WHAT IF Check report

This file was created 2012-01-30 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

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.

Verification log for pdb3h71.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.669
CA-only RMS fit for the two chains : 0.317

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

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

Note: Ramachandran plot

Chain identifier: B

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) :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 : 8.34

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: B

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

 114 TYR   ( 433-)  A
 134 TYR   ( 453-)  A
 172 TYR   ( 491-)  A
 183 TYR   ( 502-)  A
 200 TYR   ( 519-)  A
 271 TYR   ( 590-)  A
 289 TYR   ( 608-)  A
 391 TYR   ( 710-)  A
 591 TYR   ( 433-)  B
 649 TYR   ( 491-)  B
 660 TYR   ( 502-)  B
 677 TYR   ( 519-)  B
 693 TYR   ( 535-)  B
 748 TYR   ( 590-)  B
 766 TYR   ( 608-)  B

Warning: Phenylalanine convention problem

The phenylalanine residues listed in the table below have their chi-2 not between -90.0 and 90.0.

 124 PHE   ( 443-)  A
 201 PHE   ( 520-)  A
 431 PHE   ( 750-)  A
 601 PHE   ( 443-)  B
 678 PHE   ( 520-)  B

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.

 106 GLU   ( 425-)  A
 449 GLU   ( 768-)  A
 907 GLU   ( 749-)  B
 926 GLU   ( 768-)  B

Geometric checks

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.259
RMS-deviation in bond distances: 0.012

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.

  94 PRO   ( 413-)  A      N    CA   C    99.34   -5.0
 191 LYS   ( 510-)  A      N    CA   C    98.72   -4.5
 250 GLY   ( 569-)  A      N    CA   C    95.89   -5.7
 288 ILE   ( 607-)  A      N    CA   C    98.95   -4.4
 571 PRO   ( 413-)  B      N    CA   C   101.76   -4.0
 668 LYS   ( 510-)  B      N    CA   C    99.36   -4.2
 727 GLY   ( 569-)  B      N    CA   C    95.65   -5.8
 765 ILE   ( 607-)  B      N    CA   C    99.02   -4.4
 803 ASN   ( 645-)  B      N    CA   C    98.99   -4.4

Warning: Low bond angle variability

Bond angles were found to deviate less than normal from the standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond angles: 0.660
RMS-deviation in bond angles: 1.492

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.

 106 GLU   ( 425-)  A
 449 GLU   ( 768-)  A
 907 GLU   ( 749-)  B
 926 GLU   ( 768-)  B

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

 727 GLY   ( 569-)  B    6.43
 250 GLY   ( 569-)  A    6.35
  94 PRO   ( 413-)  A    5.29
 716 VAL   ( 558-)  B    5.24
 209 PHE   ( 528-)  A    5.22
 686 PHE   ( 528-)  B    5.03
 239 VAL   ( 558-)  A    4.97
 191 LYS   ( 510-)  A    4.91
 572 VAL   ( 414-)  B    4.65
 668 LYS   ( 510-)  B    4.62
  95 VAL   ( 414-)  A    4.40
 571 PRO   ( 413-)  B    4.34
 288 ILE   ( 607-)  A    4.31
 765 ILE   ( 607-)  B    4.28
 948 SER   ( 790-)  B    4.25
  26 SER   ( 345-)  A    4.01

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.501

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

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 TYR   ( 695-)  A    -2.8
 853 TYR   ( 695-)  B    -2.8
 506 ILE   ( 348-)  B    -2.7
  29 ILE   ( 348-)  A    -2.7
 755 HIS   ( 597-)  B    -2.7
 278 HIS   ( 597-)  A    -2.6
 538 ILE   ( 380-)  B    -2.5
  61 ILE   ( 380-)  A    -2.5
 861 THR   ( 703-)  B    -2.3
 287 ILE   ( 606-)  A    -2.3
 453 LYS   ( 772-)  A    -2.3
 384 THR   ( 703-)  A    -2.3
  50 HIS   ( 369-)  A    -2.2
 854 VAL   ( 696-)  B    -2.2
 764 ILE   ( 606-)  B    -2.2
 377 VAL   ( 696-)  A    -2.2
 527 HIS   ( 369-)  B    -2.1
 217 LEU   ( 536-)  A    -2.1
 579 VAL   ( 421-)  B    -2.1
 102 VAL   ( 421-)  A    -2.1
 123 ILE   ( 442-)  A    -2.1
 403 GLU   ( 722-)  A    -2.0
 873 ASN   ( 715-)  B    -2.0
 326 ASN   ( 645-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

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.

