************************************************************************ ********** REPORT OF PROTEIN ANALYSIS by the WHAT IF program ********** ************************************************************************ Date : 2003-10-26 This report was created by WHAT IF version 20030601-1154 INTRODUCTION ------------ This document contains a report of findings by the WHAT IF program during the analysis of one or more proteins. It contains a separate section for each of the proteins that have been analysed. Each reported fact has an assigned severity, one of: * error: severe errors encountered during the analyses. Items marked as errors are considered severe problems requiring immediate attention. * warning: Either less severe problems or uncommon structural features. These still need special attention. * note: Statistical values, plots, or other verbose results of tests and analyses that have been performed. If alternate conformations are present, only the first is evaluated. Hydrogen atoms are only included if explicitly requested, and even then they are not used by all checks. Legend ------ Some notations need a little explanation: RESIDUE: Residues in tables are normally given in 3-5 parts: - A number. This is the internal sequence number of the residue used by WHAT IF. - The residue name. Normally this is a three letter amino acid name. - The sequence number, between brackets. This is the residue number as it was given in the input file. It can be followed by the insertion code. - The chain identifier. A single character. If no chain identifier was given in the input file, this will be invisible. - A model number (only for NMR structures). Z-VALUE: To indicate the normality of a score, the score may be expressed as a Z-value or Z-score. This is just the number of standard deviations that the score deviates from the expected value. A property of Z-values is that the root-mean-square of a group of Z-values (the RMS Z-value) is expected to be 1.0. Z-values above 4.0 and below -4.0 are very uncommon. If a Z-score is used in WHAT IF, the accompanying text will explain how the expected value and standard deviation were obtained. ======================================================================== ==== Compound code model.pdb ==== ======================================================================== # 1 # Note: No rounded coordinates detected No significant rounding of atom coordinates has been detected. # 2 # Note: No crystallographic symmetry between molecules No extra crystallographic symmetry was observed between the independent molecules. # 3 # Error: Matthews Coefficient (Vm) very high 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. Numbers this high are almost always caused by giving the wrong value for Z on the CRYST1 card. Molecular weight of all polymer chains: 12896.757 Volume of the Unit Cell V= 168498.422 Cell multiplicity: 0 Matthews coefficient for observed atoms Vm= 13.065 # 4 # Note: Valine nomenclature OK No errors were detected in valine nomenclature. # 5 # Note: Threonine nomenclature OK No errors were detected in threonine nomenclature. # 6 # Note: Isoleucine nomenclature OK No errors were detected in isoleucine nomenclature. # 7 # Note: Leucine nomenclature OK No errors were detected in leucine nomenclature. # 8 # Note: Arginine nomenclature OK No errors were detected in arginine nomenclature. # 9 # Note: Tyrosine torsion conventions OK No errors were detected in tyrosine torsion angle conventions. # 10 # Note: Phenylalanine torsion conventions OK No errors were detected in phenylalanine torsion angle conventions. # 11 # Warning: Aspartic acid convention problem The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2. 113 ASP ( 125 ) C # 12 # Note: Glutamic acid torsion conventions OK No errors were detected in glutamic acid torsion angle conventions. # 13 # Note: Heavy atom naming OK No errors were detected in the atom names for non-hydrogen atoms. # 14 # Warning: Chirality deviations detected The atoms listed in the table below have an improper dihedral value that is deviating from expected values. 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. 