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.
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) :195.000
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
347 TYR ( 347-) A
471 ASP ( 471-) A
349 GLU ( 349-) A 484 GLU ( 484-) A 493 GLU ( 493-) A
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
| 0.998145 0.000027 -0.000129| | 0.000027 0.998970 -0.000319| | -0.000129 -0.000319 0.998769|Proposed new scale matrix
| 0.019008 0.000000 0.000002| | 0.000000 0.013389 0.000004| | 0.000000 0.000002 0.007509|With corresponding cell
A = 52.609 B = 74.689 C = 133.169 Alpha= 90.037 Beta= 90.008 Gamma= 90.001
The CRYST1 cell dimensions
A = 52.707 B = 74.768 C = 133.337 Alpha= 90.000 Beta= 90.000 Gamma= 90.000
(Under-)estimated Z-score: 4.238
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 97.47 -4.9 293 LEU ( 293-) A N CA C 99.88 -4.0
349 GLU ( 349-) A 471 ASP ( 471-) A 484 GLU ( 484-) A 493 GLU ( 493-) A
195 ARG ( 195-) A 5.54 318 ALA ( 318-) A 5.16 336 THR ( 336-) A 4.59 293 LEU ( 293-) A 4.11
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.
124 ARG ( 124-) A -2.8 376 THR ( 376-) A -2.7 45 PRO ( 45-) A -2.4 341 SER ( 341-) A -2.2 56 ARG ( 56-) 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 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 268 LYS ( 268-) A Poor phi/psi 345 PRO ( 345-) A Poor phi/psi 350 ASN ( 350-) 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 384 CYS ( 384-) 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 : -1.833
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 48 ASN ( 48-) A 0 52 HIS ( 52-) A 0 53 ASN ( 53-) A 0 54 PRO ( 54-) A 0 55 PHE ( 55-) A 0 56 ARG ( 56-) A 0 57 PRO ( 57-) 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 0And so on for a total of 230 lines.
Standard deviation of omega values : 1.432
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!
110 GLY ( 110-) A 1.69 20
130 PRO ( 130-) A 0.45 HIGH
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.
450 CYS ( 450-) A SG <-> 462 CYS ( 462-) A SG 0.93 2.52 INTRA 378 CYS ( 378-) A SG <-> 384 CYS ( 384-) A SG 0.91 2.54 INTRA 28 CYS ( 28-) A SG <-> 86 CYS ( 86-) A SG 0.86 2.59 INTRA 141 CYS ( 141-) A SG <-> 160 CYS ( 160-) A SG 0.85 2.60 INTRA 70 CYS ( 70-) A SG <-> 115 CYS ( 115-) A SG 0.72 2.73 INTRA 70 CYS ( 70-) A CB <-> 115 CYS ( 115-) A SG 0.42 2.98 INTRA BL 105 ASN ( 105-) A CG <-> 161 ARG ( 161-) A NH1 0.35 2.75 INTRA 378 CYS ( 378-) A CB <-> 384 CYS ( 384-) A SG 0.26 3.14 INTRA 61 ARG ( 61-) A CB <-> 500 HOH ( 727 ) A O 0.23 2.57 INTRA BF 305 HIS ( 305-) A C <-> 307 ALA ( 307-) A N 0.23 2.67 INTRA BF 195 ARG ( 195-) A NH2 <-> 233 GLU ( 233-) A CD 0.22 2.88 INTRA BL 200 LYS ( 200-) A NZ <-> 235 ILE ( 235-) A O 0.18 2.52 INTRA BL 170 LEU ( 170-) A CD1 <-> 202 MET ( 202-) A SD 0.18 3.22 INTRA 219 SER ( 219-) A N <-> 500 HOH ( 643 ) A O 0.17 2.53 INTRA BF 7 GLN ( 7-) A N <-> 500 HOH ( 533 ) A O 0.15 2.55 INTRA 105 ASN ( 105-) A ND2 <-> 161 ARG ( 161-) A NH1 0.14 2.71 INTRA 270 ASN ( 270-) A ND2 <-> 500 HOH ( 664 ) A O 0.13 2.57 INTRA 462 CYS ( 462-) A SG <-> 466 LYS ( 466-) A CG 0.12 3.28 INTRA 11 