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1.5.0-DEV-c9805191e3.log
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Julia Version 1.5.0-DEV.570
Commit c9805191e3 (2020-04-04 00:18 UTC)
Platform Info:
OS: Linux (x86_64-pc-linux-gnu)
CPU: Intel(R) Xeon(R) Silver 4114 CPU @ 2.20GHz
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-9.0.1 (ORCJIT, skylake)
Environment:
JULIA_DEPOT_PATH = ::/usr/local/share/julia
JULIA_NUM_THREADS = 2
Resolving package versions...
Installed PositiveFactorizations ─────── v0.2.3
Installed Media ──────────────────────── v0.5.0
Installed ColorTypes ─────────────────── v0.8.1
Installed SpecialFunctions ───────────── v0.10.0
Installed Parsers ────────────────────── v1.0.1
Installed Juno ───────────────────────── v0.8.1
Installed ProteinEnsembles ───────────── v0.3.0
Installed Optim ──────────────────────── v0.20.1
Installed JSON ───────────────────────── v0.21.0
Installed Loess ──────────────────────── v0.5.1
Installed Rmath_jll ──────────────────── v0.2.2+0
Installed OpenSpecFun_jll ────────────── v0.5.3+3
Installed DiffResults ────────────────── v1.0.2
Installed Cairo ──────────────────────── v0.8.0
Installed Parameters ─────────────────── v0.12.0
Installed CoupledFields ──────────────── v0.1.0
Installed OffsetArrays ───────────────── v1.0.4
Installed SortingAlgorithms ──────────── v0.3.1
Installed WoodburyMatrices ───────────── v0.5.2
Installed CommonSubexpressions ───────── v0.2.0
Installed FiniteDiff ─────────────────── v2.3.0
Installed QuadGK ─────────────────────── v2.3.1
Installed Graphics ───────────────────── v1.0.2
Installed DataStructures ─────────────── v0.17.11
Installed DocStringExtensions ────────── v0.8.1
Installed FFTW_jll ───────────────────── v3.3.9+5
Installed PDMats ─────────────────────── v0.9.12
Installed IntelOpenMP_jll ────────────── v2018.0.3+0
Installed Hexagons ───────────────────── v0.2.0
Installed Measures ───────────────────── v0.3.1
Installed FillArrays ─────────────────── v0.8.6
Installed StatsFuns ──────────────────── v0.9.4
Installed FFTW ───────────────────────── v1.2.0
Installed Distances ──────────────────── v0.8.2
Installed CompilerSupportLibraries_jll ─ v0.3.3+0
Installed Reexport ───────────────────── v0.2.0
Installed FixedPointNumbers ──────────── v0.6.1
Installed TextWrap ───────────────────── v0.3.0
Installed AxisAlgorithms ─────────────── v1.0.0
Installed DiffRules ──────────────────── v1.0.1
Installed CategoricalArrays ──────────── v0.7.7
Installed Colors ─────────────────────── v0.9.6
Installed DataAPI ────────────────────── v1.1.0
Installed MKL_jll ────────────────────── v2019.0.117+2
Installed AbstractFFTs ───────────────── v0.5.0
Installed OrderedCollections ─────────── v1.1.0
Installed LineSearches ───────────────── v7.0.1
Installed Showoff ────────────────────── v0.3.1
Installed StatsBase ──────────────────── v0.32.2
Installed ForwardDiff ────────────────── v0.10.10
Installed OpenBLAS_jll ───────────────── v0.3.9+1
Installed KernelDensity ──────────────── v0.5.1
Installed Rmath ──────────────────────── v0.6.1
Installed Ratios ─────────────────────── v0.4.0
Installed StaticArrays ───────────────── v0.12.1
Installed MacroTools ─────────────────── v0.5.5
Installed Compose ────────────────────── v0.8.2
Installed Gadfly ─────────────────────── v1.2.1
Installed Distributions ──────────────── v0.23.2
Installed ArrayInterface ─────────────── v2.6.2
Installed Arpack_jll ─────────────────── v3.5.0+3
Installed Requires ───────────────────── v1.0.1
Installed Compat ─────────────────────── v2.2.0
Installed NLSolversBase ──────────────── v7.6.1
Installed ProgressMeter ──────────────── v1.2.0
Installed NaNMath ────────────────────── v0.3.3
Installed Contour ────────────────────── v0.5.2
Installed ArgParse ───────────────────── v0.6.2
Installed IterTools ──────────────────── v1.3.0
Installed Missings ───────────────────── v0.4.3
Installed IndirectArrays ─────────────── v0.5.1
Installed BinaryProvider ─────────────── v0.5.8
Installed Arpack ─────────────────────── v0.4.0
Installed Interpolations ─────────────── v0.12.9
Updating `~/.julia/environments/v1.5/Project.toml`
186d2b2d + ProteinEnsembles v0.3.0
Updating `~/.julia/environments/v1.5/Manifest.toml`
621f4979 + AbstractFFTs v0.5.0
c7e460c6 + ArgParse v0.6.2
7d9fca2a + Arpack v0.4.0
68821587 + Arpack_jll v3.5.0+3
4fba245c + ArrayInterface v2.6.2
13072b0f + AxisAlgorithms v1.0.0
b99e7846 + BinaryProvider v0.5.8
159f3aea + Cairo v0.8.0
324d7699 + CategoricalArrays v0.7.7
3da002f7 + ColorTypes v0.8.1
5ae59095 + Colors v0.9.6
bbf7d656 + CommonSubexpressions v0.2.0
34da2185 + Compat v2.2.0
e66e0078 + CompilerSupportLibraries_jll v0.3.3+0
a81c6b42 + Compose v0.8.2
d38c429a + Contour v0.5.2
7ad07ef1 + CoupledFields v0.1.0
9a962f9c + DataAPI v1.1.0
864edb3b + DataStructures v0.17.11
163ba53b + DiffResults v1.0.2
b552c78f + DiffRules v1.0.1
b4f34e82 + Distances v0.8.2
31c24e10 + Distributions v0.23.2
ffbed154 + DocStringExtensions v0.8.1
7a1cc6ca + FFTW v1.2.0
f5851436 + FFTW_jll v3.3.9+5
1a297f60 + FillArrays v0.8.6
6a86dc24 + FiniteDiff v2.3.0
53c48c17 + FixedPointNumbers v0.6.1
f6369f11 + ForwardDiff v0.10.10
c91e804a + Gadfly v1.2.1
a2bd30eb + Graphics v1.0.2
a1b4810d + Hexagons v0.2.0
9b13fd28 + IndirectArrays v0.5.1
1d5cc7b8 + IntelOpenMP_jll v2018.0.3+0
a98d9a8b + Interpolations v0.12.9
c8e1da08 + IterTools v1.3.0
682c06a0 + JSON v0.21.0
e5e0dc1b + Juno v0.8.1
5ab0869b + KernelDensity v0.5.1
d3d80556 + LineSearches v7.0.1
4345ca2d + Loess v0.5.1
856f044c + MKL_jll v2019.0.117+2
1914dd2f + MacroTools v0.5.5
442fdcdd + Measures v0.3.1
e89f7d12 + Media v0.5.0
e1d29d7a + Missings v0.4.3
d41bc354 + NLSolversBase v7.6.1
77ba4419 + NaNMath v0.3.3
6fe1bfb0 + OffsetArrays v1.0.4
4536629a + OpenBLAS_jll v0.3.9+1
efe28fd5 + OpenSpecFun_jll v0.5.3+3
429524aa + Optim v0.20.1
bac558e1 + OrderedCollections v1.1.0
90014a1f + PDMats v0.9.12
d96e819e + Parameters v0.12.0
69de0a69 + Parsers v1.0.1
85a6dd25 + PositiveFactorizations v0.2.3
92933f4c + ProgressMeter v1.2.0
186d2b2d + ProteinEnsembles v0.3.0
1fd47b50 + QuadGK v2.3.1
c84ed2f1 + Ratios v0.4.0
189a3867 + Reexport v0.2.0
ae029012 + Requires v1.0.1
79098fc4 + Rmath v0.6.1
f50d1b31 + Rmath_jll v0.2.2+0
992d4aef + Showoff v0.3.1
a2af1166 + SortingAlgorithms v0.3.1
276daf66 + SpecialFunctions v0.10.0
90137ffa + StaticArrays v0.12.1
2913bbd2 + StatsBase v0.32.2
4c63d2b9 + StatsFuns v0.9.4
b718987f + TextWrap v0.3.0
efce3f68 + WoodburyMatrices v0.5.2
2a0f44e3 + Base64
ade2ca70 + Dates
8bb1440f + DelimitedFiles
8ba89e20 + Distributed
9fa8497b + Future
b77e0a4c + InteractiveUtils
76f85450 + LibGit2
8f399da3 + Libdl
37e2e46d + LinearAlgebra
56ddb016 + Logging
d6f4376e + Markdown
a63ad114 + Mmap
44cfe95a + Pkg
de0858da + Printf
9abbd945 + Profile
3fa0cd96 + REPL
9a3f8284 + Random
ea8e919c + SHA
9e88b42a + Serialization
1a1011a3 + SharedArrays
6462fe0b + Sockets