  29 ILE   ( 348-)  A  Poor phi/psi
  50 HIS   ( 369-)  A  Poor phi/psi
  53 ASP   ( 372-)  A  Poor phi/psi
  67 ASN   ( 386-)  A  Poor phi/psi
  98 ASP   ( 417-)  A  Poor phi/psi
 108 LYS   ( 427-)  A  Poor phi/psi
 138 ASP   ( 457-)  A  Poor phi/psi
 157 ARG   ( 476-)  A  Poor phi/psi
 159 ASN   ( 478-)  A  Poor phi/psi
 182 ALA   ( 501-)  A  Poor phi/psi
 214 ASP   ( 533-)  A  Poor phi/psi
 225 ASP   ( 544-)  A  Poor phi/psi
 245 LYS   ( 564-)  A  Poor phi/psi
 278 HIS   ( 597-)  A  Poor phi/psi
 286 ARG   ( 605-)  A  Poor phi/psi
 293 HIS   ( 612-)  A  Poor phi/psi
 306 ASN   ( 625-)  A  Poor phi/psi
 310 ASP   ( 629-)  A  Poor phi/psi
 327 THR   ( 646-)  A  Poor phi/psi
 376 TYR   ( 695-)  A  Poor phi/psi
 399 GLY   ( 718-)  A  PRO omega poor
 401 LYS   ( 720-)  A  Poor phi/psi
 404 ASN   ( 723-)  A  Poor phi/psi
 432 ALA   ( 751-)  A  Poor phi/psi
 441 ASN   ( 760-)  A  Poor phi/psi
 457 ALA   ( 776-)  A  omega poor
 506 ILE   ( 348-)  B  Poor phi/psi
 530 ASP   ( 372-)  B  Poor phi/psi
 544 ASN   ( 386-)  B  Poor phi/psi
 575 ASP   ( 417-)  B  Poor phi/psi
 585 LYS   ( 427-)  B  Poor phi/psi
 634 ARG   ( 476-)  B  Poor phi/psi
 636 ASN   ( 478-)  B  Poor phi/psi
 659 ALA   ( 501-)  B  Poor phi/psi
 702 ASP   ( 544-)  B  Poor phi/psi
 722 LYS   ( 564-)  B  Poor phi/psi
 755 HIS   ( 597-)  B  Poor phi/psi
 758 GLY   ( 600-)  B  Poor phi/psi
 770 HIS   ( 612-)  B  Poor phi/psi
 783 ASN   ( 625-)  B  Poor phi/psi
 804 THR   ( 646-)  B  Poor phi/psi
 842 ASP   ( 684-)  B  Poor phi/psi
 853 TYR   ( 695-)  B  Poor phi/psi
 876 GLY   ( 718-)  B  PRO omega poor
 878 LYS   ( 720-)  B  Poor phi/psi
 909 ALA   ( 751-)  B  Poor phi/psi
 918 ASN   ( 760-)  B  Poor phi/psi
 934 ALA   ( 776-)  B  omega poor
 chi-1/chi-2 correlation Z-score : -0.855

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

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 ALA   ( 322-)  A      0
  11 PHE   ( 330-)  A      0
  15 ARG   ( 334-)  A      0
  21 LYS   ( 340-)  A      0
  28 ARG   ( 347-)  A      0
  29 ILE   ( 348-)  A      0
  30 PRO   ( 349-)  A      0
  37 LYS   ( 356-)  A      0
  48 ARG   ( 367-)  A      0
  49 LEU   ( 368-)  A      0
  50 HIS   ( 369-)  A      0
  53 ASP   ( 372-)  A      0
  54 TRP   ( 373-)  A      0
  56 ASP   ( 375-)  A      0
  59 MSE   ( 378-)  A      0
  67 ASN   ( 386-)  A      0
  69 LYS   ( 388-)  A      0
  70 THR   ( 389-)  A      0
  74 ARG   ( 393-)  A      0
  78 THR   ( 397-)  A      0
  83 ASN   ( 402-)  A      0
  91 ILE   ( 410-)  A      0
  95 VAL   ( 414-)  A      0
  97 ILE   ( 416-)  A      0
  98 ASP   ( 417-)  A      0
And so on for a total of 450 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.776

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

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!

 405 GLY   ( 724-)  A   1.78   11
 250 GLY   ( 569-)  A   1.63   10

Bump checks

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.

