This notebook contains material from PyRosetta; content is available on Github.

RNA in PyRosetta

Keywords: classify_base_pairs, RNA torsions, RNA score terms, RNA motifs, mutate_position, RNA thread, RNA minimize, RNA_HelixAssembler, RNA fragment assembly, FARFAR protocol, rna_denovo

References

  1. R. Das et al., "Atomic accuracy in predicting and designing noncanonical RNA structure," Nature Methods 7:4, 291-294 (2010).
  1. A. Watkins et al., "Blind prediction of noncanonical RNA structure at atomic accuracy," Science Advances 4:5 (2018).

Introduction

In this lab, we will explore common tasks and approaches for working with RNA using Rosetta. We will be focusing on a simple system that includes a helix capped by a tetraloop for this exercise.

In [1]:
# Notebook setup
import sys
if 'google.colab' in sys.modules:
    !pip install pyrosettacolabsetup
    import pyrosettacolabsetup
    pyrosettacolabsetup.mount_pyrosetta_install()
    print ("Notebook is set for PyRosetta use in Colab.  Have fun!")
In [2]:
from pyrosetta import *
init()
PyRosetta-4 2020 [Rosetta PyRosetta4.Release.python37.mac 2020.04+release.4fcf80033aebbcdf7c379387df97fd3d51a2c079 2020-01-24T11:08:55] retrieved from: http://www.pyrosetta.org
(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.
core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init: Rosetta version: PyRosetta4.Release.python37.mac r244 2020.04+release.4fcf80033ae 4fcf80033aebbcdf7c379387df97fd3d51a2c079 http://www.pyrosetta.org 2020-01-24T11:08:55
core.init: command: PyRosetta -ex1 -ex2aro -database /Users/ramyar/Dropbox/GradSchool/Research/packages/PyRosetta4.Release.python37.mac.release-244/setup/build/lib/pyrosetta/database
basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1108316389 seed_offset=0 real_seed=1108316389
basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1108316389 RG_type=mt19937
In [3]:
from pyrosetta.rosetta import *
from pyrosetta.rosetta.core.pose.rna import *
from pyrosetta.rosetta.core.pose import *

Exploring geometry for RNA

Let's load in this structure with PyRosetta (make sure that you have the PDB file located in your current directory):

cd google_drive/My\ Drive/student-notebooks/ pose = pose_from_pdb("inputs/stem_loop.pdb")

In [4]:
### BEGIN SOLUTION
pose = pose_from_pdb("inputs/stem_loop.pdb")
### END SOLUTION
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.  Created 980 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 1.05791 seconds.
core.import_pose.import_pose: File 'inputs/stem_loop.pdb' automatically determined to be of type PDB
core.io.pose_from_sfr.chirality_resolution: Flipping atom xyz for H5' and H5'' for residue   C

Let's explore the structure in this PDB file. First, use pose.sequence() to look at the sequence:

In [6]:
# print out the sequence of the pose
### BEGIN SOLUTION
pose.sequence()
### END SOLUTION
Out[6]:
'cauccgaaaggaug'

We can see that the pose seems to contain RNA residues. To check this, let's go through the pose residue by residue, checking if each one is RNA.

In [7]:
for ii in range(pose.size()):
    print(pose.residue_type(5).is_RNA())
True
True
True
True
True
True
True
True
True
True
True
True
True
True

RNA bases interact with each other via base pairing, either through the Watson-Crick base pairs that make up standard A-form helices or through non-canonical base pairing interactions. We can use the classify_base_pairs function (this lives in core:pose:rna which was loaded above) to find and classify all the base pairs in the current pose. Let's take a look.

In [8]:
base_pairs = classify_base_pairs(pose)
for base_pair in base_pairs:
    print(base_pair)
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv
1 14 WC WC ANTI
2 13 WC WC ANTI
3 12 WC WC ANTI
4 11 WC WC ANTI
5 10 WC WC ANTI
6 9 SUGAR HOOG ANTI

We can see that the RNA molecule consists of Watson-Crick base pairs between residues 1-5 and residues 10-14 forming a standard RNA helix. We can also see that residues 6 and 9 form a non-canonical base pair interaction between the sugar and Hoogsteen edges of the respective bases. We can think of this structure as a simple stem-loop, with an idealized A-form helix between residues 1-5 and residues 10-14, and with a tetraloop connecting these chains.

Let's use some of Rosetta's tools for measuring distances and torsions to understand the typical geometry of an idealized A-form helix.

What is the distance between the phosphate atoms of two consecutive residues in one strand of a helix? Check this for a couple pairs of residues.

In [9]:
P1_xyz = pose.residue(1).xyz("P")
P2_xyz = pose.residue(2).xyz("P")
P3_xyz = pose.residue(3).xyz("P")
print((P1_xyz - P2_xyz).norm())
print((P2_xyz - P3_xyz).norm())
5.923353746008057
5.846964169549871

RNA nucleotides are quite large compared to amino acids, with many more torsion angles. In the diagram of a nucleotide below, we can see the backbone torsions applicable to RNA: $\alpha$, $\beta$, $\gamma$, $\delta$, $\epsilon$, $\zeta$, and $\chi$.

In [10]:
from IPython.display import Image
Image('./Media/nucleotide_torsions.png',width='500')
Out[10]:

We can access the values of these torsions through the pose object. Just like protein torsions can be accessed with functions like pose.phi(resid), RNA torsions can be accessed with analogous functions like pose.alpha(resid).

Exercise: Below, make a function that prints out all the torsions for a given residue. Then, using that function, check the torsions for three different residues in the RNA helix. How similar are torsion angles for different residues in an idealized helix?

In [11]:
### BEGIN SOLUTION
def print_torsions(pose, resi):
    print("%s: %f" % ("alpha", pose.alpha(resi)))
    print("%s: %f" % ("beta", pose.beta(resi)))
    print("%s: %f" % ("gamma", pose.gamma(resi)))
    print("%s: %f" % ("delta", pose.delta(resi)))
    print("%s: %f" % ("epsilon", pose.epsilon(resi)))
    print("%s: %f" % ("zeta", pose.zeta(resi)))
    print("%s: %f" % ("chi", pose.chi(resi)))
### END SOLUTION
In [12]:
### BEGIN SOLUTION
print("Torsions for residue 2:")
print_torsions(pose, 2)
print("Torsions for residue 3:")
print_torsions(pose, 3)
print("Torsions for residue 12:")
print_torsions(pose, 12)
### END SOLUTION
Torsions for residue 2:
alpha: -72.516450
beta: 178.544461
gamma: 58.327244
delta: 79.813633
epsilon: -152.375244
zeta: -70.561778
chi: 74.780524
Torsions for residue 3:
alpha: -65.899308
beta: 173.462004
gamma: 56.858161
delta: 79.609718
epsilon: -152.592269
zeta: -70.540365
chi: 77.981938
Torsions for residue 12:
alpha: -67.502850
beta: 174.408225
gamma: 56.171977
delta: 81.812182
epsilon: -149.905716
zeta: -76.028946
chi: 75.291052

Scoring RNA poses

Rosetta's energy functions provide a mechanism to score RNA structures, rewarding realistic conformations using a variety of score terms. In this section, we will see how to score RNA poses, and we will use these score terms to better understand our structure.

To score structures with RNA in Rosetta, it is best to use a high-resolution energy function designed to work with RNA, for instance stepwise/rna/rna_res_level_energy4.wts. In fact, the standard high resolution energy function used in Rosetta does not include the score terms that are quite helpful for modeling RNA. To see this, we will evaluate our RNA pose with the ref2015 score function and stepwise/rna/rna_res_level_energy4.wts, comparing the resulting score term values.

In [13]:
hires_sf = core.scoring.ScoreFunctionFactory.create_score_function("ref2015");
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb
basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop
In [14]:
hires_sf.show(pose)
core.scoring.ScoreFunction: 
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 fa_atr                       1.000    -146.195    -146.195
 fa_rep                       0.550      21.661      11.914
 fa_sol                       1.000     181.903     181.903
 fa_intra_rep                 0.005     104.969       0.525
 fa_intra_sol_xover4          1.000      43.757      43.757
 lk_ball_wtd                  1.000     -23.168     -23.168
 fa_elec                      1.000     -11.254     -11.254
 pro_close                    1.250       0.000       0.000
 hbond_sr_bb                  1.000       0.000       0.000
 hbond_lr_bb                  1.000       0.000       0.000
 hbond_bb_sc                  1.000       0.000       0.000
 hbond_sc                     1.000     -23.799     -23.799
 dslf_fa13                    1.250       0.000       0.000
 omega                        0.400       0.000       0.000
 fa_dun                       0.700       0.000       0.000
 p_aa_pp                      0.600       0.000       0.000
 yhh_planarity                0.625       0.000       0.000
 ref                          1.000       0.000       0.000
 rama_prepro                  0.450       0.000       0.000
---------------------------------------------------
 Total weighted score:                       33.681

Note that ref2015 does contain some terms that are used for RNA modeling like VDW and hydrogen bonding score terms. What extra terms are included in the RNA high resolution score function?

In [15]:
rna_hires_sf = core.scoring.ScoreFunctionFactory.create_score_function("stepwise/rna/rna_res_level_energy4.wts");
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
In [16]:
rna_hires_sf.show(pose)
core.scoring.ScoreFunction: 
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 fa_atr                       0.210    -212.399     -44.604
 fa_rep                       0.200      57.744      11.549
 fa_intra_rep                 0.003     186.211       0.540
 lk_nonpolar                  0.250      -9.222      -2.305
 fa_elec_rna_phos_phos        1.700       0.378       0.643
 rna_torsion                  1.000       3.751       3.751
 suiteness_bonus              1.000       0.000       0.000
 rna_sugar_close              0.820       3.938       3.229
 fa_stack                     0.130    -234.442     -30.477
 stack_elec                   0.760      -0.903      -0.686
 geom_sol_fast                0.170      74.843      12.723
 hbond_sr_bb_sc               0.960       0.000       0.000
 hbond_lr_bb_sc               0.960       0.000       0.000
 hbond_sc                     0.960     -23.799     -22.848
 ref                          1.000      50.440      50.440
 free_suite                   2.000       0.000       0.000
 free_2HOprime                1.000       0.000       0.000
 intermol                     1.000       0.000       0.000
 other_pose                   1.000       0.000       0.000
 loop_close                   1.000       0.000       0.000
 linear_chainbreak            5.000       0.000       0.000
---------------------------------------------------
 Total weighted score:                      -18.046

We can see that some new score terms in the high resolution RNA potential, including rna_torsion, suiteness_bonus, rna_sugar_close, and fa_stack. We will explore a few of these terms below. To learn about these and other score terms that have been included to more realistically model RNA, check out the papers referenced at the beginning of this notebook.

Analogous to the protein low-resolution potential, an RNA low-resolution potential has been developed to more quickly score RNA structures represented in centroid mode. Lets take a look at the score terms involved.

In [17]:
rna_lowres_sf = core.scoring.ScoreFunctionFactory.create_score_function("rna/denovo/rna_lores_with_rnp_aug.wts");
basic.io.database: Database file opened: scoring/rna/rna_atom_vdw.txt
basic.io.database: Database file opened: scoring/rna/rnp_atom_vdw_min_distances_reformat_MIN.txt
core.scoring.ScoringManager: Reading in: /Users/ramyar/Dropbox/GradSchool/Research/packages/PyRosetta4.Release.python37.mac.release-244/setup/build/lib/pyrosetta/database/scoring/rna/rna_base_pair_xy.dat
core.scoring.rna.RNA_LowResolutionPotential: Reading basepair x - y potential file: scoring/rna/rna_base_pair_xy.dat
core.scoring.rna.RNA_LowResolutionPotential: Finished reading basepair x - y potential file: scoring/rna/rna_base_pair_xy.dat
core.scoring.rna.RNA_LowResolutionPotential: Reading non - base - base x - y potential file: scoring/rna/rna_base_backbone_xy.dat
core.scoring.rna.RNA_LowResolutionPotential: Reading RNA backbone backbone potential file: scoring/rna/rna_backbone_backbone.dat
core.scoring.rna.RNP_LowResPotential: Reading RNP basepair x - y potential file: scoring/rna/rnp_base_pair.txt
core.scoring.rna.RNP_LowResPotential: Finished reading RNP basepair x - y potential file: scoring/rna/rnp_base_pair.txt
core.scoring.rna.RNP_LowResPotential: Reading RNP AA RNA backbone potential file: scoring/rna/rnp_backbone_potential.txt
core.scoring.rna.RNP_LowResPotential: Finished reading RNP AA RNA backbone potential file: scoring/rna/rnp_backbone_potential.txt
core.scoring.rna.RNP_LowResPairDistPotential: Reading RNP pair distance potential file: scoring/rna/rnp_pair_dist_potential_renorm.txt
core.scoring.rna.RNP_LowResPairDistPotential: Finished reading RNP pair distance potential file: scoring/rna/rnp_pair_dist_potential_renorm.txt
In [18]:
rna_lowres_sf.show(pose)
core.scoring.ScoreFunction: 
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 rna_data_backbone            2.000       0.000       0.000
 rna_vdw                      2.000       0.221       0.442
 rnp_vdw                     50.000       0.000       0.000
 rna_base_backbone            2.000      -1.884      -3.769
 rna_backbone_backbone        2.000       0.000       0.000
 rna_repulsive                5.000       0.000       0.000
 rna_base_pair                2.000     -53.214    -106.429
 rna_base_axis                0.400     -32.234     -12.894
 rna_base_stagger             2.000     -28.072     -56.143
 rna_base_stack               2.000      -3.243      -6.486
 rna_base_stack_axis          0.400     -20.598      -8.239
 rnp_base_pair                2.000       0.000       0.000
 rnp_stack                    5.000       0.000       0.000
 rnp_pair_dist                0.200       0.000       0.000
 rnp_aa_to_rna_backbone       1.000       0.000       0.000
 rna_rg                       0.500       8.609       4.304
 atom_pair_constraint         1.000       0.000       0.000
 base_pair_constraint         1.000       0.000       0.000
 linear_chainbreak            8.000       0.000       0.000
---------------------------------------------------
 Total weighted score:                     -189.213

We can see that when modeling an RNA molecule using centroid positions for nucleotides, we need to separately include terms for base pairing (rna_base_pair), base-backbone interactions (rna_base_backbone), and so on.

Returning to the high resolution RNA score function, let us see if we can decompose the energies further to understand which parts of the structure contribute positively and negatively to its energy. First, we can decompose the energies per residue like below.

