2026-03-13T03:41:56,569 Created temporary directory: /tmp/pip-ephem-wheel-cache-992251u9
2026-03-13T03:41:56,571 Created temporary directory: /tmp/pip-build-tracker-a8avkoc0
2026-03-13T03:41:56,572 Initialized build tracking at /tmp/pip-build-tracker-a8avkoc0
2026-03-13T03:41:56,572 Created build tracker: /tmp/pip-build-tracker-a8avkoc0
2026-03-13T03:41:56,573 Entered build tracker: /tmp/pip-build-tracker-a8avkoc0
2026-03-13T03:41:56,573 Created temporary directory: /tmp/pip-wheel-65vlezb4
2026-03-13T03:41:56,576 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
2026-03-13T03:41:56,579 Created temporary directory: /tmp/pip-ephem-wheel-cache-rtxeft0w
2026-03-13T03:41:56,600 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-03-13T03:41:56,603 2 location(s) to search for versions of torchref:
2026-03-13T03:41:56,603 * https://pypi.org/simple/torchref/
2026-03-13T03:41:56,603 * https://www.piwheels.org/simple/torchref/
2026-03-13T03:41:56,604 Fetching project page and analyzing links: https://pypi.org/simple/torchref/
2026-03-13T03:41:56,605 Getting page https://pypi.org/simple/torchref/
2026-03-13T03:41:56,606 Found index url https://pypi.org/simple
2026-03-13T03:41:56,896 Fetched page https://pypi.org/simple/torchref/ as application/vnd.pypi.simple.v1+json
2026-03-13T03:41:56,899   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)
2026-03-13T03:41:56,901   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
2026-03-13T03:41:56,901   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)
2026-03-13T03:41:56,902   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
2026-03-13T03:41:56,903   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)
2026-03-13T03:41:56,904   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
2026-03-13T03:41:56,905   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)
2026-03-13T03:41:56,906   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
2026-03-13T03:41:56,906   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)
2026-03-13T03:41:56,907   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
2026-03-13T03:41:56,908   Skipping link: No binaries permitted for torchref: https://files.pythonhosted.org/packages/a7/3a/847415e01c63f1d7d71316d541be7464628096ed37f5fc9020d147463263/torchref-0.4.3-py3-none-any.whl (from https://pypi.org/simple/torchref/) (requires-python:>=3.10)
2026-03-13T03:41:56,909   Found link https://files.pythonhosted.org/packages/cc/11/709f9abb6ad3da0752480f1a77de7d3c311393d6193f89d6ce18cc7d5099/torchref-0.4.3.tar.gz (from https://pypi.org/simple/torchref/) (requires-python:>=3.10), version: 0.4.3
2026-03-13T03:41:56,910 Fetching project page and analyzing links: https://www.piwheels.org/simple/torchref/
2026-03-13T03:41:56,910 Getting page https://www.piwheels.org/simple/torchref/
2026-03-13T03:41:56,911 Found index url https://www.piwheels.org/simple
2026-03-13T03:41:57,113 Fetched page https://www.piwheels.org/simple/torchref/ as text/html
2026-03-13T03:41:57,116   Skipping link: No binaries permitted for torchref: https://www.piwheels.org/simple/torchref/torchref-0.4.2-py3-none-any.whl#sha256=c4c77a7e34aad8245da2d04a76477bdf30f94ca67cd531f721e4bf47ee67114a (from https://www.piwheels.org/simple/torchref/) (requires-python:>=3.10)
2026-03-13T03:41:57,116   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)
2026-03-13T03:41:57,117   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)
2026-03-13T03:41:57,117   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)
2026-03-13T03:41:57,118   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)
2026-03-13T03:41:57,119 Skipping link: not a file: https://www.piwheels.org/simple/torchref/
2026-03-13T03:41:57,119 Skipping link: not a file: https://pypi.org/simple/torchref/
2026-03-13T03:41:57,140 Given no hashes to check 1 links for project 'torchref': discarding no candidates
2026-03-13T03:41:57,159 Collecting torchref==0.4.3
2026-03-13T03:41:57,161   Created temporary directory: /tmp/pip-unpack-5nak17qt
2026-03-13T03:41:57,303   Downloading torchref-0.4.3.tar.gz (2.9 MB)
2026-03-13T03:41:58,352   Added torchref==0.4.3 from https://files.pythonhosted.org/packages/cc/11/709f9abb6ad3da0752480f1a77de7d3c311393d6193f89d6ce18cc7d5099/torchref-0.4.3.tar.gz to build tracker '/tmp/pip-build-tracker-a8avkoc0'
2026-03-13T03:41:58,358   Created temporary directory: /tmp/pip-build-env-5ii1uptm
2026-03-13T03:41:58,363   Installing build dependencies: started
2026-03-13T03:41:58,364   Running command pip subprocess to install build dependencies
2026-03-13T03:41:58,395   Error processing line 1 of /home/piwheels/.local/lib/python3.11/site-packages/cntimer.pth:

2026-03-13T03:41:58,438     Traceback (most recent call last):
2026-03-13T03:41:58,438       File "<frozen site>", line 192, in addpackage
2026-03-13T03:41:58,439       File "<string>", line 1, in <module>
2026-03-13T03:41:58,440     ModuleNotFoundError: No module named 'cntimer'

2026-03-13T03:41:58,441   Remainder of file ignored
2026-03-13T03:41:59,534   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2026-03-13T03:42:00,111   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
2026-03-13T03:42:00,134   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-03-13T03:42:01,937   Collecting setuptools>=42
2026-03-13T03:42:02,017     Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB)
2026-03-13T03:42:02,298   Collecting wheel
2026-03-13T03:42:02,313     Using cached https://www.piwheels.org/simple/wheel/wheel-0.46.3-py3-none-any.whl (30 kB)
2026-03-13T03:42:02,506   Collecting packaging>=24.0
2026-03-13T03:42:02,524     Using cached https://www.piwheels.org/simple/packaging/packaging-26.0-py3-none-any.whl (74 kB)
2026-03-13T03:42:05,520   Installing collected packages: setuptools, packaging, wheel
2026-03-13T03:42:08,925     Creating /tmp/pip-build-env-5ii1uptm/overlay/local/bin
2026-03-13T03:42:08,927     changing mode of /tmp/pip-build-env-5ii1uptm/overlay/local/bin/wheel to 755
2026-03-13T03:42:08,948   Successfully installed packaging-26.0 setuptools-82.0.1 wheel-0.46.3
2026-03-13T03:42:09,229   Installing build dependencies: finished with status 'done'
2026-03-13T03:42:09,235   Getting requirements to build wheel: started
2026-03-13T03:42:09,236   Running command Getting requirements to build wheel
2026-03-13T03:42:09,947   running egg_info
2026-03-13T03:42:09,955   writing torchref.egg-info/PKG-INFO
2026-03-13T03:42:09,966   writing dependency_links to torchref.egg-info/dependency_links.txt
2026-03-13T03:42:09,968   writing entry points to torchref.egg-info/entry_points.txt
2026-03-13T03:42:09,973   writing requirements to torchref.egg-info/requires.txt
2026-03-13T03:42:09,974   writing top-level names to torchref.egg-info/top_level.txt
2026-03-13T03:42:10,063   reading manifest file 'torchref.egg-info/SOURCES.txt'
2026-03-13T03:42:10,076   adding license file 'LICENSE'
2026-03-13T03:42:10,087   writing manifest file 'torchref.egg-info/SOURCES.txt'
2026-03-13T03:42:10,185   Getting requirements to build wheel: finished with status 'done'
2026-03-13T03:42:10,189   Created temporary directory: /tmp/pip-modern-metadata-quutdefy
2026-03-13T03:42:10,191   Preparing metadata (pyproject.toml): started
2026-03-13T03:42:10,192   Running command Preparing metadata (pyproject.toml)
2026-03-13T03:42:10,866   running dist_info
2026-03-13T03:42:10,876   creating /tmp/pip-modern-metadata-quutdefy/torchref.egg-info
2026-03-13T03:42:10,877   writing /tmp/pip-modern-metadata-quutdefy/torchref.egg-info/PKG-INFO
2026-03-13T03:42:10,886   writing dependency_links to /tmp/pip-modern-metadata-quutdefy/torchref.egg-info/dependency_links.txt
2026-03-13T03:42:10,888   writing entry points to /tmp/pip-modern-metadata-quutdefy/torchref.egg-info/entry_points.txt
2026-03-13T03:42:10,893   writing requirements to /tmp/pip-modern-metadata-quutdefy/torchref.egg-info/requires.txt
2026-03-13T03:42:10,894   writing top-level names to /tmp/pip-modern-metadata-quutdefy/torchref.egg-info/top_level.txt
2026-03-13T03:42:10,896   writing manifest file '/tmp/pip-modern-metadata-quutdefy/torchref.egg-info/SOURCES.txt'
2026-03-13T03:42:10,966   reading manifest file '/tmp/pip-modern-metadata-quutdefy/torchref.egg-info/SOURCES.txt'
2026-03-13T03:42:10,968   adding license file 'LICENSE'
2026-03-13T03:42:10,977   writing manifest file '/tmp/pip-modern-metadata-quutdefy/torchref.egg-info/SOURCES.txt'
2026-03-13T03:42:10,979   creating '/tmp/pip-modern-metadata-quutdefy/torchref-0.4.3.dist-info'
2026-03-13T03:42:11,104   Preparing metadata (pyproject.toml): finished with status 'done'
2026-03-13T03:42:11,109   Source in /tmp/pip-wheel-65vlezb4/torchref_702f53f6e94e4959a589752e101e9833 has version 0.4.3, which satisfies requirement torchref==0.4.3 from https://files.pythonhosted.org/packages/cc/11/709f9abb6ad3da0752480f1a77de7d3c311393d6193f89d6ce18cc7d5099/torchref-0.4.3.tar.gz
2026-03-13T03:42:11,110   Removed torchref==0.4.3 from https://files.pythonhosted.org/packages/cc/11/709f9abb6ad3da0752480f1a77de7d3c311393d6193f89d6ce18cc7d5099/torchref-0.4.3.tar.gz from build tracker '/tmp/pip-build-tracker-a8avkoc0'
2026-03-13T03:42:11,116 Created temporary directory: /tmp/pip-unpack-0wv111hi
2026-03-13T03:42:11,116 Building wheels for collected packages: torchref
2026-03-13T03:42:11,120   Created temporary directory: /tmp/pip-wheel-g9si4yxg
2026-03-13T03:42:11,121   Destination directory: /tmp/pip-wheel-g9si4yxg
2026-03-13T03:42:11,123   Building wheel for torchref (pyproject.toml): started
2026-03-13T03:42:11,124   Running command Building wheel for torchref (pyproject.toml)
2026-03-13T03:42:11,791   running bdist_wheel
2026-03-13T03:42:11,808   running build
2026-03-13T03:42:11,808   running build_py
2026-03-13T03:42:11,814   creating build/lib/torchref
2026-03-13T03:42:11,816   copying torchref/_bootstrap.py -> build/lib/torchref
2026-03-13T03:42:11,818   copying torchref/__init__.py -> build/lib/torchref
2026-03-13T03:42:11,820   copying torchref/config.py -> build/lib/torchref
2026-03-13T03:42:11,822   creating build/lib/torchref/symmetry
2026-03-13T03:42:11,824   copying torchref/symmetry/map_symmetry.py -> build/lib/torchref/symmetry
2026-03-13T03:42:11,826   copying torchref/symmetry/symmetry.py -> build/lib/torchref/symmetry
2026-03-13T03:42:11,828   copying torchref/symmetry/__init__.py -> build/lib/torchref/symmetry
2026-03-13T03:42:11,830   copying torchref/symmetry/reciprocal_symmetry.py -> build/lib/torchref/symmetry
2026-03-13T03:42:11,833   copying torchref/symmetry/cell.py -> build/lib/torchref/symmetry
2026-03-13T03:42:11,835   copying torchref/symmetry/map_symmetry_interpolation.py -> build/lib/torchref/symmetry
2026-03-13T03:42:11,837   copying torchref/symmetry/grid_utils.py -> build/lib/torchref/symmetry
