YASARA Molecular Dynamics Trajectory Analysis for 4mbs

1. About the simulation

The trajectory /home/kornel/big/projects/mdanalysis/4mbs/4mbs has been analyzed with YASARA version 19.1.1.L.64 over a period of 1000.00 nanoseconds with 4001 snapshots and the AMBER14 force field. Note that the MD simulation may have been run with a different force field, but AMBER14 was used to calculate the energies in this report. To change this, edit the ForceField setting at the start of this macro.

All plots and pictures in this report [like the simulated system below] are 1024 pixels wide, you can change the figurewidth variable in this macro as needed.

Figure-1: A ray-traced picture of the simulated system. The simulation cell boundary is set to periodic. Atoms that stick out of the simulation cell will be wrapped to the opposite side of the cell during the simulation.

1.1. Composition of the system

The components of the system are shown in the table below.

TypeNumber
Protein molecules1
Protein residues346
Protein atoms5648
Nucleic acid molecules0
Nucleic acid residues0
Nucleic acid atoms0
Residue Mrv with 79 atoms1
Residue Pea with 125 atoms184
Element Zn1
Element Cl47
Element Na45
Water residues15552
Total number of atoms75476

Table-1: Composition of the simulated system

Object 1 with name 4mbs has been identified as the solute and is shown below. If this is not the intended solute, please change the soluteobj variable in this macro.

Figure-2: The solute oriented along the major axes.

1.2. The ligand

A special ligand analysis has been performed for MRV, chosen automatically by YASARA with the selection Res MRV. The number of residues matching the ligand selection is 1, with 79 atoms. To change the ligand selection, edit the ligandsel variable at the beginning of this macro.

Figure-3: A ray-traced picture of the ligand MRV. Bonds are colored by their order: Gray = 1, blue = 1.25, magenta = 1.33, red = 1.5, orange = 1.66, bright orange = 1.75, yellow = 2, lime green = 2.5, green = 3 and cyan = 4.

2. Analyses inside the simulation cell

This section shows all analyses that have been performed inside the simulation cell, when all atoms share the common coordinate system of the simulation cell.

Periodic boundaries are active and considered for distance measurements. Calculations that involve groups of atoms [center of mass, regression lines, enclosing spheres..] are ambiguous and should be placed in the next section, unless it is known that the atom group does not drift through a periodic boundary.

2.1. Simulation cell lengths

Conformational changes of the simulated solute molecules lead to fluctuations in density. If the simulation box has a constant size, changes in density lead to changes in pressure. This is not realistic, because molecules normally "live" in a constant pressure environment. During the simulation the cell is therefore rescaled to maintain a constant cell pressure. Depending on the chosen pressure control mode, the three cell axes are either rescaled together [Manometer1D], partly together [X- and Z-axes, Manometer2D, used for membrane simulations], independently [Manometer3D], or not at all [Off]. You can deduce the pressure control mode from the plot below.

Figure-4: Simulation cell lengths [vertical axis] as a function of simulation time [horizontal axis]. Note: Graph CellLengthZ completely covers graph CellLengthX, they share the same values.

2.2. Total potential energy of the system

The total potential energy of the system is plotted, according to the AMBER14 force field. If you ran the simulation with a different force field, you need to adapt the ForceField command at the top of this macro accordingly.

When the simulation is started from an energy-minimized "frozen" conformation, there is usually a sharp increase in energy during the first picoseconds, since the added kinetic energy is partly stored as potential energy. Also on a larger time-scale, the potential energy will often not decrease. A common reason are counter ions. These are initially placed at the positions with the lowest potential energy, usually close to charged solute groups, from where they detach to gain entropy, but also potential energy.

Figure-5: Total potential energy of the system [vertical axis] as a function of simulation time [horizontal axis]. Note: The first value of the plot [-968364.43], coming from the energy minimized starting structure, has been replaced with the second value of the plot [-774542.93] to show this plot with a smaller energy range and thus a higher resolution.

2.3. Potential energy components

The following individual components of the total potential energy are plotted: bond energies [Bond], bond angle energies [Angle], dihedral angle energies [Dihedral], planarity or improper dihedral energies [Planarity], Van der Waals energies [VdW] and electrostatic energies [Coulomb]. Force field energies help to judge the structural quality of a protein: distortions of local covalent geometry can be found by looking at the bond, angle and planarity energies. Unrealistically close contacts [bumps] lead to a high Van der Waals energy, just like a large number of hydrogen bonds [since they pull the atoms closer than their normal Van der Waals contact distance]. The Coulomb energy is the least informative, because it strongly depends on the amino acid composition [e.g. proteins with a net charge have a higher Coulomb energy].

Figure-6: Potential energy components [vertical axis] as a function of simulation time [horizontal axis].

2.4. Surface areas of the solute

The Van der Waals [SurfVdW], molecular [SurfMol] and solvent accessible [SurfAcc] surface areas of the solute in A^2 are plotted. The difference between these surface types can be summarized as follows:

Van der Waals surface: if you think of atoms as spheres with a given Van der Waals radius, then the Van der Waals surface consists of all the points on these spheres that are not inside another sphere. In practice, the Van der Waals surface is of limited use, because it can be found throughout a protein and does not tell much about the interaction with the solvent.

Molecular surface: this is the Van der Waals surface from the viewpoint of a solvent molecule, which is a much more useful concept. The water is assumed to be a sphere of a given radius [also called the water probe], that rolls over the solute. Those parts of the Van der Waals surface that the water probe can touch are simply copied to the molecular surface [and called the contact surface]. Clefts in the Van der Waals surface that are too narrow for the water probe to enter are replaced by the Van der Waals surface of the water probe itself [and called the reentrant surface]. So the molecular surface is a smooth composition of two Van der Waals surfaces: the one of the solute and the one of the solvent molecule while it traces the contours of the solute. Other common names for the molecular surface are solvent excluded surface or Connolly surface.

Solvent accessible surface: this surface consists of all the points that the center of the water probe [i.e. the nucleus of the oxygen atom in the water molecule] can reach while rolling over the solute. The shortest possible distance between the water oxygen nucleus and a solute atom is simply the sum of the Van der Waals radii of the solute atom and the water probe.

Figure-7: Surface areas of the solute [vertical axis] as a function of simulation time [horizontal axis], obtained with the command "SurfObj Solute".