In [19]:
rna_hires_sf(pose)
nonzero_scores = pose.energies().residue_total_energies(4).show_nonzero()
print(nonzero_scores)
 fa_atr: -16.0481 fa_rep: 4.95774 fa_intra_atr: -10.6601 fa_intra_rep: 10.4003 fa_intra_sol: 6.2042 fa_intra_atr_nonprotein: -10.6601 fa_intra_rep_nonprotein: 10.4003 fa_intra_sol_nonprotein: 6.2042 lk_nonpolar: -0.837546 fa_elec_rna_phos_phos: -0.0122409 rna_torsion: 0.105802 rna_torsion_sc: 0.054655 rna_sugar_close: 0.471854 fa_stack: -14.7643 stack_elec: 0.0989445 geom_sol_fast: 6.69203 geom_sol_fast_intra_RNA: 0.348984 hbond_sc: -2.22045 ref: 2.82 total_score: -2.10402

A lot of the RNA specific energy terms make more sense when we look at pairs of residues. The energy graph object allows you to explore pairwise energies. The function below uses the energy graph to print out all non-zero scores between residues for a particular score term.

In [20]:
def print_nonzero_pairwise_energies(pose, energy_term, sf):
    sf(pose)
    energy_graph = pose.energies().energy_graph()
    for ii in range(1, pose.size() + 1):
        for jj in range(ii + 1, pose.size() + 1):
            edge = energy_graph.find_energy_edge(ii, jj)
            if (edge != None):
                emap = edge.fill_energy_map()
                resid1 = str(ii) + " " + pose.residue(ii).name1()
                resid2 = str(jj) + " " + pose.residue(jj).name1()
                resid_pair = resid1 + " " + resid2
                score = emap[ energy_term ]
                if score != 0:
                    print("%s: %f" % (resid_pair, score))

Using the function above, we're going to look at the stacking energies in the high resolution potential.

In [21]:
print_nonzero_pairwise_energies(pose, core.scoring.ScoreType.fa_stack, rna_hires_sf)
1 c 2 a: -8.786457
1 c 13 u: -0.021402
1 c 14 g: -0.014325
2 a 3 u: -17.195315
2 a 12 a: -1.166573
2 a 13 u: -0.021531
2 a 14 g: -18.136998
3 u 4 c: -10.651433
3 u 11 g: -0.182032
3 u 12 a: -0.025817
3 u 13 u: -2.437063
4 c 5 c: -11.016306
4 c 6 g: -0.042999
4 c 10 g: -0.170933
4 c 11 g: -0.003559
4 c 12 a: -7.643363
5 c 6 g: -14.998700
5 c 9 a: -0.055888
5 c 10 g: -0.004817
5 c 11 g: -9.170599
6 g 8 a: -1.056694
6 g 9 a: -0.381851
6 g 10 g: -11.820445
7 a 8 a: -21.526270
8 a 9 a: -22.045880
9 a 10 g: -13.441684
10 g 11 g: -18.409410
11 g 12 a: -18.811699
12 a 13 u: -16.199935
13 u 14 g: -9.002159

We can see that the stacking energies are highest for consecutive residues. In the idealized helix, the best stacking energy bonuses are given to stacked purine residues.

Now lets take a look at the torsion energies. Which energies are the highest? Where are these torsions in the structure?

In [22]:
print_nonzero_pairwise_energies(pose, core.scoring.ScoreType.rna_torsion, rna_hires_sf)
1 c 2 a: 0.041018
2 a 3 u: 0.003446
3 u 4 c: 0.012547
4 c 5 c: 0.015482
5 c 6 g: 0.048322
6 g 7 a: 0.273854
7 a 8 a: 0.096358
8 a 9 a: 0.020082
9 a 10 g: 0.248952
10 g 11 g: 0.019879
11 g 12 a: 0.012364
12 a 13 u: 0.017076
13 u 14 g: 0.002773

RNA structures are often viewed as being composed of small building blocks called RNA motifs. These motifs can be as simple as stacks of base pairs, which we have seen above. Typical motifs also include stereotyped loops, junctions, and tertiary contacts present across many common RNA molecules. Let's take a look to see whether any of these common RNA motifs are present in our simple stem loop structure.

In [23]:
lowres_potential = core.scoring.rna.RNA_LowResolutionPotential( "scoring/rna/rna_base_pair_xy.dat" )
rna_scoring_info = core.scoring.rna.rna_scoring_info_from_pose(pose).rna_filtered_base_base_info()
rna_motifs = core.scoring.rna.get_rna_motifs( pose, lowres_potential, rna_scoring_info)
print(rna_motifs)
core.scoring.rna.RNA_LowResolutionPotential: Reading basepair x - y potential file: scoring/rna/rna_base_pair_xy.dat
core.scoring.rna.RNA_LowResolutionPotential: Finished reading basepair x - y potential file: scoring/rna/rna_base_pair_xy.dat
core.scoring.rna.RNA_LowResolutionPotential: Reading non - base - base x - y potential file: scoring/rna/rna_base_backbone_xy.dat
core.scoring.rna.RNA_LowResolutionPotential: Reading RNA backbone backbone potential file: scoring/rna/rna_backbone_backbone.dat
WC_STACKED_PAIR [1, 2, 13, 14]
WC_STACKED_PAIR [4, 5, 10, 11]
WC_STACKED_PAIR [11, 12, 3, 4]
WC_STACKED_PAIR [10, 11, 4, 5]
WC_STACKED_PAIR [3, 4, 11, 12]
WC_STACKED_PAIR [12, 13, 2, 3]
WC_STACKED_PAIR [2, 3, 12, 13]
WC_STACKED_PAIR [13, 14, 1, 2]
U_TURN [6, 7, 8]
GNRA_TETRALOOP [6, 7, 8, 9]

We can see that our RNA structure includes many stacked Watson-Crick base pair, making the idealized A-form helix. In addition, the loop connecting the strands of the helix in our structure is a stereotyped "GNRA" tetraloop, taking a loop conformation that is common across many RNA structures in the PDB.

Manipulating RNA poses

Rosetta allows you to not just explore a given PDB structure, but to manipulate and design structures. In this section, we discuss some basic ways to manipulate RNA structures, and we observe the effects of these manipulations on the structure's energy. For each manipulation, we will make a new copy of the pose to make sure that our changes do not affect the original structure we loaded in.

One basic manipulation we can make to an RNA structure is to change torsion angles for individual residues. Let's try this out on a residue in the A-form helix, and observe the effect on the rna_torsion score. Did the change we made make the score better or worse?

In [24]:
new_pose = Pose()
new_pose.assign(pose)
rna_hires_sf(pose)
torsion_score_before = pose.energies().total_energies()[core.scoring.ScoreType.rna_torsion]
new_pose.set_beta(2, 110)
rna_hires_sf(new_pose)
torsion_score_after = new_pose.energies().total_energies()[core.scoring.ScoreType.rna_torsion]
print("%s: %f" % ("Torsion score before", torsion_score_before))
print("%s: %f" % ("Torsion score after", torsion_score_after))
Torsion score before: 3.750853
Torsion score after: 4.166565

If you want to replace residues in an RNA molecule with their idealized versions, you can use the RNA_IdealCoord class in Rosetta. Below is an example for using that method to first replace a single residue with its idealized version, and then to replace all residues with their idealized versions across the whole pose.

In [25]:
ideal_pose_one = Pose()
ideal_pose_one.assign(pose)
resid = 2
core.pose.rna.RNA_IdealCoord().apply(ideal_pose_one, resid, core.chemical.rna.PuckerState.ANY_PUCKER, False)

ideal_pose = Pose()
ideal_pose.assign(pose)
core.pose.rna.RNA_IdealCoord().apply(ideal_pose, False)

Exercise: Figure out if the total energy of the pose went up or down after replacing one or all of the residues with their idealized versions. What can explain the difference? What about the total torsion energy only - does that go up or down in the pose with idealized residues compared to the original pose?

In [26]:
### BEGIN SOLUTION
rna_hires_sf(pose)
rna_hires_sf(ideal_pose)
rna_hires_sf(ideal_pose_one)
print(pose.energies().total_energy())
print(ideal_pose.energies().total_energy())
print(ideal_pose_one.energies().total_energy())
### END SOLUTION
-18.045673691089746
22.63480325590245
-1.1025695607212
In [27]:
### BEGIN SOLUTION
print(pose.energies().total_energies()[core.scoring.ScoreType.rna_torsion])
print(ideal_pose.energies().total_energies()[core.scoring.ScoreType.rna_torsion])
### END SOLUTION
3.7508527554837183
2.334597688825869

Another common manipulation for an RNA structure is to mutate the nucleotides to different bases. This is a manipulation that is commonly used while modeling one RNA structure using coordinates from another homologous (but not identical) structure. Below we can see how to mutate one residue of our RNA structure to another one.

In [35]:
mutated_pose = Pose()
mutated_pose.assign(pose)
print(pose.sequence())
rosetta.core.pose.rna.mutate_position(mutated_pose, 1, 'a')
print(mutated_pose.sequence())
cauccgaaaggaug
aauccgaaaggaug

Exercise: Make a function that mimics the 'rna_thread' Rosetta application, which takes in a pose and a new sequence and replaces all pose residues with the new sequence's residues. Remember to check that the pose's sequence and the new sequence have the same length.

The pose's current sequence is cauccgaaaggaug. Use the function you wrote to make a version that has sequence cauccuucgggaug and one that has sequence aaaaagaaauuuuu.

In [36]:
### BEGIN SOLUTION
def rna_thread(pose, new_seq):
    if len(pose.sequence()) != len(new_seq):
        print("Sequences have different length; cannot rethread")
        return pose
    for ii in range(1, pose.size()+1):
        rosetta.core.pose.rna.mutate_position(pose, ii, new_seq[ii-1])
    return pose
### END SOLUTION
In [37]:
### BEGIN SOLUTION
uucg_pose = Pose()
uucg_pose.assign(pose)
uucg_pose = rna_thread(uucg_pose, 'cauccuucgggaug')
print(uucg_pose.sequence())

auhelix_pose = Pose()
auhelix_pose.assign(pose)
auhelix_pose = rna_thread(auhelix_pose, 'aaaaagaaauuuuu')
print(auhelix_pose.sequence())
### END SOLUTION
cauccuucgggaug
aaaaagaaauuuuu

Exercise: The RNA high resolution potential includes hydrogen bonding terms. CG base pairs have more hydrogen bonds than AU base pairs. Compare the original pose with the pose that has all AU base pairs. What happens to the hydrogen bonding energy in the high resolution potential?

In [38]:
### BEGIN SOLUTION
rna_hires_sf(auhelix_pose)
rna_hires_sf(pose)
auhelix_hbond_sc = auhelix_pose.energies().total_energies()[core.scoring.ScoreType.hbond_sc]
pose_hbond_sc = pose.energies().total_energies()[core.scoring.ScoreType.hbond_sc]
print('%s: %f' % ("AU Helix", auhelix_hbond_sc))
print('%s: %f' % ("CG Helix", pose_hbond_sc))
### END SOLUTION
AU Helix: -18.166948
CG Helix: -23.799493

Exercise: The stacking energies of the GAAA and UUCG tetraloops differ from each other. Which tetraloop provides the most favorable stacking energies overall? Can you figure out which pairs of residues have different stacking energies when the structure has changed (hint: you can base your code here off of the function print_nonzero_pairwise_energies above)?

In [39]:
### BEGIN SOLUTION
rna_hires_sf(uucg_pose)
rna_hires_sf(pose)
uucg_fa_stack = uucg_pose.energies().total_energies()[core.scoring.ScoreType.fa_stack]
pose_fa_stack = pose.energies().total_energies()[core.scoring.ScoreType.fa_stack]
print('%s: %f' % ("UUCG Loop", uucg_fa_stack))
print('%s: %f' % ("GAAA Loop", pose_fa_stack))
### END SOLUTION
UUCG Loop: -214.060807
GAAA Loop: -234.442137
In [40]:
### BEGIN SOLUTION
# The code below goes through the original pose with the GNRA loop and the uucg_pose, 
# printing out pairs of residues and the fa_stack score term between these residues
# if this score differs between the two poses.
rna_hires_sf(uucg_pose)
rna_hires_sf(pose)
pose_energy_graph = pose.energies().energy_graph()
uucg_energy_graph = uucg_pose.energies().energy_graph()
for ii in range(1, pose.size() + 1):
    for jj in range(ii + 1, pose.size() + 1):
        pose_edge = pose_energy_graph.find_energy_edge(ii, jj)
        uucg_edge = uucg_energy_graph.find_energy_edge(ii, jj)
        if (pose_edge != None)  and (uucg_edge != None):
            pose_emap = pose_edge.fill_energy_map()
            uucg_emap = uucg_edge.fill_energy_map()
            resid1 = str(ii) + " " + pose.residue(ii).name1()
            resid1_uucg = str(ii) + " " + uucg_pose.residue(ii).name1()
            resid2 = str(jj) + " " + pose.residue(jj).name1() 
            resid2_uucg = str(jj) + " " + uucg_pose.residue(jj).name1()
            resid_pair = resid1 + ", " + resid2
            resid_pair_uucg = resid1_uucg + ", " + resid2_uucg
            pose_score = pose_emap[ core.scoring.ScoreType.fa_stack ]
            uucg_score = uucg_emap[ core.scoring.ScoreType.fa_stack ]
            if pose_score != uucg_score:
                print("%s: %f; %s: %f" % (resid_pair, pose_score, resid_pair_uucg, uucg_score))
### END SOLUTION
4 c, 6 g: -0.042999; 4 c, 6 u: -0.020146
5 c, 6 g: -14.998700; 5 c, 6 u: -14.424303
5 c, 9 a: -0.055888; 5 c, 9 g: -0.040952
6 g, 8 a: -1.056694; 6 u, 8 c: -0.798130
6 g, 9 a: -0.381851; 6 u, 9 g: -0.142689
6 g, 10 g: -11.820445; 6 u, 10 g: -5.138552
7 a, 8 a: -21.526270; 7 u, 8 c: -14.881668
8 a, 9 a: -22.045880; 8 c, 9 g: -16.479345
9 a, 10 g: -13.441684; 9 g, 10 g: -13.063297

Elements of RNA Structure Prediction

Many of the same strategies are used when modeling RNA as when modeling proteins. Below, we shall explore some of these procedures specifically applied to RNA molecules to appreciate how they may come together to give a modern structure prediction method.

Generating an ideal A-form Helix

On a not wholly unrelated tangent, let us first see how we can quickly generate poses of ideal A-form RNA. You can think of this procedure as analogous to the pose_from_seq function used to generate protein poses from primary sequences. Let's use it now to generate a single-strand RNA pose with A-form torsions and the same sequence as the hairpin we've been examining so far.

assembler = core.import_pose.RNA_HelixAssembler()
assembled_pose = assembler.build_init_pose(pose.sequence(), '')
In [41]:
### BEGIN SOLUTION
assembler = core.import_pose.RNA_HelixAssembler()
assembled_pose = assembler.build_init_pose(pose.sequence(), '')
### END SOLUTION

Let's get a PyMOLMover up and running so we can examine our new pose.

In [42]:
pmm = PyMOLMover()
pmm.set_PyMOL_model_name('assembled_pose')
pmm.apply(assembled_pose)

You can also use RNA_HelixAssmebler to generate poses that comprise two strands that form an ideal A-form helical stack, like residues 1-5 and 10-14 in the hairpin from above.

In [43]:
pmm_helix = PyMOLMover()
pmm_helix.set_PyMOL_model_name('helix_pose')
helix_pose = assembler.build_init_pose('ggg','ccc')

Looking in PyMOL, you may be able to appreciate that, true to its name, the RNA_HelixAssembler has generated a pose that looks quite helical.

In [44]:
pmm_helix.apply(helix_pose)

Exercise: Examine the torsions in several of the residues of assembled_pose using the print_torsions function you wrote earlier. How do they compare to the torsions from the starting stem loop?

RNA Fragments

Given a library of RNA torsions excised from a published structure, fragment assembly methods will choose an n-mer in the current structure and replace the backbone geometry with the geometry of a corresponding n-mer from the library. Those of you familiar with protein structure prediction methods will recognize this strategy of fragment assembly.

We will implement a rudimentary version of this protocol for RNA below.

For the present exercise, we will use the torsions file inputs/1jj2.torsions, which comes from the crystal structure of a large ribosomal subunit. This library will be used to initialize a Mover specifically designed to perform fragment assembly on RNA molecules, RNA_FragmentMover.

fragset = core.import_pose.libraries.RNA_LibraryManager.get_instance().rna_fragment_library("inputs/1jj2.torsions")
atom_level_domain_map = core.pose.toolbox.AtomLevelDomainMap(assembled_pose)
frag_mover = protocols.rna.denovo.movers.RNA_FragmentMover(fragset, atom_level_domain_map, 1, 0)

Don't worry too much about the other options that RNA_FragmentMover requires at this point, but remember to include them if using this mover outside of this notebook.

In [45]:
### BEGIN SOLUTION
fragset = core.import_pose.libraries.RNA_LibraryManager.get_instance().rna_fragment_library("./inputs/1jj2.torsions")
atom_level_domain_map = core.pose.toolbox.AtomLevelDomainMap(assembled_pose)
frag_mover = protocols.rna.denovo.movers.RNA_FragmentMover(fragset, atom_level_domain_map, 1, 0)
### END SOLUTION
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Reading in vall_torsions file: ./inputs/1jj2.torsions
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Lines read from vall_torsions file: 2754

Let's practice applying this mover to a Pose. To actually make a fragment assembly move, you can call the random_fragment_insertion method which requires two arguments:

  1. An input Pose
  2. The size of the fragment to substitute.

There is also an apply() method that can be called in a similar manner, but it simply calls random_fragment_insertion(), so the recommendation is to decrease overhead by calling random_fragment_insertion() where possible.

Let's pratice calling this method below.

practice_pose = Pose()
practice_pose.assign(assembled_pose)
frag_mover.random_fragment_insertion(practice_pose, 3)
pmm.apply(practice_pose)
In [46]:
### BEGIN SOLUTION
practice_pose = Pose()
practice_pose.assign(assembled_pose)
frag_mover.random_fragment_insertion(practice_pose, 3)
pmm.apply(practice_pose)
### END SOLUTION
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence aaa  and sec. struct XXX ... found 45 potential fragments

Now that we know how to set up a fragment assembly mover in PyRosetta, try the excise below to write a quick folding routine that uses a fragment assembly strategy to try and fold the hairpin sequence.

Exercise: Fill in the function below such that fragment_assembly

  • Accepts an input Pose, RNA_FragmentMover, fragment size to substitute (frag_size), and number of trials (n_trials).
  • Uses by default the rna_lowres_sf energy function from earlier but allows the user to specify a different energy function, if desired
  • Performs a fragment substitution and accepts the substitution subject to the Metropolis criterion (assume $kT = 1$)
  • Returns the lowest-energy pose found.

* See section 4.1 of these notebooks for a review on Monte Carlo algorithms, if desired.

Then, apply it to our newly assembled pose using the following recipe:

  1. Run fragment_assembly using 3 nucleotide fragments for 400 trials.
  2. Then, run fragment_assembly using 2 nucleotide fragments for 300 trials.
  3. Finally, run fragment_assembly using 1 nucleotide fragments for 300 trials.
In [47]:
import math
import random

def fragment_assembly(start_pose, frag_mover, frag_size, n_trials, sf=rna_lowres_sf):
    curr_pose = Pose()
    curr_pose.assign(start_pose)
    trial_pose = Pose()
    trial_pose.assign(curr_pose)
    opt_pose = Pose()
    opt_pose.assign(curr_pose)
    currE = newE = optE = sf(curr_pose)
### BEGIN SOLUTION
    for _ in range(n_trials):
        frag_mover.random_fragment_insertion(trial_pose, frag_size)
        newE = sf(trial_pose)
        if random.random() < math.exp(currE-newE):
            curr_pose.assign(trial_pose)
            currE = newE
            if currE < optE:
                optE = currE
                opt_pose.assign(curr_pose)
    return curr_pose
### END SOLUTION
    #return curr_pose

frag_pose = fragment_assembly(assembled_pose, frag_mover, 3, 400)
frag_pose = fragment_assembly(frag_pose, frag_mover, 2, 300)
frag_pose = fragment_assembly(frag_pose, frag_mover, 1, 300)
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence gau  and sec. struct XXX ... found 37 potential fragments
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence aug  and sec. struct XXX ... found 38 potential fragments
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence aag  and sec. struct XXX ... found 64 potential fragments
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence ccg  and sec. struct XXX ... found 63 potential fragments
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence gga  and sec. struct XXX ... found 62 potential fragments
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence cau  and sec. struct XXX ... found 29 potential fragments
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence cga  and sec. struct XXX ... found 77 potential fragments
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence ucc  and sec. struct XXX ... found 38 potential fragments
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence agg  and sec. struct XXX ... found 64 potential fragments
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence auc  and sec. struct XXX ... found 32 potential fragments
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence gaa  and sec. struct XXX ... found 76 potential fragments
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence ga  and sec. struct XX ... found 243 potential fragments
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence cg  and sec. struct XX ... found 214 potential fragments
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence ca  and sec. struct XX ... found 156 potential fragments
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence au  and sec. struct XX ... found 113 potential fragments
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence ag  and sec. struct XX ... found 224 potential fragments
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence cc  and sec. struct XX ... found 182 potential fragments
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence gg  and sec. struct XX ... found 235 potential fragments
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence aa  and sec. struct XX ... found 197 potential fragments
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence ug  and sec. struct XX ... found 171 potential fragments
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence uc  and sec. struct XX ... found 142 potential fragments
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence g  and sec. struct X ... found 844 potential fragments
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence a  and sec. struct X ... found 716 potential fragments
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence c  and sec. struct X ... found 690 potential fragments
protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence u  and sec. struct X ... found 504 potential fragments

Examine the fragment assembled Pose in PyMOL. Do you recognize any of the motifs from before?

frag_pmm = PyMOLMover()
frag_pmm.set_PyMOL_model_name('frag_pose')
frag_pmm.apply(frag_pose)
In [48]:
### BEGIN SOLUTION
frag_pmm = PyMOLMover()
frag_pmm.set_PyMOL_model_name('frag_pose')
frag_pmm.apply(frag_pose)
### END SOLUTION

Minimizing Structures with RNA

In principle, the standard MinMover that has been introduced previously in the context of minimizing purely protein structures can also be used to minimize poses with RNA (as long as the assigned energy function has score terms relevant to RNA and an appropriate MoveMap is provided).

However, as part of the rna_denovo protocol, Das and coworkers have developed a subroutine, RNA_Minimize, that is specifically geared toward handling minimization of poses with RNA, the use of which is detailed below.

We can access the RNA_Minimize mover from the protocols namespace. The relevant options object, RNA_MinimizerOptions, lives in the import_pose.options namespace. We will set the maximum number of iterations to 1000, using default values for other options.

rna_min_options = core.import_pose.options.RNA_MinimizerOptions()
rna_min_options.set_max_iter(1000)
rna_minmizer = protocols.rna.denovo.movers.RNA_Minimizer(rna_min_options)
In [49]:
### BEGIN SOLUTION
rna_min_options = core.import_pose.options.RNA_MinimizerOptions()
rna_min_options.set_max_iter(1000)
rna_minimizer = protocols.rna.denovo.movers.RNA_Minimizer(rna_min_options)
### END SOLUTION

Unlike in the case of using MinMover, things like an appropriate energy function and MoveMap are generated by default by the RNA_Minimizer object. By default, RNA_Minimizer uses the same high-resolution energy function as above (stepwise/rna/rna_res_level_energy4.wts).

All that remains is to apply it to the relevant pose.

rna_minimizer.apply(frag_pose)
In [50]:
### BEGIN SOLUTION
rna_minimizer.apply(frag_pose)
### END SOLUTION
protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls...
protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 1
protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls...
protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 2
protocols.rna.denovo.movers.RNA_Minimizer: 
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 fa_atr                       0.210    -213.189     -44.770
 fa_rep                       0.200      28.665       5.733
 fa_intra_rep                 0.003     171.212       0.497
 lk_nonpolar                  0.250       3.414       0.854
 fa_elec_rna_phos_phos        1.700      -0.635      -1.079
 rna_torsion                  1.000       5.304       5.304
 suiteness_bonus              1.000       0.000       0.000
 rna_sugar_close              0.820       0.474       0.388
 fa_stack                     0.130    -209.236     -27.201
 stack_elec                   0.760      -4.052      -3.079
 geom_sol_fast                0.170      64.031      10.885
 hbond_sr_bb_sc               0.960      -1.318      -1.265
 hbond_lr_bb_sc               0.960       0.000       0.000
 hbond_sc                     0.960      -8.280      -7.949
 ref                          1.000      50.440      50.440
 free_suite                   2.000       0.000       0.000
 free_2HOprime                1.000       0.000       0.000
 intermol                     1.000       0.000       0.000
 other_pose                   1.000       0.000       0.000
 loop_close                   1.000       0.000       0.000
 linear_chainbreak            5.000       0.000       0.000
---------------------------------------------------
 Total weighted score:                      -11.241
protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 12 seconds.

Let's see what changes minimization has wrought on our structure:

min_pmm = PyMOLMover()
min_pmm.set_PyMOL_model_name('min_pose')
min_pmm.apply(frag_pose)
In [51]:
### BEGIN SOLUTION
min_pmm = PyMOLMover()
min_pmm.set_PyMOL_model_name('min_pose')
min_pmm.apply(frag_pose)
### END SOLUTION

Exercise: Using the functions described in the first part of the notebook, report on the following with respect to our de novo folded sequence:

  1. Which base pairs, if any, were recovered?
  2. Which motifs, if any, were recovered?
In [52]:
### BEGIN SOLUTION
base_pairs = classify_base_pairs(frag_pose)
for base_pair in base_pairs:
    print(base_pair)

lowres_potential = core.scoring.rna.RNA_LowResolutionPotential( "scoring/rna/rna_base_pair_xy.dat" )
rna_scoring_info = core.scoring.rna.rna_scoring_info_from_pose(frag_pose).rna_filtered_base_base_info()
rna_motifs = core.scoring.rna.get_rna_motifs( frag_pose, lowres_potential, rna_scoring_info)
print(rna_motifs)
### END SOLUTION
5 10 WC WC ANTI
core.scoring.rna.RNA_LowResolutionPotential: Reading basepair x - y potential file: scoring/rna/rna_base_pair_xy.dat
core.scoring.rna.RNA_LowResolutionPotential: Finished reading basepair x - y potential file: scoring/rna/rna_base_pair_xy.dat
core.scoring.rna.RNA_LowResolutionPotential: Reading non - base - base x - y potential file: scoring/rna/rna_base_backbone_xy.dat
core.scoring.rna.RNA_LowResolutionPotential: Reading RNA backbone backbone potential file: scoring/rna/rna_backbone_backbone.dat

Additional Exercises

Post-mortem

Examine our final folded structure and the hairpin from the first part of the tutorial and think about the following questions:

  • How well did our brief structure prediction algorithm do at recovering the hairpin we examined at the beginning?
  • Which parts were more successfully recovered? Which parts less so? Why might this be?
  • What would you do to improve on this method as it stands? Feel free to implement any ideas you have.

FAR + FAR = FARFAR

Write a function analogous to the fragment_assembly function above that

  • Accepts an input Pose
  • Performs a round of minimization using an RNA_Minimizer
  • Returns the minimized structure

Using this new suboutine, craft your own farfar ( Fragment Assembly of RNA with Full Atom Refinement) routine that performs multiple rounds of fragment assembly in a low-resolution potential followed by minimization in a high-resolution energy function.

Try playing around with the various parameters and see how well you can recover the hairpin starting from just the sequence.

RNA Structure Prediction Protocol

Below we will be running a short RNA de novo modeling run for the stem-loop sequence we have been working with thus far, making use of the FARFAR protocol (which you can run with the rna_denovo command in Rosetta). As discussed above, the FARFAR protocol involves a mixture of fragment assembly moves and full atom minimization moves. We will generate a small set of structures using FARFAR and compare the energy of the resulting structures to those constructed in the previous exercise.

FARFAR builds models for a structure as specified in a FASTA file, making use of any structures of known sub-pieces (for instance, A-form helices for regions known to form stems). In this case, we will provide the helical portion of our structure between residues 1-5 and residues 10-14 as an input to the FARFAR protocol, so that the protocol only has to worry about sampling the loop. In a real modeling scenario, it is often the case that information about the secondary structure of the RNA is known, allowing us to make use of A-form helix rigid bodies to accelerate modeling.

Let's set up the fasta file and input PDB files to use as options for FARFAR; these files should be in the inputs/ folder.

In [53]:
input_pdbs = rosetta.utility.vector1_std_string()
fasta_files = rosetta.utility.vector1_std_string()
input_pdbs.append("inputs/stem.pdb")
fasta_files = rosetta.utility.vector1_std_string()
fasta_files.append("inputs/stem_loop.fasta")

We will set up options for rna_denovo below, specifying the FASTA file, the input PDBs, the number of structures we would like to generate, and the output file (silent file format).

