Structure Calculation With RDC's Using CYANA - Revision history

Jma at 21:56, 6 January 2010

2010-01-06T21:56:51Z

← Older revision		Revision as of 21:56, 6 January 2010
Line 104:		Line 104:
	LL5 365		LL5 365
	ORI 370</pre>		ORI 370</pre>
			<br>

	==== Initial model-free determination of Da and R from assigned RDCs ====		==== Initial model-free determination of Da and R from assigned RDCs ====
Line 136:		Line 136:
	The dummy values in the rdc list are read initially and they can be updated after running the FindTensor.cya routine. If no models are present (e.g. final.pdb) the program will terminate with a warning. <br>		The dummy values in the rdc list are read initially and they can be updated after running the FindTensor.cya routine. If no models are present (e.g. final.pdb) the program will terminate with a warning. <br>

			<br>

			==== The CALC.cya file ====
	==== The CALC.cya file ====

	The working directory that contains all the files necessary to start the calcualtion is ready and the CALC.cya modified for the presence of RDC constraints is used:<br>		The working directory that contains all the files necessary to start the calcualtion is ready and the CALC.cya modified for the presence of RDC constraints is used:<br>
Line 160:		Line 160:
	Notice that the 'restraints' row contain the forced stereospecifically assigned methyls and sidechain NH's and the .rdc file.  Also, the NOE vs. RDC weight is set by the weight_rdc and cut_rdc functions.  The remaining instructions are identical to the CYANA-2.1 file.		Notice that the 'restraints' row contain the forced stereospecifically assigned methyls and sidechain NH's and the .rdc file.  Also, the NOE vs. RDC weight is set by the weight_rdc and cut_rdc functions.  The remaining instructions are identical to the CYANA-2.1 file.

			<br>

			==== The init.cya file ====
	==== The init.cya file ====

	Further parameters are specified in the init.cya file below:<br>		Further parameters are specified in the init.cya file below:<br>
Line 173:		Line 173:
	The above script is intended to run off a single dual-quad core machine (nproc=8).		The above script is intended to run off a single dual-quad core machine (nproc=8).

	===== rdcdistances.cya file =====		===== rdcdistances.cya file =====

	Please note the rdcdistance.cya macro is being called by the init.cya setup file.  This file, located in the cyana-3.0/macro directory contains the supported RDC vectors, more vectors could potentially be added such as Trp N<sup>ε1</sup>-H<sup>ε1</sup> that maybe useful in deuterated sample to direct the large hydrophobic sidechain.  <br>		Please note the rdcdistance.cya macro is being called by the init.cya setup file.  This file, located in the cyana-3.0/macro directory contains the supported RDC vectors, more vectors could potentially be added such as Trp N<sup>ε1</sup>-H<sup>ε1</sup> that maybe useful in deuterated sample to direct the large hydrophobic sidechain.  <br>
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	print "    Standard RDC distances defined."		print "    Standard RDC distances defined."
	</pre>		</pre>
			<br>

			==== Notes on run execution ====
	==== Notes on run execution ====

	The command line execution form single machine or cluster using MPI implememntation (highly recommended) is carried on as usual:<br>		The command line execution form single machine or cluster using MPI implememntation (highly recommended) is carried on as usual:<br>
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	<br>		<br>

	<br>		<br>

	~~-- PaoloRossi - 14 Dec 2009~~

Prossi at 21:21, 15 December 2009

2009-12-15T21:21:16Z

← Older revision		Revision as of 21:21, 15 December 2009
Line 15:		Line 15:
	c) improved function for symmetric dimers and annotation of intermolecular NOE contacts in the peaklist using the xeasy color code notation.  <br>		c) improved function for symmetric dimers and annotation of intermolecular NOE contacts in the peaklist using the xeasy color code notation.  <br>

	Good agreement between global orientational constraints from RDC and distance information from NOEs is very important to achieve better structures by NMR~~. The program is an excellent step forward~~.  Results should always be accompanied by energy refinement in CNS or NIH-XPLOR.  Further information about the program and publication references can be found in the [http://www.cyana.org/wiki/index.php/Main_Page CYANA WIKI] page.<br>		Good agreement between global orientational constraints from RDC and distance information from NOEs is very important to achieve better structures by NMR.  Results should always be accompanied by energy refinement in CNS or NIH-XPLOR.  Further information about the program and publication references can be found in the [http://www.cyana.org/wiki/index.php/Main_Page CYANA WIKI] page.<br>

	<br>		<br>
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	== <span style="font-weight: bold;">Automated NOE and RDC and Structure Calculation Setup </span><br> ==		== <span style="font-weight: bold;">Automated NOE and RDC and Structure Calculation Setup </span><br> ==

	The structure calculation with automated noesy assignments and RDC restraints follows the canonical CYANA recipe.  Simple annealing ~~calcualtions~~ starting from a set of constraints that include RDC are easily derived by simplifying the scripts below and following the demo scripts. The program requires a sequence file (name.seq), a proton assignment list (name.prot), a noesy peaklist set (name.peaks), an RDC list (name.rdc), a CALC.cya script and an init.cya script.   <br>		The structure calculation with automated noesy assignments and RDC restraints follows the canonical CYANA recipe.  Simple annealing runs starting from a set of constraints that include RDC are easily derived by simplifying the scripts below and following the demo scripts. The program requires a sequence file (name.seq), a proton assignment list (name.prot), a noesy peaklist set (name.peaks), an RDC list (name.rdc), a CALC.cya script and an init.cya script.   <br>

	The sequence file now includes the RDC tensor origin separated by dummy linker residues: <br>		==== Sequence file<br> ====

			The sequence file now includes the RDC tensor origin separated by dummy linker residues (LL5): <br>
	<pre>MET 1		<pre>MET 1
	THR 2		THR 2
Line 44:		Line 46:

	</pre>		</pre>
	The RDC list supports multiple interatomic vectors in multiple media. RDC with distinct scaling factors and distinct ORI residue numbers are listed in a single file. The program supports the Da (magnitude) and R (Rhombicity) notation typical of programs such as PALES, REDCAT etc. Below is a sample RDC file that includes N-H, N-CA (intra), and N-C' (sequential) vectors in one medium with ~~appropriate~~ errors and [http://www.ncbi.nlm.nih.gov/pubmed/18388951 ~~scaling~~ factors]:<br>		<br>

			==== RDC constraint file<br> ====

			The RDC list supports multiple interatomic vectors in multiple media. RDC with distinct scaling factors and distinct ORI residue numbers are listed in a single file. The program supports the Da (magnitude) and R (Rhombicity) notation typical of programs such as PALES, REDCAT etc. Below is a sample RDC file that includes N-H, N-CA (intra), and N-C' (sequential) vectors in one medium with adequate error (here the following errors were used:  ~10 % the RDC spread for N-H vectors, the error determined by analysis of ''J''-modulated experiments for N-CA and N-C' RDC measurement) and <span style="text-decoration: underline;">[http://www.ncbi.nlm.nih.gov/pubmed/18388951 weight factors]:</span><br>
	<pre># Orientation Magnitude Rhombicity ORI residue number		<pre># Orientation Magnitude Rhombicity ORI residue number
	1 5.39535 0.63125 360		1 5.39535 0.63125 360
Line 98:		Line 104:
	LL5 365		LL5 365
	ORI 370</pre>		ORI 370</pre>


			==== Initial model-free determination of Da and R from assigned RDCs ====

	If the values of Da and R are not known they can be determined using any desired software OR using the FindTensor.cya script below. The program yields results that are equivalent to PALES assiuming the same fitting method is employed.<br>		If the values of Da and R are not known they can be determined using any desired software OR using the FindTensor.cya script below. The program yields results that are equivalent to PALES assiuming the same fitting method is employed.<br>
	<pre>## 8DEMOS: FindTensor - Determine alignment tensor		<pre>## 8DEMOS: FindTensor - Determine alignment tensor
Line 125:		Line 135:
	</pre>		</pre>
	The dummy values in the rdc list are read initially and they can be updated after running the FindTensor.cya routine. If no models are present (e.g. final.pdb) the program will terminate with a warning. <br>		The dummy values in the rdc list are read initially and they can be updated after running the FindTensor.cya routine. If no models are present (e.g. final.pdb) the program will terminate with a warning. <br>