2.5. Number of hydrogen bonds in the solute

The number of hydrogen bonds inside the solute is plotted below. One hydrogen bond per hydrogen atom is assigned at most, picking the better one if two acceptors are available.The following formula yields the bond energy in [kJ/mol] as a function of the Hydrogen-Acceptor distance in [A] and two scaling factors:

The first scaling factor depends on the angle formed by Donor-Hydrogen-Acceptor:

The second scaling factor is derived from the angle formed by Hydrogen-Acceptor-X, where X is the atom covalently bound to the acceptor. If X is a heavy atom:

If X is a hydrogen, slightly smaller angles are allowed:

A hydrogen bond is counted if the hydrogen bond energy obtained with this formula is better than 6.25 kJ/mol [or 1.5 kcal/mol], which is 25% of the optimum value 25 kJ/mol.

Figure-8: Number of hydrogen bonds in the solute [vertical axis] as a function of simulation time [horizontal axis].

2.6. Number of hydrogen bonds between solute and solvent

The plot shows the number of hydrogen bonds between solute and solvent. Together with the plot above, it is a good indicator for successful protein folding, indicated by a decreasing number of bonds with the solvent and a growing number of bonds within the solute.

Figure-9: Number of hydrogen bonds between solute and solvent [vertical axis] as a function of simulation time [horizontal axis].

2.7. Hydrogen bonds made by Res MRV

The following table shows all hydrogen bonds made by Res MRV. With 6 acceptors and 2 donors, a total number of 14 hydrogen bonds are possible - labeled HB1 to HB14.The first atom of the bonding pair is labeled Atm1 and the second Atm2, respectively. The atom ID separates atom name, residue ID and molecule name with dots. A lower-case "h" indicates hetgroups. E and D are short for the hydrogen bonding energy in [ kJ/mol ] and the distance between the bonding partners in [A]. To list other hydrogen bonds, edit the hbosel variable at the beginning of this macro.

Time [ns]HB1Atm1HB1Atm2HB1EHB1DHB2Atm1HB2Atm2HB2EHB2DHB3Atm1HB3Atm2HB3EHB3DHB4Atm1HB4Atm2HB4EHB4DHB5Atm1HB5Atm2HB5EHB5DHB6Atm1HB6Atm2HB6EHB6DHB7Atm1HB7Atm2HB7EHB7DHB8Atm1HB8Atm2HB8EHB8DHB9Atm1HB9Atm2HB9EHB9DHB10Atm1HB10Atm2HB10EHB10DHB11Atm1HB11Atm2HB11EHB11DHB12Atm1HB12Atm2HB12EHB12DHB13Atm1HB13Atm2HB13EHB13DHB14Atm1HB14Atm2HB14EHB14D
0.00N2.h347.AOE1.E316.A23.451.70N3.h347.AOH.Y19.A25.001.91N5.h347.AOH.Y284.A18.302.11--------------------------------------------
0.25N2.h347.AOE1.E316.A18.571.90N3.h347.AOH.Y19.A23.452.02------------------------------------------------
0.50N2.h347.AOE1.E316.A21.101.98----------------------------------------------------
0.75N2.h347.AOE1.E316.A20.731.74----------------------------------------------------
1.00N2.h347.AOE1.E316.A25.001.61N3.h347.AOH.Y19.A10.852.21------------------------------------------------
1.25N2.h347.AOE1.E316.A21.881.77N3.h347.AOH.Y19.A21.102.06------------------------------------------------
1.50N2.h347.AOE1.E316.A23.851.78N3.h347.AOH.Y19.A25.002.08------------------------------------------------
1.75N2.h347.AOE1.E316.A18.751.78----------------------------------------------------
2.00N2.h347.AOE1.E316.A21.101.79N3.h347.AOH.Y19.A25.002.08------------------------------------------------
2.25N2.h347.AOE1.E316.A24.431.99N3.h347.AOH.Y19.A21.881.80------------------------------------------------

Table-2: Hydrogen bonds made by Res MRV as a function of simulation time [first column]. Note: At most 10 table rows are shown. Change the tabrowsmax variable in the macro to adjust the number of shown table rows. The full table can be found in 4mbs_analysis.tab.

2.8. Protein secondary structure content

The total percentages of alpha helices, beta sheets, turns, coils, 3-10 helices and pi helices are calculated and plotted. For clarification, a turn is simply a stretch of four residues that are not part of other secondary structure elements and form a hydrogen bond between the O of the first and the NH of the last residue. A coil is anything that does not fit into the other categories. Note that pi-helices [helices with hydrogen bonds between residues N and N+5] are rather unstable and thus do not normally occur in proteins, except for short bulges in alpha helices [which are often the result of single residue insertions and prolines].

Figure-10: Protein secondary structure content [vertical axis] as a function of simulation time [horizontal axis], obtained with the command "SecStr". Note: Graph HelixPi has all zero values.

2.9. Per-residue protein secondary structure

The following plots show the protein secondary structure per residue as a function of simulation time. They are helpful to monitor protein folding and all other kinds of structural changes. The default secondary structure colors are used, you can change them at View > Color > Parameters > Secondary structure colors. One plot per protein molecule is shown.

Figure-11: Per-residue protein secondary structure as a function of simulation time [horizontal axis] for each residue number [vertical axis]. A table with the raw data is available here: 4mbs_plotres_secstrMolA.tab

2.10. Per-residue number of contacts

The number of contacts per residue as a function of simulation time is shown in the following plots. There is one plot for each protein or nucleic acid molecule. Even though contacts between atoms separated by up to four chemical bonds are excluded, neighboring residues in the molecule usually have enough close atoms to be counted as a contact. Consequently residues with zero contacts are very rare and often glycines. The number of contacts tells you how densely a certain residue range is packed and allows to identify structurally very important residues, e.g. a phenylalanine in the hydrophobic core can contact 15 or more other residues.

Figure-12: Per-residue number of contacts as a function of simulation time [horizontal axis] for each residue number [vertical axis]. A table with the raw data is available here: 4mbs_plotres_conMolA.tab

2.11. Per-residue contacts with ligand

The following plots show the types of contacts made with the ligand - as a function of simulation time. There is one plot for each protein or nucleic acid molecule. Three types of contacts are shown: Hydrogen bonds [red] ,hydrophobic contacts [green] and ionic interactions [blue]. Also mixtures of these three colors can show up if a certain residue is involved in more than one type of contact with the ligand [see plot legend].