In [54]:
rna_de_novo_setup = core.import_pose.RNA_DeNovoSetup()
rna_de_novo_setup.set_fasta_files(fasta_files)
rna_de_novo_setup.set_minimize_rna(True)
rna_de_novo_setup.set_input_pdbs(input_pdbs)
In [55]:
rna_de_novo_setup.initialize_from_command_line()
core.import_pose.options.RNA_DeNovoProtocolOptions: Setting silent file name based on directory: notebooks.out
core.import_pose.import_pose: File 'inputs/stem.pdb' automatically determined to be of type PDB
core.import_pose.RNA_DeNovoSetup: Sequence:            cauccgaaaggaug
core.import_pose.RNA_DeNovoSetup: Secstruct:           ..............
In [56]:
rna_de_novo_options = rna_de_novo_setup.options()
rna_de_novo_options.set_nstruct(10)
rna_de_novo_options.set_silent_file("outputs/stem_loop.out")
rna_de_novo_options.set_vall_torsions_file("./inputs/1jj2.torsions")

Now we will run FARFAR by generating an RNA_DeNovoProtocol object and running it with apply on a starting pose. This will take a few minutes to run, and will generate 10 structures to the silent file specified above. As the protocol is running, take a look at the output to understand how it works. Note that for each structure generated, the protocol goes through various rounds of fragment assembly with fragments of size 3, 2, and 1, and then runs the RNA minimizer. This is similar to the protocol you made above!

