2026-05-18T20:18:24,529 Created temporary directory: /tmp/pip-ephem-wheel-cache-hh93vbtz
2026-05-18T20:18:24,531 Created temporary directory: /tmp/pip-build-tracker-hdpit6xx
2026-05-18T20:18:24,532 Initialized build tracking at /tmp/pip-build-tracker-hdpit6xx
2026-05-18T20:18:24,532 Created build tracker: /tmp/pip-build-tracker-hdpit6xx
2026-05-18T20:18:24,533 Entered build tracker: /tmp/pip-build-tracker-hdpit6xx
2026-05-18T20:18:24,534 Created temporary directory: /tmp/pip-wheel-mpz0qx14
2026-05-18T20:18:24,536 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
2026-05-18T20:18:24,539 Created temporary directory: /tmp/pip-ephem-wheel-cache-7199e0nb
2026-05-18T20:18:24,561 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-05-18T20:18:24,564 2 location(s) to search for versions of torchref:
2026-05-18T20:18:24,564 * https://pypi.org/simple/torchref/
2026-05-18T20:18:24,564 * https://www.piwheels.org/simple/torchref/
2026-05-18T20:18:24,565 Fetching project page and analyzing links: https://pypi.org/simple/torchref/
2026-05-18T20:18:24,566 Getting page https://pypi.org/simple/torchref/
2026-05-18T20:18:24,567 Found index url https://pypi.org/simple
2026-05-18T20:18:24,807 Fetched page https://pypi.org/simple/torchref/ as application/vnd.pypi.simple.v1+json
2026-05-18T20:18:24,811   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)
2026-05-18T20:18:24,812   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
2026-05-18T20:18:24,813   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)
2026-05-18T20:18:24,814   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
2026-05-18T20:18:24,815   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)
2026-05-18T20:18:24,816   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
2026-05-18T20:18:24,816   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)
2026-05-18T20:18:24,817   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
2026-05-18T20:18:24,818   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)
2026-05-18T20:18:24,819   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
2026-05-18T20:18:24,820   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)
2026-05-18T20:18:24,821   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
2026-05-18T20:18:24,822   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)
2026-05-18T20:18:24,823   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
2026-05-18T20:18:24,823   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)
2026-05-18T20:18:24,824   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
2026-05-18T20:18:24,825   Skipping link: No binaries permitted for torchref: https://files.pythonhosted.org/packages/3b/ad/f555bfcd4d9fdf1e3d542b593b2bebadf467e161cf643ff0c263db2cfcc3/torchref-0.5.2-py3-none-any.whl (from https://pypi.org/simple/torchref/) (requires-python:>=3.10)
2026-05-18T20:18:24,825   Found link https://files.pythonhosted.org/packages/4d/d1/961979d80eaa39ceac37b9b8b641c3e2b4076705b775b3bcdcb1054f3642/torchref-0.5.2.tar.gz (from https://pypi.org/simple/torchref/) (requires-python:>=3.10), version: 0.5.2
2026-05-18T20:18:24,826 Fetching project page and analyzing links: https://www.piwheels.org/simple/torchref/
2026-05-18T20:18:24,827 Getting page https://www.piwheels.org/simple/torchref/
2026-05-18T20:18:24,828 Found index url https://www.piwheels.org/simple
2026-05-18T20:18:25,033 Fetched page https://www.piwheels.org/simple/torchref/ as text/html
2026-05-18T20:18:25,037   Skipping link: No binaries permitted for torchref: https://www.piwheels.org/simple/torchref/torchref-0.5.1-py3-none-any.whl#sha256=c9b0bd6e0eba9eb14b81da89125965a0bb458251fd153ba4216811b24c993227 (from https://www.piwheels.org/simple/torchref/) (requires-python:>=3.10)
2026-05-18T20:18:25,038   Skipping link: No binaries permitted for torchref: https://archive1.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)
2026-05-18T20:18:25,039   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)
2026-05-18T20:18:25,039   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)
2026-05-18T20:18:25,040   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)
2026-05-18T20:18:25,041   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)
2026-05-18T20:18:25,041   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)
2026-05-18T20:18:25,042   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)
2026-05-18T20:18:25,042 Skipping link: not a file: https://www.piwheels.org/simple/torchref/
2026-05-18T20:18:25,043 Skipping link: not a file: https://pypi.org/simple/torchref/
2026-05-18T20:18:25,062 Given no hashes to check 1 links for project 'torchref': discarding no candidates
2026-05-18T20:18:25,081 Collecting torchref==0.5.2
2026-05-18T20:18:25,083   Created temporary directory: /tmp/pip-unpack-ezmzq8dy
2026-05-18T20:18:25,344   Downloading torchref-0.5.2.tar.gz (3.0 MB)
2026-05-18T20:18:26,682   Added torchref==0.5.2 from https://files.pythonhosted.org/packages/4d/d1/961979d80eaa39ceac37b9b8b641c3e2b4076705b775b3bcdcb1054f3642/torchref-0.5.2.tar.gz to build tracker '/tmp/pip-build-tracker-hdpit6xx'
2026-05-18T20:18:26,688   Created temporary directory: /tmp/pip-build-env-os85dk_a
2026-05-18T20:18:26,693   Installing build dependencies: started
2026-05-18T20:18:26,694   Running command pip subprocess to install build dependencies
2026-05-18T20:18:27,847   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2026-05-18T20:18:28,316   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
2026-05-18T20:18:28,340   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-05-18T20:18:30,490   Collecting setuptools>=42
2026-05-18T20:18:30,492     Obtaining dependency information for setuptools>=42 from https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl.metadata
2026-05-18T20:18:30,514     Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB)
2026-05-18T20:18:30,781   Collecting wheel
2026-05-18T20:18:30,783     Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata
2026-05-18T20:18:30,808     Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB)
2026-05-18T20:18:30,993   Collecting packaging>=24.0
2026-05-18T20:18:30,994     Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata
2026-05-18T20:18:31,008     Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata (3.5 kB)
2026-05-18T20:18:31,218   Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB)
2026-05-18T20:18:31,238   Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB)
2026-05-18T20:18:31,315   Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB)
2026-05-18T20:18:31,360   Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB)
2026-05-18T20:18:31,388   Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB)
2026-05-18T20:18:31,499   Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB)
2026-05-18T20:18:34,248   Installing collected packages: setuptools, packaging, wheel
2026-05-18T20:18:37,739     Creating /tmp/pip-build-env-os85dk_a/overlay/local/bin
2026-05-18T20:18:37,741     changing mode of /tmp/pip-build-env-os85dk_a/overlay/local/bin/wheel to 755
2026-05-18T20:18:37,761   Successfully installed packaging-26.2 setuptools-82.0.1 wheel-0.47.0
2026-05-18T20:18:38,045   Installing build dependencies: finished with status 'done'
2026-05-18T20:18:38,051   Getting requirements to build wheel: started
2026-05-18T20:18:38,052   Running command Getting requirements to build wheel
2026-05-18T20:18:38,829   running egg_info
2026-05-18T20:18:38,835   writing torchref.egg-info/PKG-INFO
2026-05-18T20:18:38,843   writing dependency_links to torchref.egg-info/dependency_links.txt
2026-05-18T20:18:38,845   writing entry points to torchref.egg-info/entry_points.txt
2026-05-18T20:18:38,849   writing requirements to torchref.egg-info/requires.txt
2026-05-18T20:18:38,851   writing top-level names to torchref.egg-info/top_level.txt
2026-05-18T20:18:38,940   reading manifest file 'torchref.egg-info/SOURCES.txt'
2026-05-18T20:18:38,955   adding license file 'LICENSE'
2026-05-18T20:18:38,968   writing manifest file 'torchref.egg-info/SOURCES.txt'
2026-05-18T20:18:39,065   Getting requirements to build wheel: finished with status 'done'
2026-05-18T20:18:39,069   Created temporary directory: /tmp/pip-modern-metadata-1vu2xime
2026-05-18T20:18:39,072   Preparing metadata (pyproject.toml): started
2026-05-18T20:18:39,073   Running command Preparing metadata (pyproject.toml)
2026-05-18T20:18:39,744   running dist_info
2026-05-18T20:18:39,755   creating /tmp/pip-modern-metadata-1vu2xime/torchref.egg-info
2026-05-18T20:18:39,756   writing /tmp/pip-modern-metadata-1vu2xime/torchref.egg-info/PKG-INFO
2026-05-18T20:18:39,763   writing dependency_links to /tmp/pip-modern-metadata-1vu2xime/torchref.egg-info/dependency_links.txt
2026-05-18T20:18:39,765   writing entry points to /tmp/pip-modern-metadata-1vu2xime/torchref.egg-info/entry_points.txt
2026-05-18T20:18:39,770   writing requirements to /tmp/pip-modern-metadata-1vu2xime/torchref.egg-info/requires.txt
2026-05-18T20:18:39,771   writing top-level names to /tmp/pip-modern-metadata-1vu2xime/torchref.egg-info/top_level.txt
2026-05-18T20:18:39,772   writing manifest file '/tmp/pip-modern-metadata-1vu2xime/torchref.egg-info/SOURCES.txt'
2026-05-18T20:18:39,845   reading manifest file '/tmp/pip-modern-metadata-1vu2xime/torchref.egg-info/SOURCES.txt'
2026-05-18T20:18:39,847   adding license file 'LICENSE'
2026-05-18T20:18:39,857   writing manifest file '/tmp/pip-modern-metadata-1vu2xime/torchref.egg-info/SOURCES.txt'
2026-05-18T20:18:39,859   creating '/tmp/pip-modern-metadata-1vu2xime/torchref-0.5.2.dist-info'
2026-05-18T20:18:39,985   Preparing metadata (pyproject.toml): finished with status 'done'
2026-05-18T20:18:39,990   Source in /tmp/pip-wheel-mpz0qx14/torchref_a69e7239b31e423188c27004bb2f097d has version 0.5.2, which satisfies requirement torchref==0.5.2 from https://files.pythonhosted.org/packages/4d/d1/961979d80eaa39ceac37b9b8b641c3e2b4076705b775b3bcdcb1054f3642/torchref-0.5.2.tar.gz
2026-05-18T20:18:39,991   Removed torchref==0.5.2 from https://files.pythonhosted.org/packages/4d/d1/961979d80eaa39ceac37b9b8b641c3e2b4076705b775b3bcdcb1054f3642/torchref-0.5.2.tar.gz from build tracker '/tmp/pip-build-tracker-hdpit6xx'
2026-05-18T20:18:39,997 Created temporary directory: /tmp/pip-unpack-lv0e52k5
2026-05-18T20:18:39,998 Building wheels for collected packages: torchref
2026-05-18T20:18:40,003   Created temporary directory: /tmp/pip-wheel-_uot49xs
2026-05-18T20:18:40,003   Destination directory: /tmp/pip-wheel-_uot49xs
2026-05-18T20:18:40,005   Building wheel for torchref (pyproject.toml): started
2026-05-18T20:18:40,007   Running command Building wheel for torchref (pyproject.toml)
2026-05-18T20:18:40,649   running bdist_wheel
2026-05-18T20:18:40,666   running build
2026-05-18T20:18:40,667   running build_py
2026-05-18T20:18:40,673   creating build/lib/torchref
2026-05-18T20:18:40,675   copying torchref/config.py -> build/lib/torchref
2026-05-18T20:18:40,677   copying torchref/__init__.py -> build/lib/torchref
2026-05-18T20:18:40,679   copying torchref/_bootstrap.py -> build/lib/torchref
2026-05-18T20:18:40,682   creating build/lib/torchref/scripts
2026-05-18T20:18:40,683   copying torchref/scripts/generate_scattering_table.py -> build/lib/torchref/scripts
2026-05-18T20:18:40,685   copying torchref/scripts/__init__.py -> build/lib/torchref/scripts
2026-05-18T20:18:40,688   creating build/lib/torchref/model
2026-05-18T20:18:40,689   copying torchref/model/sf_ds.py -> build/lib/torchref/model
2026-05-18T20:18:40,692   copying torchref/model/internal_coordinates.py -> build/lib/torchref/model
2026-05-18T20:18:40,695   copying torchref/model/closed_segmented_internal_coordinates.py -> build/lib/torchref/model
2026-05-18T20:18:40,698   copying torchref/model/sf_fft.py -> build/lib/torchref/model
2026-05-18T20:18:40,701   copying torchref/model/model.py -> build/lib/torchref/model
2026-05-18T20:18:40,706   copying torchref/model/model_collection.py -> build/lib/torchref/model
2026-05-18T20:18:40,708   copying torchref/model/mixed_model.py -> build/lib/torchref/model
2026-05-18T20:18:40,711   copying torchref/model/model_ft.py -> build/lib/torchref/model
2026-05-18T20:18:40,715   copying torchref/model/__init__.py -> build/lib/torchref/model
2026-05-18T20:18:40,717   copying torchref/model/parameter_wrappers.py -> build/lib/torchref/model
2026-05-18T20:18:40,722   copying torchref/model/segmented_internal_coordinates.py -> build/lib/torchref/model
2026-05-18T20:18:40,727   creating build/lib/torchref/symmetry
2026-05-18T20:18:40,728   copying torchref/symmetry/symmetry.py -> build/lib/torchref/symmetry
2026-05-18T20:18:40,730   copying torchref/symmetry/map_symmetry_interpolation.py -> build/lib/torchref/symmetry
2026-05-18T20:18:40,732   copying torchref/symmetry/map_symmetry.py -> build/lib/torchref/symmetry
2026-05-18T20:18:40,735   copying torchref/symmetry/cell.py -> build/lib/torchref/symmetry
2026-05-18T20:18:40,737   copying torchref/symmetry/grid_utils.py -> build/lib/torchref/symmetry
2026-05-18T20:18:40,740   copying torchref/symmetry/spacegroup.py -> build/lib/torchref/symmetry
2026-05-18T20:18:40,743   copying torchref/symmetry/__init__.py -> build/lib/torchref/symmetry
2026-05-18T20:18:40,745   copying torchref/symmetry/reciprocal_symmetry.py -> build/lib/torchref/symmetry
2026-05-18T20:18:40,749   creating build/lib/torchref/io
2026-05-18T20:18:40,750   copying torchref/io/cif_readers.py -> build/lib/torchref/io
2026-05-18T20:18:40,753   copying torchref/io/mtz.py -> build/lib/torchref/io
2026-05-18T20:18:40,756   copying torchref/io/pdb.py -> build/lib/torchref/io
2026-05-18T20:18:40,759   copying torchref/io/cif.py -> build/lib/torchref/io
2026-05-18T20:18:40,761   copying torchref/io/metadata.py -> build/lib/torchref/io
2026-05-18T20:18:40,764   copying torchref/io/ihm_mapping.py -> build/lib/torchref/io
2026-05-18T20:18:40,767   copying torchref/io/ihm.py -> build/lib/torchref/io
2026-05-18T20:18:40,770   copying torchref/io/__init__.py -> build/lib/torchref/io
2026-05-18T20:18:40,772   copying torchref/io/data_router.py -> build/lib/torchref/io
2026-05-18T20:18:40,775   creating build/lib/torchref/kinetic
2026-05-18T20:18:40,776   copying torchref/kinetic/targets.py -> build/lib/torchref/kinetic
2026-05-18T20:18:40,779   copying torchref/kinetic/refinement.py -> build/lib/torchref/kinetic
2026-05-18T20:18:40,782   copying torchref/kinetic/occupancies.py -> build/lib/torchref/kinetic
2026-05-18T20:18:40,785   copying torchref/kinetic/__init__.py -> build/lib/torchref/kinetic
2026-05-18T20:18:40,787   copying torchref/kinetic/kinetics.py -> build/lib/torchref/kinetic
2026-05-18T20:18:40,790   creating build/lib/torchref/refinement
2026-05-18T20:18:40,792   copying torchref/refinement/loss_state.py -> build/lib/torchref/refinement
2026-05-18T20:18:40,795   copying torchref/refinement/base_refinement.py -> build/lib/torchref/refinement
2026-05-18T20:18:40,798   copying torchref/refinement/logger.py -> build/lib/torchref/refinement
2026-05-18T20:18:40,800   copying torchref/refinement/__init__.py -> build/lib/torchref/refinement
2026-05-18T20:18:40,802   copying torchref/refinement/lbfgs_refinement.py -> build/lib/torchref/refinement
2026-05-18T20:18:40,805   creating build/lib/torchref/base
2026-05-18T20:18:40,806   copying torchref/base/get_scattering_factor_torch.py -> build/lib/torchref/base
2026-05-18T20:18:40,809   copying torchref/base/math_torch.py -> build/lib/torchref/base
2026-05-18T20:18:40,811   copying torchref/base/CCTBX_related.py -> build/lib/torchref/base
2026-05-18T20:18:40,813   copying torchref/base/french_wilson.py -> build/lib/torchref/base
2026-05-18T20:18:40,816   copying torchref/base/math_numpy.py -> build/lib/torchref/base
2026-05-18T20:18:40,818   copying torchref/base/__init__.py -> build/lib/torchref/base
2026-05-18T20:18:40,821   creating build/lib/torchref/scaling
2026-05-18T20:18:40,822   copying torchref/scaling/scaler_base.py -> build/lib/torchref/scaling
2026-05-18T20:18:40,826   copying torchref/scaling/scaler.py -> build/lib/torchref/scaling
2026-05-18T20:18:40,828   copying torchref/scaling/solvent.py -> build/lib/torchref/scaling
2026-05-18T20:18:40,831   copying torchref/scaling/__init__.py -> build/lib/torchref/scaling
2026-05-18T20:18:40,833   copying torchref/scaling/collection_scaler.py -> build/lib/torchref/scaling
2026-05-18T20:18:40,836   creating build/lib/torchref/alignment
2026-05-18T20:18:40,838   copying torchref/alignment/jax_subpixel_peaks.py -> build/lib/torchref/alignment
2026-05-18T20:18:40,840   copying torchref/alignment/ball_transform.py -> build/lib/torchref/alignment
2026-05-18T20:18:40,844   copying torchref/alignment/sampling.py -> build/lib/torchref/alignment
2026-05-18T20:18:40,846   copying torchref/alignment/translation.py -> build/lib/torchref/alignment
2026-05-18T20:18:40,849   copying torchref/alignment/distributions.py -> build/lib/torchref/alignment
2026-05-18T20:18:40,851   copying torchref/alignment/transform.py -> build/lib/torchref/alignment
2026-05-18T20:18:40,854   copying torchref/alignment/pipeline.py -> build/lib/torchref/alignment
2026-05-18T20:18:40,857   copying torchref/alignment/clashscore.py -> build/lib/torchref/alignment
2026-05-18T20:18:40,859   copying torchref/alignment/rigid_body.py -> build/lib/torchref/alignment
2026-05-18T20:18:40,862   copying torchref/alignment/__init__.py -> build/lib/torchref/alignment
2026-05-18T20:18:40,864   creating build/lib/torchref/maps
2026-05-18T20:18:40,865   copying torchref/maps/difference_map.py -> build/lib/torchref/maps
2026-05-18T20:18:40,867   copying torchref/maps/map.py -> build/lib/torchref/maps
2026-05-18T20:18:40,870   copying torchref/maps/__init__.py -> build/lib/torchref/maps
2026-05-18T20:18:40,872   creating build/lib/torchref/cli
2026-05-18T20:18:40,873   copying torchref/cli/_common.py -> build/lib/torchref/cli
2026-05-18T20:18:40,876   copying torchref/cli/strip_altlocs.py -> build/lib/torchref/cli
2026-05-18T20:18:40,878   copying torchref/cli/mtz2map.py -> build/lib/torchref/cli
2026-05-18T20:18:40,880   copying torchref/cli/add_metadata.py -> build/lib/torchref/cli
2026-05-18T20:18:40,883   copying torchref/cli/validate_ded.py -> build/lib/torchref/cli
2026-05-18T20:18:40,886   copying torchref/cli/collection_difference_refine.py -> build/lib/torchref/cli
2026-05-18T20:18:40,889   copying torchref/cli/phased_difference_map.py -> build/lib/torchref/cli
2026-05-18T20:18:40,891   copying torchref/cli/refine.py -> build/lib/torchref/cli
2026-05-18T20:18:40,894   copying torchref/cli/__init__.py -> build/lib/torchref/cli
2026-05-18T20:18:40,897   creating build/lib/torchref/utils
2026-05-18T20:18:40,898   copying torchref/utils/autograd_ops.py -> build/lib/torchref/utils
2026-05-18T20:18:40,900   copying torchref/utils/timing.py -> build/lib/torchref/utils
2026-05-18T20:18:40,902   copying torchref/utils/gradnorm.py -> build/lib/torchref/utils
2026-05-18T20:18:40,904   copying torchref/utils/device_mixin.py -> build/lib/torchref/utils
2026-05-18T20:18:40,906   copying torchref/utils/utils.py -> build/lib/torchref/utils
2026-05-18T20:18:40,909   copying torchref/utils/caching.py -> build/lib/torchref/utils
2026-05-18T20:18:40,911   copying torchref/utils/loss_validation.py -> build/lib/torchref/utils
2026-05-18T20:18:40,914   copying torchref/utils/pse.py -> build/lib/torchref/utils
2026-05-18T20:18:40,916   copying torchref/utils/hyperparameters.py -> build/lib/torchref/utils
2026-05-18T20:18:40,918   copying torchref/utils/autograd_introspection.py -> build/lib/torchref/utils
2026-05-18T20:18:40,920   copying torchref/utils/__init__.py -> build/lib/torchref/utils
2026-05-18T20:18:40,922   copying torchref/utils/serialization.py -> build/lib/torchref/utils
2026-05-18T20:18:40,924   copying torchref/utils/stats.py -> build/lib/torchref/utils
2026-05-18T20:18:40,926   copying torchref/utils/debug_utils.py -> build/lib/torchref/utils
2026-05-18T20:18:40,929   creating build/lib/torchref/restraints
2026-05-18T20:18:40,930   copying torchref/restraints/library.py -> build/lib/torchref/restraints
2026-05-18T20:18:40,933   copying torchref/restraints/restraints_helper.py -> build/lib/torchref/restraints
2026-05-18T20:18:40,935   copying torchref/restraints/ramachandran.py -> build/lib/torchref/restraints
2026-05-18T20:18:40,937   copying torchref/restraints/neighbor_search.py -> build/lib/torchref/restraints
2026-05-18T20:18:40,940   copying torchref/restraints/restraints.py -> build/lib/torchref/restraints
2026-05-18T20:18:40,944   copying torchref/restraints/hydrogen_topology.py -> build/lib/torchref/restraints
2026-05-18T20:18:40,947   copying torchref/restraints/__init__.py -> build/lib/torchref/restraints
2026-05-18T20:18:40,949   copying torchref/restraints/builders.py -> build/lib/torchref/restraints
2026-05-18T20:18:40,952   copying torchref/restraints/builders_fast.py -> build/lib/torchref/restraints
2026-05-18T20:18:40,956   copying torchref/restraints/builders_numba.py -> build/lib/torchref/restraints
2026-05-18T20:18:40,964   creating build/lib/torchref/io/datasets
2026-05-18T20:18:40,965   copying torchref/io/datasets/fcalc_data.py -> build/lib/torchref/io/datasets
2026-05-18T20:18:40,968   copying torchref/io/datasets/reflection_data.py -> build/lib/torchref/io/datasets
2026-05-18T20:18:40,973   copying torchref/io/datasets/collection.py -> build/lib/torchref/io/datasets
2026-05-18T20:18:40,975   copying torchref/io/datasets/base.py -> build/lib/torchref/io/datasets
2026-05-18T20:18:40,978   copying torchref/io/datasets/__init__.py -> build/lib/torchref/io/datasets
2026-05-18T20:18:40,981   creating build/lib/torchref/refinement/targets
2026-05-18T20:18:40,982   copying torchref/refinement/targets/occupancy_floor_diagnostic.py -> build/lib/torchref/refinement/targets
2026-05-18T20:18:40,984   copying torchref/refinement/targets/realspace.py -> build/lib/torchref/refinement/targets
2026-05-18T20:18:40,987   copying torchref/refinement/targets/difference.py -> build/lib/torchref/refinement/targets
2026-05-18T20:18:40,991   copying torchref/refinement/targets/combined.py -> build/lib/torchref/refinement/targets
2026-05-18T20:18:40,993   copying torchref/refinement/targets/similarity.py -> build/lib/torchref/refinement/targets
2026-05-18T20:18:40,996   copying torchref/refinement/targets/sampled_ml_phase_target.py -> build/lib/torchref/refinement/targets
2026-05-18T20:18:40,999   copying torchref/refinement/targets/base.py -> build/lib/torchref/refinement/targets
2026-05-18T20:18:41,001   copying torchref/refinement/targets/amber_target.py -> build/lib/torchref/refinement/targets
2026-05-18T20:18:41,004   copying torchref/refinement/targets/__init__.py -> build/lib/torchref/refinement/targets
2026-05-18T20:18:41,006   copying torchref/refinement/targets/forcefield_target.py -> build/lib/torchref/refinement/targets
2026-05-18T20:18:41,009   creating build/lib/torchref/refinement/weighting
2026-05-18T20:18:41,010   copying torchref/refinement/weighting/policy_weighting.py -> build/lib/torchref/refinement/weighting
2026-05-18T20:18:41,013   copying torchref/refinement/weighting/random_weighting.py -> build/lib/torchref/refinement/weighting
2026-05-18T20:18:41,015   copying torchref/refinement/weighting/es_policy_training.py -> build/lib/torchref/refinement/weighting
2026-05-18T20:18:41,018   copying torchref/refinement/weighting/component_weighting.py -> build/lib/torchref/refinement/weighting
2026-05-18T20:18:41,020   copying torchref/refinement/weighting/__init__.py -> build/lib/torchref/refinement/weighting
2026-05-18T20:18:41,022   copying torchref/refinement/weighting/base_weighting.py -> build/lib/torchref/refinement/weighting
2026-05-18T20:18:41,024   creating build/lib/torchref/refinement/optimizers
2026-05-18T20:18:41,025   copying torchref/refinement/optimizers/adam_noise.py -> build/lib/torchref/refinement/optimizers
2026-05-18T20:18:41,027   copying torchref/refinement/optimizers/simulated_annealing.py -> build/lib/torchref/refinement/optimizers
2026-05-18T20:18:41,029   copying torchref/refinement/optimizers/internal_coord_sa.py -> build/lib/torchref/refinement/optimizers
2026-05-18T20:18:41,032   copying torchref/refinement/optimizers/langevin_sa.py -> build/lib/torchref/refinement/optimizers
2026-05-18T20:18:41,034   copying torchref/refinement/optimizers/exploratory_lbfgs.py -> build/lib/torchref/refinement/optimizers
2026-05-18T20:18:41,037   copying torchref/refinement/optimizers/momentum_sa.py -> build/lib/torchref/refinement/optimizers
2026-05-18T20:18:41,039   copying torchref/refinement/optimizers/__init__.py -> build/lib/torchref/refinement/optimizers
2026-05-18T20:18:41,041   creating build/lib/torchref/refinement/targets/adp
2026-05-18T20:18:41,042   copying torchref/refinement/targets/adp/entropy.py -> build/lib/torchref/refinement/targets/adp
2026-05-18T20:18:41,044   copying torchref/refinement/targets/adp/locality.py -> build/lib/torchref/refinement/targets/adp
2026-05-18T20:18:41,046   copying torchref/refinement/targets/adp/rigid_bond.py -> build/lib/torchref/refinement/targets/adp
2026-05-18T20:18:41,049   copying torchref/refinement/targets/adp/similarity.py -> build/lib/torchref/refinement/targets/adp
2026-05-18T20:18:41,050   copying torchref/refinement/targets/adp/scaler_log_scale.py -> build/lib/torchref/refinement/targets/adp
2026-05-18T20:18:41,052   copying torchref/refinement/targets/adp/scaler_u.py -> build/lib/torchref/refinement/targets/adp
2026-05-18T20:18:41,054   copying torchref/refinement/targets/adp/base.py -> build/lib/torchref/refinement/targets/adp
2026-05-18T20:18:41,056   copying torchref/refinement/targets/adp/__init__.py -> build/lib/torchref/refinement/targets/adp
2026-05-18T20:18:41,058   creating build/lib/torchref/refinement/targets/geometry
2026-05-18T20:18:41,059   copying torchref/refinement/targets/geometry/non_bonded_h.py -> build/lib/torchref/refinement/targets/geometry
2026-05-18T20:18:41,062   copying torchref/refinement/targets/geometry/ramachandran.py -> build/lib/torchref/refinement/targets/geometry
2026-05-18T20:18:41,064   copying torchref/refinement/targets/geometry/bonds.py -> build/lib/torchref/refinement/targets/geometry
2026-05-18T20:18:41,066   copying torchref/refinement/targets/geometry/non_bonded.py -> build/lib/torchref/refinement/targets/geometry
2026-05-18T20:18:41,068   copying torchref/refinement/targets/geometry/planarity.py -> build/lib/torchref/refinement/targets/geometry
2026-05-18T20:18:41,070   copying torchref/refinement/targets/geometry/torsions.py -> build/lib/torchref/refinement/targets/geometry
2026-05-18T20:18:41,073   copying torchref/refinement/targets/geometry/base.py -> build/lib/torchref/refinement/targets/geometry
2026-05-18T20:18:41,075   copying torchref/refinement/targets/geometry/chiral.py -> build/lib/torchref/refinement/targets/geometry
2026-05-18T20:18:41,077   copying torchref/refinement/targets/geometry/__init__.py -> build/lib/torchref/refinement/targets/geometry
2026-05-18T20:18:41,079   copying torchref/refinement/targets/geometry/angles.py -> build/lib/torchref/refinement/targets/geometry
2026-05-18T20:18:41,081   creating build/lib/torchref/refinement/targets/xray
2026-05-18T20:18:41,082   copying torchref/refinement/targets/xray/maximum_likelihood.py -> build/lib/torchref/refinement/targets/xray
2026-05-18T20:18:41,084   copying torchref/refinement/targets/xray/least_squares.py -> build/lib/torchref/refinement/targets/xray
2026-05-18T20:18:41,086   copying torchref/refinement/targets/xray/gaussian.py -> build/lib/torchref/refinement/targets/xray
2026-05-18T20:18:41,087   copying torchref/refinement/targets/xray/bhattacharyya.py -> build/lib/torchref/refinement/targets/xray
2026-05-18T20:18:41,090   copying torchref/refinement/targets/xray/base.py -> build/lib/torchref/refinement/targets/xray
2026-05-18T20:18:41,092   copying torchref/refinement/targets/xray/__init__.py -> build/lib/torchref/refinement/targets/xray
2026-05-18T20:18:41,094   creating build/lib/torchref/base/targets
2026-05-18T20:18:41,095   copying torchref/base/targets/_common.py -> build/lib/torchref/base/targets
2026-05-18T20:18:41,097   copying torchref/base/targets/xray_bhattacharyya.py -> build/lib/torchref/base/targets
2026-05-18T20:18:41,099   copying torchref/base/targets/adp.py -> build/lib/torchref/base/targets
2026-05-18T20:18:41,100   copying torchref/base/targets/xray_ml.py -> build/lib/torchref/base/targets
2026-05-18T20:18:41,102   copying torchref/base/targets/bond.py -> build/lib/torchref/base/targets
2026-05-18T20:18:41,104   copying torchref/base/targets/ramachandran.py -> build/lib/torchref/base/targets
2026-05-18T20:18:41,106   copying torchref/base/targets/torsion.py -> build/lib/torchref/base/targets
2026-05-18T20:18:41,108   copying torchref/base/targets/angle.py -> build/lib/torchref/base/targets
2026-05-18T20:18:41,110   copying torchref/base/targets/xray_ls.py -> build/lib/torchref/base/targets
2026-05-18T20:18:41,112   copying torchref/base/targets/xray_gaussian.py -> build/lib/torchref/base/targets
2026-05-18T20:18:41,113   copying torchref/base/targets/planarity.py -> build/lib/torchref/base/targets
2026-05-18T20:18:41,115   copying torchref/base/targets/_dispatch.py -> build/lib/torchref/base/targets
2026-05-18T20:18:41,117   copying torchref/base/targets/chiral.py -> build/lib/torchref/base/targets
2026-05-18T20:18:41,119   copying torchref/base/targets/nonbonded.py -> build/lib/torchref/base/targets
2026-05-18T20:18:41,121   copying torchref/base/targets/__init__.py -> build/lib/torchref/base/targets
2026-05-18T20:18:41,123   creating build/lib/torchref/base/coordinates
2026-05-18T20:18:41,124   copying torchref/base/coordinates/transforms_torch.py -> build/lib/torchref/base/coordinates
2026-05-18T20:18:41,127   copying torchref/base/coordinates/__init__.py -> build/lib/torchref/base/coordinates
2026-05-18T20:18:41,128   copying torchref/base/coordinates/periodic_boundary.py -> build/lib/torchref/base/coordinates
2026-05-18T20:18:41,130   copying torchref/base/coordinates/transforms_numpy.py -> build/lib/torchref/base/coordinates
2026-05-18T20:18:41,133   creating build/lib/torchref/base/reciprocal
2026-05-18T20:18:41,133   copying torchref/base/reciprocal/symmetry.py -> build/lib/torchref/base/reciprocal
2026-05-18T20:18:41,136   copying torchref/base/reciprocal/hkl.py -> build/lib/torchref/base/reciprocal
2026-05-18T20:18:41,138   copying torchref/base/reciprocal/interpolation.py -> build/lib/torchref/base/reciprocal
2026-05-18T20:18:41,140   copying torchref/base/reciprocal/grid_operations.py -> build/lib/torchref/base/reciprocal
2026-05-18T20:18:41,142   copying torchref/base/reciprocal/__init__.py -> build/lib/torchref/base/reciprocal
2026-05-18T20:18:41,144   copying torchref/base/reciprocal/basis.py -> build/lib/torchref/base/reciprocal
2026-05-18T20:18:41,147   creating build/lib/torchref/base/scattering
2026-05-18T20:18:41,148   copying torchref/base/scattering/scattering_table.py -> build/lib/torchref/base/scattering
2026-05-18T20:18:41,151   copying torchref/base/scattering/anomalous_table.py -> build/lib/torchref/base/scattering
2026-05-18T20:18:41,153   copying torchref/base/scattering/__init__.py -> build/lib/torchref/base/scattering
2026-05-18T20:18:41,155   copying torchref/base/scattering/itc92.py -> build/lib/torchref/base/scattering
2026-05-18T20:18:41,157   creating build/lib/torchref/base/kernels
2026-05-18T20:18:41,158   copying torchref/base/kernels/separable_triton_kernel.py -> build/lib/torchref/base/kernels
2026-05-18T20:18:41,161   copying torchref/base/kernels/jit_kernel_vectorized_add_to_map.py -> build/lib/torchref/base/kernels
2026-05-18T20:18:41,164   copying torchref/base/kernels/triton_kernel.py -> build/lib/torchref/base/kernels
2026-05-18T20:18:41,166   copying torchref/base/kernels/cpu_scatter.py -> build/lib/torchref/base/kernels
2026-05-18T20:18:41,169   copying torchref/base/kernels/optimized_ops.py -> build/lib/torchref/base/kernels
2026-05-18T20:18:41,171   copying torchref/base/kernels/__init__.py -> build/lib/torchref/base/kernels
2026-05-18T20:18:41,173   creating build/lib/torchref/base/metrics
2026-05-18T20:18:41,174   copying torchref/base/metrics/rfactor.py -> build/lib/torchref/base/metrics
2026-05-18T20:18:41,177   copying torchref/base/metrics/loss.py -> build/lib/torchref/base/metrics
2026-05-18T20:18:41,179   copying torchref/base/metrics/__init__.py -> build/lib/torchref/base/metrics
2026-05-18T20:18:41,181   creating build/lib/torchref/base/fourier
2026-05-18T20:18:41,182   copying torchref/base/fourier/grid.py -> build/lib/torchref/base/fourier
2026-05-18T20:18:41,184   copying torchref/base/fourier/fft.py -> build/lib/torchref/base/fourier
2026-05-18T20:18:41,186   copying torchref/base/fourier/__init__.py -> build/lib/torchref/base/fourier
2026-05-18T20:18:41,188   creating build/lib/torchref/base/electron_density
2026-05-18T20:18:41,189   copying torchref/base/electron_density/voxel_utils.py -> build/lib/torchref/base/electron_density
2026-05-18T20:18:41,192   copying torchref/base/electron_density/main.py -> build/lib/torchref/base/electron_density
2026-05-18T20:18:41,194   copying torchref/base/electron_density/map_building.py -> build/lib/torchref/base/electron_density
2026-05-18T20:18:41,197   copying torchref/base/electron_density/solvent_mask.py -> build/lib/torchref/base/electron_density
2026-05-18T20:18:41,199   copying torchref/base/electron_density/__init__.py -> build/lib/torchref/base/electron_density
2026-05-18T20:18:41,201   creating build/lib/torchref/base/alignment
2026-05-18T20:18:41,202   copying torchref/base/alignment/scoring.py -> build/lib/torchref/base/alignment
2026-05-18T20:18:41,204   copying torchref/base/alignment/rotation.py -> build/lib/torchref/base/alignment
2026-05-18T20:18:41,207   copying torchref/base/alignment/__init__.py -> build/lib/torchref/base/alignment
2026-05-18T20:18:41,208   copying torchref/base/alignment/superposition.py -> build/lib/torchref/base/alignment
2026-05-18T20:18:41,211   copying torchref/base/alignment/normalization.py -> build/lib/torchref/base/alignment
2026-05-18T20:18:41,213   creating build/lib/torchref/base/direct_summation
2026-05-18T20:18:41,214   copying torchref/base/direct_summation/isotropic.py -> build/lib/torchref/base/direct_summation
2026-05-18T20:18:41,217   copying torchref/base/direct_summation/corrections.py -> build/lib/torchref/base/direct_summation
2026-05-18T20:18:41,218   copying torchref/base/direct_summation/anisotropic.py -> build/lib/torchref/base/direct_summation
2026-05-18T20:18:41,221   copying torchref/base/direct_summation/__init__.py -> build/lib/torchref/base/direct_summation
2026-05-18T20:18:41,223   creating build/lib/torchref/base/chain_closure
2026-05-18T20:18:41,224   copying torchref/base/chain_closure/backbone_utils.py -> build/lib/torchref/base/chain_closure
2026-05-18T20:18:41,226   copying torchref/base/chain_closure/closure.py -> build/lib/torchref/base/chain_closure
2026-05-18T20:18:41,229   copying torchref/base/chain_closure/__init__.py -> build/lib/torchref/base/chain_closure
2026-05-18T20:18:41,231   creating build/lib/torchref/base/targets/triton
2026-05-18T20:18:41,232   copying torchref/base/targets/triton/xray_bhattacharyya.py -> build/lib/torchref/base/targets/triton
2026-05-18T20:18:41,235   copying torchref/base/targets/triton/_dihedral.py -> build/lib/torchref/base/targets/triton
2026-05-18T20:18:41,236   copying torchref/base/targets/triton/xray_ml.py -> build/lib/torchref/base/targets/triton
2026-05-18T20:18:41,239   copying torchref/base/targets/triton/bond.py -> build/lib/torchref/base/targets/triton
2026-05-18T20:18:41,242   copying torchref/base/targets/triton/ramachandran.py -> build/lib/torchref/base/targets/triton
2026-05-18T20:18:41,245   copying torchref/base/targets/triton/place_hydrogens.py -> build/lib/torchref/base/targets/triton
2026-05-18T20:18:41,248   copying torchref/base/targets/triton/torsion.py -> build/lib/torchref/base/targets/triton
2026-05-18T20:18:41,251   copying torchref/base/targets/triton/angle.py -> build/lib/torchref/base/targets/triton
2026-05-18T20:18:41,253   copying torchref/base/targets/triton/xray_ls.py -> build/lib/torchref/base/targets/triton
2026-05-18T20:18:41,256   copying torchref/base/targets/triton/xray_gaussian.py -> build/lib/torchref/base/targets/triton
2026-05-18T20:18:41,258   copying torchref/base/targets/triton/planarity.py -> build/lib/torchref/base/targets/triton
2026-05-18T20:18:41,261   copying torchref/base/targets/triton/adp_simu.py -> build/lib/torchref/base/targets/triton
2026-05-18T20:18:41,263   copying torchref/base/targets/triton/chiral.py -> build/lib/torchref/base/targets/triton
2026-05-18T20:18:41,266   copying torchref/base/targets/triton/nonbonded.py -> build/lib/torchref/base/targets/triton
2026-05-18T20:18:41,269   copying torchref/base/targets/triton/__init__.py -> build/lib/torchref/base/targets/triton
2026-05-18T20:18:41,271   running egg_info
2026-05-18T20:18:41,285   writing torchref.egg-info/PKG-INFO
2026-05-18T20:18:41,294   writing dependency_links to torchref.egg-info/dependency_links.txt
2026-05-18T20:18:41,297   writing entry points to torchref.egg-info/entry_points.txt
2026-05-18T20:18:41,302   writing requirements to torchref.egg-info/requires.txt
2026-05-18T20:18:41,303   writing top-level names to torchref.egg-info/top_level.txt
2026-05-18T20:18:41,374   reading manifest file 'torchref.egg-info/SOURCES.txt'
2026-05-18T20:18:41,389   adding license file 'LICENSE'
2026-05-18T20:18:41,402   writing manifest file 'torchref.egg-info/SOURCES.txt'
2026-05-18T20:18:41,437   creating build/lib/torchref/data
2026-05-18T20:18:41,438   copying torchref/data/atomic_vdw_radii.csv -> build/lib/torchref/data
2026-05-18T20:18:41,441   copying torchref/data/itc92_scattering_factors.pt -> build/lib/torchref/data
2026-05-18T20:18:41,443   copying torchref/data/rama_nll_surfaces.pt -> build/lib/torchref/data
2026-05-18T20:18:41,503   creating build/lib/torchref/data/monomer_library/c
2026-05-18T20:18:41,505   copying torchref/data/monomer_library/c/CYS.cif -> build/lib/torchref/data/monomer_library/c
2026-05-18T20:18:41,508   copying torchref/data/monomer_library/c/C.cif -> build/lib/torchref/data/monomer_library/c
2026-05-18T20:18:41,512   creating build/lib/torchref/data/monomer_library/d
2026-05-18T20:18:41,513   copying torchref/data/monomer_library/d/DA.cif -> build/lib/torchref/data/monomer_library/d
2026-05-18T20:18:41,519   copying torchref/data/monomer_library/d/DT.cif -> build/lib/torchref/data/monomer_library/d
2026-05-18T20:18:41,522   copying torchref/data/monomer_library/d/DC.cif -> build/lib/torchref/data/monomer_library/d
2026-05-18T20:18:41,525   copying torchref/data/monomer_library/d/DG.cif -> build/lib/torchref/data/monomer_library/d
2026-05-18T20:18:41,529   creating build/lib/torchref/data/monomer_library/p
2026-05-18T20:18:41,530   copying torchref/data/monomer_library/p/PHE.cif -> build/lib/torchref/data/monomer_library/p
2026-05-18T20:18:41,533   copying torchref/data/monomer_library/p/PRO.cif -> build/lib/torchref/data/monomer_library/p
2026-05-18T20:18:41,536   copying torchref/data/monomer_library/p/PTR.cif -> build/lib/torchref/data/monomer_library/p
2026-05-18T20:18:41,538   creating build/lib/torchref/data/monomer_library/t
2026-05-18T20:18:41,539   copying torchref/data/monomer_library/t/TYR.cif -> build/lib/torchref/data/monomer_library/t
2026-05-18T20:18:41,542   copying torchref/data/monomer_library/t/TRP.cif -> build/lib/torchref/data/monomer_library/t
2026-05-18T20:18:41,545   copying torchref/data/monomer_library/t/THR.cif -> build/lib/torchref/data/monomer_library/t
2026-05-18T20:18:41,547   copying torchref/data/monomer_library/t/TPO.cif -> build/lib/torchref/data/monomer_library/t
2026-05-18T20:18:41,550   creating build/lib/torchref/data/monomer_library/a
2026-05-18T20:18:41,551   copying torchref/data/monomer_library/a/ALA.cif -> build/lib/torchref/data/monomer_library/a
2026-05-18T20:18:41,553   copying torchref/data/monomer_library/a/ARG.cif -> build/lib/torchref/data/monomer_library/a
2026-05-18T20:18:41,556   copying torchref/data/monomer_library/a/ASP.cif -> build/lib/torchref/data/monomer_library/a
2026-05-18T20:18:41,559   copying torchref/data/monomer_library/a/ASN.cif -> build/lib/torchref/data/monomer_library/a
2026-05-18T20:18:41,561   copying torchref/data/monomer_library/a/A.cif -> build/lib/torchref/data/monomer_library/a
2026-05-18T20:18:41,564   creating build/lib/torchref/data/monomer_library/g
2026-05-18T20:18:41,565   copying torchref/data/monomer_library/g/G.cif -> build/lib/torchref/data/monomer_library/g
2026-05-18T20:18:41,568   copying torchref/data/monomer_library/g/GLU.cif -> build/lib/torchref/data/monomer_library/g
2026-05-18T20:18:41,571   copying torchref/data/monomer_library/g/GLY.cif -> build/lib/torchref/data/monomer_library/g
2026-05-18T20:18:41,573   copying torchref/data/monomer_library/g/GLN.cif -> build/lib/torchref/data/monomer_library/g
2026-05-18T20:18:41,576   creating build/lib/torchref/data/monomer_library/l
2026-05-18T20:18:41,577   copying torchref/data/monomer_library/l/LYS.cif -> build/lib/torchref/data/monomer_library/l
2026-05-18T20:18:41,579   copying torchref/data/monomer_library/l/LEU.cif -> build/lib/torchref/data/monomer_library/l
2026-05-18T20:18:41,582   creating build/lib/torchref/data/monomer_library/s
2026-05-18T20:18:41,583   copying torchref/data/monomer_library/s/SEP.cif -> build/lib/torchref/data/monomer_library/s
2026-05-18T20:18:41,585   copying torchref/data/monomer_library/s/SER.cif -> build/lib/torchref/data/monomer_library/s
2026-05-18T20:18:41,588   creating build/lib/torchref/data/monomer_library/m
2026-05-18T20:18:41,589   copying torchref/data/monomer_library/m/MSE.cif -> build/lib/torchref/data/monomer_library/m
2026-05-18T20:18:41,592   copying torchref/data/monomer_library/m/MET.cif -> build/lib/torchref/data/monomer_library/m
2026-05-18T20:18:41,594   creating build/lib/torchref/data/monomer_library/i
2026-05-18T20:18:41,595   copying torchref/data/monomer_library/i/ILE.cif -> build/lib/torchref/data/monomer_library/i
2026-05-18T20:18:41,598   creating build/lib/torchref/data/monomer_library/h
2026-05-18T20:18:41,599   copying torchref/data/monomer_library/h/HIS.cif -> build/lib/torchref/data/monomer_library/h
2026-05-18T20:18:41,602   copying torchref/data/monomer_library/h/HYP.cif -> build/lib/torchref/data/monomer_library/h
2026-05-18T20:18:41,604   copying torchref/data/monomer_library/h/HOH.cif -> build/lib/torchref/data/monomer_library/h
2026-05-18T20:18:41,607   creating build/lib/torchref/data/monomer_library/v
2026-05-18T20:18:41,607   copying torchref/data/monomer_library/v/VAL.cif -> build/lib/torchref/data/monomer_library/v
2026-05-18T20:18:41,610   creating build/lib/torchref/data/monomer_library/list
2026-05-18T20:18:41,611   copying torchref/data/monomer_library/list/mon_lib_list.cif -> build/lib/torchref/data/monomer_library/list
2026-05-18T20:18:41,676   creating build/lib/torchref/data/monomer_library/u
2026-05-18T20:18:41,677   copying torchref/data/monomer_library/u/U.cif -> build/lib/torchref/data/monomer_library/u
2026-05-18T20:18:41,726   installing to build/bdist.linux-armv7l/wheel
2026-05-18T20:18:41,726   running install
2026-05-18T20:18:41,750   running install_lib
2026-05-18T20:18:41,756   creating build/bdist.linux-armv7l/wheel
2026-05-18T20:18:41,759   creating build/bdist.linux-armv7l/wheel/torchref
2026-05-18T20:18:41,760   creating build/bdist.linux-armv7l/wheel/torchref/scripts
2026-05-18T20:18:41,761   copying build/lib/torchref/scripts/generate_scattering_table.py -> build/bdist.linux-armv7l/wheel/./torchref/scripts
2026-05-18T20:18:41,764   copying build/lib/torchref/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/scripts
2026-05-18T20:18:41,765   copying build/lib/torchref/config.py -> build/bdist.linux-armv7l/wheel/./torchref
2026-05-18T20:18:41,768   creating build/bdist.linux-armv7l/wheel/torchref/data
2026-05-18T20:18:41,769   copying build/lib/torchref/data/atomic_vdw_radii.csv -> build/bdist.linux-armv7l/wheel/./torchref/data
2026-05-18T20:18:41,771   copying build/lib/torchref/data/itc92_scattering_factors.pt -> build/bdist.linux-armv7l/wheel/./torchref/data
2026-05-18T20:18:41,774   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library
2026-05-18T20:18:41,775   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/c
2026-05-18T20:18:41,776   copying build/lib/torchref/data/monomer_library/c/CYS.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/c
2026-05-18T20:18:41,779   copying build/lib/torchref/data/monomer_library/c/C.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/c
2026-05-18T20:18:41,782   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/d
2026-05-18T20:18:41,783   copying build/lib/torchref/data/monomer_library/d/DA.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d
2026-05-18T20:18:41,786   copying build/lib/torchref/data/monomer_library/d/DT.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d
2026-05-18T20:18:41,788   copying build/lib/torchref/data/monomer_library/d/DC.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d
2026-05-18T20:18:41,791   copying build/lib/torchref/data/monomer_library/d/DG.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d
2026-05-18T20:18:41,794   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/p
2026-05-18T20:18:41,795   copying build/lib/torchref/data/monomer_library/p/PHE.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/p
2026-05-18T20:18:41,798   copying build/lib/torchref/data/monomer_library/p/PRO.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/p
2026-05-18T20:18:41,800   copying build/lib/torchref/data/monomer_library/p/PTR.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/p
2026-05-18T20:18:41,803   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/t
2026-05-18T20:18:41,804   copying build/lib/torchref/data/monomer_library/t/TYR.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t
2026-05-18T20:18:41,806   copying build/lib/torchref/data/monomer_library/t/TRP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t
2026-05-18T20:18:41,809   copying build/lib/torchref/data/monomer_library/t/THR.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t
2026-05-18T20:18:41,811   copying build/lib/torchref/data/monomer_library/t/TPO.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t
2026-05-18T20:18:41,813   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/a
2026-05-18T20:18:41,815   copying build/lib/torchref/data/monomer_library/a/ALA.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a
2026-05-18T20:18:41,817   copying build/lib/torchref/data/monomer_library/a/ARG.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a
2026-05-18T20:18:41,819   copying build/lib/torchref/data/monomer_library/a/ASP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a
2026-05-18T20:18:41,821   copying build/lib/torchref/data/monomer_library/a/ASN.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a
2026-05-18T20:18:41,824   copying build/lib/torchref/data/monomer_library/a/A.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a
2026-05-18T20:18:41,827   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/g
2026-05-18T20:18:41,828   copying build/lib/torchref/data/monomer_library/g/G.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g
2026-05-18T20:18:41,830   copying build/lib/torchref/data/monomer_library/g/GLU.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g
2026-05-18T20:18:41,832   copying build/lib/torchref/data/monomer_library/g/GLY.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g
2026-05-18T20:18:41,834   copying build/lib/torchref/data/monomer_library/g/GLN.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g
2026-05-18T20:18:41,837   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/l
2026-05-18T20:18:41,838   copying build/lib/torchref/data/monomer_library/l/LYS.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/l
2026-05-18T20:18:41,840   copying build/lib/torchref/data/monomer_library/l/LEU.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/l
2026-05-18T20:18:41,843   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/s
2026-05-18T20:18:41,844   copying build/lib/torchref/data/monomer_library/s/SEP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/s
2026-05-18T20:18:41,847   copying build/lib/torchref/data/monomer_library/s/SER.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/s
2026-05-18T20:18:41,849   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/m
2026-05-18T20:18:41,850   copying build/lib/torchref/data/monomer_library/m/MSE.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/m
2026-05-18T20:18:41,852   copying build/lib/torchref/data/monomer_library/m/MET.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/m
2026-05-18T20:18:41,855   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/i
2026-05-18T20:18:41,856   copying build/lib/torchref/data/monomer_library/i/ILE.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/i
2026-05-18T20:18:41,859   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/h
2026-05-18T20:18:41,860   copying build/lib/torchref/data/monomer_library/h/HIS.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/h
2026-05-18T20:18:41,862   copying build/lib/torchref/data/monomer_library/h/HYP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/h
2026-05-18T20:18:41,864   copying build/lib/torchref/data/monomer_library/h/HOH.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/h
2026-05-18T20:18:41,867   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/v
2026-05-18T20:18:41,868   copying build/lib/torchref/data/monomer_library/v/VAL.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/v
2026-05-18T20:18:41,871   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/list
2026-05-18T20:18:41,872   copying build/lib/torchref/data/monomer_library/list/mon_lib_list.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/list
2026-05-18T20:18:41,950   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/u
2026-05-18T20:18:41,951   copying build/lib/torchref/data/monomer_library/u/U.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/u
2026-05-18T20:18:41,954   copying build/lib/torchref/data/rama_nll_surfaces.pt -> build/bdist.linux-armv7l/wheel/./torchref/data
2026-05-18T20:18:42,003   creating build/bdist.linux-armv7l/wheel/torchref/model
2026-05-18T20:18:42,004   copying build/lib/torchref/model/sf_ds.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-05-18T20:18:42,007   copying build/lib/torchref/model/internal_coordinates.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-05-18T20:18:42,011   copying build/lib/torchref/model/closed_segmented_internal_coordinates.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-05-18T20:18:42,015   copying build/lib/torchref/model/sf_fft.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-05-18T20:18:42,018   copying build/lib/torchref/model/model.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-05-18T20:18:42,023   copying build/lib/torchref/model/model_collection.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-05-18T20:18:42,025   copying build/lib/torchref/model/mixed_model.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-05-18T20:18:42,028   copying build/lib/torchref/model/model_ft.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-05-18T20:18:42,031   copying build/lib/torchref/model/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-05-18T20:18:42,034   copying build/lib/torchref/model/parameter_wrappers.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-05-18T20:18:42,037   copying build/lib/torchref/model/segmented_internal_coordinates.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-05-18T20:18:42,042   creating build/bdist.linux-armv7l/wheel/torchref/symmetry
2026-05-18T20:18:42,043   copying build/lib/torchref/symmetry/symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-05-18T20:18:42,046   copying build/lib/torchref/symmetry/map_symmetry_interpolation.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-05-18T20:18:42,050   copying build/lib/torchref/symmetry/map_symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-05-18T20:18:42,053   copying build/lib/torchref/symmetry/cell.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-05-18T20:18:42,057   copying build/lib/torchref/symmetry/grid_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-05-18T20:18:42,060   copying build/lib/torchref/symmetry/spacegroup.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-05-18T20:18:42,065   copying build/lib/torchref/symmetry/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-05-18T20:18:42,067   copying build/lib/torchref/symmetry/reciprocal_symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-05-18T20:18:42,073   creating build/bdist.linux-armv7l/wheel/torchref/io
2026-05-18T20:18:42,075   copying build/lib/torchref/io/cif_readers.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-05-18T20:18:42,081   copying build/lib/torchref/io/mtz.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-05-18T20:18:42,084   copying build/lib/torchref/io/pdb.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-05-18T20:18:42,088   copying build/lib/torchref/io/cif.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-05-18T20:18:42,091   copying build/lib/torchref/io/metadata.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-05-18T20:18:42,095   copying build/lib/torchref/io/ihm_mapping.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-05-18T20:18:42,100   creating build/bdist.linux-armv7l/wheel/torchref/io/datasets
2026-05-18T20:18:42,101   copying build/lib/torchref/io/datasets/fcalc_data.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets
2026-05-18T20:18:42,105   copying build/lib/torchref/io/datasets/reflection_data.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets
2026-05-18T20:18:42,111   copying build/lib/torchref/io/datasets/collection.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets
2026-05-18T20:18:42,114   copying build/lib/torchref/io/datasets/base.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets
2026-05-18T20:18:42,118   copying build/lib/torchref/io/datasets/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets
2026-05-18T20:18:42,121   copying build/lib/torchref/io/ihm.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-05-18T20:18:42,125   copying build/lib/torchref/io/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-05-18T20:18:42,128   copying build/lib/torchref/io/data_router.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-05-18T20:18:42,132   creating build/bdist.linux-armv7l/wheel/torchref/kinetic
2026-05-18T20:18:42,134   copying build/lib/torchref/kinetic/targets.py -> build/bdist.linux-armv7l/wheel/./torchref/kinetic
2026-05-18T20:18:42,138   copying build/lib/torchref/kinetic/refinement.py -> build/bdist.linux-armv7l/wheel/./torchref/kinetic
2026-05-18T20:18:42,142   copying build/lib/torchref/kinetic/occupancies.py -> build/bdist.linux-armv7l/wheel/./torchref/kinetic
2026-05-18T20:18:42,145   copying build/lib/torchref/kinetic/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/kinetic
2026-05-18T20:18:42,148   copying build/lib/torchref/kinetic/kinetics.py -> build/bdist.linux-armv7l/wheel/./torchref/kinetic
2026-05-18T20:18:42,152   creating build/bdist.linux-armv7l/wheel/torchref/refinement
2026-05-18T20:18:42,153   copying build/lib/torchref/refinement/loss_state.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement
2026-05-18T20:18:42,157   creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets
2026-05-18T20:18:42,159   copying build/lib/torchref/refinement/targets/occupancy_floor_diagnostic.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-05-18T20:18:42,162   copying build/lib/torchref/refinement/targets/realspace.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-05-18T20:18:42,165   copying build/lib/torchref/refinement/targets/difference.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-05-18T20:18:42,169   creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets/adp
2026-05-18T20:18:42,170   copying build/lib/torchref/refinement/targets/adp/entropy.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-05-18T20:18:42,172   copying build/lib/torchref/refinement/targets/adp/locality.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-05-18T20:18:42,175   copying build/lib/torchref/refinement/targets/adp/rigid_bond.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-05-18T20:18:42,177   copying build/lib/torchref/refinement/targets/adp/similarity.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-05-18T20:18:42,179   copying build/lib/torchref/refinement/targets/adp/scaler_log_scale.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-05-18T20:18:42,181   copying build/lib/torchref/refinement/targets/adp/scaler_u.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-05-18T20:18:42,183   copying build/lib/torchref/refinement/targets/adp/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-05-18T20:18:42,184   copying build/lib/torchref/refinement/targets/adp/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-05-18T20:18:42,187   creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets/geometry
2026-05-18T20:18:42,188   copying build/lib/torchref/refinement/targets/geometry/non_bonded_h.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-05-18T20:18:42,190   copying build/lib/torchref/refinement/targets/geometry/ramachandran.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-05-18T20:18:42,192   copying build/lib/torchref/refinement/targets/geometry/bonds.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-05-18T20:18:42,194   copying build/lib/torchref/refinement/targets/geometry/non_bonded.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-05-18T20:18:42,197   copying build/lib/torchref/refinement/targets/geometry/planarity.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-05-18T20:18:42,199   copying build/lib/torchref/refinement/targets/geometry/torsions.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-05-18T20:18:42,201   copying build/lib/torchref/refinement/targets/geometry/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-05-18T20:18:42,203   copying build/lib/torchref/refinement/targets/geometry/chiral.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-05-18T20:18:42,205   copying build/lib/torchref/refinement/targets/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-05-18T20:18:42,207   copying build/lib/torchref/refinement/targets/geometry/angles.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-05-18T20:18:42,209   copying build/lib/torchref/refinement/targets/combined.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-05-18T20:18:42,211   copying build/lib/torchref/refinement/targets/similarity.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-05-18T20:18:42,214   copying build/lib/torchref/refinement/targets/sampled_ml_phase_target.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-05-18T20:18:42,216   copying build/lib/torchref/refinement/targets/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-05-18T20:18:42,218   copying build/lib/torchref/refinement/targets/amber_target.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-05-18T20:18:42,222   creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets/xray
2026-05-18T20:18:42,223   copying build/lib/torchref/refinement/targets/xray/maximum_likelihood.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-05-18T20:18:42,225   copying build/lib/torchref/refinement/targets/xray/least_squares.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-05-18T20:18:42,227   copying build/lib/torchref/refinement/targets/xray/gaussian.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-05-18T20:18:42,229   copying build/lib/torchref/refinement/targets/xray/bhattacharyya.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-05-18T20:18:42,231   copying build/lib/torchref/refinement/targets/xray/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-05-18T20:18:42,233   copying build/lib/torchref/refinement/targets/xray/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-05-18T20:18:42,235   copying build/lib/torchref/refinement/targets/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-05-18T20:18:42,237   copying build/lib/torchref/refinement/targets/forcefield_target.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-05-18T20:18:42,240   creating build/bdist.linux-armv7l/wheel/torchref/refinement/weighting
2026-05-18T20:18:42,241   copying build/lib/torchref/refinement/weighting/policy_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-05-18T20:18:42,243   copying build/lib/torchref/refinement/weighting/random_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-05-18T20:18:42,246   copying build/lib/torchref/refinement/weighting/es_policy_training.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-05-18T20:18:42,248   copying build/lib/torchref/refinement/weighting/component_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-05-18T20:18:42,251   copying build/lib/torchref/refinement/weighting/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-05-18T20:18:42,252   copying build/lib/torchref/refinement/weighting/base_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-05-18T20:18:42,255   creating build/bdist.linux-armv7l/wheel/torchref/refinement/optimizers
2026-05-18T20:18:42,256   copying build/lib/torchref/refinement/optimizers/adam_noise.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-05-18T20:18:42,259   copying build/lib/torchref/refinement/optimizers/simulated_annealing.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-05-18T20:18:42,261   copying build/lib/torchref/refinement/optimizers/internal_coord_sa.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-05-18T20:18:42,263   copying build/lib/torchref/refinement/optimizers/langevin_sa.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-05-18T20:18:42,266   copying build/lib/torchref/refinement/optimizers/exploratory_lbfgs.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-05-18T20:18:42,268   copying build/lib/torchref/refinement/optimizers/momentum_sa.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-05-18T20:18:42,270   copying build/lib/torchref/refinement/optimizers/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-05-18T20:18:42,271   copying build/lib/torchref/refinement/base_refinement.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement
2026-05-18T20:18:42,274   copying build/lib/torchref/refinement/logger.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement
2026-05-18T20:18:42,277   copying build/lib/torchref/refinement/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement
2026-05-18T20:18:42,279   copying build/lib/torchref/refinement/lbfgs_refinement.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement
2026-05-18T20:18:42,282   creating build/bdist.linux-armv7l/wheel/torchref/base
2026-05-18T20:18:42,283   copying build/lib/torchref/base/get_scattering_factor_torch.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-05-18T20:18:42,286   creating build/bdist.linux-armv7l/wheel/torchref/base/targets
2026-05-18T20:18:42,287   copying build/lib/torchref/base/targets/_common.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-18T20:18:42,289   copying build/lib/torchref/base/targets/xray_bhattacharyya.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-18T20:18:42,291   copying build/lib/torchref/base/targets/adp.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-18T20:18:42,293   copying build/lib/torchref/base/targets/xray_ml.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-18T20:18:42,295   copying build/lib/torchref/base/targets/bond.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-18T20:18:42,297   copying build/lib/torchref/base/targets/ramachandran.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-18T20:18:42,299   copying build/lib/torchref/base/targets/torsion.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-18T20:18:42,300   copying build/lib/torchref/base/targets/angle.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-18T20:18:42,302   copying build/lib/torchref/base/targets/xray_ls.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-18T20:18:42,304   copying build/lib/torchref/base/targets/xray_gaussian.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-18T20:18:42,306   copying build/lib/torchref/base/targets/planarity.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-18T20:18:42,308   copying build/lib/torchref/base/targets/_dispatch.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-18T20:18:42,310   copying build/lib/torchref/base/targets/chiral.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-18T20:18:42,312   copying build/lib/torchref/base/targets/nonbonded.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-18T20:18:42,314   copying build/lib/torchref/base/targets/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-18T20:18:42,316   creating build/bdist.linux-armv7l/wheel/torchref/base/targets/triton
2026-05-18T20:18:42,317   copying build/lib/torchref/base/targets/triton/xray_bhattacharyya.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-18T20:18:42,320   copying build/lib/torchref/base/targets/triton/_dihedral.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-18T20:18:42,322   copying build/lib/torchref/base/targets/triton/xray_ml.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-18T20:18:42,324   copying build/lib/torchref/base/targets/triton/bond.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-18T20:18:42,326   copying build/lib/torchref/base/targets/triton/ramachandran.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-18T20:18:42,328   copying build/lib/torchref/base/targets/triton/place_hydrogens.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-18T20:18:42,330   copying build/lib/torchref/base/targets/triton/torsion.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-18T20:18:42,333   copying build/lib/torchref/base/targets/triton/angle.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-18T20:18:42,335   copying build/lib/torchref/base/targets/triton/xray_ls.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-18T20:18:42,337   copying build/lib/torchref/base/targets/triton/xray_gaussian.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-18T20:18:42,339   copying build/lib/torchref/base/targets/triton/planarity.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-18T20:18:42,341   copying build/lib/torchref/base/targets/triton/adp_simu.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-18T20:18:42,343   copying build/lib/torchref/base/targets/triton/chiral.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-18T20:18:42,345   copying build/lib/torchref/base/targets/triton/nonbonded.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-18T20:18:42,348   copying build/lib/torchref/base/targets/triton/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-18T20:18:42,350   creating build/bdist.linux-armv7l/wheel/torchref/base/coordinates
2026-05-18T20:18:42,351   copying build/lib/torchref/base/coordinates/transforms_torch.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates
2026-05-18T20:18:42,353   copying build/lib/torchref/base/coordinates/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates
2026-05-18T20:18:42,355   copying build/lib/torchref/base/coordinates/periodic_boundary.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates
2026-05-18T20:18:42,357   copying build/lib/torchref/base/coordinates/transforms_numpy.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates
2026-05-18T20:18:42,359   copying build/lib/torchref/base/math_torch.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-05-18T20:18:42,362   creating build/bdist.linux-armv7l/wheel/torchref/base/reciprocal
2026-05-18T20:18:42,363   copying build/lib/torchref/base/reciprocal/symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-05-18T20:18:42,365   copying build/lib/torchref/base/reciprocal/hkl.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-05-18T20:18:42,367   copying build/lib/torchref/base/reciprocal/interpolation.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-05-18T20:18:42,369   copying build/lib/torchref/base/reciprocal/grid_operations.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-05-18T20:18:42,372   copying build/lib/torchref/base/reciprocal/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-05-18T20:18:42,374   copying build/lib/torchref/base/reciprocal/basis.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-05-18T20:18:42,376   copying build/lib/torchref/base/CCTBX_related.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-05-18T20:18:42,379   creating build/bdist.linux-armv7l/wheel/torchref/base/scattering
2026-05-18T20:18:42,380   copying build/lib/torchref/base/scattering/scattering_table.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering
2026-05-18T20:18:42,382   copying build/lib/torchref/base/scattering/anomalous_table.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering
2026-05-18T20:18:42,385   copying build/lib/torchref/base/scattering/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering
2026-05-18T20:18:42,386   copying build/lib/torchref/base/scattering/itc92.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering
2026-05-18T20:18:42,389   copying build/lib/torchref/base/french_wilson.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-05-18T20:18:42,392   creating build/bdist.linux-armv7l/wheel/torchref/base/kernels
2026-05-18T20:18:42,393   copying build/lib/torchref/base/kernels/separable_triton_kernel.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-05-18T20:18:42,396   copying build/lib/torchref/base/kernels/jit_kernel_vectorized_add_to_map.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-05-18T20:18:42,398   copying build/lib/torchref/base/kernels/triton_kernel.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-05-18T20:18:42,401   copying build/lib/torchref/base/kernels/cpu_scatter.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-05-18T20:18:42,403   copying build/lib/torchref/base/kernels/optimized_ops.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-05-18T20:18:42,405   copying build/lib/torchref/base/kernels/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-05-18T20:18:42,408   creating build/bdist.linux-armv7l/wheel/torchref/base/metrics
2026-05-18T20:18:42,409   copying build/lib/torchref/base/metrics/rfactor.py -> build/bdist.linux-armv7l/wheel/./torchref/base/metrics
2026-05-18T20:18:42,411   copying build/lib/torchref/base/metrics/loss.py -> build/bdist.linux-armv7l/wheel/./torchref/base/metrics
2026-05-18T20:18:42,413   copying build/lib/torchref/base/metrics/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/metrics
2026-05-18T20:18:42,416   creating build/bdist.linux-armv7l/wheel/torchref/base/fourier
2026-05-18T20:18:42,417   copying build/lib/torchref/base/fourier/grid.py -> build/bdist.linux-armv7l/wheel/./torchref/base/fourier
2026-05-18T20:18:42,419   copying build/lib/torchref/base/fourier/fft.py -> build/bdist.linux-armv7l/wheel/./torchref/base/fourier
2026-05-18T20:18:42,421   copying build/lib/torchref/base/fourier/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/fourier
2026-05-18T20:18:42,423   creating build/bdist.linux-armv7l/wheel/torchref/base/electron_density
2026-05-18T20:18:42,424   copying build/lib/torchref/base/electron_density/voxel_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density
2026-05-18T20:18:42,427   copying build/lib/torchref/base/electron_density/main.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density
2026-05-18T20:18:42,429   copying build/lib/torchref/base/electron_density/map_building.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density
2026-05-18T20:18:42,432   copying build/lib/torchref/base/electron_density/solvent_mask.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density
2026-05-18T20:18:42,434   copying build/lib/torchref/base/electron_density/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density
2026-05-18T20:18:42,436   copying build/lib/torchref/base/math_numpy.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-05-18T20:18:42,439   creating build/bdist.linux-armv7l/wheel/torchref/base/alignment
2026-05-18T20:18:42,440   copying build/lib/torchref/base/alignment/scoring.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment
2026-05-18T20:18:42,442   copying build/lib/torchref/base/alignment/rotation.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment
2026-05-18T20:18:42,444   copying build/lib/torchref/base/alignment/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment
2026-05-18T20:18:42,446   copying build/lib/torchref/base/alignment/superposition.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment
2026-05-18T20:18:42,449   copying build/lib/torchref/base/alignment/normalization.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment
2026-05-18T20:18:42,452   creating build/bdist.linux-armv7l/wheel/torchref/base/direct_summation
2026-05-18T20:18:42,453   copying build/lib/torchref/base/direct_summation/isotropic.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation
2026-05-18T20:18:42,455   copying build/lib/torchref/base/direct_summation/corrections.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation
2026-05-18T20:18:42,457   copying build/lib/torchref/base/direct_summation/anisotropic.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation
2026-05-18T20:18:42,459   copying build/lib/torchref/base/direct_summation/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation
2026-05-18T20:18:42,461   copying build/lib/torchref/base/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-05-18T20:18:42,464   creating build/bdist.linux-armv7l/wheel/torchref/base/chain_closure
2026-05-18T20:18:42,465   copying build/lib/torchref/base/chain_closure/backbone_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/base/chain_closure
2026-05-18T20:18:42,467   copying build/lib/torchref/base/chain_closure/closure.py -> build/bdist.linux-armv7l/wheel/./torchref/base/chain_closure
2026-05-18T20:18:42,470   copying build/lib/torchref/base/chain_closure/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/chain_closure
2026-05-18T20:18:42,473   creating build/bdist.linux-armv7l/wheel/torchref/scaling
2026-05-18T20:18:42,474   copying build/lib/torchref/scaling/scaler_base.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling
2026-05-18T20:18:42,477   copying build/lib/torchref/scaling/scaler.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling
2026-05-18T20:18:42,479   copying build/lib/torchref/scaling/solvent.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling
2026-05-18T20:18:42,482   copying build/lib/torchref/scaling/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling
2026-05-18T20:18:42,484   copying build/lib/torchref/scaling/collection_scaler.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling
2026-05-18T20:18:42,487   creating build/bdist.linux-armv7l/wheel/torchref/alignment
2026-05-18T20:18:42,488   copying build/lib/torchref/alignment/jax_subpixel_peaks.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-05-18T20:18:42,490   copying build/lib/torchref/alignment/ball_transform.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-05-18T20:18:42,494   copying build/lib/torchref/alignment/sampling.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-05-18T20:18:42,496   copying build/lib/torchref/alignment/translation.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-05-18T20:18:42,499   copying build/lib/torchref/alignment/distributions.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-05-18T20:18:42,501   copying build/lib/torchref/alignment/transform.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-05-18T20:18:42,504   copying build/lib/torchref/alignment/pipeline.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-05-18T20:18:42,507   copying build/lib/torchref/alignment/clashscore.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-05-18T20:18:42,510   copying build/lib/torchref/alignment/rigid_body.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-05-18T20:18:42,512   copying build/lib/torchref/alignment/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-05-18T20:18:42,515   creating build/bdist.linux-armv7l/wheel/torchref/maps
2026-05-18T20:18:42,516   copying build/lib/torchref/maps/difference_map.py -> build/bdist.linux-armv7l/wheel/./torchref/maps
2026-05-18T20:18:42,518   copying build/lib/torchref/maps/map.py -> build/bdist.linux-armv7l/wheel/./torchref/maps
2026-05-18T20:18:42,521   copying build/lib/torchref/maps/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/maps
2026-05-18T20:18:42,523   creating build/bdist.linux-armv7l/wheel/torchref/cli
2026-05-18T20:18:42,524   copying build/lib/torchref/cli/_common.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-05-18T20:18:42,527   copying build/lib/torchref/cli/strip_altlocs.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-05-18T20:18:42,529   copying build/lib/torchref/cli/mtz2map.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-05-18T20:18:42,531   copying build/lib/torchref/cli/add_metadata.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-05-18T20:18:42,534   copying build/lib/torchref/cli/validate_ded.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-05-18T20:18:42,536   copying build/lib/torchref/cli/collection_difference_refine.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-05-18T20:18:42,539   copying build/lib/torchref/cli/phased_difference_map.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-05-18T20:18:42,541   copying build/lib/torchref/cli/refine.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-05-18T20:18:42,543   copying build/lib/torchref/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-05-18T20:18:42,545   copying build/lib/torchref/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref
2026-05-18T20:18:42,547   copying build/lib/torchref/_bootstrap.py -> build/bdist.linux-armv7l/wheel/./torchref
2026-05-18T20:18:42,550   creating build/bdist.linux-armv7l/wheel/torchref/utils
2026-05-18T20:18:42,551   copying build/lib/torchref/utils/autograd_ops.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-18T20:18:42,553   copying build/lib/torchref/utils/timing.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-18T20:18:42,555   copying build/lib/torchref/utils/gradnorm.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-18T20:18:42,557   copying build/lib/torchref/utils/device_mixin.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-18T20:18:42,559   copying build/lib/torchref/utils/utils.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-18T20:18:42,562   copying build/lib/torchref/utils/caching.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-18T20:18:42,564   copying build/lib/torchref/utils/loss_validation.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-18T20:18:42,567   copying build/lib/torchref/utils/pse.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-18T20:18:42,569   copying build/lib/torchref/utils/hyperparameters.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-18T20:18:42,571   copying build/lib/torchref/utils/autograd_introspection.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-18T20:18:42,573   copying build/lib/torchref/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-18T20:18:42,575   copying build/lib/torchref/utils/serialization.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-18T20:18:42,577   copying build/lib/torchref/utils/stats.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-18T20:18:42,579   copying build/lib/torchref/utils/debug_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-18T20:18:42,583   creating build/bdist.linux-armv7l/wheel/torchref/restraints
2026-05-18T20:18:42,584   copying build/lib/torchref/restraints/library.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-05-18T20:18:42,586   copying build/lib/torchref/restraints/restraints_helper.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-05-18T20:18:42,589   copying build/lib/torchref/restraints/ramachandran.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-05-18T20:18:42,591   copying build/lib/torchref/restraints/neighbor_search.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-05-18T20:18:42,594   copying build/lib/torchref/restraints/restraints.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-05-18T20:18:42,599   copying build/lib/torchref/restraints/hydrogen_topology.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-05-18T20:18:42,601   copying build/lib/torchref/restraints/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-05-18T20:18:42,603   copying build/lib/torchref/restraints/builders.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-05-18T20:18:42,606   copying build/lib/torchref/restraints/builders_fast.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-05-18T20:18:42,611   copying build/lib/torchref/restraints/builders_numba.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-05-18T20:18:42,613   running install_egg_info
2026-05-18T20:18:42,619   Copying torchref.egg-info to build/bdist.linux-armv7l/wheel/./torchref-0.5.2-py3.11.egg-info
2026-05-18T20:18:42,631   running install_scripts
2026-05-18T20:18:42,643   creating build/bdist.linux-armv7l/wheel/torchref-0.5.2.dist-info/WHEEL
2026-05-18T20:18:42,646   creating '/tmp/pip-wheel-_uot49xs/.tmp-m0jwow_r/torchref-0.5.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2026-05-18T20:18:42,649   adding 'torchref/__init__.py'
2026-05-18T20:18:42,650   adding 'torchref/_bootstrap.py'
2026-05-18T20:18:42,652   adding 'torchref/config.py'
2026-05-18T20:18:42,654   adding 'torchref/alignment/__init__.py'
2026-05-18T20:18:42,662   adding 'torchref/alignment/ball_transform.py'
2026-05-18T20:18:42,665   adding 'torchref/alignment/clashscore.py'
2026-05-18T20:18:42,667   adding 'torchref/alignment/distributions.py'
2026-05-18T20:18:42,668   adding 'torchref/alignment/jax_subpixel_peaks.py'
2026-05-18T20:18:42,671   adding 'torchref/alignment/pipeline.py'
2026-05-18T20:18:42,673   adding 'torchref/alignment/rigid_body.py'
2026-05-18T20:18:42,675   adding 'torchref/alignment/sampling.py'
2026-05-18T20:18:42,678   adding 'torchref/alignment/transform.py'
2026-05-18T20:18:42,680   adding 'torchref/alignment/translation.py'
2026-05-18T20:18:42,682   adding 'torchref/base/CCTBX_related.py'
2026-05-18T20:18:42,684   adding 'torchref/base/__init__.py'
2026-05-18T20:18:42,688   adding 'torchref/base/french_wilson.py'
2026-05-18T20:18:42,690   adding 'torchref/base/get_scattering_factor_torch.py'
2026-05-18T20:18:42,692   adding 'torchref/base/math_numpy.py'
2026-05-18T20:18:42,695   adding 'torchref/base/math_torch.py'
2026-05-18T20:18:42,697   adding 'torchref/base/alignment/__init__.py'
2026-05-18T20:18:42,699   adding 'torchref/base/alignment/normalization.py'
2026-05-18T20:18:42,701   adding 'torchref/base/alignment/rotation.py'
2026-05-18T20:18:42,702   adding 'torchref/base/alignment/scoring.py'
2026-05-18T20:18:42,704   adding 'torchref/base/alignment/superposition.py'
2026-05-18T20:18:42,706   adding 'torchref/base/chain_closure/__init__.py'
2026-05-18T20:18:42,708   adding 'torchref/base/chain_closure/backbone_utils.py'
2026-05-18T20:18:42,711   adding 'torchref/base/chain_closure/closure.py'
2026-05-18T20:18:42,713   adding 'torchref/base/coordinates/__init__.py'
2026-05-18T20:18:42,714   adding 'torchref/base/coordinates/periodic_boundary.py'
2026-05-18T20:18:42,715   adding 'torchref/base/coordinates/transforms_numpy.py'
2026-05-18T20:18:42,717   adding 'torchref/base/coordinates/transforms_torch.py'
2026-05-18T20:18:42,718   adding 'torchref/base/direct_summation/__init__.py'
2026-05-18T20:18:42,720   adding 'torchref/base/direct_summation/anisotropic.py'
2026-05-18T20:18:42,722   adding 'torchref/base/direct_summation/corrections.py'
2026-05-18T20:18:42,723   adding 'torchref/base/direct_summation/isotropic.py'
2026-05-18T20:18:42,725   adding 'torchref/base/electron_density/__init__.py'
2026-05-18T20:18:42,729   adding 'torchref/base/electron_density/main.py'
2026-05-18T20:18:42,731   adding 'torchref/base/electron_density/map_building.py'
2026-05-18T20:18:42,733   adding 'torchref/base/electron_density/solvent_mask.py'
2026-05-18T20:18:42,734   adding 'torchref/base/electron_density/voxel_utils.py'
2026-05-18T20:18:42,736   adding 'torchref/base/fourier/__init__.py'
2026-05-18T20:18:42,737   adding 'torchref/base/fourier/fft.py'
2026-05-18T20:18:42,739   adding 'torchref/base/fourier/grid.py'
2026-05-18T20:18:42,740   adding 'torchref/base/kernels/__init__.py'
2026-05-18T20:18:42,742   adding 'torchref/base/kernels/cpu_scatter.py'
2026-05-18T20:18:42,744   adding 'torchref/base/kernels/jit_kernel_vectorized_add_to_map.py'
2026-05-18T20:18:42,746   adding 'torchref/base/kernels/optimized_ops.py'
2026-05-18T20:18:42,751   adding 'torchref/base/kernels/separable_triton_kernel.py'
2026-05-18T20:18:42,754   adding 'torchref/base/kernels/triton_kernel.py'
2026-05-18T20:18:42,756   adding 'torchref/base/metrics/__init__.py'
2026-05-18T20:18:42,758   adding 'torchref/base/metrics/loss.py'
2026-05-18T20:18:42,759   adding 'torchref/base/metrics/rfactor.py'
2026-05-18T20:18:42,761   adding 'torchref/base/reciprocal/__init__.py'
2026-05-18T20:18:42,762   adding 'torchref/base/reciprocal/basis.py'
2026-05-18T20:18:42,764   adding 'torchref/base/reciprocal/grid_operations.py'
2026-05-18T20:18:42,765   adding 'torchref/base/reciprocal/hkl.py'
2026-05-18T20:18:42,768   adding 'torchref/base/reciprocal/interpolation.py'
2026-05-18T20:18:42,770   adding 'torchref/base/reciprocal/symmetry.py'
2026-05-18T20:18:42,771   adding 'torchref/base/scattering/__init__.py'
2026-05-18T20:18:42,773   adding 'torchref/base/scattering/anomalous_table.py'
2026-05-18T20:18:42,774   adding 'torchref/base/scattering/itc92.py'
2026-05-18T20:18:42,776   adding 'torchref/base/scattering/scattering_table.py'
2026-05-18T20:18:42,778   adding 'torchref/base/targets/__init__.py'
2026-05-18T20:18:42,779   adding 'torchref/base/targets/_common.py'
2026-05-18T20:18:42,781   adding 'torchref/base/targets/_dispatch.py'
2026-05-18T20:18:42,782   adding 'torchref/base/targets/adp.py'
2026-05-18T20:18:42,783   adding 'torchref/base/targets/angle.py'
2026-05-18T20:18:42,785   adding 'torchref/base/targets/bond.py'
2026-05-18T20:18:42,786   adding 'torchref/base/targets/chiral.py'
2026-05-18T20:18:42,787   adding 'torchref/base/targets/nonbonded.py'
2026-05-18T20:18:42,789   adding 'torchref/base/targets/planarity.py'
2026-05-18T20:18:42,790   adding 'torchref/base/targets/ramachandran.py'
2026-05-18T20:18:42,791   adding 'torchref/base/targets/torsion.py'
2026-05-18T20:18:42,793   adding 'torchref/base/targets/xray_bhattacharyya.py'
2026-05-18T20:18:42,794   adding 'torchref/base/targets/xray_gaussian.py'
2026-05-18T20:18:42,795   adding 'torchref/base/targets/xray_ls.py'
2026-05-18T20:18:42,796   adding 'torchref/base/targets/xray_ml.py'
2026-05-18T20:18:42,798   adding 'torchref/base/targets/triton/__init__.py'
2026-05-18T20:18:42,800   adding 'torchref/base/targets/triton/_dihedral.py'
2026-05-18T20:18:42,801   adding 'torchref/base/targets/triton/adp_simu.py'
2026-05-18T20:18:42,803   adding 'torchref/base/targets/triton/angle.py'
2026-05-18T20:18:42,804   adding 'torchref/base/targets/triton/bond.py'
2026-05-18T20:18:42,806   adding 'torchref/base/targets/triton/chiral.py'
2026-05-18T20:18:42,808   adding 'torchref/base/targets/triton/nonbonded.py'
2026-05-18T20:18:42,810   adding 'torchref/base/targets/triton/place_hydrogens.py'
2026-05-18T20:18:42,812   adding 'torchref/base/targets/triton/planarity.py'
2026-05-18T20:18:42,814   adding 'torchref/base/targets/triton/ramachandran.py'
2026-05-18T20:18:42,816   adding 'torchref/base/targets/triton/torsion.py'
2026-05-18T20:18:42,818   adding 'torchref/base/targets/triton/xray_bhattacharyya.py'
2026-05-18T20:18:42,819   adding 'torchref/base/targets/triton/xray_gaussian.py'
2026-05-18T20:18:42,821   adding 'torchref/base/targets/triton/xray_ls.py'
2026-05-18T20:18:42,823   adding 'torchref/base/targets/triton/xray_ml.py'
2026-05-18T20:18:42,825   adding 'torchref/cli/__init__.py'
2026-05-18T20:18:42,827   adding 'torchref/cli/_common.py'
2026-05-18T20:18:42,829   adding 'torchref/cli/add_metadata.py'
2026-05-18T20:18:42,834   adding 'torchref/cli/collection_difference_refine.py'
2026-05-18T20:18:42,836   adding 'torchref/cli/mtz2map.py'
2026-05-18T20:18:42,838   adding 'torchref/cli/phased_difference_map.py'
2026-05-18T20:18:42,840   adding 'torchref/cli/refine.py'
2026-05-18T20:18:42,841   adding 'torchref/cli/strip_altlocs.py'
2026-05-18T20:18:42,844   adding 'torchref/cli/validate_ded.py'
2026-05-18T20:18:42,847   adding 'torchref/data/atomic_vdw_radii.csv'
2026-05-18T20:18:42,849   adding 'torchref/data/itc92_scattering_factors.pt'
2026-05-18T20:18:43,082   adding 'torchref/data/rama_nll_surfaces.pt'
2026-05-18T20:18:43,105   adding 'torchref/data/monomer_library/a/A.cif'
2026-05-18T20:18:43,106   adding 'torchref/data/monomer_library/a/ALA.cif'
2026-05-18T20:18:43,108   adding 'torchref/data/monomer_library/a/ARG.cif'
2026-05-18T20:18:43,109   adding 'torchref/data/monomer_library/a/ASN.cif'
2026-05-18T20:18:43,111   adding 'torchref/data/monomer_library/a/ASP.cif'
2026-05-18T20:18:43,114   adding 'torchref/data/monomer_library/c/C.cif'
2026-05-18T20:18:43,115   adding 'torchref/data/monomer_library/c/CYS.cif'
2026-05-18T20:18:43,118   adding 'torchref/data/monomer_library/d/DA.cif'
2026-05-18T20:18:43,120   adding 'torchref/data/monomer_library/d/DC.cif'
2026-05-18T20:18:43,122   adding 'torchref/data/monomer_library/d/DG.cif'
2026-05-18T20:18:43,125   adding 'torchref/data/monomer_library/d/DT.cif'
2026-05-18T20:18:43,128   adding 'torchref/data/monomer_library/g/G.cif'
2026-05-18T20:18:43,129   adding 'torchref/data/monomer_library/g/GLN.cif'
2026-05-18T20:18:43,131   adding 'torchref/data/monomer_library/g/GLU.cif'
2026-05-18T20:18:43,132   adding 'torchref/data/monomer_library/g/GLY.cif'
2026-05-18T20:18:43,134   adding 'torchref/data/monomer_library/h/HIS.cif'
2026-05-18T20:18:43,136   adding 'torchref/data/monomer_library/h/HOH.cif'
2026-05-18T20:18:43,137   adding 'torchref/data/monomer_library/h/HYP.cif'
2026-05-18T20:18:43,139   adding 'torchref/data/monomer_library/i/ILE.cif'
2026-05-18T20:18:43,142   adding 'torchref/data/monomer_library/l/LEU.cif'
2026-05-18T20:18:43,143   adding 'torchref/data/monomer_library/l/LYS.cif'
2026-05-18T20:18:43,683   adding 'torchref/data/monomer_library/list/mon_lib_list.cif'
2026-05-18T20:18:43,710   adding 'torchref/data/monomer_library/m/MET.cif'
2026-05-18T20:18:43,712   adding 'torchref/data/monomer_library/m/MSE.cif'
2026-05-18T20:18:43,714   adding 'torchref/data/monomer_library/p/PHE.cif'
2026-05-18T20:18:43,716   adding 'torchref/data/monomer_library/p/PRO.cif'
2026-05-18T20:18:43,718   adding 'torchref/data/monomer_library/p/PTR.cif'
2026-05-18T20:18:43,720   adding 'torchref/data/monomer_library/s/SEP.cif'
2026-05-18T20:18:43,721   adding 'torchref/data/monomer_library/s/SER.cif'
2026-05-18T20:18:43,723   adding 'torchref/data/monomer_library/t/THR.cif'
2026-05-18T20:18:43,725   adding 'torchref/data/monomer_library/t/TPO.cif'
2026-05-18T20:18:43,727   adding 'torchref/data/monomer_library/t/TRP.cif'
2026-05-18T20:18:43,728   adding 'torchref/data/monomer_library/t/TYR.cif'
2026-05-18T20:18:43,731   adding 'torchref/data/monomer_library/u/U.cif'
2026-05-18T20:18:43,733   adding 'torchref/data/monomer_library/v/VAL.cif'
2026-05-18T20:18:43,735   adding 'torchref/io/__init__.py'
2026-05-18T20:18:43,738   adding 'torchref/io/cif.py'
2026-05-18T20:18:43,745   adding 'torchref/io/cif_readers.py'
2026-05-18T20:18:43,747   adding 'torchref/io/data_router.py'
2026-05-18T20:18:43,752   adding 'torchref/io/ihm.py'
2026-05-18T20:18:43,754   adding 'torchref/io/ihm_mapping.py'
2026-05-18T20:18:43,757   adding 'torchref/io/metadata.py'
2026-05-18T20:18:43,759   adding 'torchref/io/mtz.py'
2026-05-18T20:18:43,762   adding 'torchref/io/pdb.py'
2026-05-18T20:18:43,765   adding 'torchref/io/datasets/__init__.py'
2026-05-18T20:18:43,766   adding 'torchref/io/datasets/base.py'
2026-05-18T20:18:43,768   adding 'torchref/io/datasets/collection.py'
2026-05-18T20:18:43,771   adding 'torchref/io/datasets/fcalc_data.py'
2026-05-18T20:18:43,783   adding 'torchref/io/datasets/reflection_data.py'
2026-05-18T20:18:43,786   adding 'torchref/kinetic/__init__.py'
2026-05-18T20:18:43,790   adding 'torchref/kinetic/kinetics.py'
2026-05-18T20:18:43,794   adding 'torchref/kinetic/occupancies.py'
2026-05-18T20:18:43,796   adding 'torchref/kinetic/refinement.py'
2026-05-18T20:18:43,799   adding 'torchref/kinetic/targets.py'
2026-05-18T20:18:43,801   adding 'torchref/maps/__init__.py'
2026-05-18T20:18:43,802   adding 'torchref/maps/difference_map.py'
2026-05-18T20:18:43,804   adding 'torchref/maps/map.py'
2026-05-18T20:18:43,806   adding 'torchref/model/__init__.py'
2026-05-18T20:18:43,814   adding 'torchref/model/closed_segmented_internal_coordinates.py'
2026-05-18T20:18:43,823   adding 'torchref/model/internal_coordinates.py'
2026-05-18T20:18:43,826   adding 'torchref/model/mixed_model.py'
2026-05-18T20:18:43,840   adding 'torchref/model/model.py'
2026-05-18T20:18:43,844   adding 'torchref/model/model_collection.py'
2026-05-18T20:18:43,849   adding 'torchref/model/model_ft.py'
2026-05-18T20:18:43,857   adding 'torchref/model/parameter_wrappers.py'
2026-05-18T20:18:43,865   adding 'torchref/model/segmented_internal_coordinates.py'
2026-05-18T20:18:43,868   adding 'torchref/model/sf_ds.py'
2026-05-18T20:18:43,871   adding 'torchref/model/sf_fft.py'
2026-05-18T20:18:43,873   adding 'torchref/refinement/__init__.py'
2026-05-18T20:18:43,878   adding 'torchref/refinement/base_refinement.py'
2026-05-18T20:18:43,881   adding 'torchref/refinement/lbfgs_refinement.py'
2026-05-18T20:18:43,883   adding 'torchref/refinement/logger.py'
2026-05-18T20:18:43,887   adding 'torchref/refinement/loss_state.py'
2026-05-18T20:18:43,889   adding 'torchref/refinement/optimizers/__init__.py'
2026-05-18T20:18:43,891   adding 'torchref/refinement/optimizers/adam_noise.py'
2026-05-18T20:18:43,894   adding 'torchref/refinement/optimizers/exploratory_lbfgs.py'
2026-05-18T20:18:43,897   adding 'torchref/refinement/optimizers/internal_coord_sa.py'
2026-05-18T20:18:43,900   adding 'torchref/refinement/optimizers/langevin_sa.py'
2026-05-18T20:18:43,901   adding 'torchref/refinement/optimizers/momentum_sa.py'
2026-05-18T20:18:43,903   adding 'torchref/refinement/optimizers/simulated_annealing.py'
2026-05-18T20:18:43,905   adding 'torchref/refinement/targets/__init__.py'
2026-05-18T20:18:43,911   adding 'torchref/refinement/targets/amber_target.py'
2026-05-18T20:18:43,913   adding 'torchref/refinement/targets/base.py'
2026-05-18T20:18:43,916   adding 'torchref/refinement/targets/combined.py'
2026-05-18T20:18:43,921   adding 'torchref/refinement/targets/difference.py'
2026-05-18T20:18:43,923   adding 'torchref/refinement/targets/forcefield_target.py'
2026-05-18T20:18:43,926   adding 'torchref/refinement/targets/occupancy_floor_diagnostic.py'
2026-05-18T20:18:43,929   adding 'torchref/refinement/targets/realspace.py'
2026-05-18T20:18:43,932   adding 'torchref/refinement/targets/sampled_ml_phase_target.py'
2026-05-18T20:18:43,934   adding 'torchref/refinement/targets/similarity.py'
2026-05-18T20:18:43,936   adding 'torchref/refinement/targets/adp/__init__.py'
2026-05-18T20:18:43,938   adding 'torchref/refinement/targets/adp/base.py'
2026-05-18T20:18:43,939   adding 'torchref/refinement/targets/adp/entropy.py'
2026-05-18T20:18:43,941   adding 'torchref/refinement/targets/adp/locality.py'
2026-05-18T20:18:43,943   adding 'torchref/refinement/targets/adp/rigid_bond.py'
2026-05-18T20:18:43,944   adding 'torchref/refinement/targets/adp/scaler_log_scale.py'
2026-05-18T20:18:43,946   adding 'torchref/refinement/targets/adp/scaler_u.py'
2026-05-18T20:18:43,947   adding 'torchref/refinement/targets/adp/similarity.py'
2026-05-18T20:18:43,949   adding 'torchref/refinement/targets/geometry/__init__.py'
2026-05-18T20:18:43,950   adding 'torchref/refinement/targets/geometry/angles.py'
2026-05-18T20:18:43,952   adding 'torchref/refinement/targets/geometry/base.py'
2026-05-18T20:18:43,953   adding 'torchref/refinement/targets/geometry/bonds.py'
2026-05-18T20:18:43,955   adding 'torchref/refinement/targets/geometry/chiral.py'
2026-05-18T20:18:43,957   adding 'torchref/refinement/targets/geometry/non_bonded.py'
2026-05-18T20:18:43,959   adding 'torchref/refinement/targets/geometry/non_bonded_h.py'
2026-05-18T20:18:43,961   adding 'torchref/refinement/targets/geometry/planarity.py'
2026-05-18T20:18:43,962   adding 'torchref/refinement/targets/geometry/ramachandran.py'
2026-05-18T20:18:43,964   adding 'torchref/refinement/targets/geometry/torsions.py'
2026-05-18T20:18:43,966   adding 'torchref/refinement/targets/xray/__init__.py'
2026-05-18T20:18:43,967   adding 'torchref/refinement/targets/xray/base.py'
2026-05-18T20:18:43,970   adding 'torchref/refinement/targets/xray/bhattacharyya.py'
2026-05-18T20:18:43,971   adding 'torchref/refinement/targets/xray/gaussian.py'
2026-05-18T20:18:43,972   adding 'torchref/refinement/targets/xray/least_squares.py'
2026-05-18T20:18:43,973   adding 'torchref/refinement/targets/xray/maximum_likelihood.py'
2026-05-18T20:18:43,975   adding 'torchref/refinement/weighting/__init__.py'
2026-05-18T20:18:43,976   adding 'torchref/refinement/weighting/base_weighting.py'
2026-05-18T20:18:43,978   adding 'torchref/refinement/weighting/component_weighting.py'
2026-05-18T20:18:43,981   adding 'torchref/refinement/weighting/es_policy_training.py'
2026-05-18T20:18:43,984   adding 'torchref/refinement/weighting/policy_weighting.py'
2026-05-18T20:18:43,987   adding 'torchref/refinement/weighting/random_weighting.py'
2026-05-18T20:18:43,989   adding 'torchref/restraints/__init__.py'
2026-05-18T20:18:43,993   adding 'torchref/restraints/builders.py'
2026-05-18T20:18:44,000   adding 'torchref/restraints/builders_fast.py'
2026-05-18T20:18:44,004   adding 'torchref/restraints/builders_numba.py'
2026-05-18T20:18:44,009   adding 'torchref/restraints/hydrogen_topology.py'
2026-05-18T20:18:44,010   adding 'torchref/restraints/library.py'
2026-05-18T20:18:44,015   adding 'torchref/restraints/neighbor_search.py'
2026-05-18T20:18:44,017   adding 'torchref/restraints/ramachandran.py'
2026-05-18T20:18:44,027   adding 'torchref/restraints/restraints.py'
2026-05-18T20:18:44,030   adding 'torchref/restraints/restraints_helper.py'
2026-05-18T20:18:44,033   adding 'torchref/scaling/__init__.py'
2026-05-18T20:18:44,035   adding 'torchref/scaling/collection_scaler.py'
2026-05-18T20:18:44,037   adding 'torchref/scaling/scaler.py'
2026-05-18T20:18:44,042   adding 'torchref/scaling/scaler_base.py'
2026-05-18T20:18:44,045   adding 'torchref/scaling/solvent.py'
2026-05-18T20:18:44,047   adding 'torchref/scripts/__init__.py'
2026-05-18T20:18:44,049   adding 'torchref/scripts/generate_scattering_table.py'
2026-05-18T20:18:44,051   adding 'torchref/symmetry/__init__.py'
2026-05-18T20:18:44,053   adding 'torchref/symmetry/cell.py'
2026-05-18T20:18:44,054   adding 'torchref/symmetry/grid_utils.py'
2026-05-18T20:18:44,056   adding 'torchref/symmetry/map_symmetry.py'
2026-05-18T20:18:44,058   adding 'torchref/symmetry/map_symmetry_interpolation.py'
2026-05-18T20:18:44,065   adding 'torchref/symmetry/reciprocal_symmetry.py'
2026-05-18T20:18:44,068   adding 'torchref/symmetry/spacegroup.py'
2026-05-18T20:18:44,070   adding 'torchref/symmetry/symmetry.py'
2026-05-18T20:18:44,072   adding 'torchref/utils/__init__.py'
2026-05-18T20:18:44,073   adding 'torchref/utils/autograd_introspection.py'
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2026-05-18T20:18:44,076   adding 'torchref/utils/caching.py'
2026-05-18T20:18:44,078   adding 'torchref/utils/debug_utils.py'
2026-05-18T20:18:44,080   adding 'torchref/utils/device_mixin.py'
2026-05-18T20:18:44,082   adding 'torchref/utils/gradnorm.py'
2026-05-18T20:18:44,084   adding 'torchref/utils/hyperparameters.py'
2026-05-18T20:18:44,086   adding 'torchref/utils/loss_validation.py'
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2026-05-18T20:18:44,089   adding 'torchref/utils/serialization.py'
2026-05-18T20:18:44,090   adding 'torchref/utils/stats.py'
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2026-05-18T20:18:44,097   adding 'torchref/utils/utils.py'
2026-05-18T20:18:44,100   adding 'torchref-0.5.2.dist-info/licenses/LICENSE'
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2026-05-18T20:18:44,398   Created wheel for torchref: filename=torchref-0.5.2-py3-none-any.whl size=3120900 sha256=243d4c01af453def03a1e0667e20d3a8dc738f6af546aa60605b8a99369e41e3
2026-05-18T20:18:44,399   Stored in directory: /tmp/pip-ephem-wheel-cache-7199e0nb/wheels/b3/74/d4/4996ff3d52fccd1ecc7463000ac6f98ed39da7169e36da07f9
2026-05-18T20:18:44,420 Successfully built torchref
2026-05-18T20:18:44,496 Removed build tracker: '/tmp/pip-build-tracker-hdpit6xx'