WHAT IF Check report

This file was created 2013-12-09 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 pdb3v3y.ent

Checks that need to be done early-on in validation

Note: No crystallographic symmetry between molecules

No extra crystallographic symmetry was observed between the independent molecules.

Note: Counting molecules and matrices

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

Space group as read from CRYST card: P 31 2 1
Number of matrices in space group: 6
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 1
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 6
Z, spacegroup, and NCS seem to agree administratively

Warning: Matthews Coefficient (Vm) 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.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 100562.797
Volume of the Unit Cell V= 3138804.8
Space group multiplicity: 6
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 5.202
Vm by authors and this calculated Vm agree only marginally
Matthews coefficient read from REMARK 280 Vm= 5.720

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.

 826 LDA   ( 702-)  M  -         OK
 827 LDA   ( 704-)  H  -         OK
 828 LDA   ( 709-)  H  -         OK
 829 BCL   ( 302-)  L  -         Atom types
 830 BPH   ( 402-)  L  -         OK
 831 U10   ( 502-)  L  -         OK
 832 DIO   ( 900-)  L  -         OK
 833 DIO   ( 901-)  L  -         OK
 834 BCL   ( 303-)  M  -         Atom types
 835 BCL   ( 304-)  M  -         Atom types
 836 BCL   ( 305-)  L  -         Atom types
 838 LDA   ( 701-)  M  -         OK
 839 LDA   ( 703-)  M  -         OK
 840 LDA   ( 705-)  M  -         OK
 841 LDA   ( 707-)  M  -         OK
 846 DIO   ( 902-)  L  -         OK
 847 LDA   ( 708-)  M  -         OK
 848 SPN   ( 600-)  M  -         OK
 849 U10   ( 501-)  M  -         OK
 850 BPH   ( 401-)  M  -         OK

Administrative problems that can generate validation failures

Note: No strange inter-chain connections detected

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

Note: No duplicate atom names in ligands

All atom names in ligands seem adequately unique.

Note: No mixed usage of alternate atom problems detected

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

Note: In all cases the primary alternate atom was used

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

Note: No residues detected inside ligands

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

Note: No attached groups interfere with hydrogen bond calculations

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

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

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

Note: No probable backbone atoms with zero occupancy detected.

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

Note: All residues have a complete backbone.

No residues have missing backbone atoms.

Note: No C-alpha only residues

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

Note: Non-canonicals

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

Non-validating, descriptive output paragraph

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

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

     1     1 (   10)   241 (  250) H Protein             pdb3v3y.ent
     2   242 (    1)   522 (  281) L Protein             pdb3v3y.ent
     3   523 (    1)   824 (  302) M Protein             pdb3v3y.ent
     4   825 (  281)   825 (  281) L G O2 <-   522       pdb3v3y.ent
     5   826 (  702)   826 (  702) M LDA                 pdb3v3y.ent
     6   827 (  704)   827 (  704) H LDA                 pdb3v3y.ent
     7   828 (  709)   828 (  709) H LDA                 pdb3v3y.ent
     8   829 (  302)   829 (  302) L BCL                 pdb3v3y.ent
     9   830 (  402)   830 (  402) L BPH                 pdb3v3y.ent
    10   831 (  502)   831 (  502) L U10                 pdb3v3y.ent
    11   832 (  900)   832 (  900) L DIO                 pdb3v3y.ent
    12   833 (  901)   833 (  901) L DIO                 pdb3v3y.ent
    13   834 (  303)   834 (  303) M BCL                 pdb3v3y.ent
    14   835 (  304)   835 (  304) M BCL                 pdb3v3y.ent
    15   836 (  305)   836 (  305) L BCL                 pdb3v3y.ent
    16   837 (  500)   837 (  500) M  FE                 pdb3v3y.ent
    17   838 (  701)   838 (  701) M LDA                 pdb3v3y.ent
    18   839 (  703)   839 (  703) M LDA                 pdb3v3y.ent
    19   840 (  705)   840 (  705) M LDA                 pdb3v3y.ent
    20   841 (  707)   841 (  707) M LDA                 pdb3v3y.ent
    21   842 (  800)   842 (  800) M PO4                 pdb3v3y.ent
    22   843 (  801)   843 (  801) M PO4                 pdb3v3y.ent
    23   844 (  306)   844 (  306) M  CL                 pdb3v3y.ent
    24   845 (  803)   845 (  803) M PO4                 pdb3v3y.ent
    25   846 (  902)   846 (  902) L DIO                 pdb3v3y.ent
    26   847 (  708)   847 (  708) M LDA                 pdb3v3y.ent
    27   848 (  600)   848 (  600) M SPN                 pdb3v3y.ent
    28   849 (  501)   849 (  501) M U10                 pdb3v3y.ent
    29   850 (  401)   850 (  401) M BPH                 pdb3v3y.ent
    30   851 ( HOH )   851 ( HOH ) H water   (   40)     pdb3v3y.ent
    31   852 ( HOH )   852 ( HOH ) L water   (   21)     pdb3v3y.ent
    32   853 ( HOH )   853 ( HOH ) M water   (   31)     pdb3v3y.ent