In [57]:
rna_de_novo_protocol = rosetta.protocols.rna.denovo.RNA_DeNovoProtocol(rna_de_novo_options, rna_de_novo_setup.rna_params())
In [58]:
rna_de_novo_pose = rna_de_novo_setup.pose()
rna_de_novo_protocol.apply(rna_de_novo_pose)
protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer: Setting desired secondary structure to: XXXXXXXXXXXXXX
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 1
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 2) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  O3'
core.import_pose.import_pose: File 'inputs/stem.pdb' automatically determined to be of type PDB
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 1
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 2) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  O3'
protocols.rna.setup.RNA_MonteCarloJobDistributor: 
protocols.rna.setup.RNA_MonteCarloJobDistributor: Embarking on structure 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving residues: 5
protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving chunks: 0
protocols.rna.denovo.RNA_FragmentMonteCarlo: Using 10000 cycles in de novo modeling.
protocols.rna.denovo.libraries.RNA_JumpLibrary: Reading RNA jump library: /Users/ramyar/Dropbox/GradSchool/Research/packages/PyRosetta4.Release.python37.mac.release-244/setup/build/lib/pyrosetta/database/sampling/rna/RNA18_HUB_2.154_2.5.jump
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.moves.TrialCounter:           frag 3 trials=    896;  accepts= 0.1496;  energy_drop/trial=  -0.02519
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    900;  accepts= 0.1078;  energy_drop/trial=   0.00455
core.scoring.rna.RNA_LowResolutionPotential: Reading basepair x - y potential file: scoring/rna/rna_base_pair_xy.dat
core.scoring.rna.RNA_LowResolutionPotential: Finished reading basepair x - y potential file: scoring/rna/rna_base_pair_xy.dat
core.scoring.rna.RNA_LowResolutionPotential: Reading non - base - base x - y potential file: scoring/rna/rna_base_backbone_xy.dat
core.scoring.rna.RNA_LowResolutionPotential: Reading RNA backbone backbone potential file: scoring/rna/rna_backbone_backbone.dat
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    920;  accepts= 0.0870;  energy_drop/trial=   0.01243
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    902;  accepts= 0.0687;  energy_drop/trial=   0.00649
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    889;  accepts= 0.0439;  energy_drop/trial=   0.00800
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    896;  accepts= 0.0357;  energy_drop/trial=   0.01042
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    894;  accepts= 0.0649;  energy_drop/trial=   0.00982
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    891;  accepts= 0.0471;  energy_drop/trial=   0.00768
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    898;  accepts= 0.0301;  energy_drop/trial=  -0.00188
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    896;  accepts= 0.0435;  energy_drop/trial=   0.00480
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000001 in 6 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -98.4243 to automatically determined cutoff: -98.4243 based on 0.2 quantile from 1 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: 
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 rna_data_backbone            1.000       0.000       0.000
 rna_vdw                      1.000       0.060       0.060
 rna_base_backbone            1.000      -7.444      -7.444
 rna_backbone_backbone        1.000       0.000       0.000
 rna_repulsive                1.000       0.000       0.000
 rna_base_pair                1.000     -56.859     -56.859
 rna_base_axis                0.200     -32.627      -6.525
 rna_base_stagger             1.000     -28.303     -28.303
 rna_base_stack               1.000      -3.516      -3.516
 rna_base_stack_axis          0.200     -23.519      -4.704
 rna_rg                       1.000       8.646       8.646
 atom_pair_constraint         1.000       0.000       0.000
 base_pair_constraint         1.000       0.000       0.000
 linear_chainbreak            5.000       0.044       0.220
---------------------------------------------------
 Total weighted score:                      -98.424
protocols.rna.denovo.RNA_FragmentMonteCarlo: 
protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls...
protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 1
protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls...
protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 2
protocols.rna.denovo.movers.RNA_Minimizer: 
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 fa_atr                       0.210    -204.738     -42.995
 fa_rep                       0.200      59.226      11.845
 fa_intra_rep                 0.003     155.483       0.451
 lk_nonpolar                  0.250      -7.480      -1.870
 fa_elec_rna_phos_phos        1.700       0.209       0.356
 rna_torsion                  1.000       4.773       4.773
 suiteness_bonus              1.000       0.000       0.000
 rna_sugar_close              0.820       3.803       3.118
 fa_stack                     0.130    -207.756     -27.008
 stack_elec                   0.760      -1.458      -1.108
 geom_sol_fast                0.170      74.773      12.711
 hbond_sr_bb_sc               0.960       0.000       0.000
 hbond_lr_bb_sc               0.960      -0.236      -0.227
 hbond_sc                     0.960     -22.237     -21.348
 ref                          1.000      50.440      50.440
 free_suite                   2.000       0.000       0.000
 free_2HOprime                1.000       0.000       0.000
 intermol                     1.000       0.000       0.000
 other_pose                   1.000       0.000       0.000
 loop_close                   1.000       0.000       0.000
 linear_chainbreak            5.000       0.015       0.074
---------------------------------------------------
 Total weighted score:                      -10.788
protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 3 seconds.
protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000011
protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: outputs/stem_loop.out
protocols.rna.setup.RNA_MonteCarloJobDistributor: 
protocols.rna.setup.RNA_MonteCarloJobDistributor: Embarking on structure 2 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving residues: 5
protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving chunks: 0
protocols.rna.denovo.RNA_FragmentMonteCarlo: Using 10000 cycles in de novo modeling.
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.moves.TrialCounter:           frag 3 trials=    912;  accepts= 0.1985;  energy_drop/trial=  -0.02832
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    902;  accepts= 0.1031;  energy_drop/trial=   0.00035
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    895;  accepts= 0.0436;  energy_drop/trial=   0.00208
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    885;  accepts= 0.0508;  energy_drop/trial=   0.00127
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    890;  accepts= 0.0258;  energy_drop/trial=   0.00626
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    911;  accepts= 0.0505;  energy_drop/trial=   0.01172
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    925;  accepts= 0.0811;  energy_drop/trial=   0.01452
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    905;  accepts= 0.0906;  energy_drop/trial=   0.00890
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    911;  accepts= 0.0659;  energy_drop/trial=   0.00931
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    905;  accepts= 0.0807;  energy_drop/trial=  -0.00160
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000002 in 6 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -92.8449 to automatically determined cutoff: -98.4243 based on 0.2 quantile from 2 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 2 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    902;  accepts= 0.1530;  energy_drop/trial=  -0.01438
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    893;  accepts= 0.0963;  energy_drop/trial=   0.00220
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    904;  accepts= 0.0675;  energy_drop/trial=   0.00678
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    895;  accepts= 0.0726;  energy_drop/trial=   0.00289
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    909;  accepts= 0.0594;  energy_drop/trial=   0.00582
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    904;  accepts= 0.0465;  energy_drop/trial=   0.01846
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    895;  accepts= 0.0525;  energy_drop/trial=   0.01473
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    890;  accepts= 0.0506;  energy_drop/trial=   0.00401
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    892;  accepts= 0.0359;  energy_drop/trial=   0.00562
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    897;  accepts= 0.0970;  energy_drop/trial=   0.01381
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000002 in 6 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -88.8255 to automatically determined cutoff: -98.4243 based on 0.2 quantile from 3 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 3 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    885;  accepts= 0.2373;  energy_drop/trial=  -0.01199
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    904;  accepts= 0.1150;  energy_drop/trial=   0.00237
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    885;  accepts= 0.0678;  energy_drop/trial=   0.00674
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    895;  accepts= 0.0860;  energy_drop/trial=   0.01003
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    894;  accepts= 0.0694;  energy_drop/trial=   0.00749
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    875;  accepts= 0.0606;  energy_drop/trial=   0.01380
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    905;  accepts= 0.1182;  energy_drop/trial=   0.01549
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    903;  accepts= 0.1240;  energy_drop/trial=   0.01240
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    909;  accepts= 0.0506;  energy_drop/trial=   0.00005
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    901;  accepts= 0.1498;  energy_drop/trial=   0.00713
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000002 in 7 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.2254 to automatically determined cutoff: -98.4243 based on 0.2 quantile from 4 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 4 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    897;  accepts= 0.2386;  energy_drop/trial=  -0.04562
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    894;  accepts= 0.2013;  energy_drop/trial=   0.00053
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    897;  accepts= 0.2107;  energy_drop/trial=   0.00063
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    897;  accepts= 0.1918;  energy_drop/trial=   0.01017
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    894;  accepts= 0.1577;  energy_drop/trial=   0.00162
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    905;  accepts= 0.1315;  energy_drop/trial=   0.01269
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    895;  accepts= 0.1821;  energy_drop/trial=   0.00288
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    901;  accepts= 0.1310;  energy_drop/trial=   0.00550
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    886;  accepts= 0.1501;  energy_drop/trial=   0.02005
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    916;  accepts= 0.2631;  energy_drop/trial=  -0.00041
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000002 in 7 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.034 to automatically determined cutoff: -92.8449 based on 0.2 quantile from 5 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 5 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    919;  accepts= 0.1262;  energy_drop/trial=  -0.02591
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    899;  accepts= 0.0868;  energy_drop/trial=   0.00592
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    904;  accepts= 0.0575;  energy_drop/trial=   0.00568
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    911;  accepts= 0.0626;  energy_drop/trial=   0.02642
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    907;  accepts= 0.0474;  energy_drop/trial=   0.00557
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    891;  accepts= 0.0438;  energy_drop/trial=   0.00816
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    888;  accepts= 0.0800;  energy_drop/trial=   0.01689
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    886;  accepts= 0.0451;  energy_drop/trial=  -0.00238
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    906;  accepts= 0.0243;  energy_drop/trial=  -0.00006
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    906;  accepts= 0.0684;  energy_drop/trial=   0.01162
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000002 in 6 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.2721 to automatically determined cutoff: -92.8449 based on 0.2 quantile from 6 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 6 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    880;  accepts= 0.2602;  energy_drop/trial=  -0.02211
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    912;  accepts= 0.1908;  energy_drop/trial=   0.00053
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    903;  accepts= 0.1872;  energy_drop/trial=   0.00702
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    900;  accepts= 0.1900;  energy_drop/trial=   0.00453
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    901;  accepts= 0.1265;  energy_drop/trial=   0.00477
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    884;  accepts= 0.1482;  energy_drop/trial=   0.00355
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    898;  accepts= 0.1526;  energy_drop/trial=   0.00675
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    910;  accepts= 0.1747;  energy_drop/trial=   0.00806
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    902;  accepts= 0.1685;  energy_drop/trial=   0.00500
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    900;  accepts= 0.2300;  energy_drop/trial=   0.00582
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000002 in 5 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -89.4801 to automatically determined cutoff: -92.8449 based on 0.2 quantile from 7 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 7 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    890;  accepts= 0.2146;  energy_drop/trial=  -0.07357
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    911;  accepts= 0.0977;  energy_drop/trial=   0.00711
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    905;  accepts= 0.0762;  energy_drop/trial=   0.01525
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    915;  accepts= 0.0710;  energy_drop/trial=   0.01902
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    901;  accepts= 0.0311;  energy_drop/trial=   0.00380
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    906;  accepts= 0.0430;  energy_drop/trial=   0.03093
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    904;  accepts= 0.0465;  energy_drop/trial=   0.02006
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    901;  accepts= 0.0832;  energy_drop/trial=   0.00790
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    908;  accepts= 0.0441;  energy_drop/trial=   0.00503
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    897;  accepts= 0.0836;  energy_drop/trial=  -0.00882
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000002 in 6 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -94.1246 to automatically determined cutoff: -94.1246 based on 0.2 quantile from 8 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: 
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 rna_data_backbone            1.000       0.000       0.000
 rna_vdw                      1.000       0.553       0.553
 rna_base_backbone            1.000      -1.587      -1.587
 rna_backbone_backbone        1.000       0.000       0.000
 rna_repulsive                1.000       0.000       0.000
 rna_base_pair                1.000     -57.648     -57.648
 rna_base_axis                0.200     -37.206      -7.441
 rna_base_stagger             1.000     -29.375     -29.375
 rna_base_stack               1.000      -4.295      -4.295
 rna_base_stack_axis          0.200     -28.297      -5.659
 rna_rg                       1.000       9.011       9.011
 atom_pair_constraint         1.000       0.000       0.000
 base_pair_constraint         1.000       0.000       0.000
 linear_chainbreak            5.000       0.464       2.318
---------------------------------------------------
 Total weighted score:                      -94.125
protocols.rna.denovo.RNA_FragmentMonteCarlo: 
protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls...
protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 1
protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls...
protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 2
protocols.rna.denovo.movers.RNA_Minimizer: 
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 fa_atr                       0.210    -209.473     -43.989
 fa_rep                       0.200     187.286      37.457
 fa_intra_rep                 0.003     144.186       0.418
 lk_nonpolar                  0.250      -8.037      -2.009
 fa_elec_rna_phos_phos        1.700       0.284       0.483
 rna_torsion                  1.000       6.401       6.401
 suiteness_bonus              1.000       0.000       0.000
 rna_sugar_close              0.820       3.730       3.058
 fa_stack                     0.130    -209.077     -27.180
 stack_elec                   0.760      -1.642      -1.248
 geom_sol_fast                0.170      73.999      12.580
 hbond_sr_bb_sc               0.960       0.000       0.000
 hbond_lr_bb_sc               0.960       0.000       0.000
 hbond_sc                     0.960     -21.604     -20.740
 ref                          1.000      50.440      50.440
 free_suite                   2.000       0.000       0.000
 free_2HOprime                1.000       0.000       0.000
 intermol                     1.000       0.000       0.000
 other_pose                   1.000       0.000       0.000
 loop_close                   1.000       0.000       0.000
 linear_chainbreak            5.000       0.069       0.346
---------------------------------------------------
 Total weighted score:                       16.017
protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 4 seconds.
protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000012
protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: outputs/stem_loop.out
protocols.rna.setup.RNA_MonteCarloJobDistributor: 
protocols.rna.setup.RNA_MonteCarloJobDistributor: Embarking on structure 3 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving residues: 5
protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving chunks: 0
protocols.rna.denovo.RNA_FragmentMonteCarlo: Using 10000 cycles in de novo modeling.
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.moves.TrialCounter:           frag 3 trials=    917;  accepts= 0.2083;  energy_drop/trial=  -0.01818
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    899;  accepts= 0.0968;  energy_drop/trial=   0.00783
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    892;  accepts= 0.0886;  energy_drop/trial=   0.00511
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    898;  accepts= 0.0713;  energy_drop/trial=   0.01621
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    889;  accepts= 0.0911;  energy_drop/trial=   0.00559
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    895;  accepts= 0.1006;  energy_drop/trial=   0.01736
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    903;  accepts= 0.1373;  energy_drop/trial=   0.00926
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    901;  accepts= 0.1121;  energy_drop/trial=   0.00939
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    901;  accepts= 0.0899;  energy_drop/trial=   0.00004
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    901;  accepts= 0.1398;  energy_drop/trial=   0.00040
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000003 in 6 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -86.7151 to automatically determined cutoff: -94.1246 based on 0.2 quantile from 9 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 2 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    892;  accepts= 0.2848;  energy_drop/trial=  -0.08165
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    911;  accepts= 0.1592;  energy_drop/trial=   0.00182
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    910;  accepts= 0.1879;  energy_drop/trial=   0.01775
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    897;  accepts= 0.2375;  energy_drop/trial=   0.02596
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    891;  accepts= 0.1437;  energy_drop/trial=   0.00590
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    911;  accepts= 0.1636;  energy_drop/trial=   0.00385
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    897;  accepts= 0.1695;  energy_drop/trial=   0.00672
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    903;  accepts= 0.1561;  energy_drop/trial=   0.00581
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    906;  accepts= 0.1711;  energy_drop/trial=   0.03649
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    893;  accepts= 0.2273;  energy_drop/trial=   0.00774
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000003 in 5 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -86.7368 to automatically determined cutoff: -92.8449 based on 0.2 quantile from 10 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 3 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    897;  accepts= 0.1394;  energy_drop/trial=  -0.01516
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    888;  accepts= 0.0923;  energy_drop/trial=   0.00973
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    901;  accepts= 0.1265;  energy_drop/trial=   0.00099
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    896;  accepts= 0.0792;  energy_drop/trial=   0.00660
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    915;  accepts= 0.0842;  energy_drop/trial=   0.00897
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    911;  accepts= 0.0889;  energy_drop/trial=   0.01005
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    899;  accepts= 0.1257;  energy_drop/trial=   0.00706
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    892;  accepts= 0.1278;  energy_drop/trial=   0.00767
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    898;  accepts= 0.1258;  energy_drop/trial=   0.01122
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    900;  accepts= 0.1578;  energy_drop/trial=   0.00888
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000003 in 8 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -89.6628 to automatically determined cutoff: -92.8449 based on 0.2 quantile from 11 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 4 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    910;  accepts= 0.1505;  energy_drop/trial=  -0.01623
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    904;  accepts= 0.1250;  energy_drop/trial=  -0.00010
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    889;  accepts= 0.0956;  energy_drop/trial=   0.00747
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    906;  accepts= 0.0905;  energy_drop/trial=   0.00601
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    890;  accepts= 0.0629;  energy_drop/trial=   0.01323
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    889;  accepts= 0.1102;  energy_drop/trial=   0.01602
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    910;  accepts= 0.1000;  energy_drop/trial=   0.00501
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    916;  accepts= 0.1135;  energy_drop/trial=   0.00533
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    898;  accepts= 0.1247;  energy_drop/trial=   0.01046
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    922;  accepts= 0.1540;  energy_drop/trial=   0.00283
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000003 in 7 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -87.6454 to automatically determined cutoff: -92.8449 based on 0.2 quantile from 12 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 5 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    902;  accepts= 0.1807;  energy_drop/trial=  -0.03472
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    912;  accepts= 0.0735;  energy_drop/trial=   0.01046
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    898;  accepts= 0.0969;  energy_drop/trial=   0.00808
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    916;  accepts= 0.0207;  energy_drop/trial=  -0.00080
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    895;  accepts= 0.0089;  energy_drop/trial=   0.01270
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    902;  accepts= 0.0144;  energy_drop/trial=   0.01826
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    902;  accepts= 0.0610;  energy_drop/trial=   0.00238
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    910;  accepts= 0.0802;  energy_drop/trial=   0.00754
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    892;  accepts= 0.0628;  energy_drop/trial=   0.00652
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    890;  accepts= 0.0933;  energy_drop/trial=  -0.00322
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000003 in 7 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -89.7438 to automatically determined cutoff: -92.8449 based on 0.2 quantile from 13 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 6 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    890;  accepts= 0.3169;  energy_drop/trial=  -0.02860
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    902;  accepts= 0.2239;  energy_drop/trial=   0.00166
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    893;  accepts= 0.1937;  energy_drop/trial=   0.00326
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    885;  accepts= 0.1989;  energy_drop/trial=   0.00574
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    905;  accepts= 0.1768;  energy_drop/trial=   0.01289
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    906;  accepts= 0.1358;  energy_drop/trial=   0.00338
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    895;  accepts= 0.1441;  energy_drop/trial=   0.01646
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    901;  accepts= 0.1543;  energy_drop/trial=   0.00178
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    911;  accepts= 0.2086;  energy_drop/trial=   0.00263
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    901;  accepts= 0.2120;  energy_drop/trial=   0.00515
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000003 in 6 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -87.1968 to automatically determined cutoff: -92.8449 based on 0.2 quantile from 14 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 7 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    915;  accepts= 0.1322;  energy_drop/trial=  -0.12232
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    906;  accepts= 0.0960;  energy_drop/trial=  -0.00369
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    909;  accepts= 0.0605;  energy_drop/trial=   0.00880
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    885;  accepts= 0.0531;  energy_drop/trial=   0.02702
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    891;  accepts= 0.0292;  energy_drop/trial=   0.00760
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    912;  accepts= 0.0318;  energy_drop/trial=   0.01114
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    905;  accepts= 0.0508;  energy_drop/trial=   0.00682
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    895;  accepts= 0.0637;  energy_drop/trial=   0.01025
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    892;  accepts= 0.0011;  energy_drop/trial=  -0.00028
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    888;  accepts= 0.0664;  energy_drop/trial=   0.00326
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000003 in 6 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -89.417 to automatically determined cutoff: -90.2721 based on 0.2 quantile from 15 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 8 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    910;  accepts= 0.1703;  energy_drop/trial=  -0.04866
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    893;  accepts= 0.1232;  energy_drop/trial=  -0.00562
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    892;  accepts= 0.0426;  energy_drop/trial=   0.00452
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    907;  accepts= 0.0452;  energy_drop/trial=   0.00239
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    901;  accepts= 0.0610;  energy_drop/trial=   0.01896
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    882;  accepts= 0.0295;  energy_drop/trial=   0.00002
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    886;  accepts= 0.0158;  energy_drop/trial=  -0.00077
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    906;  accepts= 0.0419;  energy_drop/trial=   0.00983
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    901;  accepts= 0.0189;  energy_drop/trial=   0.00994
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    892;  accepts= 0.0605;  energy_drop/trial=   0.00700
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000003 in 6 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.6275 to automatically determined cutoff: -90.6275 based on 0.2 quantile from 16 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: 
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 rna_data_backbone            1.000       0.000       0.000
 rna_vdw                      1.000       0.576       0.576
 rna_base_backbone            1.000      -0.864      -0.864
 rna_backbone_backbone        1.000       0.000       0.000
 rna_repulsive                1.000       0.000       0.000
 rna_base_pair                1.000     -56.745     -56.745
 rna_base_axis                0.200     -35.290      -7.058
 rna_base_stagger             1.000     -27.837     -27.837
 rna_base_stack               1.000      -3.503      -3.503
 rna_base_stack_axis          0.200     -21.861      -4.372
 rna_rg                       1.000       9.025       9.025
 atom_pair_constraint         1.000       0.000       0.000
 base_pair_constraint         1.000       0.000       0.000
 linear_chainbreak            5.000       0.030       0.150
---------------------------------------------------
 Total weighted score:                      -90.628
protocols.rna.denovo.RNA_FragmentMonteCarlo: 
protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls...
protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 1
protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls...
protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 2
protocols.rna.denovo.movers.RNA_Minimizer: 
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 fa_atr                       0.210    -204.435     -42.931
 fa_rep                       0.200      62.991      12.598
 fa_intra_rep                 0.003     151.437       0.439
 lk_nonpolar                  0.250      -8.047      -2.012
 fa_elec_rna_phos_phos        1.700       0.804       1.366
 rna_torsion                  1.000       5.860       5.860
 suiteness_bonus              1.000      -1.135      -1.135
 rna_sugar_close              0.820       4.053       3.324
 fa_stack                     0.130    -218.297     -28.379
 stack_elec                   0.760      -2.401      -1.825
 geom_sol_fast                0.170      74.495      12.664
 hbond_sr_bb_sc               0.960      -0.641      -0.615
 hbond_lr_bb_sc               0.960      -0.875      -0.840
 hbond_sc                     0.960     -19.934     -19.137
 ref                          1.000      50.440      50.440
 free_suite                   2.000       0.000       0.000
 free_2HOprime                1.000       0.000       0.000
 intermol                     1.000       0.000       0.000
 other_pose                   1.000       0.000       0.000
 loop_close                   1.000       0.000       0.000
 linear_chainbreak            5.000       0.006       0.028
---------------------------------------------------
 Total weighted score:                      -10.154
protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 2 seconds.
protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000013
protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: outputs/stem_loop.out
protocols.rna.setup.RNA_MonteCarloJobDistributor: 
protocols.rna.setup.RNA_MonteCarloJobDistributor: Embarking on structure 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving residues: 5
protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving chunks: 0
protocols.rna.denovo.RNA_FragmentMonteCarlo: Using 10000 cycles in de novo modeling.
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.moves.TrialCounter:           frag 3 trials=    910;  accepts= 0.1132;  energy_drop/trial=  -0.01953
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    900;  accepts= 0.0756;  energy_drop/trial=   0.00469
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    886;  accepts= 0.0835;  energy_drop/trial=   0.01171
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    905;  accepts= 0.0475;  energy_drop/trial=   0.02135
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    901;  accepts= 0.0610;  energy_drop/trial=   0.01018
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    902;  accepts= 0.0466;  energy_drop/trial=   0.00873
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    880;  accepts= 0.0932;  energy_drop/trial=   0.00164
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    908;  accepts= 0.0617;  energy_drop/trial=  -0.00153
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    897;  accepts= 0.0580;  energy_drop/trial=   0.00553
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    907;  accepts= 0.0595;  energy_drop/trial=  -0.00205
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000004 in 6 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -95.6989 to automatically determined cutoff: -92.8449 based on 0.2 quantile from 17 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: 
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 rna_data_backbone            1.000       0.000       0.000
 rna_vdw                      1.000       0.368       0.368
 rna_base_backbone            1.000      -1.619      -1.619
 rna_backbone_backbone        1.000       0.000       0.000
 rna_repulsive                1.000       0.000       0.000
 rna_base_pair                1.000     -57.032     -57.032
 rna_base_axis                0.200     -37.459      -7.492
 rna_base_stagger             1.000     -28.619     -28.619
 rna_base_stack               1.000      -4.503      -4.503
 rna_base_stack_axis          0.200     -29.887      -5.977
 rna_rg                       1.000       8.832       8.832
 atom_pair_constraint         1.000       0.000       0.000
 base_pair_constraint         1.000       0.000       0.000
 linear_chainbreak            5.000       0.069       0.344
---------------------------------------------------
 Total weighted score:                      -95.699
protocols.rna.denovo.RNA_FragmentMonteCarlo: 
protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls...
protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 1
protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls...
protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 2
protocols.rna.denovo.movers.RNA_Minimizer: 
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 fa_atr                       0.210    -207.517     -43.579
 fa_rep                       0.200      57.598      11.520
 fa_intra_rep                 0.003     142.906       0.414
 lk_nonpolar                  0.250      -4.073      -1.018
 fa_elec_rna_phos_phos        1.700       0.441       0.750
 rna_torsion                  1.000       3.921       3.921
 suiteness_bonus              1.000       0.000       0.000
 rna_sugar_close              0.820       3.625       2.973
 fa_stack                     0.130    -204.783     -26.622
 stack_elec                   0.760      -1.538      -1.169
 geom_sol_fast                0.170      72.951      12.402
 hbond_sr_bb_sc               0.960       0.000       0.000
 hbond_lr_bb_sc               0.960      -1.041      -1.000
 hbond_sc                     0.960     -20.384     -19.569
 ref                          1.000      50.440      50.440
 free_suite                   2.000       0.000       0.000
 free_2HOprime                1.000       0.000       0.000
 intermol                     1.000       0.000       0.000
 other_pose                   1.000       0.000       0.000
 loop_close                   1.000       0.000       0.000
 linear_chainbreak            5.000       0.014       0.068
---------------------------------------------------
 Total weighted score:                      -10.469
protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 3 seconds.
protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000014
protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: outputs/stem_loop.out
protocols.rna.setup.RNA_MonteCarloJobDistributor: 
protocols.rna.setup.RNA_MonteCarloJobDistributor: Embarking on structure 5 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving residues: 5
protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving chunks: 0
protocols.rna.denovo.RNA_FragmentMonteCarlo: Using 10000 cycles in de novo modeling.
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.moves.TrialCounter:           frag 3 trials=    903;  accepts= 0.1761;  energy_drop/trial=  -0.03425
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    913;  accepts= 0.0789;  energy_drop/trial=  -0.00487
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    902;  accepts= 0.0698;  energy_drop/trial=   0.01205
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    891;  accepts= 0.0763;  energy_drop/trial=   0.00566
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    901;  accepts= 0.0744;  energy_drop/trial=   0.01003
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    899;  accepts= 0.0311;  energy_drop/trial=   0.00749
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    893;  accepts= 0.0784;  energy_drop/trial=   0.01129
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    904;  accepts= 0.0465;  energy_drop/trial=   0.01077
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    895;  accepts= 0.0358;  energy_drop/trial=   0.00286
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    898;  accepts= 0.0668;  energy_drop/trial=   0.00066
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000005 in 6 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.9546 to automatically determined cutoff: -92.8449 based on 0.2 quantile from 18 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 2 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    899;  accepts= 0.2770;  energy_drop/trial=  -0.04831
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    910;  accepts= 0.2253;  energy_drop/trial=   0.00178
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    890;  accepts= 0.1955;  energy_drop/trial=   0.00921
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    905;  accepts= 0.1757;  energy_drop/trial=   0.00428
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    891;  accepts= 0.1347;  energy_drop/trial=   0.00817
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    901;  accepts= 0.1487;  energy_drop/trial=   0.00506
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    906;  accepts= 0.1733;  energy_drop/trial=   0.01042
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    894;  accepts= 0.1409;  energy_drop/trial=   0.01070
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    905;  accepts= 0.1591;  energy_drop/trial=   0.00727
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    895;  accepts= 0.2291;  energy_drop/trial=   0.01465
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000005 in 6 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -91.1003 to automatically determined cutoff: -92.8449 based on 0.2 quantile from 19 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 3 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    913;  accepts= 0.1807;  energy_drop/trial=  -0.07156
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    897;  accepts= 0.0635;  energy_drop/trial=  -0.00754
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    904;  accepts= 0.0619;  energy_drop/trial=   0.01550
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    892;  accepts= 0.0796;  energy_drop/trial=   0.00761
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    895;  accepts= 0.0536;  energy_drop/trial=   0.01487
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    904;  accepts= 0.0442;  energy_drop/trial=   0.00086
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    907;  accepts= 0.0695;  energy_drop/trial=   0.01046
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    892;  accepts= 0.0796;  energy_drop/trial=   0.01015
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    900;  accepts= 0.0233;  energy_drop/trial=   0.00458
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    889;  accepts= 0.0934;  energy_drop/trial=   0.00449
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000005 in 7 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -89.66 to automatically determined cutoff: -91.1003 based on 0.2 quantile from 20 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 4 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    897;  accepts= 0.2419;  energy_drop/trial=  -0.02891
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    895;  accepts= 0.2380;  energy_drop/trial=   0.00204
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    915;  accepts= 0.2011;  energy_drop/trial=   0.00309
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    884;  accepts= 0.1584;  energy_drop/trial=   0.00281
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    899;  accepts= 0.1413;  energy_drop/trial=   0.01224
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    877;  accepts= 0.1767;  energy_drop/trial=   0.00894
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    899;  accepts= 0.1535;  energy_drop/trial=   0.01221
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    892;  accepts= 0.1648;  energy_drop/trial=   0.00227
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    891;  accepts= 0.1358;  energy_drop/trial=   0.00348
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    903;  accepts= 0.2436;  energy_drop/trial=   0.00457
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000005 in 7 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.7851 to automatically determined cutoff: -91.1003 based on 0.2 quantile from 21 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 5 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    897;  accepts= 0.2007;  energy_drop/trial=  -0.00430
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    908;  accepts= 0.1101;  energy_drop/trial=   0.00102
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    900;  accepts= 0.0644;  energy_drop/trial=   0.00527
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    913;  accepts= 0.0307;  energy_drop/trial=   0.00793
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    909;  accepts= 0.0407;  energy_drop/trial=   0.00567
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    897;  accepts= 0.0156;  energy_drop/trial=   0.00697
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    897;  accepts= 0.0769;  energy_drop/trial=   0.01673
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    915;  accepts= 0.0874;  energy_drop/trial=   0.00232
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    908;  accepts= 0.0286;  energy_drop/trial=   0.00402
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    915;  accepts= 0.1005;  energy_drop/trial=   0.00019
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000005 in 7 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -91.1244 to automatically determined cutoff: -91.1244 based on 0.2 quantile from 22 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: 
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 rna_data_backbone            1.000       0.000       0.000
 rna_vdw                      1.000       2.420       2.420
 rna_base_backbone            1.000      -9.791      -9.791
 rna_backbone_backbone        1.000       0.000       0.000
 rna_repulsive                1.000       0.000       0.000
 rna_base_pair                1.000     -51.831     -51.831
 rna_base_axis                0.200     -33.412      -6.682
 rna_base_stagger             1.000     -26.810     -26.810
 rna_base_stack               1.000      -3.503      -3.503
 rna_base_stack_axis          0.200     -22.702      -4.540
 rna_rg                       1.000       9.372       9.372
 atom_pair_constraint         1.000       0.000       0.000
 base_pair_constraint         1.000       0.000       0.000
 linear_chainbreak            5.000       0.048       0.240
---------------------------------------------------
 Total weighted score:                      -91.124
protocols.rna.denovo.RNA_FragmentMonteCarlo: 
protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls...
protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 1
protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls...
protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 2
protocols.rna.denovo.movers.RNA_Minimizer: 
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 fa_atr                       0.210    -202.785     -42.585
 fa_rep                       0.200      56.182      11.236
 fa_intra_rep                 0.003     166.828       0.484
 lk_nonpolar                  0.250      -5.589      -1.397
 fa_elec_rna_phos_phos        1.700       0.263       0.447
 rna_torsion                  1.000       3.398       3.398
 suiteness_bonus              1.000       0.000       0.000
 rna_sugar_close              0.820       3.648       2.991
 fa_stack                     0.130    -207.102     -26.923
 stack_elec                   0.760      -1.042      -0.792
 geom_sol_fast                0.170      73.832      12.551
 hbond_sr_bb_sc               0.960       0.000       0.000
 hbond_lr_bb_sc               0.960      -1.165      -1.118
 hbond_sc                     0.960     -21.809     -20.937
 ref                          1.000      50.440      50.440
 free_suite                   2.000       0.000       0.000
 free_2HOprime                1.000       0.000       0.000
 intermol                     1.000       0.000       0.000
 other_pose                   1.000       0.000       0.000
 loop_close                   1.000       0.000       0.000
 linear_chainbreak            5.000       0.005       0.026
---------------------------------------------------
 Total weighted score:                      -12.179
protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 4 seconds.
protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000015
protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: outputs/stem_loop.out
protocols.rna.setup.RNA_MonteCarloJobDistributor: 
protocols.rna.setup.RNA_MonteCarloJobDistributor: Embarking on structure 6 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving residues: 5
protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving chunks: 0
protocols.rna.denovo.RNA_FragmentMonteCarlo: Using 10000 cycles in de novo modeling.
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.moves.TrialCounter:           frag 3 trials=    905;  accepts= 0.1171;  energy_drop/trial=  -0.00815
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    902;  accepts= 0.0787;  energy_drop/trial=   0.00797
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    901;  accepts= 0.0588;  energy_drop/trial=   0.00468
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    906;  accepts= 0.0596;  energy_drop/trial=   0.00353
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    891;  accepts= 0.0393;  energy_drop/trial=   0.00408
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    903;  accepts= 0.0465;  energy_drop/trial=   0.02471
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    905;  accepts= 0.0762;  energy_drop/trial=   0.00540
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    899;  accepts= 0.0456;  energy_drop/trial=   0.00834
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    900;  accepts= 0.0344;  energy_drop/trial=   0.00695
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    894;  accepts= 0.1174;  energy_drop/trial=   0.00646
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000006 in 6 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -87.8902 to automatically determined cutoff: -91.1244 based on 0.2 quantile from 23 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 2 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    901;  accepts= 0.2642;  energy_drop/trial=  -0.14535
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    896;  accepts= 0.2087;  energy_drop/trial=   0.00120
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    896;  accepts= 0.1842;  energy_drop/trial=   0.00266
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    888;  accepts= 0.2140;  energy_drop/trial=   0.02087
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    896;  accepts= 0.2031;  energy_drop/trial=   0.01614
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    897;  accepts= 0.1148;  energy_drop/trial=   0.00577
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    895;  accepts= 0.1475;  energy_drop/trial=   0.01753
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    896;  accepts= 0.1283;  energy_drop/trial=   0.00659
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    911;  accepts= 0.1196;  energy_drop/trial=   0.00646
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    903;  accepts= 0.2004;  energy_drop/trial=   0.00994
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000006 in 6 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -89.318 to automatically determined cutoff: -91.1244 based on 0.2 quantile from 24 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 3 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    902;  accepts= 0.1530;  energy_drop/trial=  -0.01022
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    906;  accepts= 0.0949;  energy_drop/trial=  -0.00907
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    901;  accepts= 0.0655;  energy_drop/trial=   0.00510
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    904;  accepts= 0.0321;  energy_drop/trial=   0.00447
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    901;  accepts= 0.0588;  energy_drop/trial=   0.00068
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    895;  accepts= 0.0324;  energy_drop/trial=   0.00250
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    894;  accepts= 0.0570;  energy_drop/trial=   0.00361
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    913;  accepts= 0.0591;  energy_drop/trial=   0.00757
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    901;  accepts= 0.0466;  energy_drop/trial=   0.00820
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    893;  accepts= 0.0717;  energy_drop/trial=   0.00566
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000006 in 6 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -89.333 to automatically determined cutoff: -91.1003 based on 0.2 quantile from 25 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 4 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    905;  accepts= 0.2939;  energy_drop/trial=  -0.03060
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    897;  accepts= 0.2575;  energy_drop/trial=   0.00046
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    901;  accepts= 0.1398;  energy_drop/trial=   0.00079
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    898;  accepts= 0.1782;  energy_drop/trial=   0.01059
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    895;  accepts= 0.1598;  energy_drop/trial=   0.01658
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    907;  accepts= 0.1114;  energy_drop/trial=   0.00411
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    898;  accepts= 0.1247;  energy_drop/trial=   0.01030
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    907;  accepts= 0.1389;  energy_drop/trial=  -0.00125
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    918;  accepts= 0.1383;  energy_drop/trial=  -0.00170
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    891;  accepts= 0.2514;  energy_drop/trial=   0.01313
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000006 in 5 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -89.048 to automatically determined cutoff: -91.1003 based on 0.2 quantile from 26 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 5 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    905;  accepts= 0.1326;  energy_drop/trial=  -0.01584
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    895;  accepts= 0.0961;  energy_drop/trial=  -0.00434
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    891;  accepts= 0.0808;  energy_drop/trial=   0.00096
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    899;  accepts= 0.0267;  energy_drop/trial=   0.00092
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    881;  accepts= 0.0511;  energy_drop/trial=   0.01427
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    918;  accepts= 0.0632;  energy_drop/trial=   0.00650
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    912;  accepts= 0.0603;  energy_drop/trial=   0.00217
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    907;  accepts= 0.0529;  energy_drop/trial=   0.00955
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    901;  accepts= 0.0633;  energy_drop/trial=   0.00419
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    885;  accepts= 0.1153;  energy_drop/trial=  -0.00158
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000006 in 6 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -86.1987 to automatically determined cutoff: -91.1003 based on 0.2 quantile from 27 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 6 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    893;  accepts= 0.3684;  energy_drop/trial=  -0.05196
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    896;  accepts= 0.2567;  energy_drop/trial=   0.00592
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    901;  accepts= 0.1898;  energy_drop/trial=   0.00602
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    878;  accepts= 0.1834;  energy_drop/trial=   0.00334
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    878;  accepts= 0.1241;  energy_drop/trial=   0.00500
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    915;  accepts= 0.1628;  energy_drop/trial=   0.01090
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    891;  accepts= 0.1829;  energy_drop/trial=   0.01296
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    900;  accepts= 0.1422;  energy_drop/trial=   0.01386
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    897;  accepts= 0.1494;  energy_drop/trial=   0.01247
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    910;  accepts= 0.2132;  energy_drop/trial=  -0.00038
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000006 in 6 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -85.1923 to automatically determined cutoff: -91.1003 based on 0.2 quantile from 28 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 7 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    904;  accepts= 0.2190;  energy_drop/trial=  -0.17120
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    896;  accepts= 0.1004;  energy_drop/trial=   0.00427
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    898;  accepts= 0.1147;  energy_drop/trial=   0.00529
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    896;  accepts= 0.1150;  energy_drop/trial=   0.01740
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    900;  accepts= 0.1089;  energy_drop/trial=   0.00864
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    887;  accepts= 0.0417;  energy_drop/trial=   0.01265
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    905;  accepts= 0.1072;  energy_drop/trial=   0.01097
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    904;  accepts= 0.0785;  energy_drop/trial=   0.00973
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    909;  accepts= 0.1166;  energy_drop/trial=   0.00610
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    905;  accepts= 0.1249;  energy_drop/trial=   0.01110
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000006 in 6 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -87.911 to automatically determined cutoff: -91.1003 based on 0.2 quantile from 29 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 8 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    909;  accepts= 0.1969;  energy_drop/trial=  -0.11968
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    904;  accepts= 0.1261;  energy_drop/trial=   0.01176
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    899;  accepts= 0.0968;  energy_drop/trial=  -0.00348
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    893;  accepts= 0.1153;  energy_drop/trial=   0.01616
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    914;  accepts= 0.0733;  energy_drop/trial=   0.01463
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    911;  accepts= 0.0856;  energy_drop/trial=   0.00277
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    889;  accepts= 0.1181;  energy_drop/trial=   0.00858
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    898;  accepts= 0.0924;  energy_drop/trial=   0.00293
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    891;  accepts= 0.1122;  energy_drop/trial=   0.01508
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    910;  accepts= 0.1209;  energy_drop/trial=   0.00640
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000006 in 7 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -88.754 to automatically determined cutoff: -90.9546 based on 0.2 quantile from 30 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 9 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    899;  accepts= 0.3059;  energy_drop/trial=  -0.02331
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    891;  accepts= 0.2121;  energy_drop/trial=   0.00343
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    897;  accepts= 0.1895;  energy_drop/trial=   0.00679
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    928;  accepts= 0.1562;  energy_drop/trial=   0.00462
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    910;  accepts= 0.1527;  energy_drop/trial=   0.00636
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    888;  accepts= 0.1216;  energy_drop/trial=   0.00906
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    871;  accepts= 0.1274;  energy_drop/trial=   0.00760
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    898;  accepts= 0.1615;  energy_drop/trial=   0.00803
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    895;  accepts= 0.1128;  energy_drop/trial=   0.00357
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    909;  accepts= 0.2574;  energy_drop/trial=   0.00188
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000006 in 6 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.0468 to automatically determined cutoff: -90.9546 based on 0.2 quantile from 31 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 10 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    905;  accepts= 0.1691;  energy_drop/trial=  -0.05201
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    901;  accepts= 0.1387;  energy_drop/trial=   0.00617
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    884;  accepts= 0.0577;  energy_drop/trial=   0.00002
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    903;  accepts= 0.0277;  energy_drop/trial=   0.00579
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    923;  accepts= 0.0509;  energy_drop/trial=   0.00058
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    904;  accepts= 0.0332;  energy_drop/trial=   0.00404
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    894;  accepts= 0.0772;  energy_drop/trial=   0.00487
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    900;  accepts= 0.0322;  energy_drop/trial=   0.00677
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    889;  accepts= 0.0709;  energy_drop/trial=   0.00658
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    907;  accepts= 0.0551;  energy_drop/trial=   0.00382
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000006 in 7 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -94.4195 to automatically determined cutoff: -91.1003 based on 0.2 quantile from 32 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: 
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 rna_data_backbone            1.000       0.000       0.000
 rna_vdw                      1.000       5.106       5.106
 rna_base_backbone            1.000      -7.911      -7.911
 rna_backbone_backbone        1.000       0.000       0.000
 rna_repulsive                1.000       0.000       0.000
 rna_base_pair                1.000     -58.015     -58.015
 rna_base_axis                0.200     -36.136      -7.227
 rna_base_stagger             1.000     -27.638     -27.638
 rna_base_stack               1.000      -3.503      -3.503
 rna_base_stack_axis          0.200     -22.787      -4.557
 rna_rg                       1.000       8.668       8.668
 atom_pair_constraint         1.000       0.000       0.000
 base_pair_constraint         1.000       0.000       0.000
 linear_chainbreak            5.000       0.132       0.658
---------------------------------------------------
 Total weighted score:                      -94.420
protocols.rna.denovo.RNA_FragmentMonteCarlo: 
protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls...
protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 1
protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls...
protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 2
protocols.rna.denovo.movers.RNA_Minimizer: 
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 fa_atr                       0.210    -210.742     -44.256
 fa_rep                       0.200      55.495      11.099
 fa_intra_rep                 0.003     664.439       1.927
 lk_nonpolar                  0.250      -7.290      -1.823
 fa_elec_rna_phos_phos        1.700       0.349       0.593
 rna_torsion                  1.000       5.620       5.620
 suiteness_bonus              1.000       0.000       0.000
 rna_sugar_close              0.820       3.709       3.041
 fa_stack                     0.130    -228.548     -29.711
 stack_elec                   0.760      -1.130      -0.859
 geom_sol_fast                0.170      72.140      12.264
 hbond_sr_bb_sc               0.960       0.000       0.000
 hbond_lr_bb_sc               0.960      -0.500      -0.480
 hbond_sc                     0.960     -21.573     -20.710
 ref                          1.000      50.440      50.440
 free_suite                   2.000       0.000       0.000
 free_2HOprime                1.000       0.000       0.000
 intermol                     1.000       0.000       0.000
 other_pose                   1.000       0.000       0.000
 loop_close                   1.000       0.000       0.000
 linear_chainbreak            5.000       0.005       0.026
---------------------------------------------------
 Total weighted score:                      -12.829
protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 3 seconds.
protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000016
protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: outputs/stem_loop.out
protocols.rna.setup.RNA_MonteCarloJobDistributor: 
protocols.rna.setup.RNA_MonteCarloJobDistributor: Embarking on structure 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving residues: 5
protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving chunks: 0
protocols.rna.denovo.RNA_FragmentMonteCarlo: Using 10000 cycles in de novo modeling.
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.moves.TrialCounter:           frag 3 trials=    898;  accepts= 0.2695;  energy_drop/trial=  -0.02659
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    895;  accepts= 0.1821;  energy_drop/trial=   0.00804
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    919;  accepts= 0.1621;  energy_drop/trial=   0.00739
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    919;  accepts= 0.1491;  energy_drop/trial=   0.01368
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    910;  accepts= 0.1231;  energy_drop/trial=   0.00785
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    899;  accepts= 0.1179;  energy_drop/trial=   0.00571
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    895;  accepts= 0.1385;  energy_drop/trial=   0.01038
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    892;  accepts= 0.1121;  energy_drop/trial=   0.00454
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    901;  accepts= 0.1776;  energy_drop/trial=   0.01901
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    885;  accepts= 0.1910;  energy_drop/trial=   0.00191
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000007 in 6 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.0243 to automatically determined cutoff: -91.1003 based on 0.2 quantile from 33 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 2 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    894;  accepts= 0.3020;  energy_drop/trial=  -0.01466
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    914;  accepts= 0.2046;  energy_drop/trial=   0.00502
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    911;  accepts= 0.1625;  energy_drop/trial=   0.01345
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    908;  accepts= 0.1938;  energy_drop/trial=   0.00254
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    900;  accepts= 0.1656;  energy_drop/trial=   0.00792
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    917;  accepts= 0.1189;  energy_drop/trial=   0.01190
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    914;  accepts= 0.1663;  energy_drop/trial=   0.00125
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    905;  accepts= 0.1481;  energy_drop/trial=  -0.00058
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    908;  accepts= 0.1366;  energy_drop/trial=   0.02556
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    902;  accepts= 0.2106;  energy_drop/trial=   0.00068
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000007 in 6 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -91.7874 to automatically determined cutoff: -91.1244 based on 0.2 quantile from 34 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: 
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 rna_data_backbone            1.000       0.000       0.000
 rna_vdw                      1.000       0.056       0.056
 rna_base_backbone            1.000      -7.142      -7.142
 rna_backbone_backbone        1.000       0.000       0.000
 rna_repulsive                1.000       0.000       0.000
 rna_base_pair                1.000     -52.425     -52.425
 rna_base_axis                0.200     -32.962      -6.592
 rna_base_stagger             1.000     -27.205     -27.205
 rna_base_stack               1.000      -3.503      -3.503
 rna_base_stack_axis          0.200     -21.465      -4.293
 rna_rg                       1.000       8.748       8.748
 atom_pair_constraint         1.000       0.000       0.000
 base_pair_constraint         1.000       0.000       0.000
 linear_chainbreak            5.000       0.114       0.569
---------------------------------------------------
 Total weighted score:                      -91.787
protocols.rna.denovo.RNA_FragmentMonteCarlo: 
protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls...
protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 1
protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls...
protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 2
protocols.rna.denovo.movers.RNA_Minimizer: 
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 fa_atr                       0.210    -210.969     -44.304
 fa_rep                       0.200      56.415      11.283
 fa_intra_rep                 0.003     150.392       0.436
 lk_nonpolar                  0.250      -7.509      -1.877
 fa_elec_rna_phos_phos        1.700       0.452       0.768
 rna_torsion                  1.000       3.375       3.375
 suiteness_bonus              1.000       0.000       0.000
 rna_sugar_close              0.820       4.120       3.379
 fa_stack                     0.130    -227.779     -29.611
 stack_elec                   0.760      -0.934      -0.710
 geom_sol_fast                0.170      73.909      12.564
 hbond_sr_bb_sc               0.960       0.000       0.000
 hbond_lr_bb_sc               0.960      -0.631      -0.606
 hbond_sc                     0.960     -22.279     -21.388
 ref                          1.000      50.440      50.440
 free_suite                   2.000       0.000       0.000
 free_2HOprime                1.000       0.000       0.000
 intermol                     1.000       0.000       0.000
 other_pose                   1.000       0.000       0.000
 loop_close                   1.000       0.000       0.000
 linear_chainbreak            5.000       0.005       0.024
---------------------------------------------------
 Total weighted score:                      -16.227
protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 3 seconds.
protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000017
protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: outputs/stem_loop.out
protocols.rna.setup.RNA_MonteCarloJobDistributor: 
protocols.rna.setup.RNA_MonteCarloJobDistributor: Embarking on structure 8 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving residues: 5
protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving chunks: 0
protocols.rna.denovo.RNA_FragmentMonteCarlo: Using 10000 cycles in de novo modeling.
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.moves.TrialCounter:           frag 3 trials=    900;  accepts= 0.1833;  energy_drop/trial=  -0.03416
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    903;  accepts= 0.0543;  energy_drop/trial=  -0.00269
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    892;  accepts= 0.0919;  energy_drop/trial=   0.00405
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    905;  accepts= 0.0674;  energy_drop/trial=   0.00671
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    918;  accepts= 0.0871;  energy_drop/trial=   0.00196
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    906;  accepts= 0.0342;  energy_drop/trial=   0.00638
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    901;  accepts= 0.0877;  energy_drop/trial=   0.01291
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    896;  accepts= 0.0815;  energy_drop/trial=   0.00907
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    904;  accepts= 0.0586;  energy_drop/trial=   0.00875
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    912;  accepts= 0.0746;  energy_drop/trial=  -0.00811
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000008 in 7 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -97.3472 to automatically determined cutoff: -91.1244 based on 0.2 quantile from 35 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: 
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 rna_data_backbone            1.000       0.000       0.000
 rna_vdw                      1.000       2.756       2.756
 rna_base_backbone            1.000      -8.634      -8.634
 rna_backbone_backbone        1.000       0.000       0.000
 rna_repulsive                1.000       0.000       0.000
 rna_base_pair                1.000     -57.623     -57.623
 rna_base_axis                0.200     -34.588      -6.918
 rna_base_stagger             1.000     -28.338     -28.338
 rna_base_stack               1.000      -3.503      -3.503
 rna_base_stack_axis          0.200     -22.332      -4.466
 rna_rg                       1.000       8.947       8.947
 atom_pair_constraint         1.000       0.000       0.000
 base_pair_constraint         1.000       0.000       0.000
 linear_chainbreak            5.000       0.086       0.432
---------------------------------------------------
 Total weighted score:                      -97.347
protocols.rna.denovo.RNA_FragmentMonteCarlo: 
protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls...
protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 1
protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls...
protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 2
protocols.rna.denovo.movers.RNA_Minimizer: 
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 fa_atr                       0.210    -213.669     -44.870
 fa_rep                       0.200      57.454      11.491
 fa_intra_rep                 0.003     180.164       0.522
 lk_nonpolar                  0.250      -8.156      -2.039
 fa_elec_rna_phos_phos        1.700       0.546       0.928
 rna_torsion                  1.000       4.517       4.517
 suiteness_bonus              1.000       0.000       0.000
 rna_sugar_close              0.820       3.658       3.000
 fa_stack                     0.130    -232.938     -30.282
 stack_elec                   0.760      -1.202      -0.913
 geom_sol_fast                0.170      74.637      12.688
 hbond_sr_bb_sc               0.960       0.000       0.000
 hbond_lr_bb_sc               0.960      -0.299      -0.287
 hbond_sc                     0.960     -22.053     -21.171
 ref                          1.000      50.440      50.440
 free_suite                   2.000       0.000       0.000
 free_2HOprime                1.000       0.000       0.000
 intermol                     1.000       0.000       0.000
 other_pose                   1.000       0.000       0.000
 loop_close                   1.000       0.000       0.000
 linear_chainbreak            5.000       0.005       0.027
---------------------------------------------------
 Total weighted score:                      -15.950
protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 3 seconds.
protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000018
protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: outputs/stem_loop.out
protocols.rna.setup.RNA_MonteCarloJobDistributor: 
protocols.rna.setup.RNA_MonteCarloJobDistributor: Embarking on structure 9 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving residues: 5
protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving chunks: 0
protocols.rna.denovo.RNA_FragmentMonteCarlo: Using 10000 cycles in de novo modeling.
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.moves.TrialCounter:           frag 3 trials=    890;  accepts= 0.2921;  energy_drop/trial=  -0.02343
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    894;  accepts= 0.2103;  energy_drop/trial=   0.00337
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    912;  accepts= 0.1886;  energy_drop/trial=   0.00700
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    908;  accepts= 0.1443;  energy_drop/trial=   0.00850
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    904;  accepts= 0.1527;  energy_drop/trial=   0.00892
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    899;  accepts= 0.1046;  energy_drop/trial=   0.00174
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    900;  accepts= 0.1756;  energy_drop/trial=   0.00726
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    905;  accepts= 0.1304;  energy_drop/trial=   0.01126
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    907;  accepts= 0.1433;  energy_drop/trial=   0.00653
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    906;  accepts= 0.2152;  energy_drop/trial=   0.00479
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000009 in 8 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -91.0191 to automatically determined cutoff: -91.1244 based on 0.2 quantile from 36 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 2 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    908;  accepts= 0.1652;  energy_drop/trial=  -0.02244
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    908;  accepts= 0.1388;  energy_drop/trial=   0.01026
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    907;  accepts= 0.0981;  energy_drop/trial=   0.00616
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    895;  accepts= 0.0983;  energy_drop/trial=   0.00876
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    879;  accepts= 0.0535;  energy_drop/trial=   0.00370
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    904;  accepts= 0.0841;  energy_drop/trial=   0.01281
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    895;  accepts= 0.1352;  energy_drop/trial=   0.01113
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    886;  accepts= 0.1129;  energy_drop/trial=   0.00384
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    898;  accepts= 0.0679;  energy_drop/trial=   0.01461
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    893;  accepts= 0.1422;  energy_drop/trial=   0.01164
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000009 in 7 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -85.9899 to automatically determined cutoff: -91.1244 based on 0.2 quantile from 37 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 3 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    894;  accepts= 0.1756;  energy_drop/trial=  -0.04131
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    895;  accepts= 0.1039;  energy_drop/trial=  -0.00168
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    903;  accepts= 0.1030;  energy_drop/trial=   0.01568
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    894;  accepts= 0.0358;  energy_drop/trial=   0.00607
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    905;  accepts= 0.0773;  energy_drop/trial=   0.00739
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    877;  accepts= 0.0422;  energy_drop/trial=   0.00798
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    905;  accepts= 0.0210;  energy_drop/trial=   0.00690
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    894;  accepts= 0.0570;  energy_drop/trial=   0.00920
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    896;  accepts= 0.0480;  energy_drop/trial=   0.01077
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    916;  accepts= 0.1015;  energy_drop/trial=   0.00025
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000009 in 6 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -91.9203 to automatically determined cutoff: -91.7874 based on 0.2 quantile from 38 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: 
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 rna_data_backbone            1.000       0.000       0.000
 rna_vdw                      1.000       0.276       0.276
 rna_base_backbone            1.000      -5.036      -5.036
 rna_backbone_backbone        1.000       0.000       0.000
 rna_repulsive                1.000       0.000       0.000
 rna_base_pair                1.000     -53.071     -53.071
 rna_base_axis                0.200     -34.565      -6.913
 rna_base_stagger             1.000     -28.465     -28.465
 rna_base_stack               1.000      -3.503      -3.503
 rna_base_stack_axis          0.200     -22.961      -4.592
 rna_rg                       1.000       9.230       9.230
 atom_pair_constraint         1.000       0.000       0.000
 base_pair_constraint         1.000       0.000       0.000
 linear_chainbreak            5.000       0.031       0.153
---------------------------------------------------
 Total weighted score:                      -91.920
protocols.rna.denovo.RNA_FragmentMonteCarlo: 
protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls...
protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 1
protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls...
protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 2
protocols.rna.denovo.movers.RNA_Minimizer: 
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 fa_atr                       0.210    -213.265     -44.786
 fa_rep                       0.200      56.255      11.251
 fa_intra_rep                 0.003     932.297       2.704
 lk_nonpolar                  0.250      -4.778      -1.194
 fa_elec_rna_phos_phos        1.700       0.224       0.381
 rna_torsion                  1.000       5.784       5.784
 suiteness_bonus              1.000       0.000       0.000
 rna_sugar_close              0.820       3.729       3.058
 fa_stack                     0.130    -226.979     -29.507
 stack_elec                   0.760      -1.369      -1.040
 geom_sol_fast                0.170      72.846      12.384
 hbond_sr_bb_sc               0.960       0.000       0.000
 hbond_lr_bb_sc               0.960      -0.880      -0.845
 hbond_sc                     0.960     -20.273     -19.462
 ref                          1.000      50.440      50.440
 free_suite                   2.000       0.000       0.000
 free_2HOprime                1.000       0.000       0.000
 intermol                     1.000       0.000       0.000
 other_pose                   1.000       0.000       0.000
 loop_close                   1.000       0.000       0.000
 linear_chainbreak            5.000       0.055       0.277
---------------------------------------------------
 Total weighted score:                      -10.557
protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 3 seconds.
protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000019
protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: outputs/stem_loop.out
protocols.rna.setup.RNA_MonteCarloJobDistributor: 
protocols.rna.setup.RNA_MonteCarloJobDistributor: Embarking on structure 10 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving residues: 5
protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving chunks: 0
protocols.rna.denovo.RNA_FragmentMonteCarlo: Using 10000 cycles in de novo modeling.
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.moves.TrialCounter:           frag 3 trials=    900;  accepts= 0.2944;  energy_drop/trial=  -0.02921
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    878;  accepts= 0.1993;  energy_drop/trial=   0.00128
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    903;  accepts= 0.1916;  energy_drop/trial=   0.00346
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    914;  accepts= 0.2133;  energy_drop/trial=   0.01186
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    899;  accepts= 0.1780;  energy_drop/trial=   0.00083
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    898;  accepts= 0.1336;  energy_drop/trial=   0.00585
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    896;  accepts= 0.1953;  energy_drop/trial=   0.00676
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    907;  accepts= 0.1731;  energy_drop/trial=   0.00852
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    895;  accepts= 0.1620;  energy_drop/trial=   0.00826
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    908;  accepts= 0.1795;  energy_drop/trial=   0.00086
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000010 in 6 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -88.6103 to automatically determined cutoff: -91.7874 based on 0.2 quantile from 39 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 2 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    898;  accepts= 0.1069;  energy_drop/trial=  -0.02033
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    890;  accepts= 0.1258;  energy_drop/trial=   0.01112
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    895;  accepts= 0.0626;  energy_drop/trial=   0.01057
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    896;  accepts= 0.0603;  energy_drop/trial=   0.00142
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    895;  accepts= 0.0358;  energy_drop/trial=   0.00381
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    913;  accepts= 0.0624;  energy_drop/trial=   0.00167
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    891;  accepts= 0.0920;  energy_drop/trial=   0.01310
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    887;  accepts= 0.0552;  energy_drop/trial=   0.01865
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    906;  accepts= 0.0353;  energy_drop/trial=   0.01329
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    900;  accepts= 0.0867;  energy_drop/trial=  -0.00025
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000010 in 8 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.3844 to automatically determined cutoff: -91.1244 based on 0.2 quantile from 40 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 3 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    907;  accepts= 0.2712;  energy_drop/trial=  -0.02289
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    909;  accepts= 0.2024;  energy_drop/trial=   0.01466
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    900;  accepts= 0.1533;  energy_drop/trial=   0.00649
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    909;  accepts= 0.1815;  energy_drop/trial=   0.01124
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    886;  accepts= 0.2020;  energy_drop/trial=   0.01881
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    918;  accepts= 0.1416;  energy_drop/trial=  -0.00005
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    907;  accepts= 0.1841;  energy_drop/trial=   0.00801
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    900;  accepts= 0.1700;  energy_drop/trial=   0.00025
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    897;  accepts= 0.1583;  energy_drop/trial=   0.00243
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    896;  accepts= 0.2042;  energy_drop/trial=  -0.00533
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000010 in 7 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -89.4019 to automatically determined cutoff: -91.1244 based on 0.2 quantile from 41 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 4 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    901;  accepts= 0.1765;  energy_drop/trial=  -0.03647
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    902;  accepts= 0.1519;  energy_drop/trial=   0.00565
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    891;  accepts= 0.0438;  energy_drop/trial=  -0.00142
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    889;  accepts= 0.0607;  energy_drop/trial=   0.00160
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    903;  accepts= 0.0997;  energy_drop/trial=   0.00652
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    905;  accepts= 0.1017;  energy_drop/trial=   0.00338
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    893;  accepts= 0.0918;  energy_drop/trial=   0.00957
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    908;  accepts= 0.0529;  energy_drop/trial=   0.00659
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    894;  accepts= 0.0649;  energy_drop/trial=   0.00802
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    910;  accepts= 0.1538;  energy_drop/trial=   0.00415
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000010 in 7 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -88.4029 to automatically determined cutoff: -91.1244 based on 0.2 quantile from 42 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 5 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    903;  accepts= 0.1395;  energy_drop/trial=  -0.00951
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    893;  accepts= 0.0739;  energy_drop/trial=   0.01648
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    907;  accepts= 0.0496;  energy_drop/trial=   0.00070
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    904;  accepts= 0.0896;  energy_drop/trial=   0.01028
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    906;  accepts= 0.0740;  energy_drop/trial=   0.01057
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    903;  accepts= 0.0609;  energy_drop/trial=   0.01206
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    914;  accepts= 0.0514;  energy_drop/trial=   0.02141
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    909;  accepts= 0.0583;  energy_drop/trial=   0.00667
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    912;  accepts= 0.0537;  energy_drop/trial=   0.00310
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    898;  accepts= 0.0668;  energy_drop/trial=   0.00388
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000010 in 6 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.0788 to automatically determined cutoff: -91.1244 based on 0.2 quantile from 43 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 6 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    901;  accepts= 0.2708;  energy_drop/trial=  -0.13368
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    898;  accepts= 0.2038;  energy_drop/trial=   0.01013
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    913;  accepts= 0.2092;  energy_drop/trial=   0.00911
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    894;  accepts= 0.1510;  energy_drop/trial=   0.00275
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    891;  accepts= 0.1403;  energy_drop/trial=   0.00532
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    900;  accepts= 0.1022;  energy_drop/trial=   0.00647
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    895;  accepts= 0.1061;  energy_drop/trial=   0.00951
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    901;  accepts= 0.1565;  energy_drop/trial=   0.01272
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    898;  accepts= 0.1459;  energy_drop/trial=   0.02775
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    898;  accepts= 0.2249;  energy_drop/trial=   0.00573
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000010 in 7 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -89.001 to automatically determined cutoff: -91.1244 based on 0.2 quantile from 44 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 7 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    901;  accepts= 0.2908;  energy_drop/trial=  -0.01154
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    901;  accepts= 0.2253;  energy_drop/trial=  -0.00026
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    910;  accepts= 0.2176;  energy_drop/trial=   0.00408
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    898;  accepts= 0.1871;  energy_drop/trial=   0.02081
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    901;  accepts= 0.1731;  energy_drop/trial=   0.01200
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    897;  accepts= 0.1304;  energy_drop/trial=   0.00451
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    898;  accepts= 0.1114;  energy_drop/trial=   0.00928
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    895;  accepts= 0.1441;  energy_drop/trial=   0.01042
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    900;  accepts= 0.1400;  energy_drop/trial=   0.01827
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    899;  accepts= 0.2514;  energy_drop/trial=   0.00157
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000010 in 8 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.4988 to automatically determined cutoff: -91.1003 based on 0.2 quantile from 45 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 8 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    908;  accepts= 0.2445;  energy_drop/trial=  -0.01489
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    900;  accepts= 0.2011;  energy_drop/trial=   0.00373
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    919;  accepts= 0.1926;  energy_drop/trial=   0.00195
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    903;  accepts= 0.2082;  energy_drop/trial=   0.01001
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    901;  accepts= 0.1776;  energy_drop/trial=   0.00502
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    908;  accepts= 0.1388;  energy_drop/trial=   0.00790
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    902;  accepts= 0.1619;  energy_drop/trial=  -0.00007
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    909;  accepts= 0.1540;  energy_drop/trial=   0.00224
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    881;  accepts= 0.1464;  energy_drop/trial=  -0.00073
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    883;  accepts= 0.2299;  energy_drop/trial=   0.01987
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000010 in 7 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -86.6308 to automatically determined cutoff: -91.1003 based on 0.2 quantile from 46 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 9 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    902;  accepts= 0.1486;  energy_drop/trial=  -0.01940
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    893;  accepts= 0.0784;  energy_drop/trial=   0.00524
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    911;  accepts= 0.0724;  energy_drop/trial=   0.00105
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    899;  accepts= 0.0690;  energy_drop/trial=   0.02012
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    902;  accepts= 0.0565;  energy_drop/trial=   0.01008
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    893;  accepts= 0.0437;  energy_drop/trial=   0.00134
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    885;  accepts= 0.0870;  energy_drop/trial=   0.00652
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    914;  accepts= 0.0536;  energy_drop/trial=   0.00753
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    889;  accepts= 0.0529;  energy_drop/trial=   0.01637
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    905;  accepts= 0.0917;  energy_drop/trial=   0.00344
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000010 in 6 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -87.0646 to automatically determined cutoff: -91.1003 based on 0.2 quantile from 47 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 10 out of 10
protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop...
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3
protocols.moves.TrialCounter:           frag 3 trials=    913;  accepts= 0.3384;  energy_drop/trial=  -0.08144
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10
protocols.moves.TrialCounter:           frag 3 trials=    912;  accepts= 0.2018;  energy_drop/trial=   0.00538
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10
protocols.moves.TrialCounter:           frag 3 trials=    895;  accepts= 0.1732;  energy_drop/trial=   0.00574
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2
protocols.moves.TrialCounter:           frag 2 trials=    912;  accepts= 0.1974;  energy_drop/trial=   0.01849
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10
protocols.moves.TrialCounter:           frag 2 trials=    912;  accepts= 0.1623;  energy_drop/trial=   0.00482
protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10
protocols.moves.TrialCounter:           frag 2 trials=    898;  accepts= 0.1414;  energy_drop/trial=   0.00312
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10
protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1
protocols.moves.TrialCounter:           frag 1 trials=    903;  accepts= 0.1584;  energy_drop/trial=   0.01173
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10
protocols.moves.TrialCounter:           frag 1 trials=    894;  accepts= 0.1174;  energy_drop/trial=   0.02140
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10
protocols.moves.TrialCounter:           frag 1 trials=    890;  accepts= 0.1674;  energy_drop/trial=   0.01587
protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10
protocols.moves.TrialCounter:           frag 1 trials=    921;  accepts= 0.2465;  energy_drop/trial=   0.00308
protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000010 in 6 seconds.
protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -87.9397 to automatically determined cutoff: -91.1003 based on 0.2 quantile from 48 models so far
protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter.
protocols.rna.denovo.RNA_FragmentMonteCarlo: 
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 rna_data_backbone            1.000       0.000       0.000
 rna_vdw                      1.000       0.003       0.003
 rna_base_backbone            1.000      -2.987      -2.987
 rna_backbone_backbone        1.000       0.000       0.000
 rna_repulsive                1.000       0.000       0.000
 rna_base_pair                1.000     -52.934     -52.934
 rna_base_axis                0.200     -31.866      -6.373
 rna_base_stagger             1.000     -27.222     -27.222
 rna_base_stack               1.000      -3.503      -3.503
 rna_base_stack_axis          0.200     -21.876      -4.375
 rna_rg                       1.000       8.762       8.762
 atom_pair_constraint         1.000       0.000       0.000
 base_pair_constraint         1.000       0.000       0.000
 linear_chainbreak            5.000       0.138       0.689
---------------------------------------------------
 Total weighted score:                      -87.940
protocols.rna.denovo.RNA_FragmentMonteCarlo: 
protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls...
protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 1
protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls...
protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 2
protocols.rna.denovo.movers.RNA_Minimizer: 
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 fa_atr                       0.210    -211.413     -44.397
 fa_rep                       0.200      56.224      11.245
 fa_intra_rep                 0.003     148.592       0.431
 lk_nonpolar                  0.250      -8.003      -2.001
 fa_elec_rna_phos_phos        1.700       0.387       0.658
 rna_torsion                  1.000       3.443       3.443
 suiteness_bonus              1.000       0.000       0.000
 rna_sugar_close              0.820       3.769       3.091
 fa_stack                     0.130    -230.719     -29.993
 stack_elec                   0.760      -0.805      -0.612
 geom_sol_fast                0.170      74.933      12.739
 hbond_sr_bb_sc               0.960       0.000       0.000
 hbond_lr_bb_sc               0.960      -0.407      -0.390
 hbond_sc                     0.960     -22.544     -21.643
 ref                          1.000      50.440      50.440
 free_suite                   2.000       0.000       0.000
 free_2HOprime                1.000       0.000       0.000
 intermol                     1.000       0.000       0.000
 other_pose                   1.000       0.000       0.000
 loop_close                   1.000       0.000       0.000
 linear_chainbreak            5.000       0.005       0.024
---------------------------------------------------
 Total weighted score:                      -16.966
protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 3 seconds.
protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000020
protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: outputs/stem_loop.out

Now that we've generated RNA structures with the FARFAR protocol, let's look at the top scoring structures and compare to those that you generated earlier in this module.

Run the following to get the poses from the silent file that FARFAR wrote to.

In [59]:
poses = poses_from_silent("outputs/stem_loop.out")

Exercise: Get the best scoring pose generated from FARFAR by iterating through the poses above with a loop (for pose in poses...). Make use of the rna_hires_sf that was generated earlier in this notebook to score these structures. Compare the best score with the the score of the frag_pose you generated in the previous section. Which is better?

In [60]:
### BEGIN SOLUTION
# Get the best scoring pose from fragment assembly
best_pose = Pose()
best_score = 100000 # Some high value
for pose in poses:
    cur_score = rna_hires_sf(pose)
    if cur_score < best_score:
        best_pose = pose
        best_score = cur_score
### END SOLUTION
core.io.silent.SilentFileData: Reading all structures from outputs/stem_loop.out
core.io.silent.SilentFileData: Finished reading 20 structures from outputs/stem_loop.out
In [61]:
### BEGIN SOLUTION
print(rna_hires_sf(frag_pose))
print(best_score)
### END SOLUTION
-11.241039337616563
-16.965964080330625

The FARFAR protocol in this section can generate structures with an improved Rosetta score in part because it uses an optimized number of fragment assembly moves for each structure, and in large part because we initialized this run with an idealized A-form helix for the stem portion of our structure. Let's take a look to see what the best pose we generated looks like using the PyMOLMover.

In [62]:
farfar_pmm = PyMOLMover()
farfar_pmm.set_PyMOL_model_name('farfar_pose')
farfar_pmm.apply(best_pose)

Exercise: What motifs and features can you see in the best pose for this sequence from our 10 FARFAR models? What features are missing? How might we recover those features?

In [ ]:
 

Chapter contributors:

  • Ramya Rangan (Stanford University)
  • Matt Adrianowycz (Stanford University)