2026-05-13T13:56:26,892 Created temporary directory: /tmp/pip-ephem-wheel-cache-wbd0twxr 2026-05-13T13:56:26,893 Created temporary directory: /tmp/pip-build-tracker-chgdwl6q 2026-05-13T13:56:26,894 Initialized build tracking at /tmp/pip-build-tracker-chgdwl6q 2026-05-13T13:56:26,894 Created build tracker: /tmp/pip-build-tracker-chgdwl6q 2026-05-13T13:56:26,895 Entered build tracker: /tmp/pip-build-tracker-chgdwl6q 2026-05-13T13:56:26,896 Created temporary directory: /tmp/pip-wheel-dft3f0q3 2026-05-13T13:56:26,898 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 2026-05-13T13:56:26,901 Created temporary directory: /tmp/pip-ephem-wheel-cache-mngz1gu0 2026-05-13T13:56:26,926 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-05-13T13:56:26,930 2 location(s) to search for versions of torchref: 2026-05-13T13:56:26,930 * https://pypi.org/simple/torchref/ 2026-05-13T13:56:26,930 * https://www.piwheels.org/simple/torchref/ 2026-05-13T13:56:26,930 Fetching project page and analyzing links: https://pypi.org/simple/torchref/ 2026-05-13T13:56:26,931 Getting page https://pypi.org/simple/torchref/ 2026-05-13T13:56:26,932 Found index url https://pypi.org/simple 2026-05-13T13:56:27,159 Fetched page https://pypi.org/simple/torchref/ as application/vnd.pypi.simple.v1+json 2026-05-13T13:56:27,163 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) 2026-05-13T13:56:27,164 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 2026-05-13T13:56:27,165 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) 2026-05-13T13:56:27,166 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 2026-05-13T13:56:27,167 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) 2026-05-13T13:56:27,168 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 2026-05-13T13:56:27,169 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) 2026-05-13T13:56:27,170 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 2026-05-13T13:56:27,171 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) 2026-05-13T13:56:27,172 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 2026-05-13T13:56:27,172 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) 2026-05-13T13:56:27,174 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 2026-05-13T13:56:27,174 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) 2026-05-13T13:56:27,175 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 2026-05-13T13:56:27,176 Skipping link: No binaries permitted for torchref: https://files.pythonhosted.org/packages/26/a0/7aceb00564e0dabc8d2cf6412cf7dba08013709a3ec915d33e40eabf72e0/torchref-0.5.1-py3-none-any.whl (from https://pypi.org/simple/torchref/) (requires-python:>=3.10) 2026-05-13T13:56:27,177 Found link https://files.pythonhosted.org/packages/c8/0e/388f73407fc7bfe62c48f8e6983fd0b167b0739c260c2e08953ecaaac1bb/torchref-0.5.1.tar.gz (from https://pypi.org/simple/torchref/) (requires-python:>=3.10), version: 0.5.1 2026-05-13T13:56:27,177 Fetching project page and analyzing links: https://www.piwheels.org/simple/torchref/ 2026-05-13T13:56:27,178 Getting page https://www.piwheels.org/simple/torchref/ 2026-05-13T13:56:27,179 Found index url https://www.piwheels.org/simple 2026-05-13T13:56:27,345 Fetched page https://www.piwheels.org/simple/torchref/ as text/html 2026-05-13T13:56:27,349 Skipping link: No binaries permitted for torchref: https://www.piwheels.org/simple/torchref/torchref-0.5.0-py3-none-any.whl#sha256=81412a83cb1884393fe067281c4c70763169b28f13a642e80110fdc7eb65b9d2 (from https://www.piwheels.org/simple/torchref/) (requires-python:>=3.10) 2026-05-13T13:56:27,350 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) 2026-05-13T13:56:27,350 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) 2026-05-13T13:56:27,351 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) 2026-05-13T13:56:27,351 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) 2026-05-13T13:56:27,352 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) 2026-05-13T13:56:27,352 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) 2026-05-13T13:56:27,353 Skipping link: not a file: https://www.piwheels.org/simple/torchref/ 2026-05-13T13:56:27,354 Skipping link: not a file: https://pypi.org/simple/torchref/ 2026-05-13T13:56:27,375 Given no hashes to check 1 links for project 'torchref': discarding no candidates 2026-05-13T13:56:27,394 Collecting torchref==0.5.1 2026-05-13T13:56:27,397 Created temporary directory: /tmp/pip-unpack-en7rc4qf 2026-05-13T13:56:27,541 Downloading torchref-0.5.1.tar.gz (3.0 MB) 2026-05-13T13:56:28,695 Added torchref==0.5.1 from https://files.pythonhosted.org/packages/c8/0e/388f73407fc7bfe62c48f8e6983fd0b167b0739c260c2e08953ecaaac1bb/torchref-0.5.1.tar.gz to build tracker '/tmp/pip-build-tracker-chgdwl6q' 2026-05-13T13:56:28,702 Created temporary directory: /tmp/pip-build-env-on91r6vx 2026-05-13T13:56:28,706 Installing build dependencies: started 2026-05-13T13:56:28,707 Running command pip subprocess to install build dependencies 2026-05-13T13:56:29,846 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-05-13T13:56:30,304 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 2026-05-13T13:56:30,327 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-05-13T13:56:32,162 Collecting setuptools>=42 2026-05-13T13:56:32,163 Obtaining dependency information for setuptools>=42 from https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl.metadata 2026-05-13T13:56:32,180 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB) 2026-05-13T13:56:32,423 Collecting wheel 2026-05-13T13:56:32,424 Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata 2026-05-13T13:56:32,439 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB) 2026-05-13T13:56:32,627 Collecting packaging>=24.0 2026-05-13T13:56:32,628 Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata 2026-05-13T13:56:32,643 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata (3.5 kB) 2026-05-13T13:56:32,834 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-05-13T13:56:32,855 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-05-13T13:56:32,956 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-05-13T13:56:32,996 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-05-13T13:56:33,022 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-05-13T13:56:33,105 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-05-13T13:56:35,949 Installing collected packages: setuptools, packaging, wheel 2026-05-13T13:56:39,432 Creating /tmp/pip-build-env-on91r6vx/overlay/local/bin 2026-05-13T13:56:39,435 changing mode of /tmp/pip-build-env-on91r6vx/overlay/local/bin/wheel to 755 2026-05-13T13:56:39,457 Successfully installed packaging-26.2 setuptools-82.0.1 wheel-0.47.0 2026-05-13T13:56:39,746 Installing build dependencies: finished with status 'done' 2026-05-13T13:56:39,753 Getting requirements to build wheel: started 2026-05-13T13:56:39,754 Running command Getting requirements to build wheel 2026-05-13T13:56:40,691 running egg_info 2026-05-13T13:56:40,697 writing torchref.egg-info/PKG-INFO 2026-05-13T13:56:40,704 writing dependency_links to torchref.egg-info/dependency_links.txt 2026-05-13T13:56:40,707 writing entry points to torchref.egg-info/entry_points.txt 2026-05-13T13:56:40,711 writing requirements to torchref.egg-info/requires.txt 2026-05-13T13:56:40,712 writing top-level names to torchref.egg-info/top_level.txt 2026-05-13T13:56:40,801 reading manifest file 'torchref.egg-info/SOURCES.txt' 2026-05-13T13:56:40,816 adding license file 'LICENSE' 2026-05-13T13:56:40,829 writing manifest file 'torchref.egg-info/SOURCES.txt' 2026-05-13T13:56:40,928 Getting requirements to build wheel: finished with status 'done' 2026-05-13T13:56:40,931 Created temporary directory: /tmp/pip-modern-metadata-l516djy3 2026-05-13T13:56:40,934 Preparing metadata (pyproject.toml): started 2026-05-13T13:56:40,935 Running command Preparing metadata (pyproject.toml) 2026-05-13T13:56:41,625 running dist_info 2026-05-13T13:56:41,636 creating /tmp/pip-modern-metadata-l516djy3/torchref.egg-info 2026-05-13T13:56:41,636 writing /tmp/pip-modern-metadata-l516djy3/torchref.egg-info/PKG-INFO 2026-05-13T13:56:41,644 writing dependency_links to /tmp/pip-modern-metadata-l516djy3/torchref.egg-info/dependency_links.txt 2026-05-13T13:56:41,646 writing entry points to /tmp/pip-modern-metadata-l516djy3/torchref.egg-info/entry_points.txt 2026-05-13T13:56:41,650 writing requirements to /tmp/pip-modern-metadata-l516djy3/torchref.egg-info/requires.txt 2026-05-13T13:56:41,651 writing top-level names to /tmp/pip-modern-metadata-l516djy3/torchref.egg-info/top_level.txt 2026-05-13T13:56:41,653 writing manifest file '/tmp/pip-modern-metadata-l516djy3/torchref.egg-info/SOURCES.txt' 2026-05-13T13:56:41,726 reading manifest file '/tmp/pip-modern-metadata-l516djy3/torchref.egg-info/SOURCES.txt' 2026-05-13T13:56:41,729 adding license file 'LICENSE' 2026-05-13T13:56:41,739 writing manifest file '/tmp/pip-modern-metadata-l516djy3/torchref.egg-info/SOURCES.txt' 2026-05-13T13:56:41,740 creating '/tmp/pip-modern-metadata-l516djy3/torchref-0.5.1.dist-info' 2026-05-13T13:56:41,865 Preparing metadata (pyproject.toml): finished with status 'done' 2026-05-13T13:56:41,870 Source in /tmp/pip-wheel-dft3f0q3/torchref_155f3111a60a47f7a4edf649199f0b3f has version 0.5.1, which satisfies requirement torchref==0.5.1 from https://files.pythonhosted.org/packages/c8/0e/388f73407fc7bfe62c48f8e6983fd0b167b0739c260c2e08953ecaaac1bb/torchref-0.5.1.tar.gz 2026-05-13T13:56:41,871 Removed torchref==0.5.1 from https://files.pythonhosted.org/packages/c8/0e/388f73407fc7bfe62c48f8e6983fd0b167b0739c260c2e08953ecaaac1bb/torchref-0.5.1.tar.gz from build tracker '/tmp/pip-build-tracker-chgdwl6q' 2026-05-13T13:56:41,877 Created temporary directory: /tmp/pip-unpack-km9kb5wf 2026-05-13T13:56:41,878 Building wheels for collected packages: torchref 2026-05-13T13:56:41,882 Created temporary directory: /tmp/pip-wheel-y7_t3hsg 2026-05-13T13:56:41,882 Destination directory: /tmp/pip-wheel-y7_t3hsg 2026-05-13T13:56:41,885 Building wheel for torchref (pyproject.toml): started 2026-05-13T13:56:41,886 Running command Building wheel for torchref (pyproject.toml) 2026-05-13T13:56:42,520 running bdist_wheel 2026-05-13T13:56:42,538 running build 2026-05-13T13:56:42,539 running build_py 2026-05-13T13:56:42,545 creating build/lib/torchref 2026-05-13T13:56:42,547 copying torchref/config.py -> build/lib/torchref 2026-05-13T13:56:42,550 copying torchref/_bootstrap.py -> build/lib/torchref 2026-05-13T13:56:42,552 copying torchref/__init__.py -> build/lib/torchref 2026-05-13T13:56:42,554 creating build/lib/torchref/symmetry 2026-05-13T13:56:42,555 copying torchref/symmetry/grid_utils.py -> build/lib/torchref/symmetry 2026-05-13T13:56:42,558 copying torchref/symmetry/symmetry.py -> build/lib/torchref/symmetry 2026-05-13T13:56:42,560 copying torchref/symmetry/reciprocal_symmetry.py -> build/lib/torchref/symmetry 2026-05-13T13:56:42,563 copying torchref/symmetry/map_symmetry.py -> build/lib/torchref/symmetry 2026-05-13T13:56:42,566 copying torchref/symmetry/__init__.py -> build/lib/torchref/symmetry 2026-05-13T13:56:42,568 copying torchref/symmetry/map_symmetry_interpolation.py -> build/lib/torchref/symmetry 2026-05-13T13:56:42,570 copying torchref/symmetry/cell.py -> build/lib/torchref/symmetry 2026-05-13T13:56:42,572 copying torchref/symmetry/spacegroup.py -> build/lib/torchref/symmetry 2026-05-13T13:56:42,576 creating build/lib/torchref/utils 2026-05-13T13:56:42,577 copying torchref/utils/pse.py -> build/lib/torchref/utils 2026-05-13T13:56:42,579 copying torchref/utils/hyperparameters.py -> build/lib/torchref/utils 2026-05-13T13:56:42,581 copying torchref/utils/serialization.py -> build/lib/torchref/utils 2026-05-13T13:56:42,583 copying torchref/utils/device_mixin.py -> build/lib/torchref/utils 2026-05-13T13:56:42,584 copying torchref/utils/loss_validation.py -> build/lib/torchref/utils 2026-05-13T13:56:42,587 copying torchref/utils/autograd_introspection.py -> build/lib/torchref/utils 2026-05-13T13:56:42,589 copying torchref/utils/caching.py -> build/lib/torchref/utils 2026-05-13T13:56:42,591 copying torchref/utils/autograd_ops.py -> build/lib/torchref/utils 2026-05-13T13:56:42,593 copying torchref/utils/gradnorm.py -> build/lib/torchref/utils 2026-05-13T13:56:42,595 copying torchref/utils/debug_utils.py -> build/lib/torchref/utils 2026-05-13T13:56:42,598 copying torchref/utils/__init__.py -> build/lib/torchref/utils 2026-05-13T13:56:42,600 copying torchref/utils/stats.py -> build/lib/torchref/utils 2026-05-13T13:56:42,602 copying torchref/utils/utils.py -> build/lib/torchref/utils 2026-05-13T13:56:42,605 copying torchref/utils/timing.py -> build/lib/torchref/utils 2026-05-13T13:56:42,607 creating build/lib/torchref/maps 2026-05-13T13:56:42,608 copying torchref/maps/__init__.py -> build/lib/torchref/maps 2026-05-13T13:56:42,610 copying torchref/maps/map.py -> build/lib/torchref/maps 2026-05-13T13:56:42,612 copying torchref/maps/difference_map.py -> build/lib/torchref/maps 2026-05-13T13:56:42,615 creating build/lib/torchref/io 2026-05-13T13:56:42,616 copying torchref/io/data_router.py -> build/lib/torchref/io 2026-05-13T13:56:42,618 copying torchref/io/cif_readers.py -> build/lib/torchref/io 2026-05-13T13:56:42,622 copying torchref/io/mtz.py -> build/lib/torchref/io 2026-05-13T13:56:42,624 copying torchref/io/pdb.py -> build/lib/torchref/io 2026-05-13T13:56:42,627 copying torchref/io/ihm_mapping.py -> build/lib/torchref/io 2026-05-13T13:56:42,629 copying torchref/io/metadata.py -> build/lib/torchref/io 2026-05-13T13:56:42,632 copying torchref/io/__init__.py -> build/lib/torchref/io 2026-05-13T13:56:42,634 copying torchref/io/cif.py -> build/lib/torchref/io 2026-05-13T13:56:42,636 copying torchref/io/ihm.py -> build/lib/torchref/io 2026-05-13T13:56:42,640 creating build/lib/torchref/cli 2026-05-13T13:56:42,641 copying torchref/cli/phased_difference_map.py -> build/lib/torchref/cli 2026-05-13T13:56:42,643 copying torchref/cli/mtz2map.py -> build/lib/torchref/cli 2026-05-13T13:56:42,645 copying torchref/cli/collection_difference_refine.py -> build/lib/torchref/cli 2026-05-13T13:56:42,649 copying torchref/cli/__init__.py -> build/lib/torchref/cli 2026-05-13T13:56:42,650 copying torchref/cli/add_metadata.py -> build/lib/torchref/cli 2026-05-13T13:56:42,652 copying torchref/cli/validate_ded.py -> build/lib/torchref/cli 2026-05-13T13:56:42,655 copying torchref/cli/strip_altlocs.py -> build/lib/torchref/cli 2026-05-13T13:56:42,657 copying torchref/cli/refine.py -> build/lib/torchref/cli 2026-05-13T13:56:42,660 copying torchref/cli/_common.py -> build/lib/torchref/cli 2026-05-13T13:56:42,663 creating build/lib/torchref/base 2026-05-13T13:56:42,664 copying torchref/base/math_numpy.py -> build/lib/torchref/base 2026-05-13T13:56:42,666 copying torchref/base/math_torch.py -> build/lib/torchref/base 2026-05-13T13:56:42,669 copying torchref/base/__init__.py -> build/lib/torchref/base 2026-05-13T13:56:42,672 copying torchref/base/CCTBX_related.py -> build/lib/torchref/base 2026-05-13T13:56:42,674 copying torchref/base/french_wilson.py -> build/lib/torchref/base 2026-05-13T13:56:42,676 copying torchref/base/get_scattering_factor_torch.py -> build/lib/torchref/base 2026-05-13T13:56:42,679 creating build/lib/torchref/scripts 2026-05-13T13:56:42,680 copying torchref/scripts/generate_scattering_table.py -> build/lib/torchref/scripts 2026-05-13T13:56:42,682 copying torchref/scripts/__init__.py -> build/lib/torchref/scripts 2026-05-13T13:56:42,684 creating build/lib/torchref/model 2026-05-13T13:56:42,685 copying torchref/model/sf_fft.py -> build/lib/torchref/model 2026-05-13T13:56:42,688 copying torchref/model/segmented_internal_coordinates.py -> build/lib/torchref/model 2026-05-13T13:56:42,692 copying torchref/model/__init__.py -> build/lib/torchref/model 2026-05-13T13:56:42,693 copying torchref/model/sf_ds.py -> build/lib/torchref/model 2026-05-13T13:56:42,696 copying torchref/model/mixed_model.py -> build/lib/torchref/model 2026-05-13T13:56:42,698 copying torchref/model/internal_coordinates.py -> build/lib/torchref/model 2026-05-13T13:56:42,701 copying torchref/model/model_collection.py -> build/lib/torchref/model 2026-05-13T13:56:42,704 copying torchref/model/parameter_wrappers.py -> build/lib/torchref/model 2026-05-13T13:56:42,707 copying torchref/model/closed_segmented_internal_coordinates.py -> build/lib/torchref/model 2026-05-13T13:56:42,712 copying torchref/model/model.py -> build/lib/torchref/model 2026-05-13T13:56:42,716 copying torchref/model/model_ft.py -> build/lib/torchref/model 2026-05-13T13:56:42,719 creating build/lib/torchref/alignment 2026-05-13T13:56:42,720 copying torchref/alignment/sampling.py -> build/lib/torchref/alignment 2026-05-13T13:56:42,723 copying torchref/alignment/ball_transform.py -> build/lib/torchref/alignment 2026-05-13T13:56:42,726 copying torchref/alignment/__init__.py -> build/lib/torchref/alignment 2026-05-13T13:56:42,729 copying torchref/alignment/rigid_body.py -> build/lib/torchref/alignment 2026-05-13T13:56:42,731 copying torchref/alignment/distributions.py -> build/lib/torchref/alignment 2026-05-13T13:56:42,734 copying torchref/alignment/transform.py -> build/lib/torchref/alignment 2026-05-13T13:56:42,736 copying torchref/alignment/clashscore.py -> build/lib/torchref/alignment 2026-05-13T13:56:42,739 copying torchref/alignment/translation.py -> build/lib/torchref/alignment 2026-05-13T13:56:42,741 copying torchref/alignment/jax_subpixel_peaks.py -> build/lib/torchref/alignment 2026-05-13T13:56:42,743 copying torchref/alignment/pipeline.py -> build/lib/torchref/alignment 2026-05-13T13:56:42,746 creating build/lib/torchref/refinement 2026-05-13T13:56:42,747 copying torchref/refinement/logger.py -> build/lib/torchref/refinement 2026-05-13T13:56:42,750 copying torchref/refinement/loss_state.py -> build/lib/torchref/refinement 2026-05-13T13:56:42,753 copying torchref/refinement/lbfgs_refinement.py -> build/lib/torchref/refinement 2026-05-13T13:56:42,756 copying torchref/refinement/__init__.py -> build/lib/torchref/refinement 2026-05-13T13:56:42,758 copying torchref/refinement/base_refinement.py -> build/lib/torchref/refinement 2026-05-13T13:56:42,762 creating build/lib/torchref/scaling 2026-05-13T13:56:42,763 copying torchref/scaling/scaler.py -> build/lib/torchref/scaling 2026-05-13T13:56:42,765 copying torchref/scaling/solvent.py -> build/lib/torchref/scaling 2026-05-13T13:56:42,768 copying torchref/scaling/__init__.py -> build/lib/torchref/scaling 2026-05-13T13:56:42,770 copying torchref/scaling/scaler_base.py -> build/lib/torchref/scaling 2026-05-13T13:56:42,774 copying torchref/scaling/collection_scaler.py -> build/lib/torchref/scaling 2026-05-13T13:56:42,777 creating build/lib/torchref/restraints 2026-05-13T13:56:42,778 copying torchref/restraints/neighbor_search.py -> build/lib/torchref/restraints 2026-05-13T13:56:42,781 copying torchref/restraints/builders_numba.py -> build/lib/torchref/restraints 2026-05-13T13:56:42,784 copying torchref/restraints/__init__.py -> build/lib/torchref/restraints 2026-05-13T13:56:42,786 copying torchref/restraints/restraints.py -> build/lib/torchref/restraints 2026-05-13T13:56:42,789 copying torchref/restraints/restraints_helper.py -> build/lib/torchref/restraints 2026-05-13T13:56:42,792 copying torchref/restraints/ramachandran.py -> build/lib/torchref/restraints 2026-05-13T13:56:42,794 copying torchref/restraints/library.py -> build/lib/torchref/restraints 2026-05-13T13:56:42,796 copying torchref/restraints/builders.py -> build/lib/torchref/restraints 2026-05-13T13:56:42,799 copying torchref/restraints/hydrogen_topology.py -> build/lib/torchref/restraints 2026-05-13T13:56:42,802 copying torchref/restraints/builders_fast.py -> build/lib/torchref/restraints 2026-05-13T13:56:42,806 creating build/lib/torchref/kinetic 2026-05-13T13:56:42,807 copying torchref/kinetic/refinement.py -> build/lib/torchref/kinetic 2026-05-13T13:56:42,809 copying torchref/kinetic/__init__.py -> build/lib/torchref/kinetic 2026-05-13T13:56:42,811 copying torchref/kinetic/occupancies.py -> build/lib/torchref/kinetic 2026-05-13T13:56:42,814 copying torchref/kinetic/targets.py -> build/lib/torchref/kinetic 2026-05-13T13:56:42,816 copying torchref/kinetic/kinetics.py -> build/lib/torchref/kinetic 2026-05-13T13:56:42,819 creating build/lib/torchref/io/datasets 2026-05-13T13:56:42,820 copying torchref/io/datasets/fcalc_data.py -> build/lib/torchref/io/datasets 2026-05-13T13:56:42,823 copying torchref/io/datasets/base.py -> build/lib/torchref/io/datasets 2026-05-13T13:56:42,825 copying torchref/io/datasets/__init__.py -> build/lib/torchref/io/datasets 2026-05-13T13:56:42,827 copying torchref/io/datasets/collection.py -> build/lib/torchref/io/datasets 2026-05-13T13:56:42,830 copying torchref/io/datasets/reflection_data.py -> build/lib/torchref/io/datasets 2026-05-13T13:56:42,834 creating build/lib/torchref/base/fourier 2026-05-13T13:56:42,835 copying torchref/base/fourier/fft.py -> build/lib/torchref/base/fourier 2026-05-13T13:56:42,837 copying torchref/base/fourier/grid.py -> build/lib/torchref/base/fourier 2026-05-13T13:56:42,839 copying torchref/base/fourier/__init__.py -> build/lib/torchref/base/fourier 2026-05-13T13:56:42,842 creating build/lib/torchref/base/targets 2026-05-13T13:56:42,843 copying torchref/base/targets/_dispatch.py -> build/lib/torchref/base/targets 2026-05-13T13:56:42,845 copying torchref/base/targets/xray_gaussian.py -> build/lib/torchref/base/targets 2026-05-13T13:56:42,847 copying torchref/base/targets/planarity.py -> build/lib/torchref/base/targets 2026-05-13T13:56:42,849 copying torchref/base/targets/adp.py -> build/lib/torchref/base/targets 2026-05-13T13:56:42,851 copying torchref/base/targets/xray_ls.py -> build/lib/torchref/base/targets 2026-05-13T13:56:42,852 copying torchref/base/targets/nonbonded.py -> build/lib/torchref/base/targets 2026-05-13T13:56:42,855 copying torchref/base/targets/angle.py -> build/lib/torchref/base/targets 2026-05-13T13:56:42,856 copying torchref/base/targets/__init__.py -> build/lib/torchref/base/targets 2026-05-13T13:56:42,858 copying torchref/base/targets/bond.py -> build/lib/torchref/base/targets 2026-05-13T13:56:42,860 copying torchref/base/targets/xray_bhattacharyya.py -> build/lib/torchref/base/targets 2026-05-13T13:56:42,862 copying torchref/base/targets/chiral.py -> build/lib/torchref/base/targets 2026-05-13T13:56:42,864 copying torchref/base/targets/xray_ml.py -> build/lib/torchref/base/targets 2026-05-13T13:56:42,866 copying torchref/base/targets/ramachandran.py -> build/lib/torchref/base/targets 2026-05-13T13:56:42,867 copying torchref/base/targets/torsion.py -> build/lib/torchref/base/targets 2026-05-13T13:56:42,869 copying torchref/base/targets/_common.py -> build/lib/torchref/base/targets 2026-05-13T13:56:42,872 creating build/lib/torchref/base/metrics 2026-05-13T13:56:42,873 copying torchref/base/metrics/loss.py -> build/lib/torchref/base/metrics 2026-05-13T13:56:42,877 copying torchref/base/metrics/rfactor.py -> build/lib/torchref/base/metrics 2026-05-13T13:56:42,879 copying torchref/base/metrics/__init__.py -> build/lib/torchref/base/metrics 2026-05-13T13:56:42,881 creating build/lib/torchref/base/scattering 2026-05-13T13:56:42,882 copying torchref/base/scattering/scattering_table.py -> build/lib/torchref/base/scattering 2026-05-13T13:56:42,884 copying torchref/base/scattering/anomalous_table.py -> build/lib/torchref/base/scattering 2026-05-13T13:56:42,886 copying torchref/base/scattering/__init__.py -> build/lib/torchref/base/scattering 2026-05-13T13:56:42,888 copying torchref/base/scattering/itc92.py -> build/lib/torchref/base/scattering 2026-05-13T13:56:42,891 creating build/lib/torchref/base/kernels 2026-05-13T13:56:42,892 copying torchref/base/kernels/optimized_ops.py -> build/lib/torchref/base/kernels 2026-05-13T13:56:42,894 copying torchref/base/kernels/jit_kernel_vectorized_add_to_map.py -> build/lib/torchref/base/kernels 2026-05-13T13:56:42,896 copying torchref/base/kernels/cpu_scatter.py -> build/lib/torchref/base/kernels 2026-05-13T13:56:42,899 copying torchref/base/kernels/separable_triton_kernel.py -> build/lib/torchref/base/kernels 2026-05-13T13:56:42,902 copying torchref/base/kernels/__init__.py -> build/lib/torchref/base/kernels 2026-05-13T13:56:42,904 copying torchref/base/kernels/triton_kernel.py -> build/lib/torchref/base/kernels 2026-05-13T13:56:42,907 creating build/lib/torchref/base/direct_summation 2026-05-13T13:56:42,908 copying torchref/base/direct_summation/isotropic.py -> build/lib/torchref/base/direct_summation 2026-05-13T13:56:42,911 copying torchref/base/direct_summation/corrections.py -> build/lib/torchref/base/direct_summation 2026-05-13T13:56:42,913 copying torchref/base/direct_summation/__init__.py -> build/lib/torchref/base/direct_summation 2026-05-13T13:56:42,915 copying torchref/base/direct_summation/anisotropic.py -> build/lib/torchref/base/direct_summation 2026-05-13T13:56:42,917 creating build/lib/torchref/base/coordinates 2026-05-13T13:56:42,918 copying torchref/base/coordinates/periodic_boundary.py -> build/lib/torchref/base/coordinates 2026-05-13T13:56:42,920 copying torchref/base/coordinates/transforms_numpy.py -> build/lib/torchref/base/coordinates 2026-05-13T13:56:42,923 copying torchref/base/coordinates/__init__.py -> build/lib/torchref/base/coordinates 2026-05-13T13:56:42,924 copying torchref/base/coordinates/transforms_torch.py -> build/lib/torchref/base/coordinates 2026-05-13T13:56:42,927 creating build/lib/torchref/base/alignment 2026-05-13T13:56:42,928 copying torchref/base/alignment/normalization.py -> build/lib/torchref/base/alignment 2026-05-13T13:56:42,931 copying torchref/base/alignment/scoring.py -> build/lib/torchref/base/alignment 2026-05-13T13:56:42,932 copying torchref/base/alignment/superposition.py -> build/lib/torchref/base/alignment 2026-05-13T13:56:42,935 copying torchref/base/alignment/__init__.py -> build/lib/torchref/base/alignment 2026-05-13T13:56:42,937 copying torchref/base/alignment/rotation.py -> build/lib/torchref/base/alignment 2026-05-13T13:56:42,941 creating build/lib/torchref/base/reciprocal 2026-05-13T13:56:42,942 copying torchref/base/reciprocal/symmetry.py -> build/lib/torchref/base/reciprocal 2026-05-13T13:56:42,944 copying torchref/base/reciprocal/grid_operations.py -> build/lib/torchref/base/reciprocal 2026-05-13T13:56:42,946 copying torchref/base/reciprocal/basis.py -> build/lib/torchref/base/reciprocal 2026-05-13T13:56:42,949 copying torchref/base/reciprocal/__init__.py -> build/lib/torchref/base/reciprocal 2026-05-13T13:56:42,951 copying torchref/base/reciprocal/interpolation.py -> build/lib/torchref/base/reciprocal 2026-05-13T13:56:42,953 copying torchref/base/reciprocal/hkl.py -> build/lib/torchref/base/reciprocal 2026-05-13T13:56:42,956 creating build/lib/torchref/base/electron_density 2026-05-13T13:56:42,957 copying torchref/base/electron_density/map_building.py -> build/lib/torchref/base/electron_density 2026-05-13T13:56:42,959 copying torchref/base/electron_density/solvent_mask.py -> build/lib/torchref/base/electron_density 2026-05-13T13:56:42,962 copying torchref/base/electron_density/main.py -> build/lib/torchref/base/electron_density 2026-05-13T13:56:42,965 copying torchref/base/electron_density/__init__.py -> build/lib/torchref/base/electron_density 2026-05-13T13:56:42,967 copying torchref/base/electron_density/voxel_utils.py -> build/lib/torchref/base/electron_density 2026-05-13T13:56:42,969 creating build/lib/torchref/base/chain_closure 2026-05-13T13:56:42,970 copying torchref/base/chain_closure/closure.py -> build/lib/torchref/base/chain_closure 2026-05-13T13:56:42,973 copying torchref/base/chain_closure/backbone_utils.py -> build/lib/torchref/base/chain_closure 2026-05-13T13:56:42,975 copying torchref/base/chain_closure/__init__.py -> build/lib/torchref/base/chain_closure 2026-05-13T13:56:42,978 creating build/lib/torchref/base/targets/triton 2026-05-13T13:56:42,979 copying torchref/base/targets/triton/xray_gaussian.py -> build/lib/torchref/base/targets/triton 2026-05-13T13:56:42,981 copying torchref/base/targets/triton/place_hydrogens.py -> build/lib/torchref/base/targets/triton 2026-05-13T13:56:42,984 copying torchref/base/targets/triton/planarity.py -> build/lib/torchref/base/targets/triton 2026-05-13T13:56:42,986 copying torchref/base/targets/triton/xray_ls.py -> build/lib/torchref/base/targets/triton 2026-05-13T13:56:42,988 copying torchref/base/targets/triton/nonbonded.py -> build/lib/torchref/base/targets/triton 2026-05-13T13:56:42,991 copying torchref/base/targets/triton/angle.py -> build/lib/torchref/base/targets/triton 2026-05-13T13:56:42,993 copying torchref/base/targets/triton/__init__.py -> build/lib/torchref/base/targets/triton 2026-05-13T13:56:42,995 copying torchref/base/targets/triton/bond.py -> build/lib/torchref/base/targets/triton 2026-05-13T13:56:42,997 copying torchref/base/targets/triton/xray_bhattacharyya.py -> build/lib/torchref/base/targets/triton 2026-05-13T13:56:42,999 copying torchref/base/targets/triton/chiral.py -> build/lib/torchref/base/targets/triton 2026-05-13T13:56:43,001 copying torchref/base/targets/triton/xray_ml.py -> build/lib/torchref/base/targets/triton 2026-05-13T13:56:43,004 copying torchref/base/targets/triton/_dihedral.py -> build/lib/torchref/base/targets/triton 2026-05-13T13:56:43,006 copying torchref/base/targets/triton/adp_simu.py -> build/lib/torchref/base/targets/triton 2026-05-13T13:56:43,008 copying torchref/base/targets/triton/ramachandran.py -> build/lib/torchref/base/targets/triton 2026-05-13T13:56:43,010 copying torchref/base/targets/triton/torsion.py -> build/lib/torchref/base/targets/triton 2026-05-13T13:56:43,014 creating build/lib/torchref/refinement/targets 2026-05-13T13:56:43,014 copying torchref/refinement/targets/amber_target.py -> build/lib/torchref/refinement/targets 2026-05-13T13:56:43,018 copying torchref/refinement/targets/occupancy_floor_diagnostic.py -> build/lib/torchref/refinement/targets 2026-05-13T13:56:43,020 copying torchref/refinement/targets/base.py -> build/lib/torchref/refinement/targets 2026-05-13T13:56:43,023 copying torchref/refinement/targets/realspace.py -> build/lib/torchref/refinement/targets 2026-05-13T13:56:43,026 copying torchref/refinement/targets/forcefield_target.py -> build/lib/torchref/refinement/targets 2026-05-13T13:56:43,028 copying torchref/refinement/targets/__init__.py -> build/lib/torchref/refinement/targets 2026-05-13T13:56:43,030 copying torchref/refinement/targets/combined.py -> build/lib/torchref/refinement/targets 2026-05-13T13:56:43,033 copying torchref/refinement/targets/similarity.py -> build/lib/torchref/refinement/targets 2026-05-13T13:56:43,036 copying torchref/refinement/targets/sampled_ml_phase_target.py -> build/lib/torchref/refinement/targets 2026-05-13T13:56:43,039 copying torchref/refinement/targets/difference.py -> build/lib/torchref/refinement/targets 2026-05-13T13:56:43,042 creating build/lib/torchref/refinement/weighting 2026-05-13T13:56:43,043 copying torchref/refinement/weighting/es_policy_training.py -> build/lib/torchref/refinement/weighting 2026-05-13T13:56:43,046 copying torchref/refinement/weighting/policy_weighting.py -> build/lib/torchref/refinement/weighting 2026-05-13T13:56:43,049 copying torchref/refinement/weighting/base_weighting.py -> build/lib/torchref/refinement/weighting 2026-05-13T13:56:43,051 copying torchref/refinement/weighting/component_weighting.py -> build/lib/torchref/refinement/weighting 2026-05-13T13:56:43,053 copying torchref/refinement/weighting/__init__.py -> build/lib/torchref/refinement/weighting 2026-05-13T13:56:43,055 copying torchref/refinement/weighting/random_weighting.py -> build/lib/torchref/refinement/weighting 2026-05-13T13:56:43,058 creating build/lib/torchref/refinement/optimizers 2026-05-13T13:56:43,058 copying torchref/refinement/optimizers/langevin_sa.py -> build/lib/torchref/refinement/optimizers 2026-05-13T13:56:43,061 copying torchref/refinement/optimizers/adam_noise.py -> build/lib/torchref/refinement/optimizers 2026-05-13T13:56:43,063 copying torchref/refinement/optimizers/__init__.py -> build/lib/torchref/refinement/optimizers 2026-05-13T13:56:43,065 copying torchref/refinement/optimizers/momentum_sa.py -> build/lib/torchref/refinement/optimizers 2026-05-13T13:56:43,067 copying torchref/refinement/optimizers/internal_coord_sa.py -> build/lib/torchref/refinement/optimizers 2026-05-13T13:56:43,070 copying torchref/refinement/optimizers/exploratory_lbfgs.py -> build/lib/torchref/refinement/optimizers 2026-05-13T13:56:43,073 copying torchref/refinement/optimizers/simulated_annealing.py -> build/lib/torchref/refinement/optimizers 2026-05-13T13:56:43,075 creating build/lib/torchref/refinement/targets/adp 2026-05-13T13:56:43,076 copying torchref/refinement/targets/adp/scaler_u.py -> build/lib/torchref/refinement/targets/adp 2026-05-13T13:56:43,078 copying torchref/refinement/targets/adp/base.py -> build/lib/torchref/refinement/targets/adp 2026-05-13T13:56:43,080 copying torchref/refinement/targets/adp/rigid_bond.py -> build/lib/torchref/refinement/targets/adp 2026-05-13T13:56:43,083 copying torchref/refinement/targets/adp/__init__.py -> build/lib/torchref/refinement/targets/adp 2026-05-13T13:56:43,084 copying torchref/refinement/targets/adp/scaler_log_scale.py -> build/lib/torchref/refinement/targets/adp 2026-05-13T13:56:43,086 copying torchref/refinement/targets/adp/entropy.py -> build/lib/torchref/refinement/targets/adp 2026-05-13T13:56:43,088 copying torchref/refinement/targets/adp/similarity.py -> build/lib/torchref/refinement/targets/adp 2026-05-13T13:56:43,090 copying torchref/refinement/targets/adp/locality.py -> build/lib/torchref/refinement/targets/adp 2026-05-13T13:56:43,093 creating build/lib/torchref/refinement/targets/geometry 2026-05-13T13:56:43,094 copying torchref/refinement/targets/geometry/planarity.py -> build/lib/torchref/refinement/targets/geometry 2026-05-13T13:56:43,097 copying torchref/refinement/targets/geometry/base.py -> build/lib/torchref/refinement/targets/geometry 2026-05-13T13:56:43,099 copying torchref/refinement/targets/geometry/non_bonded.py -> build/lib/torchref/refinement/targets/geometry 2026-05-13T13:56:43,101 copying torchref/refinement/targets/geometry/__init__.py -> build/lib/torchref/refinement/targets/geometry 2026-05-13T13:56:43,103 copying torchref/refinement/targets/geometry/chiral.py -> build/lib/torchref/refinement/targets/geometry 2026-05-13T13:56:43,105 copying torchref/refinement/targets/geometry/bonds.py -> build/lib/torchref/refinement/targets/geometry 2026-05-13T13:56:43,107 copying torchref/refinement/targets/geometry/torsions.py -> build/lib/torchref/refinement/targets/geometry 2026-05-13T13:56:43,110 copying torchref/refinement/targets/geometry/non_bonded_h.py -> build/lib/torchref/refinement/targets/geometry 2026-05-13T13:56:43,112 copying torchref/refinement/targets/geometry/ramachandran.py -> build/lib/torchref/refinement/targets/geometry 2026-05-13T13:56:43,114 copying torchref/refinement/targets/geometry/angles.py -> build/lib/torchref/refinement/targets/geometry 2026-05-13T13:56:43,116 creating build/lib/torchref/refinement/targets/xray 2026-05-13T13:56:43,117 copying torchref/refinement/targets/xray/bhattacharyya.py -> build/lib/torchref/refinement/targets/xray 2026-05-13T13:56:43,120 copying torchref/refinement/targets/xray/maximum_likelihood.py -> build/lib/torchref/refinement/targets/xray 2026-05-13T13:56:43,122 copying torchref/refinement/targets/xray/base.py -> build/lib/torchref/refinement/targets/xray 2026-05-13T13:56:43,124 copying torchref/refinement/targets/xray/__init__.py -> build/lib/torchref/refinement/targets/xray 2026-05-13T13:56:43,126 copying torchref/refinement/targets/xray/least_squares.py -> build/lib/torchref/refinement/targets/xray 2026-05-13T13:56:43,128 copying torchref/refinement/targets/xray/gaussian.py -> build/lib/torchref/refinement/targets/xray 2026-05-13T13:56:43,134 running egg_info 2026-05-13T13:56:43,145 writing torchref.egg-info/PKG-INFO 2026-05-13T13:56:43,152 writing dependency_links to torchref.egg-info/dependency_links.txt 2026-05-13T13:56:43,154 writing entry points to torchref.egg-info/entry_points.txt 2026-05-13T13:56:43,158 writing requirements to torchref.egg-info/requires.txt 2026-05-13T13:56:43,159 writing top-level names to torchref.egg-info/top_level.txt 2026-05-13T13:56:43,220 reading manifest file 'torchref.egg-info/SOURCES.txt' 2026-05-13T13:56:43,235 adding license file 'LICENSE' 2026-05-13T13:56:43,249 writing manifest file 'torchref.egg-info/SOURCES.txt' 2026-05-13T13:56:43,284 creating build/lib/torchref/data 2026-05-13T13:56:43,285 copying torchref/data/atomic_vdw_radii.csv -> build/lib/torchref/data 2026-05-13T13:56:43,288 copying torchref/data/itc92_scattering_factors.pt -> build/lib/torchref/data 2026-05-13T13:56:43,290 copying torchref/data/rama_nll_surfaces.pt -> build/lib/torchref/data 2026-05-13T13:56:43,343 creating build/lib/torchref/data/monomer_library/d 2026-05-13T13:56:43,345 copying torchref/data/monomer_library/d/DA.cif -> build/lib/torchref/data/monomer_library/d 2026-05-13T13:56:43,348 copying torchref/data/monomer_library/d/DG.cif -> build/lib/torchref/data/monomer_library/d 2026-05-13T13:56:43,351 copying torchref/data/monomer_library/d/DT.cif -> build/lib/torchref/data/monomer_library/d 2026-05-13T13:56:43,355 copying torchref/data/monomer_library/d/DC.cif -> build/lib/torchref/data/monomer_library/d 2026-05-13T13:56:43,358 creating build/lib/torchref/data/monomer_library/i 2026-05-13T13:56:43,359 copying torchref/data/monomer_library/i/ILE.cif -> build/lib/torchref/data/monomer_library/i 2026-05-13T13:56:43,362 creating build/lib/torchref/data/monomer_library/m 2026-05-13T13:56:43,364 copying torchref/data/monomer_library/m/MSE.cif -> build/lib/torchref/data/monomer_library/m 2026-05-13T13:56:43,367 copying torchref/data/monomer_library/m/MET.cif -> build/lib/torchref/data/monomer_library/m 2026-05-13T13:56:43,370 creating build/lib/torchref/data/monomer_library/u 2026-05-13T13:56:43,371 copying torchref/data/monomer_library/u/U.cif -> build/lib/torchref/data/monomer_library/u 2026-05-13T13:56:43,374 creating build/lib/torchref/data/monomer_library/h 2026-05-13T13:56:43,376 copying torchref/data/monomer_library/h/HOH.cif -> build/lib/torchref/data/monomer_library/h 2026-05-13T13:56:43,379 copying torchref/data/monomer_library/h/HIS.cif -> build/lib/torchref/data/monomer_library/h 2026-05-13T13:56:43,382 copying torchref/data/monomer_library/h/HYP.cif -> build/lib/torchref/data/monomer_library/h 2026-05-13T13:56:43,385 creating build/lib/torchref/data/monomer_library/c 2026-05-13T13:56:43,386 copying torchref/data/monomer_library/c/CYS.cif -> build/lib/torchref/data/monomer_library/c 2026-05-13T13:56:43,389 copying torchref/data/monomer_library/c/C.cif -> build/lib/torchref/data/monomer_library/c 2026-05-13T13:56:43,392 creating build/lib/torchref/data/monomer_library/list 2026-05-13T13:56:43,393 copying torchref/data/monomer_library/list/mon_lib_list.cif -> build/lib/torchref/data/monomer_library/list 2026-05-13T13:56:43,468 creating build/lib/torchref/data/monomer_library/p 2026-05-13T13:56:43,469 copying torchref/data/monomer_library/p/PHE.cif -> build/lib/torchref/data/monomer_library/p 2026-05-13T13:56:43,472 copying torchref/data/monomer_library/p/PTR.cif -> build/lib/torchref/data/monomer_library/p 2026-05-13T13:56:43,474 copying torchref/data/monomer_library/p/PRO.cif -> build/lib/torchref/data/monomer_library/p 2026-05-13T13:56:43,477 creating build/lib/torchref/data/monomer_library/v 2026-05-13T13:56:43,477 copying torchref/data/monomer_library/v/VAL.cif -> build/lib/torchref/data/monomer_library/v 2026-05-13T13:56:43,480 creating build/lib/torchref/data/monomer_library/a 2026-05-13T13:56:43,481 copying torchref/data/monomer_library/a/ASP.cif -> build/lib/torchref/data/monomer_library/a 2026-05-13T13:56:43,483 copying torchref/data/monomer_library/a/ASN.cif -> build/lib/torchref/data/monomer_library/a 2026-05-13T13:56:43,485 copying torchref/data/monomer_library/a/ALA.cif -> build/lib/torchref/data/monomer_library/a 2026-05-13T13:56:43,488 copying torchref/data/monomer_library/a/ARG.cif -> build/lib/torchref/data/monomer_library/a 2026-05-13T13:56:43,490 copying torchref/data/monomer_library/a/A.cif -> build/lib/torchref/data/monomer_library/a 2026-05-13T13:56:43,493 creating build/lib/torchref/data/monomer_library/l 2026-05-13T13:56:43,494 copying torchref/data/monomer_library/l/LEU.cif -> build/lib/torchref/data/monomer_library/l 2026-05-13T13:56:43,496 copying torchref/data/monomer_library/l/LYS.cif -> build/lib/torchref/data/monomer_library/l 2026-05-13T13:56:43,499 creating build/lib/torchref/data/monomer_library/t 2026-05-13T13:56:43,500 copying torchref/data/monomer_library/t/THR.cif -> build/lib/torchref/data/monomer_library/t 2026-05-13T13:56:43,502 copying torchref/data/monomer_library/t/TPO.cif -> build/lib/torchref/data/monomer_library/t 2026-05-13T13:56:43,505 copying torchref/data/monomer_library/t/TRP.cif -> build/lib/torchref/data/monomer_library/t 2026-05-13T13:56:43,508 copying torchref/data/monomer_library/t/TYR.cif -> build/lib/torchref/data/monomer_library/t 2026-05-13T13:56:43,510 creating build/lib/torchref/data/monomer_library/g 2026-05-13T13:56:43,511 copying torchref/data/monomer_library/g/GLU.cif -> build/lib/torchref/data/monomer_library/g 2026-05-13T13:56:43,514 copying torchref/data/monomer_library/g/GLN.cif -> build/lib/torchref/data/monomer_library/g 2026-05-13T13:56:43,517 copying torchref/data/monomer_library/g/G.cif -> build/lib/torchref/data/monomer_library/g 2026-05-13T13:56:43,520 copying torchref/data/monomer_library/g/GLY.cif -> build/lib/torchref/data/monomer_library/g 2026-05-13T13:56:43,522 creating build/lib/torchref/data/monomer_library/s 2026-05-13T13:56:43,523 copying torchref/data/monomer_library/s/SEP.cif -> build/lib/torchref/data/monomer_library/s 2026-05-13T13:56:43,525 copying torchref/data/monomer_library/s/SER.cif -> build/lib/torchref/data/monomer_library/s 2026-05-13T13:56:43,572 installing to build/bdist.linux-armv7l/wheel 2026-05-13T13:56:43,572 running install 2026-05-13T13:56:43,595 running install_lib 2026-05-13T13:56:43,601 creating build/bdist.linux-armv7l/wheel 2026-05-13T13:56:43,603 creating build/bdist.linux-armv7l/wheel/torchref 2026-05-13T13:56:43,605 creating build/bdist.linux-armv7l/wheel/torchref/symmetry 2026-05-13T13:56:43,606 copying build/lib/torchref/symmetry/grid_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry 2026-05-13T13:56:43,608 copying build/lib/torchref/symmetry/symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry 2026-05-13T13:56:43,610 copying build/lib/torchref/symmetry/reciprocal_symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry 2026-05-13T13:56:43,614 copying build/lib/torchref/symmetry/map_symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry 2026-05-13T13:56:43,616 copying build/lib/torchref/symmetry/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry 2026-05-13T13:56:43,618 copying build/lib/torchref/symmetry/map_symmetry_interpolation.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry 2026-05-13T13:56:43,620 copying build/lib/torchref/symmetry/cell.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry 2026-05-13T13:56:43,623 copying build/lib/torchref/symmetry/spacegroup.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry 2026-05-13T13:56:43,626 creating build/bdist.linux-armv7l/wheel/torchref/utils 2026-05-13T13:56:43,627 copying build/lib/torchref/utils/pse.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-05-13T13:56:43,630 copying build/lib/torchref/utils/hyperparameters.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-05-13T13:56:43,632 copying build/lib/torchref/utils/serialization.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-05-13T13:56:43,633 copying build/lib/torchref/utils/device_mixin.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-05-13T13:56:43,635 copying build/lib/torchref/utils/loss_validation.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-05-13T13:56:43,638 copying build/lib/torchref/utils/autograd_introspection.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-05-13T13:56:43,639 copying build/lib/torchref/utils/caching.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-05-13T13:56:43,642 copying build/lib/torchref/utils/autograd_ops.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-05-13T13:56:43,643 copying build/lib/torchref/utils/gradnorm.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-05-13T13:56:43,645 copying build/lib/torchref/utils/debug_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-05-13T13:56:43,647 copying build/lib/torchref/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-05-13T13:56:43,649 copying build/lib/torchref/utils/stats.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-05-13T13:56:43,651 copying build/lib/torchref/utils/utils.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-05-13T13:56:43,654 copying build/lib/torchref/utils/timing.py -> build/bdist.linux-armv7l/wheel/./torchref/utils 2026-05-13T13:56:43,656 copying build/lib/torchref/config.py -> build/bdist.linux-armv7l/wheel/./torchref 2026-05-13T13:56:43,659 creating build/bdist.linux-armv7l/wheel/torchref/maps 2026-05-13T13:56:43,660 copying build/lib/torchref/maps/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/maps 2026-05-13T13:56:43,662 copying build/lib/torchref/maps/map.py -> build/bdist.linux-armv7l/wheel/./torchref/maps 2026-05-13T13:56:43,664 copying build/lib/torchref/maps/difference_map.py -> build/bdist.linux-armv7l/wheel/./torchref/maps 2026-05-13T13:56:43,667 creating build/bdist.linux-armv7l/wheel/torchref/io 2026-05-13T13:56:43,668 copying build/lib/torchref/io/data_router.py -> build/bdist.linux-armv7l/wheel/./torchref/io 2026-05-13T13:56:43,671 copying build/lib/torchref/io/cif_readers.py -> build/bdist.linux-armv7l/wheel/./torchref/io 2026-05-13T13:56:43,674 copying build/lib/torchref/io/mtz.py -> build/bdist.linux-armv7l/wheel/./torchref/io 2026-05-13T13:56:43,677 copying build/lib/torchref/io/pdb.py -> build/bdist.linux-armv7l/wheel/./torchref/io 2026-05-13T13:56:43,680 copying build/lib/torchref/io/ihm_mapping.py -> build/bdist.linux-armv7l/wheel/./torchref/io 2026-05-13T13:56:43,682 copying build/lib/torchref/io/metadata.py -> build/bdist.linux-armv7l/wheel/./torchref/io 2026-05-13T13:56:43,684 copying build/lib/torchref/io/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/io 2026-05-13T13:56:43,687 creating build/bdist.linux-armv7l/wheel/torchref/io/datasets 2026-05-13T13:56:43,688 copying build/lib/torchref/io/datasets/fcalc_data.