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
R. Das et al., "Atomic accuracy in predicting and designing noncanonical RNA structure," Nature Methods 7:4, 291-294 (2010).
A. Watkins et al., "Blind prediction of noncanonical RNA structure at atomic accuracy," Science Advances 4:5 (2018).
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.
# Notebook setup
import sys
if 'google.colab' in sys.modules:
!pip install pyrosettacolabsetup
import pyrosettacolabsetup
pyrosettacolabsetup.setup()
print ("Notebook is set for PyRosetta use in Colab. Have fun!")
from pyrosetta import *
init()
PyRosetta-4 2019 [Rosetta PyRosetta4.Release.python37.mac 2019.35+release.767c1ea25c572fbc078db45ad65dddb507240ad3 2019-08-22T09:19:33] 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 r231 2019.35+release.767c1ea25c5 767c1ea25c572fbc078db45ad65dddb507240ad3 http://www.pyrosetta.org 2019-08-22T09:19:33 core.init: command: PyRosetta -ex1 -ex2aro -database /Users/ramyar/Dropbox/GradSchool/Research/packages/PyRosetta4.Release.python37.mac.release-231/setup/build/lib/pyrosetta/database basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=653634719 seed_offset=0 real_seed=653634719 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=653634719 RG_type=mt19937
from pyrosetta.rosetta import *
from pyrosetta.rosetta.core.pose.rna import *
from pyrosetta.rosetta.core.pose import *
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")
### 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 1.05936 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:
# print out the sequence of the pose
### BEGIN SOLUTION
pose.sequence()
### END SOLUTION
'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.
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.
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.
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 $\chi$.
from IPython.display import Image
Image('./Media/nucleotide_torsions.png',width='500')
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?
### 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
### 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
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.
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
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?
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. 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
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.
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-231/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
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.
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.
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.
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?
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.
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.
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?
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.
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?
### 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
### 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. We include the update_full_model_info_from_pose
command to ensure that the pose's internal data is kept up-to-date after the mutation is made.
mutated_pose = Pose()
mutated_pose.assign(pose)
print(pose.sequence())
rosetta.core.pose.rna.mutate_position(mutated_pose, 1, 'a')
core.pose.full_model_info.update_full_model_info_from_pose(mutated_pose)
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
.
### 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])
core.pose.full_model_info.update_full_model_info_from_pose(pose)
return pose
### END SOLUTION
### 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?
### 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)?
### 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
### 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
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.
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(), '')
### 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.
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.
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.
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?
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.
### 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:
Pose
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)
### 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 auc and sec. struct XXX ... found 32 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
Pose
, RNA_FragmentMover
, fragment size to substitute (frag_size
), and number of trials (n_trials
).rna_lowres_sf
energy function from earlier but allows the user to specify a different energy function, if desired* 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:
fragment_assembly
using 3 nucleotide fragments for 400 trials.fragment_assembly
using 2 nucleotide fragments for 300 trials.fragment_assembly
using 1 nucleotide fragments for 300 trials.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 gaa and sec. struct XXX ... found 76 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 gga and sec. struct XXX ... found 62 potential fragments 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 cga and sec. struct XXX ... found 77 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 aaa and sec. struct XXX ... found 45 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 ucc and sec. struct XXX ... found 38 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 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 aa and sec. struct XX ... found 197 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 cc and sec. struct XX ... found 182 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 ag and sec. struct XX ... found 224 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 au and sec. struct XX ... found 113 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 g and sec. struct X ... found 844 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 a and sec. struct X ... found 716 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)
### BEGIN SOLUTION
frag_pmm = PyMOLMover()
frag_pmm.set_PyMOL_model_name('frag_pose')
frag_pmm.apply(frag_pose)
### END SOLUTION
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)
### 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)
### 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 -199.341 -41.862 fa_rep 0.200 33.513 6.703 fa_intra_rep 0.003 172.640 0.501 lk_nonpolar 0.250 1.420 0.355 fa_elec_rna_phos_phos 1.700 -1.041 -1.769 rna_torsion 1.000 6.846 6.846 suiteness_bonus 1.000 0.000 0.000 rna_sugar_close 0.820 0.717 0.588 fa_stack 0.130 -203.316 -26.431 stack_elec 0.760 -5.900 -4.484 geom_sol_fast 0.170 57.716 9.812 hbond_sr_bb_sc 0.960 -0.692 -0.664 hbond_lr_bb_sc 0.960 -0.923 -0.886 hbond_sc 0.960 -4.804 -4.612 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: -5.464 protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 9 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)
### 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:
### 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
4 12 WC SUGAR ANTI 5 11 WC SUGAR ANTI 6 11 SUGAR 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
Examine our final folded structure and the hairpin from the first part of the tutorial and think about the following questions:
Write a function analogous to the fragment_assembly
function above that
Pose
RNA_Minimizer
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.
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.
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).
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)
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: ..............
rna_de_novo_options = rna_de_novo_setup.options()
rna_de_novo_options.set_nstruct(10)
rna_de_novo_options.set_silent_file("output/stem_loop.out")
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!
