# command:# Seed set to 1097199118
# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/
# command:# reading monomeric-50pc.atoms
# computed average trans backbone unit from 106383 examples
#	  CA= -2.2067 1.01107 -0.00976435
#	   O= -0.156391 2.24254 0.00853487
#	   C= -0.691543 1.13393 2.11219e-08
#	 N+1= 0 0 0
#	CA+1= 1.45965 1.16587e-11 8.88176e-10
# computed average cis backbone unit from 312 examples
#	  CA= -0.168209 2.45254 -0.00539451
#	   O= -2.0208 0.958499 0.0065027
#	   C= -0.795215 1.06924 2.25141e-07
#	 N+1= 0 0 0
#	CA+1= 1.46067 -3.43873e-09 -1.56176e-08
# computed average trans backbone unit before proline from 5106 examples
#	  CA= -2.20825 1.05236 9.6159e-05
#	   O= -0.131049 2.23905 0.000983042
#	   C= -0.689918 1.14203 -7.63592e-08
#	 N+1= 0 0 0
#	CA+1= 1.4642 5.07041e-09 8.55354e-10
# After reading monomeric-50pc.atoms have 448 chains in training database
#  Count of chains,residues,atoms: 448,112605,876684
#  111435 residues have no bad marker
#  665 residues lack atoms needed to compute omega
#  322 residues have cis peptide
#  number of each bad type:
#	NON_STANDARD_RESIDUE	6
#	HAS_OXT	325
#	TOO_MANY_ATOMS	1
#	TOO_FEW_ATOMS	523
#	HAS_UNKNOWN_ATOMS	2
#	HAS_DUPLICATE_ATOMS	0
#	CHAIN_BREAK_BEFORE	208
#	NON_PLANAR_PEPTIDE	143
#  Note: may sum to more than number of residues, 
#    because one residue may have multiple problems
# command:# Reading rotamer library from dunbrack-1332.rot
# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/
# command:# ReadAtomType exp-pdb.types
Read AtomType exp-pdb with 49 types.
# command:# ReadClashTable exp-pdb-1332-2symm.clash
# Read ClashTable exp-pdb-2symm checking bonds symmetric at MaxSep 2
# command:# command:CPU_time= 10.11 sec, elapsed time= 10.2893 sec)
# command:# Prefix for input files set to 
# command:# ReadTargetPDB reading from PDB file T0243.blank.pdb looking for model 1
Warning: all-zero PDB file read in ReadTargetPDB, so making up random conformation
Read PDB file T0243.blank.pdb model 1 as target.
Have 93 residues and 783 atoms.
# command:# command:# No conformations to remove in PopConform
# command:CPU_time= 12 sec, elapsed time= 12.1844 sec)
# command:# Prefix for input files set to decoys/
# command:# Prefix for output files set to decoys/
# command:# ReadConformPDB reading from PDB file T0243.try11-opt2.pdb.gz looking for model 1
# choosing archetypes in rotamer library
# Found a chain break before 76
# copying to AlignedFragments data structure
# command:# Prefix for input files set to /projects/compbio/data/pdb/
# command:# ReadConformPDB reading from PDB file 1tbx.pdb looking for chain 'A' model 1
Bad short name: MSE for alphabet: ExtAA
Replacing MSE with M
Bad short name: MSE for alphabet: ExtAA
Replacing MSE with M
Bad short name: MSE for alphabet: ExtAA
Replacing MSE with M
Bad short name: MSE for alphabet: ExtAA
Replacing MSE with M
Bad short name: MSE for alphabet: ExtAA
Replacing MSE with M
Bad short name: MSE for alphabet: ExtAA
Replacing MSE with M
Bad short name: MSE for alphabet: ExtAA
Replacing MSE with M
Bad short name: MSE for alphabet: ExtAA
Replacing MSE with M
# command:CPU_time= 14.24 sec, elapsed time= 14.4397 sec)
# command:# Prefix for output files set to 
# command:Debug: superimposing conformation 0 on the average so far
superimposing iter= 0 total_weight= 1.4751 rmsd (weighted)= 0 (unweighted)= 0
superimposing iter= 1 total_weight= 7830 rmsd (weighted)= 0 (unweighted)= 0
superimposing iter= 2 total_weight= 7830 rmsd (weighted)= 0 (unweighted)= 0
superimposing iter= 3 total_weight= 7830 rmsd (weighted)= 0 (unweighted)= 0
superimposing iter= 4 total_weight= 7830 rmsd (weighted)= 0 (unweighted)= 0
superimposing iter= 5 total_weight= 7830 rmsd (weighted)= 0 (unweighted)= 0
Debug: superimposing conformation 1 on the average so far
superimposing iter= 0 total_weight= 0.454662 rmsd (weighted)= 11.8997 (unweighted)= 95.6389
superimposing iter= 1 total_weight= 503.027 rmsd (weighted)= 8.12714 (unweighted)= 96.0025
superimposing iter= 2 total_weight= 297.629 rmsd (weighted)= 7.24458 (unweighted)= 96.5189
superimposing iter= 3 total_weight= 281.914 rmsd (weighted)= 6.65906 (unweighted)= 96.9624
superimposing iter= 4 total_weight= 274.228 rmsd (weighted)= 6.21825 (unweighted)= 97.2994
superimposing iter= 5 total_weight= 268.469 rmsd (weighted)= 5.87739 (unweighted)= 97.5344
Debug: superimposing conformation 0 on the average so far
superimposing iter= 0 total_weight= 1.4751 rmsd (weighted)= 3.48023 (unweighted)= 3.54721
superimposing iter= 1 total_weight= 5677.43 rmsd (weighted)= 0.714178 (unweighted)= 3.6017
superimposing iter= 2 total_weight= 5412.3 rmsd (weighted)= 0.151607 (unweighted)= 3.60372
superimposing iter= 3 total_weight= 5391.01 rmsd (weighted)= 0.0322539 (unweighted)= 3.60367
superimposing iter= 4 total_weight= 5390.05 rmsd (weighted)= 0.00686248 (unweighted)= 3.60367
superimposing iter= 5 total_weight= 5390 rmsd (weighted)= 0.0014601 (unweighted)= 3.60367
Debug: superimposing conformation 1 on the average so far
superimposing iter= 0 total_weight= 0.454662 rmsd (weighted)= 6.0251 (unweighted)= 96.8022
superimposing iter= 1 total_weight= 551.463 rmsd (weighted)= 3.91272 (unweighted)= 96.905
superimposing iter= 2 total_weight= 307.115 rmsd (weighted)= 3.44332 (unweighted)= 97.0936
superimposing iter= 3 total_weight= 276.773 rmsd (weighted)= 3.20136 (unweighted)= 97.2551
superimposing iter= 4 total_weight= 271.024 rmsd (weighted)= 3.01096 (unweighted)= 97.3779
superimposing iter= 5 total_weight= 262.345 rmsd (weighted)= 2.88038 (unweighted)= 97.4603
Debug: superimposing conformation 0 on the average so far
superimposing iter= 0 total_weight= 1.4751 rmsd (weighted)= 3.48309 (unweighted)= 3.5501
superimposing iter= 1 total_weight= 5677.56 rmsd (weighted)= 0.714877 (unweighted)= 3.6053
superimposing iter= 2 total_weight= 5412.41 rmsd (weighted)= 0.151755 (unweighted)= 3.60739
superimposing iter= 3 total_weight= 5391.02 rmsd (weighted)= 0.0322853 (unweighted)= 3.60735
superimposing iter= 4 total_weight= 5390.05 rmsd (weighted)= 0.00686917 (unweighted)= 3.60734
superimposing iter= 5 total_weight= 5390 rmsd (weighted)= 0.00146152 (unweighted)= 3.60734
Debug: superimposing conformation 1 on the average so far
superimposing iter= 0 total_weight= 0.454662 rmsd (weighted)= 6.02634 (unweighted)= 96.8196
superimposing iter= 1 total_weight= 551.77 rmsd (weighted)= 3.91223 (unweighted)= 96.9219
superimposing iter= 2 total_weight= 307.233 rmsd (weighted)= 3.44222 (unweighted)= 97.1101
superimposing iter= 3 total_weight= 276.814 rmsd (weighted)= 3.20008 (unweighted)= 97.2713
superimposing iter= 4 total_weight= 271.044 rmsd (weighted)= 3.00964 (unweighted)= 97.3938
superimposing iter= 5 total_weight= 262.27 rmsd (weighted)= 2.87952 (unweighted)= 97.4759
superimposing iter= 0 total_weight= 1.4751 rmsd (weighted)= 3.48472 (unweighted)= 3.55176
superimposing iter= 1 total_weight= 5677.57 rmsd (weighted)= 0.715282 (unweighted)= 3.60734
superimposing iter= 2 total_weight= 5412.47 rmsd (weighted)= 0.15184 (unweighted)= 3.60948
superimposing iter= 3 total_weight= 5391.02 rmsd (weighted)= 0.0323036 (unweighted)= 3.60944
superimposing iter= 4 total_weight= 5390.05 rmsd (weighted)= 0.00687305 (unweighted)= 3.60943
superimposing iter= 5 total_weight= 5390 rmsd (weighted)= 0.00146235 (unweighted)= 3.60943
superimposing iter= 0 total_weight= 0.454662 rmsd (weighted)= 6.02709 (unweighted)= 96.8293
superimposing iter= 1 total_weight= 551.95 rmsd (weighted)= 3.91195 (unweighted)= 96.9314
superimposing iter= 2 total_weight= 307.302 rmsd (weighted)= 3.44158 (unweighted)= 97.1193
superimposing iter= 3 total_weight= 276.841 rmsd (weighted)= 3.19931 (unweighted)= 97.2804
superimposing iter= 4 total_weight= 271.058 rmsd (weighted)= 3.00884 (unweighted)= 97.4027
superimposing iter= 5 total_weight= 262.224 rmsd (weighted)= 2.879 (unweighted)= 97.4845
# command:CPU_time= 14.27 sec, elapsed time= 14.4893 sec)
# command: