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.
498 B0D ( 503-) A - 501 B0D ( 504-) A - 502 BGC ( 502-) A - 503 B9D ( 501-) A -
For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.
197 ASP ( 197-) A - OD2 bound to 503 B9D ( 501-) A - C1
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: Tyrosine convention problem
The tyrosine residues listed in the table below have their chi-2 not between
-90.0 and 90.0
333 TYR ( 333-) A
315 PHE ( 315-) A
197 ASP ( 197-) A 472 ASP ( 472-) A
272 GLU ( 272-) A 369 GLU ( 369-) A
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.
197 ASP ( 197-) A CG OD2 1.24 -4.0
RMS Z-score for bond lengths: 0.274
RMS-deviation in bond distances: 0.006
Warning: Low bond angle variability
Bond angles were found to deviate less than normal from the 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. 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 angles: 0.549
RMS-deviation in bond angles: 1.102
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.
197 ASP ( 197-) A 272 GLU ( 272-) A 369 GLU ( 369-) A 472 ASP ( 472-) 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.
376 THR ( 376-) A -2.9 124 ARG ( 124-) A -2.6 459 ASN ( 459-) A -2.6 142 LYS ( 142-) A -2.4 239 GLY ( 239-) A -2.4 270 ASN ( 270-) A -2.4 273 LYS ( 273-) A -2.3 457 LYS ( 457-) A -2.3 347 GLN ( 347-) A -2.3 341 SER ( 341-) A -2.2 414 SER ( 414-) A -2.1 89 VAL ( 89-) A -2.1 438 LEU ( 438-) A -2.0 407 THR ( 407-) A -2.0 401 VAL ( 401-) A -2.0 66 SER ( 66-) A -2.0 444 LEU ( 444-) A -2.0 427 ILE ( 427-) A -2.0 56 ARG ( 56-) A -2.0 243 LYS ( 243-) A -2.0 69 LEU ( 69-) A -2.0
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.
5 ASN ( 5-) A Poor phi/psi 18 GLU ( 18-) A Poor phi/psi 53 ASN ( 53-) A PRO omega poor 102 MET ( 102-) A Poor phi/psi 124 ARG ( 124-) A Poor phi/psi 129 VAL ( 129-) A PRO omega poor 237 LEU ( 237-) A Poor phi/psi 239 GLY ( 239-) A Poor phi/psi 268 LYS ( 268-) A Poor phi/psi 350 ASN ( 350-) A Poor phi/psi 364 ASN ( 364-) A Poor phi/psi 376 THR ( 376-) A Poor phi/psi 380 ASN ( 380-) A Poor phi/psi 381 ASP ( 381-) A Poor phi/psi 414 SER ( 414-) A Poor phi/psi 486 PRO ( 486-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -2.661
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!
5 ASN ( 5-) A 0 8 GLN ( 8-) A 0 12 SER ( 12-) A 0 17 PHE ( 17-) A 0 18 GLU ( 18-) A 0 19 TRP ( 19-) A 0 30 ARG ( 30-) A 0 37 PHE ( 37-) A 0 45 PRO ( 45-) A 0 52 TYR ( 52-) A 0 53 ASN ( 53-) A 0 54 PRO ( 54-) A 0 55 PHE ( 55-) A 0 56 ARG ( 56-) A 0 58 TRP ( 58-) A 0 59 TRP ( 59-) A 0 62 TYR ( 62-) A 0 63 GLN ( 63-) A 0 64 PRO ( 64-) A 0 66 SER ( 66-) A 0 67 TYR ( 67-) A 0 69 LEU ( 69-) A 0 70 CYS ( 70-) A 0 73 SER ( 73-) A 0 75 ASN ( 75-) A 0And so on for a total of 229 lines.
Standard deviation of omega values : 2.093
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!
238 GLY ( 238-) A 1.92 10 110 GLY ( 110-) A 1.52 19
45 PRO ( 45-) A -59.8 half-chair C-beta/C-alpha (-54 degrees) 130 PRO ( 130-) A -37.1 envelop C-alpha (-36 degrees) 241 PRO ( 241-) A -112.1 envelop C-gamma (-108 degrees) 374 PRO ( 374-) A -115.1 envelop C-gamma (-108 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.
197 ASP ( 197-) A OD2 <-> 503 B9D ( 501-) A C1 1.01 1.39 INTRA B3 197 ASP ( 197-) A CG <-> 503 B9D ( 501-) A C1 0.90 2.30 INTRA 147 ASP ( 147-) A OD1 <-> 161 ARG ( 161-) A NH1 0.22 2.48 INTRA 200 LYS ( 200-) A NZ <-> 240 GLU ( 240-) A OE2 0.19 2.51 INTRA 216 ASN ( 216-) A ND2 <-> 227 LYS ( 227-) A NZ 0.18 2.67 INTRA 349 GLN ( 349-) A O <-> 352 ASN ( 352-) A ND2 0.17 2.53 INTRA 307 ALA ( 307-) A N <-> 504 HOH ( 668 ) A O 0.15 2.55 INTRA BF 243 LYS ( 243-) A NZ <-> 246 ASP ( 246-) A OD1 0.14 2.56 INTRA 200 LYS ( 200-) A CE <-> 240 GLU ( 240-) A OE2 0.12 2.68 INTRA 80 ARG ( 80-) A NH2 <-> 504 HOH ( 708 ) A O 0.12 2.58 INTRA 213 LYS ( 213-) A NZ <-> 504 HOH ( 686 ) A O 0.12 2.58 INTRA 218 ASN ( 218-) A ND2 <-> 220 ASN ( 220-) A CB 0.11 2.99 INTRA BL 269 TRP ( 269-) A C <-> 270 ASN ( 270-) A CG 0.10 3.00 INTRA 140 LYS ( 140-) A NZ <-> 504 HOH ( 632 ) A O 0.10 2.60 INTRA 337 ARG ( 337-) A NH2 <-> 500 CL ( 498-) A CL 0.09 3.01 INTRA BL 218 ASN ( 218-) A ND2 <-> 220 ASN ( 220-) A N 0.09 2.76 INTRA BL 410 TYR ( 410-) A CG <-> 411 ASP ( 411-) A N 0.09 2.91 INTRA 195 ARG ( 195-) A NH2 <-> 233 GLU ( 233-) A CD 0.08 3.02 INTRA 216 ASN ( 216-) A N <-> 504 HOH ( 612 ) A O 0.08 2.62 INTRA 201 HIS ( 201-) A NE2 <-> 504 HOH ( 730 ) A O 0.08 2.62 INTRA 33 ALA ( 33-) A N <-> 34 PRO ( 34-) A CD 0.08 2.92 INTRA 75 ASN ( 75-) A N <-> 78 GLU ( 78-) A OE1 0.08 2.62 INTRA 124 ARG ( 124-) A NH2 <-> 138 ASP ( 138-) A OD1 0.07 2.63 INTRA 458 ILE ( 458-) A C <-> 459 ASN ( 459-) A CG 0.07 3.03 INTRA BF 158 ARG ( 158-) A NH2 <-> 504 HOH ( 652 ) A O 0.07 2.63 INTRAAnd so on for a total of 57 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.
72 ARG ( 72-) A -6.96 8 GLN ( 8-) A -6.22 343 ARG ( 343-) A -6.11 2 TYR ( 2-) A -6.00 52 TYR ( 52-) A -5.94 237 LEU ( 237-) A -5.80 142 LYS ( 142-) A -5.75 118 TYR ( 118-) A -5.51 284 TRP ( 284-) A -5.41 279 ASN ( 279-) A -5.36 7 GLN ( 7-) A -5.32 269 TRP ( 269-) A -5.32 270 ASN ( 270-) A -5.32 88 ASN ( 88-) A -5.31 302 GLN ( 302-) A -5.25 30 ARG ( 30-) A -5.25 303 ARG ( 303-) A -5.24 53 ASN ( 53-) A -5.08 349 GLN ( 349-) A -5.03
The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.
269 TRP ( 269-) A 271 - GLY 271- ( A) -4.92
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
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.
504 HOH ( 808 ) A O -7.85 42.06 32.72
105 ASN ( 105-) A 150 ASN ( 150-) A 152 ASN ( 152-) A 185 HIS ( 185-) A 216 ASN ( 216-) A 218 ASN ( 218-) A 415 ASN ( 415-) 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.
23 ASP ( 23-) A N 59 TRP ( 59-) A N 87 ASN ( 87-) A ND2 101 HIS ( 101-) A N 142 LYS ( 142-) A N 193 GLY ( 193-) A N 195 ARG ( 195-) A NH1 195 ARG ( 195-) A NH2 273 LYS ( 273-) A N 281 GLY ( 281-) A N 295 PHE ( 295-) A N 299 HIS ( 299-) A NE2 300 ASP ( 300-) A N 306 GLY ( 306-) A N 316 TRP ( 316-) A NE1 337 ARG ( 337-) A NH2 344 TRP ( 344-) A N 357 TRP ( 357-) A N 370 VAL ( 370-) A N 434 TRP ( 434-) A N Only metal coordination for 100 ASN ( 100-) A OD1
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.
15 HIS ( 15-) A NE2 250 ASN ( 250-) A OD1 300 ASP ( 300-) A OD1
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+.
499 CA ( 497-) A 0.82 1.06 Scores about as good as NA
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.
504 HOH ( 554 ) A O 1.00 K 4 504 HOH ( 569 ) A O 1.05 K 4 504 HOH ( 713 ) A O 0.99 K 4 ION-B
236 ASP ( 236-) A H-bonding suggests Asn; but Alt-Rotamer
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 : -0.876 2nd generation packing quality : -1.277 Ramachandran plot appearance : -1.496 chi-1/chi-2 rotamer normality : -2.661 Backbone conformation : -1.326
Bond lengths : 0.274 (tight) Bond angles : 0.549 (tight) Omega angle restraints : 0.381 (tight) Side chain planarity : 0.143 (tight) Improper dihedral distribution : 0.611 B-factor distribution : 0.466 Inside/Outside distribution : 1.007
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 : 1.85
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.3 2nd generation packing quality : -1.0 Ramachandran plot appearance : -1.9 chi-1/chi-2 rotamer normality : -2.3 Backbone conformation : -1.4
Bond lengths : 0.274 (tight) Bond angles : 0.549 (tight) Omega angle restraints : 0.381 (tight) Side chain planarity : 0.143 (tight) Improper dihedral distribution : 0.611 B-factor distribution : 0.466 Inside/Outside distribution : 1.007 ==============
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.