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.
345 ATP ( 368-) 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.
223 GLU ( 228-) A 0.50 302 ARG ( 324-) A 0.50
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) :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: Arginine nomenclature problem
The arginine residues listed in the table below have their N-H-1 and N-H-2
158 ARG ( 163-) A
34 PHE ( 36-) A 122 PHE ( 127-) A 153 PHE ( 158-) A 300 PHE ( 322-) A
42 ASP ( 44-) A 157 ASP ( 162-) A 197 ASP ( 202-) A 253 ASP ( 275-) A
14 GLU ( 16-) A 223 GLU ( 228-) A 225 GLU ( 230-) A 245 GLU ( 267-) A 293 GLU ( 315-) 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.
183 ASN ( 188-) A CB CG 1.40 -4.5 233 VAL ( 238-) A CA CB 1.62 4.6 244 VAL ( 249-) A CA CB 1.61 4.2 265 VAL ( 287-) A CA CB 1.61 4.2
There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.
Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.
If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.
Unit Cell deformation matrix
| 0.999741 -0.000898 -0.001883| | -0.000898 0.997522 0.000877| | -0.001883 0.000877 0.996752|Proposed new scale matrix
| 0.012019 0.000011 0.000023| | 0.000011 0.012046 -0.000011| | 0.000019 -0.000009 0.010328|With corresponding cell
A = 83.201 B = 83.016 C = 96.829 Alpha= 89.899 Beta= 90.216 Gamma= 90.103
The CRYST1 cell dimensions
A = 83.225 B = 83.225 C = 97.143 Alpha= 90.000 Beta= 90.000 Gamma= 90.000
(Under-)estimated Z-score: 5.946
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.
15 HIS ( 17-) A CG ND1 CE1 109.72 4.1 253 ASP ( 275-) A C CA CB 101.11 -4.7 285 ALA ( 307-) A N CA C 94.67 -5.9 286 ASP ( 308-) A N CA C 129.59 6.6 287 GLY ( 309-) A -C N CA 137.16 9.7 336 GLN ( 358-) A C CA CB 102.16 -4.2 340 SER ( 362-) A -C N CA 130.13 4.7
14 GLU ( 16-) A 42 ASP ( 44-) A 157 ASP ( 162-) A 158 ARG ( 163-) A 197 ASP ( 202-) A 223 GLU ( 228-) A 225 GLU ( 230-) A 245 GLU ( 267-) A 253 ASP ( 275-) A 293 GLU ( 315-) A
285 ALA ( 307-) A 6.94 286 ASP ( 308-) A 6.20 339 ARG ( 361-) A 4.97 318 ARG ( 340-) A 4.55
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.
147 ARG ( 152-) A -2.6 342 VAL ( 364-) A -2.4 175 LEU ( 180-) A -2.4 303 ILE ( 325-) A -2.3 246 ILE ( 268-) A -2.2 2 ILE ( 4-) A -2.1 99 PRO ( 104-) A -2.1 286 ASP ( 308-) A -2.1 88 ILE ( 90-) A -2.0 96 VAL ( 101-) 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.
7 ILE ( 9-) A omega poor 12 SER ( 14-) A omega poor 36 PRO ( 38-) A omega poor 107 GLU ( 112-) A omega poor 119 ASN ( 124-) A Poor phi/psi 147 ARG ( 152-) A Poor phi/psi 152 PRO ( 157-) A omega poor 156 PHE ( 161-) A omega poor 160 THR ( 165-) A Poor phi/psi 175 LEU ( 180-) A PRO omega poor 231 ASN ( 236-) A Poor phi/psi 237 SER ( 242-) A omega poor 248 ILE ( 270-) A PRO omega poor 276 MET ( 298-) A omega poor 286 ASP ( 308-) A Poor phi/psi, omega poor 293 GLU ( 315-) A omega poor 342 VAL ( 364-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -3.565
chi-1/chi-2 correlation Z-score : -3.565
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!
8 PHE ( 10-) A 0 11 LYS ( 13-) A 0 12 SER ( 14-) A 0 33 ARG ( 35-) A 0 43 LYS ( 45-) A 0 44 GLN ( 46-) A 0 54 SER ( 56-) A 0 55 PHE ( 57-) A 0 57 LEU ( 59-) A 0 64 ARG ( 66-) A 0 65 ILE ( 67-) A 0 69 ARG ( 71-) A 0 70 SER ( 72-) A 0 72 ARG ( 74-) A 0 78 PRO ( 80-) A 0 81 GLN ( 83-) A 0 82 GLN ( 84-) A 0 83 GLN ( 85-) A 0 84 GLN ( 86-) A 0 85 LEU ( 87-) A 0 88 ILE ( 90-) A 0 89 GLN ( 91-) A 0 90 ALA ( 95-) A 0 91 LEU ( 96-) A 0 99 PRO ( 104-) A 0And so on for a total of 112 lines.
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!
73 GLY ( 75-) A 1.65 12
62 PRO ( 64-) A 0.16 LOW 78 PRO ( 80-) A 0.17 LOW 121 PRO ( 126-) A 0.09 LOW
152 PRO ( 157-) A -122.1 half-chair C-delta/C-gamma (-126 degrees) 176 PRO ( 181-) A 24.2 half-chair N/C-delta (18 degrees) 181 PRO ( 186-) A -45.1 half-chair C-beta/C-alpha (-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.