THR ( 11-) A N <-> 399 ASN ( 399-) A ND2 0.11 2.74 INTRA 343 ARG ( 343-) A N <-> 381 ASP ( 381-) A O 0.11 2.59 INTRA 450 CYS ( 450-) A CB <-> 462 CYS ( 462-) A SG 0.10 3.30 INTRA 410 TYR ( 410-) A N <-> 418 ALA ( 418-) A O 0.09 2.61 INTRA 11 THR ( 11-) A OG1 <-> 399 ASN ( 399-) A ND2 0.09 2.61 INTRA BL 28 CYS ( 28-) A SG <-> 86 CYS ( 86-) A CB 0.09 3.31 INTRA 344 TRP ( 344-) A O <-> 346 ARG ( 346-) A N 0.08 2.62 INTRAAnd so on for a total of 76 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 -7.46 8 GLN ( 8-) A -6.23 237 LEU ( 237-) A -6.19 142 LYS ( 142-) A -6.13 2 TYR ( 2-) A -5.80 118 TYR ( 118-) A -5.70 7 GLN ( 7-) A -5.56 343 ARG ( 343-) A -5.39 279 ASN ( 279-) A -5.37 88 ASN ( 88-) A -5.36 284 TRP ( 284-) A -5.32 30 ARG ( 30-) A -5.30 303 ARG ( 303-) A -5.26 302 GLN ( 302-) A -5.25 55 PHE ( 55-) A -5.16 53 ASN ( 53-) A -5.15
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.
500 HOH ( 736 ) A O -7.72 78.48 36.67
500 HOH ( 609 ) A O Marked this atom as acceptor 499 CL ( 498-) A CL Strange metal coordination for HIS 201
105 ASN ( 105-) A 399 ASN ( 399-) A 441 GLN ( 441-) 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.
2 TYR ( 2-) A N 3 SER ( 3-) A N 53 ASN ( 53-) A N 59 TRP ( 59-) A N 87 ASN ( 87-) A ND2 101 HIS ( 101-) A N 193 GLY ( 193-) A N 240 GLU ( 240-) A N 252 ARG ( 252-) A NE 271 GLY ( 271-) A N 273 LYS ( 273-) A N 281 GLY ( 281-) A N 295 PHE ( 295-) A N 300 ASP ( 300-) A N 312 ILE ( 312-) A N 316 TRP ( 316-) A NE1 337 ARG ( 337-) A NH2 344 TRP ( 344-) A N 352 LYS ( 352-) A N 355 ASN ( 355-) A ND2 370 VAL ( 370-) A N 390 GLN ( 390-) A NE2 416 GLN ( 416-) A NE2 434 TRP ( 434-) A N 462 CYS ( 462-) A N 463 THR ( 463-) A OG1 495 LYS ( 495-) 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.
147 ASP ( 147-) A OD1 215 HIS ( 215-) A NE2 290 ASP ( 290-) 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+.
498 CA ( 497-) A 0.79 1.03 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.
500 HOH ( 645 ) A O 1.12 K 4 Ion-B
188 ASP ( 188-) A H-bonding suggests Asn 246 ASP ( 246-) A H-bonding suggests Asn 353 ASP ( 353-) A H-bonding suggests Asn; but Alt-Rotamer 356 ASP ( 356-) 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 : -0.832 2nd generation packing quality : -1.456 Ramachandran plot appearance : -2.053 chi-1/chi-2 rotamer normality : -1.833 Backbone conformation : -0.946
Bond lengths : 0.279 (tight) Bond angles : 0.613 (tight) Omega angle restraints : 0.260 (tight) Side chain planarity : 0.252 (tight) Improper dihedral distribution : 0.581 B-factor distribution : 0.596 Inside/Outside distribution : 1.009
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 : -0.2 2nd generation packing quality : -0.6 Ramachandran plot appearance : -0.5 chi-1/chi-2 rotamer normality : -0.4 Backbone conformation : -0.8
Bond lengths : 0.279 (tight) Bond angles : 0.613 (tight) Omega angle restraints : 0.260 (tight) Side chain planarity : 0.252 (tight) Improper dihedral distribution : 0.581 B-factor distribution : 0.596 Inside/Outside distribution : 1.009 ==============
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.