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Project

XML Project description (version 2.1)

Presentation

The xml file describing the project contains all the information needed to run an ARIA calculation. The input data are included in the file as links to other files, whereas the parameters of the calculation are written into the file. The project file is the main file used to start a run.


List of attributes


The following attributes are contained into the Project xml file:

  • element project:
<project name="" version="1.0" author="" date="" description="" comment="" references="" 
working_directory="/home/Bis/terez/ARIA/test" temp_root="/home/Bis/terez/ARIA/test" 
run="1" file_root="my_molecule" cache="yes" cleanup="yes">
  • working_directory: Defines the root directory of your project. Every run is then stored in a separate sub-directory [working_directory]/runxxx.
  • temp_root: For every run, ARIA creates a directory [temp_root]/aria_temp.@xxxxx to store all temporary (large) files (e.g. CNS output). If omited, the current directory will be used. When calculating on multiple machines, the temporary directory *must* be accessible from all machines.
  • run: Specifies the current run of a project. Every RUN is stored in a separate directory with the project directory as its root, i.e. [working_directory]/runxxxx.
  • file_root: The file_root is used to build filenames. E.g., if the file_root is set to "my_structure", the structure PDB-files are called my_structure_1.pdb etc.
  • cache: If enabled, ARIA caches all XML data-files (i.e. molecule definition and spectra). If a RUN is executed more than once, ARIA just accesses the cache instead of reading the complete XML files; this considerably speeds-up the reading process. If the original data (i.e. those that are stored in the run's local data-directory [working_directory]/RUNxxx/data) are modified, the cache is automatically invalidated so that the data are read from their original XML files.
  • cleanup: Enable this option if you want ARIA to remove the temporary directory [temp_root]/aria_temp.@xxxxx. Of course, the main temporary directory, [temp-root], is not removed.
  • section data:
  <data>
   <ccpn_model filename=""/>
   <molecule file="/home/Bis/bardiaux/projects/tudor/xml/tudor.xml" 
       format="xml" ccpn_id="">
     <linkage_definition name="automatic" filename=""/>
     <parameter_definition name="automatic" filename=""/>
     <topology_definition name="automatic" filename=""/>
   </molecule>
   <spectrum enabled="yes" use_assignments="no" trust_assigned_peaks="no">
     <shifts file="/home/Bis/bardiaux/projects/tudor/xml/13C.ppm.xml" 
       format="xml" ccpn_id="" default_shift_error="0.0"/>
     <peaks file="/home/Bis/bardiaux/projects/tudor/xml/13C.noesy.xml" 
          format="xml" ccpn_id="" peak_size="volume" 
          freq_window_proton1="0.04" freq_window_hetero1="0.5" 
          freq_window_proton2="0.02" freq_window_hetero2="0.5">
        <lower_bound_correction value="0.0" enabled="no"/>
        <upper_bound_correction value="6.0" enabled="no"/>
     </peaks>
   </spectrum>
   <initial_structure file="" format="iupac" ccpn_id="" enabled="no"/>
  </data>
  • In the element ccpn_model, if the data are read from a CCPN project, the CCPN project filename is given in the attribute 'filename' and the other attributes 'file' should be empty. In that case, during the loading step, ccp_id attributes are automatically generated corresponding to the molecules and to the spectra picked up by the user in the CCPN project. If the data are read from xml files, all attributes 'ccpn_id' should be empty.
  • the elements linkage_definition, parameter_definition and topology_definition define the linkage, parameter and topology files used in CNS. These parameters can be 'automatic', and the files to use are then determined from the molecular system. If the parameters are 'user-defined', the corresponding filename should be given as an attribute. The attributes 'lower_bound_correction' and 'upper_bound_correction' describe the lower and upper bound values used for violated restraints, if the bound-correction is enabled. When performing a Violation Analysis on an ensemble of structures, ARIAs default approach is to deactivate a restraint for the structure calculation in the subsequent iteration, if the restraint has been violated in more than a certain fraction of all structures.
  • If lower_bound-correction is turned on (attribute enabled in the element lower_bound_correction), ARIA runs a 2-pass Violation Analysis: the 1st pass determines the set of violated restraints which is then analysed further: if the restraint is still violated with respect to the user-defined LOWER bound (attribute value in the element lower_bound_correction), nothing changes. If not, the restraint will be used (with modified lower bound) in the subsequent iteration.
