2026-03-03T23:15:39,985 Created temporary directory: /tmp/pip-ephem-wheel-cache-kkdl8owt
2026-03-03T23:15:39,987 Created temporary directory: /tmp/pip-build-tracker-m1kgrtg1
2026-03-03T23:15:39,988 Initialized build tracking at /tmp/pip-build-tracker-m1kgrtg1
2026-03-03T23:15:39,988 Created build tracker: /tmp/pip-build-tracker-m1kgrtg1
2026-03-03T23:15:39,989 Entered build tracker: /tmp/pip-build-tracker-m1kgrtg1
2026-03-03T23:15:39,989 Created temporary directory: /tmp/pip-wheel-ichynuf5
2026-03-03T23:15:39,992 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
2026-03-03T23:15:39,995 Created temporary directory: /tmp/pip-ephem-wheel-cache-v28ofeh5
2026-03-03T23:15:40,017 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-03-03T23:15:40,020 2 location(s) to search for versions of torchref:
2026-03-03T23:15:40,020 * https://pypi.org/simple/torchref/
2026-03-03T23:15:40,020 * https://www.piwheels.org/simple/torchref/
2026-03-03T23:15:40,021 Fetching project page and analyzing links: https://pypi.org/simple/torchref/
2026-03-03T23:15:40,022 Getting page https://pypi.org/simple/torchref/
2026-03-03T23:15:40,023 Found index url https://pypi.org/simple
2026-03-03T23:15:40,246 Fetched page https://pypi.org/simple/torchref/ as application/vnd.pypi.simple.v1+json
2026-03-03T23:15:40,249   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)
2026-03-03T23:15:40,250   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
2026-03-03T23:15:40,250   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)
2026-03-03T23:15:40,251   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
2026-03-03T23:15:40,252   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)
2026-03-03T23:15:40,253   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
2026-03-03T23:15:40,254   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)
2026-03-03T23:15:40,254   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
2026-03-03T23:15:40,255 Fetching project page and analyzing links: https://www.piwheels.org/simple/torchref/
2026-03-03T23:15:40,256 Getting page https://www.piwheels.org/simple/torchref/
2026-03-03T23:15:40,257 Found index url https://www.piwheels.org/simple
2026-03-03T23:15:40,422 Fetched page https://www.piwheels.org/simple/torchref/ as text/html
2026-03-03T23:15:40,424   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)
2026-03-03T23:15:40,425   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)
2026-03-03T23:15:40,425   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)
2026-03-03T23:15:40,426 Skipping link: not a file: https://www.piwheels.org/simple/torchref/
2026-03-03T23:15:40,426 Skipping link: not a file: https://pypi.org/simple/torchref/
2026-03-03T23:15:40,445 Given no hashes to check 1 links for project 'torchref': discarding no candidates
2026-03-03T23:15:40,463 Collecting torchref==0.4.1
2026-03-03T23:15:40,466   Created temporary directory: /tmp/pip-unpack-bu09nde9
2026-03-03T23:15:40,692   Downloading torchref-0.4.1.tar.gz (2.9 MB)
2026-03-03T23:15:42,017   Added torchref==0.4.1 from https://files.pythonhosted.org/packages/16/bd/cfbdc266a4fe7c8868b100eda000f82419609e89158bda8524efa51748be/torchref-0.4.1.tar.gz to build tracker '/tmp/pip-build-tracker-m1kgrtg1'
2026-03-03T23:15:42,023   Created temporary directory: /tmp/pip-build-env-j6hbjof0
2026-03-03T23:15:42,027   Installing build dependencies: started
2026-03-03T23:15:42,028   Running command pip subprocess to install build dependencies
2026-03-03T23:15:43,176   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2026-03-03T23:15:43,741   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
2026-03-03T23:15:43,764   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-03-03T23:15:45,543   Collecting setuptools>=42
2026-03-03T23:15:45,618     Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.0-py3-none-any.whl (1.0 MB)
2026-03-03T23:15:45,889   Collecting wheel
2026-03-03T23:15:45,905     Using cached https://www.piwheels.org/simple/wheel/wheel-0.46.3-py3-none-any.whl (30 kB)
2026-03-03T23:15:46,089   Collecting packaging>=24.0
2026-03-03T23:15:46,111     Using cached https://www.piwheels.org/simple/packaging/packaging-26.0-py3-none-any.whl (74 kB)
2026-03-03T23:15:49,063   Installing collected packages: setuptools, packaging, wheel
2026-03-03T23:15:52,628     Creating /tmp/pip-build-env-j6hbjof0/overlay/local/bin
2026-03-03T23:15:52,630     changing mode of /tmp/pip-build-env-j6hbjof0/overlay/local/bin/wheel to 755
2026-03-03T23:15:52,650   Successfully installed packaging-26.0 setuptools-82.0.0 wheel-0.46.3
2026-03-03T23:15:52,938   Installing build dependencies: finished with status 'done'
2026-03-03T23:15:52,944   Getting requirements to build wheel: started
2026-03-03T23:15:52,945   Running command Getting requirements to build wheel
2026-03-03T23:15:53,669   running egg_info
2026-03-03T23:15:53,675   writing torchref.egg-info/PKG-INFO
2026-03-03T23:15:53,683   writing dependency_links to torchref.egg-info/dependency_links.txt
2026-03-03T23:15:53,685   writing entry points to torchref.egg-info/entry_points.txt
2026-03-03T23:15:53,690   writing requirements to torchref.egg-info/requires.txt
2026-03-03T23:15:53,691   writing top-level names to torchref.egg-info/top_level.txt
2026-03-03T23:15:53,770   reading manifest file 'torchref.egg-info/SOURCES.txt'
2026-03-03T23:15:53,783   adding license file 'LICENSE'
2026-03-03T23:15:53,795   writing manifest file 'torchref.egg-info/SOURCES.txt'
2026-03-03T23:15:53,898   Getting requirements to build wheel: finished with status 'done'
2026-03-03T23:15:53,901   Created temporary directory: /tmp/pip-modern-metadata-_bwz0lky
2026-03-03T23:15:53,903   Preparing metadata (pyproject.toml): started
2026-03-03T23:15:53,904   Running command Preparing metadata (pyproject.toml)
2026-03-03T23:15:54,564   running dist_info
2026-03-03T23:15:54,574   creating /tmp/pip-modern-metadata-_bwz0lky/torchref.egg-info
2026-03-03T23:15:54,575   writing /tmp/pip-modern-metadata-_bwz0lky/torchref.egg-info/PKG-INFO
2026-03-03T23:15:54,583   writing dependency_links to /tmp/pip-modern-metadata-_bwz0lky/torchref.egg-info/dependency_links.txt
2026-03-03T23:15:54,585   writing entry points to /tmp/pip-modern-metadata-_bwz0lky/torchref.egg-info/entry_points.txt
2026-03-03T23:15:54,589   writing requirements to /tmp/pip-modern-metadata-_bwz0lky/torchref.egg-info/requires.txt
2026-03-03T23:15:54,590   writing top-level names to /tmp/pip-modern-metadata-_bwz0lky/torchref.egg-info/top_level.txt
2026-03-03T23:15:54,591   writing manifest file '/tmp/pip-modern-metadata-_bwz0lky/torchref.egg-info/SOURCES.txt'
2026-03-03T23:15:54,657   reading manifest file '/tmp/pip-modern-metadata-_bwz0lky/torchref.egg-info/SOURCES.txt'
2026-03-03T23:15:54,659   adding license file 'LICENSE'
2026-03-03T23:15:54,668   writing manifest file '/tmp/pip-modern-metadata-_bwz0lky/torchref.egg-info/SOURCES.txt'
2026-03-03T23:15:54,669   creating '/tmp/pip-modern-metadata-_bwz0lky/torchref-0.4.1.dist-info'
2026-03-03T23:15:54,796   Preparing metadata (pyproject.toml): finished with status 'done'
2026-03-03T23:15:54,800   Source in /tmp/pip-wheel-ichynuf5/torchref_3c7329fe726c4194b23466042b6a7e1d has version 0.4.1, which satisfies requirement torchref==0.4.1 from https://files.pythonhosted.org/packages/16/bd/cfbdc266a4fe7c8868b100eda000f82419609e89158bda8524efa51748be/torchref-0.4.1.tar.gz
2026-03-03T23:15:54,801   Removed torchref==0.4.1 from https://files.pythonhosted.org/packages/16/bd/cfbdc266a4fe7c8868b100eda000f82419609e89158bda8524efa51748be/torchref-0.4.1.tar.gz from build tracker '/tmp/pip-build-tracker-m1kgrtg1'
2026-03-03T23:15:54,807 Created temporary directory: /tmp/pip-unpack-svojosiv
2026-03-03T23:15:54,808 Building wheels for collected packages: torchref
2026-03-03T23:15:54,812   Created temporary directory: /tmp/pip-wheel-g5sidcas
2026-03-03T23:15:54,813   Destination directory: /tmp/pip-wheel-g5sidcas
2026-03-03T23:15:54,815   Building wheel for torchref (pyproject.toml): started
2026-03-03T23:15:54,816   Running command Building wheel for torchref (pyproject.toml)
2026-03-03T23:15:55,453   running bdist_wheel
2026-03-03T23:15:55,471   running build
2026-03-03T23:15:55,471   running build_py
2026-03-03T23:15:55,477   creating build/lib/torchref
2026-03-03T23:15:55,479   copying torchref/config.py -> build/lib/torchref
2026-03-03T23:15:55,481   copying torchref/_bootstrap.py -> build/lib/torchref
2026-03-03T23:15:55,483   copying torchref/__init__.py -> build/lib/torchref
2026-03-03T23:15:55,486   creating build/lib/torchref/symmetry
2026-03-03T23:15:55,487   copying torchref/symmetry/cell.py -> build/lib/torchref/symmetry
2026-03-03T23:15:55,489   copying torchref/symmetry/spacegroup.py -> build/lib/torchref/symmetry
2026-03-03T23:15:55,492   copying torchref/symmetry/map_symmetry_interpolation.py -> build/lib/torchref/symmetry
2026-03-03T23:15:55,494   copying torchref/symmetry/reciprocal_symmetry.py -> build/lib/torchref/symmetry
2026-03-03T23:15:55,497   copying torchref/symmetry/map_symmetry.py -> build/lib/torchref/symmetry
2026-03-03T23:15:55,499   copying torchref/symmetry/grid_utils.py -> build/lib/torchref/symmetry
2026-03-03T23:15:55,502   copying torchref/symmetry/__init__.py -> build/lib/torchref/symmetry
2026-03-03T23:15:55,504   copying torchref/symmetry/symmetry.py -> build/lib/torchref/symmetry
2026-03-03T23:15:55,506   creating build/lib/torchref/cli
2026-03-03T23:15:55,507   copying torchref/cli/refine_everything_policy.py -> build/lib/torchref/cli
2026-03-03T23:15:55,510   copying torchref/cli/refine_everything_static.py -> build/lib/torchref/cli
2026-03-03T23:15:55,512   copying torchref/cli/refine_everything_hyperparameters.py -> build/lib/torchref/cli
2026-03-03T23:15:55,514   copying torchref/cli/difference_refine.py -> build/lib/torchref/cli
2026-03-03T23:15:55,517   copying torchref/cli/validate_ded.py -> build/lib/torchref/cli
2026-03-03T23:15:55,520   copying torchref/cli/phased_difference_map.py -> build/lib/torchref/cli
2026-03-03T23:15:55,522   copying torchref/cli/refine_everything_random_weights.py -> build/lib/torchref/cli
2026-03-03T23:15:55,524   copying torchref/cli/mtz2map.py -> build/lib/torchref/cli
2026-03-03T23:15:55,526   copying torchref/cli/refine.py -> build/lib/torchref/cli
2026-03-03T23:15:55,529   copying torchref/cli/__init__.py -> build/lib/torchref/cli
2026-03-03T23:15:55,531   creating build/lib/torchref/scripts
2026-03-03T23:15:55,532   copying torchref/scripts/generate_scattering_table.py -> build/lib/torchref/scripts
2026-03-03T23:15:55,534   copying torchref/scripts/__init__.py -> build/lib/torchref/scripts
2026-03-03T23:15:55,537   creating build/lib/torchref/utils
2026-03-03T23:15:55,538   copying torchref/utils/caching.py -> build/lib/torchref/utils
2026-03-03T23:15:55,541   copying torchref/utils/gradnorm.py -> build/lib/torchref/utils
2026-03-03T23:15:55,543   copying torchref/utils/debug_utils.py -> build/lib/torchref/utils
2026-03-03T23:15:55,546   copying torchref/utils/serialization.py -> build/lib/torchref/utils
2026-03-03T23:15:55,548   copying torchref/utils/pse.py -> build/lib/torchref/utils
2026-03-03T23:15:55,550   copying torchref/utils/utils.py -> build/lib/torchref/utils
2026-03-03T23:15:55,553   copying torchref/utils/stats.py -> build/lib/torchref/utils
2026-03-03T23:15:55,555   copying torchref/utils/hyperparameters.py -> build/lib/torchref/utils
2026-03-03T23:15:55,558   copying torchref/utils/timing.py -> build/lib/torchref/utils
2026-03-03T23:15:55,560   copying torchref/utils/device_mixin.py -> build/lib/torchref/utils
2026-03-03T23:15:55,562   copying torchref/utils/__init__.py -> build/lib/torchref/utils
2026-03-03T23:15:55,564   creating build/lib/torchref/base
2026-03-03T23:15:55,565   copying torchref/base/math_numpy.py -> build/lib/torchref/base
2026-03-03T23:15:55,568   copying torchref/base/CCTBX_related.py -> build/lib/torchref/base
2026-03-03T23:15:55,570   copying torchref/base/get_scattering_factor_torch.py -> build/lib/torchref/base
2026-03-03T23:15:55,572   copying torchref/base/french_wilson.py -> build/lib/torchref/base
2026-03-03T23:15:55,575   copying torchref/base/math_torch.py -> build/lib/torchref/base
2026-03-03T23:15:55,578   copying torchref/base/__init__.py -> build/lib/torchref/base
2026-03-03T23:15:55,581   creating build/lib/torchref/restraints
2026-03-03T23:15:55,582   copying torchref/restraints/builders_fast.py -> build/lib/torchref/restraints
2026-03-03T23:15:55,585   copying torchref/restraints/library.py -> build/lib/torchref/restraints
2026-03-03T23:15:55,588   copying torchref/restraints/restraints_helper.py -> build/lib/torchref/restraints
2026-03-03T23:15:55,591   copying torchref/restraints/ramachandran.py -> build/lib/torchref/restraints
2026-03-03T23:15:55,593   copying torchref/restraints/restraints.py -> build/lib/torchref/restraints
2026-03-03T23:15:55,597   copying torchref/restraints/builders_numba.py -> build/lib/torchref/restraints
2026-03-03T23:15:55,600   copying torchref/restraints/builders.py -> build/lib/torchref/restraints
2026-03-03T23:15:55,603   copying torchref/restraints/__init__.py -> build/lib/torchref/restraints
2026-03-03T23:15:55,606   creating build/lib/torchref/scaling
2026-03-03T23:15:55,607   copying torchref/scaling/scaler_base.py -> build/lib/torchref/scaling
2026-03-03T23:15:55,610   copying torchref/scaling/solvent.py -> build/lib/torchref/scaling
2026-03-03T23:15:55,613   copying torchref/scaling/__init__.py -> build/lib/torchref/scaling
2026-03-03T23:15:55,616   copying torchref/scaling/scaler.py -> build/lib/torchref/scaling
2026-03-03T23:15:55,619   creating build/lib/torchref/refinement
2026-03-03T23:15:55,620   copying torchref/refinement/logger.py -> build/lib/torchref/refinement
2026-03-03T23:15:55,623   copying torchref/refinement/lbfgs_refinement.py -> build/lib/torchref/refinement
2026-03-03T23:15:55,626   copying torchref/refinement/base_refinement.py -> build/lib/torchref/refinement
2026-03-03T23:15:55,629   copying torchref/refinement/loss_state.py -> build/lib/torchref/refinement
2026-03-03T23:15:55,632   copying torchref/refinement/__init__.py -> build/lib/torchref/refinement
2026-03-03T23:15:55,635   creating build/lib/torchref/model
2026-03-03T23:15:55,636   copying torchref/model/closed_segmented_internal_coordinates.py -> build/lib/torchref/model
2026-03-03T23:15:55,641   copying torchref/model/sf_fft.py -> build/lib/torchref/model
2026-03-03T23:15:55,643   copying torchref/model/sf_ds.py -> build/lib/torchref/model
2026-03-03T23:15:55,646   copying torchref/model/internal_coordinates.py -> build/lib/torchref/model
2026-03-03T23:15:55,650   copying torchref/model/segmented_internal_coordinates.py -> build/lib/torchref/model
2026-03-03T23:15:55,654   copying torchref/model/parameter_wrappers.py -> build/lib/torchref/model
2026-03-03T23:15:55,659   copying torchref/model/mixed_model.py -> build/lib/torchref/model
2026-03-03T23:15:55,661   copying torchref/model/model.py -> build/lib/torchref/model
2026-03-03T23:15:55,666   copying torchref/model/model_ft.py -> build/lib/torchref/model
2026-03-03T23:15:55,670   copying torchref/model/__init__.py -> build/lib/torchref/model
2026-03-03T23:15:55,673   creating build/lib/torchref/maps
2026-03-03T23:15:55,674   copying torchref/maps/map.py -> build/lib/torchref/maps
2026-03-03T23:15:55,677   copying torchref/maps/difference_map.py -> build/lib/torchref/maps
2026-03-03T23:15:55,679   copying torchref/maps/__init__.py -> build/lib/torchref/maps
2026-03-03T23:15:55,682   creating build/lib/torchref/alignment
2026-03-03T23:15:55,683   copying torchref/alignment/rigid_body.py -> build/lib/torchref/alignment
2026-03-03T23:15:55,686   copying torchref/alignment/sampling.py -> build/lib/torchref/alignment
2026-03-03T23:15:55,688   copying torchref/alignment/transform.py -> build/lib/torchref/alignment
2026-03-03T23:15:55,691   copying torchref/alignment/translation.py -> build/lib/torchref/alignment
2026-03-03T23:15:55,694   copying torchref/alignment/pipeline.py -> build/lib/torchref/alignment
2026-03-03T23:15:55,697   copying torchref/alignment/ball_transform.py -> build/lib/torchref/alignment
2026-03-03T23:15:55,701   copying torchref/alignment/clashscore.py -> build/lib/torchref/alignment
2026-03-03T23:15:55,704   copying torchref/alignment/__init__.py -> build/lib/torchref/alignment
2026-03-03T23:15:55,706   copying torchref/alignment/distributions.py -> build/lib/torchref/alignment
2026-03-03T23:15:55,709   copying torchref/alignment/jax_subpixel_peaks.py -> build/lib/torchref/alignment
2026-03-03T23:15:55,712   creating build/lib/torchref/io
2026-03-03T23:15:55,713   copying torchref/io/data_router.py -> build/lib/torchref/io
2026-03-03T23:15:55,716   copying torchref/io/cif_readers.py -> build/lib/torchref/io
2026-03-03T23:15:55,720   copying torchref/io/mtz.py -> build/lib/torchref/io
2026-03-03T23:15:55,723   copying torchref/io/__init__.py -> build/lib/torchref/io
2026-03-03T23:15:55,725   copying torchref/io/pdb.py -> build/lib/torchref/io
2026-03-03T23:15:55,728   copying torchref/io/cif.py -> build/lib/torchref/io
2026-03-03T23:15:55,731   creating build/lib/torchref/base/direct_summation
2026-03-03T23:15:55,732   copying torchref/base/direct_summation/isotropic.py -> build/lib/torchref/base/direct_summation
2026-03-03T23:15:55,735   copying torchref/base/direct_summation/corrections.py -> build/lib/torchref/base/direct_summation
2026-03-03T23:15:55,737   copying torchref/base/direct_summation/anisotropic.py -> build/lib/torchref/base/direct_summation
2026-03-03T23:15:55,740   copying torchref/base/direct_summation/__init__.py -> build/lib/torchref/base/direct_summation
2026-03-03T23:15:55,743   creating build/lib/torchref/base/metrics
2026-03-03T23:15:55,744   copying torchref/base/metrics/loss.py -> build/lib/torchref/base/metrics
2026-03-03T23:15:55,747   copying torchref/base/metrics/__init__.py -> build/lib/torchref/base/metrics
2026-03-03T23:15:55,749   copying torchref/base/metrics/rfactor.py -> build/lib/torchref/base/metrics
2026-03-03T23:15:55,752   creating build/lib/torchref/base/fourier
2026-03-03T23:15:55,753   copying torchref/base/fourier/fft.py -> build/lib/torchref/base/fourier
2026-03-03T23:15:55,756   copying torchref/base/fourier/grid.py -> build/lib/torchref/base/fourier
2026-03-03T23:15:55,758   copying torchref/base/fourier/__init__.py -> build/lib/torchref/base/fourier
2026-03-03T23:15:55,761   creating build/lib/torchref/base/chain_closure
2026-03-03T23:15:55,762   copying torchref/base/chain_closure/backbone_utils.py -> build/lib/torchref/base/chain_closure
2026-03-03T23:15:55,765   copying torchref/base/chain_closure/closure.py -> build/lib/torchref/base/chain_closure
2026-03-03T23:15:55,768   copying torchref/base/chain_closure/__init__.py -> build/lib/torchref/base/chain_closure
2026-03-03T23:15:55,770   creating build/lib/torchref/base/scattering
2026-03-03T23:15:55,772   copying torchref/base/scattering/anomalous_table.py -> build/lib/torchref/base/scattering
2026-03-03T23:15:55,774   copying torchref/base/scattering/itc92.py -> build/lib/torchref/base/scattering
2026-03-03T23:15:55,777   copying torchref/base/scattering/scattering_table.py -> build/lib/torchref/base/scattering
2026-03-03T23:15:55,779   copying torchref/base/scattering/__init__.py -> build/lib/torchref/base/scattering
2026-03-03T23:15:55,782   creating build/lib/torchref/base/coordinates
2026-03-03T23:15:55,783   copying torchref/base/coordinates/periodic_boundary.py -> build/lib/torchref/base/coordinates
2026-03-03T23:15:55,786   copying torchref/base/coordinates/transforms_torch.py -> build/lib/torchref/base/coordinates
2026-03-03T23:15:55,788   copying torchref/base/coordinates/transforms_numpy.py -> build/lib/torchref/base/coordinates
2026-03-03T23:15:55,790   copying torchref/base/coordinates/__init__.py -> build/lib/torchref/base/coordinates
2026-03-03T23:15:55,793   creating build/lib/torchref/base/alignment
2026-03-03T23:15:55,794   copying torchref/base/alignment/superposition.py -> build/lib/torchref/base/alignment
2026-03-03T23:15:55,797   copying torchref/base/alignment/normalization.py -> build/lib/torchref/base/alignment
2026-03-03T23:15:55,800   copying torchref/base/alignment/rotation.py -> build/lib/torchref/base/alignment
2026-03-03T23:15:55,802   copying torchref/base/alignment/__init__.py -> build/lib/torchref/base/alignment
2026-03-03T23:15:55,804   copying torchref/base/alignment/scoring.py -> build/lib/torchref/base/alignment
2026-03-03T23:15:55,807   creating build/lib/torchref/base/electron_density
2026-03-03T23:15:55,808   copying torchref/base/electron_density/map_building.py -> build/lib/torchref/base/electron_density
2026-03-03T23:15:55,811   copying torchref/base/electron_density/solvent_mask.py -> build/lib/torchref/base/electron_density
2026-03-03T23:15:55,813   copying torchref/base/electron_density/main.py -> build/lib/torchref/base/electron_density
2026-03-03T23:15:55,816   copying torchref/base/electron_density/__init__.py -> build/lib/torchref/base/electron_density