2f01184e + SparseArrays
10745b16 + Statistics
4607b0f0 + SuiteSparse
8dfed614 + Test
cf7118a7 + UUIDs
4ec0a83e + Unicode
Building Cairo → `~/.julia/packages/Cairo/ZbzIH/deps/build.log`
Building FFTW ─→ `~/.julia/packages/FFTW/qqcBj/deps/build.log`
Testing ProteinEnsembles
Status `/tmp/jl_gPqyub/Project.toml`
c7e460c6 ArgParse v0.6.2
159f3aea Cairo v0.8.0
5ae59095 Colors v0.9.6
c91e804a Gadfly v1.2.1
92933f4c ProgressMeter v1.2.0
186d2b2d ProteinEnsembles v0.3.0
37e2e46d LinearAlgebra
9a3f8284 Random
10745b16 Statistics
8dfed614 Test
Status `/tmp/jl_gPqyub/Manifest.toml`
621f4979 AbstractFFTs v0.5.0
c7e460c6 ArgParse v0.6.2
7d9fca2a Arpack v0.4.0
68821587 Arpack_jll v3.5.0+3
4fba245c ArrayInterface v2.6.2
13072b0f AxisAlgorithms v1.0.0
b99e7846 BinaryProvider v0.5.8
159f3aea Cairo v0.8.0
324d7699 CategoricalArrays v0.7.7
3da002f7 ColorTypes v0.8.1
5ae59095 Colors v0.9.6
bbf7d656 CommonSubexpressions v0.2.0
34da2185 Compat v2.2.0
e66e0078 CompilerSupportLibraries_jll v0.3.3+0
a81c6b42 Compose v0.8.2
d38c429a Contour v0.5.2
7ad07ef1 CoupledFields v0.1.0
9a962f9c DataAPI v1.1.0
864edb3b DataStructures v0.17.11
163ba53b DiffResults v1.0.2
b552c78f DiffRules v1.0.1
b4f34e82 Distances v0.8.2
31c24e10 Distributions v0.23.2
ffbed154 DocStringExtensions v0.8.1
7a1cc6ca FFTW v1.2.0
f5851436 FFTW_jll v3.3.9+5
1a297f60 FillArrays v0.8.6
6a86dc24 FiniteDiff v2.3.0
53c48c17 FixedPointNumbers v0.6.1
f6369f11 ForwardDiff v0.10.10
c91e804a Gadfly v1.2.1
a2bd30eb Graphics v1.0.2
a1b4810d Hexagons v0.2.0
9b13fd28 IndirectArrays v0.5.1
1d5cc7b8 IntelOpenMP_jll v2018.0.3+0
a98d9a8b Interpolations v0.12.9
c8e1da08 IterTools v1.3.0
682c06a0 JSON v0.21.0
e5e0dc1b Juno v0.8.1
5ab0869b KernelDensity v0.5.1
d3d80556 LineSearches v7.0.1
4345ca2d Loess v0.5.1
856f044c MKL_jll v2019.0.117+2
1914dd2f MacroTools v0.5.5
442fdcdd Measures v0.3.1
e89f7d12 Media v0.5.0
e1d29d7a Missings v0.4.3
d41bc354 NLSolversBase v7.6.1
77ba4419 NaNMath v0.3.3
6fe1bfb0 OffsetArrays v1.0.4
4536629a OpenBLAS_jll v0.3.9+1
efe28fd5 OpenSpecFun_jll v0.5.3+3
429524aa Optim v0.20.1
bac558e1 OrderedCollections v1.1.0
90014a1f PDMats v0.9.12
d96e819e Parameters v0.12.0
69de0a69 Parsers v1.0.1
85a6dd25 PositiveFactorizations v0.2.3
92933f4c ProgressMeter v1.2.0
186d2b2d ProteinEnsembles v0.3.0
1fd47b50 QuadGK v2.3.1
c84ed2f1 Ratios v0.4.0
189a3867 Reexport v0.2.0
ae029012 Requires v1.0.1
79098fc4 Rmath v0.6.1
f50d1b31 Rmath_jll v0.2.2+0
992d4aef Showoff v0.3.1
a2af1166 SortingAlgorithms v0.3.1
276daf66 SpecialFunctions v0.10.0
90137ffa StaticArrays v0.12.1
2913bbd2 StatsBase v0.32.2
4c63d2b9 StatsFuns v0.9.4
b718987f TextWrap v0.3.0
efce3f68 WoodburyMatrices v0.5.2
2a0f44e3 Base64
ade2ca70 Dates
8bb1440f DelimitedFiles
8ba89e20 Distributed
9fa8497b Future
b77e0a4c InteractiveUtils
76f85450 LibGit2
8f399da3 Libdl
37e2e46d LinearAlgebra
56ddb016 Logging
d6f4376e Markdown
a63ad114 Mmap
44cfe95a Pkg
de0858da Printf
9abbd945 Profile
3fa0cd96 REPL
9a3f8284 Random
ea8e919c SHA
9e88b42a Serialization
1a1011a3 SharedArrays
6462fe0b Sockets
2f01184e SparseArrays
10745b16 Statistics
4607b0f0 SuiteSparse
8dfed614 Test
cf7118a7 UUIDs
4ec0a83e Unicode
Test Summary: | Pass Total
Types | 8 8
Could not find element for atom with name X
Test Summary: | Pass Total
Atoms | 26 26
Read 214 residues from DSSP file
Read 1336 atoms from PDB file
Read 141 residues from DSSP file
Read 3312 atoms from PDB file
Read 3804 atoms from PDB file
Read 3312 atoms from PDB file
Read 3312 atoms from PDB file
Read 476 pocket points from pocket points PDB file
Read 43 pocket centres from LIGSITEcs output PDB file
Test Summary: | Pass Total
IO | 31 31
Read 2035 atoms from PDB file
Read 214 residues from DSSP file
Found distance constraints from single structure
Found combined distance constraints from two structures
Test Summary: | Pass Total
Interactions | 41 41
Kept lowest scoring 2 out of 4 structures
Scores range from 10.0 to 20.0
Test Summary: | Pass Total
Generate | 12 12
Test Summary: | Pass Total
Align | 11 11
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read in protein ensemble
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read in protein ensemble
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read 2035 atoms from PDB file
Read in protein ensemble
Test Summary: | Pass Total
PCA | 10 10
Found 2 interactions between the modulator and the protein
Read 395 pocket points from LIGSITEcs pocket points PDB file
Read 43 pocket centres from LIGSITEcs output PDB file
Assigned all points
Wrote pocket number assignments to file "/tmp/jl_1VVIFV"
Test Summary: | Pass Total
Perturb | 9 9
-- ExProSE --
Arguments:
i1 - /home/pkgeval/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CLL_H.pdb
d1 - /home/pkgeval/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CLL.dssp
i2 - /home/pkgeval/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR_H.pdb
d2 - /home/pkgeval/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR.dssp
out_dir - /tmp/exprose_out
n_strucs - 4
tolerance_weight - 0.3
other_ratio - 20.0
extra_pdbs - /home/pkgeval/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_1.pdb, /home/pkgeval/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_2.pdb
mod_path - nothing
n_mods - 0
Making output directory "/tmp/exprose_out"
Proceeding with two structures
Read 1367 atoms from PDB file
Read 1336 atoms from PDB file
Read 144 residues from DSSP file
Read 141 residues from DSSP file
Found interactions:
Covalently bonded - 1313
1-3 system - 1868
Same ring system - 35
Side-chain restricted 1-4 - 116
Omega 1-4 - 540
Tight phi/psi 1-4 - 692
Loose phi/psi 1-4 - 157
Other phi/psi 1-4 - 195
Other 1-4 - 589
Secondary structure - 3684
Salt bridge - 42
H bond - 230
Tight hydrophobic - 817
Loose hydrophobic - 878
Other pairs - 835795
Found distance constraints from single structure
Found interactions:
Covalently bonded - 1313
1-3 system - 1868
Same ring system - 35
Side-chain restricted 1-4 - 116
Omega 1-4 - 540
Tight phi/psi 1-4 - 540
Loose phi/psi 1-4 - 206
Other phi/psi 1-4 - 298
Other 1-4 - 589
Secondary structure - 2544
Salt bridge - 63
H bond - 233
Tight hydrophobic - 773
Loose hydrophobic - 1055
Other pairs - 836778
Found distance constraints from single structure
Found combined distance constraints from two structures
Will generate 6 structures and keep best-scoring 4
Progress: 17%|████████▍ | ETA: 0:00:29Progress: 33%|████████████████▋ | ETA: 0:00:24Progress: 50%|█████████████████████████ | ETA: 0:00:18Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:12Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:06Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:34
Kept lowest scoring 4 out of 6 structures
Scores range from 1.5 to 103.7
Aligned ensemble to itself after 7 iteration(s)
Projections written to file "/tmp/exprose_out/pcs/pcs.tsv"
Projections written to file "/tmp/exprose_out/pcs/pcs_input_1.tsv"
Projections written to file "/tmp/exprose_out/pcs/pcs_input_2.tsv"
Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs/out.pdb"
Wrote ensemble scores to file "/tmp/exprose_out/spe_scores.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_1.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_2.tsv"
Plotted principal components to file(s) "/tmp/exprose_out/pcs/pc_x_y.png"
Plotted RMSFs to file "/tmp/exprose_out/rmsfs.png"
n_to_write is larger than the number of eigenvectors - proceeding with all possible eigenvectors
PyMol script to view principal components written to file(s) "/tmp/exprose_out/pymol/view_pc_x.pml"
Done
-- ExProSE --
Arguments:
i1 - /home/pkgeval/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CLL_H.pdb
d1 - /home/pkgeval/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CLL.dssp
i2 - nothing
d2 - nothing
out_dir - /tmp/exprose_out
n_strucs - 4
tolerance_weight - 0.3
other_ratio - 20.0
extra_pdbs - /home/pkgeval/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_1.pdb, /home/pkgeval/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_2.pdb
mod_path - nothing
n_mods - 0
Making output directory "/tmp/exprose_out"
Proceeding with one structure
Read 1367 atoms from PDB file
Read 144 residues from DSSP file
Found interactions:
Covalently bonded - 1379
1-3 system - 1966
Same ring system - 35
Side-chain restricted 1-4 - 116
Omega 1-4 - 568
Tight phi/psi 1-4 - 744
Loose phi/psi 1-4 - 157
Other phi/psi 1-4 - 195
Other 1-4 - 626
Secondary structure - 4160
Salt bridge - 42
H bond - 244
Tight hydrophobic - 865
Loose hydrophobic - 931
Other pairs - 921633
Found distance constraints from single structure
Will generate 6 structures and keep best-scoring 4
Progress: 17%|████████▍ | ETA: 0:00:28Progress: 33%|████████████████▋ | ETA: 0:00:26Progress: 50%|█████████████████████████ | ETA: 0:00:19Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:12Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:06Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:37
Kept lowest scoring 4 out of 6 structures
Scores range from 0.0 to 6.7
Aligned ensemble to itself after 2 iteration(s)
Projections written to file "/tmp/exprose_out/pcs/pcs.tsv"
Projections written to file "/tmp/exprose_out/pcs/pcs_input.tsv"
Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs/out.pdb"
Wrote ensemble scores to file "/tmp/exprose_out/spe_scores.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_1.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_2.tsv"
Plotted principal components to file(s) "/tmp/exprose_out/pcs/pc_x_y.png"
Plotted RMSFs to file "/tmp/exprose_out/rmsfs.png"
n_to_write is larger than the number of eigenvectors - proceeding with all possible eigenvectors
PyMol script to view principal components written to file(s) "/tmp/exprose_out/pymol/view_pc_x.pml"
Done
-- ExProSE --
Arguments:
i1 - /home/pkgeval/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CLL_H.pdb
d1 - /home/pkgeval/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CLL.dssp
i2 - /home/pkgeval/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR_H.pdb
d2 - /home/pkgeval/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR.dssp
out_dir - /tmp/exprose_out
n_strucs - 4
tolerance_weight - 0.3
other_ratio - 20.0
extra_pdbs - /home/pkgeval/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_1.pdb, /home/pkgeval/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_2.pdb
mod_path - /home/pkgeval/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR_pocket_points.pdb
n_mods - 1
Making output directory "/tmp/exprose_out"
Proceeding with two structures
Read 1367 atoms from PDB file
Read 1336 atoms from PDB file
Read 144 residues from DSSP file
Read 141 residues from DSSP file
Found interactions:
Covalently bonded - 1313
1-3 system - 1868
Same ring system - 35
Side-chain restricted 1-4 - 116
Omega 1-4 - 540
Tight phi/psi 1-4 - 692
Loose phi/psi 1-4 - 157
Other phi/psi 1-4 - 195
Other 1-4 - 589
Secondary structure - 3684
Salt bridge - 42
H bond - 230
Tight hydrophobic - 817
Loose hydrophobic - 878
Other pairs - 835795
Found distance constraints from single structure
Found interactions:
Covalently bonded - 1313
1-3 system - 1868
Same ring system - 35
Side-chain restricted 1-4 - 116
Omega 1-4 - 540
Tight phi/psi 1-4 - 540
Loose phi/psi 1-4 - 206
Other phi/psi 1-4 - 298
Other 1-4 - 589
Secondary structure - 2544
Salt bridge - 63
H bond - 233
Tight hydrophobic - 773
Loose hydrophobic - 1055
Other pairs - 836778
Found distance constraints from single structure
Found combined distance constraints from two structures
Will generate 6 structures and keep best-scoring 4
Progress: 17%|████████▍ | ETA: 0:00:28Progress: 33%|████████████████▋ | ETA: 0:00:22Progress: 50%|█████████████████████████ | ETA: 0:00:17Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:12Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:06Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:35
Kept lowest scoring 4 out of 6 structures
Scores range from 1.3 to 48.4
Read 1111 pocket points from pocket points PDB file
Generating ensemble with modulator 1 of 1
Found 3095 interactions between the modulator and the protein
Will generate 6 structures and keep best-scoring 4
Progress: 17%|████████▍ | ETA: 0:00:29Progress: 33%|████████████████▋ | ETA: 0:00:26Progress: 50%|█████████████████████████ | ETA: 0:00:20Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:13Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:07Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:39
Kept lowest scoring 4 out of 6 structures
Scores range from 0.5 to 14.3
Aligned ensemble to itself after 6 iteration(s)
Projections written to file "/tmp/exprose_out/pcs/pcs.tsv"
Projections written to file "/tmp/exprose_out/pcs/pcs_input_1.tsv"
Projections written to file "/tmp/exprose_out/pcs/pcs_input_2.tsv"
Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs/out.pdb"
Wrote ensemble scores to file "/tmp/exprose_out/spe_scores.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_1.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_2.tsv"
Plotted principal components to file(s) "/tmp/exprose_out/pcs/pc_x_y.png"
Plotted RMSFs to file "/tmp/exprose_out/rmsfs.png"
Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs_mod_1/out.pdb"
Projections written to file "/tmp/exprose_out/mod_1/pcs.tsv"
Wrote ensemble scores to file "/tmp/exprose_out/mod_1/spe_scores.tsv"
Plotted principal components to file(s) "/tmp/exprose_out/mod_1/pc_x_y.png"
Aligned ensemble to itself after 2 iteration(s)
Plotted RMSFs to file "/tmp/exprose_out/mod_1/rmsfs.png"
n_to_write is larger than the number of eigenvectors - proceeding with all possible eigenvectors
PyMol script to view principal components written to file(s) "/tmp/exprose_out/pymol/view_pc_x.pml"
Done
-- ExProSE --
Arguments:
i1 - /home/pkgeval/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR_H.pdb
d1 - /home/pkgeval/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR.dssp
i2 - nothing
d2 - nothing
out_dir - /tmp/exprose_out
n_strucs - 4
tolerance_weight - 0.3
other_ratio - 20.0
extra_pdbs - /home/pkgeval/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_1.pdb, /home/pkgeval/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CFF_2.pdb
mod_path - /home/pkgeval/.julia/packages/ProteinEnsembles/pvqsO/test/test_files/1CTR_pocket_points.pdb
n_mods - 1
Making output directory "/tmp/exprose_out"
Proceeding with one structure
Read 1336 atoms from PDB file
Read 141 residues from DSSP file
Found interactions:
Covalently bonded - 1347
1-3 system - 1919
Same ring system - 35
Side-chain restricted 1-4 - 120
Omega 1-4 - 552
Tight phi/psi 1-4 - 540
Loose phi/psi 1-4 - 232
Other phi/psi 1-4 - 298
Other 1-4 - 608
Secondary structure - 2544
Salt bridge - 84
H bond - 239
Tight hydrophobic - 789
Loose hydrophobic - 1084
Other pairs - 881389
Found distance constraints from single structure
Will generate 6 structures and keep best-scoring 4
Progress: 17%|████████▍ | ETA: 0:00:28Progress: 33%|████████████████▋ | ETA: 0:00:22Progress: 50%|█████████████████████████ | ETA: 0:00:17Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:11Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:06Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:34
Kept lowest scoring 4 out of 6 structures
Scores range from 0.0 to 0.3
Read 1111 pocket points from pocket points PDB file
Generating ensemble with modulator 1 of 1
Found 3305 interactions between the modulator and the protein
Will generate 6 structures and keep best-scoring 4
Progress: 17%|████████▍ | ETA: 0:00:35Progress: 33%|████████████████▋ | ETA: 0:00:26Progress: 50%|█████████████████████████ | ETA: 0:00:19Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:13Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:06Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:37
Kept lowest scoring 4 out of 6 structures
Scores range from 0.0 to 2.9
Aligned ensemble to itself after 2 iteration(s)
Projections written to file "/tmp/exprose_out/pcs/pcs.tsv"
Projections written to file "/tmp/exprose_out/pcs/pcs_input.tsv"
Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs/out.pdb"
Wrote ensemble scores to file "/tmp/exprose_out/spe_scores.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_1.tsv"
Read 2634 atoms from PDB file
Projections written to file "/tmp/exprose_out/pcs/pcs_ex_2.tsv"
Plotted principal components to file(s) "/tmp/exprose_out/pcs/pc_x_y.png"
Plotted RMSFs to file "/tmp/exprose_out/rmsfs.png"
Wrote ensemble to PDB file(s) with prefix "/tmp/exprose_out/pdbs_mod_1/out.pdb"
Projections written to file "/tmp/exprose_out/mod_1/pcs.tsv"
Wrote ensemble scores to file "/tmp/exprose_out/mod_1/spe_scores.tsv"
Plotted principal components to file(s) "/tmp/exprose_out/mod_1/pc_x_y.png"
Aligned ensemble to itself after 2 iteration(s)
Plotted RMSFs to file "/tmp/exprose_out/mod_1/rmsfs.png"
n_to_write is larger than the number of eigenvectors - proceeding with all possible eigenvectors
PyMol script to view principal components written to file(s) "/tmp/exprose_out/pymol/view_pc_x.pml"
Done
Test Summary: | Pass Total
Pipeline | 5 5
Parameterisation tests not run; to run these, set run_param_test to true in runtests.jl
Testing ProteinEnsembles tests passed