  • If upper_bound-correction is turned on (attribute enabled in the element upper_bound_correction), ARIA runs a 2-pass Violation Analysis: the 1st pass determines the set of violated restraints which is then analysed further: if the restraint is still violated with respect to the user-defined UPPER bound (attribute value in the element upper_bound_correction), nothing changes. If not, the restraint will be used (with modified upper bound) in the subsequent iteration.
  • The peak volumes or intensities can be taken as input using the peak_size attribute of the element peak. The frequence window defining the ambiguity of the chemical are defined in ppm. The attribute default_shift_error gives the default error [ppm] of chemical-shift measurementsfor which an error is not available.
  • To force the use of a given structure in place of the extended structure generated by CNS, as a starting point for the calculation, for example, in the case, one wants to filter NOE data with respect to a given already known structure, on can use the attribute 'file' in the element initial_structure.
  • section cns:
<cns local_executable="/Bis/shared/cns/intel-i686-linux/bin/cns_solve" 
   keep_output="yes" keep_restraint_files="yes" create_psf_file="yes" 
   generate_template="yes" nonbonded_parameters="PROLSQ"> 
  <annealing_parameters> 
    <unambiguous_restraints first_iteration="0" 
     k_hot="10.0" k_cool1_initial="10.0" k_cool1_final="50.0" k_cool2="50.0"/> 
    <ambiguous_restraints first_iteration="0" k_hot="10.0" k_cool1_initial="10.0" 
       k_cool1_final="50.0" k_cool2="50.0"/> 
    <hbond_restraints first_iteration="0" k_hot="10.0" k_cool1_initial="10.0" 
       k_cool1_final="50.0" k_cool2="50.0"/> 
    <dihedral_restraints k_hot="5.0" k_cool1="25.0" k_cool2="200.0"/> 
    <karplus_restraints parameter_class="1" a="6.98" b="-1.38" c="1.72" 
       d="-60.0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/> 
    <karplus_restraints parameter_class="2" a="6.98" b="-1.38" c="1.72" 
       d="-60.0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/> 
    <karplus_restraints parameter_class="3" a="6.98" b="-1.38" c="1.72" 
       d="-60.0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/> 
    <karplus_restraints parameter_class="4" a="6.98" b="-1.38" c="1.72" 
       d="-60.0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/> 
    <karplus_restraints parameter_class="5" a="6.98" b="-1.38" c="1.72" 
       d="-60.0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/> 
    <rdc_restraints parameter_class="1" method="SANI" first_iteration="0" 
       k_hot="0.0" k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" 
       border_hot_initial="0.1" border_hot_final="40.0" 
       border_cool1_initial="40.0" border_cool1_final="40.0" 
       border_cool2_initial="40.0" border_cool2_final="40.0" 
       center_hot_initial="0.1" center_hot_final="0.1" 
       center_cool1_initial="10.0" center_cool1_final="10.0" 
       center_cool2_initial="10.0" center_cool2_final="10.0"/> 
    <rdc_restraints parameter_class="2" method="SANI" first_iteration="0" 
       k_hot="0.0" k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" 
       border_hot_initial="0.1" border_hot_final="40.0" 
       border_cool1_initial="40.0" border_cool1_final="40.0" 
       border_cool2_initial="40.0" border_cool2_final="40.0" 
       center_hot_initial="0.1" center_hot_final="0.1" 
       center_cool1_initial="10.0" center_cool1_final="10.0" 
       center_cool2_initial="10.0" center_cool2_final="10.0"/> 
    <rdc_restraints parameter_class="3" method="SANI" first_iteration="0" 
       k_hot="0.0" k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" 
       border_hot_initial="0.1" border_hot_final="40.0" 
       border_cool1_initial="40.0" border_cool1_final="40.0" 
       border_cool2_initial="40.0" border_cool2_final="40.0" 
       center_hot_initial="0.1" center_hot_final="0.1" 
       center_cool1_initial="10.0" center_cool1_final="10.0" 
       center_cool2_initial="10.0" center_cool2_final="10.0"/> 
    <rdc_restraints parameter_class="4" method="SANI" first_iteration="0" 
       k_hot="0.0" k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" 
       border_hot_initial="0.1" border_hot_final="40.0" 
       border_cool1_initial="40.0" border_cool1_final="40.0" 
       border_cool2_initial="40.0" border_cool2_final="40.0" 
       center_hot_initial="0.1" center_hot_final="0.1" 