2026-03-13T03:42:11,839   copying torchref/symmetry/spacegroup.py -> build/lib/torchref/symmetry
2026-03-13T03:42:11,842   creating build/lib/torchref/io
2026-03-13T03:42:11,843   copying torchref/io/mtz.py -> build/lib/torchref/io
2026-03-13T03:42:11,846   copying torchref/io/cif_readers.py -> build/lib/torchref/io
2026-03-13T03:42:11,849   copying torchref/io/cif.py -> build/lib/torchref/io
2026-03-13T03:42:11,851   copying torchref/io/__init__.py -> build/lib/torchref/io
2026-03-13T03:42:11,853   copying torchref/io/pdb.py -> build/lib/torchref/io
2026-03-13T03:42:11,855   copying torchref/io/data_router.py -> build/lib/torchref/io
2026-03-13T03:42:11,858   creating build/lib/torchref/cli
2026-03-13T03:42:11,859   copying torchref/cli/refine_everything_hyperparameters.py -> build/lib/torchref/cli
2026-03-13T03:42:11,862   copying torchref/cli/difference_refine.py -> build/lib/torchref/cli
2026-03-13T03:42:11,864   copying torchref/cli/refine.py -> build/lib/torchref/cli
2026-03-13T03:42:11,867   copying torchref/cli/refine_everything_random_weights.py -> build/lib/torchref/cli
2026-03-13T03:42:11,869   copying torchref/cli/__init__.py -> build/lib/torchref/cli
2026-03-13T03:42:11,871   copying torchref/cli/refine_everything_policy.py -> build/lib/torchref/cli
2026-03-13T03:42:11,873   copying torchref/cli/mtz2map.py -> build/lib/torchref/cli
2026-03-13T03:42:11,875   copying torchref/cli/phased_difference_map.py -> build/lib/torchref/cli
2026-03-13T03:42:11,877   copying torchref/cli/validate_ded.py -> build/lib/torchref/cli
2026-03-13T03:42:11,880   copying torchref/cli/refine_everything_static.py -> build/lib/torchref/cli
2026-03-13T03:42:11,883   copying torchref/cli/_common.py -> build/lib/torchref/cli
2026-03-13T03:42:11,886   creating build/lib/torchref/base
2026-03-13T03:42:11,887   copying torchref/base/get_scattering_factor_torch.py -> build/lib/torchref/base
2026-03-13T03:42:11,890   copying torchref/base/CCTBX_related.py -> build/lib/torchref/base
2026-03-13T03:42:11,892   copying torchref/base/__init__.py -> build/lib/torchref/base
2026-03-13T03:42:11,894   copying torchref/base/math_torch.py -> build/lib/torchref/base
2026-03-13T03:42:11,897   copying torchref/base/math_numpy.py -> build/lib/torchref/base
2026-03-13T03:42:11,899   copying torchref/base/french_wilson.py -> build/lib/torchref/base
2026-03-13T03:42:11,903   creating build/lib/torchref/model
2026-03-13T03:42:11,903   copying torchref/model/model.py -> build/lib/torchref/model
2026-03-13T03:42:11,908   copying torchref/model/mixed_model.py -> build/lib/torchref/model
2026-03-13T03:42:11,910   copying torchref/model/closed_segmented_internal_coordinates.py -> build/lib/torchref/model
2026-03-13T03:42:11,914   copying torchref/model/__init__.py -> build/lib/torchref/model
2026-03-13T03:42:11,915   copying torchref/model/model_ft.py -> build/lib/torchref/model
2026-03-13T03:42:11,918   copying torchref/model/segmented_internal_coordinates.py -> build/lib/torchref/model
2026-03-13T03:42:11,922   copying torchref/model/sf_ds.py -> build/lib/torchref/model
2026-03-13T03:42:11,925   copying torchref/model/sf_fft.py -> build/lib/torchref/model
2026-03-13T03:42:11,928   copying torchref/model/internal_coordinates.py -> build/lib/torchref/model
2026-03-13T03:42:11,932   copying torchref/model/parameter_wrappers.py -> build/lib/torchref/model
2026-03-13T03:42:11,936   creating build/lib/torchref/scaling
2026-03-13T03:42:11,937   copying torchref/scaling/scaler_base.py -> build/lib/torchref/scaling
2026-03-13T03:42:11,940   copying torchref/scaling/__init__.py -> build/lib/torchref/scaling
2026-03-13T03:42:11,942   copying torchref/scaling/scaler.py -> build/lib/torchref/scaling
2026-03-13T03:42:11,944   copying torchref/scaling/solvent.py -> build/lib/torchref/scaling
2026-03-13T03:42:11,947   creating build/lib/torchref/utils
2026-03-13T03:42:11,948   copying torchref/utils/caching.py -> build/lib/torchref/utils
2026-03-13T03:42:11,951   copying torchref/utils/timing.py -> build/lib/torchref/utils
2026-03-13T03:42:11,952   copying torchref/utils/__init__.py -> build/lib/torchref/utils
2026-03-13T03:42:11,954   copying torchref/utils/debug_utils.py -> build/lib/torchref/utils
2026-03-13T03:42:11,957   copying torchref/utils/serialization.py -> build/lib/torchref/utils
2026-03-13T03:42:11,958   copying torchref/utils/hyperparameters.py -> build/lib/torchref/utils
2026-03-13T03:42:11,960   copying torchref/utils/device_mixin.py -> build/lib/torchref/utils
2026-03-13T03:42:11,962   copying torchref/utils/pse.py -> build/lib/torchref/utils
2026-03-13T03:42:11,965   copying torchref/utils/gradnorm.py -> build/lib/torchref/utils
2026-03-13T03:42:11,966   copying torchref/utils/utils.py -> build/lib/torchref/utils
2026-03-13T03:42:11,969   copying torchref/utils/stats.py -> build/lib/torchref/utils
2026-03-13T03:42:11,972   creating build/lib/torchref/refinement
2026-03-13T03:42:11,973   copying torchref/refinement/lbfgs_refinement.py -> build/lib/torchref/refinement
2026-03-13T03:42:11,976   copying torchref/refinement/__init__.py -> build/lib/torchref/refinement
2026-03-13T03:42:11,978   copying torchref/refinement/logger.py -> build/lib/torchref/refinement
2026-03-13T03:42:11,980   copying torchref/refinement/base_refinement.py -> build/lib/torchref/refinement
2026-03-13T03:42:11,983   copying torchref/refinement/loss_state.py -> build/lib/torchref/refinement
2026-03-13T03:42:11,986   creating build/lib/torchref/scripts
2026-03-13T03:42:11,987   copying torchref/scripts/__init__.py -> build/lib/torchref/scripts
2026-03-13T03:42:11,989   copying torchref/scripts/generate_scattering_table.py -> build/lib/torchref/scripts
2026-03-13T03:42:11,992   creating build/lib/torchref/maps
2026-03-13T03:42:11,993   copying torchref/maps/__init__.py -> build/lib/torchref/maps
2026-03-13T03:42:11,995   copying torchref/maps/difference_map.py -> build/lib/torchref/maps
2026-03-13T03:42:11,997   copying torchref/maps/map.py -> build/lib/torchref/maps
2026-03-13T03:42:12,000   creating build/lib/torchref/alignment
2026-03-13T03:42:12,001   copying torchref/alignment/translation.py -> build/lib/torchref/alignment
2026-03-13T03:42:12,004   copying torchref/alignment/ball_transform.py -> build/lib/torchref/alignment
2026-03-13T03:42:12,007   copying torchref/alignment/transform.py -> build/lib/torchref/alignment
2026-03-13T03:42:12,010   copying torchref/alignment/distributions.py -> build/lib/torchref/alignment
2026-03-13T03:42:12,012   copying torchref/alignment/__init__.py -> build/lib/torchref/alignment
2026-03-13T03:42:12,014   copying torchref/alignment/rigid_body.py -> build/lib/torchref/alignment
2026-03-13T03:42:12,017   copying torchref/alignment/pipeline.py -> build/lib/torchref/alignment
2026-03-13T03:42:12,019   copying torchref/alignment/jax_subpixel_peaks.py -> build/lib/torchref/alignment
2026-03-13T03:42:12,021   copying torchref/alignment/clashscore.py -> build/lib/torchref/alignment
2026-03-13T03:42:12,023   copying torchref/alignment/sampling.py -> build/lib/torchref/alignment
2026-03-13T03:42:12,026   creating build/lib/torchref/restraints
2026-03-13T03:42:12,027   copying torchref/restraints/builders_numba.py -> build/lib/torchref/restraints
2026-03-13T03:42:12,030   copying torchref/restraints/restraints_helper.py -> build/lib/torchref/restraints
2026-03-13T03:42:12,033   copying torchref/restraints/__init__.py -> build/lib/torchref/restraints
2026-03-13T03:42:12,035   copying torchref/restraints/library.py -> build/lib/torchref/restraints
2026-03-13T03:42:12,037   copying torchref/restraints/ramachandran.py -> build/lib/torchref/restraints
2026-03-13T03:42:12,039   copying torchref/restraints/builders_fast.py -> build/lib/torchref/restraints
2026-03-13T03:42:12,043   copying torchref/restraints/builders.py -> build/lib/torchref/restraints
2026-03-13T03:42:12,046   copying torchref/restraints/restraints.py -> build/lib/torchref/restraints
2026-03-13T03:42:12,050   creating build/lib/torchref/io/datasets
2026-03-13T03:42:12,051   copying torchref/io/datasets/reflection_data.py -> build/lib/torchref/io/datasets
2026-03-13T03:42:12,056   copying torchref/io/datasets/__init__.py -> build/lib/torchref/io/datasets
2026-03-13T03:42:12,058   copying torchref/io/datasets/collection.py -> build/lib/torchref/io/datasets
2026-03-13T03:42:12,060   copying torchref/io/datasets/base.py -> build/lib/torchref/io/datasets
2026-03-13T03:42:12,062   copying torchref/io/datasets/fcalc_data.py -> build/lib/torchref/io/datasets
2026-03-13T03:42:12,065   creating build/lib/torchref/base/chain_closure
2026-03-13T03:42:12,066   copying torchref/base/chain_closure/backbone_utils.py -> build/lib/torchref/base/chain_closure
2026-03-13T03:42:12,068   copying torchref/base/chain_closure/__init__.py -> build/lib/torchref/base/chain_closure
2026-03-13T03:42:12,070   copying torchref/base/chain_closure/closure.py -> build/lib/torchref/base/chain_closure
2026-03-13T03:42:12,073   creating build/lib/torchref/base/fourier
2026-03-13T03:42:12,074   copying torchref/base/fourier/fft.py -> build/lib/torchref/base/fourier
2026-03-13T03:42:12,076   copying torchref/base/fourier/__init__.py -> build/lib/torchref/base/fourier
2026-03-13T03:42:12,078   copying torchref/base/fourier/grid.py -> build/lib/torchref/base/fourier
2026-03-13T03:42:12,080   creating build/lib/torchref/base/direct_summation
2026-03-13T03:42:12,081   copying torchref/base/direct_summation/corrections.py -> build/lib/torchref/base/direct_summation
2026-03-13T03:42:12,083   copying torchref/base/direct_summation/anisotropic.py -> build/lib/torchref/base/direct_summation
2026-03-13T03:42:12,086   copying torchref/base/direct_summation/__init__.py -> build/lib/torchref/base/direct_summation
2026-03-13T03:42:12,087   copying torchref/base/direct_summation/isotropic.py -> build/lib/torchref/base/direct_summation
2026-03-13T03:42:12,090   creating build/lib/torchref/base/coordinates
2026-03-13T03:42:12,091   copying torchref/base/coordinates/periodic_boundary.py -> build/lib/torchref/base/coordinates
2026-03-13T03:42:12,093   copying torchref/base/coordinates/transforms_numpy.py -> build/lib/torchref/base/coordinates
2026-03-13T03:42:12,095   copying torchref/base/coordinates/__init__.py -> build/lib/torchref/base/coordinates
2026-03-13T03:42:12,097   copying torchref/base/coordinates/transforms_torch.py -> build/lib/torchref/base/coordinates
2026-03-13T03:42:12,100   creating build/lib/torchref/base/reciprocal
2026-03-13T03:42:12,101   copying torchref/base/reciprocal/hkl.py -> build/lib/torchref/base/reciprocal
2026-03-13T03:42:12,103   copying torchref/base/reciprocal/interpolation.py -> build/lib/torchref/base/reciprocal
2026-03-13T03:42:12,105   copying torchref/base/reciprocal/symmetry.py -> build/lib/torchref/base/reciprocal
