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.
347 MYS ( 500-) A - 348 CFP ( 367-) A -
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: Occupancies atoms do not add up to 1.0.
In principle, the occupancy of all alternates of one atom should add up till
1.0. A valid exception is the missing atom (i.e. an atom not seen in the
electron density) that is allowed to have a 0.0 occupancy. Sometimes this
even happens when there are no alternate atoms given...
Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.
WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.
227 MET ( 235-) A 0.50
Obviously, the temperature at which the X-ray data was collected has some importance too:
Crystal temperature (K) :125.000
Error: The B-factors of bonded atoms show signs of over-refinement
For each of the bond types in a protein a distribution was derived for the
difference between the square roots of the B-factors of the two atoms. All
bonds in the current protein were scored against these distributions. The
number given below is the RMS Z-score over the structure. For a structure
with completely restrained B-factors within residues, this value will be
around 0.35, for extremely high resolution structures refined with free
isotropic B-factors this number is expected to be near 1.0. Any value over
1.5 is sign of severe over-refinement of B-factors.
RMS Z-score : 1.514 over 2298 bonds
Average difference in B over a bond : 4.28
RMS difference in B over a bond : 6.05
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.
13 PHE ( 21-) A 18 PHE ( 26-) A 55 PHE ( 63-) A 83 PHE ( 91-) A 89 PHE ( 97-) A 94 PHE ( 102-) A 148 PHE ( 156-) A 248 PHE ( 256-) A
166 ASP ( 174-) A 181 ASP ( 189-) A 191 ASP ( 199-) A 243 ASP ( 251-) A 255 ASP ( 263-) A 326 ASP ( 337-) A 330 ASP ( 341-) A
40 GLU ( 48-) A 51 GLU ( 59-) A
40 GLU ( 48-) A 51 GLU ( 59-) A 166 ASP ( 174-) A 181 ASP ( 189-) A 191 ASP ( 199-) A 243 ASP ( 251-) A 255 ASP ( 263-) A 326 ASP ( 337-) A 330 ASP ( 341-) A
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.
309 PRO ( 320-) A -2.7 56 LEU ( 64-) A -2.5 68 THR ( 76-) A -2.4 167 ILE ( 175-) A -2.3 127 PRO ( 135-) A -2.2 99 GLY ( 107-) A -2.2 189 THR ( 197-) A -2.1 14 GLY ( 22-) A -2.1 50 ARG ( 58-) 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.
99 GLY ( 107-) A Poor phi/psi 124 LEU ( 132-) A Poor phi/psi 182 ARG ( 190-) A Poor phi/psi 191 ASP ( 199-) A Poor phi/psi 305 LYS ( 316-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -0.457
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!
13 PHE ( 21-) A 0 29 LYS ( 37-) A 0 30 CYS ( 38-) A 0 31 ARG ( 39-) A 0 38 MET ( 46-) A 0 50 ARG ( 58-) A 0 54 LEU ( 62-) A 0 55 PHE ( 63-) A 0 57 LYS ( 65-) A 0 76 ASN ( 84-) A 0 79 GLU ( 87-) A 0 83 PHE ( 91-) A 0 84 VAL ( 92-) A 0 96 LYS ( 104-) A 0 97 SER ( 105-) A 0 115 CYS ( 123-) A 0 117 LYS ( 125-) A 0 121 ARG ( 129-) A 0 124 LEU ( 132-) A 0 134 PHE ( 142-) A 0 144 ALA ( 152-) A 0 146 PRO ( 154-) A 0 147 SER ( 155-) A 0 154 THR ( 162-) A 0 157 PHE ( 165-) A 0And so on for a total of 98 lines.
Standard deviation of omega values : 1.101
Warning: Backbone oxygen evaluation
The residues listed in the table below have an unusual backbone oxygen
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!
127 PRO ( 135-) A 1.84 11
146 PRO ( 154-) A 51.4 half-chair C-delta/C-gamma (54 degrees)
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.