       center_cool1_initial="10.0" center_cool1_final="10.0" 
       center_cool2_initial="10.0" center_cool2_final="10.0"/> 
    <rdc_restraints parameter_class="5" method="SANI" first_iteration="0" 
       k_hot="0.0" k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" 
       border_hot_initial="0.1" border_hot_final="40.0" 
       border_cool1_initial="40.0" border_cool1_final="40.0" 
       border_cool2_initial="40.0" border_cool2_final="40.0" 
       center_hot_initial="0.1" center_hot_final="0.1" 
       center_cool1_initial="10.0" center_cool1_final="10.0" 
       center_cool2_initial="10.0" center_cool2_final="10.0"/> 
    <flat_bottom_harmonic_wall m_rswitch_hot="0.5" m_rswitch_cool1="0.5" 
       m_rswitch_cool2="0.5" rswitch_hot="0.5" rswitch_cool1="0.5" 
       rswitch_cool2="0.5" m_asymptote_hot="-1.0" m_asymptote_cool1="-1.0" 
       m_asymptote_cool2="-0.1" asymptote_hot="1.0" asymptote_cool1="1.0" 
       asymptote_cool2="0.1"/> 
  </annealing_parameters> 
  <md_parameters dynamics="torsion" random_seed="89764443" 
    tad_temp_high="10000.0" tad_timestep_factor="9.0" 
    cartesian_temp_high="2000.0" cartesian_first_iteration="0" 
    timestep="0.003" temp_cool1_final="1000.0" temp_cool2_final="50.0" 
    steps_high="25000" steps_refine="4000" steps_cool1="20000" 
    steps_cool2="20000"/> 
</cns>
  • The CNS simulated annealing protocol contains one hot stage and two cooling stages, and the corresponding attributes contain the substrings 'hot', 'cool1' and 'cool2'.
  • The attribute local_executable contains the complete path of the cns binary used for the cns set-up (generation of psf files, of extended structures).  Other attributes describes whether the CNS output files are kept (they may be very large files), whether the restraint .tbl files generated for CNS are kept, and  whether the initial psf (parameter file of the analyzedmolecular system) and template files should be generated. The type of non-bonded parameters used during the calculation is described using the attribute 'nonbonded_parameters'. This attribute can have the values: 'PROLSQ',  'PARMALLH6', 'PARALLHDG' and 'OPLSX' (look at Linge and Nilges (1999) J Bio NMR in the list of references).
  • The elements unambiguous_restraints, ambiguous_restraints and hbond_restraints describe the simulated annealing set-up for the distance restraints: the  force constants during the different steps of the simulated annealing are the attributes k_*. The attribute first_iteration gives the iteration number from which the corresponding restraint is applied.
  • The elements dihedral_restraints, karplus_restraints and rdc-restraints describe the set-up for the angular restraints. Karplus restraints and rdc (residual dipolar coupling) restraints can be grouped into classes. Every class has its own parameter set which the user has to specify. It contains the specification of the alignment tensor for the rdcs and settings for the simulated annealing protocol.
  • The attribute method in the element rdc-restraints describes the approcah to use rdc data. ARIA offers two approaches to use residual dipolar coupling data as restraints: SANI and VEAN. For SANI, you have to specify the rhombicity and magnitude of the alignment tensor. VEAN uses angular restraints which must be precalculated with a separate program.
  • The element flat_bottom_harmonic_wall describes the shape of the restraint potential.
  • The element md_parameters contains the molecular dynamics parameters describing the simulated annealing protocol. The attribute dynamics is equal to "torsion" in the torsion angle dynamics is used in the high temperature and cooling stages, and is equal to cartesian if no torsion angle dynamics is used. The temperature values are the attributes *_temp_* and the number of integration steps are the attributes steps_*.
  • section job_manager:
<job_manager default_command="csh -f">
   <host enabled="yes" 
     command="/Bis/SGE/bin/lx24-x86/qsub -S /bin/csh" 
     executable="/Bis/shared/centos-3/cns_solve-1.1_20041015_intel-8.1_x86/intel-i686-linux/bin/cns_solve" 
     n_cpu="2" use_absolute_path="yes"/>
   <host enabled="yes" 
     command="ssh hotsname csh" 
     executable="/Bis/shared/centos-3/cns_solve-1.1_20041015_intel-8.1_x86/intel-i686-linux/bin/cns_solve" 
     n_cpu="2" use_absolute_path="yes"/>
</job_manager>
  • In the element job_manager, the default (and recommanded) value of the attribute default_command is"csh -f".