rna_de_novo_protocol = rosetta.protocols.rna.denovo.RNA_DeNovoProtocol(rna_de_novo_options, rna_de_novo_setup.rna_params())
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.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= 911; accepts= 0.2766; energy_drop/trial= -0.03536 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 885; accepts= 0.2294; energy_drop/trial= 0.00376 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= 914; accepts= 0.1751; energy_drop/trial= 0.00587 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 901; accepts= 0.2042; energy_drop/trial= 0.00841 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 898; accepts= 0.1258; energy_drop/trial= 0.00631 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= 885; accepts= 0.1209; energy_drop/trial= 0.00560 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= 0.1801; energy_drop/trial= 0.00695 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 894; accepts= 0.1566; energy_drop/trial= 0.00347 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 886; accepts= 0.1558; energy_drop/trial= 0.00956 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 890; accepts= 0.2056; energy_drop/trial= 0.00292 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000001 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -89.8351 to automatically determined cutoff: -89.8351 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 0.902 0.902 rna_base_backbone 1.000 -4.767 -4.767 rna_backbone_backbone 1.000 0.000 0.000 rna_repulsive 1.000 0.000 0.000 rna_base_pair 1.000 -52.954 -52.954 rna_base_axis 0.200 -33.252 -6.650 rna_base_stagger 1.000 -27.282 -27.282 rna_base_stack 1.000 -3.503 -3.503 rna_base_stack_axis 0.200 -22.582 -4.516 rna_rg 1.000 8.695 8.695 atom_pair_constraint 1.000 0.000 0.000 base_pair_constraint 1.000 0.000 0.000 linear_chainbreak 5.000 0.048 0.239 --------------------------------------------------- Total weighted score: -89.835 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 -212.395 -44.603 fa_rep 0.200 57.785 11.557 fa_intra_rep 0.003 156.356 0.453 lk_nonpolar 0.250 -8.238 -2.060 fa_elec_rna_phos_phos 1.700 0.180 0.307 rna_torsion 1.000 5.115 5.115 suiteness_bonus 1.000 0.000 0.000 rna_sugar_close 0.820 3.757 3.081 fa_stack 0.130 -232.018 -30.162 stack_elec 0.760 -1.304 -0.991 geom_sol_fast 0.170 76.314 12.973 hbond_sr_bb_sc 0.960 -0.771 -0.740 hbond_lr_bb_sc 0.960 -0.418 -0.401 hbond_sc 0.960 -22.120 -21.235 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: -16.243 protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 2 seconds. protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000001 protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: inputs/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= 915; accepts= 0.1574; energy_drop/trial= -0.05502 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 901; accepts= 0.1443; energy_drop/trial= 0.00532 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= 0.0714; energy_drop/trial= 0.00288 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= 0.1225; energy_drop/trial= 0.00958 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 895; accepts= 0.0749; energy_drop/trial= 0.00115 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= 0.0746; energy_drop/trial= 0.01596 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= 0.1197; energy_drop/trial= 0.00356 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 915; accepts= 0.0798; energy_drop/trial= 0.00069 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 899; accepts= 0.0812; energy_drop/trial= 0.01018 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 915; accepts= 0.1049; energy_drop/trial= -0.00595 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000002 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -89.9549 to automatically determined cutoff: -89.9549 based on 0.2 quantile from 2 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 0.288 0.288 rna_base_backbone 1.000 -4.578 -4.578 rna_backbone_backbone 1.000 0.000 0.000 rna_repulsive 1.000 0.000 0.000 rna_base_pair 1.000 -51.631 -51.631 rna_base_axis 0.200 -31.708 -6.342 rna_base_stagger 1.000 -26.993 -26.993 rna_base_stack 1.000 -4.404 -4.404 rna_base_stack_axis 0.200 -28.967 -5.793 rna_rg 1.000 8.902 8.902 atom_pair_constraint 1.000 0.000 0.000 base_pair_constraint 1.000 0.000 0.000 linear_chainbreak 5.000 0.119 0.596 --------------------------------------------------- Total weighted score: -89.955 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 -191.485 -40.212 fa_rep 0.200 54.120 10.824 fa_intra_rep 0.003 141.027 0.409 lk_nonpolar 0.250 -9.784 -2.446 fa_elec_rna_phos_phos 1.700 0.017 0.030 rna_torsion 1.000 4.181 4.181 suiteness_bonus 1.000 0.000 0.000 rna_sugar_close 0.820 4.063 3.332 fa_stack 0.130 -207.617 -26.990 stack_elec 0.760 -0.561 -0.426 geom_sol_fast 0.170 71.405 12.139 hbond_sr_bb_sc 0.960 0.000 0.000 hbond_lr_bb_sc 0.960 0.000 0.000 hbond_sc 0.960 -21.758 -20.887 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: -9.584 protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 3 seconds. protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000002 protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: inputs/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= 898; accepts= 0.1815; energy_drop/trial= -0.07813 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 877; accepts= 0.0969; energy_drop/trial= -0.00307 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= 0.0719; energy_drop/trial= -0.00110 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= 0.0761; energy_drop/trial= 0.00648 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 914; accepts= 0.0481; energy_drop/trial= 0.00507 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= 0.0872; energy_drop/trial= 0.00674 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= 0.1278; energy_drop/trial= 0.01127 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 905; accepts= 0.1193; energy_drop/trial= 0.02087 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 902; accepts= 0.0698; energy_drop/trial= 0.01351 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 901; accepts= 0.1465; energy_drop/trial= -0.00064 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000003 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.9657 to automatically determined cutoff: -90.9657 based on 0.2 quantile from 3 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 3.434 3.434 rna_base_backbone 1.000 -1.508 -1.508 rna_backbone_backbone 1.000 0.000 0.000 rna_repulsive 1.000 0.000 0.000 rna_base_pair 1.000 -55.346 -55.346 rna_base_axis 0.200 -36.365 -7.273 rna_base_stagger 1.000 -28.892 -28.892 rna_base_stack 1.000 -4.410 -4.410 rna_base_stack_axis 0.200 -29.248 -5.850 rna_rg 1.000 8.553 8.553 atom_pair_constraint 1.000 0.000 0.000 base_pair_constraint 1.000 0.000 0.000 linear_chainbreak 5.000 0.065 0.324 --------------------------------------------------- Total weighted score: -90.966 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 -208.421 -43.768 fa_rep 0.200 56.698 11.340 fa_intra_rep 0.003 221.109 0.641 lk_nonpolar 0.250 -6.898 -1.724 fa_elec_rna_phos_phos 1.700 0.286 0.486 rna_torsion 1.000 4.346 4.346 suiteness_bonus 1.000 0.000 0.000 rna_sugar_close 0.820 4.059 3.328 fa_stack 0.130 -226.739 -29.476 stack_elec 0.760 -0.767 -0.583 geom_sol_fast 0.170 70.645 12.010 hbond_sr_bb_sc 0.960 0.000 0.000 hbond_lr_bb_sc 0.960 -0.665 -0.638 hbond_sc 0.960 -20.448 -19.630 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 