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: 49759.715
Volume of the Unit Cell V= 3041622.0
Space group multiplicity: 12
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 5.094
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 4.340
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.
451 DAN ( 601-) A - 452 NDG ( 1-) 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.
445 NAG ( 2-) A - O4 bound to 446 NAG ( 3-) A - C1 447 NAG ( 4-) A - O4 bound to 448 NAG ( 5-) A - C1
Obviously, the temperature at which the X-ray data was collected has some importance too:
Crystal temperature (K) :100.000
Nomenclature related problems
Warning: Phenylalanine convention problem
The phenylalanine residues listed in the table below have their chi-2 not
between -90.0 and 90.0.
34 PHE ( 151-) A
61 HIS ( 178-) A CG ND1 CE1 109.88 4.3
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.
27 PRO ( 144-) A N -6.6 -24.01 -2.48 The average deviation= 0.877
168 PRO ( 289-) A 4.43 13 PHE ( 130-) A 4.28
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.
436 PRO ( 557-) A -2.9 375 ILE ( 496-) A -2.7 47 ILE ( 164-) A -2.7 170 THR ( 291-) A -2.7 370 THR ( 491-) A -2.7 320 PRO ( 441-) A -2.5 321 ARG ( 442-) A -2.4 105 SER ( 226-) A -2.4 232 PHE ( 353-) A -2.3 341 VAL ( 462-) A -2.3 88 PHE ( 209-) A -2.3 339 THR ( 460-) A -2.3 96 TYR ( 217-) A -2.3 60 THR ( 177-) A -2.3 290 PRO ( 411-) A -2.2 316 THR ( 437-) A -2.2 185 TYR ( 306-) A -2.2 414 VAL ( 535-) A -2.1 200 ASN ( 321-) A -2.1 403 GLY ( 524-) A -2.1 53 THR ( 170-) A -2.1 147 ASP ( 268-) A -2.0 61 HIS ( 178-) 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.
47 ILE ( 164-) A Poor phi/psi 147 ASP ( 268-) A Poor phi/psi 161 ASP ( 282-) A Poor phi/psi 170 THR ( 291-) A Poor phi/psi 200 ASN ( 321-) A Poor phi/psi 234 ASN ( 355-) A Poor phi/psi 287 SER ( 408-) A Poor phi/psi 303 ASN ( 424-) A Poor phi/psi 319 VAL ( 440-) A Poor phi/psi 332 ARG ( 453-) A Poor phi/psi 376 ASN ( 497-) A Poor phi/psi 385 THR ( 506-) A Poor phi/psi 401 ALA ( 522-) A Poor phi/psi 414 VAL ( 535-) A Poor phi/psi 428 LEU ( 549-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -1.875
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!
6 TYR ( 123-) A 0 10 ILE ( 127-) A 0 11 ASN ( 128-) A 0 12 GLN ( 129-) A 0 14 TYR ( 131-) A 0 23 LEU ( 140-) A 0 31 MET ( 148-) A 0 34 PHE ( 151-) A 0 46 ARG ( 163-) A 0 47 ILE ( 164-) A 0 48 PRO ( 165-) A 0 55 THR ( 172-) A 0 56 HIS ( 173-) A 0 61 HIS ( 178-) A 0 66 ASN ( 183-) A 0 68 CYS ( 185-) A 0 69 GLN ( 186-) A 0 70 SER ( 191-) A 0 71 ASN ( 192-) A 0 76 MET ( 197-) A 0 80 GLU ( 201-) A 0 86 PHE ( 207-) A 0 87 PRO ( 208-) A 0 92 LEU ( 213-) A 0 98 SER ( 219-) A 0And so on for a total of 202 lines.
Standard deviation of omega values : 1.666
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!