			==== The CALC.cya file ====

	The working directory that contains all the files necessary to start the calcualtion is ready and the CALC.cya modified for the presence of RDC constraints is used:<br>		The working directory that contains all the files necessary to start the calcualtion is ready and the CALC.cya modified for the presence of RDC constraints is used:<br>
Line 144:		Line 158:

	</pre>		</pre>
	Notice the ~~restraint~~ contain the forced stereospecifically assigned methyls and sidechain NH's and the ~~RDC set~~.  Also, the NOE vs. RDC weight is set by the weight_rdc and cut_rdc functions. The remaining instructions are identical to the CYANA-2.1 file.  Further parameters are specified in the init.cya file below:<br>		Notice that the 'restraints' row contain the forced stereospecifically assigned methyls and sidechain NH's and the .rdc file.  Also, the NOE vs. RDC weight is set by the weight_rdc and cut_rdc functions.  The remaining instructions are identical to the CYANA-2.1 file.



			==== The init.cya file ====

			Further parameters are specified in the init.cya file below:<br>
	<pre>name:=RpR324		<pre>name:=RpR324
	rmsdrange:=10-80		rmsdrange:=10-80
Line 151:		Line 171:
	read seq $name.seq		read seq $name.seq
	rdcdistances</pre>		rdcdistances</pre>
	The above script is intended to run off a single dual-quad core machine (nproc=8).  Please note the rdcdistance.cya macro is being called by the init.cya setup file.  This file, located in the cyana-3.0/macro directory contains the supported RDC vectors, more vectors could potentially be added such as Trp N<sup>ε1</sup>-H<sup>ε1</sup> that maybe useful in deuterated sample to direct the large hydrophobic sidechain.  <br>		The above script is intended to run off a single dual-quad core machine (nproc=8).

			===== rdcdistances.cya file =====

			Please note the rdcdistance.cya macro is being called by the init.cya setup file.  This file, located in the cyana-3.0/macro directory contains the supported RDC vectors, more vectors could potentially be added such as Trp N<sup>ε1</sup>-H<sup>ε1</sup> that maybe useful in deuterated sample to direct the large hydrophobic sidechain.  <br>
	<pre># Copyright (c) 2002-08 Peter Guntert. All rights reserved.		<pre># Copyright (c) 2002-08 Peter Guntert. All rights reserved.
	## 7MACROS: rdcdistances - CYANA macro		## 7MACROS: rdcdistances - CYANA macro
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	print "    Standard RDC distances defined."		print "    Standard RDC distances defined."
	</pre>		</pre>


			==== Notes on run execution ====

	The command line execution form single machine or cluster using MPI implememntation (highly recommended) is carried on as usual:<br>		The command line execution form single machine or cluster using MPI implememntation (highly recommended) is carried on as usual:<br>
	<pre>/cyana-3.0/cyana CALC > & log &		<pre>/cyana-3.0/cyana CALC > & log &

Prossi at 20:26, 15 December 2009

2009-12-15T20:26:08Z

← Older revision		Revision as of 20:26, 15 December 2009
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	<br>		<br>

	The following page describes the setup and analysis ~~using~~ RDC~~ ~~constraints in the framework of CYANA-3.0.<br>		The following page describes the setup of and analysis of an automated structure determination starting from NOEs peaklists and residual dipolar coupling (RDC) constraints in the framework of CYANA 3.0.<br>

	CYANA version 3.0 incorporates many new features including:<br>		CYANA version 3.0 incorporates many new features including:<br>

Jma at 23:11, 14 December 2009

2009-12-14T23:11:58Z

← Older revision		Revision as of 23:11, 14 December 2009
Line 151:		Line 151:
	read seq $name.seq		read seq $name.seq
	rdcdistances</pre>		rdcdistances</pre>
	The above script is intended to run off a single dual-quad core machine (nproc=8).  Please note the rdcdistance.cya macro is being called by the init.cya setup file.  This file, located in the cyana-3.0/macro directory contains the supported RDC vectors, more vectors could potentially be added such as Trp ~~NE1~~-~~HE1~~ that maybe useful in deuterated sample to direct the large hydrophobic sidechain.  <br>		The above script is intended to run off a single dual-quad core machine (nproc=8).  Please note the rdcdistance.cya macro is being called by the init.cya setup file.  This file, located in the cyana-3.0/macro directory contains the supported RDC vectors, more vectors could potentially be added such as Trp N<sup>ε1</sup>-H<sup>ε1</sup> that maybe useful in deuterated sample to direct the large hydrophobic sidechain.  <br>
	<pre># Copyright (c) 2002-08 Peter Guntert. All rights reserved.		<pre># Copyright (c) 2002-08 Peter Guntert. All rights reserved.
	## 7MACROS: rdcdistances - CYANA macro		## 7MACROS: rdcdistances - CYANA macro

Prossi at 23:02, 14 December 2009

2009-12-14T23:02:25Z

Show changes

Prossi: Created page with '== '''Introduction''' == '''IMPORTANT DISCLAIMER:''' A number of NESG NMR groups are currently beta-testing sites for CYANA-3.0 and the information in this page is in…'

2009-12-14T23:00:02Z

Created page with '== '''Introduction''' == '''IMPORTANT DISCLAIMER:''' A number of NESG NMR groups are currently beta-testing sites for CYANA-3.0 and the information in this page is in…'

New page

== '''Introduction''' ==

'''IMPORTANT DISCLAIMER:''' A number of NESG NMR groups are currently beta-testing sites for CYANA-3.0 and the information in this page is intended for use by the licensed members of the NESG consortium, other beta testers, and is to be used in accordance to the program licensing agreement.

 

The following page describes the setup and analysis using RDC constraints in the framework of CYANA-3.0. 

CYANA version 3.0 incorporates many new features including: 

a) inclusion of residual dipolar coupling in structure calculation (RDC) 

b) inclusion of pseudocontact shifts from paramagnetic centers in structure calculation (PCS) 

c) improved function for symmetric dimers and annotation of intermolecular NOE contacts in the peaklist using the xeasy color code notation.   

Good agreement between global orientational constraints from RDC and distance information from NOEs is very important to achieve better structures by NMR. The program is an excellent step forward.  Results should always be accompanied by energy refinement in CNS or NIH-XPLOR.  Further information about the program and publication references can be found in the [http://www.cyana.org/wiki/index.php/Main_Page CYANA WIKI] page. 

 

== Automated NOE and RDC and Structure Calculation Setup ==

The structure calculation with automated noesy assignments and RDC restraints follows the canonical CYANA recipe.  Simple annealing calcualtions starting from a set of constraints that include RDC are easily derived by simplifying the scripts below and following the demo scripts. The program requires a sequence file (name.seq), a proton assignment list (name.prot), a noesy peaklist set (name.peaks), an RDC list (name.rdc), a CALC.cya script and an init.cya script.   

The sequence file now includes the RDC tensor origin separated by dummy linker residues: 
<pre>MET 1
THR 2
SER 3
THR 4
PHE 5
ASP 6
ARG 7
VAL 8
ALA 9
THR 10

PL 350
LL5 351
LL5 352
LL5 353
LL5 354
LL5 355
ORI 360

</pre>
The RDC list supports multiple interatomic vectors in multiple media. RDC with distinct scaling factors and distinct ORI residue numbers are listed in a single file. The program supports the Da (magnitude) and R (Rhombicity) notation typical of programs such as PALES, REDCAT etc. Below is a sample RDC file that includes N-H, N-CA (intra), and N-C' (sequential) vectors in one medium with appropriate errors and [http://www.ncbi.nlm.nih.gov/pubmed/18388951 scaling factors]: 
<pre># Orientation Magnitude Rhombicity ORI residue number
1 5.39535 0.63125 360
# First atom Second atom RDC Error Weight Orientation
7 ARG H 7 ARG N 5.936 2.000 1.000 1
8 VAL H 8 VAL N 3.827 2.000 1.000 1
9 ALA H 9 ALA N -2.822 2.000 1.000 1
10 THR H 10 THR N -0.674 2.000 1.000 1
11 ILE H 11 ILE N 4.945 2.000 1.000 1
12 ILE H 12 ILE N 1.709 2.000 1.000 1
13 ALA H 13 ALA N -1.336 2.000 1.000 1
#
4 THR N 3 SER C 1.267 0.095 8.330 1
5 PHE N 4 THR C -0.246 0.207 8.330 1
7 ARG N 6 ASP C 0.161 0.052 8.330 1
8 VAL N 7 ARG C 0.439 0.034 8.330 1
9 ALA N 8 VAL C -0.076 0.040 8.330 1
10 THR N 9 ALA C -0.957 0.048 8.330 1
11 ILE N 10 THR C 1.123 0.022 8.330 1
12 ILE N 11 ILE C -0.440 0.037 8.330 1
13 ALA N 12 ILE C 0.065 0.026 8.330 1
#
3 SER N 3 SER CA 0.251 0.199 8.330 1
4 THR N 4 THR CA -0.265 0.258 8.330 1
5 PHE N 5 PHE CA -0.499 0.281 8.330 1
7 ARG N 7 ARG CA -0.457 0.200 8.330 1
8 VAL N 8 VAL CA -0.481 0.154 8.330 1
9 ALA N 9 ALA CA 0.349 0.083 8.330 1
10 THR N 10 THR CA 0.548 0.121 8.330 1
11 ILE N 11 ILE CA -0.091 0.111 8.330 1
12 ILE N 12 ILE CA -0.678 0.078 8.330 1
13 ALA N 13 ALA CA 1.014 0.108 8.330 1</pre>
Multiple media (e.g. orientations) should be listed as follows: 
<pre># Orientation Magnitude Rhombicity ORI residue number
1 5.39535 0.63125 360
2 7.55656 0.58200 370
</pre>
and the sequence should be modified to include further links and ORI: 
<pre>ALA 9
THR 10

PL 350
LL5 351
LL5 352
LL5 353
LL5 354
LL5 355
ORI 360
LL5 361
LL5 362
LL5 363
LL5 364
LL5 365
ORI 370</pre>
If the values of Da and R are not known they can be determined using any desired software OR using the FindTensor.cya script below. The program yields results that are equivalent to PALES assiuming the same fitting method is employed. 
<pre>## 8DEMOS: FindTensor - Determine alignment tensor
##
## Determine magnitude and rhombicity of the alignment tensor
## from input RDCs

# determine tensor from histogram, no structure needed

read rdc phage_all_mono.rdc
print "    Input alignment tensor:"
do i 1 orientations
  print "    Orientation $i: magnitude = $magnitude(i) Hz, rhombicity = $rhombicity(i)."
end do

rdc fittensor method=simplex       # (can take several minutes)
#rdc fittensor method=gridsearch   # systematic search (very slow)

# alternatively, determine tensor from given structure by SVD

read rdc phage_all_mono.rdc
read pdb final.pdb
overview

</pre>
The dummy values in the rdc list are read initially and they can be updated after running the FindTensor.cya routine. If no models are present (e.g. final.pdb) the program will terminate with a warning. 

The working directory that contains all the files necessary to start the calcualtion is ready and the CALC.cya modified for the presence of RDC constraints is used: 
<pre>peaks := ali5.peaks,aro5.peaks,n3.peaks # names of NOESY peak lists
prot := RpR324.prot # names of chemical shift lists
restraints := ssa.cya,phage_all_mono.rdc # additional (non-NOE) constraints
tolerance := 0.04,0.025,0.3 # chemical shift tolerances: HX2-HX1-X1
calibration := # NOE calibration parameters
structures := 100,20 # number of initial, final structures
steps := 10000 # number of torsion angle dynamics steps
rmsdrange := 10..80 # residue range for RMSD calculation
randomseed := 56231 # random number generator seed

weight_rdc = 0.02 # weight for RDC restraints
cut_rdc = 0.2 # cutoff for RDC violation output

ssa
noeassign peaks=$peaks prot=$prot autoaco

</pre>
Notice the restraint contain the forced stereospecifically assigned methyls and sidechain NH's and the RDC set.  Also, the NOE vs. RDC weight is set by the weight_rdc and cut_rdc functions. The remaining instructions are identical to the CYANA-2.1 file.  Further parameters are specified in the init.cya file below: 
<pre>name:=RpR324
rmsdrange:=10-80
cyanalib
nproc:=8
read seq $name.seq
rdcdistances</pre>
The above script is intended to run off a single dual-quad core machine (nproc=8).  Please note the rdcdistance.cya macro is being called by the init.cya setup file.  This file, located in the cyana-3.0/macro directory contains the supported RDC vectors, more vectors could potentially be added such as Trp NE1-HE1 that maybe useful in deuterated sample to direct the large hydrophobic sidechain.  
<pre># Copyright (c) 2002-08 Peter Guntert. All rights reserved.
## 7MACROS: rdcdistances - CYANA macro
##
## Parameters: (none)
##
# dipole definition format: atom1_name atom2_name atom1_index atom2_index
# if indexes are missing, zeros are assumed

var info echo

syntax

info:=none; echo:=off
rdc distance "N  H"    distance=1.041
rdc distance "CA HA"   distance=1.117
rdc distance "C  CA"   distance=1.525
rdc distance "C  N"    distance=2.461
rdc distance "C  N -1" distance=1.329
rdc distance "CA N"    distance=1.458
rdc distance "CA N -1" distance=2.425
rdc distance "CA H"    distance=2.117
rdc distance "CA H -1" distance=2.533
rdc distance "C  H -1" distance=2.000
rdc distance "C  HA"   distance=2.144
rdc distance "CB HB"   distance=1.080
rdc distance "CA CB"   distance=1.532
unset info
print "    Standard RDC distances defined."
</pre>
The command line execution form single machine or cluster using MPI implememntation (highly recommended) is carried on as usual: 
<pre>/cyana-3.0/cyana CALC > & log &
</pre>
the MPI is launched using the script called, for example, submit_cyana: 
<pre>#!/bin/bash
#PBS -S /bin/bash
#PBS -N cyana
#PBS -lnodes=6:ppn=8
lamboot ~/bhost.def
cd /farm/users/prossi/RpR324_structure/cyana_new_mono2
/opt/openmpi/tcp-gnu/bin/mpirun /farm/software/cyana-3.0-mpi/cyana CALC.cya
lamhalt</pre>
 with the command: 
<pre>qsub -q @master3 submit_cyana
</pre>
The starting scripts are highly system specific they are almost guaranteed NOT to work on your sytem and are given here for general information only. 

 

== Output analysis ==

The output analysis is carried out in the usual manner, it should be noted that, during the calculation the specified values Da and R are kept fixed.  Following the final cycle a new model-based estimate of Da and R is calculated and used to compute the RDC violations and their contribution to the target function. The resulting target function will be increased by the number and extent of RDC violations in addition to other violations from dihedral, vdw, and NOEs restraints.

A partial output file is given below (final.ovw): 
<pre>
Structural statistics:

str target upper limits van der Waals RDCs
function # rms max # sum max # rms max
1 8.98 5 0.0089 0.40 12 18.5 0.37 13 0.2508 2.27
2 8.96 7 0.0083 0.31 15 17.4 0.38 19 0.2656 2.27
3 9.69 11 0.0122 0.54 15 18.6 0.38 18 0.2595 2.28
4 9.63 6 0.0068 0.20 16 18.9 0.38 18 0.2604 2.27
5 9.41 14 0.0089 0.22 17 20.4 0.37 14 0.2521 2.26
6 9.80 10 0.0085 0.24 17 19.7 0.38 15 0.2563 2.27
7 10.52 12 0.0158 0.78 15 19.1 0.38 13 0.2554 2.29
8 10.05 10 0.0084 0.18 18 20.3 0.42 18 0.2587 2.28
9 10.57 7 0.0079 0.29 19 18.3 0.53 16 0.3169 2.43
10 10.38 13 0.0088 0.21 22 20.5 0.37 21 0.2636 2.28
11 10.33 7 0.0067 0.16 17 19.6 0.64 15 0.2663 2.28
12 9.93 9 0.0090 0.29 19 20.6 0.38 20 0.2541 2.27
13 10.12 12 0.0098 0.23 21 19.9 0.47 13 0.2681 2.30
14 10.53 7 0.0077 0.19 23 19.3 0.38 11 0.3145 2.40
15 10.96 8 0.0089 0.31 21 22.6 0.38 12 0.2639 2.28
16 10.50 12 0.0100 0.29 23 20.1 0.37 15 0.2696 2.27
17 10.56 14 0.0119 0.30 23 21.1 0.37 16 0.2736 2.33
18 10.75 17 0.0146 0.60 21 20.0 0.37 12 0.2547 2.27
19 10.88 18 0.0125 0.38 19 23.3 0.38 10 0.2506 2.30
20 10.88 8 0.0083 0.26 23 21.4 0.42 15 0.2644 2.28

Ave 10.17 10 0.0097 0.32 19 20.0 0.41 15 0.2660 2.29
+/- 0.59 4 0.0024 0.15 3 1.4 0.07 3 0.0177 0.04
Min 8.96 5 0.0067 0.16 12 17.4 0.37 10 0.2506 2.26
Max 10.96 18 0.0158 0.78 23 23.3 0.64 21 0.3169 2.43
Cut 0.10 0.20 0.20

Constraints violated in 6 or more structures:
# mean max. 1 5 10 15 20
Upper HA PRO 19 - HB3 ARG 20 5.50 15 0.11 0.21 +++++++ ++++ ++*+ peak 970
Upper HA ILE 23 - QB SER 27 5.34 6 0.09 0.16 + ++ + +* peak 276
Upper HA ILE 30 - HB2 LEU 33 4.95 10 0.10 0.15 ++++ ++ ++ +* peak 313
VdW CB ALA 69 - H THR 70 2.55 18 0.24 0.28 ++++++++ ++++ *+++++
VdW O THR 71 - N PHE 75 2.75 12 0.20 0.32 ++* +++ + ++ +++
VdW O PHE 75 - C VAL 76 2.80 13 0.21 0.31 ++++ + *+++++++
VdW CG1 VAL 76 - HG2 LYS 78 2.60 9 0.17 0.25 ++* +++++ +
VdW HG3 LYS 78 - C LYS 78 2.50 14 0.22 0.36 +++*++ +++++ + + +
Ori 1 N ALA 69 - CA ALA 69 -2.84 20 1.95 2.04 +++++++++++++*++++++
Ori 1 H ALA 69 - N ALA 69 -3.32 20 2.01 2.33 ++++++++++++++++*+++
Ori 1 N THR 70 - C ALA 69 0.25 16 0.31 1.06 ++++++++*+++ + + ++
Ori 1 H ASN 79 - N ASN 79 -4.71 10 0.17 0.32 + *+ + ++++ + +
Ori 1 H GLY 92 - N GLY 92 -5.54 8 0.15 0.51 ++++* + ++
Ori 1 H LEU 94 - N LEU 94 0.42 6 0.14 0.54 +*+ +++
3 violated distance restraints.
5 violated van der Waals restraints.
6 violated residual dipolar coupling restraints.

RDC statistics:
Correlation coefficient : 0.906 +/- 0.003 (0.899..0.909, best in conformer 4)
Q = rms(Dcalc-Dobs)/rms(Dobs): 42.709 +/- 0.583 % (42.073..44.194)
Q normalized by tensor : 32.943 +/- 0.638 % (32.231..34.776)
Alignment tensor magnitude : 5.881 +/- 0.045 Hz (5.760..5.950, best 5.898; input 5.898)
Alignment tensor rhombicity : 0.537 +/- 0.007 (0.524..0.556, best 0.539; input 0.539)

</pre>
 

 

 

-- PaoloRossi - 14 Dec 2009