What Check for E. coli Ffh Model

# 1 # Note: Cell is 1 Angstrom cube

The unit cell in the CRYST1 card of the PDB file is given as a cube

with vertices of 1 Angstrom. This is the convention for structures

obtained using a method other than crystallography.

# 2 # Error: Missing unit cell information

No SCALE matrix is given in the PDB file.

# 3 # Note: No rounded coordinates detected

No significant rounding of atom coordinates has been detected.

# 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 # Note: Aspartic acid torsion conventions OK

No errors were detected in aspartic acid torsion angle conventions.

# 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 ( 22 ) C 9.7 17.7 -0.1

22 ASN ( 26 ) C 4.9 8.8 -0.1

27 LEU ( 31 ) CA -5.3 23.6 34.4

30 VAL ( 34 ) CB -6.7 -47.9 -33.6

46 PHE ( 50 ) CA -4.8 23.0 34.2

53 LYS ( 57 ) C 4.6 8.2 -0.1

88 LEU ( 92 ) C 7.4 13.5 -0.1

93 GLN ( 97 ) C -4.9 -8.9 -0.1

96 ALA ( 100 ) C 4.2 7.2 0.0

97 VAL ( 101 ) C 5.2 9.9 -0.3

102 GLY ( 106 ) C -7.4 -11.9 0.1

191 HIS ( 195 ) C 4.3 8.1 -0.1

192 VAL ( 196 ) CB -7.8 -50.5 -33.6

194 GLU ( 198 ) C 4.1 7.6 0.0

200 ILE ( 204 ) C -4.4 -8.6 -0.2

232 ASN ( 236 ) CA -11.9 5.4 33.8

232 ASN ( 236 ) C -10.2 -18.4 -0.1

236 PRO ( 240 ) C -4.6 -8.5 0.0

237 LEU ( 241 ) C 12.9 23.6 -0.1

242 LEU ( 246 ) CG -4.2 -42.3 -34.2

247 GLY ( 251 ) C -11.3 -18.1 0.1

252 GLY ( 256 ) C 5.6 9.1 0.1

253 ALA ( 257 ) CA 4.4 42.6 34.4

268 LEU ( 272 ) C -8.3 -15.3 -0.1

271 GLY ( 275 ) C -6.3 -10.1 0.1

285 ILE ( 289 ) C -4.4 -8.7 -0.2

291 GLY ( 295 ) C -5.1 -8.1 0.1

# 15 # Warning: High improper dihedral angle deviations

The RMS Z-score for the improper dihedrals in the structure is high.

For well refined structures this number is expected to be around 1.0.

The fact that it is higher than 1.5 in this structure could be an

indication of overrefinement.

Improper dihedral RMS Z-score : 1.972

# 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 # Note: OXT check OK

All required C-terminal oxygen atoms are present.