Figure-13: Per-residue contacts with ligand as a function of simulation time [horizontal axis] for each residue number [vertical axis]. A table with the raw data is available here: 4mbs_plotres_ligconMolA.tab

3. Analysis outside the simulation cell

The following section presents data gathered outside the simulation cell, where each object has its own local coordinate system and no periodic boundaries are present. Calculations that involve the interaction between objects [common surface areas, contacts between objects..] must be placed in the previous section.

3.1. Radius of gyration of the solute

After determining the center of mass of the solute, the radius of gyration is calculated and plotted according to this formula:

In this formula, C is the center of mass, and Ri is the position of atom i of N.

Figure-14: Radius of gyration of the solute [vertical axis] as a function of simulation time [horizontal axis], obtained with the command "RadiusObj Solute,Center=Mass,Type=Gyration".

4. Analyses performed with respect to the starting structure

Analyses performed with respect to the starting structure are shown in this section. These are also done outside the simulation cell, where each object has its own local coordinate systems and no periodic boundaries are present. To choose another reference snapshot than 0, edit the refsnapshot variable at the beginning of this macro.

4.1. Solute RMSD from the starting structure

The plot shows Calpha [RMSDCa], backbone [RMSDBb] and all-heavy atom [RMSDAll] RMSDs calculated according to this formula, where Ri is the vector linking the positions of atom i [of N atoms] in the reference snapshot and the current snapshot after optimal superposition:

The selection for the Calpha RMSD calculation is CA Protein or C1* NucAcid, this matched 346 atoms. The Calpha selection thus includes the main backbone carbon C1* of nucleic acids, so the plot also shows a Calpha RMSD if you simulate just nucleic acids. In simulations of protein-DNA complexes, the Calpha RMSD therefore considers the DNA too. To change the Calpha selection, edit the casel variable at the beginning of this macro.

Figure-15: Solute RMSD from the starting structure [vertical axis] as a function of simulation time [horizontal axis].

4.2. Ligand movement RMSD after superposing on the receptor

The following plot shows the RMSD of the ligand heavy atoms over time, measured after superposing the receptor on its reference structure. This procedure delivers information about the movement of the ligand in its binding pocket.

Figure-16: Ligand movement RMSD after superposing on the receptor [vertical axis] as a function of simulation time [horizontal axis].

4.3. Ligand conformation RMSD after superposing on the ligand

This plot displays the RMSD of the ligand atoms over time, measured after superposing on the reference structure of the ligand. The gained data summarize the conformational changes of the ligand.

Figure-17: Ligand conformation RMSD after superposing on the ligand [vertical axis] as a function of simulation time [horizontal axis].

5. Solute residue RMSF

The Root Mean Square Fluctuation [RMSF] per solute residue is calculated from the average RMSF of its constituting atoms. The RMSF of atom i with j runing from 1 to 3 for the x, y, and z coordinate of the atom position vector P and k runing over the set of N evaluated snapshots is given by following formula:

Figure-18: The Root Mean Square Fluctuation [vertical axis] per solute protein/nucleic acid residue [horizontal axis] calculated from the average RMSF of the atoms constituting the residue. A RMSF of exactly zero means that that residue number is not present in the molecule. Atom RMSF table: 4mbs_rmsf.tab

MolResidueFirst atomRMSF[A]
AMrv-34756496.40
AZn-34857283.98

Table-3: RMSF in Angstrom for non-protein/nucleic acid residues in the solute.

6. Dynamic Cross-Correlation Matrix

The dynamic cross-correlation matrix [DCCM] is a square matrix, whose rows and columns match the selected units Atom CA Protein or C1* NucAcid. To change this selection, edit the dccmsel variable at the beginning of this macro. The DCCM shows how the movements of all selected pairs correlate. The values in the DCCM range from -1 [perfectly anti-correlated] to +1 [perfectly correlated]. The values along the diagonal are always +1 [because the motion of an atom is perfectly correlated to itself]. The DCCM element for units i and j is obtained with the following formula:

Here d is the displacement between the current position and the average position of the selected unit, and the angle brackets indicate the average over all samples. The highest correlations off the diagonal can often be found for bridged cysteines.

The image below shows the correlation directly in the solute object:

Figure-19: Blue and red lines are shown between strongly anti- and correlated pairs. To change the threshold value for the correlation lines edit the dccmcut variable at the beginning of this macro. To look at this structure interactively, open the file 4mbs_dccm.yob in YASARA.

In the image below, the DCCM is visualized with colors ranging from blue [-1, fully anti-correlated] to yellow [+1, fully correlated].

Figure-20: Visualization of the dynamic cross-correlation matrix. Open the file 4mbs_dccm.sce in YASARA to look at this matrix visualization interactively. In the scene file, the zero level [0, not correlated] is indicated with a wire-frame grid.

