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.
Atoms at special positions should have an occupancy that is smaller than 1/N where N is the multiplicity of the symmetry operator. So, an atom on a 2-fold axis should have occupancy less or equal 0.5, for a 3-fold axis this is 0.33, etc. If the occupancy is too high, application of the symmetry matrices will result in the presence of more than one atom at (nearly) the same position. WHAT IF will certainly report this as bumps, but other things will also go wrong. E.g. 3 waters at the same position will make three times more hydrogen bonds, they will be counted three times in packing analysis, etc. So, I suggest you first fix this problem and run WHAT IF again on the fixed PDB file. An atom is considered to be located at a special position if it is within 0.3 Angstrom from one of its own symmetry copies. See also the next check...
361 HOH (1075 ) A O 361 HOH (1082 ) A O 361 HOH (1191 ) A O 361 HOH (1219 ) A O
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.
307 VAL ( 325-) A 0.50
Obviously, the temperature at which the X-ray data was collected has some importance too:
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: Tyrosine convention problem
The tyrosine residues listed in the table below have their chi-2 not between
-90.0 and 90.0
171 TYR ( 179-) A 277 TYR ( 295-) A 292 TYR ( 310-) A 336 TYR ( 354-) A
91 PHE ( 99-) A 94 PHE ( 102-) A 149 PHE ( 157-) A 187 PHE ( 195-) A 267 PHE ( 279-) A 349 PHE ( 367-) A
207 ASP ( 215-) A
64 GLU ( 72-) A 254 GLU ( 266-) A 343 GLU ( 361-) A
RMS Z-score for bond lengths: 0.259
RMS-deviation in bond distances: 0.006
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.
189 PHE ( 197-) A N CA C 99.92 -4.0
RMS Z-score for bond angles: 0.657
RMS-deviation in bond angles: 1.464
Error: Nomenclature error(s)
Checking for a hand-check. WHAT IF has over the course of this session
already corrected the handedness of atoms in several residues. These were
administrative corrections. These residues are listed here.
64 GLU ( 72-) A 207 ASP ( 215-) A 254 GLU ( 266-) A 343 GLU ( 361-) A
189 PHE ( 197-) A 4.21 224 ALA ( 236-) A 4.09
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.
298 PRO ( 316-) A -3.0 148 THR ( 156-) A -2.8 20 ILE ( 22-) A -2.6 135 THR ( 143-) A -2.5 257 PRO ( 269-) A -2.5 124 HIS ( 132-) A -2.3 56 HIS ( 64-) A -2.3 16 HIS ( 18-) A -2.2 187 PHE ( 195-) A -2.1 46 LEU ( 54-) 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.
16 HIS ( 18-) A Poor phi/psi 20 ILE ( 22-) A Poor phi/psi 30 GLN ( 32-) A Poor phi/psi 78 ASN ( 86-) A Poor phi/psi 124 HIS ( 132-) A Poor phi/psi 152 GLY ( 160-) A PRO omega poor 164 ARG ( 172-) A Poor phi/psi 194 HIS ( 202-) A Poor phi/psi 204 VAL ( 212-) A Poor phi/psi 207 ASP ( 215-) A Poor phi/psi 209 LEU ( 217-) A Poor phi/psi 239 ASP ( 251-) A Poor phi/psi 256 PRO ( 268-) A PRO omega poor 279 HIS ( 297-) A Poor phi/psi 288 ASP ( 306-) A Poor phi/psi 297 PRO ( 315-) A PRO omega poor 315 ALA ( 333-) A Poor phi/psi 341 TYR ( 359-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -0.485
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!
3 PRO ( 5-) A 0 10 VAL ( 12-) A 0 11 PHE ( 13-) A 0 13 SER ( 15-) A 0 17 ALA ( 19-) A 0 18 TYR ( 20-) A 0 19 ARG ( 21-) A 0 20 ILE ( 22-) A 0 21 PRO ( 23-) A 0 30 GLN ( 32-) A 0 39 ARG ( 41-) A 0 40 ALA ( 42-) A 0 41 ALA ( 49-) A 0 42 GLU ( 50-) A 0 56 HIS ( 64-) A 0 61 GLN ( 69-) A 0 64 GLU ( 72-) A 0 67 ALA ( 75-) A 0 69 ALA ( 77-) A 0 70 ARG ( 78-) A 0 71 LEU ( 79-) A 0 72 ASP ( 80-) A 0 76 SER ( 84-) A 0 77 MET ( 85-) A 0 78 ASN ( 86-) A 0And so on for a total of 169 lines.