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets 2026-05-13T13:56:43,691 copying build/lib/torchref/io/datasets/base.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets 2026-05-13T13:56:43,693 copying build/lib/torchref/io/datasets/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets 2026-05-13T13:56:43,695 copying build/lib/torchref/io/datasets/collection.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets 2026-05-13T13:56:43,697 copying build/lib/torchref/io/datasets/reflection_data.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets 2026-05-13T13:56:43,701 copying build/lib/torchref/io/cif.py -> build/bdist.linux-armv7l/wheel/./torchref/io 2026-05-13T13:56:43,703 copying build/lib/torchref/io/ihm.py -> build/bdist.linux-armv7l/wheel/./torchref/io 2026-05-13T13:56:43,707 creating build/bdist.linux-armv7l/wheel/torchref/cli 2026-05-13T13:56:43,708 copying build/lib/torchref/cli/phased_difference_map.py -> build/bdist.linux-armv7l/wheel/./torchref/cli 2026-05-13T13:56:43,710 copying build/lib/torchref/cli/mtz2map.py -> build/bdist.linux-armv7l/wheel/./torchref/cli 2026-05-13T13:56:43,712 copying build/lib/torchref/cli/collection_difference_refine.py -> build/bdist.linux-armv7l/wheel/./torchref/cli 2026-05-13T13:56:43,715 copying build/lib/torchref/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/cli 2026-05-13T13:56:43,717 copying build/lib/torchref/cli/add_metadata.py -> build/bdist.linux-armv7l/wheel/./torchref/cli 2026-05-13T13:56:43,719 copying build/lib/torchref/cli/validate_ded.py -> build/bdist.linux-armv7l/wheel/./torchref/cli 2026-05-13T13:56:43,722 copying build/lib/torchref/cli/strip_altlocs.py -> build/bdist.linux-armv7l/wheel/./torchref/cli 2026-05-13T13:56:43,723 copying build/lib/torchref/cli/refine.py -> build/bdist.linux-armv7l/wheel/./torchref/cli 2026-05-13T13:56:43,726 copying build/lib/torchref/cli/_common.py -> build/bdist.linux-armv7l/wheel/./torchref/cli 2026-05-13T13:56:43,728 copying build/lib/torchref/_bootstrap.py -> build/bdist.linux-armv7l/wheel/./torchref 2026-05-13T13:56:43,730 creating build/bdist.linux-armv7l/wheel/torchref/base 2026-05-13T13:56:43,731 copying build/lib/torchref/base/math_numpy.py -> build/bdist.linux-armv7l/wheel/./torchref/base 2026-05-13T13:56:43,734 copying build/lib/torchref/base/math_torch.py -> build/bdist.linux-armv7l/wheel/./torchref/base 2026-05-13T13:56:43,737 creating build/bdist.linux-armv7l/wheel/torchref/base/fourier 2026-05-13T13:56:43,738 copying build/lib/torchref/base/fourier/fft.py -> build/bdist.linux-armv7l/wheel/./torchref/base/fourier 2026-05-13T13:56:43,740 copying build/lib/torchref/base/fourier/grid.py -> build/bdist.linux-armv7l/wheel/./torchref/base/fourier 2026-05-13T13:56:43,742 copying build/lib/torchref/base/fourier/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/fourier 2026-05-13T13:56:43,745 creating build/bdist.linux-armv7l/wheel/torchref/base/targets 2026-05-13T13:56:43,746 copying build/lib/torchref/base/targets/_dispatch.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets 2026-05-13T13:56:43,748 copying build/lib/torchref/base/targets/xray_gaussian.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets 2026-05-13T13:56:43,750 copying build/lib/torchref/base/targets/planarity.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets 2026-05-13T13:56:43,752 copying build/lib/torchref/base/targets/adp.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets 2026-05-13T13:56:43,754 copying build/lib/torchref/base/targets/xray_ls.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets 2026-05-13T13:56:43,756 copying build/lib/torchref/base/targets/nonbonded.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets 2026-05-13T13:56:43,758 copying build/lib/torchref/base/targets/angle.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets 2026-05-13T13:56:43,760 copying build/lib/torchref/base/targets/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets 2026-05-13T13:56:43,762 copying build/lib/torchref/base/targets/bond.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets 2026-05-13T13:56:43,764 copying build/lib/torchref/base/targets/xray_bhattacharyya.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets 2026-05-13T13:56:43,766 copying build/lib/torchref/base/targets/chiral.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets 2026-05-13T13:56:43,767 copying build/lib/torchref/base/targets/xray_ml.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets 2026-05-13T13:56:43,770 creating build/bdist.linux-armv7l/wheel/torchref/base/targets/triton 2026-05-13T13:56:43,771 copying build/lib/torchref/base/targets/triton/xray_gaussian.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton 2026-05-13T13:56:43,773 copying build/lib/torchref/base/targets/triton/place_hydrogens.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton 2026-05-13T13:56:43,776 copying build/lib/torchref/base/targets/triton/planarity.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton 2026-05-13T13:56:43,778 copying build/lib/torchref/base/targets/triton/xray_ls.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton 2026-05-13T13:56:43,780 copying build/lib/torchref/base/targets/triton/nonbonded.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton 2026-05-13T13:56:43,783 copying build/lib/torchref/base/targets/triton/angle.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton 2026-05-13T13:56:43,785 copying build/lib/torchref/base/targets/triton/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton 2026-05-13T13:56:43,787 copying build/lib/torchref/base/targets/triton/bond.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton 2026-05-13T13:56:43,790 copying build/lib/torchref/base/targets/triton/xray_bhattacharyya.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton 2026-05-13T13:56:43,792 copying build/lib/torchref/base/targets/triton/chiral.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton 2026-05-13T13:56:43,795 copying build/lib/torchref/base/targets/triton/xray_ml.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton 2026-05-13T13:56:43,798 copying build/lib/torchref/base/targets/triton/_dihedral.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton 2026-05-13T13:56:43,800 copying build/lib/torchref/base/targets/triton/adp_simu.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton 2026-05-13T13:56:43,802 copying build/lib/torchref/base/targets/triton/ramachandran.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton 2026-05-13T13:56:43,804 copying build/lib/torchref/base/targets/triton/torsion.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton 2026-05-13T13:56:43,807 copying build/lib/torchref/base/targets/ramachandran.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets 2026-05-13T13:56:43,809 copying build/lib/torchref/base/targets/torsion.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets 2026-05-13T13:56:43,811 copying build/lib/torchref/base/targets/_common.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets 2026-05-13T13:56:43,813 creating build/bdist.linux-armv7l/wheel/torchref/base/metrics 2026-05-13T13:56:43,814 copying build/lib/torchref/base/metrics/loss.py -> build/bdist.linux-armv7l/wheel/./torchref/base/metrics 2026-05-13T13:56:43,817 copying build/lib/torchref/base/metrics/rfactor.py -> build/bdist.linux-armv7l/wheel/./torchref/base/metrics 2026-05-13T13:56:43,819 copying build/lib/torchref/base/metrics/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/metrics 2026-05-13T13:56:43,822 creating build/bdist.linux-armv7l/wheel/torchref/base/scattering 2026-05-13T13:56:43,823 copying build/lib/torchref/base/scattering/scattering_table.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering 2026-05-13T13:56:43,825 copying build/lib/torchref/base/scattering/anomalous_table.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering 2026-05-13T13:56:43,828 copying build/lib/torchref/base/scattering/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering 2026-05-13T13:56:43,830 copying build/lib/torchref/base/scattering/itc92.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering 2026-05-13T13:56:43,833 creating build/bdist.linux-armv7l/wheel/torchref/base/kernels 2026-05-13T13:56:43,834 copying build/lib/torchref/base/kernels/optimized_ops.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels 2026-05-13T13:56:43,837 copying build/lib/torchref/base/kernels/jit_kernel_vectorized_add_to_map.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels 2026-05-13T13:56:43,839 copying build/lib/torchref/base/kernels/cpu_scatter.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels 2026-05-13T13:56:43,842 copying build/lib/torchref/base/kernels/separable_triton_kernel.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels 2026-05-13T13:56:43,845 copying build/lib/torchref/base/kernels/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels 2026-05-13T13:56:43,847 copying build/lib/torchref/base/kernels/triton_kernel.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels 2026-05-13T13:56:43,850 copying build/lib/torchref/base/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base 2026-05-13T13:56:43,853 creating build/bdist.linux-armv7l/wheel/torchref/base/direct_summation 2026-05-13T13:56:43,854 copying build/lib/torchref/base/direct_summation/isotropic.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation 2026-05-13T13:56:43,856 copying build/lib/torchref/base/direct_summation/corrections.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation 2026-05-13T13:56:43,858 copying build/lib/torchref/base/direct_summation/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation 2026-05-13T13:56:43,860 copying build/lib/torchref/base/direct_summation/anisotropic.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation 2026-05-13T13:56:43,862 copying build/lib/torchref/base/CCTBX_related.py -> build/bdist.linux-armv7l/wheel/./torchref/base 2026-05-13T13:56:43,865 creating build/bdist.linux-armv7l/wheel/torchref/base/coordinates 2026-05-13T13:56:43,866 copying build/lib/torchref/base/coordinates/periodic_boundary.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates 2026-05-13T13:56:43,868 copying build/lib/torchref/base/coordinates/transforms_numpy.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates 2026-05-13T13:56:43,870 copying build/lib/torchref/base/coordinates/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates 2026-05-13T13:56:43,872 copying build/lib/torchref/base/coordinates/transforms_torch.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates 2026-05-13T13:56:43,874 copying build/lib/torchref/base/french_wilson.py -> build/bdist.linux-armv7l/wheel/./torchref/base 2026-05-13T13:56:43,877 copying build/lib/torchref/base/get_scattering_factor_torch.py -> build/bdist.linux-armv7l/wheel/./torchref/base 2026-05-13T13:56:43,881 creating build/bdist.linux-armv7l/wheel/torchref/base/alignment 2026-05-13T13:56:43,882 copying build/lib/torchref/base/alignment/normalization.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment 2026-05-13T13:56:43,884 copying build/lib/torchref/base/alignment/scoring.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment 2026-05-13T13:56:43,886 copying build/lib/torchref/base/alignment/superposition.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment 2026-05-13T13:56:43,889 copying build/lib/torchref/base/alignment/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment 2026-05-13T13:56:43,891 copying build/lib/torchref/base/alignment/rotation.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment 2026-05-13T13:56:43,894 creating build/bdist.linux-armv7l/wheel/torchref/base/reciprocal 2026-05-13T13:56:43,895 copying build/lib/torchref/base/reciprocal/symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal 2026-05-13T13:56:43,897 copying build/lib/torchref/base/reciprocal/grid_operations.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal 2026-05-13T13:56:43,900 copying build/lib/torchref/base/reciprocal/basis.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal 2026-05-13T13:56:43,902 copying build/lib/torchref/base/reciprocal/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal 2026-05-13T13:56:43,904 copying build/lib/torchref/base/reciprocal/interpolation.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal 2026-05-13T13:56:43,906 copying build/lib/torchref/base/reciprocal/hkl.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal 2026-05-13T13:56:43,909 creating build/bdist.linux-armv7l/wheel/torchref/base/electron_density 2026-05-13T13:56:43,910 copying build/lib/torchref/base/electron_density/map_building.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density 2026-05-13T13:56:43,912 copying build/lib/torchref/base/electron_density/solvent_mask.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density 2026-05-13T13:56:43,914 copying build/lib/torchref/base/electron_density/main.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density 2026-05-13T13:56:43,917 copying build/lib/torchref/base/electron_density/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density 2026-05-13T13:56:43,919 copying build/lib/torchref/base/electron_density/voxel_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density 2026-05-13T13:56:43,921 creating build/bdist.linux-armv7l/wheel/torchref/base/chain_closure 2026-05-13T13:56:43,922 copying build/lib/torchref/base/chain_closure/closure.py -> build/bdist.linux-armv7l/wheel/./torchref/base/chain_closure 2026-05-13T13:56:43,925 copying build/lib/torchref/base/chain_closure/backbone_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/base/chain_closure 2026-05-13T13:56:43,928 copying build/lib/torchref/base/chain_closure/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/chain_closure 2026-05-13T13:56:43,930 creating build/bdist.linux-armv7l/wheel/torchref/scripts 2026-05-13T13:56:43,931 copying build/lib/torchref/scripts/generate_scattering_table.py -> build/bdist.linux-armv7l/wheel/./torchref/scripts 2026-05-13T13:56:43,934 copying build/lib/torchref/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/scripts 2026-05-13T13:56:43,935 copying build/lib/torchref/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref 2026-05-13T13:56:43,938 creating build/bdist.linux-armv7l/wheel/torchref/model 2026-05-13T13:56:43,939 copying build/lib/torchref/model/sf_fft.py -> build/bdist.linux-armv7l/wheel/./torchref/model 2026-05-13T13:56:43,942 copying build/lib/torchref/model/segmented_internal_coordinates.py -> build/bdist.linux-armv7l/wheel/./torchref/model 2026-05-13T13:56:43,945 copying build/lib/torchref/model/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/model 2026-05-13T13:56:43,947 copying build/lib/torchref/model/sf_ds.py -> build/bdist.linux-armv7l/wheel/./torchref/model 2026-05-13T13:56:43,949 copying build/lib/torchref/model/mixed_model.py -> build/bdist.linux-armv7l/wheel/./torchref/model 2026-05-13T13:56:43,952 copying build/lib/torchref/model/internal_coordinates.py -> build/bdist.linux-armv7l/wheel/./torchref/model 2026-05-13T13:56:43,955 copying build/lib/torchref/model/model_collection.py -> build/bdist.linux-armv7l/wheel/./torchref/model 2026-05-13T13:56:43,958 copying build/lib/torchref/model/parameter_wrappers.py -> build/bdist.linux-armv7l/wheel/./torchref/model 2026-05-13T13:56:43,962 copying build/lib/torchref/model/closed_segmented_internal_coordinates.py -> build/bdist.linux-armv7l/wheel/./torchref/model 2026-05-13T13:56:43,965 copying build/lib/torchref/model/model.py -> build/bdist.linux-armv7l/wheel/./torchref/model 2026-05-13T13:56:43,970 copying build/lib/torchref/model/model_ft.py -> build/bdist.linux-armv7l/wheel/./torchref/model 2026-05-13T13:56:43,973 creating build/bdist.linux-armv7l/wheel/torchref/alignment 2026-05-13T13:56:43,974 copying build/lib/torchref/alignment/sampling.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment 2026-05-13T13:56:43,977 copying build/lib/torchref/alignment/ball_transform.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment 2026-05-13T13:56:43,980 copying build/lib/torchref/alignment/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment 2026-05-13T13:56:43,982 copying build/lib/torchref/alignment/rigid_body.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment 2026-05-13T13:56:43,984 copying build/lib/torchref/alignment/distributions.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment 2026-05-13T13:56:43,986 copying build/lib/torchref/alignment/transform.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment 2026-05-13T13:56:43,989 copying build/lib/torchref/alignment/clashscore.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment 2026-05-13T13:56:43,991 copying build/lib/torchref/alignment/translation.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment 2026-05-13T13:56:43,994 copying build/lib/torchref/alignment/jax_subpixel_peaks.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment 2026-05-13T13:56:43,996 copying build/lib/torchref/alignment/pipeline.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment 2026-05-13T13:56:43,999 creating build/bdist.linux-armv7l/wheel/torchref/refinement 2026-05-13T13:56:44,000 copying build/lib/torchref/refinement/logger.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement 2026-05-13T13:56:44,002 copying build/lib/torchref/refinement/loss_state.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement 2026-05-13T13:56:44,006 creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets 2026-05-13T13:56:44,007 copying build/lib/torchref/refinement/targets/amber_target.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets 2026-05-13T13:56:44,011 creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets/adp 2026-05-13T13:56:44,012 copying build/lib/torchref/refinement/targets/adp/scaler_u.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp 2026-05-13T13:56:44,014 copying build/lib/torchref/refinement/targets/adp/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp 2026-05-13T13:56:44,016 copying build/lib/torchref/refinement/targets/adp/rigid_bond.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp 2026-05-13T13:56:44,018 copying build/lib/torchref/refinement/targets/adp/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp 2026-05-13T13:56:44,020 copying build/lib/torchref/refinement/targets/adp/scaler_log_scale.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp 2026-05-13T13:56:44,021 copying build/lib/torchref/refinement/targets/adp/entropy.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp 2026-05-13T13:56:44,023 copying build/lib/torchref/refinement/targets/adp/similarity.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp 2026-05-13T13:56:44,025 copying build/lib/torchref/refinement/targets/adp/locality.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp 2026-05-13T13:56:44,028 copying build/lib/torchref/refinement/targets/occupancy_floor_diagnostic.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets 2026-05-13T13:56:44,030 copying build/lib/torchref/refinement/targets/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets 2026-05-13T13:56:44,032 copying build/lib/torchref/refinement/targets/realspace.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets 2026-05-13T13:56:44,035 copying build/lib/torchref/refinement/targets/forcefield_target.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets 2026-05-13T13:56:44,038 copying build/lib/torchref/refinement/targets/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets 2026-05-13T13:56:44,040 copying build/lib/torchref/refinement/targets/combined.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets 2026-05-13T13:56:44,042 copying build/lib/torchref/refinement/targets/similarity.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets 2026-05-13T13:56:44,045 creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets/geometry 2026-05-13T13:56:44,046 copying build/lib/torchref/refinement/targets/geometry/planarity.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry 2026-05-13T13:56:44,048 copying build/lib/torchref/refinement/targets/geometry/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry 2026-05-13T13:56:44,050 copying build/lib/torchref/refinement/targets/geometry/non_bonded.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry 2026-05-13T13:56:44,053 copying build/lib/torchref/refinement/targets/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry 2026-05-13T13:56:44,054 copying build/lib/torchref/refinement/targets/geometry/chiral.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry 2026-05-13T13:56:44,056 copying build/lib/torchref/refinement/targets/geometry/bonds.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry 2026-05-13T13:56:44,058 copying build/lib/torchref/refinement/targets/geometry/torsions.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry 2026-05-13T13:56:44,061 copying build/lib/torchref/refinement/targets/geometry/non_bonded_h.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry 2026-05-13T13:56:44,063 copying build/lib/torchref/refinement/targets/geometry/ramachandran.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry 2026-05-13T13:56:44,065 copying build/lib/torchref/refinement/targets/geometry/angles.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry 2026-05-13T13:56:44,067 copying build/lib/torchref/refinement/targets/sampled_ml_phase_target.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets 2026-05-13T13:56:44,070 creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets/xray 2026-05-13T13:56:44,071 copying build/lib/torchref/refinement/targets/xray/bhattacharyya.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray 2026-05-13T13:56:44,073 copying build/lib/torchref/refinement/targets/xray/maximum_likelihood.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray 2026-05-13T13:56:44,075 copying build/lib/torchref/refinement/targets/xray/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray 2026-05-13T13:56:44,078 copying build/lib/torchref/refinement/targets/xray/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray 2026-05-13T13:56:44,080 copying build/lib/torchref/refinement/targets/xray/least_squares.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray 2026-05-13T13:56:44,082 copying build/lib/torchref/refinement/targets/xray/gaussian.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray 2026-05-13T13:56:44,083 copying build/lib/torchref/refinement/targets/difference.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets 2026-05-13T13:56:44,087 copying build/lib/torchref/refinement/lbfgs_refinement.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement 2026-05-13T13:56:44,089 copying build/lib/torchref/refinement/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement 2026-05-13T13:56:44,091 copying build/lib/torchref/refinement/base_refinement.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement 2026-05-13T13:56:44,094 creating build/bdist.linux-armv7l/wheel/torchref/refinement/weighting 2026-05-13T13:56:44,095 copying build/lib/torchref/refinement/weighting/es_policy_training.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting 2026-05-13T13:56:44,098 copying build/lib/torchref/refinement/weighting/policy_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting 2026-05-13T13:56:44,101 copying build/lib/torchref/refinement/weighting/base_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting 2026-05-13T13:56:44,103 copying build/lib/torchref/refinement/weighting/component_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting 2026-05-13T13:56:44,105 copying build/lib/torchref/refinement/weighting/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting 2026-05-13T13:56:44,107 copying build/lib/torchref/refinement/weighting/random_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting 2026-05-13T13:56:44,110 creating build/bdist.linux-armv7l/wheel/torchref/refinement/optimizers 2026-05-13T13:56:44,111 copying build/lib/torchref/refinement/optimizers/langevin_sa.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers 2026-05-13T13:56:44,114 copying build/lib/torchref/refinement/optimizers/adam_noise.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers 2026-05-13T13:56:44,117 copying build/lib/torchref/refinement/optimizers/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers 2026-05-13T13:56:44,119 copying build/lib/torchref/refinement/optimizers/momentum_sa.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers 2026-05-13T13:56:44,121 copying build/lib/torchref/refinement/optimizers/internal_coord_sa.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers 2026-05-13T13:56:44,123 copying build/lib/torchref/refinement/optimizers/exploratory_lbfgs.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers 2026-05-13T13:56:44,126 copying build/lib/torchref/refinement/optimizers/simulated_annealing.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers 2026-05-13T13:56:44,129 creating build/bdist.linux-armv7l/wheel/torchref/data 2026-05-13T13:56:44,130 copying build/lib/torchref/data/itc92_scattering_factors.pt -> build/bdist.linux-armv7l/wheel/./torchref/data 2026-05-13T13:56:44,132 copying build/lib/torchref/data/rama_nll_surfaces.pt -> build/bdist.linux-armv7l/wheel/./torchref/data 2026-05-13T13:56:44,183 copying build/lib/torchref/data/atomic_vdw_radii.csv -> build/bdist.linux-armv7l/wheel/./torchref/data 2026-05-13T13:56:44,185 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library 2026-05-13T13:56:44,187 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/d 2026-05-13T13:56:44,188 copying build/lib/torchref/data/monomer_library/d/DA.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d 2026-05-13T13:56:44,191 copying build/lib/torchref/data/monomer_library/d/DG.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d 2026-05-13T13:56:44,194 copying build/lib/torchref/data/monomer_library/d/DT.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d 2026-05-13T13:56:44,196 copying build/lib/torchref/data/monomer_library/d/DC.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d 2026-05-13T13:56:44,200 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/i 2026-05-13T13:56:44,201 copying build/lib/torchref/data/monomer_library/i/ILE.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/i 2026-05-13T13:56:44,204 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/m 2026-05-13T13:56:44,205 copying build/lib/torchref/data/monomer_library/m/MSE.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/m 2026-05-13T13:56:44,208 copying build/lib/torchref/data/monomer_library/m/MET.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/m 2026-05-13T13:56:44,211 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/u 2026-05-13T13:56:44,213 copying build/lib/torchref/data/monomer_library/u/U.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/u 2026-05-13T13:56:44,216 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/h 2026-05-13T13:56:44,217 copying build/lib/torchref/data/monomer_library/h/HOH.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/h 2026-05-13T13:56:44,219 copying build/lib/torchref/data/monomer_library/h/HIS.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/h 2026-05-13T13:56:44,222 copying build/lib/torchref/data/monomer_library/h/HYP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/h 2026-05-13T13:56:44,225 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/c 2026-05-13T13:56:44,227 copying build/lib/torchref/data/monomer_library/c/CYS.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/c 2026-05-13T13:56:44,231 copying build/lib/torchref/data/monomer_library/c/C.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/c 2026-05-13T13:56:44,235 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/list 2026-05-13T13:56:44,237 copying build/lib/torchref/data/monomer_library/list/mon_lib_list.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/list 2026-05-13T13:56:44,340 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/p 2026-05-13T13:56:44,342 copying build/lib/torchref/data/monomer_library/p/PHE.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/p 2026-05-13T13:56:44,344 copying build/lib/torchref/data/monomer_library/p/PTR.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/p 2026-05-13T13:56:44,347 copying build/lib/torchref/data/monomer_library/p/PRO.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/p 2026-05-13T13:56:44,349 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/v 2026-05-13T13:56:44,351 copying build/lib/torchref/data/monomer_library/v/VAL.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/v 2026-05-13T13:56:44,354 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/a 2026-05-13T13:56:44,355 copying build/lib/torchref/data/monomer_library/a/ASP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a 2026-05-13T13:56:44,358 copying build/lib/torchref/data/monomer_library/a/ASN.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a 2026-05-13T13:56:44,360 copying build/lib/torchref/data/monomer_library/a/ALA.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a 2026-05-13T13:56:44,362 copying build/lib/torchref/data/monomer_library/a/ARG.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a 2026-05-13T13:56:44,365 copying build/lib/torchref/data/monomer_library/a/A.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a 2026-05-13T13:56:44,368 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/l 2026-05-13T13:56:44,370 copying build/lib/torchref/data/monomer_library/l/LEU.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/l 2026-05-13T13:56:44,372 copying build/lib/torchref/data/monomer_library/l/LYS.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/l 2026-05-13T13:56:44,375 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/t 2026-05-13T13:56:44,377 copying build/lib/torchref/data/monomer_library/t/THR.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t 2026-05-13T13:56:44,379 copying build/lib/torchref/data/monomer_library/t/TPO.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t 2026-05-13T13:56:44,382 copying build/lib/torchref/data/monomer_library/t/TRP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t 2026-05-13T13:56:44,384 copying build/lib/torchref/data/monomer_library/t/TYR.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t 2026-05-13T13:56:44,388 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/g 2026-05-13T13:56:44,390 copying build/lib/torchref/data/monomer_library/g/GLU.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g 2026-05-13T13:56:44,392 copying build/lib/torchref/data/monomer_library/g/GLN.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g 2026-05-13T13:56:44,395 copying build/lib/torchref/data/monomer_library/g/G.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g 2026-05-13T13:56:44,398 copying build/lib/torchref/data/monomer_library/g/GLY.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g 2026-05-13T13:56:44,400 creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/s 2026-05-13T13:56:44,402 copying build/lib/torchref/data/monomer_library/s/SEP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/s 2026-05-13T13:56:44,404 copying build/lib/torchref/data/monomer_library/s/SER.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/s 2026-05-13T13:56:44,407 creating build/bdist.linux-armv7l/wheel/torchref/scaling 2026-05-13T13:56:44,409 copying build/lib/torchref/scaling/scaler.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling 2026-05-13T13:56:44,412 copying build/lib/torchref/scaling/solvent.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling 2026-05-13T13:56:44,414 copying build/lib/torchref/scaling/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling 2026-05-13T13:56:44,416 copying build/lib/torchref/scaling/scaler_base.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling 2026-05-13T13:56:44,419 copying build/lib/torchref/scaling/collection_scaler.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling 2026-05-13T13:56:44,422 creating build/bdist.linux-armv7l/wheel/torchref/restraints 2026-05-13T13:56:44,424 copying build/lib/torchref/restraints/neighbor_search.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints 2026-05-13T13:56:44,427 copying build/lib/torchref/restraints/builders_numba.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints 2026-05-13T13:56:44,430 copying build/lib/torchref/restraints/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints 2026-05-13T13:56:44,433 copying build/lib/torchref/restraints/restraints.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints 2026-05-13T13:56:44,436 copying build/lib/torchref/restraints/restraints_helper.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints 2026-05-13T13:56:44,439 copying build/lib/torchref/restraints/ramachandran.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints 2026-05-13T13:56:44,441 copying build/lib/torchref/restraints/library.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints 2026-05-13T13:56:44,443 copying build/lib/torchref/restraints/builders.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints 2026-05-13T13:56:44,446 copying build/lib/torchref/restraints/hydrogen_topology.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints 2026-05-13T13:56:44,449 copying build/lib/torchref/restraints/builders_fast.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints 2026-05-13T13:56:44,453 creating build/bdist.linux-armv7l/wheel/torchref/kinetic 2026-05-13T13:56:44,454 copying build/lib/torchref/kinetic/refinement.py -> build/bdist.linux-armv7l/wheel/./torchref/kinetic 2026-05-13T13:56:44,457 copying build/lib/torchref/kinetic/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/kinetic 2026-05-13T13:56:44,459 copying build/lib/torchref/kinetic/occupancies.py -> build/bdist.linux-armv7l/wheel/./torchref/kinetic 2026-05-13T13:56:44,462 copying build/lib/torchref/kinetic/targets.py -> build/bdist.linux-armv7l/wheel/./torchref/kinetic 2026-05-13T13:56:44,464 copying build/lib/torchref/kinetic/kinetics.py -> build/bdist.linux-armv7l/wheel/./torchref/kinetic 2026-05-13T13:56:44,467 running install_egg_info 2026-05-13T13:56:44,472 Copying torchref.egg-info to build/bdist.linux-armv7l/wheel/./torchref-0.5.1-py3.11.egg-info 2026-05-13T13:56:44,483 running install_scripts 2026-05-13T13:56:44,494 creating build/bdist.linux-armv7l/wheel/torchref-0.5.1.dist-info/WHEEL 2026-05-13T13:56:44,497 creating '/tmp/pip-wheel-y7_t3hsg/.tmp-t99zwts_/torchref-0.5.