2026-03-13T03:42:12,107   copying torchref/base/reciprocal/__init__.py -> build/lib/torchref/base/reciprocal
2026-03-13T03:42:12,109   copying torchref/base/reciprocal/basis.py -> build/lib/torchref/base/reciprocal
2026-03-13T03:42:12,111   copying torchref/base/reciprocal/grid_operations.py -> build/lib/torchref/base/reciprocal
2026-03-13T03:42:12,114   creating build/lib/torchref/base/kernels
2026-03-13T03:42:12,114   copying torchref/base/kernels/jit_kernel_vectorized_add_to_map.py -> build/lib/torchref/base/kernels
2026-03-13T03:42:12,117   copying torchref/base/kernels/cpu_scatter.py -> build/lib/torchref/base/kernels
2026-03-13T03:42:12,120   copying torchref/base/kernels/__init__.py -> build/lib/torchref/base/kernels
2026-03-13T03:42:12,121   copying torchref/base/kernels/separable_triton_kernel.py -> build/lib/torchref/base/kernels
2026-03-13T03:42:12,124   copying torchref/base/kernels/optimized_ops.py -> build/lib/torchref/base/kernels
2026-03-13T03:42:12,127   copying torchref/base/kernels/triton_kernel.py -> build/lib/torchref/base/kernels
2026-03-13T03:42:12,130   creating build/lib/torchref/base/electron_density
2026-03-13T03:42:12,131   copying torchref/base/electron_density/__init__.py -> build/lib/torchref/base/electron_density
2026-03-13T03:42:12,133   copying torchref/base/electron_density/solvent_mask.py -> build/lib/torchref/base/electron_density
2026-03-13T03:42:12,135   copying torchref/base/electron_density/voxel_utils.py -> build/lib/torchref/base/electron_density
2026-03-13T03:42:12,138   copying torchref/base/electron_density/main.py -> build/lib/torchref/base/electron_density
2026-03-13T03:42:12,141   copying torchref/base/electron_density/map_building.py -> build/lib/torchref/base/electron_density
2026-03-13T03:42:12,143   creating build/lib/torchref/base/metrics
2026-03-13T03:42:12,144   copying torchref/base/metrics/__init__.py -> build/lib/torchref/base/metrics
2026-03-13T03:42:12,146   copying torchref/base/metrics/loss.py -> build/lib/torchref/base/metrics
2026-03-13T03:42:12,149   copying torchref/base/metrics/rfactor.py -> build/lib/torchref/base/metrics
2026-03-13T03:42:12,152   creating build/lib/torchref/base/alignment
2026-03-13T03:42:12,152   copying torchref/base/alignment/__init__.py -> build/lib/torchref/base/alignment
2026-03-13T03:42:12,154   copying torchref/base/alignment/normalization.py -> build/lib/torchref/base/alignment
2026-03-13T03:42:12,157   copying torchref/base/alignment/rotation.py -> build/lib/torchref/base/alignment
2026-03-13T03:42:12,159   copying torchref/base/alignment/superposition.py -> build/lib/torchref/base/alignment
2026-03-13T03:42:12,162   copying torchref/base/alignment/scoring.py -> build/lib/torchref/base/alignment
2026-03-13T03:42:12,164   creating build/lib/torchref/base/scattering
2026-03-13T03:42:12,165   copying torchref/base/scattering/scattering_table.py -> build/lib/torchref/base/scattering
2026-03-13T03:42:12,167   copying torchref/base/scattering/anomalous_table.py -> build/lib/torchref/base/scattering
2026-03-13T03:42:12,170   copying torchref/base/scattering/__init__.py -> build/lib/torchref/base/scattering
2026-03-13T03:42:12,172   copying torchref/base/scattering/itc92.py -> build/lib/torchref/base/scattering
2026-03-13T03:42:12,174   creating build/lib/torchref/refinement/targets
2026-03-13T03:42:12,176   copying torchref/refinement/targets/__init__.py -> build/lib/torchref/refinement/targets
2026-03-13T03:42:12,178   copying torchref/refinement/targets/sampled_ml_phase_target.py -> build/lib/torchref/refinement/targets
2026-03-13T03:42:12,180   copying torchref/refinement/targets/realspace.py -> build/lib/torchref/refinement/targets
2026-03-13T03:42:12,183   copying torchref/refinement/targets/combined.py -> build/lib/torchref/refinement/targets
2026-03-13T03:42:12,185   copying torchref/refinement/targets/difference.py -> build/lib/torchref/refinement/targets
2026-03-13T03:42:12,189   copying torchref/refinement/targets/base.py -> build/lib/torchref/refinement/targets
2026-03-13T03:42:12,191   copying torchref/refinement/targets/amber_target.py -> build/lib/torchref/refinement/targets
2026-03-13T03:42:12,194   copying torchref/refinement/targets/occupancy_floor_diagnostic.py -> build/lib/torchref/refinement/targets
2026-03-13T03:42:12,197   copying torchref/refinement/targets/forcefield_target.py -> build/lib/torchref/refinement/targets
2026-03-13T03:42:12,199   creating build/lib/torchref/refinement/optimizers
2026-03-13T03:42:12,200   copying torchref/refinement/optimizers/exploratory_lbfgs.py -> build/lib/torchref/refinement/optimizers
2026-03-13T03:42:12,203   copying torchref/refinement/optimizers/internal_coord_sa.py -> build/lib/torchref/refinement/optimizers
2026-03-13T03:42:12,206   copying torchref/refinement/optimizers/momentum_sa.py -> build/lib/torchref/refinement/optimizers
2026-03-13T03:42:12,207   copying torchref/refinement/optimizers/__init__.py -> build/lib/torchref/refinement/optimizers
2026-03-13T03:42:12,209   copying torchref/refinement/optimizers/langevin_sa.py -> build/lib/torchref/refinement/optimizers
2026-03-13T03:42:12,211   copying torchref/refinement/optimizers/simulated_annealing.py -> build/lib/torchref/refinement/optimizers
2026-03-13T03:42:12,213   copying torchref/refinement/optimizers/adam_noise.py -> build/lib/torchref/refinement/optimizers
2026-03-13T03:42:12,216   creating build/lib/torchref/refinement/weighting
2026-03-13T03:42:12,217   copying torchref/refinement/weighting/random_weighting.py -> build/lib/torchref/refinement/weighting
2026-03-13T03:42:12,220   copying torchref/refinement/weighting/__init__.py -> build/lib/torchref/refinement/weighting
2026-03-13T03:42:12,221   copying torchref/refinement/weighting/component_weighting.py -> build/lib/torchref/refinement/weighting
2026-03-13T03:42:12,224   copying torchref/refinement/weighting/policy_weighting.py -> build/lib/torchref/refinement/weighting
2026-03-13T03:42:12,226   copying torchref/refinement/weighting/es_policy_training.py -> build/lib/torchref/refinement/weighting
2026-03-13T03:42:12,229   copying torchref/refinement/weighting/base_weighting.py -> build/lib/torchref/refinement/weighting
2026-03-13T03:42:12,231   creating build/lib/torchref/refinement/targets/adp
2026-03-13T03:42:12,232   copying torchref/refinement/targets/adp/locality.py -> build/lib/torchref/refinement/targets/adp
2026-03-13T03:42:12,234   copying torchref/refinement/targets/adp/similarity.py -> build/lib/torchref/refinement/targets/adp
2026-03-13T03:42:12,236   copying torchref/refinement/targets/adp/__init__.py -> build/lib/torchref/refinement/targets/adp
2026-03-13T03:42:12,238   copying torchref/refinement/targets/adp/rigid_bond.py -> build/lib/torchref/refinement/targets/adp
2026-03-13T03:42:12,240   copying torchref/refinement/targets/adp/entropy.py -> build/lib/torchref/refinement/targets/adp
2026-03-13T03:42:12,242   copying torchref/refinement/targets/adp/base.py -> build/lib/torchref/refinement/targets/adp
2026-03-13T03:42:12,244   creating build/lib/torchref/refinement/targets/xray
2026-03-13T03:42:12,245   copying torchref/refinement/targets/xray/maximum_likelihood.py -> build/lib/torchref/refinement/targets/xray
2026-03-13T03:42:12,248   copying torchref/refinement/targets/xray/__init__.py -> build/lib/torchref/refinement/targets/xray
2026-03-13T03:42:12,250   copying torchref/refinement/targets/xray/base.py -> build/lib/torchref/refinement/targets/xray
2026-03-13T03:42:12,252   copying torchref/refinement/targets/xray/least_squares.py -> build/lib/torchref/refinement/targets/xray
2026-03-13T03:42:12,254   copying torchref/refinement/targets/xray/gaussian.py -> build/lib/torchref/refinement/targets/xray
2026-03-13T03:42:12,257   creating build/lib/torchref/refinement/targets/geometry
2026-03-13T03:42:12,258   copying torchref/refinement/targets/geometry/angles.py -> build/lib/torchref/refinement/targets/geometry
2026-03-13T03:42:12,260   copying torchref/refinement/targets/geometry/__init__.py -> build/lib/torchref/refinement/targets/geometry
2026-03-13T03:42:12,261   copying torchref/refinement/targets/geometry/ramachandran.py -> build/lib/torchref/refinement/targets/geometry
2026-03-13T03:42:12,263   copying torchref/refinement/targets/geometry/bonds.py -> build/lib/torchref/refinement/targets/geometry
2026-03-13T03:42:12,265   copying torchref/refinement/targets/geometry/non_bonded.py -> build/lib/torchref/refinement/targets/geometry
2026-03-13T03:42:12,267   copying torchref/refinement/targets/geometry/base.py -> build/lib/torchref/refinement/targets/geometry
2026-03-13T03:42:12,268   copying torchref/refinement/targets/geometry/chiral.py -> build/lib/torchref/refinement/targets/geometry
2026-03-13T03:42:12,271   copying torchref/refinement/targets/geometry/planarity.py -> build/lib/torchref/refinement/targets/geometry
2026-03-13T03:42:12,273   copying torchref/refinement/targets/geometry/torsions.py -> build/lib/torchref/refinement/targets/geometry
2026-03-13T03:42:12,279   running egg_info
2026-03-13T03:42:12,289   writing torchref.egg-info/PKG-INFO
2026-03-13T03:42:12,296   writing dependency_links to torchref.egg-info/dependency_links.txt
2026-03-13T03:42:12,298   writing entry points to torchref.egg-info/entry_points.txt
2026-03-13T03:42:12,303   writing requirements to torchref.egg-info/requires.txt
2026-03-13T03:42:12,304   writing top-level names to torchref.egg-info/top_level.txt
2026-03-13T03:42:12,358   reading manifest file 'torchref.egg-info/SOURCES.txt'
2026-03-13T03:42:12,371   adding license file 'LICENSE'
2026-03-13T03:42:12,382   writing manifest file 'torchref.egg-info/SOURCES.txt'
2026-03-13T03:42:12,417   creating build/lib/torchref/data
2026-03-13T03:42:12,418   copying torchref/data/atomic_vdw_radii.csv -> build/lib/torchref/data
2026-03-13T03:42:12,421   copying torchref/data/default_hyperparameters.json -> build/lib/torchref/data
2026-03-13T03:42:12,423   copying torchref/data/itc92_scattering_factors.pt -> build/lib/torchref/data
2026-03-13T03:42:12,426   copying torchref/data/policy_latest.pt -> build/lib/torchref/data
2026-03-13T03:42:12,432   copying torchref/data/rama_nll_surfaces.pt -> build/lib/torchref/data
2026-03-13T03:42:12,479   creating build/lib/torchref/data/monomer_library/h
2026-03-13T03:42:12,481   copying torchref/data/monomer_library/h/HIS.cif -> build/lib/torchref/data/monomer_library/h
2026-03-13T03:42:12,483   copying torchref/data/monomer_library/h/HOH.cif -> build/lib/torchref/data/monomer_library/h
2026-03-13T03:42:12,486   copying torchref/data/monomer_library/h/HYP.cif -> build/lib/torchref/data/monomer_library/h
2026-03-13T03:42:12,488   creating build/lib/torchref/data/monomer_library/i
2026-03-13T03:42:12,489   copying torchref/data/monomer_library/i/ILE.cif -> build/lib/torchref/data/monomer_library/i
