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.
The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.
273 SO4 ( 901-) A - OK 274 SO4 ( 902-) A - OK 275 ANP ( 904-) A - 276 SO4 ( 903-) A - OK 277 EDO ( 905-) A - OK
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: Missing atoms
The atoms listed in the table below are missing from the entry. If many atoms
are missing, the other checks can become less sensitive. Be aware that it
often happens that groups at the termini of DNA or RNA are really missing,
so that the absence of these atoms normally is neither an error nor the
result of poor electron density. Some of the atoms listed here might also be
listed by other checks, most noticeably by the options in the previous
section that list missing atoms in several categories. The plausible atoms
with zero occupancy are not listed here, as they already got assigned a
non-zero occupancy, and thus are no longer 'missing'.
47 GLN ( 277-) A CG 47 GLN ( 277-) A CD 47 GLN ( 277-) A OE1 47 GLN ( 277-) A NE2 79 GLN ( 309-) A CG 79 GLN ( 309-) A CD 79 GLN ( 309-) A OE1 79 GLN ( 309-) A NE2 167 ARG ( 397-) A CG 167 ARG ( 397-) A CD 167 ARG ( 397-) A NE 167 ARG ( 397-) A CZ 167 ARG ( 397-) A NH1 167 ARG ( 397-) A NH2 171 LYS ( 401-) A CG 171 LYS ( 401-) A CD 171 LYS ( 401-) A CE 171 LYS ( 401-) A NZ
In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. In many cases the N- or C-terminal residues are too disordered to see. In case of the N-terminus, you can see from the residue numbers if there are missing residues, but at the C-terminus this is impossible. Therefore, often the position of the backbone nitrogen of the first residue missing at the C-terminal end is calculated and added to indicate that there are missing residues. As a single N causes validation trouble, we remove these single-N-residues before doing the validation. But, if you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or removed N is the cause.
272 GLU ( 502-) A
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.
17 LEU ( 247-) A 0.60 29 VAL ( 259-) A 0.77 37 HIS ( 267-) A 0.49 44 SER ( 274-) A 0.65 52 PRO ( 282-) A 0.51 76 VAL ( 306-) A 0.75 84 ILE ( 314-) A 0.82 93 SER ( 323-) A 0.43 98 LEU ( 328-) A 0.40 127 GLU ( 357-) A 0.36 191 SER ( 421-) A 0.84 195 SER ( 425-) A 0.74 208 ARG ( 438-) A 0.58 210 PRO ( 440-) A 0.43 220 ILE ( 450-) A 0.60 238 GLU ( 468-) A 0.51 262 SER ( 492-) A 0.71
Obviously, the temperature at which the X-ray data was collected has some importance too:
Crystal temperature (K) :100.000
Warning: More than 5 percent of buried atoms has low B-factor
For normal protein structures, no more than about 1 percent of the B factors
of buried atoms is below 5.0. The fact that this value is much higher in the
current structure could be a signal that the B-factors were restraints or
constraints to too-low values, misuse of B-factor field in the PDB file, or
a TLS/scaling problem. If the average B factor is low too, it is probably a
low temperature structure determination.
Percentage of buried atoms with B less than 5 : 18.40
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: Glutamic acid convention problem
The glutamic acid residues listed in the table below have their chi-3
outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.
163 GLU ( 393-) A 238 GLU ( 468-) 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.
159 ILE ( 389-) 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
| 0.994819 -0.000138 -0.000621| | -0.000138 0.994067 0.000227| | -0.000621 0.000227 1.001723|Proposed new scale matrix
| 0.023871 0.000003 0.000015| | 0.000002 0.013648 -0.000003| | 0.000007 -0.000002 0.010885|With corresponding cell
A = 41.892 B = 73.271 C = 91.867 Alpha= 89.974 Beta= 90.071 Gamma= 90.016
The CRYST1 cell dimensions
A = 42.110 B = 73.710 C = 91.710 Alpha= 90.000 Beta= 90.000 Gamma= 90.000
(Under-)estimated Z-score: 8.425
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.
67 HIS ( 297-) A CG ND1 CE1 110.59 5.0 132 HIS ( 362-) A CG ND1 CE1 110.42 4.8 159 ILE ( 389-) A C CA CB 121.17 5.8 160 GLU ( 390-) A CA CB CG 104.07 -5.0 163 GLU ( 393-) A N CA C 123.41 4.4 163 GLU ( 393-) A N CA CB 103.65 -4.0 206 HIS ( 436-) A CG ND1 CE1 110.00 4.4
163 GLU ( 393-) A 238 GLU ( 468-) A
18 VAL ( 248-) A 4.34 163 GLU ( 393-) A 4.08
258 ASP ( 488-) A 4.10
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.
159 ILE ( 389-) A -2.4 189 ILE ( 419-) 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.
80 GLU ( 310-) A PRO omega poor 129 ASN ( 359-) A Poor phi/psi 133 ARG ( 363-) A Poor phi/psi 146 LEU ( 376-) A Poor phi/psi 152 ASP ( 382-) A Poor phi/psi 166 ALA ( 396-) A Poor phi/psi chi-1/chi-2 correlation Z-score : 0.395
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.
102 SER ( 332-) A 0.36
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 TRP ( 238-) A 0 26 PHE ( 256-) A 0 30 TRP ( 260-) A 0 31 MET ( 261-) A 0 34 TYR ( 264-) A 0 37 HIS ( 267-) A 0 47 GLN ( 277-) A 0 49 SER ( 279-) A 0 50 MET ( 280-) A 0 64 GLN ( 294-) A 0 65 LEU ( 295-) A 0 66 GLN ( 296-) A 0 67 HIS ( 297-) A 0 74 TYR ( 304-) A 0 75 ALA ( 305-) A 0 79 GLN ( 309-) A 0 80 GLU ( 310-) A 0 82 ILE ( 312-) A 0 91 ASN ( 321-) A 0 129 ASN ( 359-) A 0 132 HIS ( 362-) A 0 133 ARG ( 363-) A 0 134 ASP ( 364-) A 0 135 LEU ( 365-) A 0 136 ARG ( 366-) A 0And so on for a total of 88 lines.
