2026-04-17T14:02:49,668 Created temporary directory: /tmp/pip-ephem-wheel-cache-_oii3f43 2026-04-17T14:02:49,670 Created temporary directory: /tmp/pip-build-tracker-l8h86vs7 2026-04-17T14:02:49,671 Initialized build tracking at /tmp/pip-build-tracker-l8h86vs7 2026-04-17T14:02:49,671 Created build tracker: /tmp/pip-build-tracker-l8h86vs7 2026-04-17T14:02:49,672 Entered build tracker: /tmp/pip-build-tracker-l8h86vs7 2026-04-17T14:02:49,672 Created temporary directory: /tmp/pip-wheel-zifds5f4 2026-04-17T14:02:49,675 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-04-17T14:02:49,678 Created temporary directory: /tmp/pip-ephem-wheel-cache-t5vjpesz 2026-04-17T14:02:49,699 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-17T14:02:49,702 2 location(s) to search for versions of torchref: 2026-04-17T14:02:49,702 * https://pypi.org/simple/torchref/ 2026-04-17T14:02:49,702 * https://www.piwheels.org/simple/torchref/ 2026-04-17T14:02:49,703 Fetching project page and analyzing links: https://pypi.org/simple/torchref/ 2026-04-17T14:02:49,704 Getting page https://pypi.org/simple/torchref/ 2026-04-17T14:02:49,705 Found index url https://pypi.org/simple 2026-04-17T14:02:49,933 Fetched page https://pypi.org/simple/torchref/ as application/vnd.pypi.simple.v1+json 2026-04-17T14:02:49,937 Skipping link: No binaries permitted for torchref: https://files.pythonhosted.org/packages/64/ac/2604e364cc5df69ccdc7f3c9f0cdccaf9c51e96c4d622e64b508ed42d102/torchref-0.3.0-py3-none-any.whl (from https://pypi.org/simple/torchref/) (requires-python:>=3.9) 2026-04-17T14:02:49,938 Found link https://files.pythonhosted.org/packages/73/7f/9c1e4112b5dd16c6712d7a8542a20f84bfd290f42c79dbcc4124a4df4ec9/torchref-0.3.0.tar.gz (from https://pypi.org/simple/torchref/) (requires-python:>=3.9), version: 0.3.0 2026-04-17T14:02:49,939 Skipping link: No binaries permitted for torchref: https://files.pythonhosted.org/packages/2c/60/fa60e785ed08bc2e5a786869b7143e31881874cf9e87a83b7602322bb6e5/torchref-0.3.1-py3-none-any.whl (from https://pypi.org/simple/torchref/) (requires-python:>=3.9) 2026-04-17T14:02:49,940 Found link https://files.pythonhosted.org/packages/70/0e/584b23bda864347754d7b0c9fcced9ee05dc5f7d3424d8cfd74717b6bb2f/torchref-0.3.1.tar.gz (from https://pypi.org/simple/torchref/) (requires-python:>=3.9), version: 0.3.1 2026-04-17T14:02:49,940 Skipping link: No binaries permitted for torchref: https://files.pythonhosted.org/packages/e8/b3/f063b38c335c7b0c625fd7306e6b594e5ff453ab41b33317decaa6feadc3/torchref-0.3.2-py3-none-any.whl (from https://pypi.org/simple/torchref/) (requires-python:>=3.9) 2026-04-17T14:02:49,942 Found link https://files.pythonhosted.org/packages/da/78/277f71170bd394e88380562379e2fe3b292acd3eb6d95ce110671da4ef59/torchref-0.3.2.tar.gz (from https://pypi.org/simple/torchref/) (requires-python:>=3.9), version: 0.3.2 2026-04-17T14:02:49,942 Skipping link: No binaries permitted for torchref: https://files.pythonhosted.org/packages/fb/01/2471acb3667c71a9a0d2a93bdfdb998c35e85eea6487641b27ab99b7d0f0/torchref-0.4.1-py3-none-any.whl (from https://pypi.org/simple/torchref/) (requires-python:>=3.10) 2026-04-17T14:02:49,943 Found link https://files.pythonhosted.org/packages/16/bd/cfbdc266a4fe7c8868b100eda000f82419609e89158bda8524efa51748be/torchref-0.4.1.tar.gz (from https://pypi.org/simple/torchref/) (requires-python:>=3.10), version: 0.4.1 2026-04-17T14:02:49,944 Skipping link: No binaries permitted for torchref: https://files.pythonhosted.org/packages/15/37/ed32c8184a2173783ba9429a9a0b2932172539ba3cb7b23f3ca26dfba1fd/torchref-0.4.2-py3-none-any.whl (from https://pypi.org/simple/torchref/) (requires-python:>=3.10) 2026-04-17T14:02:49,945 Found link https://files.pythonhosted.org/packages/ae/0d/52864d8146269e718c1cb7b47a20f899e4035f19e0ccb7e5d59315f65bb4/torchref-0.4.2.tar.gz (from https://pypi.org/simple/torchref/) (requires-python:>=3.10), version: 0.4.2 2026-04-17T14:02:49,946 Skipping link: No binaries permitted for torchref: https://files.pythonhosted.org/packages/a7/3a/847415e01c63f1d7d71316d541be7464628096ed37f5fc9020d147463263/torchref-0.4.3-py3-none-any.whl (from https://pypi.org/simple/torchref/) (requires-python:>=3.10) 2026-04-17T14:02:49,947 Found link https://files.pythonhosted.org/packages/cc/11/709f9abb6ad3da0752480f1a77de7d3c311393d6193f89d6ce18cc7d5099/torchref-0.4.3.tar.gz (from https://pypi.org/simple/torchref/) (requires-python:>=3.10), version: 0.4.3 2026-04-17T14:02:49,948 Skipping link: No binaries permitted for torchref: https://files.pythonhosted.org/packages/1b/b8/36df377748164e20a46356722963af74331445792bdbf08a0cdf1dbdbbdd/torchref-0.5.0-py3-none-any.whl (from https://pypi.org/simple/torchref/) (requires-python:>=3.10) 2026-04-17T14:02:49,948 Found link https://files.pythonhosted.org/packages/25/f4/c18b875b712da914d708badea4ed1c2312935dc84d561b799c337185cf6e/torchref-0.5.0.tar.gz (from https://pypi.org/simple/torchref/) (requires-python:>=3.10), version: 0.5.0 2026-04-17T14:02:49,949 Fetching project page and analyzing links: https://www.piwheels.org/simple/torchref/ 2026-04-17T14:02:49,950 Getting page https://www.piwheels.org/simple/torchref/ 2026-04-17T14:02:49,951 Found index url https://www.piwheels.org/simple 2026-04-17T14:02:50,124 Fetched page https://www.piwheels.org/simple/torchref/ as text/html 2026-04-17T14:02:50,127 Skipping link: No binaries permitted for torchref: https://archive1.piwheels.org/simple/torchref/torchref-0.4.3-py3-none-any.whl#sha256=3224a4185d64c6f2b269ee377bc5c0f6dacf3a13898fd11e73a727a462a2d878 (from https://www.piwheels.org/simple/torchref/) (requires-python:>=3.10) 2026-04-17T14:02:50,128 Skipping link: No binaries permitted for torchref: https://archive1.piwheels.org/simple/torchref/torchref-0.4.2-py3-none-any.whl#sha256=c4c77a7e34aad8245da2d04a76477bdf30f94ca67cd531f721e4bf47ee67114a (from https://www.piwheels.org/simple/torchref/) (requires-python:>=3.10) 2026-04-17T14:02:50,128 Skipping link: No binaries permitted for torchref: https://archive1.piwheels.org/simple/torchref/torchref-0.4.1-py3-none-any.whl#sha256=51e933f2f0edf7f44aa74d08f32f7530006300c4b6def2437f9257d02b3e175e (from https://www.piwheels.org/simple/torchref/) (requires-python:>=3.10) 2026-04-17T14:02:50,129 Skipping link: No binaries permitted for torchref: https://archive1.piwheels.org/simple/torchref/torchref-0.3.2-py3-none-any.whl#sha256=30e0c5727c1872459a9dcff4416e224ff7486dea2f43a6c20dab66a307492093 (from https://www.piwheels.org/simple/torchref/) (requires-python:>=3.9) 2026-04-17T14:02:50,130 Skipping link: No binaries permitted for torchref: https://archive1.piwheels.org/simple/torchref/torchref-0.3.1-py3-none-any.whl#sha256=25deb48a634dda8c799c2d7c32d9749bf327e976900dbd2a5fedf435ee5e921f (from https://www.piwheels.org/simple/torchref/) (requires-python:>=3.9) 2026-04-17T14:02:50,130 Skipping link: No binaries permitted for torchref: https://archive1.piwheels.org/simple/torchref/torchref-0.3.0-py3-none-any.whl#sha256=3032f506e2c816e7e7638e151ed6e70bf0f6b0213e92f8f790dce96c53c0d65f (from https://www.piwheels.org/simple/torchref/) (requires-python:>=3.9) 2026-04-17T14:02:50,131 Skipping link: not a file: https://www.piwheels.org/simple/torchref/ 2026-04-17T14:02:50,131 Skipping link: not a file: https://pypi.org/simple/torchref/ 2026-04-17T14:02:50,152 Given no hashes to check 1 links for project 'torchref': discarding no candidates 2026-04-17T14:02:50,172 Collecting torchref==0.5.0 2026-04-17T14:02:50,174 Created temporary directory: /tmp/pip-unpack-ut9id95w 2026-04-17T14:02:50,404 Downloading torchref-0.5.0.tar.gz (2.9 MB) 2026-04-17T14:02:51,637 Added torchref==0.5.0 from https://files.pythonhosted.org/packages/25/f4/c18b875b712da914d708badea4ed1c2312935dc84d561b799c337185cf6e/torchref-0.5.0.tar.gz to build tracker '/tmp/pip-build-tracker-l8h86vs7' 2026-04-17T14:02:51,643 Created temporary directory: /tmp/pip-build-env-_kt4zbw2 2026-04-17T14:02:51,648 Installing build dependencies: started 2026-04-17T14:02:51,649 Running command pip subprocess to install build dependencies 2026-04-17T14:02:52,792 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-04-17T14:02:53,220 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-04-17T14:02:53,244 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-17T14:02:55,066 Collecting setuptools>=42 2026-04-17T14:02:55,144 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-04-17T14:02:55,414 Collecting wheel 2026-04-17T14:02:55,430 Using cached https://www.piwheels.org/simple/wheel/wheel-0.46.3-py3-none-any.whl (30 kB) 2026-04-17T14:02:55,619 Collecting packaging>=24.0 2026-04-17T14:02:55,637 Using cached https://www.piwheels.org/simple/packaging/packaging-26.1-py3-none-any.whl (95 kB) 2026-04-17T14:02:58,586 Installing collected packages: setuptools, packaging, wheel 2026-04-17T14:03:02,074 Creating /tmp/pip-build-env-_kt4zbw2/overlay/local/bin 2026-04-17T14:03:02,076 changing mode of /tmp/pip-build-env-_kt4zbw2/overlay/local/bin/wheel to 755 2026-04-17T14:03:02,098 Successfully installed packaging-26.1 setuptools-82.0.1 wheel-0.46.3 2026-04-17T14:03:02,377 Installing build dependencies: finished with status 'done' 2026-04-17T14:03:02,384 Getting requirements to build wheel: started 2026-04-17T14:03:02,385 Running command Getting requirements to build wheel 2026-04-17T14:03:03,104 running egg_info 2026-04-17T14:03:03,109 writing torchref.egg-info/PKG-INFO 2026-04-17T14:03:03,117 writing dependency_links to torchref.egg-info/dependency_links.txt 2026-04-17T14:03:03,119 writing entry points to torchref.egg-info/entry_points.txt 2026-04-17T14:03:03,123 writing requirements to torchref.egg-info/requires.txt 2026-04-17T14:03:03,124 writing top-level names to torchref.egg-info/top_level.txt 2026-04-17T14:03:03,206 reading manifest file 'torchref.egg-info/SOURCES.txt' 2026-04-17T14:03:03,219 adding license file 'LICENSE' 2026-04-17T14:03:03,232 writing manifest file 'torchref.egg-info/SOURCES.txt' 2026-04-17T14:03:03,330 Getting requirements to build wheel: finished with status 'done' 2026-04-17T14:03:03,333 Created temporary directory: /tmp/pip-modern-metadata-0p9h_mmj 2026-04-17T14:03:03,336 Preparing metadata (pyproject.toml): started 2026-04-17T14:03:03,337 Running command Preparing metadata (pyproject.toml) 2026-04-17T14:03:04,032 running dist_info 2026-04-17T14:03:04,042 creating /tmp/pip-modern-metadata-0p9h_mmj/torchref.egg-info 2026-04-17T14:03:04,043 writing /tmp/pip-modern-metadata-0p9h_mmj/torchref.egg-info/PKG-INFO 2026-04-17T14:03:04,051 writing dependency_links to /tmp/pip-modern-metadata-0p9h_mmj/torchref.egg-info/dependency_links.txt 2026-04-17T14:03:04,053 writing entry points to /tmp/pip-modern-metadata-0p9h_mmj/torchref.egg-info/entry_points.txt 2026-04-17T14:03:04,058 writing requirements to /tmp/pip-modern-metadata-0p9h_mmj/torchref.egg-info/requires.txt 2026-04-17T14:03:04,059 writing top-level names to /tmp/pip-modern-metadata-0p9h_mmj/torchref.egg-info/top_level.txt 2026-04-17T14:03:04,061 writing manifest file '/tmp/pip-modern-metadata-0p9h_mmj/torchref.egg-info/SOURCES.txt' 2026-04-17T14:03:04,134 reading manifest file '/tmp/pip-modern-metadata-0p9h_mmj/torchref.egg-info/SOURCES.txt' 2026-04-17T14:03:04,136 adding license file 'LICENSE' 2026-04-17T14:03:04,146 writing manifest file '/tmp/pip-modern-metadata-0p9h_mmj/torchref.egg-info/SOURCES.txt' 2026-04-17T14:03:04,147 creating '/tmp/pip-modern-metadata-0p9h_mmj/torchref-0.5.0.dist-info' 2026-04-17T14:03:04,274 Preparing metadata (pyproject.toml): finished with status 'done' 2026-04-17T14:03:04,279 Source in /tmp/pip-wheel-zifds5f4/torchref_01f9597e754342aeabbe1cad65952bda has version 0.5.0, which satisfies requirement