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-05-13T13:56:44,500 adding 'torchref/__init__.py' 2026-05-13T13:56:44,501 adding 'torchref/_bootstrap.py' 2026-05-13T13:56:44,503 adding 'torchref/config.py' 2026-05-13T13:56:44,505 adding 'torchref/alignment/__init__.py' 2026-05-13T13:56:44,512 adding 'torchref/alignment/ball_transform.py' 2026-05-13T13:56:44,515 adding 'torchref/alignment/clashscore.py' 2026-05-13T13:56:44,517 adding 'torchref/alignment/distributions.py' 2026-05-13T13:56:44,519 adding 'torchref/alignment/jax_subpixel_peaks.py' 2026-05-13T13:56:44,521 adding 'torchref/alignment/pipeline.py' 2026-05-13T13:56:44,523 adding 'torchref/alignment/rigid_body.py' 2026-05-13T13:56:44,525 adding 'torchref/alignment/sampling.py' 2026-05-13T13:56:44,528 adding 'torchref/alignment/transform.py' 2026-05-13T13:56:44,530 adding 'torchref/alignment/translation.py' 2026-05-13T13:56:44,532 adding 'torchref/base/CCTBX_related.py' 2026-05-13T13:56:44,534 adding 'torchref/base/__init__.py' 2026-05-13T13:56:44,538 adding 'torchref/base/french_wilson.py' 2026-05-13T13:56:44,539 adding 'torchref/base/get_scattering_factor_torch.py' 2026-05-13T13:56:44,542 adding 'torchref/base/math_numpy.py' 2026-05-13T13:56:44,544 adding 'torchref/base/math_torch.py' 2026-05-13T13:56:44,546 adding 'torchref/base/alignment/__init__.py' 2026-05-13T13:56:44,548 adding 'torchref/base/alignment/normalization.py' 2026-05-13T13:56:44,550 adding 'torchref/base/alignment/rotation.py' 2026-05-13T13:56:44,551 adding 'torchref/base/alignment/scoring.py' 2026-05-13T13:56:44,553 adding 'torchref/base/alignment/superposition.py' 2026-05-13T13:56:44,555 adding 'torchref/base/chain_closure/__init__.py' 2026-05-13T13:56:44,557 adding 'torchref/base/chain_closure/backbone_utils.py' 2026-05-13T13:56:44,560 adding 'torchref/base/chain_closure/closure.py' 2026-05-13T13:56:44,562 adding 'torchref/base/coordinates/__init__.py' 2026-05-13T13:56:44,563 adding 'torchref/base/coordinates/periodic_boundary.py' 2026-05-13T13:56:44,564 adding 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2026-05-13T13:56:44,641 adding 'torchref/base/targets/ramachandran.py' 2026-05-13T13:56:44,642 adding 'torchref/base/targets/torsion.py' 2026-05-13T13:56:44,644 adding 'torchref/base/targets/xray_bhattacharyya.py' 2026-05-13T13:56:44,645 adding 'torchref/base/targets/xray_gaussian.py' 2026-05-13T13:56:44,646 adding 'torchref/base/targets/xray_ls.py' 2026-05-13T13:56:44,647 adding 'torchref/base/targets/xray_ml.py' 2026-05-13T13:56:44,649 adding 'torchref/base/targets/triton/__init__.py' 2026-05-13T13:56:44,651 adding 'torchref/base/targets/triton/_dihedral.py' 2026-05-13T13:56:44,652 adding 'torchref/base/targets/triton/adp_simu.py' 2026-05-13T13:56:44,654 adding 'torchref/base/targets/triton/angle.py' 2026-05-13T13:56:44,655 adding 'torchref/base/targets/triton/bond.py' 2026-05-13T13:56:44,657 adding 'torchref/base/targets/triton/chiral.py' 2026-05-13T13:56:44,659 adding 'torchref/base/targets/triton/nonbonded.py' 2026-05-13T13:56:44,661 adding 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2026-05-13T13:56:45,564 adding 'torchref/data/monomer_library/m/MET.cif' 2026-05-13T13:56:45,566 adding 'torchref/data/monomer_library/m/MSE.cif' 2026-05-13T13:56:45,568 adding 'torchref/data/monomer_library/p/PHE.cif' 2026-05-13T13:56:45,570 adding 'torchref/data/monomer_library/p/PRO.cif' 2026-05-13T13:56:45,572 adding 'torchref/data/monomer_library/p/PTR.cif' 2026-05-13T13:56:45,574 adding 'torchref/data/monomer_library/s/SEP.cif' 2026-05-13T13:56:45,575 adding 'torchref/data/monomer_library/s/SER.cif' 2026-05-13T13:56:45,577 adding 'torchref/data/monomer_library/t/THR.cif' 2026-05-13T13:56:45,579 adding 'torchref/data/monomer_library/t/TPO.cif' 2026-05-13T13:56:45,581 adding 'torchref/data/monomer_library/t/TRP.cif' 2026-05-13T13:56:45,582 adding 'torchref/data/monomer_library/t/TYR.cif' 2026-05-13T13:56:45,585 adding 'torchref/data/monomer_library/u/U.cif' 2026-05-13T13:56:45,587 adding 'torchref/data/monomer_library/v/VAL.cif' 2026-05-13T13:56:45,589 adding 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2026-05-13T13:56:45,652 adding 'torchref/kinetic/refinement.py' 2026-05-13T13:56:45,655 adding 'torchref/kinetic/targets.py' 2026-05-13T13:56:45,657 adding 'torchref/maps/__init__.py' 2026-05-13T13:56:45,659 adding 'torchref/maps/difference_map.py' 2026-05-13T13:56:45,660 adding 'torchref/maps/map.py' 2026-05-13T13:56:45,663 adding 'torchref/model/__init__.py' 2026-05-13T13:56:45,672 adding 'torchref/model/closed_segmented_internal_coordinates.py' 2026-05-13T13:56:45,680 adding 'torchref/model/internal_coordinates.py' 2026-05-13T13:56:45,683 adding 'torchref/model/mixed_model.py' 2026-05-13T13:56:45,698 adding 'torchref/model/model.py' 2026-05-13T13:56:45,701 adding 'torchref/model/model_collection.py' 2026-05-13T13:56:45,706 adding 'torchref/model/model_ft.py' 2026-05-13T13:56:45,716 adding 'torchref/model/parameter_wrappers.py' 2026-05-13T13:56:45,723 adding 'torchref/model/segmented_internal_coordinates.py' 2026-05-13T13:56:45,726 adding 'torchref/model/sf_ds.py' 2026-05-13T13:56:45,730 adding 'torchref/model/sf_fft.py' 2026-05-13T13:56:45,732 adding 'torchref/refinement/__init__.py' 2026-05-13T13:56:45,736 adding 'torchref/refinement/base_refinement.py' 2026-05-13T13:56:45,739 adding 'torchref/refinement/lbfgs_refinement.py' 2026-05-13T13:56:45,741 adding 'torchref/refinement/logger.py' 2026-05-13T13:56:45,746 adding 'torchref/refinement/loss_state.py' 2026-05-13T13:56:45,748 adding 'torchref/refinement/optimizers/__init__.py' 2026-05-13T13:56:45,749 adding 'torchref/refinement/optimizers/adam_noise.py' 2026-05-13T13:56:45,753 adding 'torchref/refinement/optimizers/exploratory_lbfgs.py' 2026-05-13T13:56:45,756 adding 'torchref/refinement/optimizers/internal_coord_sa.py' 2026-05-13T13:56:45,758 adding 'torchref/refinement/optimizers/langevin_sa.py' 2026-05-13T13:56:45,760 adding 'torchref/refinement/optimizers/momentum_sa.py' 2026-05-13T13:56:45,761 adding 'torchref/refinement/optimizers/simulated_annealing.py' 2026-05-13T13:56:45,763 adding 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adding 'torchref/refinement/targets/adp/locality.py' 2026-05-13T13:56:45,801 adding 'torchref/refinement/targets/adp/rigid_bond.py' 2026-05-13T13:56:45,802 adding 'torchref/refinement/targets/adp/scaler_log_scale.py' 2026-05-13T13:56:45,804 adding 'torchref/refinement/targets/adp/scaler_u.py' 2026-05-13T13:56:45,805 adding 'torchref/refinement/targets/adp/similarity.py' 2026-05-13T13:56:45,807 adding 'torchref/refinement/targets/geometry/__init__.py' 2026-05-13T13:56:45,808 adding 'torchref/refinement/targets/geometry/angles.py' 2026-05-13T13:56:45,810 adding 'torchref/refinement/targets/geometry/base.py' 2026-05-13T13:56:45,811 adding 'torchref/refinement/targets/geometry/bonds.py' 2026-05-13T13:56:45,812 adding 'torchref/refinement/targets/geometry/chiral.py' 2026-05-13T13:56:45,815 adding 'torchref/refinement/targets/geometry/non_bonded.py' 2026-05-13T13:56:45,817 adding 'torchref/refinement/targets/geometry/non_bonded_h.py' 2026-05-13T13:56:45,819 adding 'torchref/refinement/targets/geometry/planarity.py' 2026-05-13T13:56:45,820 adding 'torchref/refinement/targets/geometry/ramachandran.py' 2026-05-13T13:56:45,822 adding 'torchref/refinement/targets/geometry/torsions.py' 2026-05-13T13:56:45,824 adding 'torchref/refinement/targets/xray/__init__.py' 2026-05-13T13:56:45,825 adding 'torchref/refinement/targets/xray/base.py' 2026-05-13T13:56:45,827 adding 'torchref/refinement/targets/xray/bhattacharyya.py' 2026-05-13T13:56:45,829 adding 'torchref/refinement/targets/xray/gaussian.py' 2026-05-13T13:56:45,830 adding 'torchref/refinement/targets/xray/least_squares.py' 2026-05-13T13:56:45,832 adding 'torchref/refinement/targets/xray/maximum_likelihood.py' 2026-05-13T13:56:45,833 adding 'torchref/refinement/weighting/__init__.py' 2026-05-13T13:56:45,835 adding 'torchref/refinement/weighting/base_weighting.py' 2026-05-13T13:56:45,837 adding 'torchref/refinement/weighting/component_weighting.py' 2026-05-13T13:56:45,839 adding 'torchref/refinement/weighting/es_policy_training.py' 2026-05-13T13:56:45,842 adding 'torchref/refinement/weighting/policy_weighting.py' 2026-05-13T13:56:45,845 adding 'torchref/refinement/weighting/random_weighting.py' 2026-05-13T13:56:45,847 adding 'torchref/restraints/__init__.py' 2026-05-13T13:56:45,851 adding 'torchref/restraints/builders.py' 2026-05-13T13:56:45,859 adding 'torchref/restraints/builders_fast.py' 2026-05-13T13:56:45,863 adding 'torchref/restraints/builders_numba.py' 2026-05-13T13:56:45,867 adding 'torchref/restraints/hydrogen_topology.py' 2026-05-13T13:56:45,868 adding 'torchref/restraints/library.py' 2026-05-13T13:56:45,873 adding 'torchref/restraints/neighbor_search.py' 2026-05-13T13:56:45,875 adding 'torchref/restraints/ramachandran.py' 2026-05-13T13:56:45,885 adding 'torchref/restraints/restraints.py' 2026-05-13T13:56:45,888 adding 'torchref/restraints/restraints_helper.py' 2026-05-13T13:56:45,890 adding 'torchref/scaling/__init__.py' 2026-05-13T13:56:45,893 adding 'torchref/scaling/collection_scaler.py' 2026-05-13T13:56:45,895 adding 'torchref/scaling/scaler.py' 2026-05-13T13:56:45,900 adding 'torchref/scaling/scaler_base.py' 2026-05-13T13:56:45,903 adding 'torchref/scaling/solvent.py' 2026-05-13T13:56:45,905 adding 'torchref/scripts/__init__.py' 2026-05-13T13:56:45,906 adding 'torchref/scripts/generate_scattering_table.py' 2026-05-13T13:56:45,908 adding 'torchref/symmetry/__init__.py' 2026-05-13T13:56:45,910 adding 'torchref/symmetry/cell.py' 2026-05-13T13:56:45,912 adding 'torchref/symmetry/grid_utils.py' 2026-05-13T13:56:45,914 adding 'torchref/symmetry/map_symmetry.py' 2026-05-13T13:56:45,916 adding 'torchref/symmetry/map_symmetry_interpolation.py' 2026-05-13T13:56:45,922 adding 'torchref/symmetry/reciprocal_symmetry.py' 2026-05-13T13:56:45,926 adding 'torchref/symmetry/spacegroup.py' 2026-05-13T13:56:45,927 adding 'torchref/symmetry/symmetry.py' 2026-05-13T13:56:45,929 adding 'torchref/utils/__init__.py' 2026-05-13T13:56:45,930 adding 'torchref/utils/autograd_introspection.py' 2026-05-13T13:56:45,932 adding 'torchref/utils/autograd_ops.py' 2026-05-13T13:56:45,933 adding 'torchref/utils/caching.py' 2026-05-13T13:56:45,935 adding 'torchref/utils/debug_utils.py' 2026-05-13T13:56:45,937 adding 'torchref/utils/device_mixin.py' 2026-05-13T13:56:45,938 adding 'torchref/utils/gradnorm.py' 2026-05-13T13:56:45,940 adding 'torchref/utils/hyperparameters.py' 2026-05-13T13:56:45,942 adding 'torchref/utils/loss_validation.py' 2026-05-13T13:56:45,944 adding 'torchref/utils/pse.py' 2026-05-13T13:56:45,945 adding 'torchref/utils/serialization.py' 2026-05-13T13:56:45,947 adding 'torchref/utils/stats.py' 2026-05-13T13:56:45,948 adding 'torchref/utils/timing.py' 2026-05-13T13:56:45,953 adding 'torchref/utils/utils.py' 2026-05-13T13:56:45,956 adding 'torchref-0.5.1.dist-info/licenses/LICENSE' 2026-05-13T13:56:45,957 adding 'torchref-0.5.1.dist-info/METADATA' 2026-05-13T13:56:45,958 adding 'torchref-0.5.1.dist-info/WHEEL' 2026-05-13T13:56:45,959 adding 'torchref-0.5.1.dist-info/entry_points.txt' 2026-05-13T13:56:45,960 adding 'torchref-0.5.1.dist-info/top_level.txt' 2026-05-13T13:56:45,964 adding 'torchref-0.5.1.dist-info/RECORD' 2026-05-13T13:56:46,002 removing build/bdist.linux-armv7l/wheel 2026-05-13T13:56:46,180 Building wheel for torchref (pyproject.toml): finished with status 'done' 2026-05-13T13:56:46,252 Created wheel for torchref: filename=torchref-0.5.1-py3-none-any.whl size=3118515 sha256=c9b0bd6e0eba9eb14b81da89125965a0bb458251fd153ba4216811b24c993227 2026-05-13T13:56:46,253 Stored in directory: /tmp/pip-ephem-wheel-cache-mngz1gu0/wheels/88/90/71/e6120d13293dd0f85e076e70b2d9dd3b302ec0ba8dd4792792 2026-05-13T13:56:46,273 Successfully built torchref 2026-05-13T13:56:46,357 Removed build tracker: '/tmp/pip-build-tracker-chgdwl6q'