2026-03-13T03:42:12,492   creating build/lib/torchref/data/monomer_library/v
2026-03-13T03:42:12,493   copying torchref/data/monomer_library/v/VAL.cif -> build/lib/torchref/data/monomer_library/v
2026-03-13T03:42:12,495   creating build/lib/torchref/data/monomer_library/u
2026-03-13T03:42:12,496   copying torchref/data/monomer_library/u/U.cif -> build/lib/torchref/data/monomer_library/u
2026-03-13T03:42:12,499   creating build/lib/torchref/data/monomer_library/g
2026-03-13T03:42:12,500   copying torchref/data/monomer_library/g/GLY.cif -> build/lib/torchref/data/monomer_library/g
2026-03-13T03:42:12,503   copying torchref/data/monomer_library/g/GLU.cif -> build/lib/torchref/data/monomer_library/g
2026-03-13T03:42:12,505   copying torchref/data/monomer_library/g/G.cif -> build/lib/torchref/data/monomer_library/g
2026-03-13T03:42:12,508   copying torchref/data/monomer_library/g/GLN.cif -> build/lib/torchref/data/monomer_library/g
2026-03-13T03:42:12,511   creating build/lib/torchref/data/monomer_library/s
2026-03-13T03:42:12,512   copying torchref/data/monomer_library/s/SER.cif -> build/lib/torchref/data/monomer_library/s
2026-03-13T03:42:12,515   copying torchref/data/monomer_library/s/SEP.cif -> build/lib/torchref/data/monomer_library/s
2026-03-13T03:42:12,517   creating build/lib/torchref/data/monomer_library/t
2026-03-13T03:42:12,518   copying torchref/data/monomer_library/t/TYR.cif -> build/lib/torchref/data/monomer_library/t
2026-03-13T03:42:12,521   copying torchref/data/monomer_library/t/THR.cif -> build/lib/torchref/data/monomer_library/t
2026-03-13T03:42:12,523   copying torchref/data/monomer_library/t/TPO.cif -> build/lib/torchref/data/monomer_library/t
2026-03-13T03:42:12,525   copying torchref/data/monomer_library/t/TRP.cif -> build/lib/torchref/data/monomer_library/t
2026-03-13T03:42:12,528   creating build/lib/torchref/data/monomer_library/d
2026-03-13T03:42:12,529   copying torchref/data/monomer_library/d/DA.cif -> build/lib/torchref/data/monomer_library/d
2026-03-13T03:42:12,532   copying torchref/data/monomer_library/d/DT.cif -> build/lib/torchref/data/monomer_library/d
2026-03-13T03:42:12,535   copying torchref/data/monomer_library/d/DC.cif -> build/lib/torchref/data/monomer_library/d
2026-03-13T03:42:12,537   copying torchref/data/monomer_library/d/DG.cif -> build/lib/torchref/data/monomer_library/d
2026-03-13T03:42:12,540   creating build/lib/torchref/data/monomer_library/m
2026-03-13T03:42:12,541   copying torchref/data/monomer_library/m/MSE.cif -> build/lib/torchref/data/monomer_library/m
2026-03-13T03:42:12,543   copying torchref/data/monomer_library/m/MET.cif -> build/lib/torchref/data/monomer_library/m
2026-03-13T03:42:12,546   creating build/lib/torchref/data/monomer_library/list
2026-03-13T03:42:12,547   copying torchref/data/monomer_library/list/mon_lib_list.cif -> build/lib/torchref/data/monomer_library/list
2026-03-13T03:42:12,608   creating build/lib/torchref/data/monomer_library/c
2026-03-13T03:42:12,610   copying torchref/data/monomer_library/c/CYS.cif -> build/lib/torchref/data/monomer_library/c
2026-03-13T03:42:12,612   copying torchref/data/monomer_library/c/C.cif -> build/lib/torchref/data/monomer_library/c
2026-03-13T03:42:12,615   creating build/lib/torchref/data/monomer_library/a
2026-03-13T03:42:12,616   copying torchref/data/monomer_library/a/A.cif -> build/lib/torchref/data/monomer_library/a
2026-03-13T03:42:12,619   copying torchref/data/monomer_library/a/ALA.cif -> build/lib/torchref/data/monomer_library/a
2026-03-13T03:42:12,622   copying torchref/data/monomer_library/a/ARG.cif -> build/lib/torchref/data/monomer_library/a
2026-03-13T03:42:12,624   copying torchref/data/monomer_library/a/ASP.cif -> build/lib/torchref/data/monomer_library/a
2026-03-13T03:42:12,627   copying torchref/data/monomer_library/a/ASN.cif -> build/lib/torchref/data/monomer_library/a
2026-03-13T03:42:12,629   creating build/lib/torchref/data/monomer_library/p
2026-03-13T03:42:12,630   copying torchref/data/monomer_library/p/PTR.cif -> build/lib/torchref/data/monomer_library/p
2026-03-13T03:42:12,633   copying torchref/data/monomer_library/p/PHE.cif -> build/lib/torchref/data/monomer_library/p
2026-03-13T03:42:12,636   copying torchref/data/monomer_library/p/PRO.cif -> build/lib/torchref/data/monomer_library/p
2026-03-13T03:42:12,638   creating build/lib/torchref/data/monomer_library/l
2026-03-13T03:42:12,639   copying torchref/data/monomer_library/l/LYS.cif -> build/lib/torchref/data/monomer_library/l
2026-03-13T03:42:12,642   copying torchref/data/monomer_library/l/LEU.cif -> build/lib/torchref/data/monomer_library/l
2026-03-13T03:42:12,687   installing to build/bdist.linux-armv7l/wheel
2026-03-13T03:42:12,687   running install
2026-03-13T03:42:12,710   running install_lib
2026-03-13T03:42:12,716   creating build/bdist.linux-armv7l/wheel
2026-03-13T03:42:12,718   creating build/bdist.linux-armv7l/wheel/torchref
2026-03-13T03:42:12,720   copying build/lib/torchref/_bootstrap.py -> build/bdist.linux-armv7l/wheel/./torchref
2026-03-13T03:42:12,722   creating build/bdist.linux-armv7l/wheel/torchref/symmetry
2026-03-13T03:42:12,723   copying build/lib/torchref/symmetry/map_symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-03-13T03:42:12,726   copying build/lib/torchref/symmetry/symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-03-13T03:42:12,728   copying build/lib/torchref/symmetry/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-03-13T03:42:12,729   copying build/lib/torchref/symmetry/reciprocal_symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-03-13T03:42:12,732   copying build/lib/torchref/symmetry/cell.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-03-13T03:42:12,735   copying build/lib/torchref/symmetry/map_symmetry_interpolation.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-03-13T03:42:12,737   copying build/lib/torchref/symmetry/grid_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-03-13T03:42:12,739   copying build/lib/torchref/symmetry/spacegroup.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-03-13T03:42:12,742   creating build/bdist.linux-armv7l/wheel/torchref/io
2026-03-13T03:42:12,743   copying build/lib/torchref/io/mtz.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-03-13T03:42:12,746   copying build/lib/torchref/io/cif_readers.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-03-13T03:42:12,749   copying build/lib/torchref/io/cif.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-03-13T03:42:12,751   copying build/lib/torchref/io/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-03-13T03:42:12,753   creating build/bdist.linux-armv7l/wheel/torchref/io/datasets
2026-03-13T03:42:12,754   copying build/lib/torchref/io/datasets/reflection_data.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets
2026-03-13T03:42:12,758   copying build/lib/torchref/io/datasets/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets
2026-03-13T03:42:12,760   copying build/lib/torchref/io/datasets/collection.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets
2026-03-13T03:42:12,762   copying build/lib/torchref/io/datasets/base.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets
2026-03-13T03:42:12,765   copying build/lib/torchref/io/datasets/fcalc_data.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets
2026-03-13T03:42:12,768   copying build/lib/torchref/io/pdb.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-03-13T03:42:12,770   copying build/lib/torchref/io/data_router.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-03-13T03:42:12,772   copying build/lib/torchref/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref
2026-03-13T03:42:12,775   creating build/bdist.linux-armv7l/wheel/torchref/cli
2026-03-13T03:42:12,776   copying build/lib/torchref/cli/refine_everything_hyperparameters.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-13T03:42:12,778   copying build/lib/torchref/cli/difference_refine.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-13T03:42:12,781   copying build/lib/torchref/cli/refine.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-13T03:42:12,784   copying build/lib/torchref/cli/refine_everything_random_weights.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-13T03:42:12,786   copying build/lib/torchref/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-13T03:42:12,788   copying build/lib/torchref/cli/refine_everything_policy.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-13T03:42:12,790   copying build/lib/torchref/cli/mtz2map.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-13T03:42:12,792   copying build/lib/torchref/cli/phased_difference_map.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-13T03:42:12,795   copying build/lib/torchref/cli/validate_ded.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-13T03:42:12,797   copying build/lib/torchref/cli/refine_everything_static.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-13T03:42:12,800   copying build/lib/torchref/cli/_common.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-03-13T03:42:12,802   copying build/lib/torchref/config.py -> build/bdist.linux-armv7l/wheel/./torchref
2026-03-13T03:42:12,805   creating build/bdist.linux-armv7l/wheel/torchref/base
2026-03-13T03:42:12,807   creating build/bdist.linux-armv7l/wheel/torchref/base/chain_closure
2026-03-13T03:42:12,808   copying build/lib/torchref/base/chain_closure/backbone_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/base/chain_closure
2026-03-13T03:42:12,810   copying build/lib/torchref/base/chain_closure/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/chain_closure
2026-03-13T03:42:12,812   copying build/lib/torchref/base/chain_closure/closure.py -> build/bdist.linux-armv7l/wheel/./torchref/base/chain_closure
2026-03-13T03:42:12,815   creating build/bdist.linux-armv7l/wheel/torchref/base/fourier
2026-03-13T03:42:12,817   copying build/lib/torchref/base/fourier/fft.py -> build/bdist.linux-armv7l/wheel/./torchref/base/fourier
2026-03-13T03:42:12,819   copying build/lib/torchref/base/fourier/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/fourier
2026-03-13T03:42:12,820   copying build/lib/torchref/base/fourier/grid.py -> build/bdist.linux-armv7l/wheel/./torchref/base/fourier
2026-03-13T03:42:12,823   creating build/bdist.linux-armv7l/wheel/torchref/base/direct_summation
2026-03-13T03:42:12,824   copying build/lib/torchref/base/direct_summation/corrections.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation
2026-03-13T03:42:12,826   copying build/lib/torchref/base/direct_summation/anisotropic.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation
2026-03-13T03:42:12,828   copying build/lib/torchref/base/direct_summation/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation
2026-03-13T03:42:12,830   copying build/lib/torchref/base/direct_summation/isotropic.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation
2026-03-13T03:42:12,832   creating build/bdist.linux-armv7l/wheel/torchref/base/coordinates
2026-03-13T03:42:12,833   copying build/lib/torchref/base/coordinates/periodic_boundary.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates
2026-03-13T03:42:12,836   copying build/lib/torchref/base/coordinates/transforms_numpy.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates
2026-03-13T03:42:12,837   copying build/lib/torchref/base/coordinates/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates
2026-03-13T03:42:12,839   copying build/lib/torchref/base/coordinates/transforms_torch.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates
2026-03-13T03:42:12,841   creating build/bdist.linux-armv7l/wheel/torchref/base/reciprocal
2026-03-13T03:42:12,842   copying build/lib/torchref/base/reciprocal/hkl.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-03-13T03:42:12,844   copying build/lib/torchref/base/reciprocal/interpolation.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-03-13T03:42:12,847   copying build/lib/torchref/base/reciprocal/symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-03-13T03:42:12,850   copying build/lib/torchref/base/reciprocal/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-03-13T03:42:12,852   copying build/lib/torchref/base/reciprocal/basis.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-03-13T03:42:12,854   copying build/lib/torchref/base/reciprocal/grid_operations.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-03-13T03:42:12,856   copying build/lib/torchref/base/get_scattering_factor_torch.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-03-13T03:42:12,858   copying build/lib/torchref/base/CCTBX_related.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-03-13T03:42:12,860   copying build/lib/torchref/base/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-03-13T03:42:12,863   creating build/bdist.linux-armv7l/wheel/torchref/base/kernels
2026-03-13T03:42:12,864   copying build/lib/torchref/base/kernels/jit_kernel_vectorized_add_to_map.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-03-13T03:42:12,867   copying build/lib/torchref/base/kernels/cpu_scatter.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-03-13T03:42:12,869   copying build/lib/torchref/base/kernels/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-03-13T03:42:12,871   copying build/lib/torchref/base/kernels/separable_triton_kernel.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-03-13T03:42:12,874   copying build/lib/torchref/base/kernels/optimized_ops.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-03-13T03:42:12,876   copying build/lib/torchref/base/kernels/triton_kernel.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-03-13T03:42:12,879   copying build/lib/torchref/base/math_torch.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-03-13T03:42:12,881   creating build/bdist.linux-armv7l/wheel/torchref/base/electron_density
2026-03-13T03:42:12,882   copying build/lib/torchref/base/electron_density/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density
2026-03-13T03:42:12,884   copying build/lib/torchref/base/electron_density/solvent_mask.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density
2026-03-13T03:42:12,887   copying build/lib/torchref/base/electron_density/voxel_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density
2026-03-13T03:42:12,889   copying build/lib/torchref/base/electron_density/main.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density
2026-03-13T03:42:12,892   copying build/lib/torchref/base/electron_density/map_building.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density
2026-03-13T03:42:12,894   creating build/bdist.linux-armv7l/wheel/torchref/base/metrics
2026-03-13T03:42:12,895   copying build/lib/torchref/base/metrics/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/metrics
2026-03-13T03:42:12,898   copying build/lib/torchref/base/metrics/loss.py -> build/bdist.linux-armv7l/wheel/./torchref/base/metrics
2026-03-13T03:42:12,900   copying build/lib/torchref/base/metrics/rfactor.py -> build/bdist.linux-armv7l/wheel/./torchref/base/metrics
2026-03-13T03:42:12,902   copying build/lib/torchref/base/math_numpy.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-03-13T03:42:12,905   creating build/bdist.linux-armv7l/wheel/torchref/base/alignment
2026-03-13T03:42:12,906   copying build/lib/torchref/base/alignment/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment
2026-03-13T03:42:12,908   copying build/lib/torchref/base/alignment/normalization.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment
2026-03-13T03:42:12,910   copying build/lib/torchref/base/alignment/rotation.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment
2026-03-13T03:42:12,913   copying build/lib/torchref/base/alignment/superposition.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment
2026-03-13T03:42:12,915   copying build/lib/torchref/base/alignment/scoring.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment
2026-03-13T03:42:12,918   creating build/bdist.linux-armv7l/wheel/torchref/base/scattering
2026-03-13T03:42:12,919   copying build/lib/torchref/base/scattering/scattering_table.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering
2026-03-13T03:42:12,921   copying build/lib/torchref/base/scattering/anomalous_table.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering
2026-03-13T03:42:12,923   copying build/lib/torchref/base/scattering/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering
2026-03-13T03:42:12,925   copying build/lib/torchref/base/scattering/itc92.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering
2026-03-13T03:42:12,928   copying build/lib/torchref/base/french_wilson.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-03-13T03:42:12,932   creating build/bdist.linux-armv7l/wheel/torchref/model
2026-03-13T03:42:12,934   copying build/lib/torchref/model/model.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-13T03:42:12,940   copying build/lib/torchref/model/mixed_model.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-13T03:42:12,943   copying build/lib/torchref/model/closed_segmented_internal_coordinates.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-13T03:42:12,948   copying build/lib/torchref/model/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-13T03:42:12,950   copying build/lib/torchref/model/model_ft.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-13T03:42:12,953   copying build/lib/torchref/model/segmented_internal_coordinates.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-13T03:42:12,957   copying build/lib/torchref/model/sf_ds.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-13T03:42:12,961   copying build/lib/torchref/model/sf_fft.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-13T03:42:12,964   copying build/lib/torchref/model/internal_coordinates.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-13T03:42:12,969   copying build/lib/torchref/model/parameter_wrappers.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-03-13T03:42:12,976   creating build/bdist.linux-armv7l/wheel/torchref/scaling
2026-03-13T03:42:12,977   copying build/lib/torchref/scaling/scaler_base.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling
2026-03-13T03:42:12,981   copying build/lib/torchref/scaling/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling
2026-03-13T03:42:12,984   copying build/lib/torchref/scaling/scaler.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling
2026-03-13T03:42:12,987   copying build/lib/torchref/scaling/solvent.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling
2026-03-13T03:42:12,990   creating build/bdist.linux-armv7l/wheel/torchref/utils
2026-03-13T03:42:12,992   copying build/lib/torchref/utils/caching.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-13T03:42:12,995   copying build/lib/torchref/utils/timing.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-13T03:42:12,997   copying build/lib/torchref/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-13T03:42:12,999   copying build/lib/torchref/utils/debug_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-13T03:42:13,002   copying build/lib/torchref/utils/serialization.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-13T03:42:13,004   copying build/lib/torchref/utils/hyperparameters.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-13T03:42:13,007   copying build/lib/torchref/utils/device_mixin.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-13T03:42:13,009   copying build/lib/torchref/utils/pse.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-13T03:42:13,012   copying build/lib/torchref/utils/gradnorm.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-13T03:42:13,014   copying build/lib/torchref/utils/utils.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-13T03:42:13,018   copying build/lib/torchref/utils/stats.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-03-13T03:42:13,022   creating build/bdist.linux-armv7l/wheel/torchref/refinement
2026-03-13T03:42:13,024   creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets
2026-03-13T03:42:13,025   copying build/lib/torchref/refinement/targets/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-13T03:42:13,028   copying build/lib/torchref/refinement/targets/sampled_ml_phase_target.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-13T03:42:13,031   copying build/lib/torchref/refinement/targets/realspace.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-13T03:42:13,034   copying build/lib/torchref/refinement/targets/combined.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-13T03:42:13,037   creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets/adp
2026-03-13T03:42:13,038   copying build/lib/torchref/refinement/targets/adp/locality.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-03-13T03:42:13,040   copying build/lib/torchref/refinement/targets/adp/similarity.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-03-13T03:42:13,042   copying build/lib/torchref/refinement/targets/adp/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-03-13T03:42:13,044   copying build/lib/torchref/refinement/targets/adp/rigid_bond.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-03-13T03:42:13,046   copying build/lib/torchref/refinement/targets/adp/entropy.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-03-13T03:42:13,048   copying build/lib/torchref/refinement/targets/adp/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-03-13T03:42:13,050   copying build/lib/torchref/refinement/targets/difference.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-13T03:42:13,053   copying build/lib/torchref/refinement/targets/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-13T03:42:13,055   copying build/lib/torchref/refinement/targets/amber_target.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-13T03:42:13,059   creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets/xray
2026-03-13T03:42:13,060   copying build/lib/torchref/refinement/targets/xray/maximum_likelihood.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-03-13T03:42:13,062   copying build/lib/torchref/refinement/targets/xray/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-03-13T03:42:13,064   copying build/lib/torchref/refinement/targets/xray/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-03-13T03:42:13,066   copying build/lib/torchref/refinement/targets/xray/least_squares.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-03-13T03:42:13,068   copying build/lib/torchref/refinement/targets/xray/gaussian.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-03-13T03:42:13,070   creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets/geometry
2026-03-13T03:42:13,071   copying build/lib/torchref/refinement/targets/geometry/angles.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-13T03:42:13,073   copying build/lib/torchref/refinement/targets/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-13T03:42:13,075   copying build/lib/torchref/refinement/targets/geometry/ramachandran.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-13T03:42:13,077   copying build/lib/torchref/refinement/targets/geometry/bonds.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-13T03:42:13,079   copying build/lib/torchref/refinement/targets/geometry/non_bonded.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-13T03:42:13,082   copying build/lib/torchref/refinement/targets/geometry/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-13T03:42:13,084   copying build/lib/torchref/refinement/targets/geometry/chiral.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-13T03:42:13,086   copying build/lib/torchref/refinement/targets/geometry/planarity.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-13T03:42:13,089   copying build/lib/torchref/refinement/targets/geometry/torsions.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-03-13T03:42:13,091   copying build/lib/torchref/refinement/targets/occupancy_floor_diagnostic.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-13T03:42:13,094   copying build/lib/torchref/refinement/targets/forcefield_target.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-03-13T03:42:13,096   copying build/lib/torchref/refinement/lbfgs_refinement.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement
2026-03-13T03:42:13,100   creating build/bdist.linux-armv7l/wheel/torchref/refinement/optimizers
2026-03-13T03:42:13,101   copying build/lib/torchref/refinement/optimizers/exploratory_lbfgs.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-03-13T03:42:13,104   copying build/lib/torchref/refinement/optimizers/internal_coord_sa.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-03-13T03:42:13,107   copying build/lib/torchref/refinement/optimizers/momentum_sa.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-03-13T03:42:13,110   copying build/lib/torchref/refinement/optimizers/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-03-13T03:42:13,112   copying build/lib/torchref/refinement/optimizers/langevin_sa.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-03-13T03:42:13,114   copying build/lib/torchref/refinement/optimizers/simulated_annealing.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-03-13T03:42:13,117   copying build/lib/torchref/refinement/optimizers/adam_noise.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-03-13T03:42:13,119   copying build/lib/torchref/refinement/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement
2026-03-13T03:42:13,122   creating build/bdist.linux-armv7l/wheel/torchref/refinement/weighting
2026-03-13T03:42:13,123   copying build/lib/torchref/refinement/weighting/random_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-03-13T03:42:13,126   copying build/lib/torchref/refinement/weighting/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-03-13T03:42:13,128   copying build/lib/torchref/refinement/weighting/component_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-03-13T03:42:13,131   copying build/lib/torchref/refinement/weighting/policy_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-03-13T03:42:13,134   copying build/lib/torchref/refinement/weighting/es_policy_training.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-03-13T03:42:13,137   copying build/lib/torchref/refinement/weighting/base_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-03-13T03:42:13,139   copying build/lib/torchref/refinement/logger.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement
2026-03-13T03:42:13,142   copying build/lib/torchref/refinement/base_refinement.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement
2026-03-13T03:42:13,145   copying build/lib/torchref/refinement/loss_state.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement
2026-03-13T03:42:13,149   creating build/bdist.linux-armv7l/wheel/torchref/scripts
2026-03-13T03:42:13,150   copying build/lib/torchref/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/scripts
2026-03-13T03:42:13,152   copying build/lib/torchref/scripts/generate_scattering_table.py -> build/bdist.linux-armv7l/wheel/./torchref/scripts
2026-03-13T03:42:13,155   creating build/bdist.linux-armv7l/wheel/torchref/maps
2026-03-13T03:42:13,157   copying build/lib/torchref/maps/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/maps
2026-03-13T03:42:13,159   copying build/lib/torchref/maps/difference_map.py -> build/bdist.linux-armv7l/wheel/./torchref/maps
2026-03-13T03:42:13,161   copying build/lib/torchref/maps/map.py -> build/bdist.linux-armv7l/wheel/./torchref/maps
2026-03-13T03:42:13,164   creating build/bdist.linux-armv7l/wheel/torchref/alignment
2026-03-13T03:42:13,166   copying build/lib/torchref/alignment/translation.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-13T03:42:13,168   copying build/lib/torchref/alignment/ball_transform.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-13T03:42:13,172   copying build/lib/torchref/alignment/transform.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-13T03:42:13,176   copying build/lib/torchref/alignment/distributions.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-13T03:42:13,178   copying build/lib/torchref/alignment/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-13T03:42:13,181   copying build/lib/torchref/alignment/rigid_body.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-13T03:42:13,183   copying build/lib/torchref/alignment/pipeline.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-13T03:42:13,186   copying build/lib/torchref/alignment/jax_subpixel_peaks.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-13T03:42:13,188   copying build/lib/torchref/alignment/clashscore.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-13T03:42:13,191   copying build/lib/torchref/alignment/sampling.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-03-13T03:42:13,193   creating build/bdist.linux-armv7l/wheel/torchref/data
2026-03-13T03:42:13,195   copying build/lib/torchref/data/itc92_scattering_factors.pt -> build/bdist.linux-armv7l/wheel/./torchref/data
2026-03-13T03:42:13,198   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library
2026-03-13T03:42:13,200   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/h
2026-03-13T03:42:13,201   copying build/lib/torchref/data/monomer_library/h/HIS.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/h
2026-03-13T03:42:13,203   copying build/lib/torchref/data/monomer_library/h/HOH.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/h
2026-03-13T03:42:13,205   copying build/lib/torchref/data/monomer_library/h/HYP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/h
2026-03-13T03:42:13,208   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/i
2026-03-13T03:42:13,209   copying build/lib/torchref/data/monomer_library/i/ILE.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/i
2026-03-13T03:42:13,212   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/v
2026-03-13T03:42:13,213   copying build/lib/torchref/data/monomer_library/v/VAL.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/v
2026-03-13T03:42:13,216   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/u
2026-03-13T03:42:13,217   copying build/lib/torchref/data/monomer_library/u/U.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/u
2026-03-13T03:42:13,220   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/g
2026-03-13T03:42:13,220   copying build/lib/torchref/data/monomer_library/g/GLY.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g
2026-03-13T03:42:13,223   copying build/lib/torchref/data/monomer_library/g/GLU.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g
2026-03-13T03:42:13,225   copying build/lib/torchref/data/monomer_library/g/G.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g
2026-03-13T03:42:13,227   copying build/lib/torchref/data/monomer_library/g/GLN.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g
2026-03-13T03:42:13,230   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/s
2026-03-13T03:42:13,231   copying build/lib/torchref/data/monomer_library/s/SER.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/s
2026-03-13T03:42:13,233   copying build/lib/torchref/data/monomer_library/s/SEP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/s
2026-03-13T03:42:13,236   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/t
2026-03-13T03:42:13,237   copying build/lib/torchref/data/monomer_library/t/TYR.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t
2026-03-13T03:42:13,239   copying build/lib/torchref/data/monomer_library/t/THR.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t
2026-03-13T03:42:13,241   copying build/lib/torchref/data/monomer_library/t/TPO.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t
2026-03-13T03:42:13,243   copying build/lib/torchref/data/monomer_library/t/TRP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t
2026-03-13T03:42:13,246   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/d
2026-03-13T03:42:13,247   copying build/lib/torchref/data/monomer_library/d/DA.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d
2026-03-13T03:42:13,250   copying build/lib/torchref/data/monomer_library/d/DT.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d
2026-03-13T03:42:13,252   copying build/lib/torchref/data/monomer_library/d/DC.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d
2026-03-13T03:42:13,254   copying build/lib/torchref/data/monomer_library/d/DG.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d
2026-03-13T03:42:13,257   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/m
2026-03-13T03:42:13,258   copying build/lib/torchref/data/monomer_library/m/MSE.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/m
2026-03-13T03:42:13,260   copying build/lib/torchref/data/monomer_library/m/MET.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/m
2026-03-13T03:42:13,263   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/list
2026-03-13T03:42:13,264   copying build/lib/torchref/data/monomer_library/list/mon_lib_list.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/list
2026-03-13T03:42:13,322   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/c
2026-03-13T03:42:13,323   copying build/lib/torchref/data/monomer_library/c/CYS.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/c
2026-03-13T03:42:13,326   copying build/lib/torchref/data/monomer_library/c/C.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/c
2026-03-13T03:42:13,329   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/a
2026-03-13T03:42:13,330   copying build/lib/torchref/data/monomer_library/a/A.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a
2026-03-13T03:42:13,332   copying build/lib/torchref/data/monomer_library/a/ALA.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a
2026-03-13T03:42:13,334   copying build/lib/torchref/data/monomer_library/a/ARG.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a
2026-03-13T03:42:13,337   copying build/lib/torchref/data/monomer_library/a/ASP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a
2026-03-13T03:42:13,339   copying build/lib/torchref/data/monomer_library/a/ASN.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a
2026-03-13T03:42:13,341   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/p
2026-03-13T03:42:13,342   copying build/lib/torchref/data/monomer_library/p/PTR.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/p
2026-03-13T03:42:13,345   copying build/lib/torchref/data/monomer_library/p/PHE.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/p
2026-03-13T03:42:13,347   copying build/lib/torchref/data/monomer_library/p/PRO.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/p
2026-03-13T03:42:13,350   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/l
2026-03-13T03:42:13,351   copying build/lib/torchref/data/monomer_library/l/LYS.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/l
2026-03-13T03:42:13,353   copying build/lib/torchref/data/monomer_library/l/LEU.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/l
2026-03-13T03:42:13,355   copying build/lib/torchref/data/policy_latest.pt -> build/bdist.linux-armv7l/wheel/./torchref/data
2026-03-13T03:42:13,361   copying build/lib/torchref/data/atomic_vdw_radii.csv -> build/bdist.linux-armv7l/wheel/./torchref/data
2026-03-13T03:42:13,363   copying build/lib/torchref/data/rama_nll_surfaces.pt -> build/bdist.linux-armv7l/wheel/./torchref/data
2026-03-13T03:42:13,416   copying build/lib/torchref/data/default_hyperparameters.json -> build/bdist.linux-armv7l/wheel/./torchref/data
2026-03-13T03:42:13,419   creating build/bdist.linux-armv7l/wheel/torchref/restraints
2026-03-13T03:42:13,420   copying build/lib/torchref/restraints/builders_numba.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-03-13T03:42:13,423   copying build/lib/torchref/restraints/restraints_helper.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-03-13T03:42:13,425   copying build/lib/torchref/restraints/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-03-13T03:42:13,427   copying build/lib/torchref/restraints/library.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-03-13T03:42:13,429   copying build/lib/torchref/restraints/ramachandran.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-03-13T03:42:13,431   copying build/lib/torchref/restraints/builders_fast.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-03-13T03:42:13,435   copying build/lib/torchref/restraints/builders.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-03-13T03:42:13,438   copying build/lib/torchref/restraints/restraints.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-03-13T03:42:13,441   running install_egg_info
2026-03-13T03:42:13,446   Copying torchref.egg-info to build/bdist.linux-armv7l/wheel/./torchref-0.4.3-py3.11.egg-info
2026-03-13T03:42:13,457   running install_scripts
2026-03-13T03:42:13,468   creating build/bdist.linux-armv7l/wheel/torchref-0.4.3.dist-info/WHEEL
2026-03-13T03:42:13,470   creating '/tmp/pip-wheel-g9si4yxg/.tmp-5fioreb3/torchref-0.4.3-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2026-03-13T03:42:13,473   adding 'torchref/__init__.py'
2026-03-13T03:42:13,474   adding 'torchref/_bootstrap.py'
2026-03-13T03:42:13,475   adding 'torchref/config.py'
2026-03-13T03:42:13,478   adding 'torchref/alignment/__init__.py'
2026-03-13T03:42:13,485   adding 'torchref/alignment/ball_transform.py'
2026-03-13T03:42:13,488   adding 'torchref/alignment/clashscore.py'
2026-03-13T03:42:13,490   adding 'torchref/alignment/distributions.py'
2026-03-13T03:42:13,491   adding 'torchref/alignment/jax_subpixel_peaks.py'
2026-03-13T03:42:13,494   adding 'torchref/alignment/pipeline.py'
2026-03-13T03:42:13,496   adding 'torchref/alignment/rigid_body.py'
2026-03-13T03:42:13,498   adding 'torchref/alignment/sampling.py'
2026-03-13T03:42:13,502   adding 'torchref/alignment/transform.py'
2026-03-13T03:42:13,503   adding 'torchref/alignment/translation.py'
2026-03-13T03:42:13,505   adding 'torchref/base/CCTBX_related.py'
2026-03-13T03:42:13,507   adding 'torchref/base/__init__.py'
2026-03-13T03:42:13,511   adding 'torchref/base/french_wilson.py'
2026-03-13T03:42:13,513   adding 'torchref/base/get_scattering_factor_torch.py'
2026-03-13T03:42:13,516   adding 'torchref/base/math_numpy.py'
2026-03-13T03:42:13,518   adding 'torchref/base/math_torch.py'
2026-03-13T03:42:13,520   adding 'torchref/base/alignment/__init__.py'
2026-03-13T03:42:13,522   adding 'torchref/base/alignment/normalization.py'
2026-03-13T03:42:13,524   adding 'torchref/base/alignment/rotation.py'
2026-03-13T03:42:13,525   adding 'torchref/base/alignment/scoring.py'
2026-03-13T03:42:13,527   adding 'torchref/base/alignment/superposition.py'
2026-03-13T03:42:13,529   adding 'torchref/base/chain_closure/__init__.py'
2026-03-13T03:42:13,531   adding 'torchref/base/chain_closure/backbone_utils.py'
2026-03-13T03:42:13,534   adding 'torchref/base/chain_closure/closure.py'
2026-03-13T03:42:13,536   adding 'torchref/base/coordinates/__init__.py'
2026-03-13T03:42:13,537   adding 'torchref/base/coordinates/periodic_boundary.py'
2026-03-13T03:42:13,539   adding 'torchref/base/coordinates/transforms_numpy.py'
2026-03-13T03:42:13,540   adding 'torchref/base/coordinates/transforms_torch.py'
2026-03-13T03:42:13,542   adding 'torchref/base/direct_summation/__init__.py'
2026-03-13T03:42:13,544   adding 'torchref/base/direct_summation/anisotropic.py'
2026-03-13T03:42:13,545   adding 'torchref/base/direct_summation/corrections.py'
2026-03-13T03:42:13,546   adding 'torchref/base/direct_summation/isotropic.py'
2026-03-13T03:42:13,548   adding 'torchref/base/electron_density/__init__.py'
2026-03-13T03:42:13,552   adding 'torchref/base/electron_density/main.py'
2026-03-13T03:42:13,553   adding 'torchref/base/electron_density/map_building.py'
2026-03-13T03:42:13,555   adding 'torchref/base/electron_density/solvent_mask.py'
2026-03-13T03:42:13,557   adding 'torchref/base/electron_density/voxel_utils.py'
2026-03-13T03:42:13,559   adding 'torchref/base/fourier/__init__.py'
2026-03-13T03:42:13,560   adding 'torchref/base/fourier/fft.py'
2026-03-13T03:42:13,562   adding 'torchref/base/fourier/grid.py'
2026-03-13T03:42:13,564   adding 'torchref/base/kernels/__init__.py'
2026-03-13T03:42:13,565   adding 'torchref/base/kernels/cpu_scatter.py'
2026-03-13T03:42:13,568   adding 'torchref/base/kernels/jit_kernel_vectorized_add_to_map.py'
2026-03-13T03:42:13,570   adding 'torchref/base/kernels/optimized_ops.py'
2026-03-13T03:42:13,574   adding 'torchref/base/kernels/separable_triton_kernel.py'
2026-03-13T03:42:13,578   adding 'torchref/base/kernels/triton_kernel.py'
2026-03-13T03:42:13,580   adding 'torchref/base/metrics/__init__.py'
2026-03-13T03:42:13,581   adding 'torchref/base/metrics/loss.py'
2026-03-13T03:42:13,583   adding 'torchref/base/metrics/rfactor.py'
2026-03-13T03:42:13,585   adding 'torchref/base/reciprocal/__init__.py'
2026-03-13T03:42:13,586   adding 'torchref/base/reciprocal/basis.py'
2026-03-13T03:42:13,588   adding 'torchref/base/reciprocal/grid_operations.py'
2026-03-13T03:42:13,589   adding 'torchref/base/reciprocal/hkl.py'
2026-03-13T03:42:13,591   adding 'torchref/base/reciprocal/interpolation.py'
2026-03-13T03:42:13,593   adding 'torchref/base/reciprocal/symmetry.py'
2026-03-13T03:42:13,595   adding 'torchref/base/scattering/__init__.py'
2026-03-13T03:42:13,597   adding 'torchref/base/scattering/anomalous_table.py'
2026-03-13T03:42:13,599   adding 'torchref/base/scattering/itc92.py'
2026-03-13T03:42:13,600   adding 'torchref/base/scattering/scattering_table.py'
2026-03-13T03:42:13,602   adding 'torchref/cli/__init__.py'
2026-03-13T03:42:13,605   adding 'torchref/cli/_common.py'
2026-03-13T03:42:13,609   adding 'torchref/cli/difference_refine.py'
2026-03-13T03:42:13,611   adding 'torchref/cli/mtz2map.py'
2026-03-13T03:42:13,613   adding 'torchref/cli/phased_difference_map.py'
2026-03-13T03:42:13,615   adding 'torchref/cli/refine.py'
2026-03-13T03:42:13,617   adding 'torchref/cli/refine_everything_hyperparameters.py'
2026-03-13T03:42:13,619   adding 'torchref/cli/refine_everything_policy.py'
2026-03-13T03:42:13,621   adding 'torchref/cli/refine_everything_random_weights.py'
2026-03-13T03:42:13,623   adding 'torchref/cli/refine_everything_static.py'
2026-03-13T03:42:13,626   adding 'torchref/cli/validate_ded.py'
2026-03-13T03:42:13,628   adding 'torchref/data/atomic_vdw_radii.csv'
2026-03-13T03:42:13,629   adding 'torchref/data/default_hyperparameters.json'
2026-03-13T03:42:13,631   adding 'torchref/data/itc92_scattering_factors.pt'
2026-03-13T03:42:13,669   adding 'torchref/data/policy_latest.pt'
2026-03-13T03:42:13,905   adding 'torchref/data/rama_nll_surfaces.pt'
2026-03-13T03:42:13,927   adding 'torchref/data/monomer_library/a/A.cif'
2026-03-13T03:42:13,929   adding 'torchref/data/monomer_library/a/ALA.cif'
2026-03-13T03:42:13,931   adding 'torchref/data/monomer_library/a/ARG.cif'
2026-03-13T03:42:13,932   adding 'torchref/data/monomer_library/a/ASN.cif'
2026-03-13T03:42:13,934   adding 'torchref/data/monomer_library/a/ASP.cif'
2026-03-13T03:42:13,936   adding 'torchref/data/monomer_library/c/C.cif'
2026-03-13T03:42:13,938   adding 'torchref/data/monomer_library/c/CYS.cif'
2026-03-13T03:42:13,940   adding 'torchref/data/monomer_library/d/DA.cif'
2026-03-13T03:42:13,943   adding 'torchref/data/monomer_library/d/DC.cif'
2026-03-13T03:42:13,945   adding 'torchref/data/monomer_library/d/DG.cif'
2026-03-13T03:42:13,947   adding 'torchref/data/monomer_library/d/DT.cif'
2026-03-13T03:42:13,950   adding 'torchref/data/monomer_library/g/G.cif'
2026-03-13T03:42:13,951   adding 'torchref/data/monomer_library/g/GLN.cif'
2026-03-13T03:42:13,953   adding 'torchref/data/monomer_library/g/GLU.cif'
2026-03-13T03:42:13,954   adding 'torchref/data/monomer_library/g/GLY.cif'
2026-03-13T03:42:13,957   adding 'torchref/data/monomer_library/h/HIS.cif'
2026-03-13T03:42:13,958   adding 'torchref/data/monomer_library/h/HOH.cif'
2026-03-13T03:42:13,960   adding 'torchref/data/monomer_library/h/HYP.cif'
2026-03-13T03:42:13,962   adding 'torchref/data/monomer_library/i/ILE.cif'
2026-03-13T03:42:13,964   adding 'torchref/data/monomer_library/l/LEU.cif'
2026-03-13T03:42:13,966   adding 'torchref/data/monomer_library/l/LYS.cif'
2026-03-13T03:42:14,508   adding 'torchref/data/monomer_library/list/mon_lib_list.cif'
2026-03-13T03:42:14,535   adding 'torchref/data/monomer_library/m/MET.cif'
2026-03-13T03:42:14,537   adding 'torchref/data/monomer_library/m/MSE.cif'
2026-03-13T03:42:14,539   adding 'torchref/data/monomer_library/p/PHE.cif'
2026-03-13T03:42:14,541   adding 'torchref/data/monomer_library/p/PRO.cif'
2026-03-13T03:42:14,542   adding 'torchref/data/monomer_library/p/PTR.cif'
2026-03-13T03:42:14,544   adding 'torchref/data/monomer_library/s/SEP.cif'
2026-03-13T03:42:14,546   adding 'torchref/data/monomer_library/s/SER.cif'
2026-03-13T03:42:14,548   adding 'torchref/data/monomer_library/t/THR.cif'
2026-03-13T03:42:14,549   adding 'torchref/data/monomer_library/t/TPO.cif'
2026-03-13T03:42:14,551   adding 'torchref/data/monomer_library/t/TRP.cif'
2026-03-13T03:42:14,553   adding 'torchref/data/monomer_library/t/TYR.cif'
2026-03-13T03:42:14,556   adding 'torchref/data/monomer_library/u/U.cif'
2026-03-13T03:42:14,558   adding 'torchref/data/monomer_library/v/VAL.cif'
2026-03-13T03:42:14,560   adding 'torchref/io/__init__.py'
2026-03-13T03:42:14,561   adding 'torchref/io/cif.py'
2026-03-13T03:42:14,569   adding 'torchref/io/cif_readers.py'
2026-03-13T03:42:14,571   adding 'torchref/io/data_router.py'
2026-03-13T03:42:14,573   adding 'torchref/io/mtz.py'
2026-03-13T03:42:14,576   adding 'torchref/io/pdb.py'
2026-03-13T03:42:14,578   adding 'torchref/io/datasets/__init__.py'
2026-03-13T03:42:14,580   adding 'torchref/io/datasets/base.py'
2026-03-13T03:42:14,582   adding 'torchref/io/datasets/collection.py'
2026-03-13T03:42:14,584   adding 'torchref/io/datasets/fcalc_data.py'
2026-03-13T03:42:14,596   adding 'torchref/io/datasets/reflection_data.py'
2026-03-13T03:42:14,598   adding 'torchref/maps/__init__.py'
2026-03-13T03:42:14,600   adding 'torchref/maps/difference_map.py'
2026-03-13T03:42:14,601   adding 'torchref/maps/map.py'
2026-03-13T03:42:14,603   adding 'torchref/model/__init__.py'
2026-03-13T03:42:14,612   adding 'torchref/model/closed_segmented_internal_coordinates.py'
2026-03-13T03:42:14,620   adding 'torchref/model/internal_coordinates.py'
2026-03-13T03:42:14,623   adding 'torchref/model/mixed_model.py'
2026-03-13T03:42:14,636   adding 'torchref/model/model.py'
2026-03-13T03:42:14,641   adding 'torchref/model/model_ft.py'
2026-03-13T03:42:14,650   adding 'torchref/model/parameter_wrappers.py'
2026-03-13T03:42:14,658   adding 'torchref/model/segmented_internal_coordinates.py'
2026-03-13T03:42:14,660   adding 'torchref/model/sf_ds.py'
2026-03-13T03:42:14,663   adding 'torchref/model/sf_fft.py'
2026-03-13T03:42:14,665   adding 'torchref/refinement/__init__.py'
2026-03-13T03:42:14,669   adding 'torchref/refinement/base_refinement.py'
2026-03-13T03:42:14,672   adding 'torchref/refinement/lbfgs_refinement.py'
2026-03-13T03:42:14,674   adding 'torchref/refinement/logger.py'
2026-03-13T03:42:14,677   adding 'torchref/refinement/loss_state.py'
2026-03-13T03:42:14,679   adding 'torchref/refinement/optimizers/__init__.py'
2026-03-13T03:42:14,680   adding 'torchref/refinement/optimizers/adam_noise.py'
2026-03-13T03:42:14,684   adding 'torchref/refinement/optimizers/exploratory_lbfgs.py'
2026-03-13T03:42:14,687   adding 'torchref/refinement/optimizers/internal_coord_sa.py'
2026-03-13T03:42:14,690   adding 'torchref/refinement/optimizers/langevin_sa.py'
2026-03-13T03:42:14,691   adding 'torchref/refinement/optimizers/momentum_sa.py'
2026-03-13T03:42:14,693   adding 'torchref/refinement/optimizers/simulated_annealing.py'
2026-03-13T03:42:14,694   adding 'torchref/refinement/targets/__init__.py'
2026-03-13T03:42:14,700   adding 'torchref/refinement/targets/amber_target.py'
2026-03-13T03:42:14,702   adding 'torchref/refinement/targets/base.py'
2026-03-13T03:42:14,705   adding 'torchref/refinement/targets/combined.py'
2026-03-13T03:42:14,710   adding 'torchref/refinement/targets/difference.py'
2026-03-13T03:42:14,712   adding 'torchref/refinement/targets/forcefield_target.py'
2026-03-13T03:42:14,714   adding 'torchref/refinement/targets/occupancy_floor_diagnostic.py'
2026-03-13T03:42:14,717   adding 'torchref/refinement/targets/realspace.py'
2026-03-13T03:42:14,721   adding 'torchref/refinement/targets/sampled_ml_phase_target.py'
2026-03-13T03:42:14,723   adding 'torchref/refinement/targets/adp/__init__.py'
2026-03-13T03:42:14,724   adding 'torchref/refinement/targets/adp/base.py'
2026-03-13T03:42:14,726   adding 'torchref/refinement/targets/adp/entropy.py'
2026-03-13T03:42:14,727   adding 'torchref/refinement/targets/adp/locality.py'
2026-03-13T03:42:14,729   adding 'torchref/refinement/targets/adp/rigid_bond.py'
2026-03-13T03:42:14,731   adding 'torchref/refinement/targets/adp/similarity.py'
2026-03-13T03:42:14,732   adding 'torchref/refinement/targets/geometry/__init__.py'
2026-03-13T03:42:14,734   adding 'torchref/refinement/targets/geometry/angles.py'
2026-03-13T03:42:14,735   adding 'torchref/refinement/targets/geometry/base.py'
2026-03-13T03:42:14,736   adding 'torchref/refinement/targets/geometry/bonds.py'
2026-03-13T03:42:14,738   adding 'torchref/refinement/targets/geometry/chiral.py'
2026-03-13T03:42:14,740   adding 'torchref/refinement/targets/geometry/non_bonded.py'
2026-03-13T03:42:14,741   adding 'torchref/refinement/targets/geometry/planarity.py'
2026-03-13T03:42:14,742   adding 'torchref/refinement/targets/geometry/ramachandran.py'
2026-03-13T03:42:14,744   adding 'torchref/refinement/targets/geometry/torsions.py'
2026-03-13T03:42:14,746   adding 'torchref/refinement/targets/xray/__init__.py'
2026-03-13T03:42:14,747   adding 'torchref/refinement/targets/xray/base.py'
2026-03-13T03:42:14,748   adding 'torchref/refinement/targets/xray/gaussian.py'
2026-03-13T03:42:14,750   adding 'torchref/refinement/targets/xray/least_squares.py'
2026-03-13T03:42:14,751   adding 'torchref/refinement/targets/xray/maximum_likelihood.py'
2026-03-13T03:42:14,753   adding 'torchref/refinement/weighting/__init__.py'
2026-03-13T03:42:14,754   adding 'torchref/refinement/weighting/base_weighting.py'
2026-03-13T03:42:14,757   adding 'torchref/refinement/weighting/component_weighting.py'
2026-03-13T03:42:14,759   adding 'torchref/refinement/weighting/es_policy_training.py'
2026-03-13T03:42:14,762   adding 'torchref/refinement/weighting/policy_weighting.py'
2026-03-13T03:42:14,765   adding 'torchref/refinement/weighting/random_weighting.py'
2026-03-13T03:42:14,767   adding 'torchref/restraints/__init__.py'
2026-03-13T03:42:14,772   adding 'torchref/restraints/builders.py'
2026-03-13T03:42:14,779   adding 'torchref/restraints/builders_fast.py'
2026-03-13T03:42:14,783   adding 'torchref/restraints/builders_numba.py'
2026-03-13T03:42:14,785   adding 'torchref/restraints/library.py'
2026-03-13T03:42:14,786   adding 'torchref/restraints/ramachandran.py'
2026-03-13T03:42:14,794   adding 'torchref/restraints/restraints.py'
2026-03-13T03:42:14,797   adding 'torchref/restraints/restraints_helper.py'
2026-03-13T03:42:14,799   adding 'torchref/scaling/__init__.py'
2026-03-13T03:42:14,801   adding 'torchref/scaling/scaler.py'
2026-03-13T03:42:14,806   adding 'torchref/scaling/scaler_base.py'
2026-03-13T03:42:14,809   adding 'torchref/scaling/solvent.py'
2026-03-13T03:42:14,810   adding 'torchref/scripts/__init__.py'
2026-03-13T03:42:14,812   adding 'torchref/scripts/generate_scattering_table.py'
2026-03-13T03:42:14,814   adding 'torchref/symmetry/__init__.py'
2026-03-13T03:42:14,816   adding 'torchref/symmetry/cell.py'
2026-03-13T03:42:14,817   adding 'torchref/symmetry/grid_utils.py'
2026-03-13T03:42:14,819   adding 'torchref/symmetry/map_symmetry.py'
2026-03-13T03:42:14,821   adding 'torchref/symmetry/map_symmetry_interpolation.py'
2026-03-13T03:42:14,828   adding 'torchref/symmetry/reciprocal_symmetry.py'
2026-03-13T03:42:14,831   adding 'torchref/symmetry/spacegroup.py'
2026-03-13T03:42:14,833   adding 'torchref/symmetry/symmetry.py'
2026-03-13T03:42:14,835   adding 'torchref/utils/__init__.py'
2026-03-13T03:42:14,836   adding 'torchref/utils/caching.py'
2026-03-13T03:42:14,838   adding 'torchref/utils/debug_utils.py'
2026-03-13T03:42:14,840   adding 'torchref/utils/device_mixin.py'
2026-03-13T03:42:14,841   adding 'torchref/utils/gradnorm.py'
2026-03-13T03:42:14,843   adding 'torchref/utils/hyperparameters.py'
2026-03-13T03:42:14,844   adding 'torchref/utils/pse.py'
2026-03-13T03:42:14,846   adding 'torchref/utils/serialization.py'
2026-03-13T03:42:14,847   adding 'torchref/utils/stats.py'
2026-03-13T03:42:14,849   adding 'torchref/utils/timing.py'
2026-03-13T03:42:14,854   adding 'torchref/utils/utils.py'
2026-03-13T03:42:14,856   adding 'torchref-0.4.3.dist-info/licenses/LICENSE'
2026-03-13T03:42:14,858   adding 'torchref-0.4.3.dist-info/METADATA'
2026-03-13T03:42:14,859   adding 'torchref-0.4.3.dist-info/WHEEL'
2026-03-13T03:42:14,860   adding 'torchref-0.4.3.dist-info/entry_points.txt'
2026-03-13T03:42:14,861   adding 'torchref-0.4.3.dist-info/top_level.txt'
2026-03-13T03:42:14,864   adding 'torchref-0.4.3.dist-info/RECORD'
2026-03-13T03:42:14,899   removing build/bdist.linux-armv7l/wheel
2026-03-13T03:42:15,090   Building wheel for torchref (pyproject.toml): finished with status 'done'
2026-03-13T03:42:15,600   Created wheel for torchref: filename=torchref-0.4.3-py3-none-any.whl size=3057084 sha256=3224a4185d64c6f2b269ee377bc5c0f6dacf3a13898fd11e73a727a462a2d878
2026-03-13T03:42:15,601   Stored in directory: /tmp/pip-ephem-wheel-cache-rtxeft0w/wheels/e5/2a/4d/6aac65bbf2506c27358c721c030a4f03eab1e597d273a3d425
2026-03-13T03:42:15,620 Successfully built torchref
2026-03-13T03:42:15,697 Removed build tracker: '/tmp/pip-build-tracker-a8avkoc0'