Erraser analyze script, running with args: {
  "daemon_id": "GrayLab.Jazz", 
  "data": "/home/rosie/rosie/rosie.back/data", 
  "debug": false, 
  "erraser_root": "/home/rosie/rosie/rosie.back/data/erraser", 
  "here": "/home/rosie/rosie/rosie.back", 
  "hpc_driver": "Condor", 
  "log_dir": "/home/rosie/rosie/rosie.back/Jobs/18362/output/logs", 
  "remote": "false", 
  "rosetta": "/home/rosie/rosie/rosie.back/data/erraser/rosetta", 
  "working_dir": "/home/rosie/rosie/rosie.back/Jobs/18362"
}
input options: {
  "fixed_residues": "", 
  "map_resolution": 1.795, 
  "protocol_variant": "erraser_standard", 
  "rebuild_residue": ""
}
Running ERRASER script...
/home/rosie/rosie/rosie.back/data/erraser/ErraserStandard-Run.sh -pdb ./../input/model.pdb -map ./../input/density_map.ccp4 -map_reso 1.795 -fixed_res  
pdb = ./../input/model.pdb
map = ./../input/density_map.ccp4
out_pdb = 
map_reso = 1.795
rna_prot_erraser = False
debug = False
rosetta_folder = 
rosetta_bin = 
rosetta_database = 
n_iterate = 1
rebuild_rmsd = True
rebuild_all = False
fixed_res = []
rebuild_extra_res = []
use_native_edensity_cutoff = False
constrain_chi = True
native_screen_RMSD = 3.0
search_syn_pyrimidine_only_when_native_syn = True
num_pose_kept = 100
num_pose_kept_cluster = 10
o2prime_legacy_mode = True
scoring_file = 
use_2prime_OH_potential = False
fcc2012_new_torsional_potential = True
fcc2012_scoring_file = True
###################################
Starting erraser...
Create temporary directory /home/rosie/rosie/rosie.back/Jobs/18362/output/model_erraser_temp/...
######Start submitting the Rosetta command for rna_rosetta_ready_set########
core.init: Rosetta version  from 
core.init: command: /home/rosie/rosie/rosie.back/data/erraser/rosetta/main/source/bin/erraser_minimizer.linuxgccrelease -database /home/rosie/rosie/rosie.back/data/erraser/rosetta/main/database/ -native start.pdb -out_pdb minimize_0.pdb -ready_set_only true
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=868755130 seed_offset=0 real_seed=868755130
core.init.random: RandomGenerator:init: Normal mode, seed=868755130 RG_type=mt19937
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set.  Created 378 residue types
core.chemical.ResidueTypeSet: Total time to initialize 0.67 seconds.
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 1 in file start.pdb. Best match rsd_type:  RGU:LowerRNA
core.io.pdb.file_data_fixup: Flipping atom xyz for  OP1 and  OP2 for residue   G
core.io.pdb.file_data_fixup: Flipping atom xyz for  H41 and  H42 for residue   C
core.io.pdb.file_data_fixup: Number of flip-atom fixups exceeds output limit. Rerun with -show_all_fixes to show everything.
core.io.pdb.file_data: [ WARNING ] can't find atom for res 1 atom  OP3 (trying to set temp)
Extract pdb: Empty silent file or illegal format! Skip the extraction.
Extract pdb: Empty silent file or illegal format! Skip the extraction.
######Rosetta section completed#############################################
fixed_res_final in Rosetta pdb file = []
cutpoint_final in Rosetta pdb file = []
extra_res_final in Rosetta pdb file = []
Starting whole-structure minimization 1...
Minimization 1 completed sucessfully.
Rebuilding 1 completed sucessfully.
Minimization 2 completed sucessfully.

DONE!...Total time taken= 5207.095935 seconds 

###################################
Running ERRASER Analyze script...
/home/rosie/rosie/rosie.back/data/erraser/ErraserStandard-Analyze.sh ./../input/model.pdb ./model_erraser.pdb
Geometric Changes Introduced by ERRASER

====Overall Statistics==================================
                       Start         ERRASER            
Clashscore              9.66            8.78
Suite  Outlier             5               5
Pucker Outlier             2               2
Bond   Outlier             0               0
Angle  Outlier             5               0


====Suite Changes=======================================
None


====Remaining Outlier Suites============================
'!!' stands for an outlier suite.

    Residue            Start         ERRASER            
   G A  16                !!              !!
   U A  22                !!              !!
   C A  54                !!              !!
   U A  63                !!              !!
   A A  64                !!              !!


====Pucker Outliers=====================================
Format: (delta torsion)/(!! or OK).

    Residue            Start         ERRASER            
   G A  15           77.1/!!         79.0/!!
   U A  63          124.1/!!        146.1/!!


====Bond Length Outliers=================================
None


====Bond Angle Outliers===================================
The values are the number of standard deviation away from ideal value.

    Residue           Angle       Start     ERRASER      
   C A  39      C5'-C4'-C3'    -5.55/!!          OK
   C A  39        OP1-P-O5'    -5.06/!!          OK
   C A  39        OP2-P-O5'     4.60/!!          OK
   U A  63      C4'-C3'-O3'    -4.88/!!          OK
   U A  63        C3'-O3'-P    -4.11/!!          OK


====Glycosidic Torsion Changes==========================
None


========================================================