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.
!pip install pyrosettacolabsetup
import pyrosettacolabsetup; pyrosettacolabsetup.install_pyrosetta()
import pyrosetta; pyrosetta.init()
from pyrosetta import *
init()
PyRosetta-4 2020 [Rosetta PyRosetta4.Release.python37.mac 2020.04+release.4fcf80033aebbcdf7c379387df97fd3d51a2c079 2020-01-24T11:08:55] retrieved from: http://www.pyrosetta.org (C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team. core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: PyRosetta4.Release.python37.mac r244 2020.04+release.4fcf80033ae 4fcf80033aebbcdf7c379387df97fd3d51a2c079 http://www.pyrosetta.org 2020-01-24T11:08:55 core.init: command: PyRosetta -ex1 -ex2aro -database /Users/ramyar/Dropbox/GradSchool/Research/packages/PyRosetta4.Release.python37.mac.release-244/setup/build/lib/pyrosetta/database basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1108316389 seed_offset=0 real_seed=1108316389 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1108316389 RG_type=mt19937
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/MyDrive/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 1.05791 seconds. core.import_pose.import_pose: File 'inputs/stem_loop.pdb' automatically determined to be of type PDB core.io.pose_from_sfr.chirality_resolution: Flipping atom xyz for H5' and H5'' for residue C
Let's explore the structure in this PDB file. First, use pose.sequence()
to look at the sequence:
# 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.
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-244/setup/build/lib/pyrosetta/database/scoring/rna/rna_base_pair_xy.dat core.scoring.rna.RNA_LowResolutionPotential: Reading basepair x - y potential file: scoring/rna/rna_base_pair_xy.dat core.scoring.rna.RNA_LowResolutionPotential: Finished reading basepair x - y potential file: scoring/rna/rna_base_pair_xy.dat core.scoring.rna.RNA_LowResolutionPotential: Reading non - base - base x - y potential file: scoring/rna/rna_base_backbone_xy.dat core.scoring.rna.RNA_LowResolutionPotential: Reading RNA backbone backbone potential file: scoring/rna/rna_backbone_backbone.dat core.scoring.rna.RNP_LowResPotential: Reading RNP basepair x - y potential file: scoring/rna/rnp_base_pair.txt core.scoring.rna.RNP_LowResPotential: Finished reading RNP basepair x - y potential file: scoring/rna/rnp_base_pair.txt core.scoring.rna.RNP_LowResPotential: Reading RNP AA RNA backbone potential file: scoring/rna/rnp_backbone_potential.txt core.scoring.rna.RNP_LowResPotential: Finished reading RNP AA RNA backbone potential file: scoring/rna/rnp_backbone_potential.txt core.scoring.rna.RNP_LowResPairDistPotential: Reading RNP pair distance potential file: scoring/rna/rnp_pair_dist_potential_renorm.txt core.scoring.rna.RNP_LowResPairDistPotential: Finished reading RNP pair distance potential file: scoring/rna/rnp_pair_dist_potential_renorm.txt
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.
mutated_pose = Pose()
mutated_pose.assign(pose)
print(pose.sequence())
rosetta.core.pose.rna.mutate_position(mutated_pose, 1, 'a')
print(mutated_pose.sequence())
cauccgaaaggaug aauccgaaaggaug
Exercise: Make a function that mimics the 'rna_thread' Rosetta application, which takes in a pose and a new sequence and replaces all pose residues with the new sequence's residues. Remember to check that the pose's sequence and the new sequence have the same length.
The pose's current sequence is cauccgaaaggaug
. Use the function you wrote to make a version that has sequence cauccuucgggaug
and one that has sequence aaaaagaaauuuuu
.
### BEGIN SOLUTION
def rna_thread(pose, new_seq):
if len(pose.sequence()) != len(new_seq):
print("Sequences have different length; cannot rethread")
return pose
for ii in range(1, pose.size()+1):
rosetta.core.pose.rna.mutate_position(pose, ii, new_seq[ii-1])
return pose
### END SOLUTION
### 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 aaa and sec. struct XXX ... found 45 potential fragments
Now that we know how to set up a fragment assembly mover in PyRosetta, try the excise below to write a quick folding routine that uses a fragment assembly strategy to try and fold the hairpin sequence.
Exercise: Fill in the function below such that fragment_assembly
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 gau and sec. struct XXX ... found 37 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence aug and sec. struct XXX ... found 38 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence aag and sec. struct XXX ... found 64 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence ccg and sec. struct XXX ... found 63 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence gga and sec. struct XXX ... found 62 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence cau and sec. struct XXX ... found 29 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence cga and sec. struct XXX ... found 77 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence ucc and sec. struct XXX ... found 38 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence agg and sec. struct XXX ... found 64 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence auc and sec. struct XXX ... found 32 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence gaa and sec. struct XXX ... found 76 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence ga and sec. struct XX ... found 243 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence cg and sec. struct XX ... found 214 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence ca and sec. struct XX ... found 156 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence au and sec. struct XX ... found 113 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence ag and sec. struct XX ... found 224 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence cc and sec. struct XX ... found 182 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence gg and sec. struct XX ... found 235 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence aa and sec. struct XX ... found 197 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence ug and sec. struct XX ... found 171 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence uc and sec. struct XX ... found 142 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence g and sec. struct X ... found 844 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence a and sec. struct X ... found 716 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence c and sec. struct X ... found 690 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence u and sec. struct X ... found 504 potential fragments
Examine the fragment assembled Pose
in PyMOL. Do you recognize any of the motifs from before?
frag_pmm = PyMOLMover()
frag_pmm.set_PyMOL_model_name('frag_pose')
frag_pmm.apply(frag_pose)
### 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 -213.189 -44.770 fa_rep 0.200 28.665 5.733 fa_intra_rep 0.003 171.212 0.497 lk_nonpolar 0.250 3.414 0.854 fa_elec_rna_phos_phos 1.700 -0.635 -1.079 rna_torsion 1.000 5.304 5.304 suiteness_bonus 1.000 0.000 0.000 rna_sugar_close 0.820 0.474 0.388 fa_stack 0.130 -209.236 -27.201 stack_elec 0.760 -4.052 -3.079 geom_sol_fast 0.170 64.031 10.885 hbond_sr_bb_sc 0.960 -1.318 -1.265 hbond_lr_bb_sc 0.960 0.000 0.000 hbond_sc 0.960 -8.280 -7.949 ref 1.000 50.440 50.440 free_suite 2.000 0.000 0.000 free_2HOprime 1.000 0.000 0.000 intermol 1.000 0.000 0.000 other_pose 1.000 0.000 0.000 loop_close 1.000 0.000 0.000 linear_chainbreak 5.000 0.000 0.000 --------------------------------------------------- Total weighted score: -11.241 protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 12 seconds.
Let's see what changes minimization has wrought on our structure:
min_pmm = PyMOLMover()
min_pmm.set_PyMOL_model_name('min_pose')
min_pmm.apply(frag_pose)
### 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
5 10 WC WC ANTI core.scoring.rna.RNA_LowResolutionPotential: Reading basepair x - y potential file: scoring/rna/rna_base_pair_xy.dat core.scoring.rna.RNA_LowResolutionPotential: Finished reading basepair x - y potential file: scoring/rna/rna_base_pair_xy.dat core.scoring.rna.RNA_LowResolutionPotential: Reading non - base - base x - y potential file: scoring/rna/rna_base_backbone_xy.dat core.scoring.rna.RNA_LowResolutionPotential: Reading RNA backbone backbone potential file: scoring/rna/rna_backbone_backbone.dat
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("outputs/stem_loop.out")
rna_de_novo_options.set_vall_torsions_file("./inputs/1jj2.torsions")
Now we will run FARFAR by generating an RNA_DeNovoProtocol
object and running it with apply
on a starting pose. This will take a few minutes to run, and will generate 10 structures to the silent file specified above. As the protocol is running, take a look at the output to understand how it works. Note that for each structure generated, the protocol goes through various rounds of fragment assembly with fragments of size 3, 2, and 1, and then runs the RNA minimizer. This is similar to the protocol you made above!