Note: Some notes regarding the PDB file contents

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

The total number of amino acids found is 824.
of which 2 have poor or missing atoms.
Number of water molecules 92

Note: Chain identifiers seem OK

All ions seem to have a logical chain identifier, or there are no ions present in the input file.

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: H

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: M

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 FDLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPKPKTFILPHG
(  10)-(  69)  HHHHHHHHHHHHHHHHHHHHHHHTTTTT T   TTTT  T   TT     SSSS TTT
                     70        80        90       100       110       120
                      |         |         |         |         |         |
   61 -  120 RGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDLPELDGHGHN
(  70)-( 129)  SSSST     TT    SSTTTTTT  SS TT HHHHT 333      TT    TTTT
                    130       140       150       160       170       180
                      |         |         |         |         |         |
  121 -  180 KIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLEVELKDGSTR
( 130)-( 189)TSSS333TTT    TT   TT SSS TTTTSSSSSSSSSSSTTTTSSSSSSSS TTT SS
                    190       200       210       220       230       240
                      |         |         |         |         |         |
  181 -  241 LLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGGLMYAAPKRKS
( 190)-( 250)SSS333 SS TT SS TT  333TTTT   TTTT   HHHHHHHHHHHHHHHHHT333
 
                   250       260       270       280       290       300
                     |         |         |         |         |         |
  242 -  301 ALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTWN
(   1)-(  60)   TTT333  T   TTTTTTT TSSTTSS HHHHHHHHHHHHHHHHHHHHHHHHT
                   310       320       330       340       350       360
                     |         |         |         |         |         |
  302 -  361 PQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPFA
(  61)-( 120)TTT SS    TTTTTT   333THHHHHHHHHHHHHHHHHHHHHHHHHHHHT  THHHHH
                   370       380       390       400       410       420
                     |         |         |         |         |         |
  362 -  421 FAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAITFF
( 121)-( 180)HHHHHHHHHHHHTHHHHHHT 333T  SSTTHHHHHHHHHHHHTTT333 HHHHHHHHHH
                   430       440       450       460       470       480
                     |         |         |         |         |         |
  422 -  481 FTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLSA
( 181)-( 240)HHHHHHHHHHHHHHHHHHT TTT     HHHHHHHHHHHTT    TTHHHHHHHHHHHHH
                   490       500       510       520
                     |         |         |         |
  482 -  522 VFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING
( 241)-( 281)HHHHHHHHHT TTT  T HHHHTHHHHT TTTTT  TTTT
 
                  530       540       550       560       570       580
                    |         |         |         |         |         |
  523 -  582 AEYQNIFTQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLSL
(   1)-(  60)    TTT TT    T      TT  333        HHHHTTT T        HHHHHHH
                  590       600       610       620       630       640
                    |         |         |         |         |         |
  583 -  642 FSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIASF
(  61)-( 120)HHHHHHHHHHHHHHHHHHTT HHHHHHTTTT       333TT T T TTTTHHHHHHHH
                  650       660       670       680       690       700
                    |         |         |         |         |         |
  643 -  702 FMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGIF
( 121)-( 180)HHHHHHHHHHHHHHHHHHHHT  THHHHHHHHHHHHHHHHHTHHHHHHT 333T   THH
                  710       720       730       740       750       760
                    |         |         |         |         |         |
  703 -  762 SHLDWTNNFSLVHGNLFYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIAD
( 181)-( 240)HHHHHHHHHHHHTT 333 HHHHHHHHHHHHHHHHHHHHHHHHHHH333TTT HHHHHHT
                  770       780       790       800       810       820
                    |         |         |         |         |         |
  763 -  824 RGTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQNHG
( 241)-( 302)  HHHHHHHHHHHHHHT    TTHHHHHHHHHHHHHHHHHHHHHHT TTT T HHHHHHH
 