2026-03-03T23:15:55,818   copying torchref/base/electron_density/voxel_utils.py -> build/lib/torchref/base/electron_density
2026-03-03T23:15:55,821   creating build/lib/torchref/base/kernels
2026-03-03T23:15:55,822   copying torchref/base/kernels/cpu_scatter.py -> build/lib/torchref/base/kernels
2026-03-03T23:15:55,824   copying torchref/base/kernels/jit_kernel_vectorized_add_to_map.py -> build/lib/torchref/base/kernels
2026-03-03T23:15:55,827   copying torchref/base/kernels/optimized_ops.py -> build/lib/torchref/base/kernels
2026-03-03T23:15:55,829   copying torchref/base/kernels/triton_kernel.py -> build/lib/torchref/base/kernels
2026-03-03T23:15:55,832   copying torchref/base/kernels/separable_triton_kernel.py -> build/lib/torchref/base/kernels
2026-03-03T23:15:55,834   copying torchref/base/kernels/__init__.py -> build/lib/torchref/base/kernels
2026-03-03T23:15:55,837   creating build/lib/torchref/base/reciprocal
2026-03-03T23:15:55,838   copying torchref/base/reciprocal/basis.py -> build/lib/torchref/base/reciprocal
2026-03-03T23:15:55,840   copying torchref/base/reciprocal/interpolation.py -> build/lib/torchref/base/reciprocal
2026-03-03T23:15:55,843   copying torchref/base/reciprocal/hkl.py -> build/lib/torchref/base/reciprocal
2026-03-03T23:15:55,844   copying torchref/base/reciprocal/grid_operations.py -> build/lib/torchref/base/reciprocal
2026-03-03T23:15:55,846   copying torchref/base/reciprocal/__init__.py -> build/lib/torchref/base/reciprocal
2026-03-03T23:15:55,848   copying torchref/base/reciprocal/symmetry.py -> build/lib/torchref/base/reciprocal
2026-03-03T23:15:55,851   creating build/lib/torchref/refinement/optimizers
2026-03-03T23:15:55,852   copying torchref/refinement/optimizers/adam_noise.py -> build/lib/torchref/refinement/optimizers
2026-03-03T23:15:55,854   copying torchref/refinement/optimizers/internal_coord_sa.py -> build/lib/torchref/refinement/optimizers
2026-03-03T23:15:55,857   copying torchref/refinement/optimizers/momentum_sa.py -> build/lib/torchref/refinement/optimizers
2026-03-03T23:15:55,858   copying torchref/refinement/optimizers/simulated_annealing.py -> build/lib/torchref/refinement/optimizers
2026-03-03T23:15:55,861   copying torchref/refinement/optimizers/exploratory_lbfgs.py -> build/lib/torchref/refinement/optimizers
2026-03-03T23:15:55,863   copying torchref/refinement/optimizers/langevin_sa.py -> build/lib/torchref/refinement/optimizers
2026-03-03T23:15:55,866   copying torchref/refinement/optimizers/__init__.py -> build/lib/torchref/refinement/optimizers
2026-03-03T23:15:55,868   creating build/lib/torchref/refinement/targets
2026-03-03T23:15:55,869   copying torchref/refinement/targets/realspace.py -> build/lib/torchref/refinement/targets
2026-03-03T23:15:55,872   copying torchref/refinement/targets/forcefield_target.py -> build/lib/torchref/refinement/targets
2026-03-03T23:15:55,874   copying torchref/refinement/targets/difference.py -> build/lib/torchref/refinement/targets
2026-03-03T23:15:55,877   copying torchref/refinement/targets/amber_target.py -> build/lib/torchref/refinement/targets
2026-03-03T23:15:55,880   copying torchref/refinement/targets/sampled_ml_phase_target.py -> build/lib/torchref/refinement/targets
2026-03-03T23:15:55,883   copying torchref/refinement/targets/combined.py -> build/lib/torchref/refinement/targets
2026-03-03T23:15:55,885   copying torchref/refinement/targets/occupancy_floor_diagnostic.py -> build/lib/torchref/refinement/targets
2026-03-03T23:15:55,888   copying torchref/refinement/targets/base.py -> build/lib/torchref/refinement/targets
2026-03-03T23:15:55,890   copying torchref/refinement/targets/__init__.py -> build/lib/torchref/refinement/targets
2026-03-03T23:15:55,892   creating build/lib/torchref/refinement/weighting
2026-03-03T23:15:55,893   copying torchref/refinement/weighting/component_weighting.py -> build/lib/torchref/refinement/weighting
2026-03-03T23:15:55,896   copying torchref/refinement/weighting/random_weighting.py -> build/lib/torchref/refinement/weighting
2026-03-03T23:15:55,898   copying torchref/refinement/weighting/base_weighting.py -> build/lib/torchref/refinement/weighting
2026-03-03T23:15:55,900   copying torchref/refinement/weighting/es_policy_training.py -> build/lib/torchref/refinement/weighting
2026-03-03T23:15:55,902   copying torchref/refinement/weighting/policy_weighting.py -> build/lib/torchref/refinement/weighting
2026-03-03T23:15:55,905   copying torchref/refinement/weighting/__init__.py -> build/lib/torchref/refinement/weighting
2026-03-03T23:15:55,907   creating build/lib/torchref/refinement/targets/xray
2026-03-03T23:15:55,908   copying torchref/refinement/targets/xray/maximum_likelihood.py -> build/lib/torchref/refinement/targets/xray
2026-03-03T23:15:55,911   copying torchref/refinement/targets/xray/base.py -> build/lib/torchref/refinement/targets/xray
2026-03-03T23:15:55,913   copying torchref/refinement/targets/xray/gaussian.py -> build/lib/torchref/refinement/targets/xray
2026-03-03T23:15:55,915   copying torchref/refinement/targets/xray/least_squares.py -> build/lib/torchref/refinement/targets/xray
2026-03-03T23:15:55,916   copying torchref/refinement/targets/xray/__init__.py -> build/lib/torchref/refinement/targets/xray
2026-03-03T23:15:55,918   creating build/lib/torchref/refinement/targets/adp
2026-03-03T23:15:55,919   copying torchref/refinement/targets/adp/locality.py -> build/lib/torchref/refinement/targets/adp
2026-03-03T23:15:55,922   copying torchref/refinement/targets/adp/similarity.py -> build/lib/torchref/refinement/targets/adp
2026-03-03T23:15:55,923   copying torchref/refinement/targets/adp/rigid_bond.py -> build/lib/torchref/refinement/targets/adp
2026-03-03T23:15:55,926   copying torchref/refinement/targets/adp/base.py -> build/lib/torchref/refinement/targets/adp
2026-03-03T23:15:55,927   copying torchref/refinement/targets/adp/entropy.py -> build/lib/torchref/refinement/targets/adp
2026-03-03T23:15:55,929   copying torchref/refinement/targets/adp/__init__.py -> build/lib/torchref/refinement/targets/adp
2026-03-03T23:15:55,931   creating build/lib/torchref/refinement/targets/geometry
2026-03-03T23:15:55,932   copying torchref/refinement/targets/geometry/planarity.py -> build/lib/torchref/refinement/targets/geometry
2026-03-03T23:15:55,935   copying torchref/refinement/targets/geometry/torsions.py -> build/lib/torchref/refinement/targets/geometry
2026-03-03T23:15:55,937   copying torchref/refinement/targets/geometry/bonds.py -> build/lib/torchref/refinement/targets/geometry
2026-03-03T23:15:55,939   copying torchref/refinement/targets/geometry/ramachandran.py -> build/lib/torchref/refinement/targets/geometry
2026-03-03T23:15:55,940   copying torchref/refinement/targets/geometry/base.py -> build/lib/torchref/refinement/targets/geometry
2026-03-03T23:15:55,942   copying torchref/refinement/targets/geometry/angles.py -> build/lib/torchref/refinement/targets/geometry
2026-03-03T23:15:55,944   copying torchref/refinement/targets/geometry/chiral.py -> build/lib/torchref/refinement/targets/geometry
2026-03-03T23:15:55,946   copying torchref/refinement/targets/geometry/__init__.py -> build/lib/torchref/refinement/targets/geometry
2026-03-03T23:15:55,948   copying torchref/refinement/targets/geometry/non_bonded.py -> build/lib/torchref/refinement/targets/geometry
2026-03-03T23:15:55,956   creating build/lib/torchref/io/datasets
2026-03-03T23:15:55,957   copying torchref/io/datasets/collection.py -> build/lib/torchref/io/datasets
2026-03-03T23:15:55,959   copying torchref/io/datasets/reflection_data.py -> build/lib/torchref/io/datasets
2026-03-03T23:15:55,964   copying torchref/io/datasets/base.py -> build/lib/torchref/io/datasets
2026-03-03T23:15:55,967   copying torchref/io/datasets/fcalc_data.py -> build/lib/torchref/io/datasets
2026-03-03T23:15:55,969   copying torchref/io/datasets/__init__.py -> build/lib/torchref/io/datasets
2026-03-03T23:15:55,971   running egg_info
2026-03-03T23:15:55,980   writing torchref.egg-info/PKG-INFO
2026-03-03T23:15:55,988   writing dependency_links to torchref.egg-info/dependency_links.txt
2026-03-03T23:15:55,990   writing entry points to torchref.egg-info/entry_points.txt
2026-03-03T23:15:55,994   writing requirements to torchref.egg-info/requires.txt
2026-03-03T23:15:55,995   writing top-level names to torchref.egg-info/top_level.txt
2026-03-03T23:15:56,049   reading manifest file 'torchref.egg-info/SOURCES.txt'
2026-03-03T23:15:56,062   adding license file 'LICENSE'
2026-03-03T23:15:56,073   writing manifest file 'torchref.egg-info/SOURCES.txt'
2026-03-03T23:15:56,106   creating build/lib/torchref/data
2026-03-03T23:15:56,107   copying torchref/data/atomic_vdw_radii.csv -> build/lib/torchref/data
2026-03-03T23:15:56,109   copying torchref/data/default_hyperparameters.json -> build/lib/torchref/data
2026-03-03T23:15:56,111   copying torchref/data/policy_latest.pt -> build/lib/torchref/data
2026-03-03T23:15:56,118   copying torchref/data/itc92_scattering_factors.pt -> build/lib/torchref/data
2026-03-03T23:15:56,120   copying torchref/data/rama_nll_surfaces.pt -> build/lib/torchref/data
2026-03-03T23:15:56,239   creating build/lib/torchref/data/monomer_library/t
2026-03-03T23:15:56,240   copying torchref/data/monomer_library/t/TRP.cif -> build/lib/torchref/data/monomer_library/t
2026-03-03T23:15:56,243   copying torchref/data/monomer_library/t/TYR.cif -> build/lib/torchref/data/monomer_library/t
2026-03-03T23:15:56,245   copying torchref/data/monomer_library/t/THR.cif -> build/lib/torchref/data/monomer_library/t
2026-03-03T23:15:56,248   copying torchref/data/monomer_library/t/TPO.cif -> build/lib/torchref/data/monomer_library/t
2026-03-03T23:15:56,250   creating build/lib/torchref/data/monomer_library/i
2026-03-03T23:15:56,251   copying torchref/data/monomer_library/i/ILE.cif -> build/lib/torchref/data/monomer_library/i
2026-03-03T23:15:56,254   creating build/lib/torchref/data/monomer_library/c
2026-03-03T23:15:56,255   copying torchref/data/monomer_library/c/C.cif -> build/lib/torchref/data/monomer_library/c
2026-03-03T23:15:56,257   copying torchref/data/monomer_library/c/CYS.cif -> build/lib/torchref/data/monomer_library/c
2026-03-03T23:15:56,260   creating build/lib/torchref/data/monomer_library/m
2026-03-03T23:15:56,260   copying torchref/data/monomer_library/m/MET.cif -> build/lib/torchref/data/monomer_library/m
2026-03-03T23:15:56,263   copying torchref/data/monomer_library/m/MSE.cif -> build/lib/torchref/data/monomer_library/m
2026-03-03T23:15:56,265   creating build/lib/torchref/data/monomer_library/d
2026-03-03T23:15:56,266   copying torchref/data/monomer_library/d/DA.cif -> build/lib/torchref/data/monomer_library/d