18 LEU ( 19 ) A CA -4.1 25.9 34.4 90 ASN ( 91 ) A CA -4.4 23.4 33.8 # 15 # Note: Improper dihedral angle distribution OK The RMS Z-score for all improper dihedrals in the structure is within normal ranges. Improper dihedral RMS Z-score : 0.883 # 16 # Note: Chain names are OK All chain names assigned to polymer molecules are unique, and all residue numbers are strictly increasing within each chain. # 17 # Note: Weights checked OK All atomic occupancy factors ('weights') fall in the 0.0--1.0 range. # 18 # Note: No missing atoms detected All expected atoms are present. # 19 # Warning: C-terminal oxygen atoms missing The C-atoms listed in the table below belong to a C-terminal residue in a protein chain, but the C-terminal oxygen ("O2" or "OXT") that it should be bound to was not found. 98 LEU ( 99 ) A C 105 LEU ( 113 ) B C 123 ARG ( 135 ) C C # 20 # Note: No extra C-terminal groups found No C-terminal groups are present for non C-terminal residues # 21 # Warning: Unusual bond lengths The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigma for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given. Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "--SS", the disulphide bridge has a deviating length. 6 TRP ( 7 ) A CB CG 1.303 -6.3 51 ILE ( 52 ) A CG1 CD1 1.346 -4.3 102 THR ( 110 ) B CB CG2 1.384 -4.1 # 22 # Note: Normal bond length variability Bond lengths were found to deviate normally from the standard bond lengths (values for Protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). RMS Z-score for bond lengths: 0.725 RMS-deviation in bond distances: 0.018 # 23 # Note: No bond length directionality Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA does not show significant systematic deviations. # 24 # 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. 4 GLY ( 5 ) A N CA C 127.444 5.2 18 LEU ( 19 ) A C CA CB 118.362 4.3 18 LEU ( 19 ) A CA CB CG 130.765 4.1 74 THR ( 75 ) A N CA C 124.392 4.7 74 THR ( 75 ) A C CA CB 102.162 -4.2 75 VAL ( 76 ) A N CA CB 118.955 5.0 102 THR ( 110 ) B N CA CB 101.069 -5.5 # 25 # Note: Normal bond angle variability Bond angles were found to deviate normally from the mean 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 around 1.0 for a normally restrained data set, and this is indeed observed for very high resolution X-ray structures. More common values are around 1.55. RMS Z-score for bond angles: 0.962 RMS-deviation in bond angles: 2.082 # 26 # Note: Side chain planarity OK All of the side chains of residues that have a planar group are planar within expected RMS deviations. # 27 # Note: Atoms connected to aromatic rings OK All of the atoms that are connected to planar aromatic rings in side chains of amino-acid residues are in the plane within expected RMS deviations. # 28 # Note: PRO puckering amplitude OK Puckering amplitudes for all PRO residues are within normal ranges. # 29 # 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. 38 PRO ( 39 ) A 29.2 envelop C-delta (36 degrees) # 30 # 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. 91 LYS ( 92 ) A -2.4474 46 GLY ( 47 ) A -2.4136 113 ASP ( 125 ) C -2.3920 58 ARG ( 59 ) A -2.2718 104 GLU ( 112 ) B -2.2184 12 GLU ( 13 ) A -2.1442 18 LEU ( 19 ) A -2.1439 21 LEU ( 22 ) A -2.0983 41 GLU ( 42 ) A -2.0712 # 31 # Warning: Backbone torsion angle evaluation shows 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. 3 ALA ( 4 ) A omega poor 4 GLY ( 5 ) A Poor phi/psi 13 ASN ( 14 ) A Poor phi/psi 38 PRO ( 39 ) A Poor PRO-phi 46 GLY ( 47 ) A Poor phi/psi 47 ASP ( 48 ) A Poor phi/psi 72 GLU ( 73 ) A Poor phi/psi 75 VAL ( 76 ) A Poor phi/psi 114 ASP ( 126 ) C Poor phi/psi # 32 # Note: Ramachandran Z-score OK The score expressing how well the backbone conformations of all residues are corresponding to the known allowed areas in the Ramachandran plot is within expected ranges for well-refined structures. Ramachandran Z-score : -0.732 # 33 # Note: Omega angle restraint OK The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation agrees with this expectation. Standard deviation of omega values : 5.681 # 34 # Warning: chi-1/chi-2 angle correlation Z-score low The score expressing how well the chi-1/chi-2 angles of all residues are corresponding to the populated areas in the database is a bit low. chi-1/chi-2 correlation Z-score : -3.807 # 35 # Note: Ramachandran plot In this Ramachandran plot X-signs represent glycines, squares represent prolines and small plus-signs represent the other residues. If too many plus-signs fall outside the contoured areas then the molecule is poorly refined (or worse). In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. "Allowed" regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. In the TeX file, a plot has been inserted here Chain identifier: A # 36 # Note: Ramachandran plot In the TeX file, a plot has been inserted here Chain identifier: C # 37 # Note: Inside/Outside residue distribution normal The distribution of residue types over the inside and the outside of the protein is normal. inside/outside RMS Z-score : 1.120 # 38 # 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. In the TeX file, a plot has been inserted here Chain identifier: A # 39 # Note: Inside/Outside RMS Z-score plot In the TeX file, a plot has been inserted here Chain identifier: C # 40 # Note: Secondary structure This is the secondary structure according to DSSP. Only helix (H), strand (S), turn (T) and coil (blank) are shown. [REF] Secondary structure assignment 10 20 30 40 50 60 | | | | | | 1 - 60 NFAGAWKAAASENFAELLKALGVNAMLRKAAVAAASKPAVEIAQAGDAFYIKTSTTVRTT 1 - 60 T T THHHHHHHTT HHHHHHHHHHTTT SSSSSSSTTSSSSSSSSTTSSS 70 80 90 | | | 61 - 98 EINFKVGEGFEEATVDGRACASLAAWEAENKAACAQAL 61 - 98 SSSSSTTT SSSS TTT SSSSSSSSSSTTSSSSSSS 100 | 99 - 105 TAWTREL 99 - 105 110 120 | | 106 - 123 LILTAGADDVVCTRAYVR 106 - 123 SSSSSSTTSSSSSS # 41 # Note: All atoms are sufficiently far away from symmetry axes None of the atoms in the structure is closer than 0.77 Angstrom to a proper symmetry axis. # 42 # Error: Abnormally short interatomic distances The pairs of atoms listed in the table below have an unusually short distance. 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 centers of the two atoms. The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. If the final column contains the text 'HB', the bump criterium 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably aren't there anyway. Bumps between atoms for which the sum of their occupancies is lower than one are not reported. In any case, each bump is listed in only one direction. 12 GLU ( 13 ) A CG -- 57 VAL ( 58 ) A O 0.279 2.521 INTER 2 PHE ( 3 ) A N -- 44 GLN ( 45 ) A NE2 0.273 2.727 INTRA 74 THR ( 75 ) A O -- 75 VAL ( 76 ) A CB 0.175 2.625 INTRA 6 TRP ( 7 ) A CD1 -- 121 TYR ( 133 ) C CB 0.124 3.076 INTRA 12 GLU ( 13 ) A CD -- 57 VAL ( 58 ) A O 0.122 2.678 INTER 112 ALA ( 124 ) C O -- 113 ASP ( 125 ) C C 0.122 2.678 INTRA 12 GLU ( 13 ) A OE1 -- 118 THR ( 130 ) C CG2 0.118 2.682 INTRA 12 GLU ( 13 ) A CD -- 118 THR ( 130 ) C CG2 0.114 3.086 INTRA 113 ASP ( 125 ) C O -- 114 ASP ( 126 ) C CB 0.108 2.692 INTRA 45 ALA ( 46 ) A O -- 46 GLY ( 47 ) A C 0.099 2.701 INTRA 24 ASN ( 25 ) A O -- 25 ALA ( 26 ) A C 0.031 2.769 INTRA 88 ALA ( 89 ) A O -- 89 GLU ( 90 ) A C 0.027 2.773 INTRA 91 LYS ( 92 ) A CE -- 102 THR ( 110 ) B CG2 0.011 3.189 INTRA 57 VAL ( 58 ) A O -- 58 ARG ( 59 ) A CB 0.006 2.794 INTRA # 43 # Note: Second generation packing environment OK None of the individual amino acid residues has a bad packing environment. # 44 # Note: No series of residues with abnormal new packing environment There are no stretches of four or more residues each having a quality control Z-score worse than -1.75. # 45 # Note: Structural average packing Z-score OK The structural average for the second generation quality control value is within normal ranges. All contacts : Average = 0.726 Z-score = 3.47 BB-BB contacts : Average = 0.802 Z-score = 4.59 BB-SC contacts : Average = 0.137 Z-score = 0.68 SC-BB contacts : Average = 0.397 Z-score = 2.33 SC-SC contacts : Average = 0.597 Z-score = 2.96 # 46 # 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. In the TeX file, a plot has been inserted here Chain identifier: A # 47 # Note: Second generation quality Z-score plot In the TeX file, a plot has been inserted here Chain identifier: C # 48 # 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 constraints on the neighboring 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! 4 GLY ( 5 ) A 3.41 12 46 GLY ( 47 ) A 3.28 20 18 LEU ( 19 ) A 2.98 72 96 GLN ( 97 ) A 2.96 68 111 GLY ( 123 ) C 2.96 18 41 GLU ( 42 ) A 2.96 80 94 CYS ( 95 ) A 2.95 44 61 GLU ( 62 ) A 2.93 57 11 SER ( 12 ) A 2.88 50 102 THR ( 110 ) B 2.85 80 121 TYR ( 133 ) C 2.83 80 117 CYS ( 129 ) C 2.80 64 119 ARG ( 131 ) C 2.78 80 54 SER ( 55 ) A 2.70 34 50 TYR ( 51 ) A 2.57 65 101 TRP ( 109 ) B 2.55 17 52 LYS ( 53 ) A 2.53 80 103 ARG ( 111 ) B 2.41 49 6 TRP ( 7 ) A 2.33 25 84 ALA ( 85 ) A 2.23 80 38 PRO ( 39 ) A 2.12 16 69 GLY ( 70 ) A 2.10 14 8 ALA ( 9 ) A 2.08 18 24 ASN ( 25 ) A 1.94 12 120 ALA ( 132 ) C 1.90 80 39 ALA ( 40 ) A 1.88 80 59 THR ( 60 ) A 1.61 80 49 PHE ( 50 ) A 1.61 24 # 49 # Warning: Unusual rotamers The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database. It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it. 72 GLU ( 73 ) A 0.36 54 SER ( 55 ) A 0.38 # 50 # Warning: Unusual backbone conformations For the residues listed in the table below, the backbone formed by itself and two neighboring 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 center. 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 ( 4 ) A 0 5 ALA ( 6 ) A 0 45 ALA ( 46 ) A 0 75 VAL ( 76 ) A 0 88 ALA ( 89 ) A 0 90 ASN ( 91 ) A 0 113 ASP ( 125 ) C 0 114 ASP ( 126 ) C 0 47 ASP ( 48 ) A 1 74 THR ( 75 ) A 1 87 GLU ( 88 ) A 1 57 VAL ( 58 ) A 2 112 ALA ( 124 ) C 2 # 51 # Error: Backbone conformation Z-score very low A comparison of the backbone conformation with database proteins shows that the backbone fold in this structure is very unusual. Backbone conformation Z-score : -4.330 # 52 # Note: Average B-factor OK The average B-factor of buried atoms is within expected values for a room-temperature X-ray study. Average B-factor for buried atoms : 15.839 # 53 # Note: Number of buried atoms with low B-factor is OK For protein structures determined at room temperature, no more than about 1 percent of the B factors of buried atoms is below 5.0. Percentage of buried atoms with B less than 5 : 0.00 # 54 # Note: B-factor distribution normal The distribution of B-factors within residues is within expected ranges. A value over 1.5 here would mean that the B-factors show signs of over-refinement. RMS Z-score : 0.588 over 798 bonds Average difference in B over a bond : 1.29 RMS difference in B over a bond : 1.88 # 55 # Note: B-factor plot The average atomic B-factor per residue is plotted as function of the residue number. In the TeX file, a plot has been inserted here Chain identifier: A # 56 # Note: B-factor plot In the TeX file, a plot has been inserted here Chain identifier: C # 57 # 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 favorable 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. If a residue is marked ``flexible'' the flipped conformation is only slightly better than the non-flipped conformation. 1 ASN ( 2 ) A 44 GLN ( 45 ) A 63 ASN ( 64 ) A # 58 # 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. 3 ALA ( 4 ) A N 42 ILE ( 43 ) A N 77 GLY ( 78 ) A N # 59 # Note: Buried hydrogen bond acceptors OK All buried polar side-chain hydrogen bond acceptors are involved in a hydrogen bond in the optimized hydrogen bond network. # 60 # 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 constraint values. The first part of the table shows a number of constraint-independent quality indicators. Structure Z-scores, positive is better than average: 2nd generation packing quality : 3.465 Ramachandran plot appearance : -0.732 chi-1/chi-2 rotamer normality : -3.807 (poor) Backbone conformation : -4.330 (bad) RMS Z-scores, should be close to 1.0: Bond lengths : 0.725 Bond angles : 0.962 Omega angle restraints : 1.033 Side chain planarity : 0.812 Improper dihedral distribution : 0.883 B-factor distribution : 0.588 Inside/Outside distribution : 1.120 REFERENCES ========== 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). 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).