Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.
In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.
Chain identifier: A
Coordinate problems, unexpected atoms, B-factor and occupancy checks
Warning: What type of B-factor?
WHAT IF does not yet know well how to cope with B-factors in case TLS has
been used. It simply assumes that the B-factor listed on the ATOM and HETATM
cards are the total B-factors. When TLS refinement is used that assumption
sometimes is not correct. TLS seems not mentioned in the header of the PDB
file. But anyway, if WHAT IF complains about your B-factors, and you think
that they are OK, then check for TLS related B-factor problems first.
Obviously, the temperature at which the X-ray data was collected has some importance too:
Crystal temperature (K) :100.000
Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
Chain identifier: A
Nomenclature related problems
Warning: Phenylalanine convention problem
The phenylalanine residues listed in the table below have their chi-2 not
between -90.0 and 90.0.
6 PHE ( 7-) A 21 PHE ( 22-) A
164 GLU ( 165-) A
RMS Z-score for bond lengths: 0.267
RMS-deviation in bond distances: 0.006
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.
22 GLU ( 23-) A N CA C 99.77 -4.1
RMS Z-score for bond angles: 0.599
RMS-deviation in bond angles: 1.315
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.
164 GLU ( 165-) A
22 GLU ( 23-) A 4.16
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.
60 MET ( 61-) A -2.3 28 VAL ( 29-) A -2.3 108 GLY ( 109-) A -2.1
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.
24 PHE ( 25-) A Poor phi/psi 86 ASN ( 87-) A Poor phi/psi 109 SER ( 110-) A Poor phi/psi 116 ALA ( 117-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -0.794
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!
11 VAL ( 12-) A 0 15 PRO ( 16-) A 0 24 PHE ( 25-) A 0 25 ALA ( 26-) A 0 27 LYS ( 28-) A 0 42 GLU ( 43-) A 0 43 LYS ( 44-) A 0 45 PHE ( 46-) A 0 47 TYR ( 48-) A 0 48 LYS ( 49-) A 0 50 SER ( 51-) A 0 52 PHE ( 53-) A 0 53 HIS ( 54-) A 0 54 ARG ( 55-) A 0 57 PRO ( 58-) A 0 59 PHE ( 60-) A 0 60 MET ( 61-) A 0 67 THR ( 68-) A 0 68 ARG ( 69-) A 0 69 HIS ( 70-) A 0 70 ASN ( 71-) A 0 72 THR ( 73-) A 0 78 TYR ( 79-) A 0 80 GLU ( 81-) A 0 82 PHE ( 83-) A 0And so on for a total of 79 lines.
Standard deviation of omega values : 1.368
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.
119 LYS ( 120-) A NZ <-> 167 HOH ( 439 ) A O 0.23 2.47 INTRA 24 PHE ( 25-) A N <-> 167 HOH ( 522 ) A O 0.22 2.48 INTRA 22 GLU ( 23-) A O <-> 167 HOH ( 522 ) A O 0.21 2.19 INTRA 1 VAL ( 2-) A N <-> 167 HOH ( 464 ) A O 0.17 2.53 INTRA 67 THR ( 68-) A OG1 <-> 74 GLY ( 75-) A N 0.16 2.54 INTRA BL 5 VAL ( 6-) A CG1 <-> 6 PHE ( 7-) A N 0.14 2.86 INTRA 24 PHE ( 25-) A CG <-> 167 HOH ( 522 ) A O 0.13 2.67 INTRA 68 ARG ( 69-) A NH2 <-> 167 HOH ( 432 ) A O 0.10 2.60 INTRA 132 LYS ( 133-) A NZ <-> 167 HOH ( 343 ) A O 0.09 2.61 INTRA 65 ASP ( 66-) A OD2 <-> 71 GLY ( 72-) A N 0.09 2.61 INTRA BL 132 LYS ( 133-) A NZ <-> 164 GLU ( 165-) A OE2 0.07 2.63 INTRA 129 GLY ( 130-) A CA <-> 167 HOH ( 522 ) A O 0.06 2.74 INTRA 2 ASN ( 3-) A N <-> 167 HOH ( 405 ) A O 0.06 2.64 INTRA 143 ARG ( 144-) A NH2 <-> 167 HOH ( 421 ) A O 0.04 2.66 INTRA BF 148 ASN ( 149-) A ND2 <-> 150 LYS ( 151-) A N 0.04 2.81 INTRA 24 PHE ( 25-) A CD1 <-> 167 HOH ( 522 ) A O 0.04 2.76 INTRA 143 ARG ( 144-) A NH2 <-> 167 HOH ( 502 ) A O 0.04 2.66 INTRA BF 117 LYS ( 118-) A NZ <-> 167 HOH ( 404 ) A O 0.03 2.67 INTRA 99 MET ( 100-) A SD <-> 128 PHE ( 129-) A CE1 0.03 3.37 INTRA BL 115 THR ( 116-) A N <-> 116 ALA ( 117-) A N 0.03 2.57 INTRA BL 75 LYS ( 76-) A NZ <-> 167 HOH ( 399 ) A O 0.03 2.67 INTRA 81 LYS ( 82-) A NZ <-> 167 HOH ( 498 ) A O 0.02 2.68 INTRA 24 PHE ( 25-) A CD2 <-> 167 HOH ( 522 ) A O 0.01 2.79 INTRA 7 PHE ( 8-) A N <-> 19 VAL ( 20-) A O 0.01 2.69 INTRA BL 125 HIS ( 126-) A NE2 <-> 167 HOH ( 435 ) A O 0.01 2.69 INTRA
Chain identifier: A
Warning: Abnormal packing environment for some residues
The residues listed in the table below have an unusual packing environment.
The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.
147 ARG ( 148-) A -7.35 143 ARG ( 144-) A -5.49
Chain identifier: A
Warning: Low packing Z-score for some residues
The residues listed in the table below have an unusual packing
environment according to the 2nd generation packing check. The score
listed in the table is a packing normality Z-score: positive means
better than average, negative means worse than average. Only residues
scoring less than -2.50 are listed here. These are the unusual
residues in the structure, so it will be interesting to take a
special look at them.
86 ASN ( 87-) A -2.63
The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.
85 GLU ( 86-) A - 88 ILE ( 89-) A -1.91
Chain identifier: A
Water, ion, and hydrogenbond related checks
Warning: Water molecules need moving
The water molecules listed in the table below were found to be significantly
closer to a symmetry related non-water molecule than to the ones given in the
coordinate file. For optimal viewing convenience revised coordinates for
these water molecules should be given.
The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.
167 HOH ( 402 ) A O 12.05 14.33 51.54 167 HOH ( 433 ) A O 27.29 26.76 56.14 167 HOH ( 474 ) A O 17.54 10.51 65.00 167 HOH ( 503 ) A O 13.25 10.86 49.68 167 HOH ( 515 ) A O 19.17 26.53 50.52 167 HOH ( 528 ) A O 44.78 13.79 40.57 167 HOH ( 538 ) A O 22.29 27.09 49.32 167 HOH ( 539 ) A O 32.28 13.74 74.38
2 ASN ( 3-) A 69 HIS ( 70-) A 101 ASN ( 102-) A 148 ASN ( 149-) A
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.
51 CYS ( 52-) A N 53 HIS ( 54-) A N 81 LYS ( 82-) A N 86 ASN ( 87-) A N 116 ALA ( 117-) A N 120 TRP ( 121-) A N 153 LYS ( 154-) A N
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+.
166 MG ( 302-) A -.- -.- Too few ligands (2)
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.
167 HOH ( 306 ) A O 0.95 K 4 167 HOH ( 324 ) A O 0.95 K 4 H2O-B 167 HOH ( 326 ) A O 1.04 K 5 167 HOH ( 327 ) A O 1.06 K 5 167 HOH ( 403 ) A O 1.01 K 5 Ion-B
84 ASP ( 85-) A H-bonding suggests Asn; but Alt-Rotamer 85 GLU ( 86-) A H-bonding suggests Gln 122 ASP ( 123-) A H-bonding suggests Asn 133 GLU ( 134-) A H-bonding suggests Gln
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 : -0.888 2nd generation packing quality : -1.732 Ramachandran plot appearance : -0.649 chi-1/chi-2 rotamer normality : -0.794 Backbone conformation : -0.443
Bond lengths : 0.267 (tight) Bond angles : 0.599 (tight) Omega angle restraints : 0.249 (tight) Side chain planarity : 0.245 (tight) Improper dihedral distribution : 0.578 B-factor distribution : 0.667 Inside/Outside distribution : 0.930
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 : 1.90
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.4 2nd generation packing quality : -1.3 Ramachandran plot appearance : -0.3 chi-1/chi-2 rotamer normality : -0.2 Backbone conformation : -0.8
Bond lengths : 0.267 (tight) Bond angles : 0.599 (tight) Omega angle restraints : 0.249 (tight) Side chain planarity : 0.245 (tight) Improper dihedral distribution : 0.578 B-factor distribution : 0.667 Inside/Outside distribution : 0.930 ==============
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.