2026-03-03T23:15:56,269   copying torchref/data/monomer_library/d/DG.cif -> build/lib/torchref/data/monomer_library/d
2026-03-03T23:15:56,272   copying torchref/data/monomer_library/d/DT.cif -> build/lib/torchref/data/monomer_library/d
2026-03-03T23:15:56,275   copying torchref/data/monomer_library/d/DC.cif -> build/lib/torchref/data/monomer_library/d
2026-03-03T23:15:56,279   creating build/lib/torchref/data/monomer_library/h
2026-03-03T23:15:56,280   copying torchref/data/monomer_library/h/HYP.cif -> build/lib/torchref/data/monomer_library/h
2026-03-03T23:15:56,283   copying torchref/data/monomer_library/h/HIS.cif -> build/lib/torchref/data/monomer_library/h
2026-03-03T23:15:56,287   copying torchref/data/monomer_library/h/HOH.cif -> build/lib/torchref/data/monomer_library/h
2026-03-03T23:15:56,291   creating build/lib/torchref/data/monomer_library/u
2026-03-03T23:15:56,293   copying torchref/data/monomer_library/u/U.cif -> build/lib/torchref/data/monomer_library/u
2026-03-03T23:15:56,298   creating build/lib/torchref/data/monomer_library/g
2026-03-03T23:15:56,299   copying torchref/data/monomer_library/g/GLN.cif -> build/lib/torchref/data/monomer_library/g
2026-03-03T23:15:56,301   copying torchref/data/monomer_library/g/GLY.cif -> build/lib/torchref/data/monomer_library/g
2026-03-03T23:15:56,303   copying torchref/data/monomer_library/g/GLU.cif -> build/lib/torchref/data/monomer_library/g
2026-03-03T23:15:56,306   copying torchref/data/monomer_library/g/G.cif -> build/lib/torchref/data/monomer_library/g
2026-03-03T23:15:56,309   creating build/lib/torchref/data/monomer_library/l
2026-03-03T23:15:56,310   copying torchref/data/monomer_library/l/LEU.cif -> build/lib/torchref/data/monomer_library/l
2026-03-03T23:15:56,312   copying torchref/data/monomer_library/l/LYS.cif -> build/lib/torchref/data/monomer_library/l
2026-03-03T23:15:56,315   creating build/lib/torchref/data/monomer_library/p
2026-03-03T23:15:56,316   copying torchref/data/monomer_library/p/PHE.cif -> build/lib/torchref/data/monomer_library/p
2026-03-03T23:15:56,320   copying torchref/data/monomer_library/p/PRO.cif -> build/lib/torchref/data/monomer_library/p
2026-03-03T23:15:56,322   copying torchref/data/monomer_library/p/PTR.cif -> build/lib/torchref/data/monomer_library/p
2026-03-03T23:15:56,325   creating build/lib/torchref/data/monomer_library/list
2026-03-03T23:15:56,326   copying torchref/data/monomer_library/list/mon_lib_list.cif -> build/lib/torchref/data/monomer_library/list
2026-03-03T23:15:56,385   creating build/lib/torchref/data/monomer_library/s
2026-03-03T23:15:56,386   copying torchref/data/monomer_library/s/SER.cif -> build/lib/torchref/data/monomer_library/s
2026-03-03T23:15:56,389   copying torchref/data/monomer_library/s/SEP.cif -> build/lib/torchref/data/monomer_library/s
2026-03-03T23:15:56,392   creating build/lib/torchref/data/monomer_library/a
2026-03-03T23:15:56,393   copying torchref/data/monomer_library/a/ALA.cif -> build/lib/torchref/data/monomer_library/a
2026-03-03T23:15:56,396   copying torchref/data/monomer_library/a/ARG.cif -> build/lib/torchref/data/monomer_library/a
2026-03-03T23:15:56,398   copying torchref/data/monomer_library/a/ASP.cif -> build/lib/torchref/data/monomer_library/a
2026-03-03T23:15:56,401   copying torchref/data/monomer_library/a/A.cif -> build/lib/torchref/data/monomer_library/a
2026-03-03T23:15:56,404   copying torchref/data/monomer_library/a/ASN.cif -> build/lib/torchref/data/monomer_library/a
2026-03-03T23:15:56,407   creating build/lib/torchref/data/monomer_library/v
2026-03-03T23:15:56,408   copying torchref/data/monomer_library/v/VAL.cif -> build/lib/torchref/data/monomer_library/v
2026-03-03T23:15:56,452   installing to build/bdist.linux-armv7l/wheel
2026-03-03T23:15:56,453   running install
2026-03-03T23:15:56,479   running install_lib
2026-03-03T23:15:56,487   creating build/bdist.linux-armv7l/wheel
2026-03-03T23:15:56,489   creating build/bdist.linux-armv7l/wheel/torchref
2026-03-03T23:15:56,492   creating build/bdist.linux-armv7l/wheel/torchref/symmetry
2026-03-03T23:15:56,493   copying build/lib/torchref/symmetry/cell.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-03-03T23:15:56,497   copying build/lib/torchref/symmetry/spacegroup.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-03-03T23:15:56,500   copying build/lib/torchref/symmetry/map_symmetry_interpolation.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-03-03T23:15:56,503   copying build/lib/torchref/symmetry/reciprocal_symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-03-03T23:15:56,507   copying build/lib/torchref/symmetry/map_symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-03-03T23:15:56,509   copying build/lib/torchref/symmetry/grid_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-03-03T23:15:56,512   copying build/lib/torchref/symmetry/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-03-03T23:15:56,514   copying build/lib/torchref/symmetry/symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-03-03T23:15:56,517   creating build/bdist.linux-armv7l/wheel/torchref/cli
2026-03-03T23:15:56,518   copying build/lib/torchref/cli/refine_everything_policy.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-03T23:15:56,521   copying build/lib/torchref/cli/refine_everything_static.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-03T23:15:56,524   copying build/lib/torchref/cli/refine_everything_hyperparameters.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-03T23:15:56,527   copying build/lib/torchref/cli/difference_refine.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-03T23:15:56,530   copying build/lib/torchref/cli/validate_ded.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-03T23:15:56,533   copying build/lib/torchref/cli/phased_difference_map.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-03T23:15:56,536   copying build/lib/torchref/cli/refine_everything_random_weights.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-03T23:15:56,539   copying build/lib/torchref/cli/mtz2map.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-03T23:15:56,542   copying build/lib/torchref/cli/refine.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-03T23:15:56,544   copying build/lib/torchref/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-03T23:15:56,547   creating build/bdist.linux-armv7l/wheel/torchref/scripts
2026-03-03T23:15:56,548   copying build/lib/torchref/scripts/generate_scattering_table.py -> build/bdist.linux-armv7l/wheel/./torchref/scripts
2026-03-03T23:15:56,551   copying build/lib/torchref/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/scripts
2026-03-03T23:15:56,554   creating build/bdist.linux-armv7l/wheel/torchref/utils
2026-03-03T23:15:56,555   copying build/lib/torchref/utils/caching.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-03T23:15:56,557   copying build/lib/torchref/utils/gradnorm.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-03T23:15:56,559   copying build/lib/torchref/utils/debug_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-03T23:15:56,562   copying build/lib/torchref/utils/serialization.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-03T23:15:56,564   copying build/lib/torchref/utils/pse.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-03T23:15:56,567   copying build/lib/torchref/utils/utils.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-03T23:15:56,570   copying build/lib/torchref/utils/stats.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-03T23:15:56,573   copying build/lib/torchref/utils/hyperparameters.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-03T23:15:56,576   copying build/lib/torchref/utils/timing.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-03T23:15:56,578   copying build/lib/torchref/utils/device_mixin.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-03T23:15:56,580   copying build/lib/torchref/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-03T23:15:56,584   creating build/bdist.linux-armv7l/wheel/torchref/base
2026-03-03T23:15:56,585   copying build/lib/torchref/base/math_numpy.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-03-03T23:15:56,588   copying build/lib/torchref/base/CCTBX_related.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-03-03T23:15:56,591   copying build/lib/torchref/base/get_scattering_factor_torch.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-03-03T23:15:56,594   creating build/bdist.linux-armv7l/wheel/torchref/base/direct_summation
2026-03-03T23:15:56,596   copying build/lib/torchref/base/direct_summation/isotropic.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation
2026-03-03T23:15:56,599   copying build/lib/torchref/base/direct_summation/corrections.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation
2026-03-03T23:15:56,601   copying build/lib/torchref/base/direct_summation/anisotropic.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation
2026-03-03T23:15:56,604   copying build/lib/torchref/base/direct_summation/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation
2026-03-03T23:15:56,607   creating build/bdist.linux-armv7l/wheel/torchref/base/metrics
2026-03-03T23:15:56,608   copying build/lib/torchref/base/metrics/loss.py -> build/bdist.linux-armv7l/wheel/./torchref/base/metrics
2026-03-03T23:15:56,611   copying build/lib/torchref/base/metrics/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/metrics
2026-03-03T23:15:56,614   copying build/lib/torchref/base/metrics/rfactor.py -> build/bdist.linux-armv7l/wheel/./torchref/base/metrics
2026-03-03T23:15:56,617   creating build/bdist.linux-armv7l/wheel/torchref/base/fourier
2026-03-03T23:15:56,618   copying build/lib/torchref/base/fourier/fft.py -> build/bdist.linux-armv7l/wheel/./torchref/base/fourier
2026-03-03T23:15:56,621   copying build/lib/torchref/base/fourier/grid.py -> build/bdist.linux-armv7l/wheel/./torchref/base/fourier
2026-03-03T23:15:56,624   copying build/lib/torchref/base/fourier/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/fourier
2026-03-03T23:15:56,627   creating build/bdist.linux-armv7l/wheel/torchref/base/chain_closure
2026-03-03T23:15:56,628   copying build/lib/torchref/base/chain_closure/backbone_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/base/chain_closure
2026-03-03T23:15:56,631   copying build/lib/torchref/base/chain_closure/closure.py -> build/bdist.linux-armv7l/wheel/./torchref/base/chain_closure
2026-03-03T23:15:56,635   copying build/lib/torchref/base/chain_closure/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/chain_closure
2026-03-03T23:15:56,638   creating build/bdist.linux-armv7l/wheel/torchref/base/scattering
2026-03-03T23:15:56,639   copying build/lib/torchref/base/scattering/anomalous_table.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering
2026-03-03T23:15:56,643   copying build/lib/torchref/base/scattering/itc92.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering
2026-03-03T23:15:56,647   copying build/lib/torchref/base/scattering/scattering_table.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering
2026-03-03T23:15:56,651   copying build/lib/torchref/base/scattering/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering
2026-03-03T23:15:56,655   copying build/lib/torchref/base/french_wilson.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-03-03T23:15:56,659   creating build/bdist.linux-armv7l/wheel/torchref/base/coordinates
2026-03-03T23:15:56,660   copying build/lib/torchref/base/coordinates/periodic_boundary.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates
2026-03-03T23:15:56,664   copying build/lib/torchref/base/coordinates/transforms_torch.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates
2026-03-03T23:15:56,667   copying build/lib/torchref/base/coordinates/transforms_numpy.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates
2026-03-03T23:15:56,670   copying build/lib/torchref/base/coordinates/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates
2026-03-03T23:15:56,673   creating build/bdist.linux-armv7l/wheel/torchref/base/alignment
2026-03-03T23:15:56,674   copying build/lib/torchref/base/alignment/superposition.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment
2026-03-03T23:15:56,677   copying build/lib/torchref/base/alignment/normalization.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment
2026-03-03T23:15:56,682   copying build/lib/torchref/base/alignment/rotation.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment
2026-03-03T23:15:56,684   copying build/lib/torchref/base/alignment/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment
2026-03-03T23:15:56,687   copying build/lib/torchref/base/alignment/scoring.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment
2026-03-03T23:15:56,690   creating build/bdist.linux-armv7l/wheel/torchref/base/electron_density
2026-03-03T23:15:56,691   copying build/lib/torchref/base/electron_density/map_building.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density
2026-03-03T23:15:56,695   copying build/lib/torchref/base/electron_density/solvent_mask.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density
2026-03-03T23:15:56,699   copying build/lib/torchref/base/electron_density/main.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density
2026-03-03T23:15:56,706   copying build/lib/torchref/base/electron_density/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density
2026-03-03T23:15:56,712   copying build/lib/torchref/base/electron_density/voxel_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density
2026-03-03T23:15:56,719   copying build/lib/torchref/base/math_torch.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-03-03T23:15:56,731   creating build/bdist.linux-armv7l/wheel/torchref/base/kernels
2026-03-03T23:15:56,734   copying build/lib/torchref/base/kernels/cpu_scatter.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-03-03T23:15:56,745   copying build/lib/torchref/base/kernels/jit_kernel_vectorized_add_to_map.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-03-03T23:15:56,757   copying build/lib/torchref/base/kernels/optimized_ops.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-03-03T23:15:56,766   copying build/lib/torchref/base/kernels/triton_kernel.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-03-03T23:15:56,774   copying build/lib/torchref/base/kernels/separable_triton_kernel.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-03-03T23:15:56,785   copying build/lib/torchref/base/kernels/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-03-03T23:15:56,793   copying build/lib/torchref/base/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-03-03T23:15:56,802   creating build/bdist.linux-armv7l/wheel/torchref/base/reciprocal
2026-03-03T23:15:56,806   copying build/lib/torchref/base/reciprocal/basis.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-03-03T23:15:56,809   copying build/lib/torchref/base/reciprocal/interpolation.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-03-03T23:15:56,812   copying build/lib/torchref/base/reciprocal/hkl.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-03-03T23:15:56,814   copying build/lib/torchref/base/reciprocal/grid_operations.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-03-03T23:15:56,817   copying build/lib/torchref/base/reciprocal/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-03-03T23:15:56,819   copying build/lib/torchref/base/reciprocal/symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-03-03T23:15:56,822   creating build/bdist.linux-armv7l/wheel/torchref/restraints
2026-03-03T23:15:56,823   copying build/lib/torchref/restraints/builders_fast.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-03-03T23:15:56,827   copying build/lib/torchref/restraints/library.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-03-03T23:15:56,830   copying build/lib/torchref/restraints/restraints_helper.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-03-03T23:15:56,833   copying build/lib/torchref/restraints/ramachandran.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-03-03T23:15:56,834   copying build/lib/torchref/restraints/restraints.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-03-03T23:15:56,838   copying build/lib/torchref/restraints/builders_numba.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-03-03T23:15:56,841   copying build/lib/torchref/restraints/builders.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-03-03T23:15:56,845   copying build/lib/torchref/restraints/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-03-03T23:15:56,847   creating build/bdist.linux-armv7l/wheel/torchref/scaling
2026-03-03T23:15:56,848   copying build/lib/torchref/scaling/scaler_base.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling
2026-03-03T23:15:56,851   copying build/lib/torchref/scaling/solvent.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling
2026-03-03T23:15:56,853   copying build/lib/torchref/scaling/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling
2026-03-03T23:15:56,855   copying build/lib/torchref/scaling/scaler.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling
2026-03-03T23:15:56,858   copying build/lib/torchref/config.py -> build/bdist.linux-armv7l/wheel/./torchref
2026-03-03T23:15:56,860   creating build/bdist.linux-armv7l/wheel/torchref/refinement
2026-03-03T23:15:56,862   creating build/bdist.linux-armv7l/wheel/torchref/refinement/optimizers
2026-03-03T23:15:56,863   copying build/lib/torchref/refinement/optimizers/adam_noise.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-03-03T23:15:56,865   copying build/lib/torchref/refinement/optimizers/internal_coord_sa.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-03-03T23:15:56,868   copying build/lib/torchref/refinement/optimizers/momentum_sa.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-03-03T23:15:56,870   copying build/lib/torchref/refinement/optimizers/simulated_annealing.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-03-03T23:15:56,872   copying build/lib/torchref/refinement/optimizers/exploratory_lbfgs.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-03-03T23:15:56,875   copying build/lib/torchref/refinement/optimizers/langevin_sa.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-03-03T23:15:56,877   copying build/lib/torchref/refinement/optimizers/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-03-03T23:15:56,879   creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets
2026-03-03T23:15:56,881   creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets/xray
2026-03-03T23:15:56,882   copying build/lib/torchref/refinement/targets/xray/maximum_likelihood.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-03-03T23:15:56,885   copying build/lib/torchref/refinement/targets/xray/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-03-03T23:15:56,887   copying build/lib/torchref/refinement/targets/xray/gaussian.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-03-03T23:15:56,889   copying build/lib/torchref/refinement/targets/xray/least_squares.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-03-03T23:15:56,890   copying build/lib/torchref/refinement/targets/xray/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-03-03T23:15:56,892   copying build/lib/torchref/refinement/targets/realspace.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-03T23:15:56,895   copying build/lib/torchref/refinement/targets/forcefield_target.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-03T23:15:56,897   copying build/lib/torchref/refinement/targets/difference.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-03T23:15:56,900   copying build/lib/torchref/refinement/targets/amber_target.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-03T23:15:56,903   copying build/lib/torchref/refinement/targets/sampled_ml_phase_target.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-03T23:15:56,906   copying build/lib/torchref/refinement/targets/combined.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-03T23:15:56,909   creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets/adp
2026-03-03T23:15:56,910   copying build/lib/torchref/refinement/targets/adp/locality.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-03-03T23:15:56,912   copying build/lib/torchref/refinement/targets/adp/similarity.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-03-03T23:15:56,914   copying build/lib/torchref/refinement/targets/adp/rigid_bond.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-03-03T23:15:56,917   copying build/lib/torchref/refinement/targets/adp/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-03-03T23:15:56,918   copying build/lib/torchref/refinement/targets/adp/entropy.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-03-03T23:15:56,920   copying build/lib/torchref/refinement/targets/adp/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-03-03T23:15:56,923   creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets/geometry
2026-03-03T23:15:56,924   copying build/lib/torchref/refinement/targets/geometry/planarity.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-03T23:15:56,926   copying build/lib/torchref/refinement/targets/geometry/torsions.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-03T23:15:56,928   copying build/lib/torchref/refinement/targets/geometry/bonds.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-03T23:15:56,929   copying build/lib/torchref/refinement/targets/geometry/ramachandran.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-03T23:15:56,931   copying build/lib/torchref/refinement/targets/geometry/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-03T23:15:56,933   copying build/lib/torchref/refinement/targets/geometry/angles.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-03T23:15:56,935   copying build/lib/torchref/refinement/targets/geometry/chiral.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-03T23:15:56,936   copying build/lib/torchref/refinement/targets/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-03T23:15:56,938   copying build/lib/torchref/refinement/targets/geometry/non_bonded.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-03T23:15:56,940   copying build/lib/torchref/refinement/targets/occupancy_floor_diagnostic.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-03T23:15:56,943   copying build/lib/torchref/refinement/targets/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-03T23:15:56,945   copying build/lib/torchref/refinement/targets/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-03T23:15:56,947   creating build/bdist.linux-armv7l/wheel/torchref/refinement/weighting
2026-03-03T23:15:56,948   copying build/lib/torchref/refinement/weighting/component_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-03-03T23:15:56,951   copying build/lib/torchref/refinement/weighting/random_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-03-03T23:15:56,954   copying build/lib/torchref/refinement/weighting/base_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-03-03T23:15:56,956   copying build/lib/torchref/refinement/weighting/es_policy_training.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-03-03T23:15:56,959   copying build/lib/torchref/refinement/weighting/policy_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-03-03T23:15:56,962   copying build/lib/torchref/refinement/weighting/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-03-03T23:15:56,964   copying build/lib/torchref/refinement/logger.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement
2026-03-03T23:15:56,966   copying build/lib/torchref/refinement/lbfgs_refinement.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement
2026-03-03T23:15:56,969   copying build/lib/torchref/refinement/base_refinement.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement
2026-03-03T23:15:56,972   copying build/lib/torchref/refinement/loss_state.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement
2026-03-03T23:15:56,975   copying build/lib/torchref/refinement/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement
2026-03-03T23:15:56,977   copying build/lib/torchref/_bootstrap.py -> build/bdist.linux-armv7l/wheel/./torchref
2026-03-03T23:15:56,979   creating build/bdist.linux-armv7l/wheel/torchref/model
2026-03-03T23:15:56,980   copying build/lib/torchref/model/closed_segmented_internal_coordinates.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-03T23:15:56,986   copying build/lib/torchref/model/sf_fft.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-03T23:15:56,989   copying build/lib/torchref/model/sf_ds.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-03T23:15:56,992   copying build/lib/torchref/model/internal_coordinates.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-03T23:15:56,996   copying build/lib/torchref/model/segmented_internal_coordinates.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-03T23:15:57,001   copying build/lib/torchref/model/parameter_wrappers.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-03T23:15:57,005   copying build/lib/torchref/model/mixed_model.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-03T23:15:57,008   copying build/lib/torchref/model/model.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-03T23:15:57,013   copying build/lib/torchref/model/model_ft.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-03T23:15:57,017   copying build/lib/torchref/model/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-03T23:15:57,019   creating build/bdist.linux-armv7l/wheel/torchref/maps
2026-03-03T23:15:57,020   copying build/lib/torchref/maps/map.py -> build/bdist.linux-armv7l/wheel/./torchref/maps
2026-03-03T23:15:57,022   copying build/lib/torchref/maps/difference_map.py -> build/bdist.linux-armv7l/wheel/./torchref/maps
2026-03-03T23:15:57,024   copying build/lib/torchref/maps/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/maps
2026-03-03T23:15:57,026   creating build/bdist.linux-armv7l/wheel/torchref/alignment
2026-03-03T23:15:57,027   copying build/lib/torchref/alignment/rigid_body.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-03T23:15:57,029   copying build/lib/torchref/alignment/sampling.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-03T23:15:57,032   copying build/lib/torchref/alignment/transform.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-03T23:15:57,034   copying build/lib/torchref/alignment/translation.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-03T23:15:57,037   copying build/lib/torchref/alignment/pipeline.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-03T23:15:57,040   copying build/lib/torchref/alignment/ball_transform.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-03T23:15:57,043   copying build/lib/torchref/alignment/clashscore.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-03T23:15:57,046   copying build/lib/torchref/alignment/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-03T23:15:57,048   copying build/lib/torchref/alignment/distributions.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-03T23:15:57,050   copying build/lib/torchref/alignment/jax_subpixel_peaks.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-03T23:15:57,053   creating build/bdist.linux-armv7l/wheel/torchref/data
2026-03-03T23:15:57,054   copying build/lib/torchref/data/policy_latest.pt -> build/bdist.linux-armv7l/wheel/./torchref/data
2026-03-03T23:15:57,065   copying build/lib/torchref/data/itc92_scattering_factors.pt -> build/bdist.linux-armv7l/wheel/./torchref/data
2026-03-03T23:15:57,068   copying build/lib/torchref/data/atomic_vdw_radii.csv -> build/bdist.linux-armv7l/wheel/./torchref/data
2026-03-03T23:15:57,070   copying build/lib/torchref/data/default_hyperparameters.json -> build/bdist.linux-armv7l/wheel/./torchref/data
2026-03-03T23:15:57,072   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library
2026-03-03T23:15:57,074   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/t
2026-03-03T23:15:57,076   copying build/lib/torchref/data/monomer_library/t/TRP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t
2026-03-03T23:15:57,079   copying build/lib/torchref/data/monomer_library/t/TYR.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t
2026-03-03T23:15:57,081   copying build/lib/torchref/data/monomer_library/t/THR.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t
2026-03-03T23:15:57,084   copying build/lib/torchref/data/monomer_library/t/TPO.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t
2026-03-03T23:15:57,087   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/i
2026-03-03T23:15:57,088   copying build/lib/torchref/data/monomer_library/i/ILE.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/i
2026-03-03T23:15:57,091   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/c
2026-03-03T23:15:57,092   copying build/lib/torchref/data/monomer_library/c/C.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/c
2026-03-03T23:15:57,095   copying build/lib/torchref/data/monomer_library/c/CYS.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/c
2026-03-03T23:15:57,099   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/m
2026-03-03T23:15:57,100   copying build/lib/torchref/data/monomer_library/m/MET.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/m
2026-03-03T23:15:57,103   copying build/lib/torchref/data/monomer_library/m/MSE.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/m
2026-03-03T23:15:57,105   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/d
2026-03-03T23:15:57,107   copying build/lib/torchref/data/monomer_library/d/DA.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d
2026-03-03T23:15:57,109   copying build/lib/torchref/data/monomer_library/d/DG.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d
2026-03-03T23:15:57,113   copying build/lib/torchref/data/monomer_library/d/DT.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d
2026-03-03T23:15:57,115   copying build/lib/torchref/data/monomer_library/d/DC.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d
2026-03-03T23:15:57,119   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/h
2026-03-03T23:15:57,120   copying build/lib/torchref/data/monomer_library/h/HYP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/h
2026-03-03T23:15:57,123   copying build/lib/torchref/data/monomer_library/h/HIS.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/h
2026-03-03T23:15:57,125   copying build/lib/torchref/data/monomer_library/h/HOH.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/h
2026-03-03T23:15:57,128   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/u
2026-03-03T23:15:57,129   copying build/lib/torchref/data/monomer_library/u/U.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/u
2026-03-03T23:15:57,132   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/g
2026-03-03T23:15:57,134   copying build/lib/torchref/data/monomer_library/g/GLN.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g
2026-03-03T23:15:57,136   copying build/lib/torchref/data/monomer_library/g/GLY.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g
2026-03-03T23:15:57,139   copying build/lib/torchref/data/monomer_library/g/GLU.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g
2026-03-03T23:15:57,141   copying build/lib/torchref/data/monomer_library/g/G.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g
2026-03-03T23:15:57,145   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/l
2026-03-03T23:15:57,146   copying build/lib/torchref/data/monomer_library/l/LEU.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/l
2026-03-03T23:15:57,149   copying build/lib/torchref/data/monomer_library/l/LYS.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/l
2026-03-03T23:15:57,152   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/p
2026-03-03T23:15:57,153   copying build/lib/torchref/data/monomer_library/p/PHE.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/p
2026-03-03T23:15:57,155   copying build/lib/torchref/data/monomer_library/p/PRO.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/p
2026-03-03T23:15:57,158   copying build/lib/torchref/data/monomer_library/p/PTR.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/p
2026-03-03T23:15:57,161   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/list
2026-03-03T23:15:57,162   copying build/lib/torchref/data/monomer_library/list/mon_lib_list.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/list
2026-03-03T23:15:57,318   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/s
2026-03-03T23:15:57,318   copying build/lib/torchref/data/monomer_library/s/SER.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/s
2026-03-03T23:15:57,321   copying build/lib/torchref/data/monomer_library/s/SEP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/s
2026-03-03T23:15:57,323   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/a
2026-03-03T23:15:57,324   copying build/lib/torchref/data/monomer_library/a/ALA.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a
2026-03-03T23:15:57,327   copying build/lib/torchref/data/monomer_library/a/ARG.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a
2026-03-03T23:15:57,329   copying build/lib/torchref/data/monomer_library/a/ASP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a
2026-03-03T23:15:57,331   copying build/lib/torchref/data/monomer_library/a/A.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a
2026-03-03T23:15:57,333   copying build/lib/torchref/data/monomer_library/a/ASN.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a
2026-03-03T23:15:57,336   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/v
2026-03-03T23:15:57,337   copying build/lib/torchref/data/monomer_library/v/VAL.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/v
2026-03-03T23:15:57,339   copying build/lib/torchref/data/rama_nll_surfaces.pt -> build/bdist.linux-armv7l/wheel/./torchref/data
2026-03-03T23:15:57,486   creating build/bdist.linux-armv7l/wheel/torchref/io
2026-03-03T23:15:57,487   copying build/lib/torchref/io/data_router.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-03-03T23:15:57,490   creating build/bdist.linux-armv7l/wheel/torchref/io/datasets
2026-03-03T23:15:57,491   copying build/lib/torchref/io/datasets/collection.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets
2026-03-03T23:15:57,494   copying build/lib/torchref/io/datasets/reflection_data.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets
2026-03-03T23:15:57,500   copying build/lib/torchref/io/datasets/base.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets
2026-03-03T23:15:57,502   copying build/lib/torchref/io/datasets/fcalc_data.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets
2026-03-03T23:15:57,505   copying build/lib/torchref/io/datasets/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets
2026-03-03T23:15:57,507   copying build/lib/torchref/io/cif_readers.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-03-03T23:15:57,511   copying build/lib/torchref/io/mtz.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-03-03T23:15:57,513   copying build/lib/torchref/io/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-03-03T23:15:57,515   copying build/lib/torchref/io/pdb.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-03-03T23:15:57,518   copying build/lib/torchref/io/cif.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-03-03T23:15:57,521   copying build/lib/torchref/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref
2026-03-03T23:15:57,523   running install_egg_info
2026-03-03T23:15:57,528   Copying torchref.egg-info to build/bdist.linux-armv7l/wheel/./torchref-0.4.1-py3.11.egg-info
2026-03-03T23:15:57,540   running install_scripts
2026-03-03T23:15:57,551   creating build/bdist.linux-armv7l/wheel/torchref-0.4.1.dist-info/WHEEL
2026-03-03T23:15:57,554   creating '/tmp/pip-wheel-g5sidcas/.tmp-ktrgraty/torchref-0.4.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2026-03-03T23:15:57,557   adding 'torchref/__init__.py'
2026-03-03T23:15:57,558   adding 'torchref/_bootstrap.py'
2026-03-03T23:15:57,560   adding 'torchref/config.py'
2026-03-03T23:15:57,562   adding 'torchref/alignment/__init__.py'
2026-03-03T23:15:57,570   adding 'torchref/alignment/ball_transform.py'
2026-03-03T23:15:57,572   adding 'torchref/alignment/clashscore.py'
2026-03-03T23:15:57,574   adding 'torchref/alignment/distributions.py'
2026-03-03T23:15:57,576   adding 'torchref/alignment/jax_subpixel_peaks.py'
2026-03-03T23:15:57,578   adding 'torchref/alignment/pipeline.py'
2026-03-03T23:15:57,581   adding 'torchref/alignment/rigid_body.py'
2026-03-03T23:15:57,583   adding 'torchref/alignment/sampling.py'
2026-03-03T23:15:57,586   adding 'torchref/alignment/transform.py'
2026-03-03T23:15:57,587   adding 'torchref/alignment/translation.py'
2026-03-03T23:15:57,589   adding 'torchref/base/CCTBX_related.py'
2026-03-03T23:15:57,591   adding 'torchref/base/__init__.py'
2026-03-03T23:15:57,595   adding 'torchref/base/french_wilson.py'
2026-03-03T23:15:57,597   adding 'torchref/base/get_scattering_factor_torch.py'
2026-03-03T23:15:57,600   adding 'torchref/base/math_numpy.py'
2026-03-03T23:15:57,602   adding 'torchref/base/math_torch.py'
2026-03-03T23:15:57,604   adding 'torchref/base/alignment/__init__.py'
2026-03-03T23:15:57,605   adding 'torchref/base/alignment/normalization.py'
2026-03-03T23:15:57,607   adding 'torchref/base/alignment/rotation.py'
2026-03-03T23:15:57,608   adding 'torchref/base/alignment/scoring.py'
2026-03-03T23:15:57,610   adding 'torchref/base/alignment/superposition.py'
2026-03-03T23:15:57,612   adding 'torchref/base/chain_closure/__init__.py'
2026-03-03T23:15:57,614   adding 'torchref/base/chain_closure/backbone_utils.py'
2026-03-03T23:15:57,617   adding 'torchref/base/chain_closure/closure.py'
2026-03-03T23:15:57,619   adding 'torchref/base/coordinates/__init__.py'
2026-03-03T23:15:57,620   adding 'torchref/base/coordinates/periodic_boundary.py'
2026-03-03T23:15:57,621   adding 'torchref/base/coordinates/transforms_numpy.py'
2026-03-03T23:15:57,623   adding 'torchref/base/coordinates/transforms_torch.py'
2026-03-03T23:15:57,625   adding 'torchref/base/direct_summation/__init__.py'
2026-03-03T23:15:57,626   adding 'torchref/base/direct_summation/anisotropic.py'
2026-03-03T23:15:57,628   adding 'torchref/base/direct_summation/corrections.py'
2026-03-03T23:15:57,629   adding 'torchref/base/direct_summation/isotropic.py'
2026-03-03T23:15:57,631   adding 'torchref/base/electron_density/__init__.py'
2026-03-03T23:15:57,635   adding 'torchref/base/electron_density/main.py'
2026-03-03T23:15:57,637   adding 'torchref/base/electron_density/map_building.py'
2026-03-03T23:15:57,639   adding 'torchref/base/electron_density/solvent_mask.py'
2026-03-03T23:15:57,640   adding 'torchref/base/electron_density/voxel_utils.py'
2026-03-03T23:15:57,642   adding 'torchref/base/fourier/__init__.py'
2026-03-03T23:15:57,643   adding 'torchref/base/fourier/fft.py'
2026-03-03T23:15:57,645   adding 'torchref/base/fourier/grid.py'
2026-03-03T23:15:57,647   adding 'torchref/base/kernels/__init__.py'
2026-03-03T23:15:57,649   adding 'torchref/base/kernels/cpu_scatter.py'
2026-03-03T23:15:57,651   adding 'torchref/base/kernels/jit_kernel_vectorized_add_to_map.py'
2026-03-03T23:15:57,653   adding 'torchref/base/kernels/optimized_ops.py'
2026-03-03T23:15:57,658   adding 'torchref/base/kernels/separable_triton_kernel.py'
2026-03-03T23:15:57,661   adding 'torchref/base/kernels/triton_kernel.py'
2026-03-03T23:15:57,663   adding 'torchref/base/metrics/__init__.py'
2026-03-03T23:15:57,665   adding 'torchref/base/metrics/loss.py'
2026-03-03T23:15:57,666   adding 'torchref/base/metrics/rfactor.py'
2026-03-03T23:15:57,668   adding 'torchref/base/reciprocal/__init__.py'
2026-03-03T23:15:57,670   adding 'torchref/base/reciprocal/basis.py'
2026-03-03T23:15:57,671   adding 'torchref/base/reciprocal/grid_operations.py'
2026-03-03T23:15:57,673   adding 'torchref/base/reciprocal/hkl.py'
2026-03-03T23:15:57,675   adding 'torchref/base/reciprocal/interpolation.py'
2026-03-03T23:15:57,677   adding 'torchref/base/reciprocal/symmetry.py'
2026-03-03T23:15:57,679   adding 'torchref/base/scattering/__init__.py'
2026-03-03T23:15:57,680   adding 'torchref/base/scattering/anomalous_table.py'
2026-03-03T23:15:57,682   adding 'torchref/base/scattering/itc92.py'
2026-03-03T23:15:57,683   adding 'torchref/base/scattering/scattering_table.py'
2026-03-03T23:15:57,685   adding 'torchref/cli/__init__.py'
2026-03-03T23:15:57,689   adding 'torchref/cli/difference_refine.py'
2026-03-03T23:15:57,691   adding 'torchref/cli/mtz2map.py'
2026-03-03T23:15:57,692   adding 'torchref/cli/phased_difference_map.py'
2026-03-03T23:15:57,694   adding 'torchref/cli/refine.py'
2026-03-03T23:15:57,696   adding 'torchref/cli/refine_everything_hyperparameters.py'
2026-03-03T23:15:57,698   adding 'torchref/cli/refine_everything_policy.py'
2026-03-03T23:15:57,700   adding 'torchref/cli/refine_everything_random_weights.py'
2026-03-03T23:15:57,702   adding 'torchref/cli/refine_everything_static.py'
2026-03-03T23:15:57,705   adding 'torchref/cli/validate_ded.py'
2026-03-03T23:15:57,707   adding 'torchref/data/atomic_vdw_radii.csv'
2026-03-03T23:15:57,709   adding 'torchref/data/default_hyperparameters.json'
2026-03-03T23:15:57,710   adding 'torchref/data/itc92_scattering_factors.pt'
2026-03-03T23:15:57,749   adding 'torchref/data/policy_latest.pt'
2026-03-03T23:15:58,015   adding 'torchref/data/rama_nll_surfaces.pt'
2026-03-03T23:15:58,037   adding 'torchref/data/monomer_library/a/A.cif'
2026-03-03T23:15:58,039   adding 'torchref/data/monomer_library/a/ALA.cif'
2026-03-03T23:15:58,040   adding 'torchref/data/monomer_library/a/ARG.cif'
2026-03-03T23:15:58,042   adding 'torchref/data/monomer_library/a/ASN.cif'
2026-03-03T23:15:58,043   adding 'torchref/data/monomer_library/a/ASP.cif'
2026-03-03T23:15:58,046   adding 'torchref/data/monomer_library/c/C.cif'
2026-03-03T23:15:58,048   adding 'torchref/data/monomer_library/c/CYS.cif'
2026-03-03T23:15:58,051   adding 'torchref/data/monomer_library/d/DA.cif'
2026-03-03T23:15:58,053   adding 'torchref/data/monomer_library/d/DC.cif'