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.libraries.RNA_JumpLibrary: Reading RNA jump library: /Users/ramyar/Dropbox/GradSchool/Research/packages/PyRosetta4.Release.python37.mac.release-244/setup/build/lib/pyrosetta/database/sampling/rna/RNA18_HUB_2.154_2.5.jump protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.moves.TrialCounter: frag 3 trials= 896; accepts= 0.1496; energy_drop/trial= -0.02519 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 900; accepts= 0.1078; energy_drop/trial= 0.00455 core.scoring.rna.RNA_LowResolutionPotential: Reading basepair x - y potential file: scoring/rna/rna_base_pair_xy.dat core.scoring.rna.RNA_LowResolutionPotential: Finished reading basepair x - y potential file: scoring/rna/rna_base_pair_xy.dat core.scoring.rna.RNA_LowResolutionPotential: Reading non - base - base x - y potential file: scoring/rna/rna_base_backbone_xy.dat core.scoring.rna.RNA_LowResolutionPotential: Reading RNA backbone backbone potential file: scoring/rna/rna_backbone_backbone.dat protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 920; accepts= 0.0870; energy_drop/trial= 0.01243 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 902; accepts= 0.0687; energy_drop/trial= 0.00649 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 889; accepts= 0.0439; energy_drop/trial= 0.00800 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 896; accepts= 0.0357; energy_drop/trial= 0.01042 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 894; accepts= 0.0649; energy_drop/trial= 0.00982 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 891; accepts= 0.0471; energy_drop/trial= 0.00768 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 898; accepts= 0.0301; energy_drop/trial= -0.00188 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 896; accepts= 0.0435; energy_drop/trial= 0.00480 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000001 in 6 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -98.4243 to automatically determined cutoff: -98.4243 based on 0.2 quantile from 1 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ rna_data_backbone 1.000 0.000 0.000 rna_vdw 1.000 0.060 0.060 rna_base_backbone 1.000 -7.444 -7.444 rna_backbone_backbone 1.000 0.000 0.000 rna_repulsive 1.000 0.000 0.000 rna_base_pair 1.000 -56.859 -56.859 rna_base_axis 0.200 -32.627 -6.525 rna_base_stagger 1.000 -28.303 -28.303 rna_base_stack 1.000 -3.516 -3.516 rna_base_stack_axis 0.200 -23.519 -4.704 rna_rg 1.000 8.646 8.646 atom_pair_constraint 1.000 0.000 0.000 base_pair_constraint 1.000 0.000 0.000 linear_chainbreak 5.000 0.044 0.220 --------------------------------------------------- Total weighted score: -98.424 protocols.rna.denovo.RNA_FragmentMonteCarlo: protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls... protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 1 protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls... protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 2 protocols.rna.denovo.movers.RNA_Minimizer: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 0.210 -204.738 -42.995 fa_rep 0.200 59.226 11.845 fa_intra_rep 0.003 155.483 0.451 lk_nonpolar 0.250 -7.480 -1.870 fa_elec_rna_phos_phos 1.700 0.209 0.356 rna_torsion 1.000 4.773 4.773 suiteness_bonus 1.000 0.000 0.000 rna_sugar_close 0.820 3.803 3.118 fa_stack 0.130 -207.756 -27.008 stack_elec 0.760 -1.458 -1.108 geom_sol_fast 0.170 74.773 12.711 hbond_sr_bb_sc 0.960 0.000 0.000 hbond_lr_bb_sc 0.960 -0.236 -0.227 hbond_sc 0.960 -22.237 -21.348 ref 1.000 50.440 50.440 free_suite 2.000 0.000 0.000 free_2HOprime 1.000 0.000 0.000 intermol 1.000 0.000 0.000 other_pose 1.000 0.000 0.000 loop_close 1.000 0.000 0.000 linear_chainbreak 5.000 0.015 0.074 --------------------------------------------------- Total weighted score: -10.788 protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 3 seconds. protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000011 protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: outputs/stem_loop.out protocols.rna.setup.RNA_MonteCarloJobDistributor: protocols.rna.setup.RNA_MonteCarloJobDistributor: Embarking on structure 2 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving residues: 5 protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving chunks: 0 protocols.rna.denovo.RNA_FragmentMonteCarlo: Using 10000 cycles in de novo modeling. protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.moves.TrialCounter: frag 3 trials= 912; accepts= 0.1985; energy_drop/trial= -0.02832 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 902; accepts= 0.1031; energy_drop/trial= 0.00035 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 895; accepts= 0.0436; energy_drop/trial= 0.00208 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 885; accepts= 0.0508; energy_drop/trial= 0.00127 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 890; accepts= 0.0258; energy_drop/trial= 0.00626 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 911; accepts= 0.0505; energy_drop/trial= 0.01172 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 925; accepts= 0.0811; energy_drop/trial= 0.01452 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 905; accepts= 0.0906; energy_drop/trial= 0.00890 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 911; accepts= 0.0659; energy_drop/trial= 0.00931 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 905; accepts= 0.0807; energy_drop/trial= -0.00160 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000002 in 6 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -92.8449 to automatically determined cutoff: -98.4243 based on 0.2 quantile from 2 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 2 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 902; accepts= 0.1530; energy_drop/trial= -0.01438 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 893; accepts= 0.0963; energy_drop/trial= 0.00220 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 904; accepts= 0.0675; energy_drop/trial= 0.00678 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 895; accepts= 0.0726; energy_drop/trial= 0.00289 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 909; accepts= 0.0594; energy_drop/trial= 0.00582 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 904; accepts= 0.0465; energy_drop/trial= 0.01846 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 895; accepts= 0.0525; energy_drop/trial= 0.01473 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 890; accepts= 0.0506; energy_drop/trial= 0.00401 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 892; accepts= 0.0359; energy_drop/trial= 0.00562 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 897; accepts= 0.0970; energy_drop/trial= 0.01381 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000002 in 6 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -88.8255 to automatically determined cutoff: -98.4243 based on 0.2 quantile from 3 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 3 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 885; accepts= 0.2373; energy_drop/trial= -0.01199 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 904; accepts= 0.1150; energy_drop/trial= 0.00237 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 885; accepts= 0.0678; energy_drop/trial= 0.00674 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 895; accepts= 0.0860; energy_drop/trial= 0.01003 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 894; accepts= 0.0694; energy_drop/trial= 0.00749 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 875; accepts= 0.0606; energy_drop/trial= 0.01380 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 905; accepts= 0.1182; energy_drop/trial= 0.01549 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 903; accepts= 0.1240; energy_drop/trial= 0.01240 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 909; accepts= 0.0506; energy_drop/trial= 0.00005 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 901; accepts= 0.1498; energy_drop/trial= 0.00713 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000002 in 7 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.2254 to automatically determined cutoff: -98.4243 based on 0.2 quantile from 4 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 4 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 897; accepts= 0.2386; energy_drop/trial= -0.04562 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 894; accepts= 0.2013; energy_drop/trial= 0.00053 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 897; accepts= 0.2107; energy_drop/trial= 0.00063 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 897; accepts= 0.1918; energy_drop/trial= 0.01017 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 894; accepts= 0.1577; energy_drop/trial= 0.00162 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 905; accepts= 0.1315; energy_drop/trial= 0.01269 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 895; accepts= 0.1821; energy_drop/trial= 0.00288 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 901; accepts= 0.1310; energy_drop/trial= 0.00550 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 886; accepts= 0.1501; energy_drop/trial= 0.02005 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 916; accepts= 0.2631; energy_drop/trial= -0.00041 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000002 in 7 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.034 to automatically determined cutoff: -92.8449 based on 0.2 quantile from 5 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 5 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 919; accepts= 0.1262; energy_drop/trial= -0.02591 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 899; accepts= 0.0868; energy_drop/trial= 0.00592 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 904; accepts= 0.0575; energy_drop/trial= 0.00568 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 911; accepts= 0.0626; energy_drop/trial= 0.02642 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 907; accepts= 0.0474; energy_drop/trial= 0.00557 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 891; accepts= 0.0438; energy_drop/trial= 0.00816 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 888; accepts= 0.0800; energy_drop/trial= 0.01689 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 886; accepts= 0.0451; energy_drop/trial= -0.00238 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 906; accepts= 0.0243; energy_drop/trial= -0.00006 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 906; accepts= 0.0684; energy_drop/trial= 0.01162 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000002 in 6 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.2721 to automatically determined cutoff: -92.8449 based on 0.2 quantile from 6 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 6 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 880; accepts= 0.2602; energy_drop/trial= -0.02211 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 912; accepts= 0.1908; energy_drop/trial= 0.00053 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 903; accepts= 0.1872; energy_drop/trial= 0.00702 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 900; accepts= 0.1900; energy_drop/trial= 0.00453 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 901; accepts= 0.1265; energy_drop/trial= 0.00477 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 884; accepts= 0.1482; energy_drop/trial= 0.00355 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 898; accepts= 0.1526; energy_drop/trial= 0.00675 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 910; accepts= 0.1747; energy_drop/trial= 0.00806 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 902; accepts= 0.1685; energy_drop/trial= 0.00500 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 900; accepts= 0.2300; energy_drop/trial= 0.00582 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000002 in 5 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -89.4801 to automatically determined cutoff: -92.8449 based on 0.2 quantile from 7 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 7 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 890; accepts= 0.2146; energy_drop/trial= -0.07357 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 911; accepts= 0.0977; energy_drop/trial= 0.00711 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 905; accepts= 0.0762; energy_drop/trial= 0.01525 