 
 

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

Note: No rounded coordinates detected

No significant rounding of atom coordinates has been detected.

Note: No artificial side chains detected

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

Note: No missing atoms detected in residues

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

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

 241 SER   ( 250-)  H    High
 300 TRP   (  59-)  L    High

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.

 241 SER   ( 250-)  H          : REAL Oxt missing
 824 GLY   ( 302-)  M          : REAL Oxt missing

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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first.

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :110.000

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

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

Percentage of buried atoms with B less than 5 : 0.00

Note: B-factor distribution normal

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

RMS Z-score : 1.177 over 5875 bonds
Average difference in B over a bond : 3.47
RMS difference in B over a bond : 4.53

Note: B-factor plot

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

Chain identifier: H

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: M

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.

 344 ARG   ( 103-)  L
 472 ARG   ( 231-)  L
 654 ARG   ( 132-)  M
 658 ARG   ( 136-)  M

Warning: Tyrosine convention problem

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

 308 TYR   (  67-)  L

Warning: Phenylalanine convention problem

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

  11 PHE   (  20-)  H
  87 PHE   (  96-)  H
 557 PHE   (  35-)  M
 645 PHE   ( 123-)  M
 719 PHE   ( 197-)  M

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.

 202 ASP   ( 211-)  H

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.

  85 GLU   (  94-)  H
 313 GLU   (  72-)  L
 524 GLU   (   2-)  M

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.

 637 TRP   ( 115-)  M      NE1  CE2   1.32   -5.0

Note: Normal bond length variability

Bond lengths were found to deviate normally from the standard bond lengths (values for Protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]).

RMS Z-score for bond lengths: 0.417
RMS-deviation in bond distances: 0.010

Note: No bond length directionality

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA does not show significant systematic deviations.

Note: All bond angles OK

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

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: 0.640
RMS-deviation in bond angles: 1.342

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.

  85 GLU   (  94-)  H
 202 ASP   ( 211-)  H
 313 GLU   (  72-)  L
 344 ARG   ( 103-)  L
 472 ARG   ( 231-)  L
 524 GLU   (   2-)  M
 654 ARG   ( 132-)  M
 658 ARG   ( 136-)  M

Note: Chirality OK

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

Note: Improper dihedral angle distribution OK

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

Improper dihedral RMS Z-score : 0.732

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.

 236 ALA   ( 245-)  H    4.91
 186 MET   ( 195-)  H    4.61
 168 ARG   ( 177-)  H    4.33

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 : 1.187

Note: Side chain planarity OK

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

Note: Atoms connected to aromatic rings OK

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

Torsion-related checks

Note: Ramachandran Z-score OK

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

Ramachandran Z-score : -2.017

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.

  59 HIS   (  68-)  H    -2.9
 780 PHE   ( 258-)  M    -2.7
 787 ILE   ( 265-)  M    -2.4
 490 ILE   ( 249-)  L    -2.4
 441 PRO   ( 200-)  L    -2.3
 287 ILE   (  46-)  L    -2.2
 374 LEU   ( 133-)  L    -2.2
 509 LYS   ( 268-)  L    -2.2
 491 ILE   ( 250-)  L    -2.2
   8 ILE   (  17-)  H    -2.1
 461 VAL   ( 220-)  L    -2.1
 265 PHE   (  24-)  L    -2.1
 214 THR   ( 223-)  H    -2.1
 323 LYS   (  82-)  L    -2.1
 448 ARG   ( 207-)  L    -2.1
 492 THR   ( 251-)  L    -2.0
 534 VAL   (  12-)  M    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

  31 TYR   (  40-)  H  PRO omega poor
  34 GLU   (  43-)  H  omega poor
  66 VAL   (  75-)  H  PRO omega poor
  71 SER   (  80-)  H  Poor phi/psi
  73 ASP   (  82-)  H  Poor phi/psi
  85 GLU   (  94-)  H  omega poor
 111 LEU   ( 120-)  H  Poor phi/psi
 149 LEU   ( 158-)  H  Poor phi/psi
 157 ASP   ( 166-)  H  Poor phi/psi
 193 ARG   ( 202-)  H  omega poor
 246 PHE   (   5-)  L  omega poor
 265 PHE   (  24-)  L  Poor phi/psi
 266 TRP   (  25-)  L  omega poor
 272 VAL   (  31-)  L  Poor phi/psi
 410 TYR   ( 169-)  L  omega poor
 527 ASN   (   5-)  M  Poor phi/psi
 544 GLU   (  22-)  M  Poor phi/psi
 570 GLY   (  48-)  M  PRO omega poor
 602 TRP   (  80-)  M  Poor phi/psi
 717 ASN   ( 195-)  M  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.956

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 : -2.956

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.

 478 SER   ( 237-)  L    0.33
 437 SER   ( 196-)  L    0.35
 581 SER   (  59-)  M    0.36
 674 SER   ( 152-)  M    0.38

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!

  27 MET   (  36-)  H      0
  28 ARG   (  37-)  H      0
  29 GLU   (  38-)  H      0
  31 TYR   (  40-)  H      0
  32 PRO   (  41-)  H      0
  33 LEU   (  42-)  H      0
  42 ALA   (  51-)  H      0
  43 ASN   (  52-)  H      0
  44 GLN   (  53-)  H      0
  46 PRO   (  55-)  H      0
  58 PRO   (  67-)  H      0
  59 HIS   (  68-)  H      0
  61 ARG   (  70-)  H      0
  63 THR   (  72-)  H      0
  66 VAL   (  75-)  H      0
  67 PRO   (  76-)  H      0
  69 PRO   (  78-)  H      0
  71 SER   (  80-)  H      0
  72 GLU   (  81-)  H      0
  77 ALA   (  86-)  H      0
  83 VAL   (  92-)  H      0
  84 SER   (  93-)  H      0
  85 GLU   (  94-)  H      0
  94 ASP   ( 103-)  H      0
 100 VAL   ( 109-)  H      0
And so on for a total of 256 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 : 0.171

Note: Omega angle restraint OK

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation agrees with this expectation.

Standard deviation of omega values : 5.445

Note: Backbone oxygen evaluation OK

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

Note: Peptide bond conformations

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

Note: PRO puckering amplitude OK

Puckering amplitudes for all PRO residues are within normal ranges.