DCCMA
Pro
1
A
Cys
2
A
Gln
3
A
Lys
4
A
Ile
5
A
Asn
6
A
Val
7
A
Lys
8
A
Gln
9
A
Ile
10
A
Ala
11
A
Ala
12
A
Arg
13
A
Leu
14
A
Leu
15
A
Pro
16
A
Pro
17
A
Leu
18
A
Tyr
19
A
Ser
20
A
Leu
21
A
Val
22
A
Phe
23
A
Ile
24
A
Phe
25
A
Gly
26
A
Phe
27
A
Val
28
A
Gly
29
A
Asn
30
A
Met
31
A
Leu
32
A
Val
33
A
Ile
34
A
Leu
35
A
Ile
36
A
Leu
37
A
Ile
38
A
Asn
39
A
Tyr
40
A
Lys
41
A
Arg
42
A
Leu
43
A
Lys
44
A
Ser
45
A
Met
46
A
Thr
47
A
Asp
48
A
Ile
49
A
Tyr
50
A
Leu
51
A
Leu
52
A
Asn
53
A
Leu
54
A
Ala
55
A
Ile
56
A
Ser
57
A
Asp
58
A
Leu
59
A
Phe
60
A
Phe
61
A
Leu
62
A
Leu
63
A
Thr
64
A
Val
65
A
Pro
66
A
Phe
67
A
Trp
68
A
Ala
69
A
His
70
A
Tyr
71
A
Ala
72
A
Ala
73
A
Ala
74
A
Gln
75
A
Trp
76
A
Asp
77
A
Phe
78
A
Gly
79
A
Asn
80
A
Thr
81
A
Met
82
A
Cys
83
A
Gln
84
A
Leu
85
A
Leu
86
A
Thr
87
A
Gly
88
A
Leu
89
A
Tyr
90
A
Phe
91
A
Ile
92
A
Gly
93
A
Phe
94
A
Phe
95
A
Ser
96
A
Gly
97
A
Ile
98
A
Phe
99
A
Phe
100
A
Ile
101
A
Ile
102
A
Leu
103
A
Leu
104
A
Thr
105
A
Ile
106
A
Asp
107
A
Arg
108
A
Tyr
109
A
Leu
110
A
Ala
111
A
Val
112
A
Val
113
A
His
114
A
Ala
115
A
Val
116
A
Phe
117
A
Ala
118
A
Leu
119
A
Lys
120
A
Ala
121
A
Arg
122
A
Thr
123
A
Val
124
A
Thr
125
A
Phe
126
A
Gly
127
A
Val
128
A
Val
129
A
Thr
130
A
Ser
131
A
Val
132
A
Ile
133
A
Thr
134
A
Trp
135
A
Val
136
A
Val
137
A
Ala
138
A
Val
139
A
Phe
140
A
Ala
141
A
Ser
142
A
Leu
143
A
Pro
144
A
Asn
145
A
Ile
146
A
Ile
147
A
Phe
148
A
Thr
149
A
Arg
150
A
Ser
151
A
Gln
152
A
Lys
153
A
Glu
154
A
Gly
155
A
Leu
156
A
His
157
A
Tyr
158
A
Thr
159
A
Cys
160
A
Ser
161
A
Ser
162
A
His
163
A
Phe
164
A
Pro
165
A
Tyr
166
A
Ser
167
A
Gln
168
A
Tyr
169
A
Gln
170
A
Phe
171
A
Trp
172
A
Lys
173
A
Asn
174
A
Phe
175
A
Gln
176
A
Thr
177
A
Leu
178
A
Lys
179
A
Ile
180
A
Val
181
A
Ile
182
A
Leu
183
A
Gly
184
A
Leu
185
A
Val
186
A
Leu
187
A
Pro
188
A
Leu
189
A
Leu
190
A
Val
191
A
Met
192
A
Val
193
A
Ile
194
A
Cys
195
A
Tyr
196
A
Ser
197
A
Gly
198
A
Ile
199
A
Leu
200
A
Lys
201
A
Thr
202
A
Leu
203
A
Leu
204
A
Arg
205
A
Met
206
A
Lys
207
A
Lys
208
A
Tyr
209
A
Thr
210
A
Cys
211
A
Thr
212
A
Val
213
A
Cys
214
A
Gly
215
A
Tyr
216
A
Ile
217
A
Tyr
218
A
Asn
219
A
Pro
220
A
Glu
221
A
Asp
222
A
Gly
223
A
Asp
224
A
Pro
225
A
Asp
226
A
Asn
227
A
Gly
228
A
Val
229
A
Asn
230
A
Pro
231
A
Gly
232
A
Thr
233
A
Asp
234
A
Phe
235
A
Lys
236
A
Asp
237
A
Ile
238
A
Pro
239
A
Asp
240
A
Asp
241
A
Trp
242
A
Val
243
A
Cys
244
A
Pro
245
A
Leu
246
A
Cys
247
A
Gly
248
A
Val
249
A
Gly
250
A
Lys
251
A
Asp
252
A
Gln
253
A
Phe
254
A
Glu
255
A
Glu
256
A
Val
257
A
Glu
258
A
Glu
259
A
Glu
260
A
Lys
261
A
Lys
262
A
Arg
263
A
His
264
A
Arg
265
A
Asp
266
A
Val
267
A
Arg
268
A
Leu
269
A
Ile
270
A
Phe
271
A
Thr
272
A
Ile
273
A
Met
274
A
Ile
275
A
Val
276
A
Tyr
277
A
Phe
278
A
Leu
279
A
Phe
280
A
Trp
281
A
Ala
282
A
Pro
283
A
Tyr
284
A
Asn
285
A
Ile
286
A
Val
287
A
Leu
288
A
Leu
289
A
Leu
290
A
Asn
291
A
Thr
292
A
Phe
293
A
Gln
294
A
Glu
295
A
Phe
296
A
Phe
297
A
Gly
298
A
Leu
299
A
Asn
300
A
Asn
301
A
Cys
302
A
Ser
303
A
Ser
304
A
Ser
305
A
Asn
306
A
Arg
307
A
Leu
308
A
Asp
309
A
Gln
310
A
Ala
311
A
Met
312
A
Gln
313
A
Val
314
A
Thr
315
A
Glu
316
A
Thr
317
A
Leu
318
A
Gly
319
A
Met
320
A
Thr
321
A
His
322
A
Cys
323
A
Cys
324
A
Ile
325
A
Asn
326
A
Pro
327
A
Ile
328
A
Ile
329
A
Tyr
330
A
Ala
331
A
Phe
332
A
Val
333
A
Gly
334
A
Glu
335
A
Glu
336
A
Phe
337
A
Arg
338
A
Asn
339
A
Tyr
340
A
Leu
341
A
Leu
342
A
Val
343
A
Phe
344
A
Phe
345
A
Gln
346
A-Pro-11.000.920.700.210.130.100.240.100.120.21-0.030.050.040.060.040.080.130.130.130.150.170.140.120.110.150.09-0.000.020.040.04-0.020.040.04-0.000.020.050.000.000.040.03-0.01-0.02-0.05-0.05-0.07-0.07-0.09-0.08-0.11-0.09-0.05-0.06-0.09-0.08-0.00-0.01-0.050.030.060.050.020.030.010.060.090.100.080.040.060.08-0.00-0.05-0.010.01-0.02-0.040.02-0.03-0.12-0.10-0.08-0.06-0.08-0.14-0.08-0.04-0.09-0.11-0.06-0.07-0.15-0.14-0.06-0.07-0.10-0.15-0.08-0.04-0.11-0.11-0.07-0.09-0.13-0.12-0.07-0.09-0.15-0.10-0.04-0.12-0.15-0.11-0.10-0.12-0.14-0.13-0.06-0.10-0.16-0.13-0.10-0.07-0.12-0.11-0.14-0.15-0.13-0.12-0.14-0.14-0.12-0.14-0.15-0.13-0.15-0.17-0.17-0.17-0.19-0.20-0.19-0.21-0.19-0.23-0.27-0.17-0.20-0.21-0.15-0.10-0.09-0.10-0.12-0.13-0.15-0.14-0.07-0.010.00-0.04-0.07-0.12-0.08-0.18-0.22-0.17-0.18-0.22-0.07-0.04-0.21-0.180.04-0.06-0.20-0.100.08-0.04-0.15-0.050.00-0.07-0.09-0.05-0.04-0.07-0.10-0.10-0.10-0.12-0.14-0.13-0.15-0.15-0.11-0.12-0.16-0.14-0.13-0.14-0.11-0.05-0.07-0.050.050.040.01-0.01-0.08-0.04-0.06-0.07-0.06-0.010.020.030.060.000.050.000.060.080.040.030.030.030.010.020.000.020.060.03-0.03-0.16-0.19-0.20-0.13-0.08-0.08-0.09-0.06-0.05-0.05-0.030.000.01-0.03-0.04-0.07-0.08-0.11-0.14-0.11-0.11-0.10-0.080.020.070.03-0.01-0.13-0.16-0.20-0.050.02-0.06-0.03-0.03-0.07-0.03-0.01-0.01-0.02-0.000.040.060.020.060.100.090.080.050.110.120.050.060.140.04-0.030.060.08-0.07-0.010.220.01-0.080.110.250.110.100.370.450.410.340.400.420.360.340.370.330.270.270.260.210.180.160.150.140.100.060.070.030.020.03-0.020.030.020.030.030.02-0.000.01-0.02-0.15-0.15-0.07-0.15-0.28-0.24-0.15-0.23-0.230.000.05-0.020.01
A-Cys-20.921.000.790.390.360.350.430.250.260.36-0.030.080.100.100.100.160.200.200.200.220.220.180.150.140.140.07-0.06-0.07-0.03-0.03-0.11-0.06-0.05-0.11-0.08-0.05-0.10-0.10-0.05-0.06-0.11-0.13-0.16-0.15-0.17-0.18-0.21-0.21-0.25-0.22-0.17-0.17-0.20-0.18-0.07-0.07-0.13-0.010.080.04-0.020.030.020.080.130.140.110.070.110.130.00-0.040.020.01-0.04-0.070.01-0.08-0.13-0.10-0.08-0.05-0.08-0.13-0.08-0.05-0.08-0.12-0.08-0.06-0.18-0.20-0.10-0.10-0.19-0.25-0.15-0.12-0.23-0.23-0.17-0.21-0.26-0.24-0.19-0.21-0.27-0.22-0.13-0.22-0.26-0.22-0.20-0.23-0.27-0.26-0.21-0.23-0.26-0.24-0.22-0.19-0.25-0.23-0.26-0.27-0.25-0.23-0.26-0.26-0.24-0.25-0.25-0.24-0.25-0.26-0.27-0.27-0.27-0.29-0.28-0.29-0.25-0.31-0.29-0.16-0.20-0.20-0.13-0.08-0.08-0.10-0.13-0.13-0.16-0.16-0.09-0.020.01-0.02-0.05-0.09-0.05-0.15-0.20-0.12-0.12-0.17-0.010.01-0.19-0.160.07-0.05-0.21-0.120.06-0.08-0.21-0.12-0.05-0.16-0.18-0.11-0.09-0.15-0.21-0.19-0.18-0.23-0.25-0.23-0.25-0.27-0.21-0.20-0.26-0.25-0.21-0.22-0.17-0.13-0.18-0.14-0.02-0.07-0.11-0.11-0.17-0.13-0.11-0.15-0.11-0.06-0.020.030.030.030.070.070.110.160.150.160.160.160.140.150.140.160.170.130.10-0.12-0.15-0.18-0.050.01-0.01-0.04-0.000.020.010.020.080.070.010.00-0.05-0.06-0.10-0.16-0.15-0.17-0.19-0.19-0.11-0.05-0.10-0.13-0.24-0.26-0.31-0.14-0.02-0.08-0.11-0.10-0.15-0.12-0.08-0.07-0.09-0.07-0.000.02-0.020.020.080.080.050.000.100.110.000.040.160.04-0.030.110.16-0.030.030.300.110.000.180.310.200.140.510.640.580.480.560.610.510.470.530.490.370.360.390.320.230.220.230.180.100.090.100.030.010.06-0.01-0.01-0.010.02-0.01-0.03-0.00-0.01-0.07-0.24-0.20-0.12-0.23-0.30-0.21-0.10-0.19-0.140.110.150.080.11
A-Gln-30.700.791.000.650.580.490.340.170.140.220.050.110.090.090.060.130.160.170.150.150.170.130.070.090.130.05-0.06-0.03-0.03-0.04-0.11-0.07-0.08-0.13-0.10-0.09-0.13-0.13-0.08-0.10-0.15-0.18-0.19-0.19-0.20-0.20-0.21-0.22-0.25-0.21-0.18-0.21-0.23-0.19-0.13-0.15-0.18-0.08-0.02-0.06-0.09-0.05-0.050.010.070.060.050.060.070.08-0.02-0.020.030.00-0.08-0.13-0.08-0.16-0.16-0.14-0.15-0.15-0.13-0.17-0.16-0.16-0.12-0.16-0.14-0.11-0.19-0.23-0.13-0.10-0.20-0.23-0.12-0.09-0.18-0.17-0.11-0.14-0.18-0.15-0.12-0.13-0.17-0.15-0.11-0.17-0.19-0.16-0.13-0.17-0.20-0.22-0.21-0.22-0.22-0.23-0.23-0.17-0.20-0.18-0.22-0.25-0.23-0.21-0.25-0.25-0.24-0.25-0.26-0.25-0.26-0.26-0.26-0.27-0.27-0.27-0.26-0.28-0.25-0.26-0.27-0.24-0.23-0.22-0.15-0.07-0.10-0.09-0.13-0.10-0.15-0.15-0.09-0.010.01-0.03-0.07-0.12-0.05-0.21-0.26-0.19-0.17-0.27-0.14-0.18-0.36-0.28-0.09-0.23-0.34-0.24-0.10-0.22-0.29-0.17-0.13-0.22-0.23-0.15-0.12-0.17-0.22-0.17-0.15-0.21-0.21-0.15-0.16-0.18-0.14-0.11-0.16-0.17-0.13-0.12-0.08-0.06-0.13-0.09-0.02-0.07-0.09-0.05-0.14-0.11-0.12-0.16-0.13-0.060.040.070.090.090.140.120.170.200.180.170.170.160.120.140.130.170.200.160.09-0.12-0.15-0.20-0.08-0.04-0.06-0.10-0.05-0.03-0.04-0.020.060.05-0.03-0.04-0.10-0.11-0.15-0.21-0.19-0.19-0.20-0.17-0.09-0.04-0.06-0.04-0.09-0.12-0.17-0.040.06-0.01-0.05-0.04-0.10-0.06-0.010.00-0.02-0.020.040.070.040.040.090.100.070.030.120.110.030.080.180.080.030.130.14-0.000.040.160.020.120.240.260.140.250.600.660.600.530.600.600.500.470.500.440.360.340.300.270.210.180.180.170.090.070.140.100.060.080.050.060.020.060.030.000.030.03-0.04-0.17-0.10-0.04-0.10-0.16-0.12-0.07-0.12-0.120.000.02-0.010.02
A-Lys-40.210.390.651.000.820.670.430.120.100.220.140.180.180.120.130.230.190.170.140.110.100.04-0.02-0.02-0.01-0.08-0.18-0.19-0.23-0.17-0.27-0.32-0.33-0.34-0.33-0.36-0.38-0.34-0.29-0.34-0.38-0.39-0.37-0.37-0.36-0.37-0.39-0.43-0.45-0.41-0.39-0.42-0.44-0.38-0.33-0.35-0.37-0.25-0.18-0.23-0.22-0.14-0.15-0.08-0.000.020.010.060.120.110.000.060.100.06-0.06-0.06-0.00-0.07-0.06-0.02-0.09-0.06-0.03-0.08-0.16-0.14-0.07-0.16-0.19-0.15-0.24-0.33-0.26-0.20-0.30-0.35-0.21-0.16-0.28-0.29-0.19-0.23-0.27-0.21-0.21-0.21-0.21-0.27-0.21-0.20-0.22-0.18-0.16-0.22-0.27-0.30-0.34-0.38-0.34-0.32-0.37-0.35-0.36-0.33-0.34-0.39-0.39-0.37-0.39-0.41-0.43-0.39-0.38-0.41-0.41-0.36-0.37-0.38-0.34-0.31-0.31-0.30-0.26-0.23-0.11-0.14-0.13-0.05-0.010.060.050.060.030.04-0.00-0.010.030.080.070.050.020.030.08-0.01-0.040.010.04-0.07-0.04-0.13-0.23-0.14-0.08-0.21-0.25-0.18-0.17-0.26-0.25-0.23-0.20-0.28-0.29-0.19-0.15-0.21-0.27-0.18-0.15-0.22-0.21-0.12-0.11-0.18-0.13-0.03-0.07-0.12-0.06-0.02-0.01-0.07-0.15-0.11-0.11-0.22-0.22-0.09-0.19-0.15-0.16-0.23-0.18-0.070.050.150.160.190.270.260.310.350.320.290.300.260.200.240.240.290.340.300.21-0.10-0.13-0.21-0.040.00-0.05-0.11-0.05-0.01-0.020.020.150.13-0.00-0.02-0.12-0.14-0.18-0.27-0.26-0.26-0.30-0.27-0.19-0.14-0.11-0.03-0.03-0.03-0.100.020.160.08-0.07-0.08-0.13-0.06-0.03-0.02-0.03-0.020.000.030.020.020.040.050.01-0.000.100.09-0.000.070.180.150.090.210.260.110.130.280.120.200.370.350.320.240.620.650.670.620.590.610.570.500.450.470.410.270.250.310.210.120.150.150.030.010.090.04-0.020.070.08-0.02-0.13-0.05-0.07-0.11-0.09-0.08-0.13-0.22-0.040.03-0.07-0.09-0.03-0.04-0.060.010.050.100.160.15
A-Ile-50.130.360.580.821.000.850.620.430.380.430.070.170.150.090.100.220.200.160.150.170.130.060.040.050.01-0.08-0.15-0.17-0.19-0.19-0.24-0.25-0.27-0.28-0.25-0.27-0.31-0.25-0.20-0.24-0.30-0.30-0.31-0.31-0.34-0.36-0.42-0.42-0.41-0.40-0.39-0.37-0.37-0.37-0.28-0.24-0.30-0.21-0.05-0.11-0.16-0.07-0.030.030.070.100.110.120.140.170.060.060.120.09-0.01-0.040.03-0.040.060.080.050.040.050.02-0.05-0.060.02-0.06-0.08-0.08-0.22-0.25-0.18-0.23-0.37-0.36-0.26-0.27-0.37-0.37-0.31-0.36-0.38-0.34-0.35-0.35-0.36-0.37-0.33-0.34-0.34-0.31-0.29-0.33-0.35-0.35-0.42-0.47-0.35-0.36-0.42-0.38-0.36-0.31-0.32-0.37-0.37-0.32-0.35-0.39-0.38-0.33-0.34-0.38-0.34-0.31-0.36-0.37-0.27-0.30-0.36-0.29-0.20-0.24-0.15-0.05-0.03-0.010.070.130.090.080.040.050.01-0.020.030.090.120.130.090.090.130.01-0.020.040.07-0.040.02-0.06-0.21-0.18-0.10-0.26-0.33-0.27-0.28-0.41-0.42-0.38-0.34-0.42-0.42-0.33-0.30-0.38-0.41-0.33-0.32-0.38-0.37-0.30-0.29-0.34-0.30-0.23-0.25-0.28-0.24-0.19-0.16-0.20-0.30-0.24-0.19-0.27-0.28-0.21-0.18-0.16-0.09-0.17-0.10-0.05-0.000.080.030.140.090.180.130.220.300.320.320.320.320.330.330.320.280.240.290.070.060.000.170.200.150.100.140.170.150.150.220.180.110.130.050.050.02-0.06-0.10-0.12-0.21-0.24-0.27-0.22-0.26-0.23-0.25-0.18-0.26-0.21-0.05-0.01-0.19-0.19-0.24-0.23-0.20-0.18-0.21-0.23-0.19-0.14-0.17-0.18-0.13-0.11-0.16-0.20-0.09-0.09-0.19-0.130.01-0.03-0.090.020.11-0.02-0.070.160.290.300.270.370.320.270.600.650.600.530.570.570.480.420.440.410.290.210.230.210.070.030.080.03-0.08-0.030.05-0.03-0.040.03-0.02-0.09-0.08-0.05-0.13-0.090.01-0.07-0.18-0.25-0.10-0.04-0.21-0.110.080.06-0.020.110.180.170.200.19
A-Asn-60.100.350.490.670.851.000.710.590.540.560.060.210.200.150.170.290.260.210.220.230.170.100.090.090.00-0.08-0.15-0.20-0.21-0.25-0.28-0.28-0.31-0.33-0.30-0.32-0.34-0.29-0.25-0.30-0.35-0.34-0.34-0.33-0.36-0.36-0.42-0.44-0.42-0.39-0.39-0.38-0.35-0.35-0.26-0.20-0.25-0.170.01-0.05-0.11-0.010.020.080.130.170.170.170.210.230.130.130.180.150.060.010.08-0.040.040.090.080.050.070.04-0.03-0.030.04-0.04-0.07-0.06-0.20-0.25-0.19-0.23-0.37-0.36-0.29-0.29-0.38-0.38-0.33-0.37-0.40-0.36-0.36-0.35-0.36-0.35-0.30-0.31-0.32-0.30-0.30-0.34-0.36-0.39-0.46-0.44-0.33-0.34-0.38-0.38-0.37-0.32-0.32-0.37-0.37-0.32-0.33-0.36-0.36-0.31-0.31-0.34-0.30-0.27-0.32-0.33-0.24-0.26-0.31-0.26-0.16-0.20-0.110.000.010.020.100.160.120.140.090.100.040.020.070.140.170.170.140.110.110.020.000.090.100.010.06-0.02-0.15-0.13-0.07-0.20-0.26-0.27-0.28-0.34-0.37-0.35-0.31-0.40-0.40-0.31-0.29-0.37-0.41-0.34-0.33-0.41-0.40-0.32-0.34-0.39-0.32-0.23-0.30-0.33-0.24-0.20-0.18-0.21-0.30-0.23-0.18-0.29-0.30-0.29-0.22-0.21-0.11-0.18-0.10-0.09-0.080.01-0.060.06-0.010.140.070.150.270.300.310.310.340.360.360.340.260.240.330.140.130.080.250.270.220.160.200.230.200.170.230.160.110.160.090.100.08-0.02-0.07-0.11-0.22-0.26-0.33-0.27-0.34-0.33-0.34-0.29-0.32-0.27-0.16-0.10-0.22-0.21-0.25-0.26-0.21-0.19-0.21-0.22-0.17-0.15-0.15-0.15-0.12-0.11-0.16-0.21-0.11-0.10-0.21-0.15-0.03-0.07-0.090.030.110.00-0.020.070.180.220.130.130.150.050.430.550.500.390.440.520.410.320.410.420.260.200.280.230.070.070.140.06-0.040.020.09-0.03-0.040.03-0.03-0.11-0.08-0.07-0.16-0.13-0.03-0.12-0.20-0.29-0.19-0.16-0.28-0.130.080.080.040.190.240.260.270.24
