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.
155 1PG ( 300-) 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: 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) :298.000
Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
Chain identifier: A
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: 0.255
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.
148 ILE ( 158-) A N CA C 97.89 -4.8
RMS Z-score for bond angles: 0.627
RMS-deviation in bond angles: 1.353
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.
100 PHE ( 110-) A 5.31 148 ILE ( 158-) A 4.79 138 GLY ( 148-) A 4.20 122 LYS ( 132-) A 4.05 99 GLN ( 109-) A 4.01
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.
109 ARG ( 119-) A -2.2
Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.
2 LEU ( 7-) A Poor phi/psi 25 ASN ( 30-) A Poor phi/psi 60 PRO ( 70-) A Poor phi/psi 109 ARG ( 119-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -1.015
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.
98 SER ( 108-) A 0.33 128 SER ( 138-) A 0.40
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!
4 PRO ( 9-) A 0 6 TRP ( 11-) A 0 9 ARG ( 14-) A 0 12 ARG ( 17-) A 0 13 SER ( 18-) A 0 14 SER ( 19-) A 0 22 HIS ( 27-) A 0 25 ASN ( 30-) A 0 33 SER ( 38-) A 0 34 GLY ( 39-) A 0 35 GLY ( 45-) A 0 36 LYS ( 46-) A 0 37 ASN ( 47-) A 0 39 GLN ( 49-) A 0 43 ALA ( 53-) A 0 49 HIS ( 59-) A 0 54 HIS ( 64-) A 0 59 ARG ( 69-) A 0 60 PRO ( 70-) A 0 61 SER ( 71-) A 0 63 TRP ( 73-) A 0 64 ARG ( 74-) A 0 65 GLN ( 75-) A 0 66 GLU ( 76-) A 0 69 THR ( 79-) A 0And so on for a total of 71 lines.
Standard deviation of omega values : 1.356
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.
118 GLY ( 128-) A N <-> 125 GLU ( 135-) A OE1 0.30 2.40 INTRA 1 LYS ( 6-) A CD <-> 2 LEU ( 7-) A N 0.27 2.73 INTRA BF 84 GLN ( 94-) A NE2 <-> 156 HOH ( 517 ) A O 0.24 2.46 INTRA 75 ALA ( 85-) A CB <-> 156 HOH ( 469 ) A O 0.22 2.58 INTRA BF 59 ARG ( 69-) A O <-> 61 SER ( 71-) A N 0.21 2.49 INTRA BF 107 LYS ( 117-) A NZ <-> 156 HOH ( 467 ) A O 0.20 2.50 INTRA BF 44 ARG ( 54-) A NH1 <-> 156 HOH ( 486 ) A O 0.19 2.51 INTRA BF 57 SER ( 67-) A N <-> 156 HOH ( 527 ) A O 0.18 2.52 INTRA BF 70 ARG ( 80-) A CG <-> 156 HOH ( 469 ) A O 0.17 2.63 INTRA BF 80 ASN ( 90-) A ND2 <-> 156 HOH ( 505 ) A O 0.17 2.53 INTRA 57 SER ( 67-) A C <-> 59 ARG ( 69-) A N 0.17 2.73 INTRA BF 104 SER ( 114-) A C <-> 106 ALA ( 116-) A N 0.17 2.73 INTRA 93 PHE ( 103-) A N <-> 156 HOH ( 424 ) A O 0.17 2.53 INTRA BL 54 HIS ( 64-) A CB <-> 156 HOH ( 469 ) A O 0.16 2.64 INTRA BF 53 LYS ( 63-) A NZ <-> 154 SO4 ( 400-) A S 0.15 3.15 INTRA 154 SO4 ( 400-) A S <-> 156 HOH ( 516 ) A O 0.14 2.86 INTRA 71 THR ( 81-) A N <-> 74 GLU ( 84-) A OE1 0.13 2.57 INTRA 87 LYS ( 97-) A NZ <-> 156 HOH ( 417 ) A O 0.12 2.58 INTRA 144 SER ( 154-) A CA <-> 156 HOH ( 464 ) A O 0.12 2.68 INTRA 57 SER ( 67-) A O <-> 59 ARG ( 69-) A N 0.12 2.58 INTRA BF 40 GLY ( 50-) A N <-> 156 HOH ( 479 ) A O 0.11 2.59 INTRA BF 58 ARG ( 68-) A NH2 <-> 156 HOH ( 516 ) A O 0.11 2.59 INTRA BF 53 LYS ( 63-) A NZ <-> 154 SO4 ( 400-) A O3 0.10 2.60 INTRA 53 LYS ( 63-) A NZ <-> 61 SER ( 71-) A O 0.09 2.61 INTRA 41 GLU ( 51-) A OE2 <-> 117 ARG ( 127-) A NE 0.09 2.61 INTRAAnd so on for a total of 61 lines.
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.
12 ARG ( 17-) A -7.05 58 ARG ( 68-) A -6.86 36 LYS ( 46-) A -6.06 64 ARG ( 74-) A -5.98 59 ARG ( 69-) A -5.81 39 GLN ( 49-) A -5.79 117 ARG ( 127-) A -5.08 99 GLN ( 109-) A -5.02
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.
156 HOH ( 441 ) A O 156 HOH ( 506 ) A O
25 ASN ( 30-) A 28 GLN ( 33-) 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.
31 ARG ( 36-) A NH1 33 SER ( 38-) A N 33 SER ( 38-) A OG 37 ASN ( 47-) A N 73 GLU ( 83-) A N 94 GLU ( 104-) A N 105 SER ( 115-) A OG 142 THR ( 152-) A OG1
77 GLU ( 87-) A H-bonding suggests Gln 91 GLU ( 101-) 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 : -1.518 2nd generation packing quality : -0.459 Ramachandran plot appearance : 0.061 chi-1/chi-2 rotamer normality : -1.015 Backbone conformation : -0.410
Bond lengths : 0.255 (tight) Bond angles : 0.627 (tight) Omega angle restraints : 0.247 (tight) Side chain planarity : 0.245 (tight) Improper dihedral distribution : 0.529 B-factor distribution : 0.511 Inside/Outside distribution : 0.967
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 : -1.1 2nd generation packing quality : -0.6 Ramachandran plot appearance : 0.5 chi-1/chi-2 rotamer normality : -0.4 Backbone conformation : -0.8
Bond lengths : 0.255 (tight) Bond angles : 0.627 (tight) Omega angle restraints : 0.247 (tight) Side chain planarity : 0.245 (tight) Improper dihedral distribution : 0.529 B-factor distribution : 0.511 Inside/Outside distribution : 0.967 ==============
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.