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

  40 PRO   (  49-)  H  -132.3 half-chair C-delta/C-gamma (-126 degrees)
 102 PRO   ( 111-)  H  -115.8 envelop C-gamma (-108 degrees)
 208 PRO   ( 217-)  H   105.8 envelop C-beta (108 degrees)
 450 PRO   ( 209-)  L   102.6 envelop C-beta (108 degrees)
 619 PRO   (  97-)  M   105.7 envelop C-beta (108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 271 TYR   (  30-)  L      O   <->  344 ARG   ( 103-)  L      NH1    0.44    2.26  INTRA BL
 102 PRO   ( 111-)  H      O   <->  769 ARG   ( 247-)  M      NH2    0.39    2.31  INTRA BL
 110 ASP   ( 119-)  H      OD2 <->  211 LYS   ( 220-)  H      NZ     0.39    2.31  INTRA
 658 ARG   ( 136-)  M      NH1 <->  853 HOH   ( 336 )  M      O      0.37    2.33  INTRA
 414 HIS   ( 173-)  L      ND1 <->  852 HOH   ( 282 )  L      O      0.32    2.38  INTRA BL
 667 HIS   ( 145-)  M      NE2 <->  842 PO4   ( 800-)  M      O3     0.30    2.40  INTRA BL
 344 ARG   ( 103-)  L      NH2 <->  777 THR   ( 255-)  M      O      0.28    2.42  INTRA BL
 609 ARG   (  87-)  M      NE  <->  610 ASP   (  88-)  M      OD1    0.23    2.47  INTRA BF
 464 SER   ( 223-)  L      O   <->  566 ASN   (  44-)  M      ND2    0.22    2.48  INTRA BL
  54 THR   (  63-)  H      OG1 <->   65 THR   (  74-)  H      OG1    0.20    2.20  INTRA BL
 497 PHE   ( 256-)  L      N   <->  852 HOH   ( 288 )  L      O      0.19    2.51  INTRA BL
 446 GLU   ( 205-)  L      O   <->  448 ARG   ( 207-)  L      NH1    0.19    2.51  INTRA
 676 ILE   ( 154-)  M      O   <->  680 MET   ( 158-)  M      N      0.19    2.51  INTRA BL
 765 THR   ( 243-)  M      OG1 <->  769 ARG   ( 247-)  M      NH1    0.19    2.51  INTRA BL
 469 GLY   ( 228-)  L      O   <->  473 LEU   ( 232-)  L      N      0.18    2.52  INTRA BL
 449 THR   ( 208-)  L      OG1 <->  452 HIS   ( 211-)  L      ND1    0.18    2.52  INTRA BL
 424 ASN   ( 183-)  L      O   <->  428 LEU   ( 187-)  L      N      0.17    2.53  INTRA BL
 558 SER   (  36-)  M      N   <->  567 ALA   (  45-)  M      O      0.17    2.53  INTRA BL
 460 LEU   ( 219-)  L      O   <->  654 ARG   ( 132-)  M      NH2    0.16    2.54  INTRA BF
  65 THR   (  74-)  H      N   <->  851 HOH   ( 260 )  H      O      0.15    2.55  INTRA BL
 809 SER   ( 287-)  M      OG  <->  816 TRP   ( 294-)  M      NE1    0.14    2.56  INTRA BL
  72 GLU   (  81-)  H      OE1 <->  249 LYS   (   8-)  L      NZ     0.14    2.56  INTRA BL
 257 LEU   (  16-)  L      N   <->  347 GLU   ( 106-)  L      OE2    0.13    2.57  INTRA BF
 221 GLU   ( 230-)  H      OE1 <->  755 ARG   ( 233-)  M      NH1    0.12    2.58  INTRA BL
 144 VAL   ( 153-)  H      N   <->  153 GLY   ( 162-)  H      O      0.12    2.58  INTRA
And so on for a total of 95 lines.

Packing, accessibility and threading

Warning: Inside/Outside residue distribution unusual

The distribution of residue types over the inside and the outside of the protein is unusual. Normal values for the RMS Z-score below are between 0.84 and 1.16. The fact that it is higher in this structure could be caused by transmembrane helices, by the fact that it is part of a multimeric active unit, or by mistraced segments in the density.

inside/outside RMS Z-score : 1.248

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: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

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.

 308 TYR   (  67-)  L      -7.43
  61 ARG   (  70-)  H      -6.35
 240 LYS   ( 249-)  H      -6.00
 175 LYS   ( 184-)  H      -5.94
  28 ARG   (  37-)  H      -5.87
 632 LYS   ( 110-)  M      -5.83
 448 ARG   ( 207-)  L      -5.80
  44 GLN   (  53-)  H      -5.65
 211 LYS   ( 220-)  H      -5.58
 540 LEU   (  18-)  M      -5.55
 822 ASN   ( 300-)  M      -5.41
  70 GLU   (  79-)  H      -5.38
  80 ARG   (  89-)  H      -5.37
 750 ARG   ( 228-)  M      -5.17
 599 GLN   (  77-)  M      -5.15
  59 HIS   (  68-)  H      -5.10
 526 GLN   (   4-)  M      -5.09
 780 PHE   ( 258-)  M      -5.05
 821 GLN   ( 299-)  M      -5.05
  51 LYS   (  60-)  H      -5.04
 695 GLU   ( 173-)  M      -5.00

Note: No series of residues with bad packing environment

There are no stretches of three or more residues each having a packing score worse than -4.0.

Note: Structural average packing environment OK

The structural average packing score is within normal ranges.

Average for range 1 - 824 : -0.979

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: 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

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.