285 ALA ( 307-) A O <-> 286 ASP ( 308-) A CG 0.41 2.29 INTRA BF 222 ARG ( 227-) A NH1 <-> 241 GLU ( 246-) A OE1 0.37 2.33 INTRA BF 285 ALA ( 307-) A N <-> 346 HOH ( 462 ) A O 0.34 2.36 INTRA BF 48 HIS ( 50-) A CD2 <-> 71 GLY ( 73-) A N 0.33 2.77 INTRA 140 LYS ( 145-) A CE <-> 216 GLU ( 221-) A OE2 0.31 2.49 INTRA BL 341 ALA ( 363-) A O <-> 342 VAL ( 364-) A CB 0.30 2.30 INTRA BF 219 VAL ( 224-) A N <-> 345 ATP ( 368-) A N1 0.29 2.71 INTRA BL 337 LEU ( 359-) A O <-> 340 SER ( 362-) A CB 0.28 2.52 INTRA BF 333 THR ( 355-) A O <-> 337 LEU ( 359-) A CD1 0.28 2.52 INTRA BF 15 HIS ( 17-) A NE2 <-> 346 HOH ( 452 ) A O 0.25 2.45 INTRA 285 ALA ( 307-) A O <-> 286 ASP ( 308-) A CB 0.22 2.38 INTRA BF 180 LYS ( 185-) A NZ <-> 345 ATP ( 368-) A N7 0.22 2.78 INTRA BL 140 LYS ( 145-) A NZ <-> 151 ALA ( 156-) A O 0.21 2.49 INTRA BL 293 GLU ( 315-) A OE2 <-> 295 ASN ( 317-) A ND2 0.18 2.52 INTRA BF 284 CYS ( 306-) A C <-> 285 ALA ( 307-) A C 0.16 2.64 INTRA BF 258 GLN ( 280-) A O <-> 262 GLN ( 284-) A CG 0.14 2.66 INTRA BF 222 ARG ( 227-) A NH1 <-> 241 GLU ( 246-) A CD 0.13 2.97 INTRA BF 188 VAL ( 193-) A CG2 <-> 209 TYR ( 214-) A CE1 0.13 3.07 INTRA BF 169 LEU ( 174-) A O <-> 173 LEU ( 178-) A N 0.13 2.57 INTRA BL 24 ASN ( 26-) A ND2 <-> 346 HOH ( 444 ) A O 0.13 2.57 INTRA BF 339 ARG ( 361-) A N <-> 340 SER ( 362-) A N 0.13 2.47 INTRA BF 140 LYS ( 145-) A NZ <-> 346 HOH ( 416 ) A O 0.12 2.58 INTRA BL 339 ARG ( 361-) A CD <-> 346 HOH ( 440 ) A O 0.12 2.68 INTRA BF 188 VAL ( 193-) A CG2 <-> 209 TYR ( 214-) A CD1 0.12 3.08 INTRA BF 11 LYS ( 13-) A CG <-> 43 LYS ( 45-) A O 0.12 2.68 INTRA BFAnd so on for a total of 56 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.
194 ARG ( 199-) A -6.98 81 GLN ( 83-) A -6.39 69 ARG ( 71-) A -6.37 11 LYS ( 13-) A -5.81 159 HIS ( 164-) A -5.73 172 GLN ( 177-) A -5.65 82 GLN ( 84-) A -5.64 88 ILE ( 90-) 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.
297 LEU ( 319-) A -2.69 89 GLN ( 91-) A -2.54
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 ASN ( 188-) A - 186 SER ( 191-) A -1.63
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.
346 HOH ( 486 ) A O 346 HOH ( 487 ) A O
48 HIS ( 50-) A 68 HIS ( 70-) A 183 ASN ( 188-) A 257 GLN ( 279-) A 311 GLN ( 333-) A 336 GLN ( 358-) 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.
91 LEU ( 96-) A N 162 ALA ( 167-) A N 163 HIS ( 168-) A N 166 VAL ( 171-) A N 167 ASP ( 172-) A N 180 LYS ( 185-) A NZ 185 GLY ( 190-) A N 211 HIS ( 216-) A N 212 LYS ( 217-) A N 219 VAL ( 224-) A N 251 ASP ( 273-) A N 256 THR ( 278-) A N 339 ARG ( 361-) A NE
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.
293 GLU ( 315-) A OE1
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+.
344 MG ( 369-) A 0.30 1.07 Is perhaps K
108 ASP ( 113-) A H-bonding suggests Asn; but Alt-Rotamer 286 ASP ( 308-) A H-bonding suggests Asn
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 : 0.537 2nd generation packing quality : -0.446 Ramachandran plot appearance : 0.115 chi-1/chi-2 rotamer normality : -3.565 (poor) Backbone conformation : 0.872
Bond lengths : 1.014 Bond angles : 0.980 Omega angle restraints : 1.148 Side chain planarity : 0.860 Improper dihedral distribution : 1.132 B-factor distribution : 0.589 Inside/Outside distribution : 1.021
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 : 2.07
Structure Z-scores, positive is better than average:
1st generation packing quality : 1.0 2nd generation packing quality : -0.3 Ramachandran plot appearance : 0.8 chi-1/chi-2 rotamer normality : -2.2 Backbone conformation : 0.9
Bond lengths : 1.014 Bond angles : 0.980 Omega angle restraints : 1.148 Side chain planarity : 0.860 Improper dihedral distribution : 1.132 B-factor distribution : 0.589 Inside/Outside distribution : 1.021 ==============
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.