  • The  element host contain the parameters related to the generation of conformers on several computers: 'enabled' is the option to enable a given host. The attribute command describes how to launch a job on the given host. Two possibilities are given in the example above: use the batch system SGE, or a simple ssh command to the host. In the first case, no hostname should be given, as sge is dispatching the CPU time between the users. The attribute executable: The absolute path of the CNS binary on the given host. WARNING: if you are using qsub or another batch system dispatching automatically the CPU time between the users, as you are not giving any hostname, the absolute path should be the same on all the computers you will use. Two ways to do so are: (i) install cns on disk exported to all computer, (ii) have exactly the same cns installation on each computer.
  • If all calculations are run on the local computer, the syntax is:

<job_manager default_command="csh -f"/>

  • section protocol:
<protocol floating_assignment="yes"> 
  <iteration number="0" n_structures="40" sort_criterion="total_energy" n_best_structures="7"> 
    <assignment/> 
    <merging method="no_merging"/> 
    <calibration distance_cutoff="6.0" estimator="ratio_of_averages"/> 
    <violation_analysis violation_tolerance="1000.0" violation_threshold="0.5"/> 
    <partial_assignment weight_threshold="1.0" max_contributions="20"/> 
  </iteration>
............................................................
  <iteration number="8" n_structures="100" sort_criterion="total_energy" n_best_structures="7"> 
    <assignment/> 
    <merging method="no_merging"/> 
    <calibration distance_cutoff="6.0"estimator="ratio_of_averages"/> 
    <violation_analysis violation_tolerance="0.1" violation_threshold="0.5"/> 
    <partial_assignment weight_threshold="0.8" max_contributions="20"/> 
  </iteration> 
  <water_refinement solvent="water" n_structures="10" enabled="yes" write_solvent_molecules="no"/> 
</protocol>
  • The attribute floating_assignment describes whether the floating chirality assignment is used (equivalent hydrogens are swapped and the energy difference is measured): floating_assignment can take the values "yes" or "no".    It is often difficult to assign the chemical shifts of the two substituents of a prochiral center stereospecifically. In proteins, these are the two methylene protons or the methyl protons of the isopropyl groups of valine or leucine. A resonance matching one of the chemical shifts in the proton dimensions potentially involves either of the two prochiral substituents. ARIA compensates this lack of information by testing both alternatives during structure calculation. For each calculated structure, the energetically preferred options are written to a file witha .float extension (see the page Results analysis).
  • Parameters specific for each iteration are contained in the element iteration.The total number of generated structures is given by n_structures, only the number  of selectecd structure for assignment statistics is given byt n_best_structures of structures. The criterion for sorting is according the total energy, which is the only possible value for the attribute sort-criterion.
  • The element merging describes how the number of peaks can be reduced by merging: the attribute method can be equal to "standard" (peaks with the same assignment are merged) or "no_merging" (no peak merging).
  • The element calibration describes the way the experimental peak intensities measured from spectra are calibrated with respect to the theoretical peak intensities calculated from the set of conformers. The attribute estimator defines how the calibration of experimental intensity with respect to the calculated ones is performed. The defalut value "ratio_of_averages" corresponds to a calibration through the ratio of the average experimental and calculated intensities/volumes and is the only possible value for the moment. The attribute distance_cutoff is used to filter the calculated intensities/volumes used for the calibration by including only those corresponding to a distance smaller than the distance_cutoff value. If no value is given, all crosspeaks are considered.
  • In the element violation_analysis, the attribute violation_tolerance is the limit of distance value for which a restraint is not considered as violated. This value decreases during the simulated annealing iterations. The violated restraints are those for which the distance is larger than the sum of the upper bound limit and of the attribute violation_threshold. 
  • In the element partial_assignment, the attribute weight_threshold a weight which is assigned to every contribution by the 'Partial Assignment' step. The sum of weights over all contributions in a restraint is always greater or equal to the attribute 'weight_threshold'. The attribute 'max_contributions' gives the maximum number of contributions possible for a given ARIA peak.
  • The element water_refinement describes the features of the final refinement step in solvent. The refinement is enables through the attribute 'enabled'. The solvent is given by the attribute 'solvent' (default value: "water", other possible value: "dmso"). The number of refined structures is given by the attribute 'n_structures', and the PDB files will include solvent molecules if the attribute 'write_solvent_molecule' is 'yes'.
  • section analysis:
<analysis> 
  <structures_analysis enabled="yes"/> 
  <procheck executable="/Bis/shared/centos-3/bin/procheck" enabled="yes"/> 
  <prosa executable="prosa" enabled="no"/> 
  <whatif executable="/Bis/shared/bin/whatif.intel-7.1" enabled="yes"/> 
</analysis>
  • The element structures_analysis enables or disables, with the attribute enable, the analysis of the final structures.
  • The elements procheck, prosa and whatif enable or disable the use of the corresponding softwares for the final structures analysis: the attributes executable contain the full path of the software executable.
  • section report:
<report> 
  <ccpn export_assignments="no" export_noe_restraint_list="last" export_structures="no"/
  <molmol enabled="yes"/> 
  <noe_restraint_list pickle_output="yes" text_output="yes" xml_output="no"/> 
  <spectra write_assigned="yes" write_assigned_force="yes" iteration="last"/> 
</report>
  • The element ccpn describes whether ARIA exports the complete project (last iteration) into a CCPN project. The attributes export_noe_restraint_list, export_structures and export_assignments describe whether the noe restraint list, the structures or assignments are exported.
  • The element molmol tells whether a molmol script is produced, if the attribute 'enabled' of the section 'molmol' is equal to "yes".
  • In the element noe_restraint, an assigned NOE restraint list can be produced, in a python binary format (attribute 'pickle_output'), in a text format (attribute 'text_output') or in a xml format (attribute 'xml_output').
  • The element spectra describes the output of an assigned peak list in the xml format of ARIA. The attribute write_assigned tells whether the assigned peak list should be written or not.  The attribute write_assigned_force tells whether already existing peak lists should be erased by the new output. The attribute iteration tells whether the assigned peak list should be written at each iteration ("all") or only at the last one ("last").

Example of file


An example of a generic project file is given below, in a format compatible with the version 2.1 of ARIA. For specific applications of ARIA, please have a look to the tutorial introduction page: 


<!DOCTYPE project SYSTEM "project1.0.dtd">
<project name="" version="1.0" author="" date="" description="" comment="" references="" 
working_directory="/home/Bis/terez/ARIA/test" temp_root="/home/Bis/terez/ARIA/test" 
run="1" file_root="my_molecule" cache="yes" cleanup="yes">
<data>
  <ccpn_model filename=""/>
  <molecule file="./xml/hrdc.xml" format="xml">
    <linkage_definition name="automatic" filename=""/>
    <parameter_definition name="automatic" filename=""/>
    <topology_definition name="automatic" filename=""/>
  </molecule>
  <spectrum enabled="yes" use_assignments="yes" trust_assigned_peaks="no">
    <shifts file="./xml/13C_ppm.xml" format="xml" default_shift_error="0.0"/>
    <peaks file="./xml/13C_noe.xml" format="xml" peak_size="volume" freq_window_proton1="0.04" freq_window_hetero1="0.5" freq_window_proton2="0.02" freq_window_hetero2="0.5"> ]]>
      <lower_bound_correction value="0.0" enabled="no"/> 
      <upper_bound_correction value="6.0" enabled="no"/>
    </peaks>
  </spectrum> 
.................................
  <initial_structure file="" format="iupac" enabled="no"/>
</data>
<structure_generation engine="cns">
  <cns local_executable="" keep_output="yes" keep_restraint_files="yes" create_psf_file="yes" 
     generate_template="yes" nonbonded_parameters="PROLSQ">
    <annealing_parameters>
      <unambiguous_restraints first_iteration="0" k_hot="10.0" k_cool1_initial="10.0" 
         k_cool1_final="50.0" k_cool2="50.0"/>
      <ambiguous_restraints first_iteration="0" k_hot="10.0" k_cool1_initial="10.0" 
         k_cool1_final="50.0" k_cool2="50.0"/>
      <hbond_restraints first_iteration="0" k_hot="10.0" k_cool1_initial="10.0" 
         k_cool1_final="50.0" k_cool2="50.0"/> 
      <dihedral_restraints k_hot="5.0" k_cool1="25.0" k_cool2="200.0"/>
      <karplus_restraints parameter_class="1" a="6.98" b="-1.38" c="1.72" d="-60.0" 
         k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/>
      <karplus_restraints parameter_class="2" a="6.98" b="-1.38" c="1.72" d="-60.0" 
         k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/> 
      <karplus_restraints parameter_class="3" a="6.98" b="-1.38" c="1.72" d="-60.0" 
         k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/> ]]> 
      <karplus_restraints parameter_class="4" a="6.98" b="-1.38" c="1.72" d="-60.0" 
         k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/> ]]>
      <karplus_restraints parameter_class="5" a="6.98" b="-1.38" c="1.72" d="-60.0" 
         k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/>
      <rdc_restraints parameter_class="1" method="SANI" first_iteration="0" k_hot="0.0" 
         k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" border_hot_initial="0.1" 
         border_hot_final="40.0" border_cool1_initial="40.0" border_cool1_final="40.0" 
         border_cool2_initial="40.0" border_cool2_final="40.0" center_hot_initial="0.1" 
         center_hot_final="0.1" center_cool1_initial="10.0" center_cool1_final="10.0" 
         center_cool2_initial="10.0" center_cool2_final="10.0"/>
      <rdc_restraints parameter_class="2" method="SANI" first_iteration="0" k_hot="0.0" 
         k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" border_hot_initial="0.1" 
         border_hot_final="40.0" border_cool1_initial="40.0" border_cool1_final="40.0" 
         border_cool2_initial="40.0" border_cool2_final="40.0" center_hot_initial="0.1" 
         center_hot_final="0.1" center_cool1_initial="10.0" center_cool1_final="10.0" 
         center_cool2_initial="10.0" center_cool2_final="10.0"/>
      <rdc_restraints parameter_class="3" method="SANI" first_iteration="0" k_hot="0.0" 
         k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" border_hot_initial="0.1" 
         border_hot_final="40.0" border_cool1_initial="40.0" border_cool1_final="40.0" 
         border_cool2_initial="40.0" border_cool2_final="40.0" center_hot_initial="0.1" 
         center_hot_final="0.1" center_cool1_initial="10.0" center_cool1_final="10.0" 
         center_cool2_initial="10.0" center_cool2_final="10.0"/>
      <rdc_restraints parameter_class="4" method="SANI" first_iteration="0" k_hot="0.0" 
         k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" border_hot_initial="0.1" 
         border_hot_final="40.0" border_cool1_initial="40.0" border_cool1_final="40.0" 
         border_cool2_initial="40.0" border_cool2_final="40.0" center_hot_initial="0.1" 
         center_hot_final="0.1" center_cool1_initial="10.0" center_cool1_final="10.0" 
         center_cool2_initial="10.0" center_cool2_final="10.0"/>
      <rdc_restraints parameter_class="5" method="SANI" first_iteration="0" k_hot="0.0" 
         k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" border_hot_initial="0.1" 
         border_hot_final="40.0" border_cool1_initial="40.0" border_cool1_final="40.0" 
         border_cool2_initial="40.0" border_cool2_final="40.0" center_hot_initial="0.1" 
         center_hot_final="0.1" center_cool1_initial="10.0" center_cool1_final="10.0" 
         center_cool2_initial="10.0" center_cool2_final="10.0"/>
      <flat_bottom_harmonic_wall m_rswitch_hot="0.5" m_rswitch_cool1="0.5" m_rswitch_cool2="0.5" 
         rswitch_hot="0.5" rswitch_cool1="0.5" rswitch_cool2="0.5" m_asymptote_hot="-1.0" 
         m_asymptote_cool1="-1.0" m_asymptote_cool2="-0.1" asymptote_hot="1.0" asymptote_cool1="1.0" 
         asymptote_cool2="0.1"/>
    </annealing_parameters>
    <md_parameters dynamics="torsion" random_seed="89764443" tad_temp_high="10000.0" 
       tad_timestep_factor="9.0" cartesian_temp_high="2000.0" cartesian_first_iteration="0" 
       timestep="0.003" temp_cool1_final="1000.0" temp_cool2_final="50.0" steps_high="10000" 
       steps_refine="4000" steps_cool1="5000" steps_cool2="4000"/>
  </cns>
  <job_manager default_command="csh -f"/>
</structure_generation>
<protocol floating_assignment="yes">
  <iteration number="0" n_structures="20" sort_criterion="total_energy" n_best_structures="7">
    <assignment/>
    <merging method="standard"/>
    <calibration estimator="ratio_of_averages" distance_cutoff="6.0"/>
    <violation_analysis violation_tolerance="1000.0" violation_threshold="0.5"/>
    <partial_assignment weight_threshold="1.0" max_contributions="20"/>
  </iteration>
  <iteration number="1" n_structures="20" sort_criterion="total_energy" n_best_structures="7"> 
    <assignment/>
    <merging method="standard"/>
    <calibration estimator="ratio_of_averages" distance_cutoff="6.0"/>
    <violation_analysis violation_tolerance="5.0" violation_threshold="0.5"/> 
    <partial_assignment weight_threshold="0.9999" max_contributions="20"/>
  </iteration>
  <iteration number="2" n_structures="20" sort_criterion="total_energy" n_best_structures="7">
    <assignment/>
    <merging method="standard"/>
    <calibration estimator="ratio_of_averages" distance_cutoff="6.0"/>
    <violation_analysis violation_tolerance="3.0" violation_threshold="0.5"/> 
    <partial_assignment weight_threshold="0.999" max_contributions="20"/>
  </iteration> 
  <iteration number="3" n_structures="20" sort_criterion="total_energy" n_best_structures="7"> 
    <assignment/>
    <merging method="standard"/>
    <calibration estimator="ratio_of_averages" distance_cutoff="6.0"/>
    <violation_analysis violation_tolerance="1.0" violation_threshold="0.5"/>
    <partial_assignment weight_threshold="0.99" max_contributions="20"/>
  </iteration>
  <iteration number="4" n_structures="20" sort_criterion="total_energy" n_best_structures="7">
    <assignment/>
    <merging method="standard"/>
    <calibration estimator="ratio_of_averages" distance_cutoff="6.0"/>
    <violation_analysis violation_tolerance="1.0" violation_threshold="0.5"/>
    <partial_assignment weight_threshold="0.98" max_contributions="20"/>
  </iteration>
  <iteration number="5" n_structures="20" sort_criterion="total_energy" n_best_structures="7">
    <assignment/>
    <merging method="standard"/>
    <calibration estimator="ratio_of_averages" distance_cutoff="6.0"/>
    <violation_analysis violation_tolerance="1.0" violation_threshold="0.5"/>
    <partial_assignment weight_threshold="0.96" max_contributions="20"/>
  </iteration>
  <iteration number="6" n_structures="20" sort_criterion="total_energy" n_best_structures="7">
    <assignment/>
    <merging method="standard"/>
    <calibration estimator="ratio_of_averages" distance_cutoff="6.0"/>
    <violation_analysis violation_tolerance="0.1" violation_threshold="0.5"/>
    <partial_assignment weight_threshold="0.93" max_contributions="20"/>
  </iteration>
  <iteration number="7" n_structures="20" sort_criterion="total_energy" n_best_structures="7">
    <assignment/>
    <merging method="standard"/>
    <calibration estimator="ratio_of_averages" distance_cutoff="6.0"/>
    <violation_analysis violation_tolerance="0.1" violation_threshold="0.5"/>
    <partial_assignment weight_threshold="0.9" max_contributions="20"/>
  </iteration> 
  <iteration number="8" n_structures="20" sort_criterion="total_energy" n_best_structures="7"> 
    <assignment/>
    <merging method="standard"/>
    <calibration estimator="ratio_of_averages" distance_cutoff="6.0"/>
    <violation_analysis violation_tolerance="0.1" violation_threshold="0.5"/>
    <partial_assignment weight_threshold="0.8" max_contributions="20"/>
  </iteration>
  <water_refinement solvent="water" n_structures="10" enabled="yes" write_solvent_molecules="no"/>
</protocol>
<analysis>
  <structures_analysis enabled="yes"/>
  <procheck executable="procheck" enabled="yes"/
  <prosa executable="prosa" enabled="yes"/>
  <whatif executable="whatif" enabled="yes"/>
</analysis>
<report> 
  <ccpn export_assignments="no" export_noe_restraint_list="last" export_structures="no"/
  <molmol enabled="yes"/> 
  <noe_restraint_list pickle_output="yes" text_output="yes" xml_output="no"/> 
  <spectra write_assigned="yes" write_assigned_force="yes" iteration="last"/> 
</report>
</project>
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