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 915; accepts= 0.0710; energy_drop/trial= 0.01902 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 901; accepts= 0.0311; energy_drop/trial= 0.00380 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 906; accepts= 0.0430; energy_drop/trial= 0.03093 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 904; accepts= 0.0465; energy_drop/trial= 0.02006 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 901; accepts= 0.0832; energy_drop/trial= 0.00790 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 908; accepts= 0.0441; energy_drop/trial= 0.00503 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 897; accepts= 0.0836; energy_drop/trial= -0.00882 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000002 in 6 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -94.1246 to automatically determined cutoff: -94.1246 based on 0.2 quantile from 8 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ rna_data_backbone 1.000 0.000 0.000 rna_vdw 1.000 0.553 0.553 rna_base_backbone 1.000 -1.587 -1.587 rna_backbone_backbone 1.000 0.000 0.000 rna_repulsive 1.000 0.000 0.000 rna_base_pair 1.000 -57.648 -57.648 rna_base_axis 0.200 -37.206 -7.441 rna_base_stagger 1.000 -29.375 -29.375 rna_base_stack 1.000 -4.295 -4.295 rna_base_stack_axis 0.200 -28.297 -5.659 rna_rg 1.000 9.011 9.011 atom_pair_constraint 1.000 0.000 0.000 base_pair_constraint 1.000 0.000 0.000 linear_chainbreak 5.000 0.464 2.318 --------------------------------------------------- Total weighted score: -94.125 protocols.rna.denovo.RNA_FragmentMonteCarlo: protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls... protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 1 protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls... protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 2 protocols.rna.denovo.movers.RNA_Minimizer: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 0.210 -209.473 -43.989 fa_rep 0.200 187.286 37.457 fa_intra_rep 0.003 144.186 0.418 lk_nonpolar 0.250 -8.037 -2.009 fa_elec_rna_phos_phos 1.700 0.284 0.483 rna_torsion 1.000 6.401 6.401 suiteness_bonus 1.000 0.000 0.000 rna_sugar_close 0.820 3.730 3.058 fa_stack 0.130 -209.077 -27.180 stack_elec 0.760 -1.642 -1.248 geom_sol_fast 0.170 73.999 12.580 hbond_sr_bb_sc 0.960 0.000 0.000 hbond_lr_bb_sc 0.960 0.000 0.000 hbond_sc 0.960 -21.604 -20.740 ref 1.000 50.440 50.440 free_suite 2.000 0.000 0.000 free_2HOprime 1.000 0.000 0.000 intermol 1.000 0.000 0.000 other_pose 1.000 0.000 0.000 loop_close 1.000 0.000 0.000 linear_chainbreak 5.000 0.069 0.346 --------------------------------------------------- Total weighted score: 16.017 protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 4 seconds. protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000012 protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: outputs/stem_loop.out protocols.rna.setup.RNA_MonteCarloJobDistributor: protocols.rna.setup.RNA_MonteCarloJobDistributor: Embarking on structure 3 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving residues: 5 protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving chunks: 0 protocols.rna.denovo.RNA_FragmentMonteCarlo: Using 10000 cycles in de novo modeling. protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.moves.TrialCounter: frag 3 trials= 917; accepts= 0.2083; energy_drop/trial= -0.01818 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 899; accepts= 0.0968; energy_drop/trial= 0.00783 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 892; accepts= 0.0886; energy_drop/trial= 0.00511 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 898; accepts= 0.0713; energy_drop/trial= 0.01621 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 889; accepts= 0.0911; energy_drop/trial= 0.00559 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 895; accepts= 0.1006; energy_drop/trial= 0.01736 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 903; accepts= 0.1373; energy_drop/trial= 0.00926 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 901; accepts= 0.1121; energy_drop/trial= 0.00939 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 901; accepts= 0.0899; energy_drop/trial= 0.00004 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 901; accepts= 0.1398; energy_drop/trial= 0.00040 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000003 in 6 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -86.7151 to automatically determined cutoff: -94.1246 based on 0.2 quantile from 9 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 2 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 892; accepts= 0.2848; energy_drop/trial= -0.08165 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 911; accepts= 0.1592; energy_drop/trial= 0.00182 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 910; accepts= 0.1879; energy_drop/trial= 0.01775 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 897; accepts= 0.2375; energy_drop/trial= 0.02596 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 891; accepts= 0.1437; energy_drop/trial= 0.00590 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 911; accepts= 0.1636; energy_drop/trial= 0.00385 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 897; accepts= 0.1695; energy_drop/trial= 0.00672 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 903; accepts= 0.1561; energy_drop/trial= 0.00581 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 906; accepts= 0.1711; energy_drop/trial= 0.03649 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 893; accepts= 0.2273; energy_drop/trial= 0.00774 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000003 in 5 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -86.7368 to automatically determined cutoff: -92.8449 based on 0.2 quantile from 10 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 3 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 897; accepts= 0.1394; energy_drop/trial= -0.01516 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 888; accepts= 0.0923; energy_drop/trial= 0.00973 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 901; accepts= 0.1265; energy_drop/trial= 0.00099 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 896; accepts= 0.0792; energy_drop/trial= 0.00660 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 915; accepts= 0.0842; energy_drop/trial= 0.00897 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 911; accepts= 0.0889; energy_drop/trial= 0.01005 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 899; accepts= 0.1257; energy_drop/trial= 0.00706 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 892; accepts= 0.1278; energy_drop/trial= 0.00767 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 898; accepts= 0.1258; energy_drop/trial= 0.01122 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 900; accepts= 0.1578; energy_drop/trial= 0.00888 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000003 in 8 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -89.6628 to automatically determined cutoff: -92.8449 based on 0.2 quantile from 11 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 4 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 910; accepts= 0.1505; energy_drop/trial= -0.01623 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 904; accepts= 0.1250; energy_drop/trial= -0.00010 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 889; accepts= 0.0956; energy_drop/trial= 0.00747 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 906; accepts= 0.0905; energy_drop/trial= 0.00601 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 890; accepts= 0.0629; energy_drop/trial= 0.01323 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 889; accepts= 0.1102; energy_drop/trial= 0.01602 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 910; accepts= 0.1000; energy_drop/trial= 0.00501 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 916; accepts= 0.1135; energy_drop/trial= 0.00533 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 898; accepts= 0.1247; energy_drop/trial= 0.01046 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 922; accepts= 0.1540; energy_drop/trial= 0.00283 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000003 in 7 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -87.6454 to automatically determined cutoff: -92.8449 based on 0.2 quantile from 12 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 5 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 902; accepts= 0.1807; energy_drop/trial= -0.03472 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 912; accepts= 0.0735; energy_drop/trial= 0.01046 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 898; accepts= 0.0969; energy_drop/trial= 0.00808 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 916; accepts= 0.0207; energy_drop/trial= -0.00080 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 895; accepts= 0.0089; energy_drop/trial= 0.01270 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 902; accepts= 0.0144; energy_drop/trial= 0.01826 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 902; accepts= 0.0610; energy_drop/trial= 0.00238 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 910; accepts= 0.0802; energy_drop/trial= 0.00754 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 892; accepts= 0.0628; energy_drop/trial= 0.00652 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 890; accepts= 0.0933; energy_drop/trial= -0.00322 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000003 in 7 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -89.7438 to automatically determined cutoff: -92.8449 based on 0.2 quantile from 13 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 6 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 890; accepts= 0.3169; energy_drop/trial= -0.02860 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 902; accepts= 0.2239; energy_drop/trial= 0.00166 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 893; accepts= 0.1937; energy_drop/trial= 0.00326 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 885; accepts= 0.1989; energy_drop/trial= 0.00574 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 905; accepts= 0.1768; energy_drop/trial= 0.01289 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 906; accepts= 0.1358; energy_drop/trial= 0.00338 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 895; accepts= 0.1441; energy_drop/trial= 0.01646 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 901; accepts= 0.1543; energy_drop/trial= 0.00178 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 911; accepts= 0.2086; energy_drop/trial= 0.00263 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 901; accepts= 0.2120; energy_drop/trial= 0.00515 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000003 in 6 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -87.1968 to automatically determined cutoff: -92.8449 based on 0.2 quantile from 14 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 7 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 915; accepts= 0.1322; energy_drop/trial= -0.12232 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 906; accepts= 0.0960; energy_drop/trial= -0.00369 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 909; accepts= 0.0605; energy_drop/trial= 0.00880 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 885; accepts= 0.0531; energy_drop/trial= 0.02702 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 891; accepts= 0.0292; energy_drop/trial= 0.00760 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 912; accepts= 0.0318; energy_drop/trial= 0.01114 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 905; accepts= 0.0508; energy_drop/trial= 0.00682 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 895; accepts= 0.0637; energy_drop/trial= 0.01025 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 892; accepts= 0.0011; energy_drop/trial= -0.00028 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 888; accepts= 0.0664; energy_drop/trial= 0.00326 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000003 in 6 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -89.417 to automatically determined cutoff: -90.2721 based on 0.2 quantile from 15 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 8 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 910; accepts= 0.1703; energy_drop/trial= -0.04866 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 