A-Val-70.240.430.340.430.620.711.000.790.790.720.080.360.440.340.280.460.490.350.370.470.360.210.290.300.120.040.05-0.03-0.07-0.15-0.09-0.13-0.24-0.24-0.15-0.22-0.33-0.24-0.15-0.22-0.32-0.31-0.38-0.39-0.48-0.54-0.59-0.55-0.54-0.55-0.50-0.44-0.44-0.47-0.26-0.18-0.29-0.130.130.03-0.030.190.220.310.370.430.420.370.440.470.330.310.380.320.220.220.310.280.300.280.260.320.310.200.180.260.240.070.110.11-0.20-0.24-0.13-0.28-0.49-0.51-0.45-0.46-0.62-0.62-0.56-0.60-0.64-0.61-0.58-0.58-0.62-0.59-0.51-0.52-0.55-0.53-0.53-0.56-0.58-0.54-0.50-0.58-0.52-0.50-0.55-0.60-0.55-0.48-0.48-0.55-0.54-0.46-0.48-0.55-0.51-0.43-0.47-0.51-0.43-0.42-0.52-0.48-0.35-0.44-0.50-0.36-0.26-0.35-0.180.090.010.050.200.290.300.240.170.140.080.060.160.260.340.370.280.210.210.100.080.160.130.040.130.05-0.13-0.12-0.01-0.19-0.32-0.25-0.22-0.38-0.48-0.47-0.42-0.54-0.53-0.44-0.45-0.54-0.57-0.53-0.53-0.58-0.59-0.53-0.54-0.59-0.55-0.44-0.47-0.52-0.46-0.41-0.44-0.46-0.48-0.46-0.40-0.44-0.51-0.49-0.37-0.32-0.14-0.25-0.13-0.11-0.24-0.02-0.140.100.010.240.130.270.440.490.500.510.540.550.550.520.410.350.490.200.210.140.390.460.410.320.390.420.370.320.400.300.240.310.200.220.180.03-0.05-0.12-0.33-0.45-0.53-0.48-0.55-0.58-0.59-0.55-0.59-0.51-0.38-0.36-0.44-0.44-0.43-0.47-0.45-0.42-0.40-0.41-0.36-0.32-0.33-0.29-0.24-0.22-0.30-0.35-0.20-0.19-0.36-0.30-0.12-0.24-0.35-0.18-0.04-0.26-0.290.150.220.020.090.330.140.150.520.640.570.470.560.620.480.420.550.490.290.270.390.260.060.070.170.03-0.12-0.030.00-0.16-0.15-0.00-0.11-0.22-0.11-0.09-0.26-0.19-0.04-0.16-0.33-0.43-0.30-0.24-0.37-0.210.030.090.060.240.400.440.420.40
A-Lys-80.100.250.170.120.430.590.791.000.890.65-0.080.230.270.160.110.310.330.180.220.380.250.120.250.290.080.020.110.060.01-0.140.040.02-0.10-0.090.02-0.05-0.13-0.040.02-0.05-0.14-0.09-0.15-0.18-0.27-0.32-0.39-0.33-0.26-0.31-0.32-0.21-0.17-0.27-0.120.03-0.08-0.050.230.170.050.230.300.340.350.400.420.350.360.400.330.260.330.300.270.230.310.290.350.320.350.350.330.280.280.330.280.190.210.15-0.11-0.07-0.03-0.25-0.40-0.35-0.39-0.40-0.50-0.49-0.51-0.53-0.54-0.56-0.53-0.51-0.55-0.49-0.46-0.48-0.50-0.50-0.52-0.50-0.47-0.41-0.39-0.42-0.32-0.33-0.34-0.40-0.31-0.25-0.23-0.28-0.28-0.18-0.20-0.27-0.21-0.12-0.19-0.24-0.13-0.13-0.27-0.24-0.08-0.19-0.32-0.17-0.04-0.14-0.090.190.170.130.250.310.310.270.230.250.210.170.210.240.330.360.250.180.190.110.140.180.120.080.130.06-0.07-0.10-0.07-0.21-0.28-0.30-0.31-0.40-0.46-0.46-0.46-0.52-0.49-0.44-0.49-0.56-0.55-0.53-0.57-0.59-0.59-0.57-0.59-0.60-0.58-0.55-0.56-0.57-0.54-0.52-0.53-0.51-0.50-0.49-0.38-0.32-0.38-0.46-0.18-0.160.06-0.020.090.01-0.21-0.06-0.23-0.00-0.250.00-0.20-0.050.210.310.310.360.460.440.430.320.140.090.380.350.380.380.510.550.550.510.540.530.490.410.380.290.340.440.400.440.410.320.240.15-0.06-0.21-0.42-0.39-0.52-0.64-0.66-0.62-0.58-0.63-0.61-0.50-0.48-0.47-0.43-0.52-0.53-0.50-0.47-0.50-0.47-0.46-0.46-0.42-0.37-0.39-0.45-0.51-0.44-0.41-0.51-0.49-0.37-0.41-0.48-0.39-0.24-0.32-0.40-0.120.170.04-0.080.09-0.000.090.210.320.170.050.210.250.050.030.240.13-0.090.000.14-0.05-0.22-0.13-0.03-0.18-0.26-0.11-0.10-0.27-0.20-0.09-0.19-0.25-0.07-0.13-0.30-0.19-0.06-0.21-0.36-0.36-0.37-0.36-0.44-0.200.060.140.110.290.420.420.360.33
A-Gln-90.120.260.140.100.380.540.790.891.000.81-0.000.340.420.300.240.440.470.310.340.490.350.190.320.350.110.050.120.02-0.03-0.16-0.02-0.07-0.19-0.18-0.08-0.17-0.26-0.15-0.08-0.16-0.26-0.21-0.29-0.31-0.42-0.46-0.52-0.46-0.40-0.44-0.44-0.33-0.30-0.38-0.20-0.06-0.17-0.080.220.140.040.260.330.390.420.490.490.420.470.510.390.340.430.360.310.280.350.290.370.340.360.390.380.300.300.360.330.190.220.18-0.12-0.12-0.06-0.27-0.48-0.44-0.47-0.51-0.60-0.59-0.61-0.62-0.62-0.65-0.61-0.57-0.61-0.58-0.51-0.51-0.55-0.56-0.59-0.57-0.55-0.50-0.46-0.47-0.39-0.40-0.41-0.51-0.44-0.37-0.34-0.41-0.42-0.31-0.32-0.40-0.35-0.25-0.31-0.37-0.25-0.24-0.38-0.35-0.18-0.29-0.41-0.24-0.12-0.22-0.100.200.130.120.270.350.350.300.240.260.190.150.220.290.410.440.330.230.220.110.130.200.130.070.140.06-0.09-0.11-0.06-0.21-0.30-0.32-0.31-0.42-0.49-0.50-0.50-0.59-0.55-0.49-0.55-0.63-0.63-0.60-0.63-0.67-0.66-0.63-0.65-0.68-0.64-0.56-0.60-0.62-0.55-0.52-0.57-0.56-0.53-0.54-0.47-0.42-0.47-0.53-0.26-0.240.00-0.100.03-0.02-0.26-0.04-0.210.07-0.160.14-0.080.080.360.450.450.490.580.580.570.480.280.230.520.390.430.400.590.640.610.540.590.600.550.470.470.350.370.480.410.450.410.280.180.09-0.16-0.34-0.54-0.52-0.64-0.74-0.73-0.70-0.66-0.69-0.65-0.57-0.56-0.56-0.51-0.59-0.58-0.56-0.52-0.54-0.51-0.48-0.48-0.43-0.39-0.40-0.47-0.53-0.43-0.40-0.52-0.50-0.37-0.40-0.47-0.38-0.22-0.29-0.38-0.110.180.01-0.090.06-0.100.110.280.390.260.140.270.330.150.090.300.22-0.020.040.210.02-0.18-0.080.05-0.14-0.23-0.07-0.08-0.27-0.21-0.06-0.18-0.29-0.11-0.15-0.34-0.26-0.10-0.24-0.44-0.46-0.41-0.41-0.44-0.180.070.180.200.380.510.520.470.43