43 GLY ( 160-) A 1.66 20
27 PRO ( 144-) A 153.8 half-chair C-alpha/N (162 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.
22 ASN ( 139-) A ND2 <-> 452 NDG ( 1-) A C1 1.24 1.46 INTRA BF 22 ASN ( 139-) A CG <-> 452 NDG ( 1-) A C1 0.78 2.42 INTRA BF 207 MET ( 328-) A CE <-> 317 GLN ( 438-) A NE2 0.35 2.75 INTRA 321 ARG ( 442-) A NH2 <-> 327 CYS ( 448-) A O 0.33 2.37 INTRA BF 198 GLN ( 319-) A CG <-> 261 ASN ( 382-) A ND2 0.27 2.83 INTRA 53 THR ( 170-) A CG2 <-> 54 LYS ( 171-) A N 0.22 2.78 INTRA BL 14 TYR ( 131-) A O <-> 409 ARG ( 530-) A NH2 0.22 2.48 INTRA 370 THR ( 491-) A CG2 <-> 373 GLN ( 494-) A O 0.19 2.61 INTRA 264 VAL ( 385-) A CG1 <-> 283 GLN ( 404-) A NE2 0.18 2.92 INTRA BL 247 ARG ( 368-) A NH1 <-> 249 ASP ( 370-) A OD1 0.18 2.52 INTRA BF 37 THR ( 154-) A CG2 <-> 38 ALA ( 155-) A N 0.16 2.84 INTRA BL 410 ASP ( 531-) A OD1 <-> 412 GLY ( 533-) A N 0.16 2.54 INTRA BL 247 ARG ( 368-) A NH1 <-> 249 ASP ( 370-) A CG 0.16 2.94 INTRA BF 391 GLN ( 512-) A OE1 <-> 439 ARG ( 560-) A NH1 0.13 2.57 INTRA 370 THR ( 491-) A CG2 <-> 373 GLN ( 494-) A N 0.12 2.98 INTRA 318 GLN ( 439-) A CG <-> 385 THR ( 506-) A C 0.12 3.08 INTRA 264 VAL ( 385-) A CG1 <-> 265 LEU ( 386-) A N 0.11 2.89 INTRA BL 1 ILE ( 118-) A N <-> 453 HOH ( 610 ) A O 0.10 2.60 INTRA 300 THR ( 421-) A O <-> 307 SER ( 428-) A N 0.10 2.60 INTRA BF 317 GLN ( 438-) A N <-> 318 GLN ( 439-) A N 0.09 2.51 INTRA B3 415 MET ( 536-) A CB <-> 440 GLN ( 561-) A NE2 0.09 3.01 INTRA 1 ILE ( 118-) A CG1 <-> 2 ASN ( 119-) A N 0.09 2.91 INTRA BL 375 ILE ( 496-) A CG2 <-> 376 ASN ( 497-) A CG 0.09 3.11 INTRA 130 TYR ( 251-) A O <-> 235 ARG ( 356-) A NE 0.08 2.62 INTRA 212 CYS ( 333-) A SG <-> 333 CYS ( 454-) A SG 0.08 3.37 INTRA BFAnd so on for a total of 56 lines.
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.
65 LEU ( 182-) A -6.11 428 LEU ( 549-) A -5.92 321 ARG ( 442-) A -5.52 393 PHE ( 514-) A -5.49 160 LEU ( 281-) A -5.35 177 LEU ( 298-) A -5.30 30 ASN ( 147-) A -5.17 247 ARG ( 368-) A -5.17
7 ILE ( 124-) A -2.68
8 ASN ( 125-) 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.
12 GLN ( 129-) A N 30 ASN ( 147-) A ND2 34 PHE ( 151-) A N 40 THR ( 157-) A OG1 46 ARG ( 163-) A NH2 56 HIS ( 173-) A N 86 PHE ( 207-) A N 165 THR ( 286-) A OG1 166 LEU ( 287-) A N 233 GLY ( 354-) A N 247 ARG ( 368-) A NH1 254 CYS ( 375-) A N 289 TRP ( 410-) A N 289 TRP ( 410-) A NE1 291 MET ( 412-) A N 305 GLN ( 426-) A N 321 ARG ( 442-) A NH2 335 GLY ( 456-) A N 341 VAL ( 462-) A N 342 TYR ( 463-) A N 345 ALA ( 466-) A N 362 THR ( 483-) A N 373 GLN ( 494-) A N 407 CYS ( 528-) A N 428 LEU ( 549-) A N 439 ARG ( 560-) 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.
167 ASN ( 288-) 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+.
450 CA ( 600-) A 0.79 1.02 Scores about as good as NA *2
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.
453 HOH ( 630 ) A O 0.93 K 4 453 HOH ( 771 ) A O 1.00 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 : -0.201 2nd generation packing quality : -1.225 Ramachandran plot appearance : -1.459 chi-1/chi-2 rotamer normality : -1.875 Backbone conformation : -0.083
Bond lengths : 0.368 (tight) Bond angles : 0.669 Omega angle restraints : 0.303 (tight) Side chain planarity : 0.275 (tight) Improper dihedral distribution : 0.733 B-factor distribution : 0.453 Inside/Outside distribution : 1.026
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 : 0.5 2nd generation packing quality : -0.4 Ramachandran plot appearance : -0.0 chi-1/chi-2 rotamer normality : -0.4 Backbone conformation : -0.0
Bond lengths : 0.368 (tight) Bond angles : 0.669 Omega angle restraints : 0.303 (tight) Side chain planarity : 0.275 (tight) Improper dihedral distribution : 0.733 B-factor distribution : 0.453 Inside/Outside distribution : 1.026 ==============
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.