Standard deviation of omega values : 3.005
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.
114 MET ( 344-) A SD <-> 277 HOH (1132 ) A O 0.65 2.35 INTRA 229 MET ( 459-) A SD <-> 277 HOH (1145 ) A O 0.57 2.43 INTRA 156 ALA ( 386-) A O <-> 277 HOH (1104 ) A O 0.27 2.13 INTRA 161 ASP ( 391-) A N <-> 277 HOH (1086 ) A O 0.23 2.47 INTRA 164 PTR ( 394-) A O1P <-> 277 HOH (1052 ) A O 0.23 2.17 INTRA 222 ASN ( 452-) A ND2 <-> 277 HOH ( 993 ) A O 0.19 2.51 INTRA 114 MET ( 344-) A CB <-> 277 HOH (1132 ) A O 0.13 2.67 INTRA 249 GLU ( 479-) A OE1 <-> 277 HOH (1138 ) A O 0.11 2.29 INTRA 179 PRO ( 409-) A CB <-> 275 SO4 ( 903-) A O1 0.10 2.70 INTRA 161 ASP ( 391-) A O <-> 163 GLU ( 393-) A N 0.10 2.60 INTRA 105 LYS ( 335-) A NZ <-> 277 HOH (1026 ) A O 0.07 2.63 INTRA 244 ARG ( 474-) A NH2 <-> 277 HOH (1136 ) A O 0.06 2.64 INTRA 37 HIS ( 267-) A CD2 <-> 277 HOH ( 942 ) A O 0.06 2.74 INTRA BL 16 LYS ( 246-) A NZ <-> 277 HOH (1130 ) A O 0.05 2.65 INTRA 167 ARG ( 397-) A O <-> 170 ALA ( 400-) A N 0.04 2.66 INTRA 99 LYS ( 329-) A NZ <-> 277 HOH (1100 ) A O 0.04 2.66 INTRA 20 ARG ( 250-) A CZ <-> 277 HOH ( 980 ) A O 0.03 2.77 INTRA 3 TRP ( 233-) A O <-> 277 HOH (1077 ) A O 0.03 2.37 INTRA 67 HIS ( 297-) A ND1 <-> 69 ARG ( 299-) A N 0.02 2.98 INTRA BL 109 ASN ( 339-) A ND2 <-> 268 PHE ( 498-) A CE1 0.01 3.09 INTRA 89 MET ( 319-) A N <-> 274 ANP ( 904-) A N1 0.01 2.99 INTRA BL
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.
208 ARG ( 438-) A -6.03 80 GLU ( 310-) A -5.71 227 TYR ( 457-) A -5.52 183 ASN ( 413-) A -5.47 230 VAL ( 460-) A -5.12 209 ILE ( 439-) A -5.02
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.
47 GLN ( 277-) A -2.98 167 ARG ( 397-) A -2.68 171 LYS ( 401-) A -2.52
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.
277 HOH ( 913 ) A O 24.97 20.04 88.48 277 HOH ( 926 ) A O 28.29 53.13 78.90 277 HOH ( 941 ) A O 29.01 34.61 64.92 277 HOH ( 948 ) A O 25.95 56.77 57.38 277 HOH ( 951 ) A O 27.25 50.61 82.07 277 HOH ( 967 ) A O 1.89 40.24 77.12 277 HOH ( 982 ) A O 15.76 35.93 66.84 277 HOH ( 990 ) A O 22.58 52.46 54.43 277 HOH (1096 ) A O 27.84 55.69 55.71 277 HOH (1144 ) A O 38.95 39.82 77.37
277 HOH (1106 ) A O
37 HIS ( 267-) A 109 ASN ( 339-) A 162 ASN ( 392-) A 216 ASN ( 446-) A 222 ASN ( 452-) 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.
4 TRP ( 234-) A N 8 TRP ( 238-) A N 12 ARG ( 242-) A NH1 50 MET ( 280-) A N 68 GLN ( 298-) A NE2 69 ARG ( 299-) A NH2 89 MET ( 319-) A N 102 SER ( 332-) A N 109 ASN ( 339-) A N 133 ARG ( 363-) A NH1 136 ARG ( 366-) A N 147 SER ( 377-) A OG 228 ARG ( 458-) A N 231 ARG ( 461-) A NH2
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.
277 HOH (1041 ) A O 1.11 K 4 Ion-B
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 : -0.416 2nd generation packing quality : -1.001 Ramachandran plot appearance : 0.765 chi-1/chi-2 rotamer normality : 0.395 Backbone conformation : 0.028
Bond lengths : 0.728 Bond angles : 0.926 Omega angle restraints : 0.546 (tight) Side chain planarity : 1.200 Improper dihedral distribution : 1.333 Inside/Outside distribution : 1.014
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 : 1.60
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.2 2nd generation packing quality : -1.2 Ramachandran plot appearance : 0.4 chi-1/chi-2 rotamer normality : 0.1 Backbone conformation : -0.3
Bond lengths : 0.728 Bond angles : 0.926 Omega angle restraints : 0.546 (tight) Side chain planarity : 1.200 Improper dihedral distribution : 1.333 Inside/Outside distribution : 1.014 ==============
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.