 885 HIS   ( 727-)  B      ND1 <->  900 HIS   ( 742-)  B      ND1    0.31    2.69  INTRA BL
  99 MSE   ( 418-)  A      CE  <->  112 SER   ( 431-)  A      CB     0.31    2.89  INTRA BL
 408 HIS   ( 727-)  A      ND1 <->  423 HIS   ( 742-)  A      ND1    0.28    2.72  INTRA BL
 502 LYS   ( 344-)  B      NZ  <->  955 HOH   (1794 )  B      O      0.27    2.43  INTRA
 214 ASP   ( 533-)  A      CG  <->  215 SER   ( 534-)  A      N      0.25    2.75  INTRA BL
 525 ARG   ( 367-)  B      NH2 <->  955 HOH   (1064 )  B      O      0.22    2.48  INTRA
 430 GLU   ( 749-)  A      O   <->  450 HIS   ( 769-)  A      ND1    0.21    2.49  INTRA BL
 691 ASP   ( 533-)  B      CG  <->  692 SER   ( 534-)  B      N      0.21    2.79  INTRA BL
 525 ARG   ( 367-)  B      NE  <->  955 HOH   (1003 )  B      O      0.19    2.51  INTRA
 907 GLU   ( 749-)  B      O   <->  927 HIS   ( 769-)  B      ND1    0.19    2.51  INTRA BL
 396 ASN   ( 715-)  A      ND2 <->  408 HIS   ( 727-)  A      NE2    0.18    2.82  INTRA BL
 198 ASN   ( 517-)  A      ND2 <->  200 TYR   ( 519-)  A      N      0.17    2.68  INTRA BL
 873 ASN   ( 715-)  B      ND2 <->  885 HIS   ( 727-)  B      NE2    0.17    2.83  INTRA BL
 786 VAL   ( 628-)  B      N   <->  789 GLN   ( 631-)  B      O      0.17    2.53  INTRA
 800 ARG   ( 642-)  B      NH2 <->  955 HOH   (1162 )  B      O      0.17    2.53  INTRA
 476 PRO   ( 318-)  B      CG  <->  949 LYS   ( 791-)  B      NZ     0.17    2.93  INTRA
  20 ASN   ( 339-)  A      ND2 <->   22 ASP   ( 341-)  A      N      0.16    2.69  INTRA BL
 888 ARG   ( 730-)  B      NH2 <->  955 HOH   (1512 )  B      O      0.16    2.54  INTRA
 621 ILE   ( 463-)  B      CG2 <->  622 LEU   ( 464-)  B      N      0.16    2.84  INTRA BL
 502 LYS   ( 344-)  B      NZ  <->  955 HOH   (1183 )  B      O      0.15    2.55  INTRA
 657 LYS   ( 499-)  B      NZ  <->  955 HOH   (1768 )  B      O      0.15    2.55  INTRA
  25 LYS   ( 344-)  A      NZ  <->  954 HOH   ( 887 )  A      O      0.15    2.55  INTRA
 498 LYS   ( 340-)  B      NZ  <->  955 HOH   (1180 )  B      O      0.15    2.55  INTRA
 675 ASN   ( 517-)  B      ND2 <->  677 TYR   ( 519-)  B      N      0.14    2.71  INTRA BL
 144 ILE   ( 463-)  A      CG2 <->  145 LEU   ( 464-)  A      N      0.13    2.87  INTRA BL
And so on for a total of 115 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

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.

 498 LYS   ( 340-)  B      -6.26
 905 LYS   ( 747-)  B      -6.26
 428 LYS   ( 747-)  A      -6.22
  21 LYS   ( 340-)  A      -6.21
 258 ARG   ( 577-)  A      -5.83
 841 LYS   ( 683-)  B      -5.82
 735 ARG   ( 577-)  B      -5.81
 414 GLU   ( 733-)  A      -5.53
 891 GLU   ( 733-)  B      -5.43
 690 LYS   ( 532-)  B      -5.39
 823 LEU   ( 665-)  B      -5.22
 833 LYS   ( 675-)  B      -5.21
 526 LEU   ( 368-)  B      -5.17
  49 LEU   ( 368-)  A      -5.15
 356 LYS   ( 675-)  A      -5.09
 159 ASN   ( 478-)  A      -5.08
 213 LYS   ( 532-)  A      -5.06
 280 ASN   ( 599-)  A      -5.06
 636 ASN   ( 478-)  B      -5.05
 757 ASN   ( 599-)  B      -5.04
  15 ARG   ( 334-)  A      -5.01

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: B

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.