2026-03-03T23:15:58,055   adding 'torchref/data/monomer_library/d/DG.cif'
2026-03-03T23:15:58,057   adding 'torchref/data/monomer_library/d/DT.cif'
2026-03-03T23:15:58,060   adding 'torchref/data/monomer_library/g/G.cif'
2026-03-03T23:15:58,062   adding 'torchref/data/monomer_library/g/GLN.cif'
2026-03-03T23:15:58,063   adding 'torchref/data/monomer_library/g/GLU.cif'
2026-03-03T23:15:58,065   adding 'torchref/data/monomer_library/g/GLY.cif'
2026-03-03T23:15:58,067   adding 'torchref/data/monomer_library/h/HIS.cif'
2026-03-03T23:15:58,068   adding 'torchref/data/monomer_library/h/HOH.cif'
2026-03-03T23:15:58,070   adding 'torchref/data/monomer_library/h/HYP.cif'
2026-03-03T23:15:58,072   adding 'torchref/data/monomer_library/i/ILE.cif'
2026-03-03T23:15:58,074   adding 'torchref/data/monomer_library/l/LEU.cif'
2026-03-03T23:15:58,076   adding 'torchref/data/monomer_library/l/LYS.cif'
2026-03-03T23:15:58,653   adding 'torchref/data/monomer_library/list/mon_lib_list.cif'
2026-03-03T23:15:58,680   adding 'torchref/data/monomer_library/m/MET.cif'
2026-03-03T23:15:58,682   adding 'torchref/data/monomer_library/m/MSE.cif'
2026-03-03T23:15:58,684   adding 'torchref/data/monomer_library/p/PHE.cif'
2026-03-03T23:15:58,685   adding 'torchref/data/monomer_library/p/PRO.cif'
2026-03-03T23:15:58,687   adding 'torchref/data/monomer_library/p/PTR.cif'
2026-03-03T23:15:58,689   adding 'torchref/data/monomer_library/s/SEP.cif'
2026-03-03T23:15:58,691   adding 'torchref/data/monomer_library/s/SER.cif'
2026-03-03T23:15:58,693   adding 'torchref/data/monomer_library/t/THR.cif'
2026-03-03T23:15:58,695   adding 'torchref/data/monomer_library/t/TPO.cif'
2026-03-03T23:15:58,696   adding 'torchref/data/monomer_library/t/TRP.cif'
2026-03-03T23:15:58,698   adding 'torchref/data/monomer_library/t/TYR.cif'
2026-03-03T23:15:58,701   adding 'torchref/data/monomer_library/u/U.cif'
2026-03-03T23:15:58,703   adding 'torchref/data/monomer_library/v/VAL.cif'
2026-03-03T23:15:58,705   adding 'torchref/io/__init__.py'
2026-03-03T23:15:58,706   adding 'torchref/io/cif.py'
2026-03-03T23:15:58,713   adding 'torchref/io/cif_readers.py'
2026-03-03T23:15:58,715   adding 'torchref/io/data_router.py'
2026-03-03T23:15:58,718   adding 'torchref/io/mtz.py'
2026-03-03T23:15:58,720   adding 'torchref/io/pdb.py'
2026-03-03T23:15:58,722   adding 'torchref/io/datasets/__init__.py'
2026-03-03T23:15:58,724   adding 'torchref/io/datasets/base.py'
2026-03-03T23:15:58,726   adding 'torchref/io/datasets/collection.py'
2026-03-03T23:15:58,728   adding 'torchref/io/datasets/fcalc_data.py'
2026-03-03T23:15:58,740   adding 'torchref/io/datasets/reflection_data.py'
2026-03-03T23:15:58,742   adding 'torchref/maps/__init__.py'
2026-03-03T23:15:58,744   adding 'torchref/maps/difference_map.py'
2026-03-03T23:15:58,745   adding 'torchref/maps/map.py'
2026-03-03T23:15:58,747   adding 'torchref/model/__init__.py'
2026-03-03T23:15:58,756   adding 'torchref/model/closed_segmented_internal_coordinates.py'
2026-03-03T23:15:58,764   adding 'torchref/model/internal_coordinates.py'
2026-03-03T23:15:58,766   adding 'torchref/model/mixed_model.py'
2026-03-03T23:15:58,779   adding 'torchref/model/model.py'
2026-03-03T23:15:58,785   adding 'torchref/model/model_ft.py'
2026-03-03T23:15:58,793   adding 'torchref/model/parameter_wrappers.py'
2026-03-03T23:15:58,801   adding 'torchref/model/segmented_internal_coordinates.py'
2026-03-03T23:15:58,803   adding 'torchref/model/sf_ds.py'
2026-03-03T23:15:58,806   adding 'torchref/model/sf_fft.py'
2026-03-03T23:15:58,808   adding 'torchref/refinement/__init__.py'
2026-03-03T23:15:58,812   adding 'torchref/refinement/base_refinement.py'
2026-03-03T23:15:58,815   adding 'torchref/refinement/lbfgs_refinement.py'
2026-03-03T23:15:58,817   adding 'torchref/refinement/logger.py'
2026-03-03T23:15:58,820   adding 'torchref/refinement/loss_state.py'
2026-03-03T23:15:58,822   adding 'torchref/refinement/optimizers/__init__.py'
2026-03-03T23:15:58,823   adding 'torchref/refinement/optimizers/adam_noise.py'
2026-03-03T23:15:58,827   adding 'torchref/refinement/optimizers/exploratory_lbfgs.py'
2026-03-03T23:15:58,830   adding 'torchref/refinement/optimizers/internal_coord_sa.py'
2026-03-03T23:15:58,832   adding 'torchref/refinement/optimizers/langevin_sa.py'
2026-03-03T23:15:58,833   adding 'torchref/refinement/optimizers/momentum_sa.py'
2026-03-03T23:15:58,835   adding 'torchref/refinement/optimizers/simulated_annealing.py'
2026-03-03T23:15:58,837   adding 'torchref/refinement/targets/__init__.py'
2026-03-03T23:15:58,842   adding 'torchref/refinement/targets/amber_target.py'
2026-03-03T23:15:58,845   adding 'torchref/refinement/targets/base.py'
2026-03-03T23:15:58,847   adding 'torchref/refinement/targets/combined.py'
2026-03-03T23:15:58,851   adding 'torchref/refinement/targets/difference.py'
2026-03-03T23:15:58,853   adding 'torchref/refinement/targets/forcefield_target.py'
2026-03-03T23:15:58,856   adding 'torchref/refinement/targets/occupancy_floor_diagnostic.py'
2026-03-03T23:15:58,859   adding 'torchref/refinement/targets/realspace.py'
2026-03-03T23:15:58,862   adding 'torchref/refinement/targets/sampled_ml_phase_target.py'
2026-03-03T23:15:58,864   adding 'torchref/refinement/targets/adp/__init__.py'
2026-03-03T23:15:58,865   adding 'torchref/refinement/targets/adp/base.py'
2026-03-03T23:15:58,867   adding 'torchref/refinement/targets/adp/entropy.py'
2026-03-03T23:15:58,868   adding 'torchref/refinement/targets/adp/locality.py'
2026-03-03T23:15:58,870   adding 'torchref/refinement/targets/adp/rigid_bond.py'
2026-03-03T23:15:58,872   adding 'torchref/refinement/targets/adp/similarity.py'
2026-03-03T23:15:58,874   adding 'torchref/refinement/targets/geometry/__init__.py'
2026-03-03T23:15:58,875   adding 'torchref/refinement/targets/geometry/angles.py'
2026-03-03T23:15:58,876   adding 'torchref/refinement/targets/geometry/base.py'
2026-03-03T23:15:58,877   adding 'torchref/refinement/targets/geometry/bonds.py'
2026-03-03T23:15:58,879   adding 'torchref/refinement/targets/geometry/chiral.py'
2026-03-03T23:15:58,881   adding 'torchref/refinement/targets/geometry/non_bonded.py'
2026-03-03T23:15:58,882   adding 'torchref/refinement/targets/geometry/planarity.py'
2026-03-03T23:15:58,883   adding 'torchref/refinement/targets/geometry/ramachandran.py'
2026-03-03T23:15:58,885   adding 'torchref/refinement/targets/geometry/torsions.py'
2026-03-03T23:15:58,886   adding 'torchref/refinement/targets/xray/__init__.py'
2026-03-03T23:15:58,888   adding 'torchref/refinement/targets/xray/base.py'
2026-03-03T23:15:58,889   adding 'torchref/refinement/targets/xray/gaussian.py'
2026-03-03T23:15:58,890   adding 'torchref/refinement/targets/xray/least_squares.py'
2026-03-03T23:15:58,892   adding 'torchref/refinement/targets/xray/maximum_likelihood.py'
2026-03-03T23:15:58,894   adding 'torchref/refinement/weighting/__init__.py'
2026-03-03T23:15:58,895   adding 'torchref/refinement/weighting/base_weighting.py'
2026-03-03T23:15:58,897   adding 'torchref/refinement/weighting/component_weighting.py'
2026-03-03T23:15:58,900   adding 'torchref/refinement/weighting/es_policy_training.py'
2026-03-03T23:15:58,903   adding 'torchref/refinement/weighting/policy_weighting.py'
2026-03-03T23:15:58,905   adding 'torchref/refinement/weighting/random_weighting.py'
2026-03-03T23:15:58,907   adding 'torchref/restraints/__init__.py'
2026-03-03T23:15:58,912   adding 'torchref/restraints/builders.py'
2026-03-03T23:15:58,919   adding 'torchref/restraints/builders_fast.py'
2026-03-03T23:15:58,923   adding 'torchref/restraints/builders_numba.py'
2026-03-03T23:15:58,925   adding 'torchref/restraints/library.py'
2026-03-03T23:15:58,927   adding 'torchref/restraints/ramachandran.py'
2026-03-03T23:15:58,934   adding 'torchref/restraints/restraints.py'
2026-03-03T23:15:58,938   adding 'torchref/restraints/restraints_helper.py'
2026-03-03T23:15:58,940   adding 'torchref/scaling/__init__.py'
2026-03-03T23:15:58,942   adding 'torchref/scaling/scaler.py'
2026-03-03T23:15:58,946   adding 'torchref/scaling/scaler_base.py'
2026-03-03T23:15:58,949   adding 'torchref/scaling/solvent.py'
2026-03-03T23:15:58,950   adding 'torchref/scripts/__init__.py'
2026-03-03T23:15:58,952   adding 'torchref/scripts/generate_scattering_table.py'
2026-03-03T23:15:58,954   adding 'torchref/symmetry/__init__.py'
2026-03-03T23:15:58,956   adding 'torchref/symmetry/cell.py'
2026-03-03T23:15:58,958   adding 'torchref/symmetry/grid_utils.py'
2026-03-03T23:15:58,960   adding 'torchref/symmetry/map_symmetry.py'
2026-03-03T23:15:58,962   adding 'torchref/symmetry/map_symmetry_interpolation.py'
2026-03-03T23:15:58,968   adding 'torchref/symmetry/reciprocal_symmetry.py'
2026-03-03T23:15:58,972   adding 'torchref/symmetry/spacegroup.py'
2026-03-03T23:15:58,973   adding 'torchref/symmetry/symmetry.py'
2026-03-03T23:15:58,975   adding 'torchref/utils/__init__.py'
2026-03-03T23:15:58,977   adding 'torchref/utils/caching.py'
2026-03-03T23:15:58,979   adding 'torchref/utils/debug_utils.py'
2026-03-03T23:15:58,980   adding 'torchref/utils/device_mixin.py'
2026-03-03T23:15:58,982   adding 'torchref/utils/gradnorm.py'
2026-03-03T23:15:58,984   adding 'torchref/utils/hyperparameters.py'
2026-03-03T23:15:58,985   adding 'torchref/utils/pse.py'
2026-03-03T23:15:58,987   adding 'torchref/utils/serialization.py'
2026-03-03T23:15:58,988   adding 'torchref/utils/stats.py'
2026-03-03T23:15:58,990   adding 'torchref/utils/timing.py'
2026-03-03T23:15:58,994   adding 'torchref/utils/utils.py'
2026-03-03T23:15:58,997   adding 'torchref-0.4.1.dist-info/licenses/LICENSE'
2026-03-03T23:15:58,998   adding 'torchref-0.4.1.dist-info/METADATA'
2026-03-03T23:15:58,999   adding 'torchref-0.4.1.dist-info/WHEEL'
2026-03-03T23:15:59,000   adding 'torchref-0.4.1.dist-info/entry_points.txt'
2026-03-03T23:15:59,001   adding 'torchref-0.4.1.dist-info/top_level.txt'
2026-03-03T23:15:59,005   adding 'torchref-0.4.1.dist-info/RECORD'
2026-03-03T23:15:59,048   removing build/bdist.linux-armv7l/wheel
2026-03-03T23:15:59,209   Building wheel for torchref (pyproject.toml): finished with status 'done'
2026-03-03T23:15:59,272   Created wheel for torchref: filename=torchref-0.4.1-py3-none-any.whl size=3051209 sha256=51e933f2f0edf7f44aa74d08f32f7530006300c4b6def2437f9257d02b3e175e
2026-03-03T23:15:59,273   Stored in directory: /tmp/pip-ephem-wheel-cache-v28ofeh5/wheels/e8/a8/06/691776af915b8771c6d7ef5ddab3250da777e9a73e257dde48
2026-03-03T23:15:59,292 Successfully built torchref
2026-03-03T23:15:59,374 Removed build tracker: '/tmp/pip-build-tracker-m1kgrtg1'