# 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.

38 ASP ( 42 ) CB CG 1.400 -4.6

46 PHE ( 50 ) CA C 1.424 -4.8

57 HIS ( 61 ) CG ND1 1.298 -4.3

204 HIS ( 208 ) CG CD2 1.294 -5.6

222 GLN ( 226 ) CD OE1 1.096 -6.8

232 ASN ( 236 ) CB CG 1.625 4.4

232 ASN ( 236 ) CG ND2 1.187 -6.7

233 GLU ( 237 ) N C 1.237 -4.6

# 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: 0.721

RMS-deviation in bond distances: 0.016

# 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.

12 ILE ( 16 ) CA CB CG1 117.413 4.1

15 ARG ( 19 ) C N CA 129.757 4.5

18 LEU ( 22 ) CD1 CG CD2 95.773 -6.8

19 THR ( 23 ) O C N 114.608 -5.2

21 ASP ( 25 ) CA CB CG 118.780 6.2

21 ASP ( 25 ) OD2 CG OD1 133.592 4.5

27 LEU ( 31 ) CA C O 129.261 5.0

27 LEU ( 31 ) N CA CB 118.542 4.7

30 VAL ( 34 ) CG1 CB CG2 83.860 -12.2

38 ASP ( 42 ) N CA CB 97.709 -7.5

38 ASP ( 42 ) C CA CB 118.078 4.2

38 ASP ( 42 ) CA CB CG 107.036 -5.6

38 ASP ( 42 ) CB CG OD2 104.812 -5.9

38 ASP ( 42 ) OD2 CG OD1 144.515 9.0

46 PHE ( 50 ) CA C O 93.833 -15.9

46 PHE ( 50 ) N CA CB 119.213 5.1

46 PHE ( 50 ) CA CB CG 100.567 -13.2

47 ILE ( 51 ) O C N 131.595 5.4

47 ILE ( 51 ) CA C N 132.350 8.1

48 ASN ( 52 ) C N CA 145.248 13.1

53 LYS ( 57 ) N CA CB 103.095 -4.4

53 LYS ( 57 ) CB CG CD 125.853 6.3

57 HIS ( 61 ) ND1 CE1 NE2 117.333 4.3

57 HIS ( 61 ) CE1 NE2 CD2 101.333 -4.3

59 VAL ( 63 ) CG1 CB CG2 101.645 -4.2

And so on for a total of 96 lines

# 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: 1.441

RMS-deviation in bond angles: 2.751

# 26 # Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a

planar group that was found to deviate from planarity by more than

4.0 times the expected value. For an amino acid residue that has a

side chain with a planar group, the RMS deviation of the atoms to a

least squares plane was determined. The number in the table is the

number of standard deviations this RMS value deviates from the

expected value (0.0).

278 GLU ( 282 ) 12.830

281 HIS ( 285 ) 9.163

57 HIS ( 61 ) 8.183

165 ASP ( 169 ) 6.981

248 ASP ( 252 ) 6.589

204 HIS ( 208 ) 5.999

123 HIS ( 127 ) 5.485

222 GLN ( 226 ) 5.395

48 ASN ( 52 ) 5.258

83 GLU ( 87 ) 4.957

232 ASN ( 236 ) 4.802

104 GLN ( 108 ) 4.526

22 ASN ( 26 ) 4.331

202 GLN ( 206 ) 4.111

# 27 # Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar

aromatic group in the sidechain of a protein residue but were found

to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a

protein residue the distance of the atom to the least squares plane

through the aromatic system was determined. This value was divided

by the standard deviation from a distribution of similar values

from a database of small molecule structures.

191 HIS ( 195 ) CB 5.042

154 PHE ( 158 ) CB 4.413

# 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.

156 PRO ( 160 ) -63.0 envelop C-beta (-72 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.

156 PRO ( 160 ) -3.1384

290 LEU ( 294 ) -2.7223

192 VAL ( 196 ) -2.5347

207 ILE ( 211 ) -2.4218

163 PRO ( 167 ) -2.3464

232 ASN ( 236 ) -2.3116

18 LEU ( 22 ) -2.3041

190 LEU ( 194 ) -2.0985

90 LEU ( 94 ) -2.0051

# 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.

15 ARG ( 19 ) Poor phi/psi

17 ARG ( 21 ) Poor phi/psi

38 ASP ( 42 ) Poor phi/psi

46 PHE ( 50 ) Poor phi/psi

47 ILE ( 51 ) Poor phi/psi

57 HIS ( 61 ) omega poor

62 SER ( 66 ) Poor phi/psi

83 GLU ( 87 ) Poor phi/psi, omega poor

94 PRO ( 98 ) Poor PRO-phi, PRO omega poor

95 PRO ( 99 ) Poor PRO-phi

123 HIS ( 127 ) Poor phi/psi

124 LYS ( 128 ) omega poor

156 PRO ( 160 ) Poor phi/psi

159 VAL ( 163 ) Poor phi/psi

163 PRO ( 167 ) Poor PRO-phi

178 PHE ( 182 ) Poor phi/psi

191 HIS ( 195 ) omega poor

200 ILE ( 204 ) omega poor

208 ASN ( 212 ) Poor phi/psi

223 ASP ( 227 ) Poor phi/psi

232 ASN ( 236 ) Poor phi/psi

237 LEU ( 241 ) omega poor

238 THR ( 242 ) Poor phi/psi, omega poor

244 LYS ( 248 ) Poor phi/psi

248 ASP ( 252 ) omega poor

257 ILE ( 261 ) omega poor

260 ILE ( 264 ) omega poor

276 ALA ( 280 ) Poor phi/psi

285 ILE ( 289 ) omega poor

290 LEU ( 294 ) Poor phi/psi

291 GLY ( 295 ) 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 : -1.851

# 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 : 6.015

# 34 # Note: chi-1/chi-2 angle correlation Z-score OK

The score expressing how well the chi-1/chi-2 angles of all residues

are corresponding to the populated areas in the database is

within expected ranges for well-refined structures.

chi-1/chi-2 correlation Z-score : -0.808

# 35 # 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 : 1.053

# 36 # 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.

81 MET ( 85 ) SD -- 285 ILE ( 289 ) CD1 0.583 2.817 INTRA BF

232 ASN ( 236 ) CA -- 263 LYS ( 267 ) NZ 0.583 2.517 INTRA

232 ASN ( 236 ) CG -- 263 LYS ( 267 ) NZ 0.558 2.542 INTRA

232 ASN ( 236 ) C -- 263 LYS ( 267 ) NZ 0.512 2.588 INTRA

191 HIS ( 195 ) N -- 192 VAL ( 196 ) CG2 0.480 2.620 INTRA BF

240 VAL ( 244 ) CB -- 258 ARG ( 262 ) CZ 0.479 2.721 INTRA

242 LEU ( 246 ) CD2 -- 258 ARG ( 262 ) NH1 0.475 2.625 INTRA

18 LEU ( 22 ) CD1 -- 21 ASP ( 25 ) N 0.473 2.627 INTRA BF

38 ASP ( 42 ) CG -- 222 GLN ( 226 ) OE1 0.433 2.367 INTRA

237 LEU ( 241 ) CA -- 238 THR ( 242 ) CG2 0.394 2.806 INTRA

81 MET ( 85 ) SD -- 285 ILE ( 289 ) CG1 0.391 3.009 INTRA BF

46 PHE ( 50 ) O -- 48 ASN ( 52 ) N 0.383 2.317 INTRA BF

102 GLY ( 106 ) C -- 108 LYS ( 112 ) NZ 0.373 2.727 INTRA

211 GLU ( 215 ) CD -- 238 THR ( 242 ) CG2 0.364 2.836 INTRA

216 VAL ( 220 ) CG1 -- 258 ARG ( 262 ) CZ 0.364 2.836 INTRA

281 HIS ( 285 ) CE1 -- 284 ARG ( 288 ) NH2 0.348 2.752 INTRA

53 LYS ( 57 ) CG -- 57 HIS ( 61 ) CE1 0.341 2.859 INTRA

281 HIS ( 285 ) NE2 -- 284 ARG ( 288 ) NH2 0.339 2.661 INTRA

285 ILE ( 289 ) CD1 -- 286 ALA ( 290 ) N 0.332 2.768 INTRA

53 LYS ( 57 ) NZ -- 75 ASN ( 79 ) ND2 0.330 2.670 INTRA BF

86 GLN ( 90 ) CG -- 281 HIS ( 285 ) CE1 0.324 2.876 INTRA

18 LEU ( 22 ) CD1 -- 21 ASP ( 25 ) CB 0.323 2.877 INTRA BF

27 LEU ( 31 ) CA -- 30 VAL ( 34 ) CG1 0.321 2.879 INTRA BF

281 HIS ( 285 ) CD2 -- 284 ARG ( 288 ) NH2 0.318 2.782 INTRA

237 LEU ( 241 ) C -- 238 THR ( 242 ) CG2 0.312 2.888 INTRA

And so on for a total of 254 lines

# 37 # 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.

189 ARG ( 193 ) -7.68

135 TYR ( 139 ) -6.15

15 ARG ( 19 ) -5.88

93 GLN ( 97 ) -5.64

104 GLN ( 108 ) -5.62

149 GLN ( 153 ) -5.50

161 GLN ( 165 ) -5.37

# 38 # Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing

environment was found. This could indicate that these residues are part

of a strange loop, but 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 score of the series.

292 MET ( 296 ) --- 294 ASP ( 298 ) -4.54

# 39 # Note: Structural average packing environment OK

The structural average quality control value is within normal ranges.

Average for range 1 - 294 : -0.739

# 40 # 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 quality 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.

87 THR ( 91 ) -3.14

123 HIS ( 127 ) -3.07

290 LEU ( 294 ) -2.98

291 GLY ( 295 ) -2.96

90 LEU ( 94 ) -2.90

178 PHE ( 182 ) -2.71

# 41 # 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.

# 42 # Note: Structural average packing Z-score OK

The structural average for the second generation quality control

value is within normal ranges.

All contacts : Average = -0.224 Z-score = -1.33

BB-BB contacts : Average = 0.219 Z-score = 1.58

BB-SC contacts : Average = -0.516 Z-score = -2.75

SC-BB contacts : Average = 0.086 Z-score = 0.69

SC-SC contacts : Average = -0.642 Z-score = -3.22

# 43 # Note: Backbone oxygen evaluation OK

All residues for which the local backbone conformation could be

found in the WHAT IF database have a normal backbone oxygen

position.

# 44 # Note: Rotamers checked OK

None of the residues that have a normal backbone environment have

abnormal rotamers.

# 45 # 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!

46 PHE ( 50 ) 0

47 ILE ( 51 ) 0

81 MET ( 85 ) 0

83 GLU ( 87 ) 0

84 GLU ( 88 ) 0

94 PRO ( 98 ) 0

122 LYS ( 126 ) 0

123 HIS ( 127 ) 0

124 LYS ( 128 ) 0

159 VAL ( 163 ) 0

191 HIS ( 195 ) 0

192 VAL ( 196 ) 0

193 ASP ( 197 ) 0

237 LEU ( 241 ) 0

238 THR ( 242 ) 0

17 ARG ( 21 ) 1

96 ALA ( 100 ) 1

106 ALA ( 110 ) 1

158 ASP ( 162 ) 1

178 PHE ( 182 ) 1

222 GLN ( 226 ) 1

248 ASP ( 252 ) 1

15 ARG ( 19 ) 2

207 ILE ( 211 ) 2

208 ASN ( 212 ) 2

244 LYS ( 248 ) 2

290 LEU ( 294 ) 2

# 46 # Note: Backbone conformation Z-score OK

The backbone conformation analysis gives a score that is normal

for well refined protein structures.

Backbone conformation Z-score : -2.727

# 47 # Warning: Buried unsatisfied hydrogen bond donors and acceptors

The buried hydrogen bond donors and acceptors listed in the table

below are not involved in a hydrogen bond.

Hydrogen bond donors and acceptors that are buried inside the

protein normally form hydrogen bonds within the protein. If there

are any non hydrogen bonded buried hydrogen bond donors/acceptors

in the structure, they will be listed here.

The polar side chain atoms of ARG, LYS, GLU, ASP, HIS, ASN and GLN

are, when they are buried, almost invariably involved in at least

one hydrogen bond. If any of these atoms are listed, an

investigation should be undertaken.

4 ARG ( 8 ) N

21 ASP ( 25 ) N

38 ASP ( 42 ) O

40 ALA ( 44 ) N

44 VAL ( 48 ) O

48 ASN ( 52 ) N

50 VAL ( 54 ) N

57 HIS ( 61 ) ND1

64 THR ( 68 ) OG1

80 ALA ( 84 ) O

87 THR ( 91 ) O

89 ASN ( 93 ) OD1

103 LEU ( 107 ) O

106 ALA ( 110 ) N

125 LYS ( 129 ) O

135 TYR ( 139 ) N

136 ARG ( 140 ) O

142 GLN ( 146 ) OE1

162 LYS ( 166 ) O

165 ASP ( 169 ) N

180 ASP ( 184 ) OD2

185 ASP ( 189 ) OD1

188 GLY ( 192 ) N

190 LEU ( 194 ) O

191 HIS ( 195 ) N

203 VAL ( 207 ) N

224 ALA ( 228 ) N

237 LEU ( 241 ) N

257 ILE ( 261 ) O

258 ARG ( 262 ) NH1

273 LYS ( 277 ) N

274 THR ( 278 ) OG1

288 ARG ( 292 ) NE

289 ILE ( 293 ) O

# 48 # 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:

1st generation packing quality : -0.597

2nd generation packing quality : -1.328

Ramachandran plot appearance : -1.851

chi-1/chi-2 rotamer normality : -0.808

Backbone conformation : -2.727

RMS Z-scores, should be close to 1.0:

Bond lengths : 0.721

Bond angles : 1.441

Omega angle restraints : 1.094

Side chain planarity : 2.909 (loose)

Improper dihedral distribution : 1.972 (loose)

Inside/Outside distribution : 1.053