 682 LYS   ( 524-)  B   -3.20
 241 ALA   ( 560-)  A   -3.01
 841 LYS   ( 683-)  B   -2.90
 681 ASN   ( 523-)  B   -2.83
 526 LEU   ( 368-)  B   -2.70
 166 ASP   ( 485-)  A   -2.68
 643 ASP   ( 485-)  B   -2.68
  49 LEU   ( 368-)  A   -2.64
 205 LYS   ( 524-)  A   -2.61

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

 524 ARG   ( 366-)  B     -  527 HIS   ( 369-)  B        -1.65

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

Note: Second generation quality Z-score plot

Chain identifier: B

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.

 954 HOH   (1164 )  A      O    102.36   26.44   55.61
 954 HOH   (1217 )  A      O     63.60   -7.59   52.25
 954 HOH   (1231 )  A      O     90.01   -7.47   65.82
 954 HOH   (1269 )  A      O     88.12  -15.49   52.77
 954 HOH   (1532 )  A      O    123.50    7.69   62.65
 954 HOH   (1679 )  A      O     89.16  -17.20   49.79
 955 HOH   (1444 )  B      O    115.13  -13.06    9.98
 955 HOH   (1616 )  B      O    118.80   21.50   39.44
 955 HOH   (1838 )  B      O    117.66   -5.58   62.19

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

 954 HOH   (1614 )  A      O
 954 HOH   (1633 )  A      O
 954 HOH   (1697 )  A      O
 954 HOH   (1761 )  A      O
 955 HOH   (1437 )  B      O
 955 HOH   (1749 )  B      O
ERROR. No convergence in HB2STD
Old,New value: 2711.250 2711.272

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

  20 ASN   ( 339-)  A
  79 ASN   ( 398-)  A
  96 ASN   ( 415-)  A
 143 GLN   ( 462-)  A
 198 ASN   ( 517-)  A
 204 ASN   ( 523-)  A
 304 ASN   ( 623-)  A
 336 ASN   ( 655-)  A
 396 ASN   ( 715-)  A
 434 ASN   ( 753-)  A
 455 GLN   ( 774-)  A
 456 ASN   ( 775-)  A
 466 ASN   ( 785-)  A
 497 ASN   ( 339-)  B
 573 ASN   ( 415-)  B
 675 ASN   ( 517-)  B
 681 ASN   ( 523-)  B
 781 ASN   ( 623-)  B
 785 GLN   ( 627-)  B
 813 ASN   ( 655-)  B
 873 ASN   ( 715-)  B
 911 ASN   ( 753-)  B
 933 ASN   ( 775-)  B
 943 ASN   ( 785-)  B

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

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.

  50 HIS   ( 369-)  A      N
  74 ARG   ( 393-)  A      NH2
  96 ASN   ( 415-)  A      ND2
 120 GLY   ( 439-)  A      N
 127 SER   ( 446-)  A      N
 164 THR   ( 483-)  A      OG1
 207 SER   ( 526-)  A      N
 207 SER   ( 526-)  A      OG
 215 SER   ( 534-)  A      N
 243 TRP   ( 562-)  A      N
 265 ARG   ( 584-)  A      NH1
 344 ARG   ( 663-)  A      NE
 371 GLN   ( 690-)  A      N
 378 GLN   ( 697-)  A      N
 420 TRP   ( 739-)  A      NE1
 424 ASN   ( 743-)  A      ND2
 451 THR   ( 770-)  A      N
 475 LEU   ( 317-)  B      N
 527 HIS   ( 369-)  B      N
 551 ARG   ( 393-)  B      NH1
 570 SER   ( 412-)  B      N
 573 ASN   ( 415-)  B      ND2
 597 GLY   ( 439-)  B      N
 620 GLN   ( 462-)  B      NE2
 632 THR   ( 474-)  B      OG1
 635 GLU   ( 477-)  B      N
 684 SER   ( 526-)  B      OG
 692 SER   ( 534-)  B      N
 720 TRP   ( 562-)  B      N
 755 HIS   ( 597-)  B      NE2
 821 ARG   ( 663-)  B      NE
 855 GLN   ( 697-)  B      N
 897 TRP   ( 739-)  B      NE1
 928 THR   ( 770-)  B      N
 932 GLN   ( 774-)  B      NE2
 949 LYS   ( 791-)  B      NZ

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

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.

 371 GLN   ( 690-)  A      OE1

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

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.

 954 HOH   (   7 )  A      O  1.05 NA  6
 954 HOH   (  74 )  A      O  0.86  K  4
 954 HOH   ( 146 )  A      O  1.13  K  4
 954 HOH   ( 834 )  A      O  0.86  K  5
 954 HOH   ( 842 )  A      O  0.98  K  5
 954 HOH   ( 895 )  A      O  1.04  K  4
 954 HOH   ( 904 )  A      O  1.04  K  4
 954 HOH   ( 912 )  A      O  1.03  K  6
 954 HOH   ( 913 )  A      O  1.08  K  4 Ion-B
 954 HOH   ( 992 )  A      O  0.87  K  4
 954 HOH   ( 994 )  A      O  0.98  K  4
 954 HOH   (1042 )  A      O  1.02  K  5 Ion-B
 954 HOH   (1108 )  A      O  1.12  K  4 Ion-B
 954 HOH   (1150 )  A      O  1.00  K  4 Ion-B
 954 HOH   (1158 )  A      O  0.86  K  4
 954 HOH   (1393 )  A      O  0.94  K  4 Ion-B
 954 HOH   (1565 )  A      O  0.95  K  6 Ion-B
 954 HOH   (1583 )  A      O  1.08  K  6 ION-B
 954 HOH   (1647 )  A      O  0.94  K  4 Ion-B
 955 HOH   ( 172 )  B      O  0.95  K  4
 955 HOH   ( 195 )  B      O  1.05  K  4
 955 HOH   ( 239 )  B      O  0.93  K  4
 955 HOH   ( 817 )  B      O  1.09  K  4
 955 HOH   ( 833 )  B      O  0.85  K  4
 955 HOH   ( 845 )  B      O  0.95  K  4
 955 HOH   ( 949 )  B      O  0.88  K  6
 955 HOH   (1028 )  B      O  0.86  K  4 Ion-B
 955 HOH   (1066 )  B      O  1.12  K  4
 955 HOH   (1122 )  B      O  0.87  K  5
 955 HOH   (1152 )  B      O  1.04  K  4
 955 HOH   (1200 )  B      O  0.89  K  5 Ion-B
 955 HOH   (1212 )  B      O  0.90  K  4 Ion-B
 955 HOH   (1213 )  B      O  0.96  K  7 ION-B
 955 HOH   (1296 )  B      O  0.95  K  5 Ion-B
 955 HOH   (1374 )  B      O  1.03  K  5 Ion-B
 955 HOH   (1525 )  B      O  0.94  K  7 Ion-B
 955 HOH   (1745 )  B      O  1.13  K  5 Ion-B

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

  66 ASP   ( 385-)  A   H-bonding suggests Asn; but Alt-Rotamer
 224 ASP   ( 543-)  A   H-bonding suggests Asn; but Alt-Rotamer
 374 ASP   ( 693-)  A   H-bonding suggests Asn; but Alt-Rotamer
 468 ASP   ( 787-)  A   H-bonding suggests Asn
 543 ASP   ( 385-)  B   H-bonding suggests Asn; but Alt-Rotamer
 701 ASP   ( 543-)  B   H-bonding suggests Asn
 769 ASP   ( 611-)  B   H-bonding suggests Asn; but Alt-Rotamer
 851 ASP   ( 693-)  B   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

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 :  -0.736
  2nd generation packing quality :  -1.994
  Ramachandran plot appearance   :  -0.738
  chi-1/chi-2 rotamer normality  :  -0.855
  Backbone conformation          :  -0.475

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.259 (tight)
  Bond angles                    :   0.660 (tight)
  Omega angle restraints         :   0.323 (tight)
  Side chain planarity           :   0.251 (tight)
  Improper dihedral distribution :   0.628
  Inside/Outside distribution    :   0.962

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

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 : 1.70


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.6
  2nd generation packing quality :  -1.5
  Ramachandran plot appearance   :  -1.1
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :  -0.8

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.259 (tight)
  Bond angles                    :   0.660 (tight)
  Omega angle restraints         :   0.323 (tight)
  Side chain planarity           :   0.251 (tight)
  Improper dihedral distribution :   0.628
  Inside/Outside distribution    :   0.962
==============

WHAT IF
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      WHAT IF: a molecular modelling and drug design program,
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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.