FME   (   1-)  O  -   C
3285 THR   (   2-)  V  -   N   bound to 3627 SAC   (   1-)  V  -   C

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 (    2)   513 (  514) A Prote<-             pdb1v54.ent
     2   514 (    2)   739 (  227) B Prote<-             pdb1v54.ent
     3   740 (    3)   998 (  261) C Protein             pdb1v54.ent
     4   999 (    4)  1142 (  147) D Protein             pdb1v54.ent
     5  1143 (    5)  1247 (  109) E Protein             pdb1v54.ent
     6  1248 (    1)  1345 (   98) F Protein             pdb1v54.ent
     7  1346 (    1)  1429 (   84) G Protein             pdb1v54.ent
     8  1430 (    7)  1508 (   85) H Protein             pdb1v54.ent
     9  1509 (    2)  1580 (   73) I Prote<-             pdb1v54.ent
    10  1581 (    1)  1638 (   58) J Protein             pdb1v54.ent
    11  1639 (    6)  1687 (   54) K Protein             pdb1v54.ent
    12  1688 (    2)  1733 (   47) L Protein             pdb1v54.ent
    13  1734 (    1)  1776 (   43) M Protein             pdb1v54.ent
    14  1777 (    2)  2289 (  514) N Prote<-             pdb1v54.ent
    15  2290 (    2)  2515 (  227) O Prote<-             pdb1v54.ent
    16  2516 (    3)  2774 (  261) P Protein             pdb1v54.ent
    17  2775 (    4)  2918 (  147) Q Protein             pdb1v54.ent
    18  2919 (    5)  3023 (  109) R Protein             pdb1v54.ent
    19  3024 (    1)  3121 (   98) S Protein             pdb1v54.ent
    20  3122 (    1)  3205 (   84) T Protein             pdb1v54.ent
    21  3206 (    7)  3284 (   85) U Protein             pdb1v54.ent
    22  3285 (    2)  3356 (   73) V Prote<-             pdb1v54.ent
    23  3357 (    1)  3414 (   58) W Protein             pdb1v54.ent
    24  3415 (    6)  3463 (   54) X Protein             pdb1v54.ent
    25  3464 (    2)  3509 (   47) Y Protein             pdb1v54.ent
And so on for a total of 128 lines.

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 3552.
of which 28 have poor or missing atoms.
Number of water molecules 1970

Warning: Ions bound to the wrong chain

The ions listed in the table have a chain identifier that is the same as one of the protein, nucleic acid, or sugar chains. However, the ion seems bound to protein, nucleic acid, or sugar, with another chain identifier.

Obviously, this is not wrong, but it is confusing for users of this PDB file.

3576  MG   (3518-)  B  -
3602  MG   (4518-)  O  -

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: Q

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: U

Note: Ramachandran plot

Chain identifier: V

Note: Ramachandran plot

Chain identifier: W

Note: Ramachandran plot

Chain identifier: X

Note: Ramachandran plot

Chain identifier: Y

Note: Ramachandran plot

Chain identifier: Z

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 FINRWLFSTNHKDIGTLYLLFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAH
(   2)-(  61) HHHHTT   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT TT THHHHHHHHHHH
                     70        80        90       100       110       120
                      |         |         |         |         |         |
   61 -  120 AFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLLASSMVEAG
(  62)-( 121)HHHHHHTTHHHHHTTHHHHHHHHHHTT TT TTHHHHHHHHHTHHHHHHHHHHHHHTTT
                    130       140       150       160       170       180
                      |         |         |         |         |         |
  121 -  180 AGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTIINMKPPAMSQYQT
( 122)-( 181)  TTTTT TTTTTTTTT TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT TT  333T
                    190       200       210       220       230       240
                      |         |         |         |         |         |
  181 -  240 PLFVWSVMITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHP
( 182)-( 241) HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT   TT 333T  HHHHHHHHHHHHHH
                    250       260       270       280       290       300
                      |         |         |         |         |         |
  241 -  300 EVYILILPGFGMISHIVTYYSGKKEPFGYMGMVWAMMSIGFLGFIVWAHHMFTVGMDVDT
( 242)-( 301)HHHHHHHHHHHHHHHHHHHHTT TT TTHHHHHHHHHHHHHHTTT 3333 TTT   HHH
                    310       320       330       340       350       360
                      |         |         |         |         |         |
  301 -  360 RAYFTSATMIIAIPTGVKVFSWLATLHGGNIKWSPAMMWALGFIFLFTVGGLTGIVLANS
( 302)-( 361)HHHHHHHHHHTHHHHHHHHHHHHHHHTT      HHHHHHHHHHHHHHHHHHHHHHHH H
                    370       380       390       400       410       420
                      |         |         |         |         |         |
  361 -  420 SLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGFVHWFPLFSGYTLNDTWAKIHFAIMFVGV
( 362)-( 421)HHHHHHTT HHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHT    HHHHHHHHHHHHHHH
                    430       440       450       460       470       480
                      |         |         |         |         |         |
  421 -  480 NMTFFPQHFLGLSGMPRRYSDYPDAYTMWNTISSMGSFISLTAVMLMVFIIWEAFASKRE
( 422)-( 481)HHHHTHHHHHHHTT  TT TT  333HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
                    490       500       510
                      |         |         |
  481 -  513 VLTVDLTTTNLEWLNGCPPPYHTFEEPTYVNLK
( 482)-( 514)    TT333 333TT TT  TT  TT
 
                 520       530       540       550       560       570
                   |         |         |         |         |         |
  514 -  573 AYPMQLGFQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEV
(   2)-(  61)  TT  T     THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT T    T    TTH
                 580       590       600       610       620       630
                   |         |         |         |         |         |
  574 -  633 ETIWTILPAIILILIALPSLRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDLSFDSY
(  62)-( 121)HHHHHHHHHHHHHHHHHHHHHHHHHHH     TSSSSSSSSTTSSSSSS TTT SSSSS
                 640       650       660       670       680       690
                   |         |         |         |         |         |
  634 -  693 MIPTSELKPGELRLLEVDNRVVLPMEMTIRMLVSSEDVLHSWAVPSLGLKTDAIPGRLNQ
( 122)-( 181)   333  TT  TTT  TT SSSSTTT SSSSSSSTTT SSSSS333TSSSSS TT  SS
                 700       710       720       730
                   |         |         |         |
  694 -  739 TTLMSSRPGLYYGQCSEICGSNHSFMPIVLELVPLKYFEKWSASML
( 182)-( 227)SSS  TT SSSSS   T  TTT333  SSSSSS HHHHHHHHHHT
 
           740       750       760       770       780       790
             |         |         |         |         |         |
  740 -  799 HQTHAYHMVNPSPWPLTGALSALLMTSGLTMWFHFNSMTLLMIGLTTNMLTMYQWWRDVI
(   3)-(  62)   T        THHHHHHHHHHHHHHHHHHHHHHT  HHHHHHHHHHHHHHHHHHHHHH
           800       810       820       830       840       850
             |         |         |         |         |         |
  800 -  859 RESTFQGHHTPAVQKGLRYGMILFIISEVLFFTGFFWAFYHSSLAPTPELGGCWPPTGIH
(  63)-( 122)HHHTTT    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT  333TTTTT TT
           860       870       880       890       900       910
             |         |         |         |         |         |
  860 -  919 PLNPLEVPLLNTSVLLASGVSITWAHHSLMEGDRKHMLQALFITITLGVYFTLLQASEYY
( 123)-( 182)   TTTHHHHHHHHHHHHHHHHHHHHHHHHTT HHHHHHHHHHHHHHHHHHHHHHHHHHH
           920       930       940       950       960       970
             |         |         |         |         |         |
  920 -  979 EAPFTISDGVYGSTFFVATGFHGLHVIIGSTFLIVCFFRQLKFHFTSNHHFGFEAAAWYW
( 183)-( 242)H TT TTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT   TT  HHHHHHHHHH
           980       990
             |         |
  980 -  998 HFVDVVWLFLYVSIYWWGS
( 243)-( 261)HHHHHHHHHHHHHTTTTT
 
           1000      1010      1020      1030      1040      1050
              |         |         |         |         |         |
  999 - 1058 SVVKSEDYALPSYVDRRDYPLPDVAHVKNLSASQKALKEKEKASWSSLSIDEKVELYRLK
(   4)-(  63)    333TTT      TT  T TT T     HHHHHHHHHTTT 333T HHHHHHHHHHH
           1060      1070      1080      1090      1100      1110
              |         |         |         |         |         |
 1059 - 1118 FKESFAEMNRSTNEWKTVVGAAMFFIGFTALLLIWEKHYVYGPIPHTFEEEWVAKQTKRM
(  64)-( 123) TT HHHHT   THHHHHHHHHHHHHHHHHHHHHHHHHHT     333THHHHHHHHHHH
           1120      1130      1140
              |         |         |
 1119 - 1142 LDMKVAPIQGFSAKWDYDKNEWKK
( 124)-( 147)HHTTTTTTTTT333SSTTTTSS
 
                 1150      1160      1170      1180      1190      1200
                    |         |         |         |         |         |
 1143 - 1202 HETDEEFDARWVTYFNKPDIDAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASA
(   5)-(  64)   HHHHHHHHHHHHT TT  HHHHHHHHHHHTTTTT   HHHHHHHHHHHHHTT HHHH
                 1210      1220      1230      1240
                    |         |         |         |
 1203 - 1247 VRILEVVKDKAGPHKEIYPYVIQELRPTLNELGISTPEELGLDKV
(  65)-( 109)HHHHHHHHHHTTT TTHHHHHHHHHHHHHHHHT   TTTTTTT
 
            1250      1260      1270      1280      1290      1300
               |         |         |         |         |         |
 1248 - 1307 ASGGGVPTDEEQATGLEREVMLAARKGQDPYNILAPKATSGTKEDPNLVPSITNKRIVGC
(   1)-(  60)        HHHH  HHHHHHHHHHHTT  TT  T        TTT SSSS TTTSSSSSS
            1310      1320      1330      1340
               |         |         |         |
 1308 - 1345 ICEEDNSTVIWFWLHKGEAQRCPSCGTHYKLVPHQLAH
(  61)-(  98)  TTT T  SSSSSSTTT SS TTT  SSSSS   T
 
              1350      1360      1370      1380      1390      1400
                 |         |         |         |         |         |
 1346 - 1405 ASAAKGDHGGZGARTWRFLTFGLALPSVALCTLNSWLHSGHRERPAFIPYHHLRIRTKPF
(   1)-(  60)  TT    T   HHHHHHHHHHTHHHHHHHHHHHHTTT T          TTTT  TT
              1410      1420
                 |         |
 1406 - 1429 SWGDGNHTFFHNPRVNPLPTGYEK
(  61)-(  84)TTTTTTT TT  TTT   TT
 
          1430      1440      1450      1460      1470      1480
             |         |         |         |         |         |
 1430 - 1489 KIKNYQTAPFDSRFPNQNQTRNCWQNYLDFHRCEKAMTAKGGDVSVCEWYRRVYKSLCPI
(   7)-(  66)      T    TTT TT  HHHHHHHHHHHHHHHHHHHHHT  3333HHHHHHHHHHT H
          1490      1500
             |         |
 1490 - 1508 SWVSTWDDRRAEGTFPGKI
(  67)-(  85)HHHHHHHHHHHHT   T
 
           1510      1520      1530      1540      1550      1560
              |         |         |         |         |         |
 1509 - 1568 TALAKPQMRGLLARRLRFHIVGAFMVSLGFATFYKFAVAEKRKKAYADFYRNYDSMKDFE
(   2)-(  61)        TTHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHT  HHHHHH
           1570      1580
              |         |
 1569 - 1580 EMRKAGIFQSAK
(  62)-(  73)HHHHTT  TT
 
                   1590      1600      1610      1620      1630
                      |         |         |         |         |
 1581 - 1638 FENRVAEKQKLFQEDNGLPVHLKGGATDNILYRVTMTLCLGGTLYSLYCLGWASFPHK
(   1)-(  58)    HHHHHHHHH TT   TTTTT HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
 
           1640      1650      1660      1670      1680
              |         |         |         |         |
 1639 - 1687 APDFHDKYGNAVLASGATFCVAVWVYMATQIGIEWNPSPVGRVTPKEWR
(   6)-(  54)   HHHHHHHHHHHHHHHHHHHHHHHHHHHT        TTT
 
            1690      1700      1710      1720      1730
               |         |         |         |         |
 1688 - 1733 HYEEGPGKNIPFSVENKWRLLAMMTLFFGSGFAAPFFIVRHQLLKK
(   2)-(  47)    TTTTTTTT  TTHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
 
                1740      1750      1760      1770
                   |         |         |         |
 1734 - 1776 ITAKPAKTPTSPKEQAIGLSVTFLSFLLPAGWVLYHLDNYKKS
(   1)-(  43)      TT   HHHHHHHHHHHHHHHHHHHHHHHHTHHHHHT
 
             1780      1790      1800      1810      1820      1830
                |         |         |         |         |         |
 1777 - 1836 FINRWLFSTNHKDIGTLYLLFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAH
(   2)-(  61) HHHHTT   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT TT THHHHHHHHHHH
             1840      1850      1860      1870      1880      1890
                |         |         |         |         |         |
 1837 - 1896 AFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLLASSMVEAG
(  62)-( 121)HHHHHHTTHHHHHTTTHHHHHHHHHTT TT TTHHHHHHHHHTHHHHHHHHHHHHHTTT
             1900      1910      1920      1930      1940      1950
                |         |         |         |         |         |
 1897 - 1956 AGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTIINMKPPAMSQYQT
( 122)-( 181)  TTTTT TTTTTTTTT TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT TT  333T
             1960      1970      1980      1990      2000      2010
                |         |         |         |         |         |
 1957 - 2016 PLFVWSVMITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHP
( 182)-( 241) HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT   TT 333T  HHHHHHHHHHHHHH
             2020      2030      2040      2050      2060      2070
                |         |         |         |         |         |
 2017 - 2076 EVYILILPGFGMISHIVTYYSGKKEPFGYMGMVWAMMSIGFLGFIVWAHHMFTVGMDVDT
( 242)-( 301)HHHHHHHHHHHHHHHHHHHHTT TT TTHHHHHHHHHHHHHHTTT 3333 TTT   HHH
             2080      2090      2100      2110      2120      2130
                |         |         |         |         |         |
 2077 - 2136 RAYFTSATMIIAIPTGVKVFSWLATLHGGNIKWSPAMMWALGFIFLFTVGGLTGIVLANS
( 302)-( 361)HHHHHHHHHHTHHHHHHHHHHHHHHHTT      HHHHHHHHHHHHHHHHHHHHHHHT H
             2140      2150      2160      2170      2180      2190
                |         |         |         |         |         |
 2137 - 2196 SLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGFVHWFPLFSGYTLNDTWAKIHFAIMFVGV
( 362)-( 421)HHHHHHTT HHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHT    HHHHHHHHHHHHHHH
             2200      2210      2220      2230      2240      2250
                |         |         |         |         |         |
 2197 - 2256 NMTFFPQHFLGLSGMPRRYSDYPDAYTMWNTISSMGSFISLTAVMLMVFIIWEAFASKRE
( 422)-( 481)HHHHTHHHHHHHTT  TT TT  333HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
             2260      2270      2280
                |         |         |
 2257 - 2289 VLTVDLTTTNLEWLNGCPPPYHTFEEPTYVNLK
( 482)-( 514)    T 333 333TT TT  TT  TT
 
          2290      2300      2310      2320      2330      2340
             |         |         |         |         |         |
 2290 - 2349 AYPMQLGFQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEV
(   2)-(  61)  TT  T     THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT T    T    TTH
          2350      2360      2370      2380      2390      2400
             |         |         |         |         |         |
 2350 - 2409 ETIWTILPAIILILIALPSLRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDLSFDSY
(  62)-( 121)HHHHHHHHHHHHHHHHHHHHHHHHHHH     TSSSSSSSSTTSSSSSS TTT SSSSS
          2410      2420      2430      2440      2450      2460
             |         |         |         |         |         |
 2410 - 2469 MIPTSELKPGELRLLEVDNRVVLPMEMTIRMLVSSEDVLHSWAVPSLGLKTDAIPGRLNQ
( 122)-( 181)   333  TT  TTT  TT SSSSTTT SSSSSSSTTT SSSSS333TSSSSS TT  SS
          2470      2480      2490      2500      2510
             |         |         |         |         |
 2470 - 2515 TTLMSSRPGLYYGQCSEICGSNHSFMPIVLELVPLKYFEKWSASML
( 182)-( 227)SSS  TT SSSSS   T  TTT333  SSSSSS HHHHHHHHHHT
 