0.025 --------------------------------------------------- Total weighted score: -13.205 protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 2 seconds. protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000003 protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: inputs/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= 896; accepts= 0.0893; energy_drop/trial= -0.02692 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 908; accepts= 0.0639; energy_drop/trial= 0.00485 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= 0.0612; energy_drop/trial= 0.00365 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= 0.1051; energy_drop/trial= 0.01982 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 895; accepts= 0.0425; energy_drop/trial= 0.01237 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= 0.0344; energy_drop/trial= 0.01082 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= 0.0965; energy_drop/trial= 0.01014 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 898; accepts= 0.0891; energy_drop/trial= 0.01490 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 908; accepts= 0.0782; energy_drop/trial= 0.01443 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 898; accepts= 0.1047; energy_drop/trial= -0.00516 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000004 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -95.1198 to automatically determined cutoff: -95.1198 based on 0.2 quantile from 4 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 1.079 1.079 rna_base_backbone 1.000 -9.401 -9.401 rna_backbone_backbone 1.000 0.000 0.000 rna_repulsive 1.000 0.000 0.000 rna_base_pair 1.000 -57.025 -57.025 rna_base_axis 0.200 -33.792 -6.758 rna_base_stagger 1.000 -26.618 -26.618 rna_base_stack 1.000 -3.503 -3.503 rna_base_stack_axis 0.200 -21.574 -4.315 rna_rg 1.000 9.092 9.092 atom_pair_constraint 1.000 0.000 0.000 base_pair_constraint 1.000 0.000 0.000 linear_chainbreak 5.000 0.466 2.330 --------------------------------------------------- Total weighted score: -95.120 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 -212.367 -44.597 fa_rep 0.200 59.261 11.852 fa_intra_rep 0.003 222.563 0.645 lk_nonpolar 0.250 -8.918 -2.230 fa_elec_rna_phos_phos 1.700 0.099 0.169 rna_torsion 1.000 5.680 5.680 suiteness_bonus 1.000 0.000 0.000 rna_sugar_close 0.820 3.778 3.098 fa_stack 0.130 -233.047 -30.296 stack_elec 0.760 -0.719 -0.547 geom_sol_fast 0.170 75.712 12.871 hbond_sr_bb_sc 0.960 0.000 0.000 hbond_lr_bb_sc 0.960 0.000 0.000 hbond_sc 0.960 -23.890 -22.935 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 0.007 0.034 --------------------------------------------------- Total weighted score: -15.815 protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 3 seconds. protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000004 protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: inputs/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= 891; accepts= 0.3120; energy_drop/trial= -0.02064 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 901; accepts= 0.2042; energy_drop/trial= 0.00559 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= 0.1761; energy_drop/trial= 0.00314 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= 0.00407 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 887; accepts= 0.1398; energy_drop/trial= -0.00015 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= 0.1437; energy_drop/trial= 0.00419 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= 0.1344; energy_drop/trial= 0.01280 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 910; accepts= 0.1363; energy_drop/trial= 0.00409 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 877; accepts= 0.1391; energy_drop/trial= 0.01803 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 894; accepts= 0.2069; energy_drop/trial= 0.00139 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000005 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.092 to automatically determined cutoff: -90.9657 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 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= 907; accepts= 0.3098; energy_drop/trial= -0.05083 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 905; accepts= 0.2033; energy_drop/trial= -0.00078 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= 0.1840; energy_drop/trial= 0.00454 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 881; accepts= 0.1782; energy_drop/trial= 0.00976 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 905; accepts= 0.1646; energy_drop/trial= 0.01946 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= 892; accepts= 0.1592; energy_drop/trial= 0.00987 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= 0.1587; energy_drop/trial= 0.00808 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 887; accepts= 0.1601; energy_drop/trial= 0.00859 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 894; accepts= 0.1186; energy_drop/trial= 0.00830 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 902; accepts= 0.2461; energy_drop/trial= 0.00051 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000005 in 5 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.1072 to automatically determined cutoff: -90.9657 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 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= 900; accepts= 0.1389; energy_drop/trial= -0.04372 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 911; accepts= 0.0714; energy_drop/trial= 0.01126 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= 887; accepts= 0.0338; energy_drop/trial= 0.00643 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 910; accepts= 0.0495; energy_drop/trial= 0.00615 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 881; accepts= 0.0352; energy_drop/trial= 0.00796 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= 0.0254; energy_drop/trial= 0.01641 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= 0.0773; energy_drop/trial= 0.01241 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 900; accepts= 0.0589; energy_drop/trial= 0.00798 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 914; accepts= 0.0635; energy_drop/trial= 0.00020 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 898; accepts= 0.0958; energy_drop/trial= -0.00128 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000005 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -92.7041 to automatically determined cutoff: -92.7041 based on 0.2 quantile from 7 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 1.573 1.573 rna_base_backbone 1.000 -10.421 -10.421 rna_backbone_backbone 1.000 0.000 0.000 rna_repulsive 1.000 0.000 0.000 rna_base_pair 1.000 -52.498 -52.498 rna_base_axis 0.200 -34.234 -6.847 rna_base_stagger 1.000 -25.706 -25.706 rna_base_stack 1.000 -3.503 -3.503 rna_base_stack_axis 0.200 -22.159 -4.432 rna_rg 1.000 8.817 8.817 atom_pair_constraint 1.000 0.000 0.000 base_pair_constraint 1.000 0.000 0.000 linear_chainbreak 5.000 0.062 0.312 --------------------------------------------------- Total weighted score: -92.704 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 -216.059 -45.372 fa_rep 0.200 56.498 11.300 fa_intra_rep 0.003 1043.218 3.025 lk_nonpolar 0.250 -4.939 -1.235 fa_elec_rna_phos_phos 1.700 0.188 0.319 rna_torsion 1.000 6.351 6.351 suiteness_bonus 1.000 0.000 0.000 rna_sugar_close 0.820 3.712 3.044 fa_stack 0.130 -228.254 -29.673 stack_elec 0.760 -1.436 -1.091 geom_sol_fast 0.170 77.441 13.165 hbond_sr_bb_sc 0.960 0.000 