2026-03-06T10:15:17,487 Created temporary directory: /tmp/pip-ephem-wheel-cache-6z2746im
2026-03-06T10:15:17,489 Created temporary directory: /tmp/pip-build-tracker-pgx5i65x
2026-03-06T10:15:17,490 Initialized build tracking at /tmp/pip-build-tracker-pgx5i65x
2026-03-06T10:15:17,490 Created build tracker: /tmp/pip-build-tracker-pgx5i65x
2026-03-06T10:15:17,491 Entered build tracker: /tmp/pip-build-tracker-pgx5i65x
2026-03-06T10:15:17,492 Created temporary directory: /tmp/pip-wheel-bz5ad079
2026-03-06T10:15:17,494 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
2026-03-06T10:15:17,497 Created temporary directory: /tmp/pip-ephem-wheel-cache-kz5jfo8f
2026-03-06T10:15:17,518 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-03-06T10:15:17,522 2 location(s) to search for versions of torchref:
2026-03-06T10:15:17,522 * https://pypi.org/simple/torchref/
2026-03-06T10:15:17,522 * https://www.piwheels.org/simple/torchref/
2026-03-06T10:15:17,523 Fetching project page and analyzing links: https://pypi.org/simple/torchref/
2026-03-06T10:15:17,524 Getting page https://pypi.org/simple/torchref/
2026-03-06T10:15:17,525 Found index url https://pypi.org/simple
2026-03-06T10:15:17,736 Fetched page https://pypi.org/simple/torchref/ as application/vnd.pypi.simple.v1+json
2026-03-06T10:15:17,739   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)
2026-03-06T10:15:17,740   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
2026-03-06T10:15:17,741   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)
2026-03-06T10:15:17,742   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
2026-03-06T10:15:17,742   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)
2026-03-06T10:15:17,743   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
2026-03-06T10:15:17,744   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)
2026-03-06T10:15:17,745   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
2026-03-06T10:15:17,745   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)
2026-03-06T10:15:17,746   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
2026-03-06T10:15:17,747 Fetching project page and analyzing links: https://www.piwheels.org/simple/torchref/
2026-03-06T10:15:17,748 Getting page https://www.piwheels.org/simple/torchref/
2026-03-06T10:15:17,749 Found index url https://www.piwheels.org/simple
2026-03-06T10:15:17,902 Fetched page https://www.piwheels.org/simple/torchref/ as text/html
2026-03-06T10:15:17,905   Skipping link: No binaries permitted for torchref: https://www.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)
2026-03-06T10:15:17,906   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)
2026-03-06T10:15:17,906   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)
2026-03-06T10:15:17,907   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)
2026-03-06T10:15:17,907 Skipping link: not a file: https://www.piwheels.org/simple/torchref/
2026-03-06T10:15:17,908 Skipping link: not a file: https://pypi.org/simple/torchref/
2026-03-06T10:15:17,927 Given no hashes to check 1 links for project 'torchref': discarding no candidates
2026-03-06T10:15:17,945 Collecting torchref==0.4.2
2026-03-06T10:15:17,947   Created temporary directory: /tmp/pip-unpack-yd8olt99
2026-03-06T10:15:18,161   Downloading torchref-0.4.2.tar.gz (2.9 MB)
2026-03-06T10:15:19,357   Added torchref==0.4.2 from https://files.pythonhosted.org/packages/ae/0d/52864d8146269e718c1cb7b47a20f899e4035f19e0ccb7e5d59315f65bb4/torchref-0.4.2.tar.gz to build tracker '/tmp/pip-build-tracker-pgx5i65x'
2026-03-06T10:15:19,363   Created temporary directory: /tmp/pip-build-env-7yg36t0y
2026-03-06T10:15:19,367   Installing build dependencies: started
2026-03-06T10:15:19,368   Running command pip subprocess to install build dependencies
2026-03-06T10:15:20,497   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2026-03-06T10:15:21,092   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
2026-03-06T10:15:21,115   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-03-06T10:15:22,887   Collecting setuptools>=42
2026-03-06T10:15:22,969     Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.0-py3-none-any.whl (1.0 MB)
2026-03-06T10:15:23,240   Collecting wheel
2026-03-06T10:15:23,256     Using cached https://www.piwheels.org/simple/wheel/wheel-0.46.3-py3-none-any.whl (30 kB)
2026-03-06T10:15:23,470   Collecting packaging>=24.0
2026-03-06T10:15:23,488     Using cached https://www.piwheels.org/simple/packaging/packaging-26.0-py3-none-any.whl (74 kB)
2026-03-06T10:15:26,414   Installing collected packages: setuptools, packaging, wheel
2026-03-06T10:15:29,719     Creating /tmp/pip-build-env-7yg36t0y/overlay/local/bin
2026-03-06T10:15:29,722     changing mode of /tmp/pip-build-env-7yg36t0y/overlay/local/bin/wheel to 755
2026-03-06T10:15:29,744   Successfully installed packaging-26.0 setuptools-82.0.0 wheel-0.46.3
2026-03-06T10:15:30,018   Installing build dependencies: finished with status 'done'
2026-03-06T10:15:30,025   Getting requirements to build wheel: started
2026-03-06T10:15:30,026   Running command Getting requirements to build wheel
2026-03-06T10:15:30,765   running egg_info
2026-03-06T10:15:30,771   writing torchref.egg-info/PKG-INFO
2026-03-06T10:15:30,779   writing dependency_links to torchref.egg-info/dependency_links.txt
2026-03-06T10:15:30,781   writing entry points to torchref.egg-info/entry_points.txt
2026-03-06T10:15:30,786   writing requirements to torchref.egg-info/requires.txt
2026-03-06T10:15:30,787   writing top-level names to torchref.egg-info/top_level.txt
2026-03-06T10:15:30,868   reading manifest file 'torchref.egg-info/SOURCES.txt'
2026-03-06T10:15:30,880   adding license file 'LICENSE'
2026-03-06T10:15:30,892   writing manifest file 'torchref.egg-info/SOURCES.txt'
2026-03-06T10:15:30,987   Getting requirements to build wheel: finished with status 'done'
2026-03-06T10:15:30,991   Created temporary directory: /tmp/pip-modern-metadata-uwe_u08t
2026-03-06T10:15:30,993   Preparing metadata (pyproject.toml): started
2026-03-06T10:15:30,994   Running command Preparing metadata (pyproject.toml)
2026-03-06T10:15:31,652   running dist_info
2026-03-06T10:15:31,662   creating /tmp/pip-modern-metadata-uwe_u08t/torchref.egg-info
2026-03-06T10:15:31,663   writing /tmp/pip-modern-metadata-uwe_u08t/torchref.egg-info/PKG-INFO
2026-03-06T10:15:31,671   writing dependency_links to /tmp/pip-modern-metadata-uwe_u08t/torchref.egg-info/dependency_links.txt
2026-03-06T10:15:31,673   writing entry points to /tmp/pip-modern-metadata-uwe_u08t/torchref.egg-info/entry_points.txt
2026-03-06T10:15:31,678   writing requirements to /tmp/pip-modern-metadata-uwe_u08t/torchref.egg-info/requires.txt
2026-03-06T10:15:31,679   writing top-level names to /tmp/pip-modern-metadata-uwe_u08t/torchref.egg-info/top_level.txt
2026-03-06T10:15:31,680   writing manifest file '/tmp/pip-modern-metadata-uwe_u08t/torchref.egg-info/SOURCES.txt'
2026-03-06T10:15:31,748   reading manifest file '/tmp/pip-modern-metadata-uwe_u08t/torchref.egg-info/SOURCES.txt'
2026-03-06T10:15:31,750   adding license file 'LICENSE'
2026-03-06T10:15:31,758   writing manifest file '/tmp/pip-modern-metadata-uwe_u08t/torchref.egg-info/SOURCES.txt'
2026-03-06T10:15:31,760   creating '/tmp/pip-modern-metadata-uwe_u08t/torchref-0.4.2.dist-info'
2026-03-06T10:15:31,887   Preparing metadata (pyproject.toml): finished with status 'done'
2026-03-06T10:15:31,892   Source in /tmp/pip-wheel-bz5ad079/torchref_ea56e68d8bcb4f25bb12e9f29692965c has version 0.4.2, which satisfies requirement torchref==0.4.2 from https://files.pythonhosted.org/packages/ae/0d/52864d8146269e718c1cb7b47a20f899e4035f19e0ccb7e5d59315f65bb4/torchref-0.4.2.tar.gz
2026-03-06T10:15:31,893   Removed torchref==0.4.2 from https://files.pythonhosted.org/packages/ae/0d/52864d8146269e718c1cb7b47a20f899e4035f19e0ccb7e5d59315f65bb4/torchref-0.4.2.tar.gz from build tracker '/tmp/pip-build-tracker-pgx5i65x'
2026-03-06T10:15:31,899 Created temporary directory: /tmp/pip-unpack-k1h57wdo
2026-03-06T10:15:31,900 Building wheels for collected packages: torchref
2026-03-06T10:15:31,904   Created temporary directory: /tmp/pip-wheel-lhl2727u
2026-03-06T10:15:31,904   Destination directory: /tmp/pip-wheel-lhl2727u
2026-03-06T10:15:31,906   Building wheel for torchref (pyproject.toml): started
2026-03-06T10:15:31,908   Running command Building wheel for torchref (pyproject.toml)
2026-03-06T10:15:32,550   running bdist_wheel
2026-03-06T10:15:32,568   running build
2026-03-06T10:15:32,568   running build_py
2026-03-06T10:15:32,574   creating build/lib/torchref
2026-03-06T10:15:32,576   copying torchref/config.py -> build/lib/torchref
2026-03-06T10:15:32,579   copying torchref/_bootstrap.py -> build/lib/torchref
2026-03-06T10:15:32,581   copying torchref/__init__.py -> build/lib/torchref
2026-03-06T10:15:32,584   creating build/lib/torchref/model
2026-03-06T10:15:32,585   copying torchref/model/segmented_internal_coordinates.py -> build/lib/torchref/model
2026-03-06T10:15:32,588   copying torchref/model/internal_coordinates.py -> build/lib/torchref/model
2026-03-06T10:15:32,592   copying torchref/model/sf_fft.py -> build/lib/torchref/model
2026-03-06T10:15:32,594   copying torchref/model/sf_ds.py -> build/lib/torchref/model
2026-03-06T10:15:32,597   copying torchref/model/parameter_wrappers.py -> build/lib/torchref/model
2026-03-06T10:15:32,600   copying torchref/model/__init__.py -> build/lib/torchref/model
2026-03-06T10:15:32,602   copying torchref/model/closed_segmented_internal_coordinates.py -> build/lib/torchref/model
2026-03-06T10:15:32,605   copying torchref/model/mixed_model.py -> build/lib/torchref/model
2026-03-06T10:15:32,608   copying torchref/model/model.py -> build/lib/torchref/model
2026-03-06T10:15:32,611   copying torchref/model/model_ft.py -> build/lib/torchref/model
2026-03-06T10:15:32,615   creating build/lib/torchref/refinement
2026-03-06T10:15:32,616   copying torchref/refinement/loss_state.py -> build/lib/torchref/refinement
2026-03-06T10:15:32,618   copying torchref/refinement/base_refinement.py -> build/lib/torchref/refinement
2026-03-06T10:15:32,621   copying torchref/refinement/lbfgs_refinement.py -> build/lib/torchref/refinement
2026-03-06T10:15:32,623   copying torchref/refinement/__init__.py -> build/lib/torchref/refinement
2026-03-06T10:15:32,625   copying torchref/refinement/logger.py -> build/lib/torchref/refinement
2026-03-06T10:15:32,628   creating build/lib/torchref/cli
2026-03-06T10:15:32,629   copying torchref/cli/refine_everything_static.py -> build/lib/torchref/cli
2026-03-06T10:15:32,632   copying torchref/cli/refine_everything_policy.py -> build/lib/torchref/cli
2026-03-06T10:15:32,634   copying torchref/cli/mtz2map.py -> build/lib/torchref/cli
2026-03-06T10:15:32,636   copying torchref/cli/refine_everything_random_weights.py -> build/lib/torchref/cli
2026-03-06T10:15:32,639   copying torchref/cli/phased_difference_map.py -> build/lib/torchref/cli
2026-03-06T10:15:32,641   copying torchref/cli/validate_ded.py -> build/lib/torchref/cli
2026-03-06T10:15:32,643   copying torchref/cli/__init__.py -> build/lib/torchref/cli
2026-03-06T10:15:32,645   copying torchref/cli/difference_refine.py -> build/lib/torchref/cli
2026-03-06T10:15:32,648   copying torchref/cli/refine.py -> build/lib/torchref/cli
2026-03-06T10:15:32,650   copying torchref/cli/refine_everything_hyperparameters.py -> build/lib/torchref/cli
2026-03-06T10:15:32,653   creating build/lib/torchref/maps
2026-03-06T10:15:32,655   copying torchref/maps/map.py -> build/lib/torchref/maps
2026-03-06T10:15:32,657   copying torchref/maps/difference_map.py -> build/lib/torchref/maps
2026-03-06T10:15:32,659   copying torchref/maps/__init__.py -> build/lib/torchref/maps
2026-03-06T10:15:32,661   creating build/lib/torchref/utils
2026-03-06T10:15:32,663   copying torchref/utils/utils.py -> build/lib/torchref/utils
2026-03-06T10:15:32,666   copying torchref/utils/hyperparameters.py -> build/lib/torchref/utils
2026-03-06T10:15:32,668   copying torchref/utils/serialization.py -> build/lib/torchref/utils
2026-03-06T10:15:32,670   copying torchref/utils/device_mixin.py -> build/lib/torchref/utils
2026-03-06T10:15:32,672   copying torchref/utils/debug_utils.py -> build/lib/torchref/utils
2026-03-06T10:15:32,675   copying torchref/utils/gradnorm.py -> build/lib/torchref/utils
2026-03-06T10:15:32,676   copying torchref/utils/stats.py -> build/lib/torchref/utils
2026-03-06T10:15:32,679   copying torchref/utils/caching.py -> build/lib/torchref/utils
2026-03-06T10:15:32,681   copying torchref/utils/__init__.py -> build/lib/torchref/utils
2026-03-06T10:15:32,683   copying torchref/utils/pse.py -> build/lib/torchref/utils
2026-03-06T10:15:32,686   copying torchref/utils/timing.py -> build/lib/torchref/utils
2026-03-06T10:15:32,688   creating build/lib/torchref/base
2026-03-06T10:15:32,689   copying torchref/base/math_numpy.py -> build/lib/torchref/base
2026-03-06T10:15:32,692   copying torchref/base/french_wilson.py -> build/lib/torchref/base
2026-03-06T10:15:32,695   copying torchref/base/get_scattering_factor_torch.py -> build/lib/torchref/base
2026-03-06T10:15:32,697   copying torchref/base/CCTBX_related.py -> build/lib/torchref/base
2026-03-06T10:15:32,699   copying torchref/base/__init__.py -> build/lib/torchref/base
2026-03-06T10:15:32,702   copying torchref/base/math_torch.py -> build/lib/torchref/base
2026-03-06T10:15:32,705   creating build/lib/torchref/io
2026-03-06T10:15:32,706   copying torchref/io/cif_readers.py -> build/lib/torchref/io
2026-03-06T10:15:32,709   copying torchref/io/mtz.py -> build/lib/torchref/io
2026-03-06T10:15:32,711   copying torchref/io/__init__.py -> build/lib/torchref/io
2026-03-06T10:15:32,713   copying torchref/io/cif.py -> build/lib/torchref/io
2026-03-06T10:15:32,715   copying torchref/io/pdb.py -> build/lib/torchref/io
2026-03-06T10:15:32,718   copying torchref/io/data_router.py -> build/lib/torchref/io
2026-03-06T10:15:32,720   creating build/lib/torchref/scaling
2026-03-06T10:15:32,721   copying torchref/scaling/scaler.py -> build/lib/torchref/scaling
2026-03-06T10:15:32,724   copying torchref/scaling/solvent.py -> build/lib/torchref/scaling
2026-03-06T10:15:32,726   copying torchref/scaling/scaler_base.py -> build/lib/torchref/scaling
2026-03-06T10:15:32,729   copying torchref/scaling/__init__.py -> build/lib/torchref/scaling
2026-03-06T10:15:32,731   creating build/lib/torchref/restraints
2026-03-06T10:15:32,732   copying torchref/restraints/restraints.py -> build/lib/torchref/restraints
2026-03-06T10:15:32,735   copying torchref/restraints/builders_numba.py -> build/lib/torchref/restraints
2026-03-06T10:15:32,739   copying torchref/restraints/ramachandran.py -> build/lib/torchref/restraints
2026-03-06T10:15:32,740   copying torchref/restraints/builders_fast.py -> build/lib/torchref/restraints
2026-03-06T10:15:32,744   copying torchref/restraints/library.py -> build/lib/torchref/restraints
2026-03-06T10:15:32,746   copying torchref/restraints/builders.py -> build/lib/torchref/restraints
2026-03-06T10:15:32,749   copying torchref/restraints/restraints_helper.py -> build/lib/torchref/restraints
2026-03-06T10:15:32,752   copying torchref/restraints/__init__.py -> build/lib/torchref/restraints
2026-03-06T10:15:32,755   creating build/lib/torchref/symmetry
2026-03-06T10:15:32,756   copying torchref/symmetry/grid_utils.py -> build/lib/torchref/symmetry
2026-03-06T10:15:32,758   copying torchref/symmetry/spacegroup.py -> build/lib/torchref/symmetry
2026-03-06T10:15:32,761   copying torchref/symmetry/map_symmetry.py -> build/lib/torchref/symmetry
2026-03-06T10:15:32,763   copying torchref/symmetry/cell.py -> build/lib/torchref/symmetry
2026-03-06T10:15:32,766   copying torchref/symmetry/__init__.py -> build/lib/torchref/symmetry
2026-03-06T10:15:32,767   copying torchref/symmetry/map_symmetry_interpolation.py -> build/lib/torchref/symmetry
2026-03-06T10:15:32,770   copying torchref/symmetry/symmetry.py -> build/lib/torchref/symmetry
2026-03-06T10:15:32,772   copying torchref/symmetry/reciprocal_symmetry.py -> build/lib/torchref/symmetry
2026-03-06T10:15:32,775   creating build/lib/torchref/scripts
2026-03-06T10:15:32,776   copying torchref/scripts/generate_scattering_table.py -> build/lib/torchref/scripts
2026-03-06T10:15:32,778   copying torchref/scripts/__init__.py -> build/lib/torchref/scripts
2026-03-06T10:15:32,781   creating build/lib/torchref/alignment
2026-03-06T10:15:32,782   copying torchref/alignment/transform.py -> build/lib/torchref/alignment
2026-03-06T10:15:32,785   copying torchref/alignment/distributions.py -> build/lib/torchref/alignment
2026-03-06T10:15:32,787   copying torchref/alignment/jax_subpixel_peaks.py -> build/lib/torchref/alignment
2026-03-06T10:15:32,789   copying torchref/alignment/translation.py -> build/lib/torchref/alignment
2026-03-06T10:15:32,791   copying torchref/alignment/rigid_body.py -> build/lib/torchref/alignment
2026-03-06T10:15:32,794   copying torchref/alignment/clashscore.py -> build/lib/torchref/alignment
2026-03-06T10:15:32,796   copying torchref/alignment/pipeline.py -> build/lib/torchref/alignment
2026-03-06T10:15:32,799   copying torchref/alignment/sampling.py -> build/lib/torchref/alignment
2026-03-06T10:15:32,801   copying torchref/alignment/__init__.py -> build/lib/torchref/alignment
2026-03-06T10:15:32,803   copying torchref/alignment/ball_transform.py -> build/lib/torchref/alignment
2026-03-06T10:15:32,811   creating build/lib/torchref/refinement/weighting
2026-03-06T10:15:32,812   copying torchref/refinement/weighting/component_weighting.py -> build/lib/torchref/refinement/weighting
2026-03-06T10:15:32,815   copying torchref/refinement/weighting/policy_weighting.py -> build/lib/torchref/refinement/weighting
2026-03-06T10:15:32,818   copying torchref/refinement/weighting/base_weighting.py -> build/lib/torchref/refinement/weighting
2026-03-06T10:15:32,819   copying torchref/refinement/weighting/random_weighting.py -> build/lib/torchref/refinement/weighting
2026-03-06T10:15:32,822   copying torchref/refinement/weighting/__init__.py -> build/lib/torchref/refinement/weighting
2026-03-06T10:15:32,823   copying torchref/refinement/weighting/es_policy_training.py -> build/lib/torchref/refinement/weighting
2026-03-06T10:15:32,827   creating build/lib/torchref/refinement/targets
2026-03-06T10:15:32,828   copying torchref/refinement/targets/occupancy_floor_diagnostic.py -> build/lib/torchref/refinement/targets
2026-03-06T10:15:32,830   copying torchref/refinement/targets/amber_target.py -> build/lib/torchref/refinement/targets
2026-03-06T10:15:32,833   copying torchref/refinement/targets/base.py -> build/lib/torchref/refinement/targets
2026-03-06T10:15:32,835   copying torchref/refinement/targets/combined.py -> build/lib/torchref/refinement/targets
2026-03-06T10:15:32,838   copying torchref/refinement/targets/sampled_ml_phase_target.py -> build/lib/torchref/refinement/targets
2026-03-06T10:15:32,840   copying torchref/refinement/targets/__init__.py -> build/lib/torchref/refinement/targets
2026-03-06T10:15:32,842   copying torchref/refinement/targets/difference.py -> build/lib/torchref/refinement/targets
2026-03-06T10:15:32,845   copying torchref/refinement/targets/forcefield_target.py -> build/lib/torchref/refinement/targets
2026-03-06T10:15:32,847   copying torchref/refinement/targets/realspace.py -> build/lib/torchref/refinement/targets
2026-03-06T10:15:32,850   creating build/lib/torchref/refinement/optimizers
2026-03-06T10:15:32,851   copying torchref/refinement/optimizers/simulated_annealing.py -> build/lib/torchref/refinement/optimizers
2026-03-06T10:15:32,853   copying torchref/refinement/optimizers/adam_noise.py -> build/lib/torchref/refinement/optimizers
2026-03-06T10:15:32,855   copying torchref/refinement/optimizers/momentum_sa.py -> build/lib/torchref/refinement/optimizers
2026-03-06T10:15:32,857   copying torchref/refinement/optimizers/exploratory_lbfgs.py -> build/lib/torchref/refinement/optimizers
2026-03-06T10:15:32,860   copying torchref/refinement/optimizers/__init__.py -> build/lib/torchref/refinement/optimizers
2026-03-06T10:15:32,862   copying torchref/refinement/optimizers/langevin_sa.py -> build/lib/torchref/refinement/optimizers
2026-03-06T10:15:32,864   copying torchref/refinement/optimizers/internal_coord_sa.py -> build/lib/torchref/refinement/optimizers
2026-03-06T10:15:32,868   creating build/lib/torchref/refinement/targets/geometry
2026-03-06T10:15:32,869   copying torchref/refinement/targets/geometry/base.py -> build/lib/torchref/refinement/targets/geometry
2026-03-06T10:15:32,871   copying torchref/refinement/targets/geometry/ramachandran.py -> build/lib/torchref/refinement/targets/geometry
2026-03-06T10:15:32,872   copying torchref/refinement/targets/geometry/angles.py -> build/lib/torchref/refinement/targets/geometry
2026-03-06T10:15:32,874   copying torchref/refinement/targets/geometry/torsions.py -> build/lib/torchref/refinement/targets/geometry
2026-03-06T10:15:32,876   copying torchref/refinement/targets/geometry/planarity.py -> build/lib/torchref/refinement/targets/geometry
2026-03-06T10:15:32,878   copying torchref/refinement/targets/geometry/chiral.py -> build/lib/torchref/refinement/targets/geometry
2026-03-06T10:15:32,881   copying torchref/refinement/targets/geometry/__init__.py -> build/lib/torchref/refinement/targets/geometry
2026-03-06T10:15:32,882   copying torchref/refinement/targets/geometry/non_bonded.py -> build/lib/torchref/refinement/targets/geometry
2026-03-06T10:15:32,884   copying torchref/refinement/targets/geometry/bonds.py -> build/lib/torchref/refinement/targets/geometry
2026-03-06T10:15:32,887   creating build/lib/torchref/refinement/targets/xray
2026-03-06T10:15:32,888   copying torchref/refinement/targets/xray/maximum_likelihood.py -> build/lib/torchref/refinement/targets/xray
2026-03-06T10:15:32,890   copying torchref/refinement/targets/xray/base.py -> build/lib/torchref/refinement/targets/xray
2026-03-06T10:15:32,892   copying torchref/refinement/targets/xray/least_squares.py -> build/lib/torchref/refinement/targets/xray
2026-03-06T10:15:32,894   copying torchref/refinement/targets/xray/__init__.py -> build/lib/torchref/refinement/targets/xray
2026-03-06T10:15:32,895   copying torchref/refinement/targets/xray/gaussian.py -> build/lib/torchref/refinement/targets/xray
2026-03-06T10:15:32,897   creating build/lib/torchref/refinement/targets/adp
2026-03-06T10:15:32,898   copying torchref/refinement/targets/adp/entropy.py -> build/lib/torchref/refinement/targets/adp
2026-03-06T10:15:32,900   copying torchref/refinement/targets/adp/base.py -> build/lib/torchref/refinement/targets/adp
2026-03-06T10:15:32,902   copying torchref/refinement/targets/adp/similarity.py -> build/lib/torchref/refinement/targets/adp
2026-03-06T10:15:32,904   copying torchref/refinement/targets/adp/__init__.py -> build/lib/torchref/refinement/targets/adp
2026-03-06T10:15:32,905   copying torchref/refinement/targets/adp/locality.py -> build/lib/torchref/refinement/targets/adp
2026-03-06T10:15:32,908   copying torchref/refinement/targets/adp/rigid_bond.py -> build/lib/torchref/refinement/targets/adp
2026-03-06T10:15:32,910   creating build/lib/torchref/base/fourier
2026-03-06T10:15:32,911   copying torchref/base/fourier/__init__.py -> build/lib/torchref/base/fourier
2026-03-06T10:15:32,913   copying torchref/base/fourier/grid.py -> build/lib/torchref/base/fourier
2026-03-06T10:15:32,916   copying torchref/base/fourier/fft.py -> build/lib/torchref/base/fourier
2026-03-06T10:15:32,918   creating build/lib/torchref/base/coordinates
2026-03-06T10:15:32,919   copying torchref/base/coordinates/periodic_boundary.py -> build/lib/torchref/base/coordinates
2026-03-06T10:15:32,921   copying torchref/base/coordinates/__init__.py -> build/lib/torchref/base/coordinates
2026-03-06T10:15:32,923   copying torchref/base/coordinates/transforms_torch.py -> build/lib/torchref/base/coordinates
2026-03-06T10:15:32,924   copying torchref/base/coordinates/transforms_numpy.py -> build/lib/torchref/base/coordinates
2026-03-06T10:15:32,927   creating build/lib/torchref/base/kernels
2026-03-06T10:15:32,928   copying torchref/base/kernels/optimized_ops.py -> build/lib/torchref/base/kernels
2026-03-06T10:15:32,930   copying torchref/base/kernels/cpu_scatter.py -> build/lib/torchref/base/kernels
2026-03-06T10:15:32,933   copying torchref/base/kernels/jit_kernel_vectorized_add_to_map.py -> build/lib/torchref/base/kernels
2026-03-06T10:15:32,935   copying torchref/base/kernels/triton_kernel.py -> build/lib/torchref/base/kernels
2026-03-06T10:15:32,938   copying torchref/base/kernels/__init__.py -> build/lib/torchref/base/kernels
2026-03-06T10:15:32,940   copying torchref/base/kernels/separable_triton_kernel.py -> build/lib/torchref/base/kernels
2026-03-06T10:15:32,944   creating build/lib/torchref/base/electron_density
2026-03-06T10:15:32,945   copying torchref/base/electron_density/main.py -> build/lib/torchref/base/electron_density
2026-03-06T10:15:32,947   copying torchref/base/electron_density/__init__.py -> build/lib/torchref/base/electron_density
2026-03-06T10:15:32,949   copying torchref/base/electron_density/map_building.py -> build/lib/torchref/base/electron_density
2026-03-06T10:15:32,951   copying torchref/base/electron_density/voxel_utils.py -> build/lib/torchref/base/electron_density
2026-03-06T10:15:32,954   copying torchref/base/electron_density/solvent_mask.py -> build/lib/torchref/base/electron_density
2026-03-06T10:15:32,957   creating build/lib/torchref/base/metrics
2026-03-06T10:15:32,958   copying torchref/base/metrics/rfactor.py -> build/lib/torchref/base/metrics
2026-03-06T10:15:32,960   copying torchref/base/metrics/loss.py -> build/lib/torchref/base/metrics
2026-03-06T10:15:32,962   copying torchref/base/metrics/__init__.py -> build/lib/torchref/base/metrics
2026-03-06T10:15:32,964   creating build/lib/torchref/base/chain_closure
2026-03-06T10:15:32,965   copying torchref/base/chain_closure/closure.py -> build/lib/torchref/base/chain_closure
2026-03-06T10:15:32,968   copying torchref/base/chain_closure/__init__.py -> build/lib/torchref/base/chain_closure
2026-03-06T10:15:32,969   copying torchref/base/chain_closure/backbone_utils.py -> build/lib/torchref/base/chain_closure
2026-03-06T10:15:32,972   creating build/lib/torchref/base/scattering
2026-03-06T10:15:32,973   copying torchref/base/scattering/scattering_table.py -> build/lib/torchref/base/scattering
2026-03-06T10:15:32,976   copying torchref/base/scattering/itc92.py -> build/lib/torchref/base/scattering
2026-03-06T10:15:32,978   copying torchref/base/scattering/__init__.py -> build/lib/torchref/base/scattering
2026-03-06T10:15:32,980   copying torchref/base/scattering/anomalous_table.py -> build/lib/torchref/base/scattering
2026-03-06T10:15:32,982   creating build/lib/torchref/base/direct_summation
2026-03-06T10:15:32,983   copying torchref/base/direct_summation/anisotropic.py -> build/lib/torchref/base/direct_summation
2026-03-06T10:15:32,986   copying torchref/base/direct_summation/corrections.py -> build/lib/torchref/base/direct_summation
2026-03-06T10:15:32,988   copying torchref/base/direct_summation/isotropic.py -> build/lib/torchref/base/direct_summation
2026-03-06T10:15:32,990   copying torchref/base/direct_summation/__init__.py -> build/lib/torchref/base/direct_summation
2026-03-06T10:15:32,992   creating build/lib/torchref/base/reciprocal
2026-03-06T10:15:32,993   copying torchref/base/reciprocal/grid_operations.py -> build/lib/torchref/base/reciprocal
2026-03-06T10:15:32,995   copying torchref/base/reciprocal/interpolation.py -> build/lib/torchref/base/reciprocal
2026-03-06T10:15:32,998   copying torchref/base/reciprocal/basis.py -> build/lib/torchref/base/reciprocal
2026-03-06T10:15:33,000   copying torchref/base/reciprocal/__init__.py -> build/lib/torchref/base/reciprocal
2026-03-06T10:15:33,002   copying torchref/base/reciprocal/hkl.py -> build/lib/torchref/base/reciprocal
2026-03-06T10:15:33,004   copying torchref/base/reciprocal/symmetry.py -> build/lib/torchref/base/reciprocal
2026-03-06T10:15:33,006   creating build/lib/torchref/base/alignment
2026-03-06T10:15:33,007   copying torchref/base/alignment/superposition.py -> build/lib/torchref/base/alignment
2026-03-06T10:15:33,010   copying torchref/base/alignment/normalization.py -> build/lib/torchref/base/alignment
2026-03-06T10:15:33,034   copying torchref/base/alignment/rotation.py -> build/lib/torchref/base/alignment
2026-03-06T10:15:33,037   copying torchref/base/alignment/__init__.py -> build/lib/torchref/base/alignment
2026-03-06T10:15:33,039   copying torchref/base/alignment/scoring.py -> build/lib/torchref/base/alignment
2026-03-06T10:15:33,041   creating build/lib/torchref/io/datasets
2026-03-06T10:15:33,043   copying torchref/io/datasets/base.py -> build/lib/torchref/io/datasets
2026-03-06T10:15:33,046   copying torchref/io/datasets/__init__.py -> build/lib/torchref/io/datasets
2026-03-06T10:15:33,048   copying torchref/io/datasets/fcalc_data.py -> build/lib/torchref/io/datasets
2026-03-06T10:15:33,051   copying torchref/io/datasets/reflection_data.py -> build/lib/torchref/io/datasets
2026-03-06T10:15:33,055   copying torchref/io/datasets/collection.py -> build/lib/torchref/io/datasets
2026-03-06T10:15:33,058   running egg_info
2026-03-06T10:15:33,068   writing torchref.egg-info/PKG-INFO
2026-03-06T10:15:33,075   writing dependency_links to torchref.egg-info/dependency_links.txt
2026-03-06T10:15:33,077   writing entry points to torchref.egg-info/entry_points.txt
2026-03-06T10:15:33,082   writing requirements to torchref.egg-info/requires.txt
2026-03-06T10:15:33,083   writing top-level names to torchref.egg-info/top_level.txt
2026-03-06T10:15:33,141   reading manifest file 'torchref.egg-info/SOURCES.txt'
2026-03-06T10:15:33,153   adding license file 'LICENSE'
2026-03-06T10:15:33,165   writing manifest file 'torchref.egg-info/SOURCES.txt'
2026-03-06T10:15:33,198   creating build/lib/torchref/data
2026-03-06T10:15:33,199   copying torchref/data/atomic_vdw_radii.csv -> build/lib/torchref/data
2026-03-06T10:15:33,201   copying torchref/data/default_hyperparameters.json -> build/lib/torchref/data
2026-03-06T10:15:33,203   copying torchref/data/policy_latest.pt -> build/lib/torchref/data
2026-03-06T10:15:33,210   copying torchref/data/rama_nll_surfaces.pt -> build/lib/torchref/data
2026-03-06T10:15:33,271   copying torchref/data/itc92_scattering_factors.pt -> build/lib/torchref/data
2026-03-06T10:15:33,274   creating build/lib/torchref/data/monomer_library/l
2026-03-06T10:15:33,275   copying torchref/data/monomer_library/l/LEU.cif -> build/lib/torchref/data/monomer_library/l
2026-03-06T10:15:33,278   copying torchref/data/monomer_library/l/LYS.cif -> build/lib/torchref/data/monomer_library/l
2026-03-06T10:15:33,280   creating build/lib/torchref/data/monomer_library/h
2026-03-06T10:15:33,281   copying torchref/data/monomer_library/h/HOH.cif -> build/lib/torchref/data/monomer_library/h
2026-03-06T10:15:33,284   copying torchref/data/monomer_library/h/HYP.cif -> build/lib/torchref/data/monomer_library/h
2026-03-06T10:15:33,286   copying torchref/data/monomer_library/h/HIS.cif -> build/lib/torchref/data/monomer_library/h
2026-03-06T10:15:33,288   creating build/lib/torchref/data/monomer_library/p
2026-03-06T10:15:33,289   copying torchref/data/monomer_library/p/PRO.cif -> build/lib/torchref/data/monomer_library/p
2026-03-06T10:15:33,292   copying torchref/data/monomer_library/p/PHE.cif -> build/lib/torchref/data/monomer_library/p
2026-03-06T10:15:33,295   copying torchref/data/monomer_library/p/PTR.cif -> build/lib/torchref/data/monomer_library/p
2026-03-06T10:15:33,297   creating build/lib/torchref/data/monomer_library/u
2026-03-06T10:15:33,298   copying torchref/data/monomer_library/u/U.cif -> build/lib/torchref/data/monomer_library/u
2026-03-06T10:15:33,301   creating build/lib/torchref/data/monomer_library/v
2026-03-06T10:15:33,302   copying torchref/data/monomer_library/v/VAL.cif -> build/lib/torchref/data/monomer_library/v
2026-03-06T10:15:33,304   creating build/lib/torchref/data/monomer_library/s
2026-03-06T10:15:33,306   copying torchref/data/monomer_library/s/SEP.cif -> build/lib/torchref/data/monomer_library/s
2026-03-06T10:15:33,308   copying torchref/data/monomer_library/s/SER.cif -> build/lib/torchref/data/monomer_library/s
2026-03-06T10:15:33,311   creating build/lib/torchref/data/monomer_library/m
2026-03-06T10:15:33,312   copying torchref/data/monomer_library/m/MSE.cif -> build/lib/torchref/data/monomer_library/m
2026-03-06T10:15:33,314   copying torchref/data/monomer_library/m/MET.cif -> build/lib/torchref/data/monomer_library/m
2026-03-06T10:15:33,317   creating build/lib/torchref/data/monomer_library/t
2026-03-06T10:15:33,318   copying torchref/data/monomer_library/t/TYR.cif -> build/lib/torchref/data/monomer_library/t
2026-03-06T10:15:33,320   copying torchref/data/monomer_library/t/TPO.cif -> build/lib/torchref/data/monomer_library/t
2026-03-06T10:15:33,323   copying torchref/data/monomer_library/t/THR.cif -> build/lib/torchref/data/monomer_library/t
2026-03-06T10:15:33,326   copying torchref/data/monomer_library/t/TRP.cif -> build/lib/torchref/data/monomer_library/t
2026-03-06T10:15:33,328   creating build/lib/torchref/data/monomer_library/g
2026-03-06T10:15:33,329   copying torchref/data/monomer_library/g/G.cif -> build/lib/torchref/data/monomer_library/g
2026-03-06T10:15:33,333   copying torchref/data/monomer_library/g/GLY.cif -> build/lib/torchref/data/monomer_library/g
2026-03-06T10:15:33,335   copying torchref/data/monomer_library/g/GLN.cif -> build/lib/torchref/data/monomer_library/g
2026-03-06T10:15:33,339   copying torchref/data/monomer_library/g/GLU.cif -> build/lib/torchref/data/monomer_library/g
2026-03-06T10:15:33,342   creating build/lib/torchref/data/monomer_library/c
2026-03-06T10:15:33,343   copying torchref/data/monomer_library/c/CYS.cif -> build/lib/torchref/data/monomer_library/c
2026-03-06T10:15:33,347   copying torchref/data/monomer_library/c/C.cif -> build/lib/torchref/data/monomer_library/c
2026-03-06T10:15:33,350   creating build/lib/torchref/data/monomer_library/a
2026-03-06T10:15:33,351   copying torchref/data/monomer_library/a/ARG.cif -> build/lib/torchref/data/monomer_library/a
2026-03-06T10:15:33,354   copying torchref/data/monomer_library/a/ASN.cif -> build/lib/torchref/data/monomer_library/a
2026-03-06T10:15:33,358   copying torchref/data/monomer_library/a/ALA.cif -> build/lib/torchref/data/monomer_library/a
2026-03-06T10:15:33,361   copying torchref/data/monomer_library/a/A.cif -> build/lib/torchref/data/monomer_library/a
2026-03-06T10:15:33,364   copying torchref/data/monomer_library/a/ASP.cif -> build/lib/torchref/data/monomer_library/a
2026-03-06T10:15:33,368   creating build/lib/torchref/data/monomer_library/i
2026-03-06T10:15:33,369   copying torchref/data/monomer_library/i/ILE.cif -> build/lib/torchref/data/monomer_library/i
2026-03-06T10:15:33,372   creating build/lib/torchref/data/monomer_library/list
2026-03-06T10:15:33,374   copying torchref/data/monomer_library/list/mon_lib_list.cif -> build/lib/torchref/data/monomer_library/list
2026-03-06T10:15:33,471   creating build/lib/torchref/data/monomer_library/d
2026-03-06T10:15:33,472   copying torchref/data/monomer_library/d/DC.cif -> build/lib/torchref/data/monomer_library/d
2026-03-06T10:15:33,475   copying torchref/data/monomer_library/d/DG.cif -> build/lib/torchref/data/monomer_library/d
2026-03-06T10:15:33,479   copying torchref/data/monomer_library/d/DA.cif -> build/lib/torchref/data/monomer_library/d
2026-03-06T10:15:33,482   copying torchref/data/monomer_library/d/DT.cif -> build/lib/torchref/data/monomer_library/d
2026-03-06T10:15:33,541   installing to build/bdist.linux-armv7l/wheel
2026-03-06T10:15:33,542   running install
2026-03-06T10:15:33,565   running install_lib
2026-03-06T10:15:33,570   creating build/bdist.linux-armv7l/wheel
2026-03-06T10:15:33,572   creating build/bdist.linux-armv7l/wheel/torchref
2026-03-06T10:15:33,574   creating build/bdist.linux-armv7l/wheel/torchref/data
2026-03-06T10:15:33,575   copying build/lib/torchref/data/default_hyperparameters.json -> build/bdist.linux-armv7l/wheel/./torchref/data
2026-03-06T10:15:33,577   copying build/lib/torchref/data/policy_latest.pt -> build/bdist.linux-armv7l/wheel/./torchref/data
2026-03-06T10:15:33,582   copying build/lib/torchref/data/atomic_vdw_radii.csv -> build/bdist.linux-armv7l/wheel/./torchref/data
2026-03-06T10:15:33,584   copying build/lib/torchref/data/rama_nll_surfaces.pt -> build/bdist.linux-armv7l/wheel/./torchref/data
2026-03-06T10:15:33,683   copying build/lib/torchref/data/itc92_scattering_factors.pt -> build/bdist.linux-armv7l/wheel/./torchref/data
2026-03-06T10:15:33,686   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library
2026-03-06T10:15:33,687   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/l
2026-03-06T10:15:33,689   copying build/lib/torchref/data/monomer_library/l/LEU.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/l
2026-03-06T10:15:33,691   copying build/lib/torchref/data/monomer_library/l/LYS.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/l
2026-03-06T10:15:33,694   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/h
2026-03-06T10:15:33,695   copying build/lib/torchref/data/monomer_library/h/HOH.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/h
2026-03-06T10:15:33,697   copying build/lib/torchref/data/monomer_library/h/HYP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/h
2026-03-06T10:15:33,699   copying build/lib/torchref/data/monomer_library/h/HIS.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/h
2026-03-06T10:15:33,702   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/p
2026-03-06T10:15:33,703   copying build/lib/torchref/data/monomer_library/p/PRO.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/p
2026-03-06T10:15:33,705   copying build/lib/torchref/data/monomer_library/p/PHE.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/p
2026-03-06T10:15:33,708   copying build/lib/torchref/data/monomer_library/p/PTR.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/p
2026-03-06T10:15:33,710   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/u
2026-03-06T10:15:33,711   copying build/lib/torchref/data/monomer_library/u/U.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/u
2026-03-06T10:15:33,714   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/v
2026-03-06T10:15:33,715   copying build/lib/torchref/data/monomer_library/v/VAL.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/v
2026-03-06T10:15:33,718   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/s
2026-03-06T10:15:33,719   copying build/lib/torchref/data/monomer_library/s/SEP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/s
2026-03-06T10:15:33,721   copying build/lib/torchref/data/monomer_library/s/SER.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/s
2026-03-06T10:15:33,724   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/m
2026-03-06T10:15:33,725   copying build/lib/torchref/data/monomer_library/m/MSE.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/m
2026-03-06T10:15:33,728   copying build/lib/torchref/data/monomer_library/m/MET.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/m
2026-03-06T10:15:33,730   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/t
2026-03-06T10:15:33,731   copying build/lib/torchref/data/monomer_library/t/TYR.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t
2026-03-06T10:15:33,734   copying build/lib/torchref/data/monomer_library/t/TPO.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t
2026-03-06T10:15:33,736   copying build/lib/torchref/data/monomer_library/t/THR.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t
2026-03-06T10:15:33,739   copying build/lib/torchref/data/monomer_library/t/TRP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t
2026-03-06T10:15:33,741   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/g
2026-03-06T10:15:33,742   copying build/lib/torchref/data/monomer_library/g/G.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g
2026-03-06T10:15:33,745   copying build/lib/torchref/data/monomer_library/g/GLY.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g
2026-03-06T10:15:33,747   copying build/lib/torchref/data/monomer_library/g/GLN.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g
2026-03-06T10:15:33,749   copying build/lib/torchref/data/monomer_library/g/GLU.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g
2026-03-06T10:15:33,752   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/c
2026-03-06T10:15:33,753   copying build/lib/torchref/data/monomer_library/c/CYS.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/c
2026-03-06T10:15:33,755   copying build/lib/torchref/data/monomer_library/c/C.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/c
2026-03-06T10:15:33,758   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/a
2026-03-06T10:15:33,759   copying build/lib/torchref/data/monomer_library/a/ARG.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a
2026-03-06T10:15:33,762   copying build/lib/torchref/data/monomer_library/a/ASN.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a
2026-03-06T10:15:33,764   copying build/lib/torchref/data/monomer_library/a/ALA.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a
2026-03-06T10:15:33,766   copying build/lib/torchref/data/monomer_library/a/A.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a
2026-03-06T10:15:33,768   copying build/lib/torchref/data/monomer_library/a/ASP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a
2026-03-06T10:15:33,771   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/i
2026-03-06T10:15:33,772   copying build/lib/torchref/data/monomer_library/i/ILE.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/i
2026-03-06T10:15:33,775   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/list
2026-03-06T10:15:33,776   copying build/lib/torchref/data/monomer_library/list/mon_lib_list.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/list
2026-03-06T10:15:33,836   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/d
2026-03-06T10:15:33,838   copying build/lib/torchref/data/monomer_library/d/DC.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d
2026-03-06T10:15:33,840   copying build/lib/torchref/data/monomer_library/d/DG.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d
2026-03-06T10:15:33,843   copying build/lib/torchref/data/monomer_library/d/DA.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d
2026-03-06T10:15:33,845   copying build/lib/torchref/data/monomer_library/d/DT.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d
2026-03-06T10:15:33,848   creating build/bdist.linux-armv7l/wheel/torchref/model
2026-03-06T10:15:33,849   copying build/lib/torchref/model/segmented_internal_coordinates.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-06T10:15:33,854   copying build/lib/torchref/model/internal_coordinates.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-06T10:15:33,858   copying build/lib/torchref/model/sf_fft.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-06T10:15:33,860   copying build/lib/torchref/model/sf_ds.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-06T10:15:33,863   copying build/lib/torchref/model/parameter_wrappers.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-06T10:15:33,866   copying build/lib/torchref/model/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-06T10:15:33,868   copying build/lib/torchref/model/closed_segmented_internal_coordinates.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-06T10:15:33,872   copying build/lib/torchref/model/mixed_model.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-06T10:15:33,874   copying build/lib/torchref/model/model.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-06T10:15:33,879   copying build/lib/torchref/model/model_ft.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-06T10:15:33,882   creating build/bdist.linux-armv7l/wheel/torchref/refinement
2026-03-06T10:15:33,883   copying build/lib/torchref/refinement/loss_state.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement
2026-03-06T10:15:33,886   copying build/lib/torchref/refinement/base_refinement.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement
2026-03-06T10:15:33,889   creating build/bdist.linux-armv7l/wheel/torchref/refinement/weighting
2026-03-06T10:15:33,890   copying build/lib/torchref/refinement/weighting/component_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-03-06T10:15:33,893   copying build/lib/torchref/refinement/weighting/policy_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-03-06T10:15:33,896   copying build/lib/torchref/refinement/weighting/base_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-03-06T10:15:33,898   copying build/lib/torchref/refinement/weighting/random_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-03-06T10:15:33,900   copying build/lib/torchref/refinement/weighting/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-03-06T10:15:33,902   copying build/lib/torchref/refinement/weighting/es_policy_training.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-03-06T10:15:33,904   copying build/lib/torchref/refinement/lbfgs_refinement.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement
2026-03-06T10:15:33,907   copying build/lib/torchref/refinement/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement
2026-03-06T10:15:33,910   creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets
2026-03-06T10:15:33,911   copying build/lib/torchref/refinement/targets/occupancy_floor_diagnostic.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-06T10:15:33,913   copying build/lib/torchref/refinement/targets/amber_target.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-06T10:15:33,916   copying build/lib/torchref/refinement/targets/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-06T10:15:33,918   copying build/lib/torchref/refinement/targets/combined.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-06T10:15:33,921   copying build/lib/torchref/refinement/targets/sampled_ml_phase_target.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-06T10:15:33,924   creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets/geometry
2026-03-06T10:15:33,925   copying build/lib/torchref/refinement/targets/geometry/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-06T10:15:33,927   copying build/lib/torchref/refinement/targets/geometry/ramachandran.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-06T10:15:33,929   copying build/lib/torchref/refinement/targets/geometry/angles.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-06T10:15:33,931   copying build/lib/torchref/refinement/targets/geometry/torsions.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-06T10:15:33,933   copying build/lib/torchref/refinement/targets/geometry/planarity.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-06T10:15:33,935   copying build/lib/torchref/refinement/targets/geometry/chiral.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-06T10:15:33,937   copying build/lib/torchref/refinement/targets/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-06T10:15:33,939   copying build/lib/torchref/refinement/targets/geometry/non_bonded.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-06T10:15:33,941   copying build/lib/torchref/refinement/targets/geometry/bonds.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-06T10:15:33,944   creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets/xray
2026-03-06T10:15:33,945   copying build/lib/torchref/refinement/targets/xray/maximum_likelihood.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-03-06T10:15:33,947   copying build/lib/torchref/refinement/targets/xray/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-03-06T10:15:33,949   copying build/lib/torchref/refinement/targets/xray/least_squares.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-03-06T10:15:33,951   copying build/lib/torchref/refinement/targets/xray/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-03-06T10:15:33,953   copying build/lib/torchref/refinement/targets/xray/gaussian.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-03-06T10:15:33,955   copying build/lib/torchref/refinement/targets/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-06T10:15:33,957   copying build/lib/torchref/refinement/targets/difference.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-06T10:15:33,960   creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets/adp
2026-03-06T10:15:33,961   copying build/lib/torchref/refinement/targets/adp/entropy.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-03-06T10:15:33,963   copying build/lib/torchref/refinement/targets/adp/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-03-06T10:15:33,964   copying build/lib/torchref/refinement/targets/adp/similarity.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-03-06T10:15:33,966   copying build/lib/torchref/refinement/targets/adp/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-03-06T10:15:33,968   copying build/lib/torchref/refinement/targets/adp/locality.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-03-06T10:15:33,970   copying build/lib/torchref/refinement/targets/adp/rigid_bond.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-03-06T10:15:33,972   copying build/lib/torchref/refinement/targets/forcefield_target.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-06T10:15:33,974   copying build/lib/torchref/refinement/targets/realspace.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-06T10:15:33,977   copying build/lib/torchref/refinement/logger.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement
2026-03-06T10:15:33,980   creating build/bdist.linux-armv7l/wheel/torchref/refinement/optimizers
2026-03-06T10:15:33,981   copying build/lib/torchref/refinement/optimizers/simulated_annealing.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-03-06T10:15:33,983   copying build/lib/torchref/refinement/optimizers/adam_noise.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-03-06T10:15:33,985   copying build/lib/torchref/refinement/optimizers/momentum_sa.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-03-06T10:15:33,987   copying build/lib/torchref/refinement/optimizers/exploratory_lbfgs.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-03-06T10:15:33,990   copying build/lib/torchref/refinement/optimizers/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-03-06T10:15:33,991   copying build/lib/torchref/refinement/optimizers/langevin_sa.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-03-06T10:15:33,994   copying build/lib/torchref/refinement/optimizers/internal_coord_sa.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-03-06T10:15:33,996   copying build/lib/torchref/config.py -> build/bdist.linux-armv7l/wheel/./torchref
2026-03-06T10:15:33,999   creating build/bdist.linux-armv7l/wheel/torchref/cli