266 ARG ( 274-) A NH1 <-> 286 ALA ( 297-) A CB 0.23 2.87 INTRA BF 285 ARG ( 293-) A C <-> 286 ALA ( 297-) A N 0.23 2.67 INTRA BF 322 LYS ( 333-) A NZ <-> 330 ASP ( 341-) A OD2 0.20 2.50 INTRA 8 ASN ( 16-) A N <-> 79 GLU ( 87-) A OE1 0.16 2.54 INTRA 15 SER ( 23-) A OG <-> 37 HIS ( 45-) A ND1 0.16 2.54 INTRA 137 SER ( 145-) A N <-> 138 PRO ( 146-) A CD 0.16 2.84 INTRA BF 5 LEU ( 13-) A CD2 <-> 175 ARG ( 183-) A NH2 0.14 2.96 INTRA BF 172 ARG ( 180-) A NE <-> 349 HOH ( 617 ) A O 0.13 2.57 INTRA BF 243 ASP ( 251-) A OD1 <-> 245 SER ( 253-) A N 0.11 2.59 INTRA BL 137 SER ( 145-) A O <-> 140 LEU ( 148-) A N 0.09 2.61 INTRA BF 9 LYS ( 17-) A NZ <-> 76 ASN ( 84-) A O 0.08 2.62 INTRA 303 GLN ( 314-) A NE2 <-> 349 HOH ( 626 ) A O 0.08 2.62 INTRA BF 232 GLU ( 240-) A OE2 <-> 310 LEU ( 321-) A N 0.06 2.64 INTRA BL 47 ASN ( 55-) A O <-> 50 ARG ( 58-) A CD 0.06 2.74 INTRA BF 128 ALA ( 136-) A N <-> 196 GLU ( 204-) A OE2 0.04 2.66 INTRA BL 98 GLY ( 106-) A O <-> 102 ILE ( 110-) A N 0.04 2.66 INTRA BL 3 GLU ( 11-) A O <-> 175 ARG ( 183-) A NH1 0.04 2.66 INTRA BF 51 GLU ( 59-) A OE2 <-> 58 GLY ( 66-) A N 0.04 2.66 INTRA BF 84 VAL ( 92-) A N <-> 85 ILE ( 93-) A N 0.03 2.57 INTRA BL 150 ILE ( 158-) A CG2 <-> 151 GLU ( 159-) A N 0.03 2.97 INTRA 81 ILE ( 89-) A O <-> 113 LEU ( 121-) A N 0.02 2.68 INTRA BL 121 ARG ( 129-) A NE <-> 349 HOH ( 652 ) A O 0.02 2.68 INTRA BF 120 GLU ( 128-) A O <-> 124 LEU ( 132-) A N 0.02 2.68 INTRA BL 149 ALA ( 157-) A O <-> 153 ALA ( 161-) A N 0.01 2.69 INTRA BL 137 SER ( 145-) A C <-> 139 LEU ( 147-) A N 0.01 2.89 INTRA BF
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.
336 LEU ( 347-) A -7.00 345 PHE ( 356-) A -6.69 307 LYS ( 318-) A -6.29 117 LYS ( 125-) A -5.94 341 LEU ( 352-) A -5.78 344 LEU ( 355-) A -5.40 38 MET ( 46-) A -5.04
The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.
95 GLU ( 103-) A 97 - SER 105- ( A) -4.17 336 LEU ( 347-) A 339 - GLU 350- ( A) -5.16
Chain identifier: A
Note: Second generation quality Z-score plot
The second generation quality Z-score smoothed over a 10 residue window
is plotted as function of the residue number. Low areas in the plot (below
-1.3) indicate unusual packing.
Chain identifier: A
Water, ion, and hydrogenbond related checks
Error: Water molecules without hydrogen bonds
The water molecules listed in the table below do not form any hydrogen bonds,
neither with the protein or DNA/RNA, nor with other water molecules. This is
a strong indication of a refinement problem. The last number on each line is
the identifier of the water molecule in the input file.
349 HOH ( 643 ) A O Marked this atom as acceptor 348 CFP ( 367-) A CL6 Marked this atom as acceptor 348 CFP ( 367-) A F2
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.
39 ASN ( 47-) A N 80 ILE ( 88-) A N 87 THR ( 95-) A OG1 175 ARG ( 183-) A NH1 244 GLY ( 252-) A N 257 GLN ( 265-) A NE2 281 GLU ( 289-) A N 295 ASP ( 306-) A N
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.
349 HOH ( 513 ) A O 1.07 K 4
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 : 0.369 2nd generation packing quality : -0.969 Ramachandran plot appearance : -0.252 chi-1/chi-2 rotamer normality : -0.457 Backbone conformation : 0.749
Bond lengths : 0.244 (tight) Bond angles : 0.509 (tight) Omega angle restraints : 0.200 (tight) Side chain planarity : 0.197 (tight) Improper dihedral distribution : 0.527 B-factor distribution : 1.514 (loose) Inside/Outside distribution : 1.006
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 : 2.20
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.9 2nd generation packing quality : -0.4 Ramachandran plot appearance : 0.9 chi-1/chi-2 rotamer normality : 0.7 Backbone conformation : 0.7
Bond lengths : 0.244 (tight) Bond angles : 0.509 (tight) Omega angle restraints : 0.200 (tight) Side chain planarity : 0.197 (tight) Improper dihedral distribution : 0.527 B-factor distribution : 1.514 (loose) Inside/Outside distribution : 1.006 ==============
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.