torchref==0.5.0 from https://files.pythonhosted.org/packages/25/f4/c18b875b712da914d708badea4ed1c2312935dc84d561b799c337185cf6e/torchref-0.5.0.tar.gz 2026-04-17T14:03:04,280 Removed torchref==0.5.0 from https://files.pythonhosted.org/packages/25/f4/c18b875b712da914d708badea4ed1c2312935dc84d561b799c337185cf6e/torchref-0.5.0.tar.gz from build tracker '/tmp/pip-build-tracker-l8h86vs7' 2026-04-17T14:03:04,286 Created temporary directory: /tmp/pip-unpack-d8e64hmi 2026-04-17T14:03:04,287 Building wheels for collected packages: torchref 2026-04-17T14:03:04,291 Created temporary directory: /tmp/pip-wheel-rlxf9ge2 2026-04-17T14:03:04,292 Destination directory: /tmp/pip-wheel-rlxf9ge2 2026-04-17T14:03:04,294 Building wheel for torchref (pyproject.toml): started 2026-04-17T14:03:04,295 Running command Building wheel for torchref (pyproject.toml) 2026-04-17T14:03:04,932 running bdist_wheel 2026-04-17T14:03:04,949 running build 2026-04-17T14:03:04,950 running build_py 2026-04-17T14:03:04,956 creating build/lib/torchref 2026-04-17T14:03:04,958 copying torchref/__init__.py -> build/lib/torchref 2026-04-17T14:03:04,960 copying torchref/config.py -> build/lib/torchref 2026-04-17T14:03:04,962 copying torchref/_bootstrap.py -> build/lib/torchref 2026-04-17T14:03:04,964 creating build/lib/torchref/maps 2026-04-17T14:03:04,965 copying torchref/maps/__init__.py -> build/lib/torchref/maps 2026-04-17T14:03:04,967 copying torchref/maps/difference_map.py -> build/lib/torchref/maps 2026-04-17T14:03:04,969 copying torchref/maps/map.py -> build/lib/torchref/maps 2026-04-17T14:03:04,972 creating build/lib/torchref/utils 2026-04-17T14:03:04,973 copying torchref/utils/debug_utils.py -> build/lib/torchref/utils 2026-04-17T14:03:04,975 copying torchref/utils/__init__.py -> build/lib/torchref/utils 2026-04-17T14:03:04,977 copying torchref/utils/gradnorm.py -> build/lib/torchref/utils 2026-04-17T14:03:04,979 copying torchref/utils/serialization.py -> build/lib/torchref/utils 2026-04-17T14:03:04,981 copying torchref/utils/loss_validation.py -> build/lib/torchref/utils 2026-04-17T14:03:04,983 copying torchref/utils/hyperparameters.py -> build/lib/torchref/utils 2026-04-17T14:03:04,986 copying torchref/utils/stats.py -> build/lib/torchref/utils 2026-04-17T14:03:04,988 copying torchref/utils/caching.py -> build/lib/torchref/utils 2026-04-17T14:03:04,990 copying torchref/utils/autograd_introspection.py -> build/lib/torchref/utils 2026-04-17T14:03:04,993 copying torchref/utils/device_mixin.py -> build/lib/torchref/utils 2026-04-17T14:03:04,995 copying torchref/utils/timing.py -> build/lib/torchref/utils 2026-04-17T14:03:04,997 copying torchref/utils/pse.py -> build/lib/torchref/utils 2026-04-17T14:03:04,999 copying torchref/utils/utils.py -> build/lib/torchref/utils 2026-04-17T14:03:05,003 creating build/lib/torchref/base 2026-04-17T14:03:05,004 copying torchref/base/get_scattering_factor_torch.py -> build/lib/torchref/base 2026-04-17T14:03:05,007 copying torchref/base/__init__.py -> build/lib/torchref/base 2026-04-17T14:03:05,010 copying torchref/base/french_wilson.py -> build/lib/torchref/base 2026-04-17T14:03:05,013 copying torchref/base/math_numpy.py -> build/lib/torchref/base 2026-04-17T14:03:05,015 copying torchref/base/math_torch.py -> build/lib/torchref/base 2026-04-17T14:03:05,018 copying torchref/base/CCTBX_related.py -> build/lib/torchref/base 2026-04-17T14:03:05,020 creating build/lib/torchref/cli 2026-04-17T14:03:05,021 copying torchref/cli/__init__.py -> build/lib/torchref/cli 2026-04-17T14:03:05,023 copying torchref/cli/_common.py -> build/lib/torchref/cli 2026-04-17T14:03:05,026 copying torchref/cli/validate_ded.py -> build/lib/torchref/cli 2026-04-17T14:03:05,029 copying torchref/cli/phased_difference_map.py -> build/lib/torchref/cli 2026-04-17T14:03:05,031 copying torchref/cli/collection_difference_refine.py -> build/lib/torchref/cli 2026-04-17T14:03:05,034 copying torchref/cli/add_metadata.py -> build/lib/torchref/cli 2026-04-17T14:03:05,036 copying torchref/cli/strip_altlocs.py -> build/lib/torchref/cli 2026-04-17T14:03:05,038 copying torchref/cli/refine.py -> build/lib/torchref/cli 2026-04-17T14:03:05,040 copying torchref/cli/mtz2map.py -> build/lib/torchref/cli 2026-04-17T14:03:05,043 creating build/lib/torchref/alignment 2026-04-17T14:03:05,044 copying torchref/alignment/pipeline.py -> build/lib/torchref/alignment 2026-04-17T14:03:05,047 copying torchref/alignment/sampling.py -> build/lib/torchref/alignment 2026-04-17T14:03:05,049 copying torchref/alignment/jax_subpixel_peaks.py -> build/lib/torchref/alignment 2026-04-17T14:03:05,051 copying torchref/alignment/clashscore.py -> build/lib/torchref/alignment 2026-04-17T14:03:05,053 copying torchref/alignment/rigid_body.py -> build/lib/torchref/alignment 2026-04-17T14:03:05,056 copying torchref/alignment/__init__.py -> build/lib/torchref/alignment 2026-04-17T14:03:05,058 copying torchref/alignment/ball_transform.py -> build/lib/torchref/alignment 2026-04-17T14:03:05,061 copying torchref/alignment/translation.py -> build/lib/torchref/alignment 2026-04-17T14:03:05,063 copying torchref/alignment/distributions.py -> build/lib/torchref/alignment 2026-04-17T14:03:05,065 copying torchref/alignment/transform.py -> build/lib/torchref/alignment 2026-04-17T14:03:05,069 creating build/lib/torchref/io 2026-04-17T14:03:05,070 copying torchref/io/metadata.py -> build/lib/torchref/io 2026-04-17T14:03:05,072 copying torchref/io/ihm.py -> build/lib/torchref/io 2026-04-17T14:03:05,075 copying torchref/io/mtz.py -> build/lib/torchref/io 2026-04-17T14:03:05,078 copying torchref/io/__init__.py -> build/lib/torchref/io 2026-04-17T14:03:05,079 copying torchref/io/ihm_mapping.py -> build/lib/torchref/io 2026-04-17T14:03:05,082 copying torchref/io/data_router.py -> build/lib/torchref/io 2026-04-17T14:03:05,084 copying torchref/io/pdb.py -> build/lib/torchref/io 2026-04-17T14:03:05,087 copying torchref/io/cif_readers.py -> build/lib/torchref/io 2026-04-17T14:03:05,090 copying torchref/io/cif.py -> build/lib/torchref/io 2026-04-17T14:03:05,093 creating build/lib/torchref/refinement 2026-04-17T14:03:05,094 copying torchref/refinement/__init__.py -> build/lib/torchref/refinement 2026-04-17T14:03:05,096 copying torchref/refinement/base_refinement.py -> build/lib/torchref/refinement 2026-04-17T14:03:05,099 copying torchref/refinement/loss_state.py -> build/lib/torchref/refinement 2026-04-17T14:03:05,102 copying torchref/refinement/lbfgs_refinement.py -> build/lib/torchref/refinement 2026-04-17T14:03:05,104 copying torchref/refinement/logger.py -> build/lib/torchref/refinement 2026-04-17T14:03:05,107 creating build/lib/torchref/scaling 2026-04-17T14:03:05,108 copying torchref/scaling/scaler_base.py -> build/lib/torchref/scaling 2026-04-17T14:03:05,111 copying torchref/scaling/__init__.py -> build/lib/torchref/scaling 2026-04-17T14:03:05,113 copying torchref/scaling/solvent.py -> build/lib/torchref/scaling 2026-04-17T14:03:05,116 copying torchref/scaling/scaler.py -> build/lib/torchref/scaling 2026-04-17T14:03:05,118 copying torchref/scaling/collection_scaler.py -> build/lib/torchref/scaling 2026-04-17T14:03:05,121 creating build/lib/torchref/model 2026-04-17T14:03:05,122 copying torchref/model/closed_segmented_internal_coordinates.py -> build/lib/torchref/model 2026-04-17T14:03:05,126 copying torchref/model/__init__.py -> build/lib/torchref/model 2026-04-17T14:03:05,128 copying torchref/model/sf_ds.py -> build/lib/torchref/model 2026-04-17T14:03:05,131 copying torchref/model/model_ft.py -> build/lib/torchref/model 2026-04-17T14:03:05,134 copying torchref/model/segmented_internal_coordinates.py -> build/lib/torchref/model 2026-04-17T14:03:05,137 copying torchref/model/parameter_wrappers.py -> build/lib/torchref/model 2026-04-17T14:03:05,141 copying torchref/model/internal_coordinates.py -> build/lib/torchref/model 2026-04-17T14:03:05,144 copying torchref/model/model_collection.py -> build/lib/torchref/model 2026-04-17T14:03:05,147 copying torchref/model/model.py -> build/lib/torchref/model 2026-04-17T14:03:05,151 copying torchref/model/sf_fft.py -> build/lib/torchref/model 2026-04-17T14:03:05,153 copying torchref/model/mixed_model.py -> build/lib/torchref/model 2026-04-17T14:03:05,156 creating build/lib/torchref/restraints 2026-04-17T14:03:05,157 copying torchref/restraints/ramachandran.py -> build/lib/torchref/restraints 2026-04-17T14:03:05,159 copying torchref/restraints/builders_numba.py -> build/lib/torchref/restraints 2026-04-17T14:03:05,162 copying torchref/restraints/restraints_helper.py -> build/lib/torchref/restraints 2026-04-17T14:03:05,165 copying torchref/restraints/__init__.py -> build/lib/torchref/restraints 2026-04-17T14:03:05,166 copying torchref/restraints/library.py -> build/lib/torchref/restraints 2026-04-17T14:03:05,169 copying torchref/restraints/hydrogen_topology.py -> build/lib/torchref/restraints 2026-04-17T14:03:05,171 copying torchref/restraints/builders_fast.py -> build/lib/torchref/restraints 2026-04-17T14:03:05,175 copying torchref/restraints/restraints.py -> build/lib/torchref/restraints 2026-04-17T14:03:05,179 copying torchref/restraints/neighbor_search.py -> build/lib/torchref/restraints 2026-04-17T14:03:05,182 copying torchref/restraints/builders.py -> build/lib/torchref/restraints 2026-04-17T14:03:05,185 creating build/lib/torchref/kinetic 2026-04-17T14:03:05,186 copying torchref/kinetic/refinement.py -> build/lib/torchref/kinetic 2026-04-17T14:03:05,189 copying torchref/kinetic/__init__.py -> build/lib/torchref/kinetic 2026-04-17T14:03:05,191 copying torchref/kinetic/occupancies.py -> build/lib/torchref/kinetic 2026-04-17T14:03:05,193 copying torchref/kinetic/kinetics.py -> build/lib/torchref/kinetic 2026-04-17T14:03:05,196 copying torchref/kinetic/targets.py -> build/lib/torchref/kinetic 2026-04-17T14:03:05,199 creating build/lib/torchref/symmetry 2026-04-17T14:03:05,200 copying torchref/symmetry/spacegroup.py -> build/lib/torchref/symmetry 2026-04-17T14:03:05,203 copying torchref/symmetry/__init__.py -> build/lib/torchref/symmetry 2026-04-17T14:03:05,205 copying torchref/symmetry/symmetry.py -> build/lib/torchref/symmetry 2026-04-17T14:03:05,206 copying torchref/symmetry/cell.py -> build/lib/torchref/symmetry 2026-04-17T14:03:05,209 copying torchref/symmetry/reciprocal_symmetry.py -> build/lib/torchref/symmetry 2026-04-17T14:03:05,212 copying torchref/symmetry/grid_utils.py -> build/lib/torchref/symmetry 2026-04-17T14:03:05,214 copying torchref/symmetry/map_symmetry_interpolation.py -> build/lib/torchref/symmetry 2026-04-17T14:03:05,217 copying torchref/symmetry/map_symmetry.py -> build/lib/torchref/symmetry 2026-04-17T14:03:05,219 creating build/lib/torchref/scripts 2026-04-17T14:03:05,220 copying torchref/scripts/__init__.py -> build/lib/torchref/scripts 2026-04-17T14:03:05,222 copying torchref/scripts/generate_scattering_table.py -> build/lib/torchref/scripts 2026-04-17T14:03:05,225 creating build/lib/torchref/base/fourier 2026-04-17T14:03:05,226 copying torchref/base/fourier/fft.py -> build/lib/torchref/base/fourier 2026-04-17T14:03:05,228 copying torchref/base/fourier/__init__.py -> build/lib/torchref/base/fourier 2026-04-17T14:03:05,230 copying torchref/base/fourier/grid.py -> build/lib/torchref/base/fourier 2026-04-17T14:03:05,232 creating build/lib/torchref/base/scattering 2026-04-17T14:03:05,233 copying torchref/base/scattering/scattering_table.py -> build/lib/torchref/base/scattering 2026-04-17T14:03:05,236 copying torchref/base/scattering/__init__.py -> build/lib/torchref/base/scattering 2026-04-17T14:03:05,238 copying torchref/base/scattering/itc92.py -> build/lib/torchref/base/scattering 