 778 MET   ( 256-)  M   -3.23
 718 LEU   ( 196-)  M   -2.80
 103 ALA   ( 112-)  H   -2.73
  45 GLY   (  54-)  H   -2.58
  66 VAL   (  75-)  H   -2.56

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.

 183 PRO   ( 192-)  H     -  186 MET   ( 195-)  H        -1.05

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: H

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: M

Water, ion, and hydrogenbond related checks

Note: Water contacts OK

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

Note: No waters need moving

All water molecules are sufficiently close to the asymmetric unit given in the input file.

Note: Water hydrogen bonds OK

All water molecules can form hydrogen bonds.

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.

  59 HIS   (  68-)  H
 521 ASN   ( 280-)  L
 821 GLN   ( 299-)  M

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.

  59 HIS   (  68-)  H     HIS-H   0.11 HIS-E   0.58
  89 HIS   (  98-)  H     HIS-H   0.11 HIS-E   0.56
 117 HIS   ( 126-)  H     HIS-H   0.06 HIS-E   0.56
 119 HIS   ( 128-)  H     HIS-H   0.16 HIS-E   0.58
 132 HIS   ( 141-)  H     HIS-H   0.14 HIS-D   0.54
 195 HIS   ( 204-)  H     HIS-H   0.05 HIS-E   0.56
 357 HIS   ( 116-)  L     HIS-H   0.10 HIS-E   0.62
 394 HIS   ( 153-)  L     HIS-H   0.21 HIS-D   0.57
 409 HIS   ( 168-)  L     HIS-H   0.10 HIS-E   0.61
 414 HIS   ( 173-)  L     HIS-H   0.24 HIS-D   0.62
 431 HIS   ( 190-)  L     HIS-H   0.13 HIS-D   0.57
 452 HIS   ( 211-)  L     HIS-H   0.14 HIS-E   0.61
 471 HIS   ( 230-)  L     HIS-H   0.23 HIS-D   0.58
 667 HIS   ( 145-)  M     HIS-H   0.21 HIS-E   0.63
 704 HIS   ( 182-)  M     HIS-H   0.23 HIS-D   0.60
 715 HIS   ( 193-)  M     HIS-H   0.09 HIS-D   0.55
 724 HIS   ( 202-)  M     HIS-H   0.11 HIS-D   0.56
 741 HIS   ( 219-)  M     HIS-H   0.24 HIS-D   0.66
 788 HIS   ( 266-)  M     HIS-H   0.23 HIS-D   0.59
 823 HIS   ( 301-)  M     HIS-H   0.15 HIS-E   0.56

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.

  23 GLN   (  32-)  H      NE2
  26 ASN   (  35-)  H      ND2
  28 ARG   (  37-)  H      N
  29 GLU   (  38-)  H      N
  83 VAL   (  92-)  H      N
  84 SER   (  93-)  H      N
  87 PHE   (  96-)  H      N
  89 HIS   (  98-)  H      NE2
 105 TRP   ( 114-)  H      N
 108 ARG   ( 117-)  H      N
 168 ARG   ( 177-)  H      NH2
 181 LEU   ( 190-)  H      N
 193 ARG   ( 202-)  H      N
 199 LEU   ( 208-)  H      N
 201 SER   ( 210-)  H      N
 246 PHE   (   5-)  L      N
 248 ARG   (   7-)  L      NE
 264 ASP   (  23-)  L      N
 266 TRP   (  25-)  L      NE1
 299 THR   (  58-)  L      N
 306 SER   (  65-)  L      N
 306 SER   (  65-)  L      OG
 308 TYR   (  67-)  L      OH
 312 LEU   (  71-)  L      N
 313 GLU   (  72-)  L      N
And so on for a total of 67 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.

  70 GLU   (  79-)  H      OE1
 345 GLU   ( 104-)  L      OE1
 345 GLU   ( 104-)  L      OE2
 754 GLU   ( 232-)  M      OE2
 823 HIS   ( 301-)  M      ND1

Note: Crystallisation conditions from REMARK 280

Crystallisation conditions as found in the PDB file header.