Table-4: Dynamic cross-correlation matrix. The full table is also available in text format, you need a proper text editor without line wrapping to look at this file: 4mbs_dccm.tab. Note: At most 10 rows of the DCCM are shown above. Change the tabrowsmax variable in the macro to adjust this number.

7. Additional files

The following additional files have been created:

7.1. The main data table

The main table contains all collected data in a single file. The column names match the names used above for graphs in plots and columns in tables. You can find a more detailed explanation of this table in the user manual at Recipes > Run a molecular dynamics simulation > Analyzing a trajectory. If you parse this file automatically, keep in mind that the number of columns can change any time, so you have to use the names in the first table row to find the columns of interest: 4mbs_analysis.tab

7.2. Per-residue data tables

Data of the per-residue plots:

4mbs_plotres_secstrMolA.tab
4mbs_plotres_conMolA.tab
4mbs_plotres_ligconMolA.tab

7.3. The structures

The time averaged structure in PDB format: 4mbs_average.pdb

The snapshot with the minimum solute energy. Either just the solute in PDB format 4mbs_energymin.pdb, or the complete system including solvent as a YASARA scene 4mbs_energymin.sce.

The last snapshot of the simulation. Either just the solute in PDB format 4mbs_last.pdb, or the complete system including solvent as a YASARA scene 4mbs_last.sce

7.4. The RMSF table

A table that lists the Root Mean Square Fluctuations [RMSFs] of all atoms in [A] is available here: 4mbs_rmsf.tab. The RMSFs have also been converted to B-factors and stored in the B-factor field of the time-average structure above.

7.5. High resolution plots

To facilitate publication, high resolution versions of the plots above have been created with a 4:3 aspect ratio suited for printing in a single column of a typical journal article. Just look at the figure number above to find the right file:

4mbs_report_figure4_hires.png

4mbs_report_figure5_hires.png

4mbs_report_figure6_hires.png

4mbs_report_figure7_hires.png

4mbs_report_figure8_hires.png

4mbs_report_figure9_hires.png

4mbs_report_figure10_hires.png

4mbs_report_figure11_hires.png

4mbs_report_figure12_hires.png

4mbs_report_figure13_hires.png

4mbs_report_figure14_hires.png

4mbs_report_figure15_hires.png

4mbs_report_figure16_hires.png

4mbs_report_figure17_hires.png

4mbs_report_figure18_hires.png