2026-04-17T14:03:05,240 copying torchref/base/scattering/anomalous_table.py -> build/lib/torchref/base/scattering 2026-04-17T14:03:05,242 creating build/lib/torchref/base/chain_closure 2026-04-17T14:03:05,243 copying torchref/base/chain_closure/closure.py -> build/lib/torchref/base/chain_closure 2026-04-17T14:03:05,246 copying torchref/base/chain_closure/__init__.py -> build/lib/torchref/base/chain_closure 2026-04-17T14:03:05,248 copying torchref/base/chain_closure/backbone_utils.py -> build/lib/torchref/base/chain_closure 2026-04-17T14:03:05,250 creating build/lib/torchref/base/electron_density 2026-04-17T14:03:05,251 copying torchref/base/electron_density/__init__.py -> build/lib/torchref/base/electron_density 2026-04-17T14:03:05,253 copying torchref/base/electron_density/solvent_mask.py -> build/lib/torchref/base/electron_density 2026-04-17T14:03:05,255 copying torchref/base/electron_density/main.py -> build/lib/torchref/base/electron_density 2026-04-17T14:03:05,258 copying torchref/base/electron_density/voxel_utils.py -> build/lib/torchref/base/electron_density 2026-04-17T14:03:05,260 copying torchref/base/electron_density/map_building.py -> build/lib/torchref/base/electron_density 2026-04-17T14:03:05,263 creating build/lib/torchref/base/alignment 2026-04-17T14:03:05,264 copying torchref/base/alignment/__init__.py -> build/lib/torchref/base/alignment 2026-04-17T14:03:05,266 copying torchref/base/alignment/scoring.py -> build/lib/torchref/base/alignment 2026-04-17T14:03:05,268 copying torchref/base/alignment/rotation.py -> build/lib/torchref/base/alignment 2026-04-17T14:03:05,270 copying torchref/base/alignment/normalization.py -> build/lib/torchref/base/alignment 2026-04-17T14:03:05,272 copying torchref/base/alignment/superposition.py -> build/lib/torchref/base/alignment 2026-04-17T14:03:05,275 creating build/lib/torchref/base/kernels 2026-04-17T14:03:05,276 copying torchref/base/kernels/separable_triton_kernel.py -> build/lib/torchref/base/kernels 2026-04-17T14:03:05,279 copying torchref/base/kernels/triton_kernel.py -> build/lib/torchref/base/kernels 2026-04-17T14:03:05,281 copying torchref/base/kernels/__init__.py -> build/lib/torchref/base/kernels 2026-04-17T14:03:05,283 copying torchref/base/kernels/cpu_scatter.py -> build/lib/torchref/base/kernels 2026-04-17T14:03:05,285 copying torchref/base/kernels/jit_kernel_vectorized_add_to_map.py -> build/lib/torchref/base/kernels 2026-04-17T14:03:05,288 copying torchref/base/kernels/optimized_ops.py -> build/lib/torchref/base/kernels 2026-04-17T14:03:05,291 creating build/lib/torchref/base/reciprocal 2026-04-17T14:03:05,292 copying torchref/base/reciprocal/__init__.py -> build/lib/torchref/base/reciprocal 2026-04-17T14:03:05,294 copying torchref/base/reciprocal/symmetry.py -> build/lib/torchref/base/reciprocal 2026-04-17T14:03:05,296 copying torchref/base/reciprocal/interpolation.py -> build/lib/torchref/base/reciprocal 2026-04-17T14:03:05,299 copying torchref/base/reciprocal/basis.py -> build/lib/torchref/base/reciprocal 2026-04-17T14:03:05,301 copying torchref/base/reciprocal/grid_operations.py -> build/lib/torchref/base/reciprocal 2026-04-17T14:03:05,303 copying torchref/base/reciprocal/hkl.py -> build/lib/torchref/base/reciprocal 2026-04-17T14:03:05,305 creating build/lib/torchref/base/metrics 2026-04-17T14:03:05,306 copying torchref/base/metrics/__init__.py -> build/lib/torchref/base/metrics 2026-04-17T14:03:05,308 copying torchref/base/metrics/rfactor.py -> build/lib/torchref/base/metrics 2026-04-17T14:03:05,310 copying torchref/base/metrics/loss.py -> build/lib/torchref/base/metrics 2026-04-17T14:03:05,313 creating build/lib/torchref/base/coordinates 2026-04-17T14:03:05,314 copying torchref/base/coordinates/periodic_boundary.py -> build/lib/torchref/base/coordinates 2026-04-17T14:03:05,316 copying torchref/base/coordinates/__init__.py -> build/lib/torchref/base/coordinates 2026-04-17T14:03:05,318 copying torchref/base/coordinates/transforms_torch.py -> build/lib/torchref/base/coordinates 2026-04-17T14:03:05,320 copying torchref/base/coordinates/transforms_numpy.py -> build/lib/torchref/base/coordinates 2026-04-17T14:03:05,322 creating build/lib/torchref/base/direct_summation 2026-04-17T14:03:05,323 copying torchref/base/direct_summation/isotropic.py -> build/lib/torchref/base/direct_summation 2026-04-17T14:03:05,326 copying torchref/base/direct_summation/__init__.py -> build/lib/torchref/base/direct_summation 2026-04-17T14:03:05,327 copying torchref/base/direct_summation/corrections.py -> build/lib/torchref/base/direct_summation 2026-04-17T14:03:05,329 copying torchref/base/direct_summation/anisotropic.py -> build/lib/torchref/base/direct_summation 2026-04-17T14:03:05,337 creating build/lib/torchref/io/datasets 2026-04-17T14:03:05,338 copying torchref/io/datasets/__init__.py -> build/lib/torchref/io/datasets 2026-04-17T14:03:05,339 copying torchref/io/datasets/fcalc_data.py -> build/lib/torchref/io/datasets 2026-04-17T14:03:05,342 copying torchref/io/datasets/base.py -> build/lib/torchref/io/datasets 2026-04-17T14:03:05,344 copying torchref/io/datasets/reflection_data.py -> build/lib/torchref/io/datasets 2026-04-17T14:03:05,348 copying torchref/io/datasets/collection.py -> build/lib/torchref/io/datasets 2026-04-17T14:03:05,351 creating build/lib/torchref/refinement/targets 2026-04-17T14:03:05,352 copying torchref/refinement/targets/forcefield_target.py -> build/lib/torchref/refinement/targets 2026-04-17T14:03:05,354 copying torchref/refinement/targets/realspace.py -> build/lib/torchref/refinement/targets 2026-04-17T14:03:05,356 copying torchref/refinement/targets/__init__.py -> build/lib/torchref/refinement/targets 2026-04-17T14:03:05,358 copying torchref/refinement/targets/base.py -> build/lib/torchref/refinement/targets 2026-04-17T14:03:05,361 copying torchref/refinement/targets/difference.py -> build/lib/torchref/refinement/targets 2026-04-17T14:03:05,364 copying torchref/refinement/targets/sampled_ml_phase_target.py -> build/lib/torchref/refinement/targets 2026-04-17T14:03:05,366 copying torchref/refinement/targets/similarity.py -> build/lib/torchref/refinement/targets 2026-04-17T14:03:05,368 copying torchref/refinement/targets/occupancy_floor_diagnostic.py -> build/lib/torchref/refinement/targets 2026-04-17T14:03:05,371 copying torchref/refinement/targets/amber_target.py -> build/lib/torchref/refinement/targets 2026-04-17T14:03:05,374 copying torchref/refinement/targets/combined.py -> build/lib/torchref/refinement/targets 2026-04-17T14:03:05,377 creating build/lib/torchref/refinement/weighting 2026-04-17T14:03:05,378 copying torchref/refinement/weighting/__init__.py -> build/lib/torchref/refinement/weighting 2026-04-17T14:03:05,380 copying torchref/refinement/weighting/es_policy_training.py -> build/lib/torchref/refinement/weighting 2026-04-17T14:03:05,382 copying torchref/refinement/weighting/policy_weighting.py -> build/lib/torchref/refinement/weighting 2026-04-17T14:03:05,385 copying torchref/refinement/weighting/base_weighting.py -> build/lib/torchref/refinement/weighting 2026-04-17T14:03:05,386 copying torchref/refinement/weighting/random_weighting.py -> build/lib/torchref/refinement/weighting 2026-04-17T14:03:05,389 copying torchref/refinement/weighting/component_weighting.py -> build/lib/torchref/refinement/weighting 2026-04-17T14:03:05,392 creating build/lib/torchref/refinement/optimizers 2026-04-17T14:03:05,393 copying torchref/refinement/optimizers/exploratory_lbfgs.py -> build/lib/torchref/refinement/optimizers 2026-04-17T14:03:05,396 copying torchref/refinement/optimizers/__init__.py -> build/lib/torchref/refinement/optimizers 2026-04-17T14:03:05,398 copying torchref/refinement/optimizers/internal_coord_sa.py -> build/lib/torchref/refinement/optimizers 2026-04-17T14:03:05,401 copying torchref/refinement/optimizers/momentum_sa.py -> build/lib/torchref/refinement/optimizers 2026-04-17T14:03:05,402 copying torchref/refinement/optimizers/langevin_sa.py -> build/lib/torchref/refinement/optimizers 2026-04-17T14:03:05,405 copying torchref/refinement/optimizers/adam_noise.py -> build/lib/torchref/refinement/optimizers 2026-04-17T14:03:05,407 copying torchref/refinement/optimizers/simulated_annealing.py -> build/lib/torchref/refinement/optimizers 2026-04-17T14:03:05,410 creating build/lib/torchref/refinement/targets/adp 2026-04-17T14:03:05,410 copying torchref/refinement/targets/adp/rigid_bond.py -> build/lib/torchref/refinement/targets/adp 2026-04-17T14:03:05,413 copying torchref/refinement/targets/adp/entropy.py -> build/lib/torchref/refinement/targets/adp 2026-04-17T14:03:05,414 copying torchref/refinement/targets/adp/__init__.py -> build/lib/torchref/refinement/targets/adp 2026-04-17T14:03:05,416 copying torchref/refinement/targets/adp/base.py -> build/lib/torchref/refinement/targets/adp 2026-04-17T14:03:05,418 copying torchref/refinement/targets/adp/similarity.py -> build/lib/torchref/refinement/targets/adp 2026-04-17T14:03:05,420 copying torchref/refinement/targets/adp/scaler_log_scale.py -> build/lib/torchref/refinement/targets/adp 2026-04-17T14:03:05,421 copying torchref/refinement/targets/adp/scaler_u.py -> build/lib/torchref/refinement/targets/adp 2026-04-17T14:03:05,423 copying torchref/refinement/targets/adp/locality.py -> build/lib/torchref/refinement/targets/adp 2026-04-17T14:03:05,426 creating build/lib/torchref/refinement/targets/geometry 2026-04-17T14:03:05,427 copying torchref/refinement/targets/geometry/ramachandran.py -> build/lib/torchref/refinement/targets/geometry 2026-04-17T14:03:05,429 copying torchref/refinement/targets/geometry/non_bonded.py -> build/lib/torchref/refinement/targets/geometry 2026-04-17T14:03:05,432 copying torchref/refinement/targets/geometry/angles.py -> build/lib/torchref/refinement/targets/geometry 2026-04-17T14:03:05,433 copying torchref/refinement/targets/geometry/non_bonded_h.py -> build/lib/torchref/refinement/targets/geometry 2026-04-17T14:03:05,436 copying torchref/refinement/targets/geometry/__init__.py -> build/lib/torchref/refinement/targets/geometry 2026-04-17T14:03:05,437 copying torchref/refinement/targets/geometry/planarity.py -> build/lib/torchref/refinement/targets/geometry 2026-04-17T14:03:05,440 copying torchref/refinement/targets/geometry/base.py -> build/lib/torchref/refinement/targets/geometry 2026-04-17T14:03:05,442 copying torchref/refinement/targets/geometry/torsions.py -> build/lib/torchref/refinement/targets/geometry 2026-04-17T14:03:05,444 copying torchref/refinement/targets/geometry/chiral.py -> build/lib/torchref/refinement/targets/geometry 2026-04-17T14:03:05,446 copying torchref/refinement/targets/geometry/bonds.py -> build/lib/torchref/refinement/targets/geometry 2026-04-17T14:03:05,449 creating build/lib/torchref/refinement/targets/xray 2026-04-17T14:03:05,450 copying torchref/refinement/targets/xray/__init__.py -> build/lib/torchref/refinement/targets/xray 2026-04-17T14:03:05,451 copying torchref/refinement/targets/xray/base.py -> build/lib/torchref/refinement/targets/xray 2026-04-17T14:03:05,454 copying torchref/refinement/targets/xray/maximum_likelihood.py -> build/lib/torchref/refinement/targets/xray 2026-04-17T14:03:05,456 copying torchref/refinement/targets/xray/bhattacharyya.py -> build/lib/torchref/refinement/targets/xray 2026-04-17T14:03:05,458 copying torchref/refinement/targets/xray/gaussian.py -> build/lib/torchref/refinement/targets/xray 2026-04-17T14:03:05,460 copying torchref/refinement/targets/xray/least_squares.py -> build/lib/torchref/refinement/targets/xray 2026-04-17T14:03:05,462 running egg_info 2026-04-17T14:03:05,471 writing torchref.egg-info/PKG-INFO 2026-04-17T14:03:05,479 writing