CRYSTAL
SOLVENT CONTENT, VS   (%): 78.51
MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.72
CRYSTALLIZATION CONDITIONS: 3.5% 1,2,3 -HEPTANETRIOL, 2% DIOXANE,
       0.1% LDAO, 1M POTASSIUM PHOSPHATE , PH 7.4, VAPOR DIFFUSION,
       HANGING DROP, TEMPERATURE 289K

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

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

Note: Water packing OK

All waters seem properly packed, or at least not packed like an ion. This method is experimental. See: swift.cmbi.ru.nl/teach/theory/

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.

  70 GLU   (  79-)  H   H-bonding suggests Gln; but Alt-Rotamer
 454 ASP   ( 213-)  L   H-bonding suggests Asn

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 (   10)   241 (  250) H Protein             pdb3v3y.ent
     2   242 (    1)   522 (  281) L Protein             pdb3v3y.ent
     3   523 (    1)   824 (  302) M Protein             pdb3v3y.ent
     4   825 (  281)   825 (  281) L G O2 <-   522       pdb3v3y.ent
     5   826 (  702)   826 (  702) M LDA                 pdb3v3y.ent
     6   827 (  704)   827 (  704) H LDA                 pdb3v3y.ent
     7   828 (  709)   828 (  709) H LDA                 pdb3v3y.ent
     8   829 (  302)   829 (  302) L BCL                 pdb3v3y.ent
     9   830 (  402)   830 (  402) L BPH                 pdb3v3y.ent
    10   831 (  502)   831 (  502) L U10                 pdb3v3y.ent
    11   832 (  900)   832 (  900) L DIO                 pdb3v3y.ent
    12   833 (  901)   833 (  901) L DIO                 pdb3v3y.ent
    13   834 (  303)   834 (  303) M BCL                 pdb3v3y.ent
    14   835 (  304)   835 (  304) M BCL                 pdb3v3y.ent
    15   836 (  305)   836 (  305) L BCL                 pdb3v3y.ent
    16   837 (  500)   837 (  500) M  FE                 pdb3v3y.ent
    17   838 (  701)   838 (  701) M LDA                 pdb3v3y.ent
    18   839 (  703)   839 (  703) M LDA                 pdb3v3y.ent
    19   840 (  705)   840 (  705) M LDA                 pdb3v3y.ent
    20   841 (  707)   841 (  707) M LDA                 pdb3v3y.ent
    21   842 (  800)   842 (  800) M PO4                 pdb3v3y.ent
    22   843 (  801)   843 (  801) M PO4                 pdb3v3y.ent
    23   844 (  306)   844 (  306) M  CL                 pdb3v3y.ent
    24   845 (  803)   845 (  803) M PO4                 pdb3v3y.ent
    25   846 (  902)   846 (  902) L DIO                 pdb3v3y.ent
    26   847 (  708)   847 (  708) M LDA                 pdb3v3y.ent
    27   848 (  600)   848 (  600) M SPN                 pdb3v3y.ent
    28   849 (  501)   849 (  501) M U10                 pdb3v3y.ent
    29   850 (  401)   850 (  401) M BPH                 pdb3v3y.ent
    30   851 ( HOH )   851 ( HOH ) H water   (   40)     pdb3v3y.ent
    31   852 ( HOH )   852 ( HOH ) L water   (   21)     pdb3v3y.ent
    32   853 ( HOH )   853 ( HOH ) M water   (   31)     pdb3v3y.ent

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.198
  2nd generation packing quality :  -1.580
  Ramachandran plot appearance   :  -2.017
  chi-1/chi-2 rotamer normality  :  -2.956
  Backbone conformation          :   0.171

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.417 (tight)
  Bond angles                    :   0.640 (tight)
  Omega angle restraints         :   0.990
  Side chain planarity           :   0.429 (tight)
  Improper dihedral distribution :   0.732
  B-factor distribution          :   1.177
  Inside/Outside distribution    :   1.248 (unusual)

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.2
  2nd generation packing quality :   0.0
  Ramachandran plot appearance   :   0.4
  chi-1/chi-2 rotamer normality  :  -0.8
  Backbone conformation          :   0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.417 (tight)
  Bond angles                    :   0.640 (tight)
  Omega angle restraints         :   0.990
  Side chain planarity           :   0.429 (tight)
  Improper dihedral distribution :   0.732
  B-factor distribution          :   1.177
  Inside/Outside distribution    :   1.248 (unusual)
==============

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.