Standard deviation of omega values : 1.605
Warning: Unusual PRO puckering phases
The proline residues listed in the table below have a puckering phase that is
not expected to occur in protein structures. Puckering parameters were
calculated by the method of Cremer and Pople [REF]. Normal PRO rings
approximately show a so-called envelope conformation with the C-gamma atom
above the plane of the ring (phi=+72 degrees), or a half-chair conformation
with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees).
If phi deviates strongly from these values, this is indicative of a very
strange conformation for a PRO residue, and definitely requires a manual
check of the data. Be aware that this is a warning with a low confidence
level. See: Who checks the checkers? Four validation tools applied to eight
atomic resolution structures [REF].
298 PRO ( 316-) A 41.6 envelop C-delta (36 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.
86 GLN ( 94-) A NE2 <-> 194 HIS ( 202-) A NE2 0.24 2.76 INTRA BF 106 GLN ( 114-) A NE2 <-> 361 HOH (1082 ) A O 0.22 2.48 INTRA 200 ARG ( 208-) A NH1 <-> 361 HOH (1116 ) A O 0.18 2.52 INTRA 1 SER ( 3-) A N <-> 307 VAL ( 325-) A A CG1 0.16 2.94 INTRA BF 80 CYS ( 88-) A A SG <-> 151 VAL ( 159-) A C 0.16 3.24 INTRA BL 179 ILE ( 187-) A CG2 <-> 180 GLN ( 188-) A N 0.13 2.87 INTRA BF 233 GLN ( 245-) A NE2 <-> 298 PRO ( 316-) A O 0.13 2.57 INTRA 320 GLN ( 338-) A NE2 <-> 361 HOH (1144 ) A O 0.12 2.58 INTRA 174 ARG ( 182-) A NH1 <-> 361 HOH (1094 ) A O 0.12 2.58 INTRA 229 ARG ( 241-) A NH2 <-> 361 HOH (1192 ) A O 0.11 2.59 INTRA BF 84 ASP ( 92-) A O <-> 88 GLY ( 96-) A N 0.11 2.59 INTRA 52 ASP ( 60-) A O <-> 56 HIS ( 64-) A N 0.11 2.59 INTRA 132 ARG ( 140-) A NE <-> 134 LEU ( 142-) A CD2 0.10 3.00 INTRA 29 GLN ( 31-) A NE2 <-> 124 HIS ( 132-) A ND1 0.10 2.90 INTRA 80 CYS ( 88-) A A SG <-> 152 GLY ( 160-) A CA 0.10 3.30 INTRA BL 2 LEU ( 4-) A CB <-> 3 PRO ( 5-) A CD 0.09 3.01 INTRA BF 155 HIS ( 163-) A CD2 <-> 318 ASP ( 336-) A OD1 0.08 2.72 INTRA BL 356 PRO ( 374-) A O <-> 359 TYR ( 377-) A N 0.07 2.63 INTRA BF 177 HIS ( 185-) A CD2 <-> 179 ILE ( 187-) A CG2 0.07 3.13 INTRA BF 1 SER ( 3-) A N <-> 309 LEU ( 327-) A CD2 0.06 3.04 INTRA BF 48 ARG ( 56-) A NH2 <-> 125 GLY ( 133-) A C 0.05 3.05 INTRA 356 PRO ( 374-) A C <-> 358 GLU ( 376-) A N 0.05 2.85 INTRA BF 296 ARG ( 314-) A N <-> 297 PRO ( 315-) A CD 0.05 2.95 INTRA BL 19 ARG ( 21-) A NE <-> 337 GLU ( 355-) A OE2 0.05 2.65 INTRA BL 32 LEU ( 34-) A N <-> 49 GLY ( 57-) A O 0.04 2.66 INTRA 174 ARG ( 182-) A NE <-> 361 HOH (1095 ) A O 0.04 2.66 INTRA 84 ASP ( 92-) A OD2 <-> 194 HIS ( 202-) A ND1 0.04 2.66 INTRA 53 ALA ( 61-) A N <-> 54 PRO ( 62-) A CD 0.03 2.97 INTRA 5 LEU ( 7-) A O <-> 57 GLN ( 65-) A NE2 0.03 2.67 INTRA 209 LEU ( 217-) A CB <-> 210 GLU ( 218-) A N 0.03 2.67 INTRA BL 177 HIS ( 185-) A ND1 <-> 178 PRO ( 186-) A CD 0.02 3.08 INTRA BF 165 SER ( 173-) A OG <-> 192 HIS ( 200-) A ND1 0.02 2.68 INTRA BL 271 ARG ( 283-) A NH2 <-> 358 GLU ( 376-) A OE1 0.02 2.68 INTRA BF 315 ALA ( 333-) A CB <-> 316 TYR ( 334-) A N 0.02 2.68 INTRA BL 233 GLN ( 245-) A O <-> 247 GLN ( 259-) A N 0.01 2.69 INTRA BL 219 VAL ( 231-) A CG1 <-> 220 VAL ( 232-) A N 0.01 2.99 INTRA 88 GLY ( 96-) A N <-> 89 THR ( 97-) A N 0.01 2.59 INTRA B3 227 HIS ( 239-) A N <-> 228 LEU ( 240-) A N 0.01 2.59 INTRA BL 279 HIS ( 297-) A ND1 <-> 280 PRO ( 298-) A CD 0.01 3.09 INTRA BL 37 GLU ( 39-) A OE2 <-> 78 ASN ( 86-) A N 0.01 2.69 INTRA
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.
39 ARG ( 41-) A -6.74 258 GLN ( 270-) A -6.25 176 LEU ( 184-) A -6.25 296 ARG ( 314-) A -6.24 126 ARG ( 134-) A -6.17 181 ARG ( 189-) A -6.12 180 GLN ( 188-) A -5.95 86 GLN ( 94-) A -5.89 311 LYS ( 329-) A -5.50 29 GLN ( 31-) A -5.44 229 ARG ( 241-) A -5.43 196 ARG ( 204-) A -5.17
The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.
179 ILE ( 187-) A 181 - ARG 189- ( A) -5.40
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.
302 ALA ( 320-) A -2.79
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.
361 HOH (1072 ) A O -27.66 30.12 54.38 361 HOH (1092 ) A O -0.87 42.12 23.06 361 HOH (1170 ) A O -17.52 41.81 41.85 361 HOH (1212 ) A O 0.09 43.31 28.22
361 HOH (1189 ) A O 361 HOH (1219 ) A O Marked this atom as acceptor 360 CL (1001-) A CL
56 HIS ( 64-) A 78 ASN ( 86-) A 124 HIS ( 132-) A 244 GLN ( 256-) A 258 GLN ( 270-) A 285 GLN ( 303-) A 320 GLN ( 338-) 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.
1 SER ( 3-) A N 1 SER ( 3-) A OG 2 LEU ( 4-) A N 60 TRP ( 68-) A NE1 100 GLN ( 108-) A N 102 THR ( 110-) A OG1 112 ASN ( 120-) A ND2 148 THR ( 156-) A N 151 VAL ( 159-) A N 171 TYR ( 179-) A OH 179 ILE ( 187-) A N 180 GLN ( 188-) A N 180 GLN ( 188-) A NE2 185 SER ( 193-) A OG 210 GLU ( 218-) A N 230 ALA ( 242-) A N 261 GLN ( 273-) A N 285 GLN ( 303-) A NE2 294 ASN ( 312-) A ND2 301 GLU ( 319-) A N
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.
42 GLU ( 50-) A OE2 50 ASP ( 58-) A OD1 118 GLN ( 126-) A OE1
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.
361 HOH (1024 ) A O 1.20 K 4 *2
42 GLU ( 50-) A H-bonding suggests Gln 123 ASP ( 131-) A H-bonding suggests Asn; but Alt-Rotamer 254 GLU ( 266-) A H-bonding suggests Gln; 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 : -0.350 2nd generation packing quality : -1.237 Ramachandran plot appearance : -1.651 chi-1/chi-2 rotamer normality : -0.485 Backbone conformation : -0.994
Bond lengths : 0.259 (tight) Bond angles : 0.657 (tight) Omega angle restraints : 0.292 (tight) Side chain planarity : 0.202 (tight) Improper dihedral distribution : 0.588 B-factor distribution : 0.465 Inside/Outside distribution : 0.984
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 : 1.76
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.0 2nd generation packing quality : -1.1 Ramachandran plot appearance : -1.7 chi-1/chi-2 rotamer normality : -0.3 Backbone conformation : -1.4
Bond lengths : 0.259 (tight) Bond angles : 0.657 (tight) Omega angle restraints : 0.292 (tight) Side chain planarity : 0.202 (tight) Improper dihedral distribution : 0.588 B-factor distribution : 0.465 Inside/Outside distribution : 0.984 ==============
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.