dependency_links to torchref.egg-info/dependency_links.txt 2026-04-17T14:03:05,480 writing entry points to torchref.egg-info/entry_points.txt 2026-04-17T14:03:05,484 writing requirements to torchref.egg-info/requires.txt 2026-04-17T14:03:05,485 writing top-level names to torchref.egg-info/top_level.txt 2026-04-17T14:03:05,542 reading manifest file 'torchref.egg-info/SOURCES.txt' 2026-04-17T14:03:05,555 adding license file 'LICENSE' 2026-04-17T14:03:05,567 writing manifest file 'torchref.egg-info/SOURCES.txt' 2026-04-17T14:03:05,600 creating build/lib/torchref/data 2026-04-17T14:03:05,601 copying torchref/data/atomic_vdw_radii.csv -> build/lib/torchref/data 2026-04-17T14:03:05,604 copying torchref/data/rama_nll_surfaces.pt -> build/lib/torchref/data 2026-04-17T14:03:05,667 copying torchref/data/itc92_scattering_factors.pt -> build/lib/torchref/data 2026-04-17T14:03:05,669 creating build/lib/torchref/data/monomer_library/list 2026-04-17T14:03:05,671 copying torchref/data/monomer_library/list/mon_lib_list.cif -> build/lib/torchref/data/monomer_library/list 2026-04-17T14:03:05,771 creating build/lib/torchref/data/monomer_library/d 2026-04-17T14:03:05,771 copying torchref/data/monomer_library/d/DT.cif -> build/lib/torchref/data/monomer_library/d 2026-04-17T14:03:05,775 copying torchref/data/monomer_library/d/DA.cif -> build/lib/torchref/data/monomer_library/d 2026-04-17T14:03:05,778 copying torchref/data/monomer_library/d/DG.cif -> build/lib/torchref/data/monomer_library/d 2026-04-17T14:03:05,781 copying torchref/data/monomer_library/d/DC.cif -> build/lib/torchref/data/monomer_library/d 2026-04-17T14:03:05,783 creating build/lib/torchref/data/monomer_library/i 2026-04-17T14:03:05,784 copying torchref/data/monomer_library/i/ILE.cif -> build/lib/torchref/data/monomer_library/i 2026-04-17T14:03:05,787 creating build/lib/torchref/data/monomer_library/a 2026-04-17T14:03:05,788 copying torchref/data/monomer_library/a/ASN.cif -> build/lib/torchref/data/monomer_library/a 2026-04-17T14:03:05,791 copying torchref/data/monomer_library/a/A.cif -> build/lib/torchref/data/monomer_library/a 2026-04-17T14:03:05,795 copying torchref/data/monomer_library/a/ASP.cif -> build/lib/torchref/data/monomer_library/a 2026-04-17T14:03:05,799 copying torchref/data/monomer_library/a/ARG.cif -> build/lib/torchref/data/monomer_library/a 2026-04-17T14:03:05,802 copying torchref/data/monomer_library/a/ALA.cif -> build/lib/torchref/data/monomer_library/a 2026-04-17T14:03:05,806 creating build/lib/torchref/data/monomer_library/t 2026-04-17T14:03:05,807 copying torchref/data/monomer_library/t/THR.cif -> build/lib/torchref/data/monomer_library/t 2026-04-17T14:03:05,811 copying torchref/data/monomer_library/t/TYR.cif -> build/lib/torchref/data/monomer_library/t 2026-04-17T14:03:05,814 copying torchref/data/monomer_library/t/TPO.cif -> build/lib/torchref/data/monomer_library/t 2026-04-17T14:03:05,817 copying torchref/data/monomer_library/t/TRP.cif -> build/lib/torchref/data/monomer_library/t 2026-04-17T14:03:05,821 creating build/lib/torchref/data/monomer_library/m 2026-04-17T14:03:05,822 copying torchref/data/monomer_library/m/MET.cif -> build/lib/torchref/data/monomer_library/m 2026-04-17T14:03:05,827 copying torchref/data/monomer_library/m/MSE.cif -> build/lib/torchref/data/monomer_library/m 2026-04-17T14:03:05,832 creating build/lib/torchref/data/monomer_library/c 2026-04-17T14:03:05,834 copying torchref/data/monomer_library/c/CYS.cif -> build/lib/torchref/data/monomer_library/c 2026-04-17T14:03:05,840 copying torchref/data/monomer_library/c/C.cif -> build/lib/torchref/data/monomer_library/c 2026-04-17T14:03:05,847 creating build/lib/torchref/data/monomer_library/s 2026-04-17T14:03:05,849 copying torchref/data/monomer_library/s/SER.cif -> build/lib/torchref/data/monomer_library/s 2026-04-17T14:03:05,858 copying torchref/data/monomer_library/s/SEP.cif -> build/lib/torchref/data/monomer_library/s 2026-04-17T14:03:05,866 creating build/lib/torchref/data/monomer_library/p 2026-04-17T14:03:05,869 copying torchref/data/monomer_library/p/PTR.cif -> build/lib/torchref/data/monomer_library/p 2026-04-17T14:03:05,880 copying torchref/data/monomer_library/p/PRO.cif -> build/lib/torchref/data/monomer_library/p 2026-04-17T14:03:05,890 copying torchref/data/monomer_library/p/PHE.cif -> build/lib/torchref/data/monomer_library/p 2026-04-17T14:03:05,893 creating build/lib/torchref/data/monomer_library/g 2026-04-17T14:03:05,894 copying torchref/data/monomer_library/g/GLU.cif -> build/lib/torchref/data/monomer_library/g 2026-04-17T14:03:05,897 copying torchref/data/monomer_library/g/G.cif -> build/lib/torchref/data/monomer_library/g 2026-04-17T14:03:05,899 copying torchref/data/monomer_library/g/GLY.cif -> build/lib/torchref/data/monomer_library/g 2026-04-17T14:03:05,901 copying torchref/data/monomer_library/g/GLN.cif -> build/lib/torchref/data/monomer_library/g 2026-04-17T14:03:05,904 creating build/lib/torchref/data/monomer_library/u 2026-04-17T14:03:05,904 copying torchref/data/monomer_library/u/U.cif -> build/lib/torchref/data/monomer_library/u 2026-04-17T14:03:05,907 creating build/lib/torchref/data/monomer_library/l 2026-04-17T14:03:05,908 copying torchref/data/monomer_library/l/LYS.cif -> build/lib/torchref/data/monomer_library/l 2026-04-17T14:03:05,910 copying torchref/data/monomer_library/l/LEU.cif -> build/lib/torchref/data/monomer_library/l 2026-04-17T14:03:05,913 creating build/lib/torchref/data/monomer_library/h 2026-04-17T14:03:05,914 copying torchref/data/monomer_library/h/HYP.cif -> build/lib/torchref/data/monomer_library/h 2026-04-17T14:03:05,916 copying torchref/data/monomer_library/h/HIS.cif -> build/lib/torchref/data/monomer_library/h 2026-04-17T14:03:05,918 copying torchref/data/monomer_library/h/HOH.cif -> build/lib/torchref/data/monomer_library/h 2026-04-17T14:03:05,920 creating build/lib/torchref/data/monomer_library/v 2026-04-17T14:03:05,921 copying torchref/data/monomer_library/v/VAL.cif -> build/lib/torchref/data/monomer_library/v 2026-04-17T14:03:05,965 installing to build/bdist.linux-armv7l/wheel 2026-04-17T14:03:05,966 running install 2026-04-17T14:03:05,989 running install_lib 2026-04-17T14:03:05,994 creating build/bdist.linux-armv7l/wheel 2026-04-17T14:03:05,996 creating build/bdist.linux-armv7l/wheel/torchref 2026-04-17T14:03:05,998 creating build/bdist.linux-armv7l/wheel/torchref/maps 2026-04-17T14:03:05,999 copying build/lib/torchref/maps/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/maps 2026-04-17T14:03:06,001 copying build/lib/torchref/maps/difference_map.py -> build/bdist.linux-armv7l/wheel/./torchref/maps 2026-04-17T14:03:06,003 copying build/lib/torchref/maps/map.py -> build/bdist.linux-armv7l/wheel/./torchref/maps 2026-04-17T14:03:06,005 creating build/bdist.linux-armv7l/wheel/torchref/utils 2026-04-17T14:03:06,006 copying build/lib/torchref/utils/debug_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-04-17T14:03:06,009 copying build/lib/torchref/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-04-17T14:03:06,011 copying build/lib/torchref/utils/gradnorm.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-04-17T14:03:06,012 copying build/lib/torchref/utils/serialization.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-04-17T14:03:06,014 copying build/lib/torchref/utils/loss_validation.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-04-17T14:03:06,016 copying build/lib/torchref/utils/hyperparameters.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-04-17T14:03:06,019 copying build/lib/torchref/utils/stats.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-04-17T14:03:06,021 copying build/lib/torchref/utils/caching.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-04-17T14:03:06,023 copying build/lib/torchref/utils/autograd_introspection.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-04-17T14:03:06,025 copying build/lib/torchref/utils/device_mixin.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-04-17T14:03:06,027 copying build/lib/torchref/utils/timing.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-04-17T14:03:06,028 copying build/lib/torchref/utils/pse.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-04-17T14:03:06,030 copying build/lib/torchref/utils/utils.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-04-17T14:03:06,033 copying build/lib/torchref/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref 2026-04-17T14:03:06,036 creating build/bdist.linux-armv7l/wheel/torchref/base 2026-04-17T14:03:06,037 copying build/lib/torchref/base/get_scattering_factor_torch.py -> build/bdist.linux-armv7l/wheel/./torchref/base 2026-04-17T14:03:06,040 creating build/bdist.linux-armv7l/wheel/torchref/base/fourier 2026-04-17T14:03:06,041 copying build/lib/torchref/base/fourier/fft.py -> build/bdist.linux-armv7l/wheel/./torchref/base/fourier 2026-04-17T14:03:06,044 copying build/lib/torchref/base/fourier/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/fourier 2026-04-17T14:03:06,046 copying build/lib/torchref/base/fourier/grid.py -> build/bdist.linux-armv7l/wheel/./torchref/base/fourier 2026-04-17T14:03:06,048 copying build/lib/torchref/base/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base 2026-04-17T14:03:06,051 creating build/bdist.linux-armv7l/wheel/torchref/base/scattering 2026-04-17T14:03:06,052 copying build/lib/torchref/base/scattering/scattering_table.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering 2026-04-17T14:03:06,054 copying build/lib/torchref/base/scattering/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering 2026-04-17T14:03:06,056 copying build/lib/torchref/base/scattering/itc92.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering 2026-04-17T14:03:06,058 copying build/lib/torchref/base/scattering/anomalous_table.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering 2026-04-17T14:03:06,060 copying build/lib/torchref/base/french_wilson.py -> build/bdist.linux-armv7l/wheel/./torchref/base 2026-04-17T14:03:06,063 copying build/lib/torchref/base/math_numpy.py -> build/bdist.linux-armv7l/wheel/./torchref/base 2026-04-17T14:03:06,066 copying build/lib/torchref/base/math_torch.py -> build/bdist.linux-armv7l/wheel/./torchref/base 2026-04-17T14:03:06,069 creating build/bdist.linux-armv7l/wheel/torchref/base/chain_closure 2026-04-17T14:03:06,070 copying build/lib/torchref/base/chain_closure/closure.py -> build/bdist.linux-armv7l/wheel/./torchref/base/chain_closure 2026-04-17T14:03:06,072 copying build/lib/torchref/base/chain_closure/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/chain_closure 2026-04-17T14:03:06,074 copying build/lib/torchref/base/chain_closure/backbone_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/base/chain_closure 2026-04-17T14:03:06,077 creating build/bdist.linux-armv7l/wheel/torchref/base/electron_density 2026-04-17T14:03:06,079 copying build/lib/torchref/base/electron_density/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density 2026-04-17T14:03:06,080 copying build/lib/torchref/base/electron_density/solvent_mask.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density 2026-04-17T14:03:06,083 copying build/lib/torchref/base/electron_density/main.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density 2026-04-17T14:03:06,086 copying build/lib/torchref/base/electron_density/voxel_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density 2026-04-17T14:03:06,088 copying build/lib/torchref/base/electron_density/map_building.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density 2026-04-17T14:03:06,091 creating build/bdist.linux-armv7l/wheel/torchref/base/alignment 2026-04-17T14:03:06,092 copying build/lib/torchref/base/alignment/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment 2026-04-17T14:03:06,094 copying build/lib/torchref/base/alignment/scoring.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment 2026-04-17T14:03:06,096 copying build/lib/torchref/base/alignment/rotation.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment 2026-04-17T14:03:06,098 copying build/lib/torchref/base/alignment/normalization.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment 2026-04-17T14:03:06,100 copying build/lib/torchref/base/alignment/superposition.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment 2026-04-17T14:03:06,103 creating build/bdist.linux-armv7l/wheel/torchref/base/kernels 2026-04-17T14:03:06,104 copying build/lib/torchref/base/kernels/separable_triton_kernel.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels 2026-04-17T14:03:06,107 copying build/lib/torchref/base/kernels/triton_kernel.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels 2026-04-17T14:03:06,110 copying build/lib/torchref/base/kernels/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels 2026-04-17T14:03:06,111 copying build/lib/torchref/base/kernels/cpu_scatter.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels 2026-04-17T14:03:06,114 copying build/lib/torchref/base/kernels/jit_kernel_vectorized_add_to_map.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels 2026-04-17T14:03:06,116 copying build/lib/torchref/base/kernels/optimized_ops.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels 2026-04-17T14:03:06,119 creating build/bdist.linux-armv7l/wheel/torchref/base/reciprocal 2026-04-17T14:03:06,120 copying build/lib/torchref/base/reciprocal/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal 2026-04-17T14:03:06,122 copying build/lib/torchref/base/reciprocal/symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal 2026-04-17T14:03:06,124 copying build/lib/torchref/base/reciprocal/interpolation.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal 2026-04-17T14:03:06,126 copying build/lib/torchref/base/reciprocal/basis.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal 2026-04-17T14:03:06,128 copying build/lib/torchref/base/reciprocal/grid_operations.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal 2026-04-17T14:03:06,130 copying build/lib/torchref/base/reciprocal/hkl.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal 2026-04-17T14:03:06,133 creating build/bdist.linux-armv7l/wheel/torchref/base/metrics 2026-04-17T14:03:06,134 copying build/lib/torchref/base/metrics/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/metrics 2026-04-17T14:03:06,136 copying build/lib/torchref/base/metrics/rfactor.py -> build/bdist.linux-armv7l/wheel/./torchref/base/metrics 2026-04-17T14:03:06,138 copying build/lib/torchref/base/metrics/loss.py -> build/bdist.linux-armv7l/wheel/./torchref/base/metrics 2026-04-17T14:03:06,140 copying build/lib/torchref/base/CCTBX_related.py -> build/bdist.linux-armv7l/wheel/./torchref/base 2026-04-17T14:03:06,142 creating build/bdist.linux-armv7l/wheel/torchref/base/coordinates 2026-04-17T14:03:06,144 copying build/lib/torchref/base/coordinates/periodic_boundary.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates 2026-04-17T14:03:06,145 copying build/lib/torchref/base/coordinates/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates 2026-04-17T14:03:06,147 copying build/lib/torchref/base/coordinates/transforms_torch.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates 2026-04-17T14:03:06,149 copying build/lib/torchref/base/coordinates/transforms_numpy.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates 2026-04-17T14:03:06,152 creating build/bdist.linux-armv7l/wheel/torchref/base/direct_summation 2026-04-17T14:03:06,153 copying build/lib/torchref/base/direct_summation/isotropic.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation 2026-04-17T14:03:06,155 copying build/lib/torchref/base/direct_summation/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation 2026-04-17T14:03:06,157 copying build/lib/torchref/base/direct_summation/corrections.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation 2026-04-17T14:03:06,159 copying build/lib/torchref/base/direct_summation/anisotropic.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation 2026-04-17T14:03:06,161 copying build/lib/torchref/config.py -> build/bdist.linux-armv7l/wheel/./torchref 2026-04-17T14:03:06,164 creating build/bdist.linux-armv7l/wheel/torchref/cli 2026-04-17T14:03:06,165 copying build/lib/torchref/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/cli 2026-04-17T14:03:06,167 copying build/lib/torchref/cli/_common.py -> build/bdist.linux-armv7l/wheel/./torchref/cli 2026-04-17T14:03:06,169 copying build/lib/torchref/cli/validate_ded.py -> build/bdist.linux-armv7l/wheel/./torchref/cli 2026-04-17T14:03:06,172 copying build/lib/torchref/cli/phased_difference_map.py -> build/bdist.linux-armv7l/wheel/./torchref/cli 2026-04-17T14:03:06,174 copying build/lib/torchref/cli/collection_difference_refine.py -> build/bdist.linux-armv7l/wheel/./torchref/cli 2026-04-17T14:03:06,177 copying build/lib/torchref/cli/add_metadata.py -> build/bdist.linux-armv7l/wheel/./torchref/cli 2026-04-17T14:03:06,179 copying build/lib/torchref/cli/strip_altlocs.py -> build/bdist.linux-armv7l/wheel/./torchref/cli 2026-04-17T14:03:06,181 copying build/lib/torchref/cli/refine.py -> build/bdist.linux-armv7l/wheel/./torchref/cli 2026-04-17T14:03:06,183 copying build/lib/torchref/cli/mtz2map.py -> build/bdist.linux-armv7l/wheel/./torchref/cli 2026-04-17T14:03:06,186 creating build/bdist.linux-armv7l/wheel/torchref/alignment 2026-04-17T14:03:06,187 copying build/lib/torchref/alignment/pipeline.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment 2026-04-17T14:03:06,190 copying build/lib/torchref/alignment/sampling.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment 2026-04-17T14:03:06,192 copying build/lib/torchref/alignment/jax_subpixel_peaks.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment 2026-04-17T14:03:06,194 copying build/lib/torchref/alignment/clashscore.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment 2026-04-17T14:03:06,196 copying build/lib/torchref/alignment/rigid_body.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment 2026-04-17T14:03:06,199 copying build/lib/torchref/alignment/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment 2026-04-17T14:03:06,201 copying build/lib/torchref/alignment/ball_transform.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment 2026-04-17T14:03:06,204 copying build/lib/torchref/alignment/translation.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment 2026-04-17T14:03:06,206 copying build/lib/torchref/alignment/distributions.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment 2026-04-17T14:03:06,209 copying build/lib/torchref/alignment/transform.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment 2026-04-17T14:03:06,212 creating build/bdist.linux-armv7l/wheel/torchref/data 2026-04-17T14:03:06,214 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library 2026-04-17T14:03:06,215 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/list 2026-04-17T14:03:06,216 copying build/lib/torchref/data/monomer_library/list/mon_lib_list.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/list 2026-04-17T14:03:06,285 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/d 2026-04-17T14:03:06,286 copying build/lib/torchref/data/monomer_library/d/DT.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d 2026-04-17T14:03:06,289 copying build/lib/torchref/data/monomer_library/d/DA.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d 2026-04-17T14:03:06,292 copying build/lib/torchref/data/monomer_library/d/DG.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d 2026-04-17T14:03:06,296 copying build/lib/torchref/data/monomer_library/d/DC.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d 2026-04-17T14:03:06,299 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/i 2026-04-17T14:03:06,300 copying build/lib/torchref/data/monomer_library/i/ILE.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/i 2026-04-17T14:03:06,304 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/a 2026-04-17T14:03:06,305 copying build/lib/torchref/data/monomer_library/a/ASN.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a 2026-04-17T14:03:06,307 copying build/lib/torchref/data/monomer_library/a/A.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a 2026-04-17T14:03:06,309 copying build/lib/torchref/data/monomer_library/a/ASP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a 2026-04-17T14:03:06,311 copying build/lib/torchref/data/monomer_library/a/ARG.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a 2026-04-17T14:03:06,314 copying build/lib/torchref/data/monomer_library/a/ALA.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a 2026-04-17T14:03:06,316 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/t 2026-04-17T14:03:06,317 copying build/lib/torchref/data/monomer_library/t/THR.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t 2026-04-17T14:03:06,319 copying build/lib/torchref/data/monomer_library/t/TYR.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t 2026-04-17T14:03:06,321 copying build/lib/torchref/data/monomer_library/t/TPO.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t 2026-04-17T14:03:06,324 copying build/lib/torchref/data/monomer_library/t/TRP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t 2026-04-17T14:03:06,326 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/m 2026-04-17T14:03:06,327 copying build/lib/torchref/data/monomer_library/m/MET.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/m 2026-04-17T14:03:06,329 copying build/lib/torchref/data/monomer_library/m/MSE.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/m 2026-04-17T14:03:06,332 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/c 2026-04-17T14:03:06,333 copying build/lib/torchref/data/monomer_library/c/CYS.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/c 2026-04-17T14:03:06,335 copying build/lib/torchref/data/monomer_library/c/C.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/c 2026-04-17T14:03:06,338 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/s 2026-04-17T14:03:06,339 copying build/lib/torchref/data/monomer_library/s/SER.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/s 2026-04-17T14:03:06,342 copying build/lib/torchref/data/monomer_library/s/SEP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/s 2026-04-17T14:03:06,344 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/p 2026-04-17T14:03:06,345 copying build/lib/torchref/data/monomer_library/p/PTR.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/p 2026-04-17T14:03:06,347 copying build/lib/torchref/data/monomer_library/p/PRO.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/p 2026-04-17T14:03:06,350 copying build/lib/torchref/data/monomer_library/p/PHE.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/p 2026-04-17T14:03:06,352 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/g 2026-04-17T14:03:06,353 copying build/lib/torchref/data/monomer_library/g/GLU.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g 2026-04-17T14:03:06,356 copying build/lib/torchref/data/monomer_library/g/G.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g 2026-04-17T14:03:06,358 copying build/lib/torchref/data/monomer_library/g/GLY.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g 2026-04-17T14:03:06,360 copying build/lib/torchref/data/monomer_library/g/GLN.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g 2026-04-17T14:03:06,363 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/u 2026-04-17T14:03:06,364 copying build/lib/torchref/data/monomer_library/u/U.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/u 2026-04-17T14:03:06,367 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/l 2026-04-17T14:03:06,368 copying build/lib/torchref/data/monomer_library/l/LYS.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/l 2026-04-17T14:03:06,370 copying build/lib/torchref/data/monomer_library/l/LEU.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/l 2026-04-17T14:03:06,373 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/h 2026-04-17T14:03:06,374 copying build/lib/torchref/data/monomer_library/h/HYP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/h 2026-04-17T14:03:06,376 copying build/lib/torchref/data/monomer_library/h/HIS.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/h 2026-04-17T14:03:06,378 copying build/lib/torchref/data/monomer_library/h/HOH.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/h 2026-04-17T14:03:06,381 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/v 2026-04-17T14:03:06,381 copying build/lib/torchref/data/monomer_library/v/VAL.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/v 2026-04-17T14:03:06,384 copying build/lib/torchref/data/atomic_vdw_radii.csv -> build/bdist.linux-armv7l/wheel/./torchref/data 2026-04-17T14:03:06,385 copying build/lib/torchref/data/rama_nll_surfaces.pt -> build/bdist.linux-armv7l/wheel/./torchref/data 2026-04-17T14:03:06,440 copying build/lib/torchref/data/itc92_scattering_factors.pt -> build/bdist.linux-armv7l/wheel/./torchref/data 2026-04-17T14:03:06,443 creating build/bdist.linux-armv7l/wheel/torchref/io 2026-04-17T14:03:06,444 copying build/lib/torchref/io/metadata.py -> build/bdist.linux-armv7l/wheel/./torchref/io 2026-04-17T14:03:06,447 copying build/lib/torchref/io/ihm.py -> build/bdist.linux-armv7l/wheel/./torchref/io 2026-04-17T14:03:06,450 copying build/lib/torchref/io/mtz.py -> build/bdist.linux-armv7l/wheel/./torchref/io 2026-04-17T14:03:06,453 creating build/bdist.linux-armv7l/wheel/torchref/io/datasets 2026-04-17T14:03:06,454 copying build/lib/torchref/io/datasets/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets 2026-04-17T14:03:06,456 copying build/lib/torchref/io/datasets/fcalc_data.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets 2026-04-17T14:03:06,459 copying build/lib/torchref/io/datasets/base.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets 2026-04-17T14:03:06,462 copying build/lib/torchref/io/datasets/reflection_data.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets 2026-04-17T14:03:06,466 copying build/lib/torchref/io/datasets/collection.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets 2026-04-17T14:03:06,469 copying build/lib/torchref/io/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/io 2026-04-17T14:03:06,471 copying build/lib/torchref/io/ihm_mapping.py -> build/bdist.linux-armv7l/wheel/./torchref/io 2026-04-17T14:03:06,473 copying build/lib/torchref/io/data_router.py -> build/bdist.linux-armv7l/wheel/./torchref/io 2026-04-17T14:03:06,476 copying build/lib/torchref/io/pdb.py -> build/bdist.linux-armv7l/wheel/./torchref/io 2026-04-17T14:03:06,478 copying build/lib/torchref/io/cif_readers.py -> build/bdist.linux-armv7l/wheel/./torchref/io 2026-04-17T14:03:06,482 copying build/lib/torchref/io/cif.py -> build/bdist.linux-armv7l/wheel/./torchref/io 2026-04-17T14:03:06,485 creating build/bdist.linux-armv7l/wheel/torchref/refinement 2026-04-17T14:03:06,486 copying build/lib/torchref/refinement/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement 2026-04-17T14:03:06,488 creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets 2026-04-17T14:03:06,489 copying build/lib/torchref/refinement/targets/forcefield_target.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets 2026-04-17T14:03:06,492 creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets/adp 2026-04-17T14:03:06,493 copying build/lib/torchref/refinement/targets/adp/rigid_bond.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp 2026-04-17T14:03:06,496 copying build/lib/torchref/refinement/targets/adp/entropy.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp 2026-04-17T14:03:06,498 copying build/lib/torchref/refinement/targets/adp/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp 2026-04-17T14:03:06,499 copying build/lib/torchref/refinement/targets/adp/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp 2026-04-17T14:03:06,501 copying build/lib/torchref/refinement/targets/adp/similarity.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp 2026-04-17T14:03:06,503 copying build/lib/torchref/refinement/targets/adp/scaler_log_scale.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp 2026-04-17T14:03:06,505 copying build/lib/torchref/refinement/targets/adp/scaler_u.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp 2026-04-17T14:03:06,506 copying build/lib/torchref/refinement/targets/adp/locality.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp 2026-04-17T14:03:06,509 copying build/lib/torchref/refinement/targets/realspace.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets 2026-04-17T14:03:06,512 copying build/lib/torchref/refinement/targets/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets 2026-04-17T14:03:06,514 creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets/geometry 2026-04-17T14:03:06,515 copying build/lib/torchref/refinement/targets/geometry/ramachandran.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry 2026-04-17T14:03:06,517 copying build/lib/torchref/refinement/targets/geometry/non_bonded.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry 2026-04-17T14:03:06,520 copying build/lib/torchref/refinement/targets/geometry/angles.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry 2026-04-17T14:03:06,522 copying build/lib/torchref/refinement/targets/geometry/non_bonded_h.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry 2026-04-17T14:03:06,524 copying build/lib/torchref/refinement/targets/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry 2026-04-17T14:03:06,526 copying build/lib/torchref/refinement/targets/geometry/planarity.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry 2026-04-17T14:03:06,528 copying build/lib/torchref/refinement/targets/geometry/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry 2026-04-17T14:03:06,530 copying build/lib/torchref/refinement/targets/geometry/torsions.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry 2026-04-17T14:03:06,532 copying build/lib/torchref/refinement/targets/geometry/chiral.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry 2026-04-17T14:03:06,535 copying build/lib/torchref/refinement/targets/geometry/bonds.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry 2026-04-17T14:03:06,537 copying build/lib/torchref/refinement/targets/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets 2026-04-17T14:03:06,539 copying build/lib/torchref/refinement/targets/difference.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets 2026-04-17T14:03:06,542 copying build/lib/torchref/refinement/targets/sampled_ml_phase_target.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets 2026-04-17T14:03:06,546 creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets/xray 2026-04-17T14:03:06,547 copying build/lib/torchref/refinement/targets/xray/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray 2026-04-17T14:03:06,549 copying build/lib/torchref/refinement/targets/xray/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray 2026-04-17T14:03:06,551 copying build/lib/torchref/refinement/targets/xray/maximum_likelihood.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray 2026-04-17T14:03:06,553 copying build/lib/torchref/refinement/targets/xray/bhattacharyya.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray 2026-04-17T14:03:06,556 copying build/lib/torchref/refinement/targets/xray/gaussian.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray 2026-04-17T14:03:06,558 copying build/lib/torchref/refinement/targets/xray/least_squares.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray 2026-04-17T14:03:06,560 copying build/lib/torchref/refinement/targets/similarity.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets 2026-04-17T14:03:06,562 copying build/lib/torchref/refinement/targets/occupancy_floor_diagnostic.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets 2026-04-17T14:03:06,564 copying build/lib/torchref/refinement/targets/amber_target.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets 2026-04-17T14:03:06,567 copying build/lib/torchref/refinement/targets/combined.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets 2026-04-17T14:03:06,570 creating build/bdist.linux-armv7l/wheel/torchref/refinement/weighting 2026-04-17T14:03:06,571 copying build/lib/torchref/refinement/weighting/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting 2026-04-17T14:03:06,573 copying build/lib/torchref/refinement/weighting/es_policy_training.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting 2026-04-17T14:03:06,575 copying build/lib/torchref/refinement/weighting/policy_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting 2026-04-17T14:03:06,578 copying build/lib/torchref/refinement/weighting/base_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting 2026-04-17T14:03:06,580 copying build/lib/torchref/refinement/weighting/random_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting 2026-04-17T14:03:06,582 copying build/lib/torchref/refinement/weighting/component_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting 2026-04-17T14:03:06,585 creating build/bdist.linux-armv7l/wheel/torchref/refinement/optimizers 2026-04-17T14:03:06,586 copying build/lib/torchref/refinement/optimizers/exploratory_lbfgs.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers 2026-04-17T14:03:06,589 copying build/lib/torchref/refinement/optimizers/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers 2026-04-17T14:03:06,591 copying build/lib/torchref/refinement/optimizers/internal_coord_sa.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers 2026-04-17T14:03:06,594 copying build/lib/torchref/refinement/optimizers/momentum_sa.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers 2026-04-17T14:03:06,596 copying build/lib/torchref/refinement/optimizers/langevin_sa.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers 2026-04-17T14:03:06,598 copying build/lib/torchref/refinement/optimizers/adam_noise.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers 2026-04-17T14:03:06,601 copying build/lib/torchref/refinement/optimizers/simulated_annealing.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers 2026-04-17T14:03:06,603 copying build/lib/torchref/refinement/base_refinement.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement 2026-04-17T14:03:06,607 copying build/lib/torchref/refinement/loss_state.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement 2026-04-17T14:03:06,610 copying build/lib/torchref/refinement/lbfgs_refinement.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement 2026-04-17T14:03:06,613 copying build/lib/torchref/refinement/logger.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement 2026-04-17T14:03:06,617 creating build/bdist.linux-armv7l/wheel/torchref/scaling 2026-04-17T14:03:06,618 copying build/lib/torchref/scaling/scaler_base.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling 2026-04-17T14:03:06,622 copying build/lib/torchref/scaling/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling 2026-04-17T14:03:06,624 copying build/lib/torchref/scaling/solvent.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling 2026-04-17T14:03:06,627 copying build/lib/torchref/scaling/scaler.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling 2026-04-17T14:03:06,630 copying build/lib/torchref/scaling/collection_scaler.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling 2026-04-17T14:03:06,634 creating build/bdist.linux-armv7l/wheel/torchref/model 2026-04-17T14:03:06,635 copying build/lib/torchref/model/closed_segmented_internal_coordinates.py -> build/bdist.linux-armv7l/wheel/./torchref/model 2026-04-17T14:03:06,640 copying build/lib/torchref/model/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/model 2026-04-17T14:03:06,642 copying build/lib/torchref/model/sf_ds.py -> build/bdist.linux-armv7l/wheel/./torchref/model 2026-04-17T14:03:06,645 copying build/lib/torchref/model/model_ft.py -> build/bdist.linux-armv7l/wheel/./torchref/model 2026-04-17T14:03:06,648 copying build/lib/torchref/model/segmented_internal_coordinates.py -> build/bdist.linux-armv7l/wheel/./torchref/model 2026-04-17T14:03:06,653 copying build/lib/torchref/model/parameter_wrappers.py -> build/bdist.linux-armv7l/wheel/./torchref/model 2026-04-17T14:03:06,658 copying build/lib/torchref/model/internal_coordinates.py -> build/bdist.linux-armv7l/wheel/./torchref/model 2026-04-17T14:03:06,663 copying build/lib/torchref/model/model_collection.py -> build/bdist.linux-armv7l/wheel/./torchref/model 2026-04-17T14:03:06,667 copying build/lib/torchref/model/model.py -> build/bdist.linux-armv7l/wheel/./torchref/model 2026-04-17T14:03:06,672 copying build/lib/torchref/model/sf_fft.py -> build/bdist.linux-armv7l/wheel/./torchref/model 2026-04-17T14:03:06,675 copying build/lib/torchref/model/mixed_model.py -> build/bdist.linux-armv7l/wheel/./torchref/model 2026-04-17T14:03:06,679 creating build/bdist.linux-armv7l/wheel/torchref/restraints 2026-04-17T14:03:06,680 copying build/lib/torchref/restraints/ramachandran.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints 2026-04-17T14:03:06,683 copying build/lib/torchref/restraints/builders_numba.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints 2026-04-17T14:03:06,687 copying build/lib/torchref/restraints/restraints_helper.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints 2026-04-17T14:03:06,690 copying build/lib/torchref/restraints/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints 2026-04-17T14:03:06,693 copying build/lib/torchref/restraints/library.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints 2026-04-17T14:03:06,696 copying build/lib/torchref/restraints/hydrogen_topology.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints 2026-04-17T14:03:06,700 copying build/lib/torchref/restraints/builders_fast.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints 2026-04-17T14:03:06,704 copying build/lib/torchref/restraints/restraints.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints 2026-04-17T14:03:06,709 copying build/lib/torchref/restraints/neighbor_search.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints 2026-04-17T14:03:06,712 copying build/lib/torchref/restraints/builders.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints 2026-04-17T14:03:06,716 copying build/lib/torchref/_bootstrap.py -> build/bdist.linux-armv7l/wheel/./torchref 2026-04-17T14:03:06,719 creating build/bdist.linux-armv7l/wheel/torchref/kinetic 2026-04-17T14:03:06,720 copying build/lib/torchref/kinetic/refinement.py -> build/bdist.linux-armv7l/wheel/./torchref/kinetic 2026-04-17T14:03:06,723 copying build/lib/torchref/kinetic/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/kinetic 2026-04-17T14:03:06,725 copying build/lib/torchref/kinetic/occupancies.py -> build/bdist.linux-armv7l/wheel/./torchref/kinetic 2026-04-17T14:03:06,728 copying build/lib/torchref/kinetic/kinetics.py -> build/bdist.linux-armv7l/wheel/./torchref/kinetic 2026-04-17T14:03:06,731 copying build/lib/torchref/kinetic/targets.py -> build/bdist.linux-armv7l/wheel/./torchref/kinetic 2026-04-17T14:03:06,735 creating build/bdist.linux-armv7l/wheel/torchref/symmetry 2026-04-17T14:03:06,736 copying build/lib/torchref/symmetry/spacegroup.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry 2026-04-17T14:03:06,739 copying build/lib/torchref/symmetry/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry 2026-04-17T14:03:06,741 copying build/lib/torchref/symmetry/symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry 2026-04-17T14:03:06,743 copying build/lib/torchref/symmetry/cell.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry 2026-04-17T14:03:06,745 copying build/lib/torchref/symmetry/reciprocal_symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry 2026-04-17T14:03:06,749 copying build/lib/torchref/symmetry/grid_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry 2026-04-17T14:03:06,751 copying build/lib/torchref/symmetry/map_symmetry_interpolation.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry 2026-04-17T14:03:06,754 copying build/lib/torchref/symmetry/map_symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry 2026-04-17T14:03:06,757 creating build/bdist.linux-armv7l/wheel/torchref/scripts 2026-04-17T14:03:06,758 copying build/lib/torchref/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/scripts 2026-04-17T14:03:06,760 copying build/lib/torchref/scripts/generate_scattering_table.py -> build/bdist.linux-armv7l/wheel/./torchref/scripts 2026-04-17T14:03:06,763 running install_egg_info 2026-04-17T14:03:06,768 Copying torchref.egg-info to build/bdist.linux-armv7l/wheel/./torchref-0.5.0-py3.11.egg-info 2026-04-17T14:03:06,781 running install_scripts 2026-04-17T14:03:06,793 creating build/bdist.linux-armv7l/wheel/torchref-0.5.0.dist-info/WHEEL 2026-04-17T14:03:06,796 creating '/tmp/pip-wheel-rlxf9ge2/.tmp-t3x2is31/torchref-0.5.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-04-17T14:03:06,799 adding 'torchref/__init__.py' 2026-04-17T14:03:06,801 adding 'torchref/_bootstrap.py' 2026-04-17T14:03:06,803 adding 'torchref/config.py' 2026-04-17T14:03:06,805 adding 'torchref/alignment/__init__.py' 2026-04-17T14:03:06,813 adding 'torchref/alignment/ball_transform.py' 2026-04-17T14:03:06,816 adding 'torchref/alignment/clashscore.py' 2026-04-17T14:03:06,818 adding 'torchref/alignment/distributions.py' 2026-04-17T14:03:06,820 adding 'torchref/alignment/jax_subpixel_peaks.py' 2026-04-17T14:03:06,823 adding 'torchref/alignment/pipeline.py' 2026-04-17T14:03:06,825 adding 'torchref/alignment/rigid_body.py' 2026-04-17T14:03:06,828 adding 'torchref/alignment/sampling.py' 2026-04-17T14:03:06,831 adding 'torchref/alignment/transform.py' 2026-04-17T14:03:06,833 adding 'torchref/alignment/translation.py' 2026-04-17T14:03:06,836 adding 'torchref/base/CCTBX_related.py' 2026-04-17T14:03:06,838 adding 'torchref/base/__init__.py' 2026-04-17T14:03:06,842 adding 'torchref/base/french_wilson.py' 2026-04-17T14:03:06,845 adding 'torchref/base/get_scattering_factor_torch.py' 2026-04-17T14:03:06,848 adding 'torchref/base/math_numpy.py' 2026-04-17T14:03:06,850 adding 'torchref/base/math_torch.py' 2026-04-17T14:03:06,853 adding 'torchref/base/alignment/__init__.py' 2026-04-17T14:03:06,855 adding 'torchref/base/alignment/normalization.py' 2026-04-17T14:03:06,857 adding 'torchref/base/alignment/rotation.py' 2026-04-17T14:03:06,859 adding 'torchref/base/alignment/scoring.py' 2026-04-17T14:03:06,861 adding 'torchref/base/alignment/superposition.py' 2026-04-17T14:03:06,863 adding 'torchref/base/chain_closure/__init__.py' 2026-04-17T14:03:06,866 adding 'torchref/base/chain_closure/backbone_utils.py' 2026-04-17T14:03:06,869 adding 'torchref/base/chain_closure/closure.py' 2026-04-17T14:03:06,871 adding 'torchref/base/coordinates/__init__.py' 2026-04-17T14:03:06,873 adding 'torchref/base/coordinates/periodic_boundary.py' 2026-04-17T14:03:06,875 adding 'torchref/base/coordinates/transforms_numpy.py' 2026-04-17T14:03:06,876 adding 'torchref/base/coordinates/transforms_torch.py' 2026-04-17T14:03:06,878 adding 'torchref/base/direct_summation/__init__.py' 2026-04-17T14:03:06,880 adding 'torchref/base/direct_summation/anisotropic.py' 2026-04-17T14:03:06,881 adding 'torchref/base/direct_summation/corrections.py' 2026-04-17T14:03:06,883 adding 'torchref/base/direct_summation/isotropic.py' 2026-04-17T14:03:06,884 adding 'torchref/base/electron_density/__init__.py' 2026-04-17T14:03:06,888 adding 'torchref/base/electron_density/main.py' 2026-04-17T14:03:06,890 adding 'torchref/base/electron_density/map_building.py' 2026-04-17T14:03:06,892 adding 'torchref/base/electron_density/solvent_mask.py' 2026-04-17T14:03:06,894 adding 'torchref/base/electron_density/voxel_utils.py' 2026-04-17T14:03:06,896 adding 'torchref/base/fourier/__init__.py' 2026-04-17T14:03:06,897 adding 'torchref/base/fourier/fft.py' 2026-04-17T14:03:06,898 adding 'torchref/base/fourier/grid.py' 2026-04-17T14:03:06,900 adding 'torchref/base/kernels/__init__.py' 2026-04-17T14:03:06,902 adding 'torchref/base/kernels/cpu_scatter.py' 2026-04-17T14:03:06,905 adding 'torchref/base/kernels/jit_kernel_vectorized_add_to_map.py' 2026-04-17T14:03:06,907 adding 'torchref/base/kernels/optimized_ops.py' 2026-04-17T14:03:06,911 adding 'torchref/base/kernels/separable_triton_kernel.py' 2026-04-17T14:03:06,915 adding 'torchref/base/kernels/triton_kernel.py' 2026-04-17T14:03:06,917 adding 'torchref/base/metrics/__init__.py' 2026-04-17T14:03:06,919 adding 'torchref/base/metrics/loss.py' 2026-04-17T14:03:06,920 adding 'torchref/base/metrics/rfactor.py' 2026-04-17T14:03:06,922 adding 'torchref/base/reciprocal/__init__.py' 2026-04-17T14:03:06,923 adding 'torchref/base/reciprocal/basis.py' 2026-04-17T14:03:06,925 adding 'torchref/base/reciprocal/grid_operations.py' 2026-04-17T14:03:06,926 adding 'torchref/base/reciprocal/hkl.py' 2026-04-17T14:03:06,929 adding 'torchref/base/reciprocal/interpolation.py' 2026-04-17T14:03:06,931 adding 'torchref/base/reciprocal/symmetry.py' 2026-04-17T14:03:06,933 adding 'torchref/base/scattering/__init__.py' 2026-04-17T14:03:06,934 adding 'torchref/base/scattering/anomalous_table.py' 2026-04-17T14:03:06,936 adding 'torchref/base/scattering/itc92.py' 2026-04-17T14:03:06,938 adding 'torchref/base/scattering/scattering_table.py' 2026-04-17T14:03:06,940 adding 'torchref/cli/__init__.py' 2026-04-17T14:03:06,942 adding 'torchref/cli/_common.py' 2026-04-17T14:03:06,944 adding 'torchref/cli/add_metadata.py' 2026-04-17T14:03:06,950 adding 'torchref/cli/collection_difference_refine.py' 2026-04-17T14:03:06,951 adding 'torchref/cli/mtz2map.py' 2026-04-17T14:03:06,953 adding 'torchref/cli/phased_difference_map.py' 2026-04-17T14:03:06,955 adding 'torchref/cli/refine.py' 2026-04-17T14:03:06,957 adding 'torchref/cli/strip_altlocs.py' 2026-04-17T14:03:06,960 adding 'torchref/cli/validate_ded.py' 2026-04-17T14:03:06,963 adding 'torchref/data/atomic_vdw_radii.csv' 2026-04-17T14:03:06,965 adding 'torchref/data/itc92_scattering_factors.pt' 2026-04-17T14:03:07,199 adding 'torchref/data/rama_nll_surfaces.pt' 2026-04-17T14:03:07,222 adding 'torchref/data/monomer_library/a/A.cif' 2026-04-17T14:03:07,223 adding 'torchref/data/monomer_library/a/ALA.cif' 2026-04-17T14:03:07,225 adding 'torchref/data/monomer_library/a/ARG.cif' 2026-04-17T14:03:07,227 adding 'torchref/data/monomer_library/a/ASN.cif' 2026-04-17T14:03:07,229 adding 'torchref/data/monomer_library/a/ASP.cif' 2026-04-17T14:03:07,232 adding 'torchref/data/monomer_library/c/C.cif' 2026-04-17T14:03:07,233 adding 'torchref/data/monomer_library/c/CYS.cif' 2026-04-17T14:03:07,236 adding 'torchref/data/monomer_library/d/DA.cif' 2026-04-17T14:03:07,238 adding 'torchref/data/monomer_library/d/DC.cif' 2026-04-17T14:03:07,241 adding 'torchref/data/monomer_library/d/DG.cif' 2026-04-17T14:03:07,243 adding 'torchref/data/monomer_library/d/DT.cif' 2026-04-17T14:03:07,246 adding 'torchref/data/monomer_library/g/G.cif' 2026-04-17T14:03:07,247 adding 'torchref/data/monomer_library/g/GLN.cif' 2026-04-17T14:03:07,249 adding 'torchref/data/monomer_library/g/GLU.cif' 2026-04-17T14:03:07,250 adding 'torchref/data/monomer_library/g/GLY.cif' 2026-04-17T14:03:07,252 adding 'torchref/data/monomer_library/h/HIS.cif' 2026-04-17T14:03:07,254 adding 'torchref/data/monomer_library/h/HOH.cif' 2026-04-17T14:03:07,255 adding 'torchref/data/monomer_library/h/HYP.cif' 2026-04-17T14:03:07,257 adding 'torchref/data/monomer_library/i/ILE.cif' 2026-04-17T14:03:07,259 adding 'torchref/data/monomer_library/l/LEU.cif' 2026-04-17T14:03:07,261 adding 'torchref/data/monomer_library/l/LYS.cif' 2026-04-17T14:03:07,807 adding 'torchref/data/monomer_library/list/mon_lib_list.cif' 2026-04-17T14:03:07,834 adding 'torchref/data/monomer_library/m/MET.cif' 2026-04-17T14:03:07,836 adding 'torchref/data/monomer_library/m/MSE.cif' 2026-04-17T14:03:07,838 adding 'torchref/data/monomer_library/p/PHE.cif' 2026-04-17T14:03:07,839 adding 'torchref/data/monomer_library/p/PRO.cif' 2026-04-17T14:03:07,841 adding 'torchref/data/monomer_library/p/PTR.cif' 2026-04-17T14:03:07,843 adding 'torchref/data/monomer_library/s/SEP.cif' 2026-04-17T14:03:07,845 adding 'torchref/data/monomer_library/s/SER.cif' 2026-04-17T14:03:07,847 adding 'torchref/data/monomer_library/t/THR.cif' 2026-04-17T14:03:07,848 adding 'torchref/data/monomer_library/t/TPO.cif' 2026-04-17T14:03:07,850 adding 'torchref/data/monomer_library/t/TRP.cif' 2026-04-17T14:03:07,852 adding 'torchref/data/monomer_library/t/TYR.cif' 2026-04-17T14:03:07,855 adding 'torchref/data/monomer_library/u/U.cif' 2026-04-17T14:03:07,857 adding 'torchref/data/monomer_library/v/VAL.cif' 2026-04-17T14:03:07,859 adding 'torchref/io/__init__.py' 2026-04-17T14:03:07,861 adding 'torchref/io/cif.py' 2026-04-17T14:03:07,869 adding 'torchref/io/cif_readers.py' 2026-04-17T14:03:07,871 adding 'torchref/io/data_router.py' 2026-04-17T14:03:07,876 adding 'torchref/io/ihm.py' 2026-04-17T14:03:07,878 adding 'torchref/io/ihm_mapping.py' 2026-04-17T14:03:07,880 adding 'torchref/io/metadata.py' 2026-04-17T14:03:07,883 adding 'torchref/io/mtz.py' 2026-04-17T14:03:07,885 adding 'torchref/io/pdb.py' 2026-04-17T14:03:07,887 adding 'torchref/io/datasets/__init__.py' 2026-04-17T14:03:07,889 adding 'torchref/io/datasets/base.py' 2026-04-17T14:03:07,891 adding 'torchref/io/datasets/collection.py' 2026-04-17T14:03:07,893 adding 'torchref/io/datasets/fcalc_data.py' 2026-04-17T14:03:07,906 adding 'torchref/io/datasets/reflection_data.py' 2026-04-17T14:03:07,908 adding 'torchref/kinetic/__init__.py' 2026-04-17T14:03:07,913 adding 'torchref/kinetic/kinetics.py' 2026-04-17T14:03:07,917 adding 'torchref/kinetic/occupancies.py' 2026-04-17T14:03:07,919 adding 'torchref/kinetic/refinement.py' 2026-04-17T14:03:07,922 adding 'torchref/kinetic/targets.py' 2026-04-17T14:03:07,924 adding 'torchref/maps/__init__.py' 2026-04-17T14:03:07,925 adding 'torchref/maps/difference_map.py' 2026-04-17T14:03:07,927 adding 'torchref/maps/map.py' 2026-04-17T14:03:07,929 adding 'torchref/model/__init__.py' 2026-04-17T14:03:07,937 adding 'torchref/model/closed_segmented_internal_coordinates.py' 2026-04-17T14:03:07,947 adding 'torchref/model/internal_coordinates.py' 2026-04-17T14:03:07,950 adding 'torchref/model/mixed_model.py' 2026-04-17T14:03:07,963 adding 'torchref/model/model.py' 2026-04-17T14:03:07,967 adding 'torchref/model/model_collection.py' 2026-04-17T14:03:07,972 adding 'torchref/model/model_ft.py' 2026-04-17T14:03:07,980 adding 'torchref/model/parameter_wrappers.py' 2026-04-17T14:03:07,988 adding 'torchref/model/segmented_internal_coordinates.py' 2026-04-17T14:03:07,991 adding 'torchref/model/sf_ds.py' 2026-04-17T14:03:07,994 adding 'torchref/model/sf_fft.py' 2026-04-17T14:03:07,996 adding 'torchref/refinement/__init__.py' 2026-04-17T14:03:08,000 adding 'torchref/refinement/base_refinement.py' 2026-04-17T14:03:08,003 adding 'torchref/refinement/lbfgs_refinement.py' 2026-04-17T14:03:08,005 adding 'torchref/refinement/logger.py' 2026-04-17T14:03:08,010 adding 'torchref/refinement/loss_state.py' 2026-04-17T14:03:08,012 adding 'torchref/refinement/optimizers/__init__.py' 2026-04-17T14:03:08,013 adding 'torchref/refinement/optimizers/adam_noise.py' 2026-04-17T14:03:08,016 adding 'torchref/refinement/optimizers/exploratory_lbfgs.py' 2026-04-17T14:03:08,020 adding 'torchref/refinement/optimizers/internal_coord_sa.py' 2026-04-17T14:03:08,022 adding 'torchref/refinement/optimizers/langevin_sa.py' 2026-04-17T14:03:08,024 adding 'torchref/refinement/optimizers/momentum_sa.py' 2026-04-17T14:03:08,025 adding 'torchref/refinement/optimizers/simulated_annealing.py' 2026-04-17T14:03:08,027 adding 'torchref/refinement/targets/__init__.py' 2026-04-17T14:03:08,033 adding 'torchref/refinement/targets/amber_target.py' 2026-04-17T14:03:08,036 adding 'torchref/refinement/targets/base.py' 2026-04-17T14:03:08,038 adding 'torchref/refinement/targets/combined.py' 2026-04-17T14:03:08,043 adding 'torchref/refinement/targets/difference.py' 2026-04-17T14:03:08,045 adding 'torchref/refinement/targets/forcefield_target.py' 2026-04-17T14:03:08,048 adding 'torchref/refinement/targets/occupancy_floor_diagnostic.py' 2026-04-17T14:03:08,051 adding 'torchref/refinement/targets/realspace.py' 2026-04-17T14:03:08,054 adding 'torchref/refinement/targets/sampled_ml_phase_target.py' 2026-04-17T14:03:08,056 adding 'torchref/refinement/targets/similarity.py' 2026-04-17T14:03:08,058 adding 'torchref/refinement/targets/adp/__init__.py' 2026-04-17T14:03:08,059 adding 'torchref/refinement/targets/adp/base.py' 2026-04-17T14:03:08,061 adding 'torchref/refinement/targets/adp/entropy.py' 2026-04-17T14:03:08,062 adding 'torchref/refinement/targets/adp/locality.py' 2026-04-17T14:03:08,064 adding 'torchref/refinement/targets/adp/rigid_bond.py' 2026-04-17T14:03:08,066 adding 'torchref/refinement/targets/adp/scaler_log_scale.py' 2026-04-17T14:03:08,067 adding 'torchref/refinement/targets/adp/scaler_u.py' 2026-04-17T14:03:08,069 adding 'torchref/refinement/targets/adp/similarity.py' 2026-04-17T14:03:08,071 adding 'torchref/refinement/targets/geometry/__init__.py' 2026-04-17T14:03:08,072 adding 'torchref/refinement/targets/geometry/angles.py' 2026-04-17T14:03:08,073 adding 'torchref/refinement/targets/geometry/base.py' 2026-04-17T14:03:08,075 adding 'torchref/refinement/targets/geometry/bonds.py' 2026-04-17T14:03:08,076 adding 'torchref/refinement/targets/geometry/chiral.py' 2026-04-17T14:03:08,079 adding 'torchref/refinement/targets/geometry/non_bonded.py' 2026-04-17T14:03:08,081 adding 'torchref/refinement/targets/geometry/non_bonded_h.py' 2026-04-17T14:03:08,083 adding 'torchref/refinement/targets/geometry/planarity.py' 2026-04-17T14:03:08,084 adding 'torchref/refinement/targets/geometry/ramachandran.py' 2026-04-17T14:03:08,086 adding 'torchref/refinement/targets/geometry/torsions.py' 2026-04-17T14:03:08,088 adding 'torchref/refinement/targets/xray/__init__.py' 2026-04-17T14:03:08,089 adding 'torchref/refinement/targets/xray/base.py' 2026-04-17T14:03:08,091 adding 'torchref/refinement/targets/xray/bhattacharyya.py' 2026-04-17T14:03:08,093 adding 'torchref/refinement/targets/xray/gaussian.py' 2026-04-17T14:03:08,094 adding 'torchref/refinement/targets/xray/least_squares.py' 2026-04-17T14:03:08,096 adding 'torchref/refinement/targets/xray/maximum_likelihood.py' 2026-04-17T14:03:08,098 adding 'torchref/refinement/weighting/__init__.py' 2026-04-17T14:03:08,099 adding 'torchref/refinement/weighting/base_weighting.py' 2026-04-17T14:03:08,101 adding 'torchref/refinement/weighting/component_weighting.py' 2026-04-17T14:03:08,104 adding 'torchref/refinement/weighting/es_policy_training.py' 2026-04-17T14:03:08,107 adding 'torchref/refinement/weighting/policy_weighting.py' 2026-04-17T14:03:08,109 adding 'torchref/refinement/weighting/random_weighting.py' 2026-04-17T14:03:08,111 adding 'torchref/restraints/__init__.py' 2026-04-17T14:03:08,116 adding 'torchref/restraints/builders.py' 2026-04-17T14:03:08,123 adding 'torchref/restraints/builders_fast.py' 2026-04-17T14:03:08,127 adding 'torchref/restraints/builders_numba.py' 2026-04-17T14:03:08,132 adding 'torchref/restraints/hydrogen_topology.py' 2026-04-17T14:03:08,133 adding 'torchref/restraints/library.py' 2026-04-17T14:03:08,139 adding 'torchref/restraints/neighbor_search.py' 2026-04-17T14:03:08,140 adding 'torchref/restraints/ramachandran.py' 2026-04-17T14:03:08,150 adding 'torchref/restraints/restraints.py' 2026-04-17T14:03:08,153 adding 'torchref/restraints/restraints_helper.py' 2026-04-17T14:03:08,155 adding 'torchref/scaling/__init__.py' 2026-04-17T14:03:08,158 adding 'torchref/scaling/collection_scaler.py' 2026-04-17T14:03:08,160 adding 'torchref/scaling/scaler.py' 2026-04-17T14:03:08,165 adding 'torchref/scaling/scaler_base.py' 2026-04-17T14:03:08,168 adding 'torchref/scaling/solvent.py' 2026-04-17T14:03:08,170 adding 'torchref/scripts/__init__.py' 2026-04-17T14:03:08,171 adding 'torchref/scripts/generate_scattering_table.py' 2026-04-17T14:03:08,173 adding 'torchref/symmetry/__init__.py' 2026-04-17T14:03:08,175 adding 'torchref/symmetry/cell.py' 2026-04-17T14:03:08,177 adding 'torchref/symmetry/grid_utils.py' 2026-04-17T14:03:08,178 adding 'torchref/symmetry/map_symmetry.py' 2026-04-17T14:03:08,180 adding 'torchref/symmetry/map_symmetry_interpolation.py' 2026-04-17T14:03:08,187 adding 'torchref/symmetry/reciprocal_symmetry.py' 2026-04-17T14:03:08,191 adding 'torchref/symmetry/spacegroup.py' 2026-04-17T14:03:08,192 adding 'torchref/symmetry/symmetry.py' 2026-04-17T14:03:08,194 adding 'torchref/utils/__init__.py' 2026-04-17T14:03:08,195 adding 'torchref/utils/autograd_introspection.py' 2026-04-17T14:03:08,197 adding 'torchref/utils/caching.py' 2026-04-17T14:03:08,199 adding 'torchref/utils/debug_utils.py' 2026-04-17T14:03:08,200 adding 'torchref/utils/device_mixin.py' 2026-04-17T14:03:08,201 adding 'torchref/utils/gradnorm.py' 2026-04-17T14:03:08,203 adding 'torchref/utils/hyperparameters.py' 2026-04-17T14:03:08,205 adding 'torchref/utils/loss_validation.py' 2026-04-17T14:03:08,207 adding 'torchref/utils/pse.py' 2026-04-17T14:03:08,208 adding 'torchref/utils/serialization.py' 2026-04-17T14:03:08,210 adding 'torchref/utils/stats.py' 2026-04-17T14:03:08,211 adding 'torchref/utils/timing.py' 2026-04-17T14:03:08,216 adding 'torchref/utils/utils.py' 2026-04-17T14:03:08,219 adding 'torchref-0.5.0.dist-info/licenses/LICENSE' 2026-04-17T14:03:08,220 adding 'torchref-0.5.0.dist-info/METADATA' 2026-04-17T14:03:08,222 adding 'torchref-0.5.0.dist-info/WHEEL' 2026-04-17T14:03:08,223 adding 'torchref-0.5.0.dist-info/entry_points.txt' 2026-04-17T14:03:08,224 adding 'torchref-0.5.0.dist-info/top_level.txt' 2026-04-17T14:03:08,227 adding 'torchref-0.5.0.dist-info/RECORD' 2026-04-17T14:03:08,267 removing build/bdist.linux-armv7l/wheel 2026-04-17T14:03:08,433 Building wheel for torchref (pyproject.toml): finished with status 'done' 2026-04-17T14:03:08,505 Created wheel for torchref: filename=torchref-0.5.0-py3-none-any.whl size=3061191 sha256=81412a83cb1884393fe067281c4c70763169b28f13a642e80110fdc7eb65b9d2 2026-04-17T14:03:08,506 Stored in directory: /tmp/pip-ephem-wheel-cache-t5vjpesz/wheels/d0/10/8c/22b2976c73adf85db19f0fefd5d46c7c62376d489aac4d5802 2026-04-17T14:03:08,526 Successfully built torchref 2026-04-17T14:03:08,615 Removed build tracker: '/tmp/pip-build-tracker-l8h86vs7'