893; accepts= 0.1232; energy_drop/trial= -0.00562 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 892; accepts= 0.0426; energy_drop/trial= 0.00452 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 907; accepts= 0.0452; energy_drop/trial= 0.00239 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 901; accepts= 0.0610; energy_drop/trial= 0.01896 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 882; accepts= 0.0295; energy_drop/trial= 0.00002 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 886; accepts= 0.0158; energy_drop/trial= -0.00077 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 906; accepts= 0.0419; energy_drop/trial= 0.00983 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 901; accepts= 0.0189; energy_drop/trial= 0.00994 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 892; accepts= 0.0605; energy_drop/trial= 0.00700 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000003 in 6 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.6275 to automatically determined cutoff: -90.6275 based on 0.2 quantile from 16 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ rna_data_backbone 1.000 0.000 0.000 rna_vdw 1.000 0.576 0.576 rna_base_backbone 1.000 -0.864 -0.864 rna_backbone_backbone 1.000 0.000 0.000 rna_repulsive 1.000 0.000 0.000 rna_base_pair 1.000 -56.745 -56.745 rna_base_axis 0.200 -35.290 -7.058 rna_base_stagger 1.000 -27.837 -27.837 rna_base_stack 1.000 -3.503 -3.503 rna_base_stack_axis 0.200 -21.861 -4.372 rna_rg 1.000 9.025 9.025 atom_pair_constraint 1.000 0.000 0.000 base_pair_constraint 1.000 0.000 0.000 linear_chainbreak 5.000 0.030 0.150 --------------------------------------------------- Total weighted score: -90.628 protocols.rna.denovo.RNA_FragmentMonteCarlo: protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls... protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 1 protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls... protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 2 protocols.rna.denovo.movers.RNA_Minimizer: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 0.210 -204.435 -42.931 fa_rep 0.200 62.991 12.598 fa_intra_rep 0.003 151.437 0.439 lk_nonpolar 0.250 -8.047 -2.012 fa_elec_rna_phos_phos 1.700 0.804 1.366 rna_torsion 1.000 5.860 5.860 suiteness_bonus 1.000 -1.135 -1.135 rna_sugar_close 0.820 4.053 3.324 fa_stack 0.130 -218.297 -28.379 stack_elec 0.760 -2.401 -1.825 geom_sol_fast 0.170 74.495 12.664 hbond_sr_bb_sc 0.960 -0.641 -0.615 hbond_lr_bb_sc 0.960 -0.875 -0.840 hbond_sc 0.960 -19.934 -19.137 ref 1.000 50.440 50.440 free_suite 2.000 0.000 0.000 free_2HOprime 1.000 0.000 0.000 intermol 1.000 0.000 0.000 other_pose 1.000 0.000 0.000 loop_close 1.000 0.000 0.000 linear_chainbreak 5.000 0.006 0.028 --------------------------------------------------- Total weighted score: -10.154 protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 2 seconds. protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000013 protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: outputs/stem_loop.out protocols.rna.setup.RNA_MonteCarloJobDistributor: protocols.rna.setup.RNA_MonteCarloJobDistributor: Embarking on structure 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving residues: 5 protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving chunks: 0 protocols.rna.denovo.RNA_FragmentMonteCarlo: Using 10000 cycles in de novo modeling. protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.moves.TrialCounter: frag 3 trials= 910; accepts= 0.1132; energy_drop/trial= -0.01953 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 900; accepts= 0.0756; energy_drop/trial= 0.00469 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 886; accepts= 0.0835; energy_drop/trial= 0.01171 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 905; accepts= 0.0475; energy_drop/trial= 0.02135 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 901; accepts= 0.0610; energy_drop/trial= 0.01018 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 902; accepts= 0.0466; energy_drop/trial= 0.00873 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 880; accepts= 0.0932; energy_drop/trial= 0.00164 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 908; accepts= 0.0617; energy_drop/trial= -0.00153 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 897; accepts= 0.0580; energy_drop/trial= 0.00553 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 907; accepts= 0.0595; energy_drop/trial= -0.00205 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000004 in 6 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -95.6989 to automatically determined cutoff: -92.8449 based on 0.2 quantile from 17 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ rna_data_backbone 1.000 0.000 0.000 rna_vdw 1.000 0.368 0.368 rna_base_backbone 1.000 -1.619 -1.619 rna_backbone_backbone 1.000 0.000 0.000 rna_repulsive 1.000 0.000 0.000 rna_base_pair 1.000 -57.032 -57.032 rna_base_axis 0.200 -37.459 -7.492 rna_base_stagger 1.000 -28.619 -28.619 rna_base_stack 1.000 -4.503 -4.503 rna_base_stack_axis 0.200 -29.887 -5.977 rna_rg 1.000 8.832 8.832 atom_pair_constraint 1.000 0.000 0.000 base_pair_constraint 1.000 0.000 0.000 linear_chainbreak 5.000 0.069 0.344 --------------------------------------------------- Total weighted score: -95.699 protocols.rna.denovo.RNA_FragmentMonteCarlo: protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls... protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 1 protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls... protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 2 protocols.rna.denovo.movers.RNA_Minimizer: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 0.210 -207.517 -43.579 fa_rep 0.200 57.598 11.520 fa_intra_rep 0.003 142.906 0.414 lk_nonpolar 0.250 -4.073 -1.018 fa_elec_rna_phos_phos 1.700 0.441 0.750 rna_torsion 1.000 3.921 3.921 suiteness_bonus 1.000 0.000 0.000 rna_sugar_close 0.820 3.625 2.973 fa_stack 0.130 -204.783 -26.622 stack_elec 0.760 -1.538 -1.169 geom_sol_fast 0.170 72.951 12.402 hbond_sr_bb_sc 0.960 0.000 0.000 hbond_lr_bb_sc 0.960 -1.041 -1.000 hbond_sc 0.960 -20.384 -19.569 ref 1.000 50.440 50.440 free_suite 2.000 0.000 0.000 free_2HOprime 1.000 0.000 0.000 intermol 1.000 0.000 0.000 other_pose 1.000 0.000 0.000 loop_close 1.000 0.000 0.000 linear_chainbreak 5.000 0.014 0.068 --------------------------------------------------- Total weighted score: -10.469 protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 3 seconds. protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000014 protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: outputs/stem_loop.out protocols.rna.setup.RNA_MonteCarloJobDistributor: protocols.rna.setup.RNA_MonteCarloJobDistributor: Embarking on structure 5 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving residues: 5 protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving chunks: 0 protocols.rna.denovo.RNA_FragmentMonteCarlo: Using 10000 cycles in de novo modeling. protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.moves.TrialCounter: frag 3 trials= 903; accepts= 0.1761; energy_drop/trial= -0.03425 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 913; accepts= 0.0789; energy_drop/trial= -0.00487 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 902; accepts= 0.0698; energy_drop/trial= 0.01205 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 891; accepts= 0.0763; energy_drop/trial= 0.00566 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 901; accepts= 0.0744; energy_drop/trial= 0.01003 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 899; accepts= 0.0311; energy_drop/trial= 0.00749 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 893; accepts= 0.0784; energy_drop/trial= 0.01129 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 904; accepts= 0.0465; energy_drop/trial= 0.01077 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 895; accepts= 0.0358; energy_drop/trial= 0.00286 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 898; accepts= 0.0668; energy_drop/trial= 0.00066 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000005 in 6 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.9546 to automatically determined cutoff: -92.8449 based on 0.2 quantile from 18 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 2 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 899; accepts= 0.2770; energy_drop/trial= -0.04831 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 910; accepts= 0.2253; energy_drop/trial= 0.00178 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 890; accepts= 0.1955; energy_drop/trial= 0.00921 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 905; accepts= 0.1757; energy_drop/trial= 0.00428 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 891; accepts= 0.1347; energy_drop/trial= 0.00817 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 901; accepts= 0.1487; energy_drop/trial= 0.00506 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 906; accepts= 0.1733; energy_drop/trial= 0.01042 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 894; accepts= 0.1409; energy_drop/trial= 0.01070 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 905; accepts= 0.1591; energy_drop/trial= 0.00727 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 895; accepts= 0.2291; energy_drop/trial= 0.01465 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000005 in 6 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -91.1003 to automatically determined cutoff: -92.8449 based on 0.2 quantile from 19 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 3 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 913; accepts= 0.1807; energy_drop/trial= -0.07156 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 897; accepts= 0.0635; energy_drop/trial= -0.00754 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 904; accepts= 0.0619; energy_drop/trial= 0.01550 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 892; accepts= 0.0796; energy_drop/trial= 0.00761 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 895; accepts= 0.0536; energy_drop/trial= 0.01487 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 904; accepts= 0.0442; energy_drop/trial= 0.00086 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 907; accepts= 0.0695; energy_drop/trial= 0.01046 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 892; accepts= 0.0796; energy_drop/trial= 0.01015 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 900; accepts= 0.0233; energy_drop/trial= 0.00458 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 889; accepts= 0.0934; energy_drop/trial= 0.00449 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000005 in 7 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -89.66 to automatically determined cutoff: -91.1003 based on 0.2 quantile from 20 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 4 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 897; accepts= 0.2419; energy_drop/trial= -0.02891 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 895; accepts= 0.2380; energy_drop/trial= 0.00204 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 915; accepts= 0.2011; energy_drop/trial= 0.00309 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 884; accepts= 0.1584; energy_drop/trial= 0.00281 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 899; accepts= 0.1413; energy_drop/trial= 0.01224 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 877; accepts= 0.1767; energy_drop/trial= 0.00894 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 899; accepts= 0.1535; energy_drop/trial= 0.01221 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 892; accepts= 0.1648; energy_drop/trial= 0.00227 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 891; accepts= 0.1358; energy_drop/trial= 0.00348 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 903; accepts= 0.2436; energy_drop/trial= 0.00457 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000005 in 7 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.7851 to automatically determined cutoff: -91.1003 based on 0.2 quantile from 21 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 5 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 897; accepts= 0.2007; energy_drop/trial= -0.00430 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 908; accepts= 0.1101; energy_drop/trial= 0.00102 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 900; accepts= 0.0644; energy_drop/trial= 0.00527 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 913; accepts= 0.0307; energy_drop/trial= 0.00793 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 909; accepts= 0.0407; energy_drop/trial= 0.00567 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 897; accepts= 0.0156; energy_drop/trial= 0.00697 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 897; accepts= 0.0769; energy_drop/trial= 0.01673 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 915; accepts= 0.0874; energy_drop/trial= 0.00232 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 908; accepts= 0.0286; energy_drop/trial= 0.00402 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 915; accepts= 0.1005; energy_drop/trial= 0.00019 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000005 in 7 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -91.1244 to automatically determined cutoff: -91.1244 based on 0.2 quantile from 22 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ rna_data_backbone 1.000 0.000 0.000 rna_vdw 1.000 2.420 2.420 rna_base_backbone 1.000 -9.791 -9.791 rna_backbone_backbone 1.000 0.000 0.000 rna_repulsive 1.000 0.000 0.000 rna_base_pair 1.000 -51.831 -51.831 rna_base_axis 0.200 -33.412 -6.682 rna_base_stagger 1.000 -26.810 -26.810 rna_base_stack 1.000 -3.503 -3.503 rna_base_stack_axis 0.200 -22.702 -4.540 rna_rg 1.000 9.372 9.372 atom_pair_constraint 1.000 0.000 0.000 base_pair_constraint 1.000 0.000 0.000 linear_chainbreak 5.000 0.048 0.240 --------------------------------------------------- Total weighted score: -91.124 protocols.rna.denovo.RNA_FragmentMonteCarlo: protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls... protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 1 protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls... protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 2 protocols.rna.denovo.movers.RNA_Minimizer: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 0.210 -202.785 -42.585 fa_rep 0.200 56.182 11.236 fa_intra_rep 0.003 166.828 0.484 lk_nonpolar 0.250 -5.589 -1.397 fa_elec_rna_phos_phos 1.700 0.263 0.447 rna_torsion 1.000 3.398 3.398 suiteness_bonus 1.000 0.000 0.000 rna_sugar_close 0.820 3.648 2.991 fa_stack 0.130 -207.102 -26.923 stack_elec 0.760 -1.042 -0.792 geom_sol_fast 0.170 73.832 12.551 hbond_sr_bb_sc 0.960 0.000 0.000 hbond_lr_bb_sc 0.960 -1.165 -1.118 hbond_sc 0.960 -21.809 -20.937 ref 1.000 50.440 50.440 free_suite 2.000 0.000 0.000 free_2HOprime 1.000 0.000 0.000 intermol 1.000 0.000 0.000 other_pose 1.000 0.000 0.000 loop_close 1.000 0.000 0.000 linear_chainbreak 5.000 0.005 0.026 --------------------------------------------------- Total weighted score: -12.179 protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 4 seconds. protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000015 protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: outputs/stem_loop.out protocols.rna.setup.RNA_MonteCarloJobDistributor: protocols.rna.setup.RNA_MonteCarloJobDistributor: Embarking on structure 6 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving residues: 5 protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving chunks: 0 protocols.rna.denovo.RNA_FragmentMonteCarlo: Using 10000 cycles in de novo modeling. protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.moves.TrialCounter: frag 3 trials= 905; accepts= 0.1171; energy_drop/trial= -0.00815 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 902; accepts= 0.0787; energy_drop/trial= 0.00797 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 901; accepts= 0.0588; energy_drop/trial= 0.00468 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 906; accepts= 0.0596; energy_drop/trial= 0.00353 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 891; accepts= 0.0393; energy_drop/trial= 0.00408 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 903; accepts= 0.0465; energy_drop/trial= 0.02471 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 905; accepts= 0.0762; energy_drop/trial= 0.00540 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 899; accepts= 0.0456; energy_drop/trial= 0.00834 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 900; accepts= 0.0344; energy_drop/trial= 0.00695 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 894; accepts= 0.1174; energy_drop/trial= 0.00646 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000006 in 6 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -87.8902 to automatically determined cutoff: -91.1244 based on 0.2 quantile from 23 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 2 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 901; accepts= 0.2642; energy_drop/trial= -0.14535 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 896; accepts= 0.2087; energy_drop/trial= 0.00120 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 896; accepts= 0.1842; energy_drop/trial= 0.00266 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 888; accepts= 0.2140; energy_drop/trial= 0.02087 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 896; accepts= 0.2031; energy_drop/trial= 0.01614 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 897; accepts= 0.1148; energy_drop/trial= 0.00577 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 895; accepts= 0.1475; energy_drop/trial= 0.01753 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 896; accepts= 0.1283; energy_drop/trial= 0.00659 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 911; accepts= 0.1196; energy_drop/trial= 0.00646 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 903; accepts= 0.2004; energy_drop/trial= 0.00994 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000006 in 6 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -89.318 to automatically determined cutoff: -91.1244 based on 0.2 quantile from 24 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 3 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 902; accepts= 0.1530; energy_drop/trial= -0.01022 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 906; accepts= 0.0949; energy_drop/trial= -0.00907 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 901; accepts= 0.0655; energy_drop/trial= 0.00510 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 904; accepts= 0.0321; energy_drop/trial= 0.00447 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 901; accepts= 0.0588; energy_drop/trial= 0.00068 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 895; accepts= 0.0324; energy_drop/trial= 0.00250 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 894; accepts= 0.0570; energy_drop/trial= 0.00361 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 913; accepts= 0.0591; energy_drop/trial= 0.00757 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 901; accepts= 0.0466; energy_drop/trial= 0.00820 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 893; accepts= 0.0717; energy_drop/trial= 0.00566 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000006 in 6 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -89.333 to automatically determined cutoff: -91.1003 based on 0.2 quantile from 25 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 4 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 905; accepts= 0.2939; energy_drop/trial= -0.03060 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 897; accepts= 0.2575; energy_drop/trial= 0.00046 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 901; accepts= 0.1398; energy_drop/trial= 0.00079 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 898; accepts= 0.1782; energy_drop/trial= 0.01059 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 895; accepts= 0.1598; energy_drop/trial= 0.01658 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 907; accepts= 0.1114; energy_drop/trial= 0.00411 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 898; accepts= 0.1247; energy_drop/trial= 0.01030 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 907; accepts= 0.1389; energy_drop/trial= -0.00125 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 918; accepts= 0.1383; energy_drop/trial= -0.00170 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 891; accepts= 0.2514; energy_drop/trial= 0.01313 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000006 in 5 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -89.048 to automatically determined cutoff: -91.1003 based on 0.2 quantile from 26 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 5 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 905; accepts= 0.1326; energy_drop/trial= -0.01584 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 895; accepts= 0.0961; energy_drop/trial= -0.00434 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 891; accepts= 0.0808; energy_drop/trial= 0.00096 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 899; accepts= 0.0267; energy_drop/trial= 0.00092 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 881; accepts= 0.0511; energy_drop/trial= 0.01427 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 918; accepts= 0.0632; energy_drop/trial= 0.00650 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 912; accepts= 0.0603; energy_drop/trial= 0.00217 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 907; accepts= 0.0529; energy_drop/trial= 0.00955 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 901; accepts= 0.0633; energy_drop/trial= 0.00419 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 885; accepts= 0.1153; energy_drop/trial= -0.00158 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000006 in 6 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -86.1987 to automatically determined cutoff: -91.1003 based on 0.2 quantile from 27 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 6 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 893; accepts= 0.3684; energy_drop/trial= -0.05196 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 896; accepts= 0.2567; energy_drop/trial= 0.00592 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 901; accepts= 0.1898; energy_drop/trial= 0.00602 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 878; accepts= 0.1834; energy_drop/trial= 0.00334 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 878; accepts= 0.1241; energy_drop/trial= 0.00500 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 915; accepts= 0.1628; energy_drop/trial= 0.01090 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 891; accepts= 0.1829; energy_drop/trial= 0.01296 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 900; accepts= 0.1422; energy_drop/trial= 0.01386 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 897; accepts= 0.1494; energy_drop/trial= 0.01247 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 910; accepts= 0.2132; energy_drop/trial= -0.00038 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000006 in 6 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -85.1923 to automatically determined cutoff: -91.1003 based on 0.2 quantile from 28 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 7 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 904; accepts= 0.2190; energy_drop/trial= -0.17120 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 896; accepts= 0.1004; energy_drop/trial= 0.00427 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 898; accepts= 0.1147; energy_drop/trial= 0.00529 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 896; accepts= 0.1150; energy_drop/trial= 0.01740 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 900; accepts= 0.1089; energy_drop/trial= 0.00864 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 887; accepts= 0.0417; energy_drop/trial= 0.01265 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 905; accepts= 0.1072; energy_drop/trial= 0.01097 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 904; accepts= 0.0785; energy_drop/trial= 0.00973 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 909; accepts= 0.1166; energy_drop/trial= 0.00610 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 905; accepts= 0.1249; energy_drop/trial= 0.01110 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000006 in 6 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -87.911 to automatically determined cutoff: -91.1003 based on 0.2 quantile from 29 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 8 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 909; accepts= 0.1969; energy_drop/trial= -0.11968 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 904; accepts= 0.1261; energy_drop/trial= 0.01176 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 899; accepts= 0.0968; energy_drop/trial= -0.00348 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 893; accepts= 0.1153; energy_drop/trial= 0.01616 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 914; accepts= 0.0733; energy_drop/trial= 0.01463 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 911; accepts= 0.0856; energy_drop/trial= 0.00277 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 889; accepts= 0.1181; energy_drop/trial= 0.00858 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 898; accepts= 0.0924; energy_drop/trial= 0.00293 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 891; accepts= 0.1122; energy_drop/trial= 0.01508 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 910; accepts= 0.1209; energy_drop/trial= 0.00640 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000006 in 7 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -88.754 to automatically determined cutoff: -90.9546 based on 0.2 quantile from 30 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 9 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 899; accepts= 0.3059; energy_drop/trial= -0.02331 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 891; accepts= 0.2121; energy_drop/trial= 0.00343 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 897; accepts= 0.1895; energy_drop/trial= 0.00679 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 928; accepts= 0.1562; energy_drop/trial= 0.00462 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 910; accepts= 0.1527; energy_drop/trial= 0.00636 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 888; accepts= 0.1216; energy_drop/trial= 0.00906 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 871; accepts= 0.1274; energy_drop/trial= 0.00760 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 898; accepts= 0.1615; energy_drop/trial= 0.00803 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 895; accepts= 0.1128; energy_drop/trial= 0.00357 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 909; accepts= 0.2574; energy_drop/trial= 0.00188 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000006 in 6 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.0468 to automatically determined cutoff: -90.9546 based on 0.2 quantile from 31 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 10 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 905; accepts= 0.1691; energy_drop/trial= -0.05201 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 901; accepts= 0.1387; energy_drop/trial= 0.00617 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 884; accepts= 0.0577; energy_drop/trial= 0.00002 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 903; accepts= 0.0277; energy_drop/trial= 0.00579 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 923; accepts= 0.0509; energy_drop/trial= 0.00058 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 904; accepts= 0.0332; energy_drop/trial= 0.00404 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 894; accepts= 0.0772; energy_drop/trial= 0.00487 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 900; accepts= 0.0322; energy_drop/trial= 0.00677 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 889; accepts= 0.0709; energy_drop/trial= 0.00658 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 907; accepts= 0.0551; energy_drop/trial= 0.00382 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000006 in 7 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -94.4195 to automatically determined cutoff: -91.1003 based on 0.2 quantile from 32 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ rna_data_backbone 1.000 0.000 0.000 rna_vdw 1.000 5.106 5.106 rna_base_backbone 1.000 -7.911 -7.911 rna_backbone_backbone 1.000 0.000 0.000 rna_repulsive 1.000 0.000 0.000 rna_base_pair 1.000 -58.015 -58.015 rna_base_axis 0.200 -36.136 -7.227 rna_base_stagger 1.000 -27.638 -27.638 rna_base_stack 1.000 -3.503 -3.503 rna_base_stack_axis 0.200 -22.787 -4.557 rna_rg 1.000 8.668 8.668 atom_pair_constraint 1.000 0.000 0.000 base_pair_constraint 1.000 0.000 0.000 linear_chainbreak 5.000 0.132 0.658 --------------------------------------------------- Total weighted score: -94.420 protocols.rna.denovo.RNA_FragmentMonteCarlo: protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls... protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 1 protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls... protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 2 protocols.rna.denovo.movers.RNA_Minimizer: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 0.210 -210.742 -44.256 fa_rep 0.200 55.495 11.099 fa_intra_rep 0.003 664.439 1.927 lk_nonpolar 0.250 -7.290 -1.823 fa_elec_rna_phos_phos 1.700 0.349 0.593 rna_torsion 1.000 5.620 5.620 suiteness_bonus 1.000 0.000 0.000 rna_sugar_close 0.820 3.709 3.041 fa_stack 0.130 -228.548 -29.711 stack_elec 0.760 -1.130 -0.859 geom_sol_fast 0.170 72.140 12.264 hbond_sr_bb_sc 0.960 0.000 0.000 hbond_lr_bb_sc 0.960 -0.500 -0.480 hbond_sc 0.960 -21.573 -20.710 ref 1.000 50.440 50.440 free_suite 2.000 0.000 0.000 free_2HOprime 1.000 0.000 0.000 intermol 1.000 0.000 0.000 other_pose 1.000 0.000 0.000 loop_close 1.000 0.000 0.000 linear_chainbreak 5.000 0.005 0.026 --------------------------------------------------- Total weighted score: -12.829 protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 3 seconds. protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000016 protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: outputs/stem_loop.out protocols.rna.setup.RNA_MonteCarloJobDistributor: protocols.rna.setup.RNA_MonteCarloJobDistributor: Embarking on structure 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving residues: 5 protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving chunks: 0 protocols.rna.denovo.RNA_FragmentMonteCarlo: Using 10000 cycles in de novo modeling. protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.moves.TrialCounter: frag 3 trials= 898; accepts= 0.2695; energy_drop/trial= -0.02659 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 895; accepts= 0.1821; energy_drop/trial= 0.00804 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 919; accepts= 0.1621; energy_drop/trial= 0.00739 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 919; accepts= 0.1491; energy_drop/trial= 0.01368 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 910; accepts= 0.1231; energy_drop/trial= 0.00785 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 899; accepts= 0.1179; energy_drop/trial= 0.00571 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 895; accepts= 0.1385; energy_drop/trial= 0.01038 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 892; accepts= 0.1121; energy_drop/trial= 0.00454 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 901; accepts= 0.1776; energy_drop/trial= 0.01901 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 885; accepts= 0.1910; energy_drop/trial= 0.00191 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000007 in 6 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.0243 to automatically determined cutoff: -91.1003 based on 0.2 quantile from 33 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 2 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 894; accepts= 0.3020; energy_drop/trial= -0.01466 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 914; accepts= 0.2046; energy_drop/trial= 0.00502 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 911; accepts= 0.1625; energy_drop/trial= 0.01345 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 908; accepts= 0.1938; energy_drop/trial= 0.00254 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 900; accepts= 0.1656; energy_drop/trial= 0.00792 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 917; accepts= 0.1189; energy_drop/trial= 0.01190 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 914; accepts= 0.1663; energy_drop/trial= 0.00125 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 905; accepts= 0.1481; energy_drop/trial= -0.00058 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 908; accepts= 0.1366; energy_drop/trial= 0.02556 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 902; accepts= 0.2106; energy_drop/trial= 0.00068 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000007 in 6 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -91.7874 to automatically determined cutoff: -91.1244 based on 0.2 quantile from 34 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ rna_data_backbone 1.000 0.000 0.000 rna_vdw 1.000 0.056 0.056 rna_base_backbone 1.000 -7.142 -7.142 rna_backbone_backbone 1.000 0.000 0.000 rna_repulsive 1.000 0.000 0.000 rna_base_pair 1.000 -52.425 -52.425 rna_base_axis 0.200 -32.962 -6.592 rna_base_stagger 1.000 -27.205 -27.205 rna_base_stack 1.000 -3.503 -3.503 rna_base_stack_axis 0.200 -21.465 -4.293 rna_rg 1.000 8.748 8.748 atom_pair_constraint 1.000 0.000 0.000 base_pair_constraint 1.000 0.000 0.000 linear_chainbreak 5.000 0.114 0.569 --------------------------------------------------- Total weighted score: -91.787 protocols.rna.denovo.RNA_FragmentMonteCarlo: protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls... protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 1 protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls... protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 2 protocols.rna.denovo.movers.RNA_Minimizer: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 0.210 -210.969 -44.304 fa_rep 0.200 56.415 11.283 fa_intra_rep 0.003 150.392 0.436 lk_nonpolar 0.250 -7.509 -1.877 fa_elec_rna_phos_phos 1.700 0.452 0.768 rna_torsion 1.000 3.375 3.375 suiteness_bonus 1.000 0.000 0.000 rna_sugar_close 0.820 4.120 3.379 fa_stack 0.130 -227.779 -29.611 stack_elec 0.760 -0.934 -0.710 geom_sol_fast 0.170 73.909 12.564 hbond_sr_bb_sc 0.960 0.000 0.000 hbond_lr_bb_sc 0.960 -0.631 -0.606 hbond_sc 0.960 -22.279 -21.388 ref 1.000 50.440 50.440 free_suite 2.000 0.000 0.000 free_2HOprime 1.000 0.000 0.000 intermol 1.000 0.000 0.000 other_pose 1.000 0.000 0.000 loop_close 1.000 0.000 0.000 linear_chainbreak 5.000 0.005 0.024 --------------------------------------------------- Total weighted score: -16.227 protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 3 seconds. protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000017 protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: outputs/stem_loop.out protocols.rna.setup.RNA_MonteCarloJobDistributor: protocols.rna.setup.RNA_MonteCarloJobDistributor: Embarking on structure 8 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving residues: 5 protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving chunks: 0 protocols.rna.denovo.RNA_FragmentMonteCarlo: Using 10000 cycles in de novo modeling. protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.moves.TrialCounter: frag 3 trials= 900; accepts= 0.1833; energy_drop/trial= -0.03416 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 903; accepts= 0.0543; energy_drop/trial= -0.00269 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 892; accepts= 0.0919; energy_drop/trial= 0.00405 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 905; accepts= 0.0674; energy_drop/trial= 0.00671 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 918; accepts= 0.0871; energy_drop/trial= 0.00196 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 906; accepts= 0.0342; energy_drop/trial= 0.00638 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 901; accepts= 0.0877; energy_drop/trial= 0.01291 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 896; accepts= 0.0815; energy_drop/trial= 0.00907 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 904; accepts= 0.0586; energy_drop/trial= 0.00875 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 912; accepts= 0.0746; energy_drop/trial= -0.00811 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000008 in 7 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -97.3472 to automatically determined cutoff: -91.1244 based on 0.2 quantile from 35 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ rna_data_backbone 1.000 0.000 0.000 rna_vdw 1.000 2.756 2.756 rna_base_backbone 1.000 -8.634 -8.634 rna_backbone_backbone 1.000 0.000 0.000 rna_repulsive 1.000 0.000 0.000 rna_base_pair 1.000 -57.623 -57.623 rna_base_axis 0.200 -34.588 -6.918 rna_base_stagger 1.000 -28.338 -28.338 rna_base_stack 1.000 -3.503 -3.503 rna_base_stack_axis 0.200 -22.332 -4.466 rna_rg 1.000 8.947 8.947 atom_pair_constraint 1.000 0.000 0.000 base_pair_constraint 1.000 0.000 0.000 linear_chainbreak 5.000 0.086 0.432 --------------------------------------------------- Total weighted score: -97.347 protocols.rna.denovo.RNA_FragmentMonteCarlo: protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls... protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 1 protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls... protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 2 protocols.rna.denovo.movers.RNA_Minimizer: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 0.210 -213.669 -44.870 fa_rep 0.200 57.454 11.491 fa_intra_rep 0.003 180.164 0.522 lk_nonpolar 0.250 -8.156 -2.039 fa_elec_rna_phos_phos 1.700 0.546 0.928 rna_torsion 1.000 4.517 4.517 suiteness_bonus 1.000 0.000 0.000 rna_sugar_close 0.820 3.658 3.000 fa_stack 0.130 -232.938 -30.282 stack_elec 0.760 -1.202 -0.913 geom_sol_fast 0.170 74.637 12.688 hbond_sr_bb_sc 0.960 0.000 0.000 hbond_lr_bb_sc 0.960 -0.299 -0.287 hbond_sc 0.960 -22.053 -21.171 ref 1.000 50.440 50.440 free_suite 2.000 0.000 0.000 free_2HOprime 1.000 0.000 0.000 intermol 1.000 0.000 0.000 other_pose 1.000 0.000 0.000 loop_close 1.000 0.000 0.000 linear_chainbreak 5.000 0.005 0.027 --------------------------------------------------- Total weighted score: -15.950 protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 3 seconds. protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000018 protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: outputs/stem_loop.out protocols.rna.setup.RNA_MonteCarloJobDistributor: protocols.rna.setup.RNA_MonteCarloJobDistributor: Embarking on structure 9 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving residues: 5 protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving chunks: 0 protocols.rna.denovo.RNA_FragmentMonteCarlo: Using 10000 cycles in de novo modeling. protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.moves.TrialCounter: frag 3 trials= 890; accepts= 0.2921; energy_drop/trial= -0.02343 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 894; accepts= 0.2103; energy_drop/trial= 0.00337 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 912; accepts= 0.1886; energy_drop/trial= 0.00700 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 908; accepts= 0.1443; energy_drop/trial= 0.00850 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 904; accepts= 0.1527; energy_drop/trial= 0.00892 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 899; accepts= 0.1046; energy_drop/trial= 0.00174 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 900; accepts= 0.1756; energy_drop/trial= 0.00726 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 905; accepts= 0.1304; energy_drop/trial= 0.01126 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 907; accepts= 0.1433; energy_drop/trial= 0.00653 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 906; accepts= 0.2152; energy_drop/trial= 0.00479 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000009 in 8 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -91.0191 to automatically determined cutoff: -91.1244 based on 0.2 quantile from 36 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 2 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 908; accepts= 0.1652; energy_drop/trial= -0.02244 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 908; accepts= 0.1388; energy_drop/trial= 0.01026 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 907; accepts= 0.0981; energy_drop/trial= 0.00616 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 895; accepts= 0.0983; energy_drop/trial= 0.00876 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 879; accepts= 0.0535; energy_drop/trial= 0.00370 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 904; accepts= 0.0841; energy_drop/trial= 0.01281 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 895; accepts= 0.1352; energy_drop/trial= 0.01113 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 886; accepts= 0.1129; energy_drop/trial= 0.00384 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 898; accepts= 0.0679; energy_drop/trial= 0.01461 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 893; accepts= 0.1422; energy_drop/trial= 0.01164 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000009 in 7 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -85.9899 to automatically determined cutoff: -91.1244 based on 0.2 quantile from 37 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 3 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 894; accepts= 0.1756; energy_drop/trial= -0.04131 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 895; accepts= 0.1039; energy_drop/trial= -0.00168 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 903; accepts= 0.1030; energy_drop/trial= 0.01568 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 894; accepts= 0.0358; energy_drop/trial= 0.00607 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 905; accepts= 0.0773; energy_drop/trial= 0.00739 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 877; accepts= 0.0422; energy_drop/trial= 0.00798 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 905; accepts= 0.0210; energy_drop/trial= 0.00690 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 894; accepts= 0.0570; energy_drop/trial= 0.00920 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 896; accepts= 0.0480; energy_drop/trial= 0.01077 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 916; accepts= 0.1015; energy_drop/trial= 0.00025 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000009 in 6 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -91.9203 to automatically determined cutoff: -91.7874 based on 0.2 quantile from 38 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ rna_data_backbone 1.000 0.000 0.000 rna_vdw 1.000 0.276 0.276 rna_base_backbone 1.000 -5.036 -5.036 rna_backbone_backbone 1.000 0.000 0.000 rna_repulsive 1.000 0.000 0.000 rna_base_pair 1.000 -53.071 -53.071 rna_base_axis 0.200 -34.565 -6.913 rna_base_stagger 1.000 -28.465 -28.465 rna_base_stack 1.000 -3.503 -3.503 rna_base_stack_axis 0.200 -22.961 -4.592 rna_rg 1.000 9.230 9.230 atom_pair_constraint 1.000 0.000 0.000 base_pair_constraint 1.000 0.000 0.000 linear_chainbreak 5.000 0.031 0.153 --------------------------------------------------- Total weighted score: -91.920 protocols.rna.denovo.RNA_FragmentMonteCarlo: protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls... protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 1 protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls... protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 2 protocols.rna.denovo.movers.RNA_Minimizer: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 0.210 -213.265 -44.786 fa_rep 0.200 56.255 11.251 fa_intra_rep 0.003 932.297 2.704 lk_nonpolar 0.250 -4.778 -1.194 fa_elec_rna_phos_phos 1.700 0.224 0.381 rna_torsion 1.000 5.784 5.784 suiteness_bonus 1.000 0.000 0.000 rna_sugar_close 0.820 3.729 3.058 fa_stack 0.130 -226.979 -29.507 stack_elec 0.760 -1.369 -1.040 geom_sol_fast 0.170 72.846 12.384 hbond_sr_bb_sc 0.960 0.000 0.000 hbond_lr_bb_sc 0.960 -0.880 -0.845 hbond_sc 0.960 -20.273 -19.462 ref 1.000 50.440 50.440 free_suite 2.000 0.000 0.000 free_2HOprime 1.000 0.000 0.000 intermol 1.000 0.000 0.000 other_pose 1.000 0.000 0.000 loop_close 1.000 0.000 0.000 linear_chainbreak 5.000 0.055 0.277 --------------------------------------------------- Total weighted score: -10.557 protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 3 seconds. protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000019 protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: outputs/stem_loop.out protocols.rna.setup.RNA_MonteCarloJobDistributor: protocols.rna.setup.RNA_MonteCarloJobDistributor: Embarking on structure 10 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving residues: 5 protocols.rna.denovo.RNA_FragmentMonteCarlo: Number of moving chunks: 0 protocols.rna.denovo.RNA_FragmentMonteCarlo: Using 10000 cycles in de novo modeling. protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.moves.TrialCounter: frag 3 trials= 900; accepts= 0.2944; energy_drop/trial= -0.02921 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 878; accepts= 0.1993; energy_drop/trial= 0.00128 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 903; accepts= 0.1916; energy_drop/trial= 0.00346 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 914; accepts= 0.2133; energy_drop/trial= 0.01186 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 899; accepts= 0.1780; energy_drop/trial= 0.00083 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 898; accepts= 0.1336; energy_drop/trial= 0.00585 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 896; accepts= 0.1953; energy_drop/trial= 0.00676 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 907; accepts= 0.1731; energy_drop/trial= 0.00852 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 895; accepts= 0.1620; energy_drop/trial= 0.00826 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 908; accepts= 0.1795; energy_drop/trial= 0.00086 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000010 in 6 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -88.6103 to automatically determined cutoff: -91.7874 based on 0.2 quantile from 39 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 2 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 898; accepts= 0.1069; energy_drop/trial= -0.02033 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 890; accepts= 0.1258; energy_drop/trial= 0.01112 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 895; accepts= 0.0626; energy_drop/trial= 0.01057 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 896; accepts= 0.0603; energy_drop/trial= 0.00142 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 895; accepts= 0.0358; energy_drop/trial= 0.00381 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 913; accepts= 0.0624; energy_drop/trial= 0.00167 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 891; accepts= 0.0920; energy_drop/trial= 0.01310 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 887; accepts= 0.0552; energy_drop/trial= 0.01865 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 906; accepts= 0.0353; energy_drop/trial= 0.01329 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 900; accepts= 0.0867; energy_drop/trial= -0.00025 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000010 in 8 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.3844 to automatically determined cutoff: -91.1244 based on 0.2 quantile from 40 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 3 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 907; accepts= 0.2712; energy_drop/trial= -0.02289 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 909; accepts= 0.2024; energy_drop/trial= 0.01466 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 900; accepts= 0.1533; energy_drop/trial= 0.00649 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 909; accepts= 0.1815; energy_drop/trial= 0.01124 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 886; accepts= 0.2020; energy_drop/trial= 0.01881 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 918; accepts= 0.1416; energy_drop/trial= -0.00005 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 907; accepts= 0.1841; energy_drop/trial= 0.00801 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 900; accepts= 0.1700; energy_drop/trial= 0.00025 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 897; accepts= 0.1583; energy_drop/trial= 0.00243 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 896; accepts= 0.2042; energy_drop/trial= -0.00533 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000010 in 7 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -89.4019 to automatically determined cutoff: -91.1244 based on 0.2 quantile from 41 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 4 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 901; accepts= 0.1765; energy_drop/trial= -0.03647 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 902; accepts= 0.1519; energy_drop/trial= 0.00565 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 891; accepts= 0.0438; energy_drop/trial= -0.00142 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 889; accepts= 0.0607; energy_drop/trial= 0.00160 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 903; accepts= 0.0997; energy_drop/trial= 0.00652 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 905; accepts= 0.1017; energy_drop/trial= 0.00338 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 893; accepts= 0.0918; energy_drop/trial= 0.00957 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 908; accepts= 0.0529; energy_drop/trial= 0.00659 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 894; accepts= 0.0649; energy_drop/trial= 0.00802 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 910; accepts= 0.1538; energy_drop/trial= 0.00415 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000010 in 7 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -88.4029 to automatically determined cutoff: -91.1244 based on 0.2 quantile from 42 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 5 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 903; accepts= 0.1395; energy_drop/trial= -0.00951 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 893; accepts= 0.0739; energy_drop/trial= 0.01648 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 907; accepts= 0.0496; energy_drop/trial= 0.00070 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 904; accepts= 0.0896; energy_drop/trial= 0.01028 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 906; accepts= 0.0740; energy_drop/trial= 0.01057 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 903; accepts= 0.0609; energy_drop/trial= 0.01206 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 914; accepts= 0.0514; energy_drop/trial= 0.02141 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 909; accepts= 0.0583; energy_drop/trial= 0.00667 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 912; accepts= 0.0537; energy_drop/trial= 0.00310 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 898; accepts= 0.0668; energy_drop/trial= 0.00388 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000010 in 6 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.0788 to automatically determined cutoff: -91.1244 based on 0.2 quantile from 43 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 6 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 901; accepts= 0.2708; energy_drop/trial= -0.13368 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 898; accepts= 0.2038; energy_drop/trial= 0.01013 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 913; accepts= 0.2092; energy_drop/trial= 0.00911 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 894; accepts= 0.1510; energy_drop/trial= 0.00275 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 891; accepts= 0.1403; energy_drop/trial= 0.00532 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 900; accepts= 0.1022; energy_drop/trial= 0.00647 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 895; accepts= 0.1061; energy_drop/trial= 0.00951 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 901; accepts= 0.1565; energy_drop/trial= 0.01272 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 898; accepts= 0.1459; energy_drop/trial= 0.02775 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 898; accepts= 0.2249; energy_drop/trial= 0.00573 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000010 in 7 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -89.001 to automatically determined cutoff: -91.1244 based on 0.2 quantile from 44 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 7 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 901; accepts= 0.2908; energy_drop/trial= -0.01154 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 901; accepts= 0.2253; energy_drop/trial= -0.00026 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 910; accepts= 0.2176; energy_drop/trial= 0.00408 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 898; accepts= 0.1871; energy_drop/trial= 0.02081 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 901; accepts= 0.1731; energy_drop/trial= 0.01200 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 897; accepts= 0.1304; energy_drop/trial= 0.00451 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 898; accepts= 0.1114; energy_drop/trial= 0.00928 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 895; accepts= 0.1441; energy_drop/trial= 0.01042 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 900; accepts= 0.1400; energy_drop/trial= 0.01827 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 899; accepts= 0.2514; energy_drop/trial= 0.00157 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000010 in 8 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -90.4988 to automatically determined cutoff: -91.1003 based on 0.2 quantile from 45 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 8 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 908; accepts= 0.2445; energy_drop/trial= -0.01489 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 900; accepts= 0.2011; energy_drop/trial= 0.00373 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 919; accepts= 0.1926; energy_drop/trial= 0.00195 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 903; accepts= 0.2082; energy_drop/trial= 0.01001 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 901; accepts= 0.1776; energy_drop/trial= 0.00502 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 908; accepts= 0.1388; energy_drop/trial= 0.00790 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 902; accepts= 0.1619; energy_drop/trial= -0.00007 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 909; accepts= 0.1540; energy_drop/trial= 0.00224 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 881; accepts= 0.1464; energy_drop/trial= -0.00073 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 883; accepts= 0.2299; energy_drop/trial= 0.01987 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000010 in 7 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -86.6308 to automatically determined cutoff: -91.1003 based on 0.2 quantile from 46 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 9 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 902; accepts= 0.1486; energy_drop/trial= -0.01940 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 893; accepts= 0.0784; energy_drop/trial= 0.00524 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 911; accepts= 0.0724; energy_drop/trial= 0.00105 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 899; accepts= 0.0690; energy_drop/trial= 0.02012 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 902; accepts= 0.0565; energy_drop/trial= 0.01008 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 893; accepts= 0.0437; energy_drop/trial= 0.00134 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 885; accepts= 0.0870; energy_drop/trial= 0.00652 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 914; accepts= 0.0536; energy_drop/trial= 0.00753 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 889; accepts= 0.0529; energy_drop/trial= 0.01637 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 905; accepts= 0.0917; energy_drop/trial= 0.00344 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000010 in 6 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -87.0646 to automatically determined cutoff: -91.1003 based on 0.2 quantile from 47 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: Did not pass filters. Trying the model again: trial 10 out of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 42 cycles. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 3 protocols.moves.TrialCounter: frag 3 trials= 913; accepts= 0.3384; energy_drop/trial= -0.08144 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.moves.TrialCounter: frag 3 trials= 912; accepts= 0.2018; energy_drop/trial= 0.00538 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking base pairs early! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.moves.TrialCounter: frag 3 trials= 895; accepts= 0.1732; energy_drop/trial= 0.00574 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.moves.TrialCounter: frag 2 trials= 912; accepts= 0.1974; energy_drop/trial= 0.01849 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.moves.TrialCounter: frag 2 trials= 912; accepts= 0.1623; energy_drop/trial= 0.00482 protocols.rna.denovo.RNA_FragmentMonteCarlo: Checking loop closure with tolerance of 12 Angstroms! Result: 1 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.moves.TrialCounter: frag 2 trials= 898; accepts= 0.1414; energy_drop/trial= 0.00312 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.moves.TrialCounter: frag 1 trials= 903; accepts= 0.1584; energy_drop/trial= 0.01173 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.moves.TrialCounter: frag 1 trials= 894; accepts= 0.1174; energy_drop/trial= 0.02140 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.moves.TrialCounter: frag 1 trials= 890; accepts= 0.1674; energy_drop/trial= 0.01587 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.moves.TrialCounter: frag 1 trials= 921; accepts= 0.2465; energy_drop/trial= 0.00308 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of S_000010 in 6 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: Comparing current lores score -87.9397 to automatically determined cutoff: -91.1003 based on 0.2 quantile from 48 models so far protocols.rna.denovo.RNA_FragmentMonteCarlo: Failed score filter. protocols.rna.denovo.RNA_FragmentMonteCarlo: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ rna_data_backbone 1.000 0.000 0.000 rna_vdw 1.000 0.003 0.003 rna_base_backbone 1.000 -2.987 -2.987 rna_backbone_backbone 1.000 0.000 0.000 rna_repulsive 1.000 0.000 0.000 rna_base_pair 1.000 -52.934 -52.934 rna_base_axis 0.200 -31.866 -6.373 rna_base_stagger 1.000 -27.222 -27.222 rna_base_stack 1.000 -3.503 -3.503 rna_base_stack_axis 0.200 -21.876 -4.375 rna_rg 1.000 8.762 8.762 atom_pair_constraint 1.000 0.000 0.000 base_pair_constraint 1.000 0.000 0.000 linear_chainbreak 5.000 0.138 0.689 --------------------------------------------------- Total weighted score: -87.940 protocols.rna.denovo.RNA_FragmentMonteCarlo: protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls... protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 1 protocols.rna.denovo.movers.RNA_Minimizer: Orienting 2' hydroxyls... protocols.rna.denovo.movers.RNA_Minimizer: Minimizing...round= 2 protocols.rna.denovo.movers.RNA_Minimizer: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 0.210 -211.413 -44.397 fa_rep 0.200 56.224 11.245 fa_intra_rep 0.003 148.592 0.431 lk_nonpolar 0.250 -8.003 -2.001 fa_elec_rna_phos_phos 1.700 0.387 0.658 rna_torsion 1.000 3.443 3.443 suiteness_bonus 1.000 0.000 0.000 rna_sugar_close 0.820 3.769 3.091 fa_stack 0.130 -230.719 -29.993 stack_elec 0.760 -0.805 -0.612 geom_sol_fast 0.170 74.933 12.739 hbond_sr_bb_sc 0.960 0.000 0.000 hbond_lr_bb_sc 0.960 -0.407 -0.390 hbond_sc 0.960 -22.544 -21.643 ref 1.000 50.440 50.440 free_suite 2.000 0.000 0.000 free_2HOprime 1.000 0.000 0.000 intermol 1.000 0.000 0.000 other_pose 1.000 0.000 0.000 loop_close 1.000 0.000 0.000 linear_chainbreak 5.000 0.005 0.024 --------------------------------------------------- Total weighted score: -16.966 protocols.rna.denovo.movers.RNA_Minimizer: RNA minimizer finished in 3 seconds. protocols.rna.denovo.RNA_DeNovoProtocol: Making silent struct for S_000020 protocols.rna.denovo.RNA_DeNovoProtocol: Outputting to silent file: outputs/stem_loop.out
Now that we've generated RNA structures with the FARFAR protocol, let's look at the top scoring structures and compare to those that you generated earlier in this module.
Run the following to get the poses from the silent file that FARFAR wrote to.
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 20 structures from outputs/stem_loop.out
### BEGIN SOLUTION
print(rna_hires_sf(frag_pose))
print(best_score)
### END SOLUTION
-11.241039337616563 -16.965964080330625
The FARFAR protocol in this section can generate structures with an improved Rosetta score in part because it uses an optimized number of fragment assembly moves for each structure, and in large part because we initialized this run with an idealized A-form helix for the stem portion of our structure. Let's take a look to see what the best pose we generated looks like using the PyMOLMover.
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: