Package evaluation of ProteinEnsembles on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T19:23:03.742 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.83s ################################################################################ # Installation # Installing ProteinEnsembles... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [186d2b2d] + ProteinEnsembles v0.3.1 Updating `~/.julia/environments/v1.11/Manifest.toml` [621f4979] + AbstractFFTs v1.5.0 [79e6a3ab] + Adapt v4.3.0 [66dad0bd] + AliasTables v1.1.3 [c7e460c6] + ArgParse v1.2.0 [13072b0f] + AxisAlgorithms v1.1.0 [159f3aea] + Cairo v1.1.1 [324d7699] + CategoricalArrays v0.10.8 [d360d2e6] + ChainRulesCore v1.25.1 ⌅ [3da002f7] + ColorTypes v0.11.5 ⌅ [5ae59095] + Colors v0.12.11 [34da2185] + Compat v4.16.0 [a81c6b42] + Compose v0.9.5 [d38c429a] + Contour v0.6.3 ⌅ [7ad07ef1] + CoupledFields v0.2.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.22 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.118 [ffbed154] + DocStringExtensions v0.9.4 [7a1cc6ca] + FFTW v1.8.1 [1a297f60] + FillArrays v1.13.0 [53c48c17] + FixedPointNumbers v0.8.5 [c91e804a] + Gadfly v1.4.0 [a2bd30eb] + Graphics v1.1.3 [42e2da0e] + Grisu v1.0.2 [a1b4810d] + Hexagons v0.2.0 [34004b35] + HypergeometricFunctions v0.3.28 [9b13fd28] + IndirectArrays v1.0.0 [a98d9a8b] + Interpolations v0.15.1 [92d709cd] + IrrationalConstants v0.2.4 [c8e1da08] + IterTools v1.10.0 [692b3bcd] + JLLWrappers v1.7.0 [682c06a0] + JSON v0.21.4 [e5e0dc1b] + Juno v0.8.4 [5ab0869b] + KernelDensity v0.6.9 [4345ca2d] + Loess v0.6.4 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.15 [442fdcdd] + Measures v0.3.2 [e89f7d12] + Media v0.5.0 [e1d29d7a] + Missings v1.2.0 [77ba4419] + NaNMath v1.1.3 [6fe1bfb0] + OffsetArrays v1.16.0 [bac558e1] + OrderedCollections v1.8.0 [90014a1f] + PDMats v0.11.33 [69de0a69] + Parsers v2.8.1 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [92933f4c] + ProgressMeter v1.10.4 [186d2b2d] + ProteinEnsembles v0.3.1 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [c84ed2f1] + Ratios v0.4.5 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.8.0 [992d4aef] + Showoff v1.0.3 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.0 [90137ffa] + StaticArrays v1.9.13 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.0 ⌅ [2913bbd2] + StatsBase v0.33.21 [4c63d2b9] + StatsFuns v1.4.0 [b718987f] + TextWrap v1.0.2 [efce3f68] + WoodburyMatrices v1.0.0 [6e34b625] + Bzip2_jll v1.0.9+0 [83423d85] + Cairo_jll v1.18.4+0 [2e619515] + Expat_jll v2.6.5+0 [f5851436] + FFTW_jll v3.3.11+0 [a3f928ae] + Fontconfig_jll v2.16.0+0 [d7e528f0] + FreeType2_jll v2.13.4+0 [559328eb] + FriBidi_jll v1.0.17+0 [78b55507] + Gettext_jll v0.21.0+0 ⌃ [7746bdde] + Glib_jll v2.82.4+0 [3b182d85] + Graphite2_jll v1.3.15+0 [2e76f6c2] + HarfBuzz_jll v8.5.0+0 [1d5cc7b8] + IntelOpenMP_jll v2025.0.4+0 [1d63c593] + LLVMOpenMP_jll v18.1.7+0 [dd4b983a] + LZO_jll v2.10.3+0 ⌅ [e9f186c6] + Libffi_jll v3.2.2+2 [d4300ac3] + Libgcrypt_jll v1.11.1+0 [7add5ba3] + Libgpg_error_jll v1.51.1+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [4b2f31a3] + Libmount_jll v2.41.0+0 [38a345b3] + Libuuid_jll v2.41.0+0 [856f044c] + MKL_jll v2025.0.1+1 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [36c8627f] + Pango_jll v1.56.1+0 [30392449] + Pixman_jll v0.44.2+0 [f50d1b31] + Rmath_jll v0.5.1+0 [02c8fc9c] + XML2_jll v2.13.6+1 [aed1982a] + XSLT_jll v1.1.43+0 [4f6342f7] + Xorg_libX11_jll v1.8.6+3 [0c0b7dd1] + Xorg_libXau_jll v1.0.12+0 [a3789734] + Xorg_libXdmcp_jll v1.1.5+0 [1082639a] + Xorg_libXext_jll v1.3.6+3 [ea2f1a96] + Xorg_libXrender_jll v0.9.11+1 [14d82f49] + Xorg_libpthread_stubs_jll v0.1.2+0 [c7cfdc94] + Xorg_libxcb_jll v1.17.0+3 [c5fb5394] + Xorg_xtrans_jll v1.6.0+0 [b53b4c65] + libpng_jll v1.6.47+0 [1317d2d5] + oneTBB_jll v2022.0.0+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.6.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.11.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg v1.11.0 [de0858da] + Printf v1.11.0 [9abbd945] + Profile v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [1a1011a3] + SharedArrays v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.11.0 [f489334b] + StyledStrings v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] + LibCURL_jll v8.6.0+0 [e37daf67] + LibGit2_jll v1.7.2+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.6+0 [14a3606d] + MozillaCACerts_jll v2023.12.12 [4536629a] + OpenBLAS_jll v0.3.27+1 [05823500] + OpenLibm_jll v0.8.5+0 [efcefdf7] + PCRE2_jll v10.42.0+1 [bea87d4a] + SuiteSparse_jll v7.7.0+0 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.59.0+0 [3f19e933] + p7zip_jll v17.4.0+2 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Installation completed after 4.74s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 45.09s ################################################################################ # Testing # Testing ProteinEnsembles Status `/tmp/jl_Vepn6P/Project.toml` [c7e460c6] ArgParse v1.2.0 [159f3aea] Cairo v1.1.1 ⌅ [5ae59095] Colors v0.12.11 [c91e804a] Gadfly v1.4.0 [92933f4c] ProgressMeter v1.10.4 [186d2b2d] ProteinEnsembles v0.3.1 [10745b16] Statistics v1.11.1 [37e2e46d] LinearAlgebra v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_Vepn6P/Manifest.toml` [621f4979] AbstractFFTs v1.5.0 [79e6a3ab] Adapt v4.3.0 [66dad0bd] AliasTables v1.1.3 [c7e460c6] ArgParse v1.2.0 [13072b0f] AxisAlgorithms v1.1.0 [159f3aea] Cairo v1.1.1 [324d7699] CategoricalArrays v0.10.8 [d360d2e6] ChainRulesCore v1.25.1 ⌅ [3da002f7] ColorTypes v0.11.5 ⌅ [5ae59095] Colors v0.12.11 [34da2185] Compat v4.16.0 [a81c6b42] Compose v0.9.5 [d38c429a] Contour v0.6.3 ⌅ [7ad07ef1] CoupledFields v0.2.0 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.18.22 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.118 [ffbed154] DocStringExtensions v0.9.4 [7a1cc6ca] FFTW v1.8.1 [1a297f60] FillArrays v1.13.0 [53c48c17] FixedPointNumbers v0.8.5 [c91e804a] Gadfly v1.4.0 [a2bd30eb] Graphics v1.1.3 [42e2da0e] Grisu v1.0.2 [a1b4810d] Hexagons v0.2.0 [34004b35] HypergeometricFunctions v0.3.28 [9b13fd28] IndirectArrays v1.0.0 [a98d9a8b] Interpolations v0.15.1 [92d709cd] IrrationalConstants v0.2.4 [c8e1da08] IterTools v1.10.0 [692b3bcd] JLLWrappers v1.7.0 [682c06a0] JSON v0.21.4 [e5e0dc1b] Juno v0.8.4 [5ab0869b] KernelDensity v0.6.9 [4345ca2d] Loess v0.6.4 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.15 [442fdcdd] Measures v0.3.2 [e89f7d12] Media v0.5.0 [e1d29d7a] Missings v1.2.0 [77ba4419] NaNMath v1.1.3 [6fe1bfb0] OffsetArrays v1.16.0 [bac558e1] OrderedCollections v1.8.0 [90014a1f] PDMats v0.11.33 [69de0a69] Parsers v2.8.1 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [92933f4c] ProgressMeter v1.10.4 [186d2b2d] ProteinEnsembles v0.3.1 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [c84ed2f1] Ratios v0.4.5 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.8.0 [992d4aef] Showoff v1.0.3 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.0 [90137ffa] StaticArrays v1.9.13 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.0 ⌅ [2913bbd2] StatsBase v0.33.21 [4c63d2b9] StatsFuns v1.4.0 [b718987f] TextWrap v1.0.2 [efce3f68] WoodburyMatrices v1.0.0 [6e34b625] Bzip2_jll v1.0.9+0 [83423d85] Cairo_jll v1.18.4+0 [2e619515] Expat_jll v2.6.5+0 [f5851436] FFTW_jll v3.3.11+0 [a3f928ae] Fontconfig_jll v2.16.0+0 [d7e528f0] FreeType2_jll v2.13.4+0 [559328eb] FriBidi_jll v1.0.17+0 [78b55507] Gettext_jll v0.21.0+0 ⌃ [7746bdde] Glib_jll v2.82.4+0 [3b182d85] Graphite2_jll v1.3.15+0 [2e76f6c2] HarfBuzz_jll v8.5.0+0 [1d5cc7b8] IntelOpenMP_jll v2025.0.4+0 [1d63c593] LLVMOpenMP_jll v18.1.7+0 [dd4b983a] LZO_jll v2.10.3+0 ⌅ [e9f186c6] Libffi_jll v3.2.2+2 [d4300ac3] Libgcrypt_jll v1.11.1+0 [7add5ba3] Libgpg_error_jll v1.51.1+0 [94ce4f54] Libiconv_jll v1.18.0+0 [4b2f31a3] Libmount_jll v2.41.0+0 [38a345b3] Libuuid_jll v2.41.0+0 [856f044c] MKL_jll v2025.0.1+1 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [36c8627f] Pango_jll v1.56.1+0 [30392449] Pixman_jll v0.44.2+0 [f50d1b31] Rmath_jll v0.5.1+0 [02c8fc9c] XML2_jll v2.13.6+1 [aed1982a] XSLT_jll v1.1.43+0 [4f6342f7] Xorg_libX11_jll v1.8.6+3 [0c0b7dd1] Xorg_libXau_jll v1.0.12+0 [a3789734] Xorg_libXdmcp_jll v1.1.5+0 [1082639a] Xorg_libXext_jll v1.3.6+3 [ea2f1a96] Xorg_libXrender_jll v0.9.11+1 [14d82f49] Xorg_libpthread_stubs_jll v0.1.2+0 [c7cfdc94] Xorg_libxcb_jll v1.17.0+3 [c5fb5394] Xorg_xtrans_jll v1.6.0+0 [b53b4c65] libpng_jll v1.6.47+0 [1317d2d5] oneTBB_jll v2022.0.0+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.6.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [4af54fe1] LazyArtifacts v1.11.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.11.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.2.0 [44cfe95a] Pkg v1.11.0 [de0858da] Printf v1.11.0 [9abbd945] Profile v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [1a1011a3] SharedArrays v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.11.0 [f489334b] StyledStrings v1.11.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] LibCURL_jll v8.6.0+0 [e37daf67] LibGit2_jll v1.7.2+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.6+0 [14a3606d] MozillaCACerts_jll v2023.12.12 [4536629a] OpenBLAS_jll v0.3.27+1 [05823500] OpenLibm_jll v0.8.5+0 [efcefdf7] PCRE2_jll v10.42.0+1 [bea87d4a] SuiteSparse_jll v7.7.0+0 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.59.0+0 [3f19e933] p7zip_jll v17.4.0+2 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... WARNING: Method definition PNG(Any...) in module Compose at /home/pkgeval/.julia/packages/Compose/9ma5l/src/Compose.jl:138 overwritten at /home/pkgeval/.julia/packages/Compose/9ma5l/src/cairo_backends.jl:208. WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(Compose.PNG), Any...) in module Compose at /home/pkgeval/.julia/packages/Compose/9ma5l/src/Compose.jl:138 overwritten at /home/pkgeval/.julia/packages/Compose/9ma5l/src/cairo_backends.jl:208. WARNING: Method definition PDF(Any...) in module Compose at /home/pkgeval/.julia/packages/Compose/9ma5l/src/Compose.jl:138 overwritten at /home/pkgeval/.julia/packages/Compose/9ma5l/src/cairo_backends.jl:208. WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(Compose.PDF), Any...) in module Compose at /home/pkgeval/.julia/packages/Compose/9ma5l/src/Compose.jl:138 overwritten at /home/pkgeval/.julia/packages/Compose/9ma5l/src/cairo_backends.jl:208. WARNING: Method definition PS(Any...) in module Compose at /home/pkgeval/.julia/packages/Compose/9ma5l/src/Compose.jl:138 overwritten at /home/pkgeval/.julia/packages/Compose/9ma5l/src/cairo_backends.jl:208. WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(Compose.PS), Any...) in module Compose at /home/pkgeval/.julia/packages/Compose/9ma5l/src/Compose.jl:138 overwritten at /home/pkgeval/.julia/packages/Compose/9ma5l/src/cairo_backends.jl:208. Test Summary: | Pass Total Time Types | 8 8 1.8s Could not find element for atom with name X Test Summary: | Pass Total Time Atoms | 26 26 1.8s 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 Time IO | 31 31 4.3s 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 Time Interactions | 41 41 12.6s Kept lowest scoring 2 out of 4 structures Scores range from 10.0 to 20.0 Test Summary: | Pass Total Time Generate | 12 12 7.0s Test Summary: | Pass Total Time Align | 11 11 20.0s 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 Time PCA | 10 10 6.4s 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_BMdO3SPKDw" Test Summary: | Pass Total Time Perturb | 9 9 2.9s -- ExProSE -- Arguments: i1 - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CLL_H.pdb d1 - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CLL.dssp i2 - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CTR_H.pdb d2 - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/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/TB23o/test/test_files/1CFF_1.pdb, /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/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 ┌ Warning: `Progress(n::Integer, dt::Real, desc::AbstractString = "Progress: ", barlen = nothing, color::Symbol = :green, output::IO = stderr; offset::Integer = 0)` is deprecated, use `Progress(n; dt = dt, desc = desc, barlen = barlen, color = color, output = output, offset = offset)` instead. │ caller = ip:0x0 └ @ Core :-1 Progress: 33%|████████████████▋ | ETA: 0:00:20 Progress: 50%|█████████████████████████ | ETA: 0:00:15 Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:10 Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:05 Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:27 Kept lowest scoring 4 out of 6 structures Scores range from 0.3 to 96.4 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" 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/TB23o/test/test_files/1CLL_H.pdb d1 - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/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/TB23o/test/test_files/1CFF_1.pdb, /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/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: 33%|████████████████▋ | ETA: 0:00:22 Progress: 50%|█████████████████████████ | ETA: 0:00:17 Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:11 Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:06 Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:33 Kept lowest scoring 4 out of 6 structures Scores range from 0.0 to 1.7 Aligned ensemble to itself after 3 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/TB23o/test/test_files/1CLL_H.pdb d1 - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CLL.dssp i2 - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CTR_H.pdb d2 - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/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/TB23o/test/test_files/1CFF_1.pdb, /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CFF_2.pdb mod_path - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/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: 33%|████████████████▋ | ETA: 0:00:22 Progress: 50%|█████████████████████████ | ETA: 0:00:16 Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:10 Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:05 Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:31 Kept lowest scoring 4 out of 6 structures Scores range from 0.3 to 4.1 Read 1111 pocket points from pocket points PDB file Generating ensemble with modulator 1 of 1 Found 3125 interactions between the modulator and the protein Will generate 6 structures and keep best-scoring 4 Progress: 33%|████████████████▋ | ETA: 0:00:30 Progress: 50%|█████████████████████████ | ETA: 0:00:24 Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:15 Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:07 Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:42 Kept lowest scoring 4 out of 6 structures Scores range from 2.0 to 143.8 Aligned ensemble to itself after 3 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/TB23o/test/test_files/1CTR_H.pdb d1 - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/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/TB23o/test/test_files/1CFF_1.pdb, /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/test/test_files/1CFF_2.pdb mod_path - /home/pkgeval/.julia/packages/ProteinEnsembles/TB23o/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: 33%|████████████████▋ | ETA: 0:00:23 Progress: 50%|█████████████████████████ | ETA: 0:00:17 Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:12 Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:06 Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:34 Kept lowest scoring 4 out of 6 structures Scores range from 0.0 to 0.2 Read 1111 pocket points from pocket points PDB file Generating ensemble with modulator 1 of 1 Found 3326 interactions between the modulator and the protein Will generate 6 structures and keep best-scoring 4 Progress: 33%|████████████████▋ | ETA: 0:00:25 Progress: 50%|█████████████████████████ | ETA: 0:00:19 Progress: 67%|█████████████████████████████████▍ | ETA: 0:00:13 Progress: 83%|█████████████████████████████████████████▋ | ETA: 0:00:06 Progress: 100%|██████████████████████████████████████████████████| Time: 0:00:38 Kept lowest scoring 4 out of 6 structures Scores range from 0.0 to 2.4 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 Time Pipeline | 5 5 5m45.1s Parameterisation tests not run; to run these, set run_param_test to true in runtests.jl Testing ProteinEnsembles tests passed Testing completed after 425.05s PkgEval succeeded after 512.87s