2026-03-06T10:15:34,000   copying build/lib/torchref/cli/refine_everything_static.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-06T10:15:34,003   copying build/lib/torchref/cli/refine_everything_policy.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-06T10:15:34,005   copying build/lib/torchref/cli/mtz2map.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-06T10:15:34,007   copying build/lib/torchref/cli/refine_everything_random_weights.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-06T10:15:34,010   copying build/lib/torchref/cli/phased_difference_map.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-06T10:15:34,012   copying build/lib/torchref/cli/validate_ded.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-06T10:15:34,015   copying build/lib/torchref/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-06T10:15:34,016   copying build/lib/torchref/cli/difference_refine.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-06T10:15:34,019   copying build/lib/torchref/cli/refine.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-06T10:15:34,021   copying build/lib/torchref/cli/refine_everything_hyperparameters.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-06T10:15:34,024   creating build/bdist.linux-armv7l/wheel/torchref/maps
2026-03-06T10:15:34,025   copying build/lib/torchref/maps/map.py -> build/bdist.linux-armv7l/wheel/./torchref/maps
2026-03-06T10:15:34,027   copying build/lib/torchref/maps/difference_map.py -> build/bdist.linux-armv7l/wheel/./torchref/maps
2026-03-06T10:15:34,029   copying build/lib/torchref/maps/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/maps
2026-03-06T10:15:34,031   creating build/bdist.linux-armv7l/wheel/torchref/utils
2026-03-06T10:15:34,032   copying build/lib/torchref/utils/utils.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-06T10:15:34,035   copying build/lib/torchref/utils/hyperparameters.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-06T10:15:34,037   copying build/lib/torchref/utils/serialization.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-06T10:15:34,039   copying build/lib/torchref/utils/device_mixin.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-06T10:15:34,041   copying build/lib/torchref/utils/debug_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-06T10:15:34,043   copying build/lib/torchref/utils/gradnorm.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-06T10:15:34,045   copying build/lib/torchref/utils/stats.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-06T10:15:34,047   copying build/lib/torchref/utils/caching.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-06T10:15:34,049   copying build/lib/torchref/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-06T10:15:34,051   copying build/lib/torchref/utils/pse.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-06T10:15:34,053   copying build/lib/torchref/utils/timing.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-06T10:15:34,056   creating build/bdist.linux-armv7l/wheel/torchref/base
2026-03-06T10:15:34,057   copying build/lib/torchref/base/math_numpy.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-03-06T10:15:34,060   creating build/bdist.linux-armv7l/wheel/torchref/base/fourier
2026-03-06T10:15:34,061   copying build/lib/torchref/base/fourier/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/fourier
2026-03-06T10:15:34,063   copying build/lib/torchref/base/fourier/grid.py -> build/bdist.linux-armv7l/wheel/./torchref/base/fourier
2026-03-06T10:15:34,065   copying build/lib/torchref/base/fourier/fft.py -> build/bdist.linux-armv7l/wheel/./torchref/base/fourier
2026-03-06T10:15:34,068   creating build/bdist.linux-armv7l/wheel/torchref/base/coordinates
2026-03-06T10:15:34,069   copying build/lib/torchref/base/coordinates/periodic_boundary.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates
2026-03-06T10:15:34,070   copying build/lib/torchref/base/coordinates/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates
2026-03-06T10:15:34,072   copying build/lib/torchref/base/coordinates/transforms_torch.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates
2026-03-06T10:15:34,074   copying build/lib/torchref/base/coordinates/transforms_numpy.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates
2026-03-06T10:15:34,076   copying build/lib/torchref/base/french_wilson.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-03-06T10:15:34,079   creating build/bdist.linux-armv7l/wheel/torchref/base/kernels
2026-03-06T10:15:34,080   copying build/lib/torchref/base/kernels/optimized_ops.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-03-06T10:15:34,082   copying build/lib/torchref/base/kernels/cpu_scatter.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-03-06T10:15:34,085   copying build/lib/torchref/base/kernels/jit_kernel_vectorized_add_to_map.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-03-06T10:15:34,088   copying build/lib/torchref/base/kernels/triton_kernel.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-03-06T10:15:34,090   copying build/lib/torchref/base/kernels/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-03-06T10:15:34,092   copying build/lib/torchref/base/kernels/separable_triton_kernel.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-03-06T10:15:34,096   creating build/bdist.linux-armv7l/wheel/torchref/base/electron_density
2026-03-06T10:15:34,096   copying build/lib/torchref/base/electron_density/main.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density
2026-03-06T10:15:34,099   copying build/lib/torchref/base/electron_density/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density
2026-03-06T10:15:34,101   copying build/lib/torchref/base/electron_density/map_building.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density
2026-03-06T10:15:34,103   copying build/lib/torchref/base/electron_density/voxel_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density
2026-03-06T10:15:34,105   copying build/lib/torchref/base/electron_density/solvent_mask.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density
2026-03-06T10:15:34,107   copying build/lib/torchref/base/get_scattering_factor_torch.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-03-06T10:15:34,109   copying build/lib/torchref/base/CCTBX_related.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-03-06T10:15:34,111   copying build/lib/torchref/base/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-03-06T10:15:34,114   creating build/bdist.linux-armv7l/wheel/torchref/base/metrics
2026-03-06T10:15:34,115   copying build/lib/torchref/base/metrics/rfactor.py -> build/bdist.linux-armv7l/wheel/./torchref/base/metrics
2026-03-06T10:15:34,118   copying build/lib/torchref/base/metrics/loss.py -> build/bdist.linux-armv7l/wheel/./torchref/base/metrics
2026-03-06T10:15:34,120   copying build/lib/torchref/base/metrics/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/metrics
2026-03-06T10:15:34,122   copying build/lib/torchref/base/math_torch.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-03-06T10:15:34,125   creating build/bdist.linux-armv7l/wheel/torchref/base/chain_closure
2026-03-06T10:15:34,126   copying build/lib/torchref/base/chain_closure/closure.py -> build/bdist.linux-armv7l/wheel/./torchref/base/chain_closure
2026-03-06T10:15:34,128   copying build/lib/torchref/base/chain_closure/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/chain_closure
2026-03-06T10:15:34,130   copying build/lib/torchref/base/chain_closure/backbone_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/base/chain_closure
2026-03-06T10:15:34,133   creating build/bdist.linux-armv7l/wheel/torchref/base/scattering
2026-03-06T10:15:34,134   copying build/lib/torchref/base/scattering/scattering_table.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering
2026-03-06T10:15:34,136   copying build/lib/torchref/base/scattering/itc92.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering
2026-03-06T10:15:34,138   copying build/lib/torchref/base/scattering/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering
2026-03-06T10:15:34,140   copying build/lib/torchref/base/scattering/anomalous_table.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering
2026-03-06T10:15:34,143   creating build/bdist.linux-armv7l/wheel/torchref/base/direct_summation
2026-03-06T10:15:34,144   copying build/lib/torchref/base/direct_summation/anisotropic.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation
2026-03-06T10:15:34,147   copying build/lib/torchref/base/direct_summation/corrections.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation
2026-03-06T10:15:34,148   copying build/lib/torchref/base/direct_summation/isotropic.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation
2026-03-06T10:15:34,150   copying build/lib/torchref/base/direct_summation/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation
2026-03-06T10:15:34,153   creating build/bdist.linux-armv7l/wheel/torchref/base/reciprocal
2026-03-06T10:15:34,154   copying build/lib/torchref/base/reciprocal/grid_operations.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-03-06T10:15:34,156   copying build/lib/torchref/base/reciprocal/interpolation.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-03-06T10:15:34,158   copying build/lib/torchref/base/reciprocal/basis.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-03-06T10:15:34,160   copying build/lib/torchref/base/reciprocal/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-03-06T10:15:34,162   copying build/lib/torchref/base/reciprocal/hkl.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-03-06T10:15:34,164   copying build/lib/torchref/base/reciprocal/symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-03-06T10:15:34,166   creating build/bdist.linux-armv7l/wheel/torchref/base/alignment
2026-03-06T10:15:34,167   copying build/lib/torchref/base/alignment/superposition.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment
2026-03-06T10:15:34,170   copying build/lib/torchref/base/alignment/normalization.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment
2026-03-06T10:15:34,172   copying build/lib/torchref/base/alignment/rotation.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment
2026-03-06T10:15:34,174   copying build/lib/torchref/base/alignment/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment
2026-03-06T10:15:34,176   copying build/lib/torchref/base/alignment/scoring.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment
2026-03-06T10:15:34,178   copying build/lib/torchref/_bootstrap.py -> build/bdist.linux-armv7l/wheel/./torchref
2026-03-06T10:15:34,180   creating build/bdist.linux-armv7l/wheel/torchref/io
2026-03-06T10:15:34,181   creating build/bdist.linux-armv7l/wheel/torchref/io/datasets
2026-03-06T10:15:34,182   copying build/lib/torchref/io/datasets/base.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets
2026-03-06T10:15:34,185   copying build/lib/torchref/io/datasets/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets
2026-03-06T10:15:34,187   copying build/lib/torchref/io/datasets/fcalc_data.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets
2026-03-06T10:15:34,189   copying build/lib/torchref/io/datasets/reflection_data.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets
2026-03-06T10:15:34,193   copying build/lib/torchref/io/datasets/collection.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets
2026-03-06T10:15:34,195   copying build/lib/torchref/io/cif_readers.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-03-06T10:15:34,198   copying build/lib/torchref/io/mtz.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-03-06T10:15:34,201   copying build/lib/torchref/io/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-03-06T10:15:34,203   copying build/lib/torchref/io/cif.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-03-06T10:15:34,205   copying build/lib/torchref/io/pdb.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-03-06T10:15:34,207   copying build/lib/torchref/io/data_router.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-03-06T10:15:34,210   copying build/lib/torchref/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref
2026-03-06T10:15:34,212   creating build/bdist.linux-armv7l/wheel/torchref/scaling
2026-03-06T10:15:34,213   copying build/lib/torchref/scaling/scaler.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling
2026-03-06T10:15:34,216   copying build/lib/torchref/scaling/solvent.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling
2026-03-06T10:15:34,218   copying build/lib/torchref/scaling/scaler_base.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling
2026-03-06T10:15:34,221   copying build/lib/torchref/scaling/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling
2026-03-06T10:15:34,223   creating build/bdist.linux-armv7l/wheel/torchref/restraints
2026-03-06T10:15:34,224   copying build/lib/torchref/restraints/restraints.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-03-06T10:15:34,227   copying build/lib/torchref/restraints/builders_numba.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-03-06T10:15:34,230   copying build/lib/torchref/restraints/ramachandran.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-03-06T10:15:34,232   copying build/lib/torchref/restraints/builders_fast.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-03-06T10:15:34,235   copying build/lib/torchref/restraints/library.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-03-06T10:15:34,237   copying build/lib/torchref/restraints/builders.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-03-06T10:15:34,241   copying build/lib/torchref/restraints/restraints_helper.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-03-06T10:15:34,245   copying build/lib/torchref/restraints/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-03-06T10:15:34,248   creating build/bdist.linux-armv7l/wheel/torchref/symmetry
2026-03-06T10:15:34,249   copying build/lib/torchref/symmetry/grid_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-03-06T10:15:34,252   copying build/lib/torchref/symmetry/spacegroup.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-03-06T10:15:34,256   copying build/lib/torchref/symmetry/map_symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-03-06T10:15:34,258   copying build/lib/torchref/symmetry/cell.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-03-06T10:15:34,261   copying build/lib/torchref/symmetry/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-03-06T10:15:34,264   copying build/lib/torchref/symmetry/map_symmetry_interpolation.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-03-06T10:15:34,267   copying build/lib/torchref/symmetry/symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-03-06T10:15:34,269   copying build/lib/torchref/symmetry/reciprocal_symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-03-06T10:15:34,274   creating build/bdist.linux-armv7l/wheel/torchref/scripts
2026-03-06T10:15:34,275   copying build/lib/torchref/scripts/generate_scattering_table.py -> build/bdist.linux-armv7l/wheel/./torchref/scripts
2026-03-06T10:15:34,278   copying build/lib/torchref/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/scripts
2026-03-06T10:15:34,282   creating build/bdist.linux-armv7l/wheel/torchref/alignment
2026-03-06T10:15:34,283   copying build/lib/torchref/alignment/transform.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-06T10:15:34,287   copying build/lib/torchref/alignment/distributions.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-06T10:15:34,290   copying build/lib/torchref/alignment/jax_subpixel_peaks.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-06T10:15:34,292   copying build/lib/torchref/alignment/translation.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-06T10:15:34,295   copying build/lib/torchref/alignment/rigid_body.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-06T10:15:34,298   copying build/lib/torchref/alignment/clashscore.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-06T10:15:34,301   copying build/lib/torchref/alignment/pipeline.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-06T10:15:34,305   copying build/lib/torchref/alignment/sampling.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-06T10:15:34,308   copying build/lib/torchref/alignment/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-06T10:15:34,311   copying build/lib/torchref/alignment/ball_transform.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-06T10:15:34,315   running install_egg_info
2026-03-06T10:15:34,323   Copying torchref.egg-info to build/bdist.linux-armv7l/wheel/./torchref-0.4.2-py3.11.egg-info
2026-03-06T10:15:34,341   running install_scripts
2026-03-06T10:15:34,352   creating build/bdist.linux-armv7l/wheel/torchref-0.4.2.dist-info/WHEEL
2026-03-06T10:15:34,355   creating '/tmp/pip-wheel-lhl2727u/.tmp-jc0yi9vk/torchref-0.4.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2026-03-06T10:15:34,357   adding 'torchref/__init__.py'
2026-03-06T10:15:34,359   adding 'torchref/_bootstrap.py'
2026-03-06T10:15:34,360   adding 'torchref/config.py'
2026-03-06T10:15:34,363   adding 'torchref/alignment/__init__.py'
2026-03-06T10:15:34,370   adding 'torchref/alignment/ball_transform.py'
2026-03-06T10:15:34,373   adding 'torchref/alignment/clashscore.py'
2026-03-06T10:15:34,374   adding 'torchref/alignment/distributions.py'
2026-03-06T10:15:34,376   adding 'torchref/alignment/jax_subpixel_peaks.py'
2026-03-06T10:15:34,378   adding 'torchref/alignment/pipeline.py'
2026-03-06T10:15:34,381   adding 'torchref/alignment/rigid_body.py'
2026-03-06T10:15:34,383   adding 'torchref/alignment/sampling.py'
2026-03-06T10:15:34,386   adding 'torchref/alignment/transform.py'
2026-03-06T10:15:34,387   adding 'torchref/alignment/translation.py'
2026-03-06T10:15:34,389   adding 'torchref/base/CCTBX_related.py'
2026-03-06T10:15:34,391   adding 'torchref/base/__init__.py'
2026-03-06T10:15:34,395   adding 'torchref/base/french_wilson.py'
2026-03-06T10:15:34,397   adding 'torchref/base/get_scattering_factor_torch.py'
2026-03-06T10:15:34,400   adding 'torchref/base/math_numpy.py'
2026-03-06T10:15:34,402   adding 'torchref/base/math_torch.py'
2026-03-06T10:15:34,404   adding 'torchref/base/alignment/__init__.py'
2026-03-06T10:15:34,406   adding 'torchref/base/alignment/normalization.py'
2026-03-06T10:15:34,408   adding 'torchref/base/alignment/rotation.py'
2026-03-06T10:15:34,409   adding 'torchref/base/alignment/scoring.py'
2026-03-06T10:15:34,411   adding 'torchref/base/alignment/superposition.py'
2026-03-06T10:15:34,413   adding 'torchref/base/chain_closure/__init__.py'
2026-03-06T10:15:34,415   adding 'torchref/base/chain_closure/backbone_utils.py'
2026-03-06T10:15:34,418   adding 'torchref/base/chain_closure/closure.py'
2026-03-06T10:15:34,420   adding 'torchref/base/coordinates/__init__.py'
2026-03-06T10:15:34,421   adding 'torchref/base/coordinates/periodic_boundary.py'
2026-03-06T10:15:34,422   adding 'torchref/base/coordinates/transforms_numpy.py'
2026-03-06T10:15:34,424   adding 'torchref/base/coordinates/transforms_torch.py'
2026-03-06T10:15:34,426   adding 'torchref/base/direct_summation/__init__.py'
2026-03-06T10:15:34,427   adding 'torchref/base/direct_summation/anisotropic.py'
2026-03-06T10:15:34,429   adding 'torchref/base/direct_summation/corrections.py'
2026-03-06T10:15:34,430   adding 'torchref/base/direct_summation/isotropic.py'
2026-03-06T10:15:34,432   adding 'torchref/base/electron_density/__init__.py'
2026-03-06T10:15:34,436   adding 'torchref/base/electron_density/main.py'
2026-03-06T10:15:34,438   adding 'torchref/base/electron_density/map_building.py'
2026-03-06T10:15:34,440   adding 'torchref/base/electron_density/solvent_mask.py'
2026-03-06T10:15:34,441   adding 'torchref/base/electron_density/voxel_utils.py'
2026-03-06T10:15:34,443   adding 'torchref/base/fourier/__init__.py'
2026-03-06T10:15:34,445   adding 'torchref/base/fourier/fft.py'
2026-03-06T10:15:34,446   adding 'torchref/base/fourier/grid.py'
2026-03-06T10:15:34,448   adding 'torchref/base/kernels/__init__.py'
2026-03-06T10:15:34,450   adding 'torchref/base/kernels/cpu_scatter.py'
2026-03-06T10:15:34,452   adding 'torchref/base/kernels/jit_kernel_vectorized_add_to_map.py'
2026-03-06T10:15:34,454   adding 'torchref/base/kernels/optimized_ops.py'
2026-03-06T10:15:34,458   adding 'torchref/base/kernels/separable_triton_kernel.py'
2026-03-06T10:15:34,462   adding 'torchref/base/kernels/triton_kernel.py'
2026-03-06T10:15:34,464   adding 'torchref/base/metrics/__init__.py'
2026-03-06T10:15:34,466   adding 'torchref/base/metrics/loss.py'
2026-03-06T10:15:34,467   adding 'torchref/base/metrics/rfactor.py'
2026-03-06T10:15:34,469   adding 'torchref/base/reciprocal/__init__.py'
2026-03-06T10:15:34,470   adding 'torchref/base/reciprocal/basis.py'
2026-03-06T10:15:34,472   adding 'torchref/base/reciprocal/grid_operations.py'
2026-03-06T10:15:34,473   adding 'torchref/base/reciprocal/hkl.py'
2026-03-06T10:15:34,475   adding 'torchref/base/reciprocal/interpolation.py'
2026-03-06T10:15:34,477   adding 'torchref/base/reciprocal/symmetry.py'
2026-03-06T10:15:34,479   adding 'torchref/base/scattering/__init__.py'
2026-03-06T10:15:34,481   adding 'torchref/base/scattering/anomalous_table.py'
2026-03-06T10:15:34,482   adding 'torchref/base/scattering/itc92.py'
2026-03-06T10:15:34,484   adding 'torchref/base/scattering/scattering_table.py'
2026-03-06T10:15:34,486   adding 'torchref/cli/__init__.py'
2026-03-06T10:15:34,490   adding 'torchref/cli/difference_refine.py'
2026-03-06T10:15:34,492   adding 'torchref/cli/mtz2map.py'
2026-03-06T10:15:34,494   adding 'torchref/cli/phased_difference_map.py'
2026-03-06T10:15:34,495   adding 'torchref/cli/refine.py'
2026-03-06T10:15:34,497   adding 'torchref/cli/refine_everything_hyperparameters.py'
2026-03-06T10:15:34,499   adding 'torchref/cli/refine_everything_policy.py'
2026-03-06T10:15:34,501   adding 'torchref/cli/refine_everything_random_weights.py'
2026-03-06T10:15:34,503   adding 'torchref/cli/refine_everything_static.py'
2026-03-06T10:15:34,506   adding 'torchref/cli/validate_ded.py'
2026-03-06T10:15:34,508   adding 'torchref/data/atomic_vdw_radii.csv'
2026-03-06T10:15:34,510   adding 'torchref/data/default_hyperparameters.json'
2026-03-06T10:15:34,512   adding 'torchref/data/itc92_scattering_factors.pt'
2026-03-06T10:15:34,551   adding 'torchref/data/policy_latest.pt'
2026-03-06T10:15:34,786   adding 'torchref/data/rama_nll_surfaces.pt'
2026-03-06T10:15:34,808   adding 'torchref/data/monomer_library/a/A.cif'
2026-03-06T10:15:34,810   adding 'torchref/data/monomer_library/a/ALA.cif'
2026-03-06T10:15:34,812   adding 'torchref/data/monomer_library/a/ARG.cif'
2026-03-06T10:15:34,813   adding 'torchref/data/monomer_library/a/ASN.cif'
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2026-03-06T10:15:34,819   adding 'torchref/data/monomer_library/c/CYS.cif'
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2026-03-06T10:15:34,831   adding 'torchref/data/monomer_library/g/G.cif'
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2026-03-06T10:15:34,838   adding 'torchref/data/monomer_library/h/HIS.cif'
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2026-03-06T10:15:34,843   adding 'torchref/data/monomer_library/i/ILE.cif'
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2026-03-06T10:15:34,847   adding 'torchref/data/monomer_library/l/LYS.cif'
2026-03-06T10:15:35,385   adding 'torchref/data/monomer_library/list/mon_lib_list.cif'
2026-03-06T10:15:35,412   adding 'torchref/data/monomer_library/m/MET.cif'
2026-03-06T10:15:35,414   adding 'torchref/data/monomer_library/m/MSE.cif'
2026-03-06T10:15:35,416   adding 'torchref/data/monomer_library/p/PHE.cif'
2026-03-06T10:15:35,418   adding 'torchref/data/monomer_library/p/PRO.cif'
2026-03-06T10:15:35,420   adding 'torchref/data/monomer_library/p/PTR.cif'
2026-03-06T10:15:35,422   adding 'torchref/data/monomer_library/s/SEP.cif'
2026-03-06T10:15:35,423   adding 'torchref/data/monomer_library/s/SER.cif'
2026-03-06T10:15:35,425   adding 'torchref/data/monomer_library/t/THR.cif'
2026-03-06T10:15:35,427   adding 'torchref/data/monomer_library/t/TPO.cif'
2026-03-06T10:15:35,428   adding 'torchref/data/monomer_library/t/TRP.cif'
2026-03-06T10:15:35,430   adding 'torchref/data/monomer_library/t/TYR.cif'
2026-03-06T10:15:35,433   adding 'torchref/data/monomer_library/u/U.cif'
2026-03-06T10:15:35,435   adding 'torchref/data/monomer_library/v/VAL.cif'
2026-03-06T10:15:35,437   adding 'torchref/io/__init__.py'
2026-03-06T10:15:35,438   adding 'torchref/io/cif.py'
2026-03-06T10:15:35,447   adding 'torchref/io/cif_readers.py'
2026-03-06T10:15:35,449   adding 'torchref/io/data_router.py'
2026-03-06T10:15:35,451   adding 'torchref/io/mtz.py'
2026-03-06T10:15:35,453   adding 'torchref/io/pdb.py'
2026-03-06T10:15:35,455   adding 'torchref/io/datasets/__init__.py'
2026-03-06T10:15:35,457   adding 'torchref/io/datasets/base.py'
2026-03-06T10:15:35,459   adding 'torchref/io/datasets/collection.py'
2026-03-06T10:15:35,461   adding 'torchref/io/datasets/fcalc_data.py'
2026-03-06T10:15:35,473   adding 'torchref/io/datasets/reflection_data.py'
2026-03-06T10:15:35,476   adding 'torchref/maps/__init__.py'
2026-03-06T10:15:35,477   adding 'torchref/maps/difference_map.py'
2026-03-06T10:15:35,479   adding 'torchref/maps/map.py'
2026-03-06T10:15:35,481   adding 'torchref/model/__init__.py'
2026-03-06T10:15:35,491   adding 'torchref/model/closed_segmented_internal_coordinates.py'
2026-03-06T10:15:35,499   adding 'torchref/model/internal_coordinates.py'
2026-03-06T10:15:35,501   adding 'torchref/model/mixed_model.py'
2026-03-06T10:15:35,514   adding 'torchref/model/model.py'
2026-03-06T10:15:35,520   adding 'torchref/model/model_ft.py'
2026-03-06T10:15:35,530   adding 'torchref/model/parameter_wrappers.py'
2026-03-06T10:15:35,538   adding 'torchref/model/segmented_internal_coordinates.py'
2026-03-06T10:15:35,540   adding 'torchref/model/sf_ds.py'
2026-03-06T10:15:35,543   adding 'torchref/model/sf_fft.py'
2026-03-06T10:15:35,545   adding 'torchref/refinement/__init__.py'
2026-03-06T10:15:35,549   adding 'torchref/refinement/base_refinement.py'
2026-03-06T10:15:35,552   adding 'torchref/refinement/lbfgs_refinement.py'
2026-03-06T10:15:35,554   adding 'torchref/refinement/logger.py'
2026-03-06T10:15:35,557   adding 'torchref/refinement/loss_state.py'
2026-03-06T10:15:35,558   adding 'torchref/refinement/optimizers/__init__.py'
2026-03-06T10:15:35,560   adding 'torchref/refinement/optimizers/adam_noise.py'
2026-03-06T10:15:35,563   adding 'torchref/refinement/optimizers/exploratory_lbfgs.py'
2026-03-06T10:15:35,566   adding 'torchref/refinement/optimizers/internal_coord_sa.py'
2026-03-06T10:15:35,569   adding 'torchref/refinement/optimizers/langevin_sa.py'
2026-03-06T10:15:35,570   adding 'torchref/refinement/optimizers/momentum_sa.py'
2026-03-06T10:15:35,572   adding 'torchref/refinement/optimizers/simulated_annealing.py'
2026-03-06T10:15:35,574   adding 'torchref/refinement/targets/__init__.py'
2026-03-06T10:15:35,579   adding 'torchref/refinement/targets/amber_target.py'
2026-03-06T10:15:35,581   adding 'torchref/refinement/targets/base.py'
2026-03-06T10:15:35,584   adding 'torchref/refinement/targets/combined.py'
2026-03-06T10:15:35,588   adding 'torchref/refinement/targets/difference.py'
2026-03-06T10:15:35,590   adding 'torchref/refinement/targets/forcefield_target.py'
2026-03-06T10:15:35,592   adding 'torchref/refinement/targets/occupancy_floor_diagnostic.py'
2026-03-06T10:15:35,595   adding 'torchref/refinement/targets/realspace.py'
2026-03-06T10:15:35,599   adding 'torchref/refinement/targets/sampled_ml_phase_target.py'
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2026-03-06T10:15:35,602   adding 'torchref/refinement/targets/adp/base.py'
2026-03-06T10:15:35,603   adding 'torchref/refinement/targets/adp/entropy.py'
2026-03-06T10:15:35,605   adding 'torchref/refinement/targets/adp/locality.py'
2026-03-06T10:15:35,607   adding 'torchref/refinement/targets/adp/rigid_bond.py'
2026-03-06T10:15:35,608   adding 'torchref/refinement/targets/adp/similarity.py'
2026-03-06T10:15:35,610   adding 'torchref/refinement/targets/geometry/__init__.py'
2026-03-06T10:15:35,611   adding 'torchref/refinement/targets/geometry/angles.py'
2026-03-06T10:15:35,612   adding 'torchref/refinement/targets/geometry/base.py'
2026-03-06T10:15:35,614   adding 'torchref/refinement/targets/geometry/bonds.py'
2026-03-06T10:15:35,615   adding 'torchref/refinement/targets/geometry/chiral.py'
2026-03-06T10:15:35,617   adding 'torchref/refinement/targets/geometry/non_bonded.py'
2026-03-06T10:15:35,619   adding 'torchref/refinement/targets/geometry/planarity.py'
2026-03-06T10:15:35,620   adding 'torchref/refinement/targets/geometry/ramachandran.py'
2026-03-06T10:15:35,621   adding 'torchref/refinement/targets/geometry/torsions.py'
2026-03-06T10:15:35,623   adding 'torchref/refinement/targets/xray/__init__.py'
2026-03-06T10:15:35,624   adding 'torchref/refinement/targets/xray/base.py'
2026-03-06T10:15:35,626   adding 'torchref/refinement/targets/xray/gaussian.py'
2026-03-06T10:15:35,627   adding 'torchref/refinement/targets/xray/least_squares.py'
2026-03-06T10:15:35,628   adding 'torchref/refinement/targets/xray/maximum_likelihood.py'
2026-03-06T10:15:35,630   adding 'torchref/refinement/weighting/__init__.py'
2026-03-06T10:15:35,631   adding 'torchref/refinement/weighting/base_weighting.py'
2026-03-06T10:15:35,634   adding 'torchref/refinement/weighting/component_weighting.py'
2026-03-06T10:15:35,636   adding 'torchref/refinement/weighting/es_policy_training.py'
2026-03-06T10:15:35,639   adding 'torchref/refinement/weighting/policy_weighting.py'
2026-03-06T10:15:35,642   adding 'torchref/refinement/weighting/random_weighting.py'
2026-03-06T10:15:35,643   adding 'torchref/restraints/__init__.py'
2026-03-06T10:15:35,648   adding 'torchref/restraints/builders.py'
2026-03-06T10:15:35,655   adding 'torchref/restraints/builders_fast.py'
2026-03-06T10:15:35,659   adding 'torchref/restraints/builders_numba.py'
2026-03-06T10:15:35,661   adding 'torchref/restraints/library.py'
2026-03-06T10:15:35,662   adding 'torchref/restraints/ramachandran.py'
2026-03-06T10:15:35,670   adding 'torchref/restraints/restraints.py'
2026-03-06T10:15:35,673   adding 'torchref/restraints/restraints_helper.py'
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2026-03-06T10:15:35,686   adding 'torchref/scripts/__init__.py'
2026-03-06T10:15:35,688   adding 'torchref/scripts/generate_scattering_table.py'
2026-03-06T10:15:35,690   adding 'torchref/symmetry/__init__.py'
2026-03-06T10:15:35,691   adding 'torchref/symmetry/cell.py'
2026-03-06T10:15:35,693   adding 'torchref/symmetry/grid_utils.py'
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2026-03-06T10:15:35,703   adding 'torchref/symmetry/reciprocal_symmetry.py'
2026-03-06T10:15:35,707   adding 'torchref/symmetry/spacegroup.py'
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2026-03-06T10:15:35,938   Building wheel for torchref (pyproject.toml): finished with status 'done'
2026-03-06T10:15:36,026   Created wheel for torchref: filename=torchref-0.4.2-py3-none-any.whl size=3051438 sha256=c4c77a7e34aad8245da2d04a76477bdf30f94ca67cd531f721e4bf47ee67114a
2026-03-06T10:15:36,027   Stored in directory: /tmp/pip-ephem-wheel-cache-kz5jfo8f/wheels/37/62/a4/a21115cd75dca258cc07249ee95f4b9c1080685aaabd2d40b9
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2026-03-06T10:15:36,163 Removed build tracker: '/tmp/pip-build-tracker-pgx5i65x'