              2520      2530      2540      2550      2560      2570
                 |         |         |         |         |         |
 2516 - 2575 HQTHAYHMVNPSPWPLTGALSALLMTSGLTMWFHFNSMTLLMIGLTTNMLTMYQWWRDVI
(   3)-(  62)   T        THHHHHHHHHHHHHHHHHHHHHH   HHHHHHHHHHHHHHHHHHHHHH
              2580      2590      2600      2610      2620      2630
                 |         |         |         |         |         |
 2576 - 2635 RESTFQGHHTPAVQKGLRYGMILFIISEVLFFTGFFWAFYHSSLAPTPELGGCWPPTGIH
(  63)-( 122)HHHTTT    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT  333TTTTT TT
              2640      2650      2660      2670      2680      2690
                 |         |         |         |         |         |
 2636 - 2695 PLNPLEVPLLNTSVLLASGVSITWAHHSLMEGDRKHMLQALFITITLGVYFTLLQASEYY
( 123)-( 182)   TTTHHHHHHHHHHHHHHHHHHHHHHHHTT HHHHHHHHHHHHHHHHHHHHHHHHHHH
              2700      2710      2720      2730      2740      2750
                 |         |         |         |         |         |
 2696 - 2755 EAPFTISDGVYGSTFFVATGFHGLHVIIGSTFLIVCFFRQLKFHFTSNHHFGFEAAAWYW
( 183)-( 242)H TT TTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT   TT  HHHHHHHHHH
              2760      2770
                 |         |
 2756 - 2774 HFVDVVWLFLYVSIYWWGS
( 243)-( 261)HHHHHHHHHHHHHTTTTT
 
               2780      2790      2800      2810      2820      2830
                  |         |         |         |         |         |
 2775 - 2834 SVVKSEDYALPSYVDRRDYPLPDVAHVKNLSASQKALKEKEKASWSSLSIDEKVELYRLK
(   4)-(  63)    333TTT      TT  T TT T  T  HHHHHHHHHTTT 333T HHHHHHHHHHH
               2840      2850      2860      2870      2880      2890
                  |         |         |         |         |         |
 2835 - 2894 FKESFAEMNRSTNEWKTVVGAAMFFIGFTALLLIWEKHYVYGPIPHTFEEEWVAKQTKRM
(  64)-( 123) TT HHHHT   THHHHHHHHHHHHHHHHHHHHHHHHHHT     333THHHHHHHHHHH
               2900      2910
                  |         |
 2895 - 2918 LDMKVAPIQGFSAKWDYDKNEWKK
( 124)-( 147)HHTTTTTTTTT333SSTTTTSS
 
           2920      2930      2940      2950      2960      2970
              |         |         |         |         |         |
 2919 - 2978 HETDEEFDARWVTYFNKPDIDAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASA
(   5)-(  64)   HHHHHHHHHHHHT TT  HHHHHHHHHHHTTTTT   HHHHHHHHHHHHHTT HHHH
           2980      2990      3000      3010      3020
              |         |         |         |         |
 2979 - 3023 VRILEVVKDKAGPHKEIYPYVIQELRPTLNELGISTPEELGLDKV
(  65)-( 109)HHHHHHHHHHTTT TTHHHHHHHHHHHHHHHHT   TTTTTTT
 
                3030      3040      3050      3060      3070      3080
                   |         |         |         |         |         |
 3024 - 3083 ASGGGVPTDEEQATGLEREVMLAARKGQDPYNILAPKATSGTKEDPNLVPSITNKRIVGC
(   1)-(  60)        HHHH  HHHHHHHHHHHTT  TT  T        TTT SSSS TTTSSSSSS
                3090      3100      3110      3120
                   |         |         |         |
 3084 - 3121 ICEEDNSTVIWFWLHKGEAQRCPSCGTHYKLVPHQLAH
(  61)-(  98)  TTT T  SSSSSSTTT SS TTT  SSSSS   T
 
                  3130      3140      3150      3160      3170      3180
                     |         |         |         |         |         |
 3122 - 3181 ASAAKGDHGGZGARTWRFLTFGLALPSVALCTLNSWLHSGHRERPAFIPYHHLRIRTKPF
(   1)-(  60)  TT    T   HHHHHHHHHHTHHHHHHHHHHHHTTT T          TTTT  TT
                  3190      3200
                     |         |
 3182 - 3205 SWGDGNHTFFHNPRVNPLPTGYEK
(  61)-(  84)TTTTTTT TT  TTT   TT
 
              3210      3220      3230      3240      3250      3260
                 |         |         |         |         |         |
 3206 - 3265 KIKNYQTAPFDSRFPNQNQTRNCWQNYLDFHRCEKAMTAKGGDVSVCEWYRRVYKSLCPI
(   7)-(  66)      T    TTT TT  HHHHHHHHHHHHHHHHHHHHHT  3333HHHHHHHHHHT H
              3270      3280
                 |         |
 3266 - 3284 SWVSTWDDRRAEGTFPGKI
(  67)-(  85)HHHHHHHHHHHHT   T
 
               3290      3300      3310      3320      3330      3340
                  |         |         |         |         |         |
 3285 - 3344 TALAKPQMRGLLARRLRFHIVGAFMVSLGFATFYKFAVAEKRKKAYADFYRNYDSMKDFE
(   2)-(  61)        T HHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHT  HHHHHH
               3350
                  |
 3345 - 3356 EMRKAGIFQSAK
(  62)-(  73)HHHHTT  TT
 
             3360      3370      3380      3390      3400      3410
                |         |         |         |         |         |
 3357 - 3414 FENRVAEKQKLFQEDNGLPVHLKGGATDNILYRVTMTLCLGGTLYSLYCLGWASFPHK
(   1)-(  58)    HHHHHHHHH  T   TTTTT HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
 
               3420      3430      3440      3450      3460
                  |         |         |         |         |
 3415 - 3463 APDFHDKYGNAVLASGATFCVAVWVYMATQIGIEWNPSPVGRVTPKEWR
(   6)-(  54)   HHHHHHHHHHHHHHHHHHHHHHHHHHHT        TTT
 
                3470      3480      3490      3500
                   |         |         |         |
 3464 - 3509 HYEEGPGKNIPFSVENKWRLLAMMTLFFGSGFAAPFFIVRHQLLKK
(   2)-(  47)    TTTTTTTT  TTHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
 
          3510      3520      3530      3540      3550
             |         |         |         |         |
 3510 - 3552 ITAKPAKTPTSPKEQAIGLSVTFLSFLLPAGWVLYHLDNYKKS
(   1)-(  43)      TT   HHHHHHHHHHHHHHHHHHHHHHHHTHHHHHT
 
 
 

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

Note: No rounded coordinates detected

No significant rounding of atom coordinates has been detected.

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

1356 TPO   (  11-)  G
3132 TPO   (  11-)  T

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: C-terminus capping

The residues listed in the table below either are pseudo C-terminal residues, or have two groups attached of which neither is the normal C-terminal O. In this table REAL means that the C-terminal residue is likely to be the real C-terminus of its chain; OX means that an incorrect second oxygen (OXT) was detected that should not be there; -O indicates that the 'normal' oxygen (i.e. not the OXT) is missing; OT indicates the detection of any other capping group. C-terminal nitrogen atoms, if any, have already been dealt with in a previous check and are indicated here by -N. PSEUDO means that this is the last visible residue in the chain, but not the real C-terminus, i.e. all residues after this one are missing in this chain. BREAK means that this is the last residue before a chain-break, i.e. the chain continues but after this residue a number of residues is missing. In case a break is observed the number of residues that seems to be missing is shown in brackets. OK means that given the status (REAL, PSEUDO, BREAK), no problems were found.

Be aware that we cannot easily see the difference between these errors and errors in the chain and residue numbering schemes. So do not blindly trust the table below.

1429 LYS   (  84-)  G          : PSEUDO OK
1638 LYS   (  58-)  J          : REAL Oxt missing
1687 ARG   (  54-)  K          : PSEUDO OK
1776 SER   (  43-)  M          : PSEUDO OK
3205 LYS   (  84-)  T          : PSEUDO OK
3414 LYS   (  58-)  W          : REAL Oxt missing
3463 ARG   (  54-)  X          : PSEUDO OK
3552 SER   (  43-)  Z          : PSEUDO OK

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.

Note: All occupancies seem to add up to 0.0 - 1.0.

In principle, the occupancy of all alternates of one atom should add up till 0.0 - 1.0. 0.0 is used for the missing atom (i.e. an atom not seen in the electron density). Obviously, there is nothing terribly wrong when a few occupancies add up to a bit more than 1.0, because the mathematics of refinement allow for that. However, if it happens often, it seems worth evaluating this in light of the refinement protocol used.

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: 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 : 0.594 over 25655 bonds
Average difference in B over a bond : 1.74
RMS difference in B over a bond : 2.41

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

Note: B-factor plot

Chain identifier: Q

Note: B-factor plot

Chain identifier: R

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: T

Note: B-factor plot

Chain identifier: U

Note: B-factor plot

Chain identifier: V

Note: B-factor plot

Chain identifier: W

Note: B-factor plot

Chain identifier: X

Note: B-factor plot

Chain identifier: Y

Note: B-factor plot

Chain identifier: Z

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.

1014 ARG   (  19-)  D
1687 ARG   (  54-)  K
2790 ARG   (  19-)  Q
3463 ARG   (  54-)  X

Warning: Tyrosine convention problem

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

  53 TYR   (  54-)  A
 128 TYR   ( 129-)  A
 259 TYR   ( 260-)  A
 269 TYR   ( 270-)  A
 370 TYR   ( 371-)  A
 439 TYR   ( 440-)  A
 501 TYR   ( 502-)  A
 515 TYR   (   3-)  B
 597 TYR   (  85-)  B
 622 TYR   ( 110-)  B
 633 TYR   ( 121-)  B
 704 TYR   ( 192-)  B
 705 TYR   ( 193-)  B
 730 TYR   ( 218-)  B
 839 TYR   ( 102-)  C
 919 TYR   ( 182-)  C
 930 TYR   ( 193-)  C
 994 TYR   ( 257-)  C
1099 TYR   ( 104-)  D
1156 TYR   (  18-)  E
1220 TYR   (  82-)  E
1278 TYR   (  31-)  F
1336 TYR   (  89-)  F
1479 TYR   (  56-)  H
1542 TYR   (  35-)  I
And so on for a total of 55 lines.

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   (  78-)  A
 108 PHE   ( 109-)  A
 163 PHE   ( 164-)  A
 218 PHE   ( 219-)  A
 236 PHE   ( 237-)  A
 250 PHE   ( 251-)  A
 267 PHE   ( 268-)  A
 320 PHE   ( 321-)  A
 376 PHE   ( 377-)  A
 386 PHE   ( 387-)  A
 396 PHE   ( 397-)  A
 424 PHE   ( 425-)  A
 458 PHE   ( 459-)  A
 475 PHE   ( 476-)  A
 521 PHE   (   9-)  B
 535 PHE   (  23-)  B
 544 PHE   (  32-)  B
 718 PHE   ( 206-)  B
 804 PHE   (  67-)  C
 831 PHE   (  94-)  C
 910 PHE   ( 173-)  C
 934 PHE   ( 197-)  C
 935 PHE   ( 198-)  C
 970 PHE   ( 233-)  C
 981 PHE   ( 244-)  C
And so on for a total of 104 lines.

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.

  13 ASP   (  14-)  A
  49 ASP   (  50-)  A
  50 ASP   (  51-)  A
 143 ASP   ( 144-)  A
 211 ASP   ( 212-)  A
 226 ASP   ( 227-)  A
 363 ASP   ( 364-)  A
 368 ASP   ( 369-)  A
 406 ASP   ( 407-)  A
 441 ASP   ( 442-)  A
 444 ASP   ( 445-)  A
 523 ASP   (  11-)  B
 600 ASP   (  88-)  B
 627 ASP   ( 115-)  B
 651 ASP   ( 139-)  B
1013 ASP   (  18-)  D
1049 ASP   (  54-)  D
1120 ASP   ( 125-)  D
1136 ASP   ( 141-)  D
1150 ASP   (  12-)  E
1161 ASP   (  23-)  E
1178 ASP   (  40-)  E
1187 ASP   (  49-)  E
1198 ASP   (  60-)  E
1245 ASP   ( 107-)  E
And so on for a total of 71 lines.

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.

  39 GLU   (  40-)  A
 118 GLU   ( 119-)  A
 241 GLU   ( 242-)  A
 473 GLU   ( 474-)  A
 480 GLU   ( 481-)  A
 506 GLU   ( 507-)  A
 530 GLU   (  18-)  B
 572 GLU   (  60-)  B
 574 GLU   (  62-)  B
 621 GLU   ( 109-)  B
 626 GLU   ( 114-)  B
 639 GLU   ( 127-)  B
 644 GLU   ( 132-)  B
 649 GLU   ( 137-)  B
 659 GLU   ( 147-)  B
 669 GLU   ( 157-)  B
 732 GLU   ( 220-)  B
 801 GLU   (  64-)  C
 865 GLU   ( 128-)  C
 890 GLU   ( 153-)  C
 917 GLU   ( 180-)  C
 920 GLU   ( 183-)  C
1004 GLU   (   9-)  D
1037 GLU   (  42-)  D
1050 GLU   (  55-)  D
And so on for a total of 106 lines.

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

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

  79 ASN   (  80-)  A      CG   OD1   1.33    5.0
  79 ASN   (  80-)  A      CG   ND2   1.23   -4.6
 375 HIS   ( 376-)  A      CG   CD2   1.40    4.2
 375 HIS   ( 376-)  A      ND1  CE1   1.37    4.3
1836 HIS   (  61-)  N      CG   CD2   1.40    4.1
1855 ASN   (  80-)  N      CG   OD1   1.33    4.8
1855 ASN   (  80-)  N      CG   ND2   1.22   -4.9

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: 0.449
RMS-deviation in bond distances: 0.010

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

 |  0.998203 -0.000197 -0.000093|
 | -0.000197  0.998737 -0.000145|
 | -0.000093 -0.000145  0.998401|
Proposed new scale matrix

 |  0.005487  0.000001  0.000000|
 |  0.000000  0.004881  0.000000|
 |  0.000000  0.000000  0.005619|
With corresponding cell

    A    = 182.254  B   = 204.869  C    = 177.968
    Alpha=  90.002  Beta=  90.002  Gamma=  90.012

The CRYST1 cell dimensions

    A    = 182.590  B   = 205.140  C    = 178.250
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 298.657
(Under-)estimated Z-score: 12.737

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.

  60 HIS   (  61-)  A      CA   CB   CG  118.21    4.4
  60 HIS   (  61-)  A      CB   CG   ND1 131.02    6.3
  60 HIS   (  61-)  A      CB   CG   CD2 119.19   -7.6
 128 TYR   ( 129-)  A      C    CA   CB  102.44   -4.0
 330 ASN   ( 331-)  A      N    CA   C    99.64   -4.1
 377 HIS   ( 378-)  A      CA   CB   CG  107.20   -6.6
 377 HIS   ( 378-)  A      CB   CG   CD2 123.56   -4.3
 434 GLY   ( 435-)  A      N    CA   C   125.12    4.4
 506 GLU   ( 507-)  A      N    CA   C    99.68   -4.1
 564 HIS   (  52-)  B      CG   ND1  CE1 109.61    4.0
 616 TRP   ( 104-)  B     -CA  -C    N   103.55   -6.3
 616 TRP   ( 104-)  B     -C    N    CA  133.94    6.8
 616 TRP   ( 104-)  B      N    CA   C   125.78    5.2
 673 HIS   ( 161-)  B      N    CA   C    99.97   -4.0
1128 GLY   ( 133-)  D      N    CA   C   127.17    5.1
1180 VAL   (  42-)  E      N    CA   C    99.29   -4.3
1340 PRO   (  93-)  F      N    CA   C   126.90    6.0
1341 HIS   (  94-)  F     -C    N    CA  130.20    4.7
1341 HIS   (  94-)  F      N    CA   C   127.18    5.7
1341 HIS   (  94-)  F      CG   ND1  CE1 109.68    4.1
1342 GLN   (  95-)  F     -C    N    CA  130.72    5.0
1351 GLY   (   6-)  G      N    CA   C   124.32    4.1
1434 TYR   (  11-)  H     -C    N    CA  129.34    4.2
1836 HIS   (  61-)  N      CB   CG   ND1 127.72    4.1
1836 HIS   (  61-)  N      CD2  CG   ND1 111.67    5.6
1836 HIS   (  61-)  N      CB   CG   CD2 120.54   -6.6
1904 TYR   ( 129-)  N      C    CA   CB  102.35   -4.1
1905 PRO   ( 130-)  N      N    CA   C   101.06   -4.3
2106 ASN   ( 331-)  N      N    CA   C    99.11   -4.3
2153 HIS   ( 378-)  N      CA   CB   CG  105.44   -8.4
2153 HIS   ( 378-)  N      CD2  CG   ND1 110.34    4.2
2210 GLY   ( 435-)  N      N    CA   C   124.97    4.3
2392 TRP   ( 104-)  O     -CA  -C    N   104.40   -5.9
2392 TRP   ( 104-)  O     -C    N    CA  132.89    6.2
2392 TRP   ( 104-)  O      N    CA   C   125.23    5.0
2904 GLY   ( 133-)  Q      N    CA   C   126.68    4.9
2956 VAL   (  42-)  R      N    CA   C    97.68   -4.8
2992 HIS   (  78-)  R      CG   ND1  CE1 109.66    4.1
3116 PRO   (  93-)  S      N    CA   C   125.95    5.7
3117 HIS   (  94-)  S     -C    N    CA  134.09    6.9
3117 HIS   (  94-)  S      N    CA   C   127.89    6.0
3117 HIS   (  94-)  S      CG   ND1  CE1 110.52    4.9
3118 GLN   (  95-)  S     -C    N    CA  129.84    4.5
3138 ARG   (  17-)  T      CB   CG   CD  104.39   -4.9

Note: Normal bond angle variability

Bond angles were found to deviate normally from the mean 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, and this is indeed observed for very high resolution X-ray structures.

RMS Z-score for bond angles: 0.722
RMS-deviation in bond angles: 1.518

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.

  13 ASP   (  14-)  A
  39 GLU   (  40-)  A
  49 ASP   (  50-)  A
  50 ASP   (  51-)  A
 118 GLU   ( 119-)  A
 143 ASP   ( 144-)  A
 211 ASP   ( 212-)  A
 226 ASP   ( 227-)  A
 241 GLU   ( 242-)  A
 363 ASP   ( 364-)  A
 368 ASP   ( 369-)  A
 406 ASP   ( 407-)  A
 441 ASP   ( 442-)  A
 444 ASP   ( 445-)  A
 473 GLU   ( 474-)  A
 480 GLU   ( 481-)  A
 506 GLU   ( 507-)  A
 523 ASP   (  11-)  B
 530 GLU   (  18-)  B
 572 GLU   (  60-)  B
 574 GLU   (  62-)  B
 600 ASP   (  88-)  B
 621 GLU   ( 109-)  B
 626 GLU   ( 114-)  B
 627 ASP   ( 115-)  B
And so on for a total of 181 lines.

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 615 GLN   ( 103-)  B      C     -8.4   -12.89     0.15
 616 TRP   ( 104-)  B      CA    -7.9    20.63    34.04
2391 GLN   ( 103-)  O      C     -8.1   -12.55     0.15
2392 TRP   ( 104-)  O      CA    -6.6    22.89    34.04
3117 HIS   (  94-)  S      CA    -6.2    22.71    34.11
The average deviation= 1.085

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 : 0.915

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.

1259 GLN   (  12-)  F    6.47
3035 GLN   (  12-)  S    6.22
  81 LEU   (  82-)  A    6.18
1857 LEU   (  82-)  N    5.92
 616 TRP   ( 104-)  B    5.52
1340 PRO   (  93-)  F    5.50
 424 PHE   ( 425-)  A    5.48
2200 PHE   ( 425-)  N    5.41
3117 HIS   (  94-)  S    5.40
3444 GLN   (  35-)  X    5.32
2392 TRP   ( 104-)  O    5.31
 169 ASN   ( 170-)  A    5.29
1341 HIS   (  94-)  F    5.17
3116 PRO   (  93-)  S    5.13
 213 ASN   ( 214-)  A    5.05
1831 VAL   (  56-)  N    4.97
1128 GLY   ( 133-)  D    4.88
1989 ASN   ( 214-)  N    4.86
2956 VAL   (  42-)  R    4.78
1668 GLN   (  35-)  K    4.74
3482 ARG   (  20-)  Y    4.71
2904 GLY   ( 133-)  Q    4.70
3262 LEU   (  63-)  U    4.66
2223 THR   ( 448-)  N    4.62
1905 PRO   ( 130-)  N    4.62
And so on for a total of 61 lines.

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 : 1.488

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

2151 HIS   ( 376-)  N    4.24

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

2015 HIS   ( 240-)  N      CB  12.10
 239 HIS   ( 240-)  A      CB  12.10
2153 HIS   ( 378-)  N      CB   4.11
1877 PHE   ( 102-)  N      CB   4.03
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -0.046

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 : -0.046

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.

3117 HIS   (  94-)  S    -3.2
1431 ILE   (   8-)  H    -2.9
3207 ILE   (   8-)  U    -2.9
 616 TRP   ( 104-)  B    -2.9
2392 TRP   ( 104-)  O    -2.8
1444 PRO   (  21-)  H    -2.8
2745 HIS   ( 232-)  P    -2.7
 969 HIS   ( 232-)  C    -2.7
3220 PRO   (  21-)  U    -2.6
2955 LEU   (  41-)  R    -2.5
1903 VAL   ( 128-)  N    -2.5
 127 VAL   ( 128-)  A    -2.5
2936 PRO   (  22-)  R    -2.5
1179 LEU   (  41-)  E    -2.5
3076 THR   (  53-)  S    -2.5
1993 THR   ( 218-)  N    -2.5
1436 THR   (  13-)  H    -2.5
3119 LEU   (  96-)  S    -2.4
1342 GLN   (  95-)  F    -2.4
1353 HIS   (   8-)  G    -2.4
1775 LYS   (  42-)  M    -2.3
 246 ILE   ( 247-)  A    -2.3
2022 ILE   ( 247-)  N    -2.3
1261 THR   (  14-)  F    -2.3
1343 LEU   (  96-)  F    -2.3
And so on for a total of 70 lines.

Warning: Backbone evaluation reveals unusual conformations

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

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

  90 ASP   (  91-)  A  Poor phi/psi
 118 GLU   ( 119-)  A  Poor phi/psi
 129 PRO   ( 130-)  A  PRO omega poor
 213 ASN   ( 214-)  A  Poor phi/psi
 215 ASN   ( 216-)  A  Poor phi/psi
 333 TRP   ( 334-)  A  Poor phi/psi
 368 ASP   ( 369-)  A  Poor phi/psi
 438 ARG   ( 439-)  A  Poor phi/psi
 478 LYS   ( 479-)  A  Poor phi/psi
 482 LEU   ( 483-)  A  Poor phi/psi
 486 LEU   ( 487-)  A  Poor phi/psi
 497 CYS   ( 498-)  A  PRO omega poor
 504 PHE   ( 505-)  A  Poor phi/psi
 517 MET   (   5-)  B  Poor phi/psi
 571 GLN   (  59-)  B  Poor phi/psi
 603 ASN   (  91-)  B  Poor phi/psi
 604 ASN   (  92-)  B  Poor phi/psi
 616 TRP   ( 104-)  B  Poor phi/psi
 617 TYR   ( 105-)  B  Poor phi/psi
 647 LEU   ( 135-)  B  Poor phi/psi
 659 GLU   ( 147-)  B  Poor phi/psi
 670 ASP   ( 158-)  B  Poor phi/psi
 775 ASN   (  38-)  C  Poor phi/psi
 853 TRP   ( 116-)  C  PRO omega poor
 865 GLU   ( 128-)  C  Poor phi/psi
And so on for a total of 87 lines.

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 : -1.154

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.

1883 SER   ( 108-)  N    0.36
 841 SER   ( 104-)  C    0.36
2030 SER   ( 255-)  N    0.36
2617 SER   ( 104-)  P    0.36
2807 SER   (  36-)  Q    0.36
 100 SER   ( 101-)  A    0.37
 107 SER   ( 108-)  A    0.37
 254 SER   ( 255-)  A    0.37
1876 SER   ( 101-)  N    0.39
 155 SER   ( 156-)  A    0.40
1931 SER   ( 156-)  N    0.40

Warning: Unusual backbone conformations

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

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

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

   9 THR   (  10-)  A      0
  11 HIS   (  12-)  A      0
  43 PRO   (  44-)  A      0
  45 THR   (  46-)  A      0
  47 LEU   (  48-)  A      0
  49 ASP   (  50-)  A      0
  66 PHE   (  67-)  A      0
  67 PHE   (  68-)  A      0
  73 MET   (  74-)  A      0
  88 ALA   (  89-)  A      0
  89 PRO   (  90-)  A      0
  91 MET   (  92-)  A      0
 116 MET   ( 117-)  A      0
 117 VAL   ( 118-)  A      0
 118 GLU   ( 119-)  A      0
 119 ALA   ( 120-)  A      0
 121 ALA   ( 122-)  A      0
 123 THR   ( 124-)  A      0
 125 TRP   ( 126-)  A      0
 127 VAL   ( 128-)  A      0
 128 TYR   ( 129-)  A      0
 129 PRO   ( 130-)  A      0
 137 HIS   ( 138-)  A      0
 138 ALA   ( 139-)  A      0
 140 ALA   ( 141-)  A      0
And so on for a total of 1100 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 : -0.095

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 : 1.591

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!

1470 GLY   (  47-)  H   2.01   80
3246 GLY   (  47-)  U   2.01   80

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

1341 HIS   (  94-)  F   3.37

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

 266 PRO   ( 267-)  A    0.45 HIGH
 642 PRO   ( 130-)  B    0.45 HIGH
1103 PRO   ( 108-)  D    0.45 HIGH
1160 PRO   (  22-)  E    0.46 HIGH
2292 PRO   (   4-)  O    0.46 HIGH
2418 PRO   ( 130-)  O    0.45 HIGH
2586 PRO   (  73-)  P    0.45 HIGH
2623 PRO   ( 110-)  P    0.47 HIGH

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].

 314 PRO   ( 315-)  A  -112.1 envelop C-gamma (-108 degrees)
1394 PRO   (  49-)  G    36.1 envelop C-delta (36 degrees)
2016 PRO   ( 241-)  N   100.0 envelop C-beta (108 degrees)
2090 PRO   ( 315-)  N  -116.9 envelop C-gamma (-108 degrees)
3170 PRO   (  49-)  T    49.0 half-chair C-delta/C-gamma (54 degrees)
3220 PRO   (  21-)  U   -60.7 half-chair C-beta/C-alpha (-54 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short 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.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

2015 HIS   ( 240-)  N      NE2  <->  2019 TYR   ( 244-)  N      CE2  1.74    1.36  INTRA BL
 239 HIS   ( 240-)  A      NE2  <->   243 TYR   ( 244-)  A      CE2  1.73    1.37  INTRA BL
2290 ALA   (   2-)  O      N    <->  3628 FME   (   1-)  O      C    1.37    1.33  INTRA B3
3285 THR   (   2-)  V      N    <->  3627 SAC   (   1-)  V      C    1.37    1.33  INTRA BF
2015 HIS   ( 240-)  N      CE1  <->  2019 TYR   ( 244-)  N      CE2  0.88    2.32  INTRA BL
2015 HIS   ( 240-)  N      NE2  <->  2019 TYR   ( 244-)  N      CD2  0.87    2.23  INTRA BL
 239 HIS   ( 240-)  A      CE1  <->   243 TYR   ( 244-)  A      CE2  0.84    2.36  INTRA BL
 239 HIS   ( 240-)  A      NE2  <->   243 TYR   ( 244-)  A      CD2  0.82    2.28  INTRA BL
2290 ALA   (   2-)  O      CA   <->  3628 FME   (   1-)  O      C    0.76    2.44  INTRA
3285 THR   (   2-)  V      CA   <->  3627 SAC   (   1-)  V      C    0.76    2.44  INTRA BF
2015 HIS   ( 240-)  N      CD2  <->  2019 TYR   ( 244-)  N      CE2  0.70    2.50  INTRA BL
 239 HIS   ( 240-)  A      CD2  <->   243 TYR   ( 244-)  A      CE2  0.70    2.50  INTRA BL
2745 HIS   ( 232-)  P      NE2  <->  3618 UNX   (4262-)  P     UNK   0.67    2.43  INTRA
 885 HIS   ( 148-)  C      NE2  <->  3592 UNX   (3262-)  C     UNK   0.66    2.44  INTRA BF
 969 HIS   ( 232-)  C      NE2  <->  3592 UNX   (3262-)  C     UNK   0.65    2.45  INTRA
2661 HIS   ( 148-)  P      NE2  <->  3618 UNX   (4262-)  P     UNK   0.65    2.45  INTRA
2015 HIS   ( 240-)  N      NE2  <->  2019 TYR   ( 244-)  N      CZ   0.61    2.49  INTRA BL
 239 HIS   ( 240-)  A      NE2  <->   243 TYR   ( 244-)  A      CZ   0.60    2.50  INTRA BL
3117 HIS   (  94-)  S      CD2  <->  3118 GLN   (  95-)  S      N    0.37    2.63  INTRA BF
2015 HIS   ( 240-)  N      CD2  <->  2019 TYR   ( 244-)  N      CD2  0.37    2.83  INTRA BL
2421 LEU   ( 133-)  O      CD1  <->  3628 FME   (   1-)  O      SD   0.36    3.04  INTRA
3348 LYS   (  65-)  V      O    <->  3463 ARG   (  54-)  X      NH2  0.35    2.35  INTRA BF
 377 HIS   ( 378-)  A      NE2  <->  3578 HEA   ( 515-)  A      NC   0.35    2.65  INTRA BL
 239 HIS   ( 240-)  A      CD2  <->   243 TYR   ( 244-)  A      CD2  0.35    2.85  INTRA BL
3482 ARG   (  20-)  Y      NH1  <->  3653 HOH   (1514 )  Y      O    0.34    2.36  INTRA BF
And so on for a total of 302 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 : 1.137

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

Note: Inside/Outside RMS Z-score plot

Chain identifier: Q

Note: Inside/Outside RMS Z-score plot

Chain identifier: R

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Inside/Outside RMS Z-score plot

Chain identifier: U

Note: Inside/Outside RMS Z-score plot

Chain identifier: V

Note: Inside/Outside RMS Z-score plot

Chain identifier: W

Note: Inside/Outside RMS Z-score plot

Chain identifier: X

Note: Inside/Outside RMS Z-score plot

Chain identifier: Y

Note: Inside/Outside RMS Z-score plot

Chain identifier: Z

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.

 625 TYR   ( 113-)  B      -6.55
1507 LYS   (  84-)  H      -6.49
2401 TYR   ( 113-)  O      -6.41
3283 LYS   (  84-)  U      -6.41
2347 GLN   (  59-)  O      -6.35
 571 GLN   (  59-)  B      -6.23
1342 GLN   (  95-)  F      -6.12
1353 HIS   (   8-)  G      -6.01
1387 ARG   (  42-)  G      -6.00
2875 TYR   ( 104-)  Q      -5.97
3129 HIS   (   8-)  T      -5.97
3118 GLN   (  95-)  S      -5.94
 859 HIS   ( 122-)  C      -5.84
2635 HIS   ( 122-)  P      -5.83
3551 LYS   (  42-)  Z      -5.81
2476 ARG   ( 188-)  O      -5.78
1099 TYR   ( 104-)  D      -5.78
 700 ARG   ( 188-)  B      -5.77
1775 LYS   (  42-)  M      -5.73
1818 GLN   (  43-)  N      -5.73
3195 ARG   (  74-)  T      -5.72
3051 GLN   (  28-)  S      -5.71
3163 ARG   (  42-)  T      -5.67
3048 ARG   (  25-)  S      -5.63
1389 ARG   (  44-)  G      -5.58
And so on for a total of 79 lines.

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.

 772 PHE   (  35-)  C       774 - PHE     37- ( C)         -4.65
1386 HIS   (  41-)  G      1389 - ARG     44- ( G)         -5.23
1430 LYS   (   7-)  H      1433 - ASN     10- ( H)         -4.65
1689 TYR   (   3-)  L      1691 - GLU      5- ( L)         -4.78
2548 PHE   (  35-)  P      2550 - PHE     37- ( P)         -4.60
3162 HIS   (  41-)  T      3165 - ARG     44- ( T)         -5.14
3465 TYR   (   3-)  Y      3467 - GLU      5- ( Y)         -4.95

Note: Structural average packing environment OK

The structural average packing score is within normal ranges.

Average for range 1 - 3552 : -0.722

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

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: E

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: F

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: G

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: H

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: I

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: J

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: K

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: L

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: M

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: N

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: O

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: P

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: Q

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: R

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: S

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: T

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: U

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: V

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: W

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: X

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: Y

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: Z

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.

1432 LYS   (   9-)  H   -2.90
3221 ASN   (  22-)  U   -2.80
3196 VAL   (  75-)  T   -2.79
3208 LYS   (   9-)  U   -2.76
1420 VAL   (  75-)  G   -2.76
1277 PRO   (  30-)  F   -2.63
2066 HIS   ( 291-)  N   -2.57
 290 HIS   ( 291-)  A   -2.55
1475 VAL   (  52-)  H   -2.52

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.

 285 ILE   ( 286-)  A     -  288 ALA   ( 289-)  A        -1.78

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: Q

Note: Second generation quality Z-score plot

Chain identifier: R

Note: Second generation quality Z-score plot

Chain identifier: S

Note: Second generation quality Z-score plot

Chain identifier: T

Note: Second generation quality Z-score plot

Chain identifier: U

Note: Second generation quality Z-score plot

Chain identifier: V

Note: Second generation quality Z-score plot

Chain identifier: W

Note: Second generation quality Z-score plot

Chain identifier: X

Note: Second generation quality Z-score plot

Chain identifier: Y

Note: Second generation quality Z-score plot

Chain identifier: Z

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.

3630 HOH   (4154 )  B      O     34.76  292.64  255.18
3630 HOH   (4166 )  B      O     41.37  299.55  243.05
3630 HOH   (4231 )  B      O     34.56  291.81  250.87
3639 HOH   (  87 )  K      O     57.22  312.06  236.27
3644 HOH   (1484 )  P      O    143.03  317.18  146.12

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.

3629 HOH   (3639 )  A      O
3629 HOH   (3680 )  A      O
3629 HOH   (3749 )  A      O
3629 HOH   (3751 )  A      O
3630 HOH   (4181 )  B      O
3630 HOH   (4244 )  B      O
3631 HOH   (3526 )  C      O
3631 HOH   (3541 )  C      O
3631 HOH   (3617 )  C      O
3631 HOH   (3618 )  C      O
3631 HOH   (3635 )  C      O
3631 HOH   (3640 )  C      O
3632 HOH   (3560 )  D      O
3632 HOH   (3579 )  D      O
3632 HOH   (3582 )  D      O
3633 HOH   (3249 )  E      O
3633 HOH   (3284 )  E      O
3634 HOH   ( 147 )  F      O
3635 HOH   (2474 )  G      O
3635 HOH   (2634 )  G      O
3636 HOH   ( 664 )  H      O
3636 HOH   (2652 )  H      O
3636 HOH   (2662 )  H      O
3637 HOH   ( 532 )  I      O
3637 HOH   (2599 )  I      O
And so on for a total of 52 lines.

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.

  79 ASN   (  80-)  A
  97 ASN   (  98-)  A
 177 GLN   ( 178-)  A
 179 GLN   ( 180-)  A
 522 GLN   (  10-)  B
 740 HIS   (   3-)  C
 787 ASN   (  50-)  C
 805 GLN   (  68-)  C
 813 GLN   (  76-)  C
 967 ASN   ( 230-)  C
1032 GLN   (  37-)  D
1216 HIS   (  78-)  E
1232 ASN   (  94-)  E
1353 HIS   (   8-)  G
1379 ASN   (  34-)  G
1454 GLN   (  31-)  H
1515 GLN   (   8-)  I
1668 GLN   (  35-)  K
1855 ASN   (  80-)  N
1873 ASN   (  98-)  N
1953 GLN   ( 178-)  N
1955 GLN   ( 180-)  N
2298 GLN   (  10-)  O
2516 HIS   (   3-)  P
2563 ASN   (  50-)  P
2581 GLN   (  68-)  P
2589 GLN   (  76-)  P
2800 HIS   (  29-)  Q
2808 GLN   (  37-)  Q
2992 HIS   (  78-)  R
3077 ASN   (  54-)  S
3103 GLN   (  80-)  S
3155 ASN   (  34-)  T
3230 GLN   (  31-)  U
3291 GLN   (   8-)  V
3444 GLN   (  35-)  X

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.

  11 HIS   (  12-)  A     HIS-H   0.09 HIS-D   0.55
  60 HIS   (  61-)  A     HIS-D   2.14
 137 HIS   ( 138-)  A     HIS-H   0.10 HIS-D   0.56
 150 HIS   ( 151-)  A     HIS-H   0.08 HIS-E   0.57
 232 HIS   ( 233-)  A     HIS-H   0.24 HIS-E   0.59
 239 HIS   ( 240-)  A     HIS-H   0.20 HIS-E   0.51
 255 HIS   ( 256-)  A     HIS-H   0.14 HIS-D   0.62
 289 HIS   ( 290-)  A     HIS-D   0.44
 290 HIS   ( 291-)  A     HIS-D   0.25
 327 HIS   ( 328-)  A     HIS-H   0.08 HIS-E   0.57
 367 HIS   ( 368-)  A     HIS-D   0.22
 375 HIS   ( 376-)  A     HIS-D   2.21
 377 HIS   ( 378-)  A     HIS-D   2.15
 394 HIS   ( 395-)  A     HIS-H   0.08 HIS-E   0.61
 412 HIS   ( 413-)  A     HIS-H   0.14 HIS-E   0.64
 428 HIS   ( 429-)  A     HIS-H   0.24 HIS-D   0.53
 502 HIS   ( 503-)  A     HIS-H   0.22 HIS-D   0.58
 534 HIS   (  22-)  B     HIS-H   0.16 HIS-D   0.53
 536 HIS   (  24-)  B     HIS-H   0.12 HIS-D   0.58
 538 HIS   (  26-)  B     HIS-H   0.14 HIS-E   0.58
 564 HIS   (  52-)  B     HIS-H   0.18 HIS-D   0.56
 614 HIS   ( 102-)  B     HIS-H   0.16 HIS-E   0.56
 673 HIS   ( 161-)  B     HIS-E   0.39
 716 HIS   ( 204-)  B     HIS-E   0.32
 740 HIS   (   3-)  C     HIS-H   0.12 HIS-E   0.57
 743 HIS   (   6-)  C     HIS-H   0.14 HIS-D   0.56
 746 HIS   (   9-)  C     HIS-H   0.13 HIS-E   0.54
 773 HIS   (  36-)  C     HIS-H   0.13 HIS-E   0.56
 807 HIS   (  70-)  C     HIS-H   0.14 HIS-E   0.57
 808 HIS   (  71-)  C     HIS-H   0.18 HIS-D   0.61
 840 HIS   ( 103-)  C     HIS-H   0.08 HIS-E   0.55
 859 HIS   ( 122-)  C     HIS-H   0.09 HIS-D   0.56
 885 HIS   ( 148-)  C     HIS-D   0.27 HIS-E   1.15
 886 HIS   ( 149-)  C     HIS-H   0.08 HIS-E   0.59
 895 HIS   ( 158-)  C     HIS-H   0.16 HIS-D   0.61
 941 HIS   ( 204-)  C     HIS-H   0.15 HIS-E   0.57
 944 HIS   ( 207-)  C     HIS-H   0.13 HIS-E   0.60
 963 HIS   ( 226-)  C     HIS-H   0.11 HIS-E   0.60
 968 HIS   ( 231-)  C     HIS-H   0.14 HIS-D   0.56
 969 HIS   ( 232-)  C     HIS-D   0.37
 980 HIS   ( 243-)  C     HIS-H   0.09 HIS-D   0.55
1024 HIS   (  29-)  D     HIS-H   0.18 HIS-E   0.52
1096 HIS   ( 101-)  D     HIS-H   0.13 HIS-D   0.55
1104 HIS   ( 109-)  D     HIS-H   0.11 HIS-E   0.56
1143 HIS   (   5-)  E     HIS-H   0.25 HIS-E   0.60
1216 HIS   (  78-)  E     HIS-H   0.16 HIS-D   0.62
1322 HIS   (  75-)  F     HIS-H   0.07 HIS-E   0.56
1335 HIS   (  88-)  F     HIS-H   0.22 HIS-E   0.62
1341 HIS   (  94-)  F     HIS-H   0.34 HIS-D   0.53
1345 HIS   (  98-)  F     HIS-H   0.27 HIS-E   0.56
And so on for a total of 130 lines.

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 ASN   (   4-)  A      N
   4 ARG   (   5-)  A      N
  37 ARG   (  38-)  A      NH1
  42 GLN   (  43-)  A      N
  84 LEU   (  85-)  A      N
  90 ASP   (  91-)  A      N
  95 ARG   (  96-)  A      N
  95 ARG   (  96-)  A      NE
  95 ARG   (  96-)  A      NH2
 125 TRP   ( 126-)  A      N
 125 TRP   ( 126-)  A      NE1
 213 ASN   ( 214-)  A      ND2
 215 ASN   ( 216-)  A      ND2
 239 HIS   ( 240-)  A      NE2
 243 TYR   ( 244-)  A      OH
 265 GLU   ( 266-)  A      N
 288 ALA   ( 289-)  A      N
 300 THR   ( 301-)  A      N
 301 ARG   ( 302-)  A      NH2
 367 HIS   ( 368-)  A      ND1
 370 TYR   ( 371-)  A      OH
 421 ASN   ( 422-)  A      ND2
 427 GLN   ( 428-)  A      NE2
 437 ARG   ( 438-)  A      NH2
 438 ARG   ( 439-)  A      N
And so on for a total of 225 lines.

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.

  54 ASN   (  55-)  A      OD1
 150 HIS   ( 151-)  A      ND1
 241 GLU   ( 242-)  A      OE1
 241 GLU   ( 242-)  A      OE2
 363 ASP   ( 364-)  A      OD1
 427 GLN   ( 428-)  A      OE1
 574 GLU   (  62-)  B      OE1
 746 HIS   (   9-)  C      ND1
 808 HIS   (  71-)  C      NE2
 840 HIS   ( 103-)  C      ND1
 870 ASN   ( 133-)  C      OD1
 895 HIS   ( 158-)  C      NE2
1301 ASN   (  54-)  F      OD1
1352 ASP   (   7-)  G      OD2
1379 ASN   (  34-)  G      OD1
1383 HIS   (  38-)  G      NE2
1926 HIS   ( 151-)  N      ND1
2017 GLU   ( 242-)  N      OE1
2017 GLU   ( 242-)  N      OE2
2139 ASP   ( 364-)  N      OD1
2203 GLN   ( 428-)  N      OE1
2298 GLN   (  10-)  O      OE1
2350 GLU   (  62-)  O      OE1
2522 HIS   (   9-)  P      ND1
2584 HIS   (  71-)  P      NE2
2603 GLU   (  90-)  P      OE1
2616 HIS   ( 103-)  P      ND1
2646 ASN   ( 133-)  P      OD1
2661 HIS   ( 148-)  P      NE2
2671 HIS   ( 158-)  P      NE2
2674 GLN   ( 161-)  P      OE1
2720 HIS   ( 207-)  P      NE2
2745 HIS   ( 232-)  P      NE2
2880 HIS   ( 109-)  Q      ND1
3117 HIS   (  94-)  S      ND1
3118 GLN   (  95-)  S      OE1
3128 ASP   (   7-)  T      OD2
3129 HIS   (   8-)  T      ND1
3155 ASN   (  34-)  T      OD1

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

Note: Overview of ions

When ions are located at special positions, their occupancy should be reduce by a factor that is the same as the multiplicity of that special position. This seems to have been done OK in this PDB file.

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+.

3577  NA   (3519-)  A     1.16   0.96 Scores about as good as CA
3603  NA   (4519-)  N     1.19   0.99 Scores about as good as CA

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.

3629 HOH   (3652 )  A      O  1.00  K  4 NCS 1/1
3629 HOH   (3720 )  A      O  0.91  K  4 NCS 1/1
3630 HOH   (4104 )  B      O  1.01  K  4 NCS 1/1
3630 HOH   (4158 )  B      O  0.93  K  4
3636 HOH   (2099 )  H      O  1.00  K  4
3647 HOH   (1507 )  S      O  0.87  K  4 NCS 1/1

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.

 211 ASP   ( 212-)  A   H-bonding suggests Asn; but Alt-Rotamer
 572 GLU   (  60-)  B   H-bonding suggests Gln
1039 GLU   (  44-)  D   H-bonding suggests Gln
1107 GLU   ( 112-)  D   H-bonding suggests Gln
1497 ASP   (  74-)  H   H-bonding suggests Asn
1987 ASP   ( 212-)  N   H-bonding suggests Asn; but Alt-Rotamer
2348 GLU   (  60-)  O   H-bonding suggests Gln
3234 ASP   (  35-)  U   H-bonding suggests Asn; but Alt-Rotamer
3272 ASP   (  73-)  U   H-bonding suggests Asn
3273 ASP   (  74-)  U   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 (    2)   513 (  514) A Prote<-             pdb1v54.ent
     2   514 (    2)   739 (  227) B Prote<-             pdb1v54.ent
     3   740 (    3)   998 (  261) C Protein             pdb1v54.ent
     4   999 (    4)  1142 (  147) D Protein             pdb1v54.ent
     5  1143 (    5)  1247 (  109) E Protein             pdb1v54.ent
     6  1248 (    1)  1345 (   98) F Protein             pdb1v54.ent
     7  1346 (    1)  1429 (   84) G Protein             pdb1v54.ent
     8  1430 (    7)  1508 (   85) H Protein             pdb1v54.ent
     9  1509 (    2)  1580 (   73) I Prote<-             pdb1v54.ent
    10  1581 (    1)  1638 (   58) J Protein             pdb1v54.ent
    11  1639 (    6)  1687 (   54) K Protein             pdb1v54.ent
    12  1688 (    2)  1733 (   47) L Protein             pdb1v54.ent
    13  1734 (    1)  1776 (   43) M Protein             pdb1v54.ent
    14  1777 (    2)  2289 (  514) N Prote<-             pdb1v54.ent
    15  2290 (    2)  2515 (  227) O Prote<-             pdb1v54.ent
    16  2516 (    3)  2774 (  261) P Protein             pdb1v54.ent
    17  2775 (    4)  2918 (  147) Q Protein             pdb1v54.ent
    18  2919 (    5)  3023 (  109) R Protein             pdb1v54.ent
    19  3024 (    1)  3121 (   98) S Protein             pdb1v54.ent
    20  3122 (    1)  3205 (   84) T Protein             pdb1v54.ent
    21  3206 (    7)  3284 (   85) U Protein             pdb1v54.ent
    22  3285 (    2)  3356 (   73) V Prote<-             pdb1v54.ent
    23  3357 (    1)  3414 (   58) W Protein             pdb1v54.ent
    24  3415 (    6)  3463 (   54) X Protein             pdb1v54.ent
    25  3464 (    2)  3509 (   47) Y Protein             pdb1v54.ent
And so on for a total of 128 lines.

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 :  -0.555
  2nd generation packing quality :  -1.272
  Ramachandran plot appearance   :  -0.046
  chi-1/chi-2 rotamer normality  :  -1.154
  Backbone conformation          :  -0.095

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.449 (tight)
  Bond angles                    :   0.722
  Omega angle restraints         :   0.289 (tight)
  Side chain planarity           :   0.539 (tight)
  Improper dihedral distribution :   0.915
  B-factor distribution          :   0.594
  Inside/Outside distribution    :   1.137

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 : 1.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.2
  2nd generation packing quality :  -1.1
  Ramachandran plot appearance   :   0.0
  chi-1/chi-2 rotamer normality  :  -0.8
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.449 (tight)
  Bond angles                    :   0.722
  Omega angle restraints         :   0.289 (tight)
  Side chain planarity           :   0.539 (tight)
  Improper dihedral distribution :   0.915
  B-factor distribution          :   0.594
  Inside/Outside distribution    :   1.137
==============

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.