0.000 hbond_lr_bb_sc 0.960 -0.711 -0.683 hbond_sc 0.960 -22.182 -21.295 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 0.051 0.253 --------------------------------------------------- Total weighted score: -11.451 protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 2 seconds. protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000005 protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: inputs/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= 907; accepts= 0.3186; energy_drop/trial= -0.00489 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 918; accepts= 0.2538; energy_drop/trial= 0.01175 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= 0.1170; energy_drop/trial= -0.00409 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= 0.1509; energy_drop/trial= 0.01033 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 883; accepts= 0.1314; energy_drop/trial= 0.01202 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= 0.1225; energy_drop/trial= 0.00967 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 908; accepts= 0.1509; energy_drop/trial= 0.00476 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 886; accepts= 0.1174; energy_drop/trial= 0.00713 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 903; accepts= 0.1517; energy_drop/trial= 0.01847 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 897; accepts= 0.2709; energy_drop/trial= 0.00632 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000006 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -93.2821 to automatically determined cutoff: -93.2821 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 0.253 0.253 rna_base_backbone 1.000 -3.955 -3.955 rna_backbone_backbone 1.000 0.000 0.000 rna_repulsive 1.000 0.000 0.000 rna_base_pair 1.000 -57.154 -57.154 rna_base_axis 0.200 -33.665 -6.733 rna_base_stagger 1.000 -27.063 -27.063 rna_base_stack 1.000 -3.503 -3.503 rna_base_stack_axis 0.200 -21.991 -4.398 rna_rg 1.000 8.736 8.736 atom_pair_constraint 1.000 0.000 0.000 base_pair_constraint 1.000 0.000 0.000 linear_chainbreak 5.000 0.107 0.533 --------------------------------------------------- Total weighted score: -93.282 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 -212.568 -44.639 fa_rep 0.200 57.647 11.529 fa_intra_rep 0.003 151.863 0.440 lk_nonpolar 0.250 -8.252 -2.063 fa_elec_rna_phos_phos 1.700 0.226 0.385 rna_torsion 1.000 5.104 5.104 suiteness_bonus 1.000 0.000 0.000 rna_sugar_close 0.820 3.939 3.230 fa_stack 0.130 -230.794 -30.003 stack_elec 0.760 -1.278 -0.971 geom_sol_fast 0.170 76.511 13.007 hbond_sr_bb_sc 0.960 -0.744 -0.714 hbond_lr_bb_sc 0.960 -0.445 -0.427 hbond_sc 0.960 -22.128 -21.242 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: -15.902 protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 2 seconds. protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000006 protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: inputs/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= 890; accepts= 0.2551; energy_drop/trial= -0.03388 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 895; accepts= 0.2089; energy_drop/trial= 0.00669 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= 0.1473; energy_drop/trial= 0.00273 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= 0.1604; energy_drop/trial= 0.00552 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 911; accepts= 0.2075; energy_drop/trial= 0.00371 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= 916; accepts= 0.1441; energy_drop/trial= 0.00853 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= 0.1612; energy_drop/trial= 0.00542 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 897; accepts= 0.1862; energy_drop/trial= 0.00895 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 889; accepts= 0.1800; energy_drop/trial= 0.01132 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 896; accepts= 0.2612; energy_drop/trial= -0.00291 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000007 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -87.2691 to automatically determined cutoff: -93.2821 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= 904; accepts= 0.1327; energy_drop/trial= -0.05142 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 885; accepts= 0.1028; energy_drop/trial= 0.01700 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= 908; accepts= 0.0573; energy_drop/trial= 0.00965 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= 0.0549; energy_drop/trial= 0.00250 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 898; accepts= 0.0401; energy_drop/trial= 0.01016 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= 0.0212; energy_drop/trial= 0.00062 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= 0.0706; energy_drop/trial= 0.01833 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 901; accepts= 0.0400; energy_drop/trial= 0.01115 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 891; accepts= 0.0382; energy_drop/trial= 0.01241 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 897; accepts= 0.0814; energy_drop/trial= 0.00198 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000007 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -94.8098 to automatically determined cutoff: -93.2821 based on 0.2 quantile from 10 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 2.809 2.809 rna_base_backbone 1.000 -6.455 -6.455 rna_backbone_backbone 1.000 0.000 0.000 rna_repulsive 1.000 0.000 0.000 rna_base_pair 1.000 -57.845 -57.845 rna_base_axis 0.200 -32.642 -6.528 rna_base_stagger 1.000 -28.621 -28.621 rna_base_stack 1.000 -3.503 -3.503 rna_base_stack_axis 0.200 -21.685 -4.337 rna_rg 1.000 8.823 8.823 atom_pair_constraint 1.000 0.000 0.000 base_pair_constraint 1.000 0.000 0.000 linear_chainbreak 5.000 0.169 0.846 --------------------------------------------------- Total weighted score: -94.810 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 -212.318 -44.587 fa_rep 0.200 56.743 11.349 fa_intra_rep 0.003 825.280 2.393 lk_nonpolar 0.250 -7.161 -1.790 fa_elec_rna_phos_phos 1.700 0.366 0.622 rna_torsion 1.000 5.280 5.280 suiteness_bonus 1.000 0.000 0.000 rna_sugar_close 0.820 3.896 3.194 fa_stack 0.130 -229.365 -29.817 stack_elec 0.760 -1.105 -0.840 geom_sol_fast 0.170 76.153 12.946 hbond_sr_bb_sc 0.960 0.000 0.000 hbond_lr_bb_sc 0.960 0.000 0.000 hbond_sc 0.960 -22.490 -21.590 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 0.179 0.896 --------------------------------------------------- Total weighted score: -11.504 protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 2 seconds. protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000007 protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: inputs/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= 912; accepts= 0.3048; energy_drop/trial= -0.01977 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 908; accepts= 0.1883; energy_drop/trial= 0.02082 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= 0.1761; 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= 906; accepts= 0.1700; energy_drop/trial= 0.00690 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 919; accepts= 0.1469; 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= 893; accepts= 0.1489; energy_drop/trial= 0.00854 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= 0.1656; energy_drop/trial= 0.01309 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 893; accepts= 0.1310; energy_drop/trial= 0.00924 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 910; accepts= 0.1176; energy_drop/trial= 0.00425 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 903; accepts= 0.2403; energy_drop/trial= 0.00073 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000008 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -89.7239 to automatically determined cutoff: -93.2821 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 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= 905; accepts= 0.2541; energy_drop/trial= -0.04426 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 906; accepts= 0.2031; energy_drop/trial= 0.00416 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= 0.1606; energy_drop/trial= 0.00894 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 901; accepts= 0.1820; energy_drop/trial= 0.00159 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 895; accepts= 0.1184; energy_drop/trial= 0.00080 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= 0.1413; energy_drop/trial= 0.00245 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= 0.1909; energy_drop/trial= 0.01406 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 907; accepts= 0.1224; energy_drop/trial= 0.00624 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 899; accepts= 0.0912; energy_drop/trial= 0.00671 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 888; accepts= 0.2117; energy_drop/trial= 0.00978 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000008 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.2821 to automatically determined cutoff: -93.2821 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 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= 908; accepts= 0.2599; energy_drop/trial= -0.01939 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 894; accepts= 0.2315; energy_drop/trial= 0.00470 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= 0.1859; energy_drop/trial= 0.00669 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= 0.1998; energy_drop/trial= 0.00998 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 898; accepts= 0.1392; energy_drop/trial= 0.00451 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= 914; accepts= 0.1138; energy_drop/trial= 0.00969 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 909; accepts= 0.1562; energy_drop/trial= 0.00399 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 881; accepts= 0.1884; energy_drop/trial= 0.00698 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 914; accepts= 0.1575; energy_drop/trial= 0.00792 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 900; accepts= 0.2289; energy_drop/trial= -0.00092 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000008 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -88.5914 to automatically determined cutoff: -93.2821 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 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= 917; accepts= 0.3544; energy_drop/trial= -0.01584 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 885; accepts= 0.1616; energy_drop/trial= 0.00111 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= 0.1765; energy_drop/trial= -0.00094 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= 0.1678; energy_drop/trial= 0.01557 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 900; accepts= 0.1233; energy_drop/trial= 0.00730 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= 0.1106; energy_drop/trial= 0.00889 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= 0.1437; energy_drop/trial= 0.00057 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 911; accepts= 0.1647; energy_drop/trial= 0.01347 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 897; accepts= 0.1237; energy_drop/trial= -0.00012 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 895; accepts= 0.2022; energy_drop/trial= 0.01363 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000008 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -86.5883 to automatically determined cutoff: -93.2821 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 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= 898; accepts= 0.2817; energy_drop/trial= -0.03208 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 903; accepts= 0.1938; energy_drop/trial= 0.00098 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= 0.1862; energy_drop/trial= 0.00898 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= 0.1422; energy_drop/trial= 0.01082 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 886; accepts= 0.1727; energy_drop/trial= 0.00572 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= 0.1094; energy_drop/trial= -0.00081 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= 0.1511; energy_drop/trial= 0.01157 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 899; accepts= 0.1524; energy_drop/trial= 0.01119 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 896; accepts= 0.1339; energy_drop/trial= 0.00728 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 902; accepts= 0.2428; energy_drop/trial= 0.01159 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000008 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.9812 to automatically determined cutoff: -92.7041 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 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= 905; accepts= 0.2718; energy_drop/trial= -0.15875 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 893; accepts= 0.2430; energy_drop/trial= 0.00407 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= 918; accepts= 0.1580; energy_drop/trial= 0.00334 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 901; accepts= 0.1443; energy_drop/trial= 0.00266 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 882; accepts= 0.1156; energy_drop/trial= 0.00679 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= 914; accepts= 0.1236; energy_drop/trial= 0.00117 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= 0.1456; energy_drop/trial= 0.01015 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 900; accepts= 0.1144; energy_drop/trial= 0.00503 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 898; accepts= 0.1258; energy_drop/trial= 0.00959 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 896; accepts= 0.1853; energy_drop/trial= 0.00601 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000008 in 3 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -91.2876 to automatically determined cutoff: -92.7041 based on 0.2 quantile from 16 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= 898; accepts= 0.1693; energy_drop/trial= -0.05115 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 909; accepts= 0.0990; energy_drop/trial= -0.00230 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= 0.0365; energy_drop/trial= 0.00498 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= 0.0675; energy_drop/trial= 0.00381 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 889; accepts= 0.0439; energy_drop/trial= 0.00209 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= 0.0211; energy_drop/trial= 0.00470 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= 0.0932; energy_drop/trial= 0.01302 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 895; accepts= 0.0827; energy_drop/trial= 0.00792 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 898; accepts= 0.0713; energy_drop/trial= 0.01122 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 910; accepts= 0.1220; energy_drop/trial= 0.00009 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000008 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -91.5317 to automatically determined cutoff: -92.7041 based on 0.2 quantile from 17 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= 895; accepts= 0.1654; energy_drop/trial= -0.32085 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 912; accepts= 0.0658; energy_drop/trial= -0.00412 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= 908; accepts= 0.0308; energy_drop/trial= -0.00173 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= 0.0830; energy_drop/trial= 0.00187 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 891; accepts= 0.0325; energy_drop/trial= 0.01012 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= 0.0191; energy_drop/trial= 0.00113 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= 0.0803; energy_drop/trial= 0.00439 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 903; accepts= 0.0709; energy_drop/trial= 0.01375 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 911; accepts= 0.0845; energy_drop/trial= 0.01129 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 896; accepts= 0.0949; energy_drop/trial= 0.00443 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000008 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -91.1926 to automatically determined cutoff: -92.7041 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 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= 895; accepts= 0.1743; energy_drop/trial= -0.06677 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 910; accepts= 0.0396; energy_drop/trial= 0.00817 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= 0.1056; energy_drop/trial= 0.00179 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= 0.1100; energy_drop/trial= -0.00134 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 910; accepts= 0.0791; energy_drop/trial= 0.00311 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= 0.0244; energy_drop/trial= 0.01399 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= 0.0871; energy_drop/trial= 0.00315 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 903; accepts= 0.0653; energy_drop/trial= 0.00626 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 894; accepts= 0.0973; energy_drop/trial= 0.00597 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 908; accepts= 0.1278; energy_drop/trial= 0.00161 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000008 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -92.2129 to automatically determined cutoff: -92.7041 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 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= 899; accepts= 0.1468; energy_drop/trial= -0.01520 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 898; accepts= 0.0490; energy_drop/trial= 0.00961 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= 0.1166; energy_drop/trial= 0.00329 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= 0.0613; energy_drop/trial= 0.00246 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 883; accepts= 0.0985; energy_drop/trial= 0.00234 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= 0.0858; energy_drop/trial= 0.00586 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= 0.1419; energy_drop/trial= 0.00670 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 891; accepts= 0.1279; energy_drop/trial= 0.00373 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 900; accepts= 0.1389; energy_drop/trial= 0.02513 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 890; accepts= 0.1685; energy_drop/trial= -0.00007 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000008 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.3376 to automatically determined cutoff: -92.2129 based on 0.2 quantile from 20 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 0.251 0.251 rna_base_backbone 1.000 -3.278 -3.278 rna_backbone_backbone 1.000 0.000 0.000 rna_repulsive 1.000 0.000 0.000 rna_base_pair 1.000 -53.644 -53.644 rna_base_axis 0.200 -34.750 -6.950 rna_base_stagger 1.000 -27.713 -27.713 rna_base_stack 1.000 -3.465 -3.465 rna_base_stack_axis 0.200 -22.763 -4.553 rna_rg 1.000 8.915 8.915 atom_pair_constraint 1.000 0.000 0.000 base_pair_constraint 1.000 0.000 0.000 linear_chainbreak 5.000 0.020 0.098 --------------------------------------------------- Total weighted score: -90.338 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 -210.441 -44.193 fa_rep 0.200 57.003 11.401 fa_intra_rep 0.003 140.468 0.407 lk_nonpolar 0.250 -6.950 -1.738 fa_elec_rna_phos_phos 1.700 0.186 0.316 rna_torsion 1.000 4.150 4.150 suiteness_bonus 1.000 0.000 0.000 rna_sugar_close 0.820 4.275 3.506 fa_stack 0.130 -228.089 -29.652 stack_elec 0.760 -0.826 -0.628 geom_sol_fast 0.170 71.040 12.077 hbond_sr_bb_sc 0.960 0.000 0.000 hbond_lr_bb_sc 0.960 -0.640 -0.614 hbond_sc 0.960 -20.498 -19.678 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: -14.181 protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 3 seconds. protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000008 protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: inputs/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= 909; accepts= 0.3630; energy_drop/trial= -0.05615 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 897; accepts= 0.2441; energy_drop/trial= 0.00122 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= 0.1794; energy_drop/trial= 0.00467 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= 0.1618; energy_drop/trial= 0.00530 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 911; accepts= 0.1614; energy_drop/trial= 0.00810 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= 0.1175; energy_drop/trial= 0.01292 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= 0.1596; energy_drop/trial= 0.01399 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 901; accepts= 0.1365; energy_drop/trial= 0.00740 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 896; accepts= 0.1105; energy_drop/trial= 0.00854 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 890; accepts= 0.2236; energy_drop/trial= -0.00238 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000009 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.0804 to automatically determined cutoff: -92.2129 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 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= 890; accepts= 0.2978; energy_drop/trial= -0.04121 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 905; accepts= 0.2133; energy_drop/trial= 0.00219 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= 0.1789; energy_drop/trial= 0.00141 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= 0.1611; energy_drop/trial= 0.00296 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 888; accepts= 0.1565; energy_drop/trial= 0.00418 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= 0.1672; energy_drop/trial= 0.00306 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= 0.1823; energy_drop/trial= 0.01010 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 912; accepts= 0.1294; energy_drop/trial= 0.00884 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 900; accepts= 0.1711; energy_drop/trial= 0.00647 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 902; accepts= 0.2306; energy_drop/trial= -0.00180 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000009 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -89.8654 to automatically determined cutoff: -92.2129 based on 0.2 quantile from 22 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= 908; accepts= 0.2610; energy_drop/trial= -0.03853 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 898; accepts= 0.1904; energy_drop/trial= 0.00658 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= 883; accepts= 0.1767; energy_drop/trial= 0.01007 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= 0.1991; energy_drop/trial= 0.00589 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 904; accepts= 0.1881; energy_drop/trial= 0.01126 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= 0.1544; energy_drop/trial= 0.00993 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= 0.1874; energy_drop/trial= 0.00561 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 903; accepts= 0.1960; energy_drop/trial= 0.01379 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 920; accepts= 0.1880; energy_drop/trial= 0.00627 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 891; accepts= 0.2391; energy_drop/trial= 0.00474 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000009 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -80.0935 to automatically determined cutoff: -92.2129 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 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= 893; accepts= 0.2945; energy_drop/trial= -0.02371 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 893; accepts= 0.2296; energy_drop/trial= 0.00216 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= 0.2206; energy_drop/trial= 0.01864 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= 0.1854; energy_drop/trial= 0.01159 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 904; accepts= 0.1383; energy_drop/trial= 0.00032 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= 894; accepts= 0.1510; energy_drop/trial= 0.01246 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= 0.1588; energy_drop/trial= 0.00141 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 905; accepts= 0.1580; energy_drop/trial= 0.00625 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 902; accepts= 0.1541; energy_drop/trial= 0.01254 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 899; accepts= 0.2247; energy_drop/trial= 0.00878 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000009 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -82.7993 to automatically determined cutoff: -92.2129 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 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= 922; accepts= 0.1616; energy_drop/trial= -0.04411 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 917; accepts= 0.0785; energy_drop/trial= 0.00707 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= 0.0820; energy_drop/trial= 0.00313 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= 0.0520; energy_drop/trial= 0.00713 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 909; accepts= 0.0198; energy_drop/trial= 0.00923 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= 920; accepts= 0.0304; energy_drop/trial= 0.00670 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= 0.1232; energy_drop/trial= 0.03025 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 900; accepts= 0.0700; energy_drop/trial= 0.01258 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 888; accepts= 0.0867; energy_drop/trial= 0.00956 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 902; accepts= 0.0820; energy_drop/trial= 0.00540 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000009 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -91.3146 to automatically determined cutoff: -91.5317 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 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= 911; accepts= 0.1251; energy_drop/trial= -0.03553 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 886; accepts= 0.0214; energy_drop/trial= 0.00084 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= 0.0412; energy_drop/trial= -0.00190 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= 0.0585; energy_drop/trial= 0.00617 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 915; accepts= 0.0459; energy_drop/trial= 0.00934 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= 0.0278; energy_drop/trial= 0.00536 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= 0.1237; energy_drop/trial= 0.00664 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 895; accepts= 0.0816; energy_drop/trial= 0.00989 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 900; accepts= 0.0856; energy_drop/trial= 0.01567 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 898; accepts= 0.0902; energy_drop/trial= 0.00296 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000009 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.1262 to automatically determined cutoff: -91.5317 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 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= 903; accepts= 0.1030; energy_drop/trial= -0.02559 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 896; accepts= 0.0603; energy_drop/trial= -0.00203 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= 887; accepts= 0.0710; 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= 890; accepts= 0.0551; energy_drop/trial= 0.00370 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 890; accepts= 0.0899; energy_drop/trial= 0.02292 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= 0.0631; energy_drop/trial= 0.01894 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 877; accepts= 0.1163; energy_drop/trial= 0.01539 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 910; accepts= 0.0505; energy_drop/trial= 0.00804 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 893; accepts= 0.0526; energy_drop/trial= 0.00193 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 889; accepts= 0.1226; energy_drop/trial= 0.01050 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000009 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -87.6637 to automatically determined cutoff: -91.5317 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 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= 906; accepts= 0.3157; energy_drop/trial= -0.02314 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 906; accepts= 0.2152; energy_drop/trial= -0.00064 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= 0.1940; energy_drop/trial= 0.01207 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= 0.1526; energy_drop/trial= 0.00613 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 912; accepts= 0.1327; energy_drop/trial= 0.00654 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= 0.1077; energy_drop/trial= 0.00594 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 915; accepts= 0.1727; energy_drop/trial= 0.00707 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 909; accepts= 0.1782; energy_drop/trial= 0.00204 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 894; accepts= 0.1007; energy_drop/trial= 0.00945 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 891; accepts= 0.2447; energy_drop/trial= 0.00711 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000009 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -89.8229 to automatically determined cutoff: -91.5317 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 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= 907; accepts= 0.3407; energy_drop/trial= -0.02799 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 900; accepts= 0.1233; energy_drop/trial= 0.00097 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= 0.1492; energy_drop/trial= 0.00331 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= 0.1947; energy_drop/trial= 0.00801 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 918; accepts= 0.1078; energy_drop/trial= 0.00198 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= 909; accepts= 0.1155; energy_drop/trial= 0.01410 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= 0.1419; energy_drop/trial= 0.01287 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 918; accepts= 0.1285; energy_drop/trial= -0.00202 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 923; accepts= 0.1278; energy_drop/trial= 0.00094 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 896; accepts= 0.2277; energy_drop/trial= 0.00878 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000009 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -86.7647 to automatically determined cutoff: -91.5317 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 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= 896; accepts= 0.1607; energy_drop/trial= -0.15826 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 906; accepts= 0.0651; 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= 897; accepts= 0.0513; energy_drop/trial= 0.00563 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 886; accepts= 0.0971; energy_drop/trial= -0.00024 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 919; accepts= 0.0925; energy_drop/trial= 0.00399 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= 0.0486; 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= 897; accepts= 0.1137; energy_drop/trial= 0.01124 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 907; accepts= 0.0551; energy_drop/trial= 0.00661 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 914; accepts= 0.0897; energy_drop/trial= -0.00526 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 911; accepts= 0.0955; energy_drop/trial= 0.00379 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000009 in 4 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -93.5395 to automatically determined cutoff: -91.5317 based on 0.2 quantile from 30 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 0.523 0.523 rna_base_backbone 1.000 -9.727 -9.727 rna_backbone_backbone 1.000 0.000 0.000 rna_repulsive 1.000 0.000 0.000 rna_base_pair 1.000 -52.488 -52.488 rna_base_axis 0.200 -32.017 -6.403 rna_base_stagger 1.000 -26.956 -26.956 rna_base_stack 1.000 -3.503 -3.503 rna_base_stack_axis 0.200 -22.926 -4.585 rna_rg 1.000 9.235 9.235 atom_pair_constraint 1.000 0.000 0.000 base_pair_constraint 1.000 0.000 0.000 linear_chainbreak 5.000 0.073 0.363 --------------------------------------------------- Total weighted score: -93.539 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 -204.850 -43.019 fa_rep 0.200 57.037 11.407 fa_intra_rep 0.003 152.542 0.442 lk_nonpolar 0.250 -5.757 -1.439 fa_elec_rna_phos_phos 1.700 0.164 0.279 rna_torsion 1.000 3.825 3.825 suiteness_bonus 1.000 0.000 0.000 rna_sugar_close 0.820 3.885 3.186 fa_stack 0.130 -207.529 -26.979 stack_elec 0.760 -1.344 -1.021 geom_sol_fast 0.170 75.229 12.789 hbond_sr_bb_sc 0.960 0.000 0.000 hbond_lr_bb_sc 0.960 -0.964 -0.925 hbond_sc 0.960 -21.427 -20.570 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: -11.559 protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 1 seconds. protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000009 protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: inputs/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= 888; accepts= 0.1408; energy_drop/trial= -0.09342 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 900; accepts= 0.1156; energy_drop/trial= 0.00338 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= 0.1150; energy_drop/trial= -0.00395 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= 0.0554; energy_drop/trial= 0.01713 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 911; accepts= 0.0944; energy_drop/trial= 0.01395 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= 0.0210; energy_drop/trial= 0.00510 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= 0.1352; energy_drop/trial= 0.01593 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 892; accepts= 0.1076; energy_drop/trial= 0.00536 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 926; accepts= 0.0972; energy_drop/trial= 0.00782 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 891; accepts= 0.1403; energy_drop/trial= 0.00310 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000010 in 5 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -91.2706 to automatically determined cutoff: -91.5317 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 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= 886; accepts= 0.0880; energy_drop/trial= -0.03125 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 908; accepts= 0.0848; energy_drop/trial= 0.01052 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= 0.0597; energy_drop/trial= 0.01419 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= 0.0346; energy_drop/trial= 0.00145 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 901; accepts= 0.0322; energy_drop/trial= 0.00453 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= 0.0419; energy_drop/trial= 0.01110 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 892; accepts= 0.0583; energy_drop/trial= 0.00564 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 907; accepts= 0.0595; energy_drop/trial= -0.00103 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 902; accepts= 0.0377; energy_drop/trial= 0.00374 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 904; accepts= 0.0962; energy_drop/trial= 0.00100 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000010 in 3 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -93.0452 to automatically determined cutoff: -92.2129 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 1.412 1.412 rna_base_backbone 1.000 -5.014 -5.014 rna_backbone_backbone 1.000 0.000 0.000 rna_repulsive 1.000 0.000 0.000 rna_base_pair 1.000 -56.413 -56.413 rna_base_axis 0.200 -34.611 -6.922 rna_base_stagger 1.000 -28.271 -28.271 rna_base_stack 1.000 -3.503 -3.503 rna_base_stack_axis 0.200 -22.902 -4.580 rna_rg 1.000 9.077 9.077 atom_pair_constraint 1.000 0.000 0.000 base_pair_constraint 1.000 0.000 0.000 linear_chainbreak 5.000 0.234 1.170 --------------------------------------------------- Total weighted score: -93.045 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 -208.758 -43.839 fa_rep 0.200 85.362 17.072 fa_intra_rep 0.003 153.603 0.445 lk_nonpolar 0.250 -10.694 -2.673 fa_elec_rna_phos_phos 1.700 0.246 0.418 rna_torsion 1.000 5.678 5.678 suiteness_bonus 1.000 0.000 0.000 rna_sugar_close 0.820 3.719 3.049 fa_stack 0.130 -234.941 -30.542 stack_elec 0.760 -0.666 -0.506 geom_sol_fast 0.170 72.883 12.390 hbond_sr_bb_sc 0.960 0.000 0.000 hbond_lr_bb_sc 0.960 0.000 0.000 hbond_sc 0.960 -23.932 -22.975 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: -11.018 protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 4 seconds. protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000010 protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: inputs/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.
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?
### 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 10 structures from outputs/stem_loop.out
### BEGIN SOLUTION
print(rna_hires_sf(frag_pose))
print(best_score)
### END SOLUTION
7.741146964073884 -16.242744103490725
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.
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?
Chapter contributors: