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 Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.
Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).
Molecular weight of all polymer chains: 56395.039
Volume of the Unit Cell V= 959635.375
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 4.254
Vm by authors and this calculated Vm agree well
Matthews coefficient read from REMARK 280 Vm= 4.330
Warning: Ligands for which a topology was generated automatically
The topology for the ligands in the table below were determined
automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG
server to automatically generate topology information for ligands. For this
PDB file that seems to have gone fine, but be aware that automatic topology
generation is a complicated task. So, if you get messages that you fail to
understand or that you believe are wrong, and one of these ligands is
involved, then check the ligand topology first.
499 AC1 ( 990-) A - 500 BGC ( 993-) A - 503 BGC ( 996-) A - 504 AC1 ( 992-) 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.
497 GLC ( 991-) A - O4 bound to 499 AC1 ( 990-) A - C1
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.
347 ASN ( 347-) A 0.50 348 PHE ( 348-) A 0.50 349 VAL ( 349-) A 0.50 351 GLY ( 351-) A 0.50
Obviously, the temperature at which the X-ray data was collected has some importance too:
Temperature cannot be read from the PDB file. This most likely means that
the temperature is listed as NULL (meaning unknown) in the PDB file.
Warning: More than 2 percent of buried atoms has low B-factor
For protein structures determined at room temperature, no more than
about 1 percent of the B factors of buried atoms is below 5.0.
Percentage of buried atoms with B less than 5 : 2.39
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.
195 ARG ( 195-) A N CA C 99.76 -4.1 323 VAL ( 323-) A CA CB CG1 117.31 4.0 323 VAL ( 323-) A CA CB CG2 132.32 12.8
Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.
Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.
323 VAL ( 323-) A CB 14.8 -13.62 -32.96 The average deviation= 0.949
292 ALA ( 292-) A 4.69 336 THR ( 336-) A 4.61 195 ARG ( 195-) A 4.47 318 ALA ( 318-) A 4.45 382 TRP ( 382-) A 4.15 293 LEU ( 293-) A 4.02
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 -3.0 92 ARG ( 92-) A -2.3 163 VAL ( 163-) A -2.2 227 ARG ( 227-) A -2.2 56 ARG ( 56-) A -2.2 66 SER ( 66-) A -2.1 270 SER ( 270-) A -2.1 341 SER ( 341-) A -2.1 237 LEU ( 237-) A -2.1 69 LEU ( 69-) A -2.1 401 VAL ( 401-) 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.
5 GLN ( 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 221 TRP ( 221-) 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 : -1.974
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 GLN ( 5-) A 0 8 SER ( 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 35 LYS ( 35-) A 0 45 PRO ( 45-) A 0 48 ASN ( 48-) A 0 52 THR ( 52-) A 0 53 ASN ( 53-) A 0 54 PRO ( 54-) A 0 55 SER ( 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 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 216 lines.
Standard deviation of omega values : 1.496
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.
500 BGC ( 993-) A O4 <-> 504 AC1 ( 992-) A C1 1.00 1.40 INTRA B3 500 BGC ( 993-) A C4 <-> 504 AC1 ( 992-) A C1 0.78 2.42 INTRA 10 ARG ( 10-) A NH2 <-> 33 GLY ( 33-) A O 0.24 2.46 INTRA 404 GLU ( 404-) A O <-> 421 ARG ( 421-) A NH1 0.24 2.46 INTRA 195 ARG ( 195-) A NH1 <-> 501 CL ( 498-) A CL 0.20 2.90 INTRA BL 100 ASN ( 100-) A ND2 <-> 101 HIS ( 101-) A CD2 0.11 2.99 INTRA BL 11 THR ( 11-) A OG1 <-> 399 ASN ( 399-) A ND2 0.10 2.60 INTRA BL 170 LEU ( 170-) A O <-> 176 ARG ( 176-) A CD 0.09 2.71 INTRA BL 421 ARG ( 421-) A NH2 <-> 505 HOH (1069 ) A O 0.09 2.61 INTRA 158 ARG ( 158-) A NH1 <-> 247 TYR ( 247-) A OH 0.08 2.62 INTRA BL 214 LEU ( 214-) A O <-> 227 ARG ( 227-) A NH2 0.07 2.63 INTRA 103 CYS ( 103-) A SG <-> 121 PRO ( 121-) A CG 0.06 3.34 INTRA 291 ARG ( 291-) A N <-> 292 ALA ( 292-) A N 0.05 2.55 INTRA BL 389 ARG ( 389-) A NH1 <-> 453 ILE ( 453-) A O 0.05 2.65 INTRA 494 SER ( 494-) A N <-> 495 LYS ( 495-) A N 0.04 2.56 INTRA BL 201 HIS ( 201-) A NE2 <-> 504 AC1 ( 992-) A O2 0.03 2.67 INTRA 259 GLY ( 259-) A N <-> 505 HOH (1012 ) A O 0.02 2.68 INTRA 195 ARG ( 195-) A NH2 <-> 197 ASP ( 197-) A OD1 0.02 2.68 INTRA BL 337 ARG ( 337-) A NH2 <-> 501 CL ( 498-) A CL 0.02 3.08 INTRA BL
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 -6.98 7 GLN ( 7-) A -5.74 2 TYR ( 2-) A -5.64 118 TYR ( 118-) A -5.42 284 TRP ( 284-) A -5.38 30 ARG ( 30-) A -5.33 279 ASN ( 279-) A -5.32 88 ASN ( 88-) A -5.30 302 GLN ( 302-) A -5.29 343 ARG ( 343-) A -5.26 303 ARG ( 303-) A -5.24 53 ASN ( 53-) A -5.22 267 ARG ( 267-) A -5.12
The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.
235 ILE ( 235-) A - 238 GLY ( 238-) A -1.86
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.
506 HOH (1240 ) A O 54.12 28.39 10.72 507 HOH (1271 ) A O 46.84 -1.07 31.08 507 HOH (1366 ) A O 22.99 44.01 -10.18 507 HOH (1382 ) A O 40.20 36.17 -9.55
507 HOH (1279 ) A O 507 HOH (1304 ) A O 507 HOH (1375 ) A O 507 HOH (1380 ) A O 507 HOH (1382 ) A O 507 HOH (1396 ) A O Marked this atom as acceptor 501 CL ( 498-) A CL Strange metal coordination for HIS 201
15 HIS ( 15-) A 101 HIS ( 101-) A 152 ASN ( 152-) A 279 ASN ( 279-) A 373 ASN ( 373-) A 399 ASN ( 399-) A 408 ASN ( 408-) A 435 GLN ( 435-) 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.
59 TRP ( 59-) A N 87 ASN ( 87-) A ND2 101 HIS ( 101-) A N 158 ARG ( 158-) A NE 175 VAL ( 175-) A N 193 GLY ( 193-) A N 195 ARG ( 195-) A NH1 241 ALA ( 241-) A N 273 LYS ( 273-) A N 281 GLY ( 281-) A N 295 PHE ( 295-) A N 299 HIS ( 299-) A NE2 308 GLY ( 308-) A N 314 THR ( 314-) A N 316 TRP ( 316-) A NE1 337 ARG ( 337-) A NH2 344 TRP ( 344-) A N 364 ASN ( 364-) A ND2 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.
201 HIS ( 201-) A NE2 300 ASP ( 300-) A OD1
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.
505 HOH (1032 ) A O 0.95 K 4 505 HOH (1070 ) A O 1.12 K 4 507 HOH (1339 ) A O 1.00 K 4 507 HOH (1394 ) A O 0.96 K 4 ION-B
181 ASP ( 181-) A H-bonding suggests Asn 352 GLU ( 352-) 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 : -0.997 2nd generation packing quality : -1.846 Ramachandran plot appearance : -1.426 chi-1/chi-2 rotamer normality : -1.974 Backbone conformation : -1.001
Bond lengths : 0.309 (tight) Bond angles : 0.647 (tight) Omega angle restraints : 0.272 (tight) Side chain planarity : 0.299 (tight) Improper dihedral distribution : 0.880 B-factor distribution : 1.078 Inside/Outside distribution : 0.996
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 : 2.30
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.4 2nd generation packing quality : -0.9 Ramachandran plot appearance : 0.0 chi-1/chi-2 rotamer normality : -0.5 Backbone conformation : -0.9
Bond lengths : 0.309 (tight) Bond angles : 0.647 (tight) Omega angle restraints : 0.272 (tight) Side chain planarity : 0.299 (tight) Improper dihedral distribution : 0.880 B-factor distribution : 1.078 Inside/Outside distribution : 0.996 ==============
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.