[2026-05-12 11:26:49] Pipeline started. Working dir: /Users/ario/conserved_site_project
venv created
Python 3.11.9
    Uninstalling pip-24.0:
      Successfully uninstalled pip-24.0
Successfully installed packaging-26.2 pip-26.1.1 setuptools-82.0.1 wheel-0.47.0
--- Trying optional/heavy deps ---
      Directories searched: conda env, /usr/local/include and /usr/include.
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed to build 'vina' when getting requirements to build wheel
--- Brew installs ---
==> Running `brew cleanup mafft`...
Disable this behaviour by setting `HOMEBREW_NO_INSTALL_CLEANUP=1`.
Hide these hints with `HOMEBREW_NO_ENV_HINTS=1` (see `man brew`).
Running these by name will not invoke the version provided by Homebrew.
Disable this behaviour by setting `HOMEBREW_NO_PATH_SHADOW_CHECK=1`.
Hide these hints with `HOMEBREW_NO_ENV_HINTS=1` (see `man brew`).
--- Final check ---
/opt/homebrew/bin/mafft
/Users/ario/conserved_site_project/.venv/bin/obabel
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/ario/conserved_site_project/.venv/lib/python3.11/site-packages/meeko/__init__.py", line 27, in <module>
    from .polymer import Polymer
  File "/Users/ario/conserved_site_project/.venv/lib/python3.11/site-packages/meeko/polymer.py", line 33, in <module>
    from .chemtempgen import export_chem_templates_to_json
  File "/Users/ario/conserved_site_project/.venv/lib/python3.11/site-packages/meeko/chemtempgen.py", line 1, in <module>
    import gemmi
ModuleNotFoundError: No module named 'gemmi'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'vina'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/ario/conserved_site_project/.venv/lib/python3.11/site-packages/pymol/__init__.py", line 558, in <module>
    import pymol._cmd
ImportError: dlopen(/Users/ario/conserved_site_project/.venv/lib/python3.11/site-packages/pymol/_cmd.cpython-311-darwin.so, 0x0002): Library not loaded: @rpath/libxml2.2.dylib
  Referenced from: <E5AC15DC-1F64-3F79-83A0-2E66C328B776> /Users/ario/conserved_site_project/.venv/lib/python3.11/site-packages/pymol/_cmd.cpython-311-darwin.so
  Reason: tried: '/Users/Martin/.local/share/mamba/envs/pymol_311/lib/libxml2.2.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/Martin/.local/share/mamba/envs/pymol_311/lib/libxml2.2.dylib' (no such file), '/Users/Martin/.local/share/mamba/envs/pymol_311/lib/libxml2.2.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/Martin/.local/share/mamba/envs/pymol_311/lib/libxml2.2.dylib' (no such file), '/Users/ario/.pyenv/versions/3.11.9/lib/libxml2.2.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/ario/.pyenv/versions/3.11.9/lib/libxml2.2.dylib' (no such file), '/opt/homebrew/lib/libxml2.2.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/lib/libxml2.2.dylib' (no such file), '/Users/ario/.pyenv/versions/3.11.9/lib/libxml2.2.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/ario/.pyenv/versions/3.11.9/lib/libxml2.2.dylib' (no such file), '/opt/homebrew/lib/libxml2.2.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/lib/libxml2.2.dylib' (no such file)
=== installing gemmi for meeko ===
=== brew autodock-vina ===
==> Casks
autodesk-fusion

To install autodesk-fusion, run:
  brew install --cask autodesk-fusion
=== brew pymol via brewsci/bio ===
The following pymol executables are shadowed by other commands earlier in your PATH:
  pymol (shadowed by /Users/ario/conserved_site_project/.venv/bin/pymol)
Running these by name will not invoke the version provided by Homebrew.
Disable this behaviour by setting `HOMEBREW_NO_PATH_SHADOW_CHECK=1`.
Hide these hints with `HOMEBREW_NO_ENV_HINTS=1` (see `man brew`).
=== libxml2 for python pymol ===
/opt/homebrew/opt/libxml2/lib/libxml2.2.dylib
/opt/homebrew/opt/libxml2/lib/libxml2.dylib
=== rechecks ===
vina not found
/Users/ario/conserved_site_project/.venv/bin/pymol
/opt/homebrew/bin/mafft
/Users/ario/conserved_site_project/.venv/bin/obabel
meeko OK
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/ario/conserved_site_project/.venv/lib/python3.11/site-packages/pymol/__init__.py", line 558, in <module>
    import pymol._cmd
ImportError: dlopen(/Users/ario/conserved_site_project/.venv/lib/python3.11/site-packages/pymol/_cmd.cpython-311-darwin.so, 0x0002): Library not loaded: @rpath/libGLEW.2.1.dylib
  Referenced from: <E5AC15DC-1F64-3F79-83A0-2E66C328B776> /Users/ario/conserved_site_project/.venv/lib/python3.11/site-packages/pymol/_cmd.cpython-311-darwin.so
  Reason: tried: '/Users/Martin/.local/share/mamba/envs/pymol_311/lib/libGLEW.2.1.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/Martin/.local/share/mamba/envs/pymol_311/lib/libGLEW.2.1.dylib' (no such file), '/Users/Martin/.local/share/mamba/envs/pymol_311/lib/libGLEW.2.1.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/Martin/.local/share/mamba/envs/pymol_311/lib/libGLEW.2.1.dylib' (no such file), '/Users/ario/.pyenv/versions/3.11.9/lib/libGLEW.2.1.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/ario/.pyenv/versions/3.11.9/lib/libGLEW.2.1.dylib' (no such file), '/opt/homebrew/lib/libGLEW.2.1.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/lib/libGLEW.2.1.dylib' (no such file), '/Users/ario/.pyenv/versions/3.11.9/lib/libGLEW.2.1.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/ario/.pyenv/versions/3.11.9/lib/libGLEW.2.1.dylib' (no such file), '/opt/homebrew/lib/libGLEW.2.1.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/lib/libGLEW.2.1.dylib' (no such file), '/opt/homebrew/opt/libxml2/lib/libGLEW.2.1.dylib' (no such file)
(eval):15: command not found: vina
[2026-05-12 11:40:23] Environment ready
vina=/opt/homebrew/bin/vina | pymol=/opt/homebrew/bin/pymol | mafft=/opt/homebrew/bin/mafft | obabel=/Users/ario/conserved_site_project/.venv/bin/obabel
venv: python: aliased to python3 (Python 3.11.9)
[2026-05-12 11:41:10] PROTEIN CHOICE: TYMS (Thymidylate Synthase, P04818, 313 aa)
RATIONALE:
- Direct CRC link: TYMS is the molecular target of 5-fluorouracil (5-FU), the
  backbone of CRC chemotherapy for >50 years. TYMS expression predicts 5-FU
  response and is itself a CRC prognostic marker.
- Size: 313 aa (within 150-400 aa window).
- Bound natural substrate: dUMP (2'-deoxyuridine 5'-monophosphate) is present
  in many human TS PDB structures (e.g., 1HVY, 1HW4, 2RD8). The methylene-
  THF cofactor or analogs co-bind. dUMP is the true natural substrate, not
  an inhibitor.
- Conservation: TYMS is one of the most ancient/conserved enzymes — clear
  orthologs in Bacteria, Archaea, Fungi, Plants, Animals.
- Active site is a tight pocket (not a 30 A cleft) with well-defined
  catalytic residues: Cys195 (nucleophile, Michael addition to C6 of dUMP),
  Arg50/176/215 (phosphate clamp), His196/Asn226/Tyr135 (proton shuttle &
  substrate orientation).
PDB: 1HVY (human TS, 1.9 A, dUMP + raltitrexed). dUMP is the natural substrate;
the polyglutamylated CB3717/raltitrexed mimics the methylene-THF cofactor.
[2026-05-12 11:44:03] STAGE1: Stage 1 starting
[2026-05-12 11:44:03] STAGE1: Fetching sequences from UniProt
[2026-05-12 11:44:04] STAGE1: got P04818 (Homo_sapiens)
[2026-05-12 11:44:05] STAGE1: got P07607 (Mus_musculus)
[2026-05-12 11:44:06] STAGE1: got P04394 (Escherichia_coli)
[2026-05-12 11:44:07] STAGE1: got P04996 (Lactobacillus_casei)
[2026-05-12 11:44:08] STAGE1: got P0CG53 (Saccharomyces_cerevisiae)
[2026-05-12 11:44:09] STAGE1: got O44019 (Caenorhabditis_elegans)
[2026-05-12 11:44:11] STAGE1: FAILED Q9V3K2 (Drosophila_melanogaster)
[2026-05-12 11:44:13] STAGE1: got P11849 (Bacteriophage_T4)
[2026-05-12 11:44:14] STAGE1: got P21520 (Plasmodium_falciparum)
[2026-05-12 11:44:14] STAGE1: Fetched 8 sequences: ['Homo_sapiens', 'Mus_musculus', 'Escherichia_coli', 'Lactobacillus_casei', 'Saccharomyces_cerevisiae', 'Caenorhabditis_elegans', 'Bacteriophage_T4', 'Plasmodium_falciparum']
[2026-05-12 11:44:14] STAGE1: Wrote input.fa with 8 sequences
[2026-05-12 11:44:14] STAGE1: Running MAFFT --auto
[2026-05-12 11:44:17] STAGE1: MAFFT done
[2026-05-12 11:44:17] STAGE1: Aligned 8 sequences, length 970
[2026-05-12 11:44:17] STAGE1: Reference is row 0, ungapped length 313
[2026-05-12 11:44:17] STAGE1: Wrote /Users/ario/conserved_site_project/01_msa/conservation_scores.csv (313 rows)
[2026-05-12 11:44:18] STAGE1: Wrote /Users/ario/conserved_site_project/01_msa/conservation_plot.png
[2026-05-12 11:44:18] STAGE1: Stage 1 DONE
[2026-05-12 11:45:00] STAGE2: Stage 2 starting
[2026-05-12 11:45:00] STAGE2: Fetching UniProt P04818 features
[2026-05-12 11:45:01] STAGE2: UniProt: 14 unique annotated positions
[2026-05-12 11:45:01] STAGE2: Fetching PDBe binding sites for 1HVY
[2026-05-12 11:46:08] STAGE2: Stage 2 starting
[2026-05-12 11:46:08] STAGE2: Fetching UniProt P04818 features
[2026-05-12 11:46:09] STAGE2: UniProt: 14 unique annotated positions
[2026-05-12 11:46:09] STAGE2: Fetching PDBe ligand monomers for 1HVY
[2026-05-12 11:46:10] STAGE2: Chain-A target ligands: [('bm1', 'D16'), ('bm2', 'UMP')]
[2026-05-12 11:46:13] STAGE2: PDBe: 21 unique residues binding UMP/D16
[2026-05-12 11:46:13] STAGE2: Wrote active_site_residues.csv with 24 residues
[2026-05-12 11:46:13] STAGE2: Wrote overlap_table.csv
[2026-05-12 11:46:13] STAGE2: Wrote overlap_figure.png
[2026-05-12 11:46:13] STAGE2: Final selected residues (6, threshold top-25%): [80, 217, 218, 225, 226, 258]
[2026-05-12 11:46:13] STAGE2: Stage 2 DONE
[2026-05-12 11:46:46] STAGE2: Stage 2 starting
[2026-05-12 11:46:46] STAGE2: Fetching UniProt P04818 features
[2026-05-12 11:46:47] STAGE2: UniProt: 14 unique annotated positions
[2026-05-12 11:46:47] STAGE2: Fetching PDBe ligand monomers for 1HVY
[2026-05-12 11:46:48] STAGE2: Chain-A target ligands: [('bm1', 'D16'), ('bm2', 'UMP')]
[2026-05-12 11:46:51] STAGE2: PDBe: 21 unique residues binding UMP/D16
[2026-05-12 11:46:51] STAGE2: Wrote active_site_residues.csv with 24 residues
[2026-05-12 11:46:51] STAGE2: Wrote overlap_table.csv
[2026-05-12 11:46:51] STAGE2: Wrote overlap_figure.png
[2026-05-12 11:46:51] STAGE2: Augmented with catalytic residue 195
[2026-05-12 11:46:51] STAGE2: Augmented with catalytic residue 196
[2026-05-12 11:46:51] STAGE2: Final selected residues (8, threshold top-25% +catalytic): [80, 195, 196, 217, 218, 225, 226, 258]
[2026-05-12 11:46:51] STAGE2: Stage 2 DONE
[2026-05-12 11:47:23] STAGE3: Downloading 1HVY
[2026-05-12 11:47:23] STAGE3: Got from RCSB
[2026-05-12 11:47:23] STAGE3: raw 1hvy size: 896022 bytes
[2026-05-12 11:47:23] STAGE3: wrote /Users/ario/conserved_site_project/03_structure/protein_chainA.pdb
[2026-05-12 11:47:23] STAGE3: wrote /Users/ario/conserved_site_project/03_structure/ligand.pdb
[2026-05-12 11:47:23] STAGE3: wrote /Users/ario/conserved_site_project/03_structure/cofactor.pdb
[2026-05-12 11:47:23] STAGE3: Adding hydrogens to protein with obabel
[2026-05-12 11:48:21] STAGE3: protein_h.pdb size 701977
[2026-05-12 11:48:21] STAGE3: Adding hydrogens to ligand with obabel
[2026-05-12 11:48:21] STAGE3: ligand_h.pdb size 5576
[2026-05-12 11:48:21] STAGE3: Selected residues check: 8 requested, 0 missing: []
[2026-05-12 11:48:21] STAGE3: Stage 3 DONE
[2026-05-12 11:48:49] STAGE4: Selected residues: [80, 195, 196, 217, 218, 225, 226, 258]
[2026-05-12 11:48:49] STAGE4: wrote /Users/ario/conserved_site_project/03_structure/protein_cons.pdb
[2026-05-12 11:48:49] STAGE4: running pymol script 01_overview
[2026-05-12 11:48:51] STAGE4: pymol 01_overview: rc=0
[2026-05-12 11:48:51] STAGE4: running pymol script 02_closeup
[2026-05-12 11:48:52] STAGE4: pymol 02_closeup: rc=0
[2026-05-12 11:48:52] STAGE4: running pymol script 03_conservation
[2026-05-12 11:48:53] STAGE4: pymol 03_conservation: rc=0
[2026-05-12 11:48:53] STAGE4: running pymol script 04_cavity
[2026-05-12 11:48:53] STAGE4: pymol 04_cavity: rc=0
[2026-05-12 11:48:53] STAGE4: OK 01_overview.png (561771 bytes)
[2026-05-12 11:48:53] STAGE4: OK 02_closeup.png (668353 bytes)
[2026-05-12 11:48:53] STAGE4: OK 03_conservation.png (517382 bytes)
[2026-05-12 11:48:53] STAGE4: OK 04_cavity.png (60960 bytes)
[2026-05-12 11:48:53] STAGE4: Stage 4 DONE
[2026-05-12 11:49:57] STAGE5_6: Stage 5: ligand prep
[2026-05-12 11:49:57] STAGE5_6: obabel ligand→pdbqt rc=0
[2026-05-12 11:49:57] STAGE5_6: ligand.pdbqt size=2509, has_UNK=False
[2026-05-12 11:49:57] STAGE5_6: Stage 5 DONE
[2026-05-12 11:49:57] STAGE5_6: Stage 6: WT docking
[2026-05-12 11:49:59] STAGE5_6: meeko receptor WT rc=2
[2026-05-12 11:49:59] STAGE5_6: meeko failed: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 11:49:59] STAGE5_6: obabel receptor WT rc=0
[2026-05-12 11:49:59] STAGE5_6: centroid from 8 CA atoms: [-1.286625   9.1467495 12.0295   ]
[2026-05-12 11:49:59] STAGE5_6: vina cmd: /opt/homebrew/bin/vina --receptor /Users/ario/conserved_site_project/06_docking_wt/protein_wt.pdbqt --ligand /Users/ario/conserved_site_project/05_ligand/ligand.pdbqt --center_x -1.287 --center_y 9.147 --center_z 12.030 --size_x 22 --size_y 22 --size_z 22 --exhaustiveness 16 --num_modes 20 --seed 42 --out /Users/ario/conserved_site_project/06_docking_wt/wt_poses.pdbqt --cpu 4
[2026-05-12 11:50:08] STAGE5_6: vina affinities: []
[2026-05-12 11:50:08] STAGE5_6: top affinity nan kcal/mol, mean_top3 nan, rmsd_to_native 1.08 A
[2026-05-12 11:50:09] STAGE5_6: wrote wt_topdock.png (741525 bytes)
[2026-05-12 11:50:09] STAGE5_6: Stage 6 DONE
[2026-05-12 11:52:06] STAGE7: Stage 7 starting
[2026-05-12 11:52:06] STAGE7: Active site residues: [80, 195, 196, 217, 218, 225, 226, 258]
[2026-05-12 11:52:07] STAGE7: Control: T170A (distance 32.3 Å from active centroid)
[2026-05-12 11:52:07] STAGE7: Total mutations to test: 21
[2026-05-12 11:52:07] STAGE7: [1/21] F80A (single_ala)
[2026-05-12 11:52:09] STAGE5_6: meeko receptor F80A rc=2
[2026-05-12 11:52:09] STAGE5_6: meeko failed: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 11:52:10] STAGE5_6: obabel receptor F80A rc=0
[2026-05-12 11:52:17] STAGE7:   F80A: top=-7.73 Δ=-0.00 rmsd=1.09
[2026-05-12 11:52:17] STAGE7: [2/21] F80D (single_opposite)
[2026-05-12 11:52:19] STAGE5_6: meeko receptor F80D rc=2
[2026-05-12 11:52:19] STAGE5_6: meeko failed: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 11:52:20] STAGE5_6: obabel receptor F80D rc=0
[2026-05-12 11:52:27] STAGE7:   F80D: top=-7.69 Δ=+0.04 rmsd=1.04
[2026-05-12 11:52:27] STAGE7: [3/21] C195A (single_ala)
[2026-05-12 11:52:29] STAGE5_6: meeko receptor C195A rc=2
[2026-05-12 11:52:29] STAGE5_6: meeko failed: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 11:52:29] STAGE5_6: obabel receptor C195A rc=0
[2026-05-12 11:52:36] STAGE7:   C195A: top=-8.00 Δ=-0.27 rmsd=0.89
[2026-05-12 11:52:36] STAGE7: [4/21] C195S (single_opposite)
[2026-05-12 11:52:39] STAGE5_6: meeko receptor C195S rc=2
[2026-05-12 11:52:39] STAGE5_6: meeko failed: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 11:52:39] STAGE5_6: obabel receptor C195S rc=0
[2026-05-12 11:52:46] STAGE7:   C195S: top=-8.11 Δ=-0.38 rmsd=0.55
[2026-05-12 11:52:46] STAGE7: [5/21] H196A (single_ala)
[2026-05-12 11:52:48] STAGE5_6: meeko receptor H196A rc=2
[2026-05-12 11:52:48] STAGE5_6: meeko failed: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 11:52:49] STAGE5_6: obabel receptor H196A rc=0
[2026-05-12 11:52:56] STAGE7:   H196A: top=-7.61 Δ=+0.12 rmsd=1.08
[2026-05-12 11:52:56] STAGE7: [6/21] H196F (single_opposite)
[2026-05-12 11:52:58] STAGE5_6: meeko receptor H196F rc=2
[2026-05-12 11:52:58] STAGE5_6: meeko failed: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 11:52:59] STAGE5_6: obabel receptor H196F rc=0
[2026-05-12 11:53:06] STAGE7:   H196F: top=-7.73 Δ=-0.00 rmsd=1.05
[2026-05-12 11:53:06] STAGE7: [7/21] G217A (single_ala)
[2026-05-12 11:53:08] STAGE5_6: meeko receptor G217A rc=2
[2026-05-12 11:53:08] STAGE5_6: meeko failed: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 11:53:08] STAGE5_6: obabel receptor G217A rc=0
[2026-05-12 11:53:16] STAGE7:   G217A: top=-7.73 Δ=-0.00 rmsd=1.07
[2026-05-12 11:53:16] STAGE7: [8/21] G217W (single_opposite)
[2026-05-12 11:53:18] STAGE5_6: meeko receptor G217W rc=2
[2026-05-12 11:53:18] STAGE5_6: meeko failed: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 11:53:18] STAGE5_6: obabel receptor G217W rc=0
[2026-05-12 11:53:25] STAGE7:   G217W: top=-7.90 Δ=-0.17 rmsd=1.08
[2026-05-12 11:53:25] STAGE7: [9/21] D218A (single_ala)
[2026-05-12 11:53:27] STAGE5_6: meeko receptor D218A rc=2
[2026-05-12 11:53:27] STAGE5_6: meeko failed: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 11:53:28] STAGE5_6: obabel receptor D218A rc=0
[2026-05-12 11:53:35] STAGE7:   D218A: top=-7.63 Δ=+0.09 rmsd=1.10
[2026-05-12 11:53:35] STAGE7: [10/21] D218K (single_opposite)
[2026-05-12 11:53:37] STAGE5_6: meeko receptor D218K rc=2
[2026-05-12 11:53:37] STAGE5_6: meeko failed: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 11:53:37] STAGE5_6: obabel receptor D218K rc=0
[2026-05-12 11:53:46] STAGE7:   D218K: top=-6.61 Δ=+1.12 rmsd=7.34
[2026-05-12 11:53:46] STAGE7: [11/21] F225A (single_ala)
[2026-05-12 11:53:48] STAGE5_6: meeko receptor F225A rc=2
[2026-05-12 11:53:48] STAGE5_6: meeko failed: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 11:53:48] STAGE5_6: obabel receptor F225A rc=0
[2026-05-12 11:53:55] STAGE7:   F225A: top=-7.70 Δ=+0.03 rmsd=1.09
[2026-05-12 11:53:55] STAGE7: [12/21] F225D (single_opposite)
[2026-05-12 11:53:57] STAGE5_6: meeko receptor F225D rc=2
[2026-05-12 11:53:57] STAGE5_6: meeko failed: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 11:53:58] STAGE5_6: obabel receptor F225D rc=0
[2026-05-12 11:54:05] STAGE7:   F225D: top=-7.62 Δ=+0.11 rmsd=1.05
[2026-05-12 11:54:05] STAGE7: [13/21] N226A (single_ala)
[2026-05-12 11:54:08] STAGE5_6: meeko receptor N226A rc=2
[2026-05-12 11:54:08] STAGE5_6: meeko failed: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 11:54:08] STAGE5_6: obabel receptor N226A rc=0
[2026-05-12 11:54:16] STAGE7:   N226A: top=-7.00 Δ=+0.73 rmsd=5.88
[2026-05-12 11:54:16] STAGE7: [14/21] N226D (single_opposite)
[2026-05-12 11:54:18] STAGE5_6: meeko receptor N226D rc=2
[2026-05-12 11:54:18] STAGE5_6: meeko failed: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 11:54:19] STAGE5_6: obabel receptor N226D rc=0
[2026-05-12 11:54:26] STAGE7:   N226D: top=-7.50 Δ=+0.23 rmsd=1.09
[2026-05-12 11:54:26] STAGE7: [15/21] Y258A (single_ala)
[2026-05-12 11:54:29] STAGE5_6: meeko receptor Y258A rc=2
[2026-05-12 11:54:29] STAGE5_6: meeko failed: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 11:54:29] STAGE5_6: obabel receptor Y258A rc=0
[2026-05-12 11:54:39] STAGE7:   Y258A: top=-6.89 Δ=+0.84 rmsd=4.51
[2026-05-12 11:54:39] STAGE7: [16/21] C195A_H196A (double_catalytic_dyad)
[2026-05-12 11:54:42] STAGE5_6: meeko receptor C195A_H196A rc=2
[2026-05-12 11:54:42] STAGE5_6: meeko failed: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 11:54:42] STAGE5_6: obabel receptor C195A_H196A rc=0
[2026-05-12 11:54:51] STAGE7:   C195A_H196A: top=-7.83 Δ=-0.10 rmsd=0.87
[2026-05-12 11:54:51] STAGE7: [17/21] R175E_R176E (double_arg_clamp_swap)
[2026-05-12 11:54:54] STAGE5_6: meeko receptor R175E_R176E rc=2
[2026-05-12 11:54:54] STAGE5_6: meeko failed: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 11:54:54] STAGE5_6: obabel receptor R175E_R176E rc=0
[2026-05-12 11:55:02] STAGE7:   R175E_R176E: top=-7.69 Δ=+0.04 rmsd=1.05
[2026-05-12 11:55:02] STAGE7: [18/21] D218N_N226D (double_charge_swap)
[2026-05-12 11:55:04] STAGE5_6: meeko receptor D218N_N226D rc=2
[2026-05-12 11:55:04] STAGE5_6: meeko failed: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 11:55:05] STAGE5_6: obabel receptor D218N_N226D rc=0
[2026-05-12 11:55:13] STAGE7:   D218N_N226D: top=-7.53 Δ=+0.20 rmsd=1.07
[2026-05-12 11:55:13] STAGE7: [19/21] Y258F_F225Y (double_aromatic_swap)
[2026-05-12 11:55:15] STAGE5_6: meeko receptor Y258F_F225Y rc=2
[2026-05-12 11:55:15] STAGE5_6: meeko failed: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 11:55:15] STAGE5_6: obabel receptor Y258F_F225Y rc=0
[2026-05-12 11:55:23] STAGE7:   Y258F_F225Y: top=-7.12 Δ=+0.61 rmsd=4.43
[2026-05-12 11:55:23] STAGE7: [20/21] C195S_H196N (double_polar_neutral)
[2026-05-12 11:55:25] STAGE5_6: meeko receptor C195S_H196N rc=2
[2026-05-12 11:55:25] STAGE5_6: meeko failed: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 11:55:25] STAGE5_6: obabel receptor C195S_H196N rc=0
[2026-05-12 11:55:33] STAGE7:   C195S_H196N: top=-7.98 Δ=-0.25 rmsd=0.65
[2026-05-12 11:55:33] STAGE7: [21/21] CTRL_T170A (control_surface)
[2026-05-12 11:55:35] STAGE5_6: meeko receptor CTRL_T170A rc=2
[2026-05-12 11:55:35] STAGE5_6: meeko failed: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 11:55:36] STAGE5_6: obabel receptor CTRL_T170A rc=0
[2026-05-12 11:55:43] STAGE7:   CTRL_T170A: top=-7.69 Δ=+0.04 rmsd=1.05
[2026-05-12 11:55:43] STAGE7: Wrote /Users/ario/conserved_site_project/07_mut_docking/results_full.csv with 22 rows
[2026-05-12 11:55:43] STAGE7: Stage 7 DONE
[2026-05-12 11:56:52] STAGE8: Stage 8 starting
[2026-05-12 11:56:52] STAGE8: WT top affinity: -7.729
[2026-05-12 11:56:52] STAGE8: delta_affinity_bar.png done
[2026-05-12 11:56:52] STAGE8: residue_substitution_heatmap.png done
[2026-05-12 11:56:52] STAGE8: conservation_vs_effect.png done
[2026-05-12 11:56:52] STAGE8: analysis.md done
[2026-05-12 11:56:52] STAGE8: Stage 8 DONE
[2026-05-12 11:58:24] STAGE9: Stage 9 starting
[2026-05-12 11:58:24] STAGE9: wrote /Users/ario/conserved_site_project/09_report/report.html
[2026-05-12 11:58:25] STAGE9: wrote /Users/ario/conserved_site_project/09_report/report.pdf (2650016 bytes)
[2026-05-12 11:58:25] STAGE9: Stage 9 DONE
wrote /Users/ario/conserved_site_project/09_report/report.docx (3017739 bytes)
[V2] 2026-05-12 12:17:58 Pipeline v2 starting
[2026-05-12 12:19:10] [V2] STAGE1: Stage 1 v2 starting
[2026-05-12 12:19:10] [V2] STAGE1: Fetching P04818 (Homo_sapiens)
[2026-05-12 12:19:11] [V2] STAGE1:   ACCEPT P04818 (Homo_sapiens): ok(len=313)
[2026-05-12 12:19:11] [V2] STAGE1: Fetching P07607 (Mus_musculus)
[2026-05-12 12:19:12] [V2] STAGE1:   ACCEPT P07607 (Mus_musculus): ok(len=307)
[2026-05-12 12:19:12] [V2] STAGE1: Fetching P45352 (Rattus_norvegicus)
[2026-05-12 12:19:13] [V2] STAGE1:   ACCEPT P45352 (Rattus_norvegicus): ok(len=307)
[2026-05-12 12:19:13] [V2] STAGE1: Fetching P0A884 (Escherichia_coli)
[2026-05-12 12:19:15] [V2] STAGE1:   REJECT P0A884 (Escherichia_coli): no_TS_motif; trying search fallback
[2026-05-12 12:19:16] [V2] STAGE1: Fetching P00469 (Lactobacillus_casei)
[2026-05-12 12:19:17] [V2] STAGE1:   REJECT P00469 (Lactobacillus_casei): no_TS_motif; trying search fallback
[2026-05-12 12:19:18] [V2] STAGE1: Fetching P07807 (Saccharomyces_cerevisiae)
[2026-05-12 12:19:19] [V2] STAGE1:   REJECT P07807 (Saccharomyces_cerevisiae): no_TS_motif; trying search fallback
[2026-05-12 12:19:21] [V2] STAGE1: Fetching Q23381 (Caenorhabditis_elegans)
[2026-05-12 12:19:22] [V2] STAGE1:   REJECT Q23381 (Caenorhabditis_elegans): no_TS_motif; trying search fallback
[2026-05-12 12:19:23] [V2] STAGE1: Fetching Q9V3K2 (Drosophila_melanogaster)
[2026-05-12 12:19:24] [V2] STAGE1: fetch Q9V3K2 status 200
[2026-05-12 12:19:25] [V2] STAGE1: fetch Q9V3K2 status 200
[2026-05-12 12:19:26] [V2] STAGE1: fetch Q9V3K2 status 200
[2026-05-12 12:19:26] [V2] STAGE1:   primary fetch failed for Q9V3K2, trying search fallback
[2026-05-12 12:19:28] [V2] STAGE1:   REJECT Q9V3K2 (Drosophila_melanogaster): no_TS_motif; trying search fallback
[2026-05-12 12:19:29] [V2] STAGE1: Fetching Q05762 (Arabidopsis_thaliana)
[2026-05-12 12:19:30] [V2] STAGE1:   REJECT Q05762 (Arabidopsis_thaliana): no_TS_motif; trying search fallback
[2026-05-12 12:19:31] [V2] STAGE1: Fetching P04019 (Bacteriophage_T4)
[2026-05-12 12:19:33] [V2] STAGE1:   REJECT P04019 (Bacteriophage_T4): no_TS_motif; trying search fallback
[2026-05-12 12:19:34] [V2] STAGE1: Fetching P13922 (Plasmodium_falciparum)
[2026-05-12 12:19:35] [V2] STAGE1:   Pf TS trim: 608 -> 328 aa
[2026-05-12 12:19:35] [V2] STAGE1:   REJECT P13922 (Plasmodium_falciparum): no_TS_motif; trying search fallback
[2026-05-12 12:19:37] [V2] STAGE1: Final ortholog set: 3 valid, 8 rejected
[2026-05-12 12:19:37] [V2] STAGE1:   rejected: P0A884 Escherichia_coli (no_TS_motif)
[2026-05-12 12:19:37] [V2] STAGE1:   rejected: P00469 Lactobacillus_casei (no_TS_motif)
[2026-05-12 12:19:37] [V2] STAGE1:   rejected: P07807 Saccharomyces_cerevisiae (no_TS_motif)
[2026-05-12 12:19:37] [V2] STAGE1:   rejected: Q23381 Caenorhabditis_elegans (too_long(1059))
[2026-05-12 12:19:37] [V2] STAGE1:   rejected: Q9V3K2 Drosophila_melanogaster (no_TS_motif)
[2026-05-12 12:19:37] [V2] STAGE1:   rejected: Q05762 Arabidopsis_thaliana (no_TS_motif)
[2026-05-12 12:19:37] [V2] STAGE1:   rejected: P04019 Bacteriophage_T4 (no_TS_motif)
[2026-05-12 12:19:37] [V2] STAGE1:   rejected: P13922 Plasmodium_falciparum (no_TS_motif)
[2026-05-12 12:19:37] [V2] STAGE1: WARNING: only 3 orthologs (target was >=10), proceeding anyway
[2026-05-12 12:19:37] [V2] STAGE1: FATAL: fewer than 5 sequences validated
[2026-05-12 12:21:25] [V2] STAGE1: Stage 1 v2 starting
[2026-05-12 12:21:25] [V2] STAGE1: Fetching P04818 (Homo_sapiens)
[2026-05-12 12:21:27] [V2] STAGE1:   ACCEPT P04818 (Homo_sapiens): ok(len=313)
[2026-05-12 12:21:27] [V2] STAGE1: Fetching P07607 (Mus_musculus)
[2026-05-12 12:21:28] [V2] STAGE1:   ACCEPT P07607 (Mus_musculus): ok(len=307)
[2026-05-12 12:21:28] [V2] STAGE1: Fetching P45352 (Rattus_norvegicus)
[2026-05-12 12:21:29] [V2] STAGE1:   ACCEPT P45352 (Rattus_norvegicus): ok(len=307)
[2026-05-12 12:21:29] [V2] STAGE1: Fetching P0A884 (Escherichia_coli)
[2026-05-12 12:21:31] [V2] STAGE1:   ACCEPT P0A884 (Escherichia_coli): ok(len=264)
[2026-05-12 12:21:31] [V2] STAGE1: Fetching P00469 (Lactobacillus_casei)
[2026-05-12 12:21:32] [V2] STAGE1:   ACCEPT P00469 (Lactobacillus_casei): ok(len=316)
[2026-05-12 12:21:32] [V2] STAGE1: Fetching P06785 (Saccharomyces_cerevisiae)
[2026-05-12 12:21:33] [V2] STAGE1:   ACCEPT P06785 (Saccharomyces_cerevisiae): ok(len=304)
[2026-05-12 12:21:33] [V2] STAGE1: Fetching Q9N588 (Caenorhabditis_elegans)
[2026-05-12 12:21:34] [V2] STAGE1:   REJECT Q9N588 (Caenorhabditis_elegans): no_TS_motif; trying search fallback
[2026-05-12 12:21:35] [V2] STAGE1: Fetching O76511 (Drosophila_melanogaster)
[2026-05-12 12:21:36] [V2] STAGE1:   ACCEPT O76511 (Drosophila_melanogaster): ok(len=321)
[2026-05-12 12:21:36] [V2] STAGE1: Fetching Q05762 (Arabidopsis_thaliana)
[2026-05-12 12:21:37] [V2] STAGE1:   Arabidopsis_thaliana bifunctional trim: 519 -> 315 aa
[2026-05-12 12:21:37] [V2] STAGE1:   ACCEPT Q05762 (Arabidopsis_thaliana): ok(len=315)
[2026-05-12 12:21:37] [V2] STAGE1: Fetching P00471 (Bacteriophage_T4)
[2026-05-12 12:21:39] [V2] STAGE1:   ACCEPT P00471 (Bacteriophage_T4): ok(len=286)
[2026-05-12 12:21:39] [V2] STAGE1: Fetching P13922 (Plasmodium_falciparum)
[2026-05-12 12:21:40] [V2] STAGE1:   Plasmodium_falciparum bifunctional trim: 608 -> 315 aa
[2026-05-12 12:21:40] [V2] STAGE1:   ACCEPT P13922 (Plasmodium_falciparum): ok(len=315)
[2026-05-12 12:21:40] [V2] STAGE1: Final ortholog set: 10 valid, 1 rejected
[2026-05-12 12:21:40] [V2] STAGE1:   rejected: Q9N588 Caenorhabditis_elegans (too_long(1059))
[2026-05-12 12:21:40] [V2] STAGE1: Wrote /Users/ario/conserved_site_project/01b_msa_v2/input.fa with 10 sequences
[2026-05-12 12:21:40] [V2] STAGE1: Running MAFFT --auto
[2026-05-12 12:21:40] [V2] STAGE1: MAFFT done
[2026-05-12 12:21:40] [V2] STAGE1: Aligned 10 sequences, length 399
[2026-05-12 12:21:40] [V2] STAGE1: Reference row 0, ungapped len 313
[2026-05-12 12:21:40] [V2] STAGE1: Wrote /Users/ario/conserved_site_project/01b_msa_v2/conservation_scores.csv (313 rows, 306 eligible for percentile)
[2026-05-12 12:21:40] [V2] STAGE1: Sanity check (catalytic / known):
[2026-05-12 12:21:40] [V2] STAGE1:   pos 50 (R): js=0.219, pct=94.1, gap_frac=0.00
[2026-05-12 12:21:40] [V2] STAGE1:   pos 175 (R): js=0.209, pct=89.5, gap_frac=0.00
[2026-05-12 12:21:40] [V2] STAGE1:   pos 176 (R): js=0.210, pct=90.8, gap_frac=0.00
[2026-05-12 12:21:40] [V2] STAGE1:   pos 195 (C): js=0.253, pct=100.0, gap_frac=0.00
[2026-05-12 12:21:40] [V2] STAGE1:   pos 196 (H): js=0.227, pct=96.1, gap_frac=0.00
[2026-05-12 12:21:40] [V2] STAGE1:   pos 215 (R): js=0.219, pct=94.4, gap_frac=0.00
[2026-05-12 12:21:40] [V2] STAGE1:   pos 226 (N): js=0.229, pct=97.1, gap_frac=0.00
[2026-05-12 12:21:40] [V2] STAGE1:   pos 258 (Y): js=0.178, pct=64.1, gap_frac=0.00
[2026-05-12 12:21:40] [V2] STAGE1: Wrote /Users/ario/conserved_site_project/01b_msa_v2/conservation_plot.png
[2026-05-12 12:21:40] [V2] STAGE1: Stage 1 v2 DONE
[2026-05-12 12:22:29] [V2] STAGE2: Stage 2 v2 starting
[2026-05-12 12:22:31] [V2] STAGE2: UniProt: 14 annotated positions
[2026-05-12 12:22:32] [V2] STAGE2: chain-A/B target ligands: [('bm1', 'D16', 'A'), ('bm4', 'D16', 'B'), ('bm2', 'UMP', 'A'), ('bm5', 'UMP', 'B')]
[2026-05-12 12:22:37] [V2] STAGE2: PDBe: 26 unique residues binding UMP/D16
[2026-05-12 12:22:37] [V2] STAGE2: Wrote active_site_residues.csv (27 rows)
[2026-05-12 12:22:37] [V2] STAGE2: Wrote overlap_table.csv
[2026-05-12 12:22:37] [V2] STAGE2: DB-annotated set: 27; top25%: 77; top10%: 31
[2026-05-12 12:22:37] [V2] STAGE2: DB ∩ top25%: 17; DB ∩ top10%: 9
[2026-05-12 12:22:37] [V2] STAGE2: Capped to 10 highest-cons: [50, 109, 175, 176, 195, 196, 214, 215, 225, 226]
[2026-05-12 12:22:37] [V2] STAGE2: Final selected (10, threshold top-25%): [50, 109, 175, 176, 195, 196, 214, 215, 225, 226]
[2026-05-12 12:22:37] [V2] STAGE2: Stage 2 v2 DONE
[2026-05-12 12:23:23] [V2] STAGE3: Stage 3 v2 starting
[2026-05-12 12:23:23] [V2] STAGE3: using raw 1hvy: /Users/ario/conserved_site_project/03_structure/1hvy.pdb
[2026-05-12 12:23:23] [V2] STAGE3: CME->CYS conversion: 40 CME lines, 24 kept (heavy), 16 hydroxyethyl atoms dropped
[2026-05-12 12:23:23] [V2] STAGE3: wrote /Users/ario/conserved_site_project/03b_structure_v2/protein_dimer.pdb
[2026-05-12 12:23:23] [V2] STAGE3: wrote /Users/ario/conserved_site_project/03b_structure_v2/ligand.pdb
[2026-05-12 12:23:23] [V2] STAGE3: wrote /Users/ario/conserved_site_project/03b_structure_v2/cofactor_chainA.pdb
[2026-05-12 12:23:23] [V2] STAGE3: wrote /Users/ario/conserved_site_project/03b_structure_v2/cofactor_chainB.pdb
[2026-05-12 12:23:23] [V2] STAGE3: protein_dimer_h.pdb size 1406500
[2026-05-12 12:23:24] [V2] STAGE3: obabel ligand_h rc=0, size 5580
[2026-05-12 12:23:24] [V2] STAGE3:   cofactor_chainA.pdb -> cofactor_chainA_h.pdb rc=0
[2026-05-12 12:23:24] [V2] STAGE3:   cofactor_chainB.pdb -> cofactor_chainB_h.pdb rc=0
[2026-05-12 12:23:24] [V2] STAGE3: chains in dimer_h: ['A', 'B']
[2026-05-12 12:23:24] [V2] STAGE3:   chain A: 288 residues
[2026-05-12 12:23:24] [V2] STAGE3:   chain A Cys43 heavy atoms: ['C', 'CA', 'CB', 'N', 'O', 'SG']
[2026-05-12 12:23:24] [V2] STAGE3:   chain B: 288 residues
[2026-05-12 12:23:24] [V2] STAGE3:   chain B Cys43 heavy atoms: ['C', 'CA', 'CB', 'N', 'O', 'SG']
[2026-05-12 12:23:24] [V2] STAGE3: selected residues missing in A: []; in B: []
[2026-05-12 12:23:24] [V2] STAGE3: Stage 3 v2 DONE
[2026-05-12 12:24:00] [V2] STAGE4: Stage 4 v2 starting
[2026-05-12 12:24:00] [V2] STAGE4: wrote b-factor PDB: /Users/ario/conserved_site_project/04b_pymol_v2/protein_dimer_jsd_bfactor.pdb
[2026-05-12 12:24:01] [V2] STAGE4:   rendered dimer_overview.png rc=0 size=744334
[2026-05-12 12:24:02] [V2] STAGE4:   rendered active_site_chainA.png rc=0 size=1075627
[2026-05-12 12:24:03] [V2] STAGE4:   rendered active_site_chainB.png rc=0 size=1113904
[2026-05-12 12:24:05] [V2] STAGE4:   rendered conservation_surface.png rc=0 size=814827
[2026-05-12 12:24:06] [V2] STAGE4:   rendered catalytic_dyad.png rc=0 size=1182981
[2026-05-12 12:24:06] [V2] STAGE4: Stage 4 v2 DONE
[2026-05-12 12:24:31] [V2] STAGE5: Stage 5 v2 starting
[2026-05-12 12:24:31] [V2] STAGE5: wrote /Users/ario/conserved_site_project/05b_ligand_v2/dump.pdb
[2026-05-12 12:24:32] [V2] STAGE5: obabel mol2 rc=0 size=3700
[2026-05-12 12:24:32] [V2] STAGE5: obabel sdf --gen3d rc=0 size=3589
[2026-05-12 12:24:32] [V2] STAGE5: obabel pdbqt rc=0 size=2513
[2026-05-12 12:24:32] [V2] STAGE5: pdbqt has_UNK=False, n_atoms=22
[2026-05-12 12:24:32] [V2] STAGE5: Stage 5 v2 DONE
[2026-05-12 12:25:33] [V2] STAGE6: Stage 6 v2 starting
[2026-05-12 12:25:33] [V2] STAGE6: chain-A active site centroid from 10 CA: [3.4655004 4.7408    7.7776003]
[2026-05-12 12:25:35] [V2] STAGE6:   meeko receptor APO_dimer rc=2
[2026-05-12 12:25:35] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:25:36] [V2] STAGE6:   obabel receptor APO_dimer rc=0
[2026-05-12 12:25:38] [V2] STAGE6:   meeko receptor HOLO_dimer rc=2
[2026-05-12 12:25:38] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:25:38] [V2] STAGE6:   obabel receptor HOLO_dimer rc=0
[2026-05-12 12:25:38] [V2] STAGE6:   vina WT_apo: cmd=/opt/homebrew/bin/vina --receptor /Users/ario/conserved_site_project/06b_docking_wt_v2/protein_dimer_apo.pdbqt --ligand ... center=(3.47,4.74,7.78)
[2026-05-12 12:25:55] [V2] STAGE6:   WT apo affinities (from PDBQT): [-6.798, -6.505, -6.446, -6.371, -6.346]
[2026-05-12 12:25:55] [V2] STAGE6:   WT apo: top=-6.80, mean_top3=-6.58, RMSD=5.60
[2026-05-12 12:25:55] [V2] STAGE6:   vina WT_holo: cmd=/opt/homebrew/bin/vina --receptor /Users/ario/conserved_site_project/06b_docking_wt_v2/protein_dimer_holo.pdbqt --ligand ... center=(3.47,4.74,7.78)
[2026-05-12 12:26:09] [V2] STAGE6:   WT holo affinities (from PDBQT): [-3.215, -1.355, -0.495]
[2026-05-12 12:26:10] [V2] STAGE6:   WT holo: top=-3.21, mean_top3=-1.69, RMSD=4.32
[2026-05-12 12:26:10] [V2] STAGE6: Stage 6 v2 DONE
[2026-05-12 12:27:57] [V2] STAGE7: Stage 7 v2 starting
[2026-05-12 12:27:58] [V2] STAGE7: ref seq len=313
[2026-05-12 12:27:58] [V2] STAGE7: Built panel of 20 mutants
[2026-05-12 12:27:58] [V2] STAGE7: Final panel size: 21
[2026-05-12 12:27:58] [V2] STAGE7: centroid: [3.4655004 4.7408    7.7776003]
[2026-05-12 12:27:58] [V2] STAGE7: [1/21] R50A (ala_scan)
[2026-05-12 12:27:59] [V2] STAGE7:   PyMOL>print("ROTAMER_PICK resi=50 aa=ALA best_idx=" + str(best_idx) + " strain=" + str(best_strain))
[2026-05-12 12:27:59] [V2] STAGE7:   ROTAMER_PICK resi=50 aa=ALA best_idx=0 strain=1e+30
[2026-05-12 12:28:02] [V2] STAGE6:   meeko receptor R50A_apo rc=2
[2026-05-12 12:28:02] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:28:03] [V2] STAGE6:   obabel receptor R50A_apo rc=0
[2026-05-12 12:28:04] [V2] STAGE6:   meeko receptor R50A_holo rc=2
[2026-05-12 12:28:04] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:28:05] [V2] STAGE6:   obabel receptor R50A_holo rc=0
[2026-05-12 12:28:22] [V2] STAGE7:   R50A apo: top=-7.07, ddG=-0.27, rmsd=5.52
[2026-05-12 12:28:36] [V2] STAGE7:   R50A holo: top=-6.01, ddG=-2.79, rmsd=2.23
[2026-05-12 12:28:36] [V2] STAGE7: [2/21] W109A (ala_scan)
[2026-05-12 12:28:36] [V2] STAGE7:   PyMOL>print("ROTAMER_PICK resi=109 aa=ALA best_idx=" + str(best_idx) + " strain=" + str(best_strain))
[2026-05-12 12:28:36] [V2] STAGE7:   ROTAMER_PICK resi=109 aa=ALA best_idx=0 strain=1e+30
[2026-05-12 12:28:39] [V2] STAGE6:   meeko receptor W109A_apo rc=2
[2026-05-12 12:28:39] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:28:41] [V2] STAGE6:   obabel receptor W109A_apo rc=0
[2026-05-12 12:28:42] [V2] STAGE6:   meeko receptor W109A_holo rc=2
[2026-05-12 12:28:42] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:28:42] [V2] STAGE6:   obabel receptor W109A_holo rc=0
[2026-05-12 12:29:00] [V2] STAGE7:   W109A apo: top=-7.85, ddG=-1.05, rmsd=5.83
[2026-05-12 12:29:15] [V2] STAGE7:   W109A holo: top=-6.19, ddG=-2.97, rmsd=2.23
[2026-05-12 12:29:15] [V2] STAGE7: [3/21] R175A (ala_scan)
[2026-05-12 12:29:15] [V2] STAGE7:   PyMOL>print("ROTAMER_PICK resi=175 aa=ALA best_idx=" + str(best_idx) + " strain=" + str(best_strain))
[2026-05-12 12:29:15] [V2] STAGE7:   ROTAMER_PICK resi=175 aa=ALA best_idx=0 strain=1e+30
[2026-05-12 12:29:18] [V2] STAGE6:   meeko receptor R175A_apo rc=2
[2026-05-12 12:29:18] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:29:20] [V2] STAGE6:   obabel receptor R175A_apo rc=0
[2026-05-12 12:29:21] [V2] STAGE6:   meeko receptor R175A_holo rc=2
[2026-05-12 12:29:21] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:29:21] [V2] STAGE6:   obabel receptor R175A_holo rc=0
[2026-05-12 12:29:38] [V2] STAGE7:   R175A apo: top=-7.10, ddG=-0.30, rmsd=5.58
[2026-05-12 12:29:53] [V2] STAGE7:   R175A holo: top=-6.36, ddG=-3.15, rmsd=2.21
[2026-05-12 12:29:53] [V2] STAGE7: [4/21] R176A (ala_scan)
[2026-05-12 12:29:53] [V2] STAGE7:   PyMOL>print("ROTAMER_PICK resi=176 aa=ALA best_idx=" + str(best_idx) + " strain=" + str(best_strain))
[2026-05-12 12:29:53] [V2] STAGE7:   ROTAMER_PICK resi=176 aa=ALA best_idx=0 strain=1e+30
[2026-05-12 12:29:56] [V2] STAGE6:   meeko receptor R176A_apo rc=2
[2026-05-12 12:29:56] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:29:58] [V2] STAGE6:   obabel receptor R176A_apo rc=0
[2026-05-12 12:29:59] [V2] STAGE6:   meeko receptor R176A_holo rc=2
[2026-05-12 12:29:59] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:29:59] [V2] STAGE6:   obabel receptor R176A_holo rc=0
[2026-05-12 12:30:16] [V2] STAGE7:   R176A apo: top=-7.16, ddG=-0.36, rmsd=5.75
[2026-05-12 12:30:30] [V2] STAGE7:   R176A holo: top=-6.32, ddG=-3.10, rmsd=2.15
[2026-05-12 12:30:30] [V2] STAGE7: [5/21] C195A (ala_scan)
[2026-05-12 12:30:31] [V2] STAGE7:   PyMOL>print("ROTAMER_PICK resi=195 aa=ALA best_idx=" + str(best_idx) + " strain=" + str(best_strain))
[2026-05-12 12:30:31] [V2] STAGE7:   ROTAMER_PICK resi=195 aa=ALA best_idx=0 strain=1e+30
[2026-05-12 12:30:34] [V2] STAGE6:   meeko receptor C195A_apo rc=2
[2026-05-12 12:30:34] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:30:35] [V2] STAGE6:   obabel receptor C195A_apo rc=0
[2026-05-12 12:30:36] [V2] STAGE6:   meeko receptor C195A_holo rc=2
[2026-05-12 12:30:36] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:30:37] [V2] STAGE6:   obabel receptor C195A_holo rc=0
[2026-05-12 12:30:53] [V2] STAGE7:   C195A apo: top=-7.93, ddG=-1.13, rmsd=3.09
[2026-05-12 12:31:08] [V2] STAGE7:   C195A holo: top=-8.34, ddG=-5.13, rmsd=2.08
[2026-05-12 12:31:08] [V2] STAGE7: [6/21] H196A (ala_scan)
[2026-05-12 12:31:08] [V2] STAGE7:   PyMOL>print("ROTAMER_PICK resi=196 aa=ALA best_idx=" + str(best_idx) + " strain=" + str(best_strain))
[2026-05-12 12:31:08] [V2] STAGE7:   ROTAMER_PICK resi=196 aa=ALA best_idx=0 strain=1e+30
[2026-05-12 12:31:11] [V2] STAGE6:   meeko receptor H196A_apo rc=2
[2026-05-12 12:31:11] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:31:13] [V2] STAGE6:   obabel receptor H196A_apo rc=0
[2026-05-12 12:31:14] [V2] STAGE6:   meeko receptor H196A_holo rc=2
[2026-05-12 12:31:14] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:31:14] [V2] STAGE6:   obabel receptor H196A_holo rc=0
[2026-05-12 12:31:31] [V2] STAGE7:   H196A apo: top=-7.18, ddG=-0.38, rmsd=8.05
[2026-05-12 12:31:45] [V2] STAGE7:   H196A holo: top=-4.38, ddG=-1.17, rmsd=7.48
[2026-05-12 12:31:45] [V2] STAGE7: [7/21] Q214A (ala_scan)
[2026-05-12 12:31:46] [V2] STAGE7:   PyMOL>print("ROTAMER_PICK resi=214 aa=ALA best_idx=" + str(best_idx) + " strain=" + str(best_strain))
[2026-05-12 12:31:46] [V2] STAGE7:   ROTAMER_PICK resi=214 aa=ALA best_idx=0 strain=1e+30
[2026-05-12 12:31:49] [V2] STAGE6:   meeko receptor Q214A_apo rc=2
[2026-05-12 12:31:49] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:31:50] [V2] STAGE6:   obabel receptor Q214A_apo rc=0
[2026-05-12 12:31:51] [V2] STAGE6:   meeko receptor Q214A_holo rc=2
[2026-05-12 12:31:51] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:31:52] [V2] STAGE6:   obabel receptor Q214A_holo rc=0
[2026-05-12 12:32:09] [V2] STAGE7:   Q214A apo: top=-6.67, ddG=+0.13, rmsd=5.75
[2026-05-12 12:32:25] [V2] STAGE7:   Q214A holo: top=-6.35, ddG=-3.14, rmsd=2.18
[2026-05-12 12:32:25] [V2] STAGE7: [8/21] R215A (ala_scan)
[2026-05-12 12:32:25] [V2] STAGE7:   PyMOL>print("ROTAMER_PICK resi=215 aa=ALA best_idx=" + str(best_idx) + " strain=" + str(best_strain))
[2026-05-12 12:32:25] [V2] STAGE7:   ROTAMER_PICK resi=215 aa=ALA best_idx=0 strain=1e+30
[2026-05-12 12:32:28] [V2] STAGE6:   meeko receptor R215A_apo rc=2
[2026-05-12 12:32:28] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:32:29] [V2] STAGE6:   obabel receptor R215A_apo rc=0
[2026-05-12 12:32:31] [V2] STAGE6:   meeko receptor R215A_holo rc=2
[2026-05-12 12:32:31] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:32:31] [V2] STAGE6:   obabel receptor R215A_holo rc=0
[2026-05-12 12:32:47] [V2] STAGE7:   R215A apo: top=-7.84, ddG=-1.04, rmsd=2.25
[2026-05-12 12:33:03] [V2] STAGE7:   R215A holo: top=-7.15, ddG=-3.93, rmsd=2.19
[2026-05-12 12:33:03] [V2] STAGE7: [9/21] R50E (opposite)
[2026-05-12 12:33:04] [V2] STAGE7:   PyMOL>print("ROTAMER_PICK resi=50 aa=GLU best_idx=" + str(best_idx) + " strain=" + str(best_strain))
[2026-05-12 12:33:04] [V2] STAGE7:   ROTAMER_PICK resi=50 aa=GLU best_idx=0 strain=1e+30
[2026-05-12 12:33:07] [V2] STAGE6:   meeko receptor R50E_apo rc=2
[2026-05-12 12:33:07] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:33:08] [V2] STAGE6:   obabel receptor R50E_apo rc=0
[2026-05-12 12:33:10] [V2] STAGE6:   meeko receptor R50E_holo rc=2
[2026-05-12 12:33:10] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:33:10] [V2] STAGE6:   obabel receptor R50E_holo rc=0
[2026-05-12 12:33:27] [V2] STAGE7:   R50E apo: top=-7.00, ddG=-0.20, rmsd=5.76
[2026-05-12 12:33:41] [V2] STAGE7:   R50E holo: top=-5.39, ddG=-2.17, rmsd=2.18
[2026-05-12 12:33:41] [V2] STAGE7: [10/21] R175E (opposite)
[2026-05-12 12:33:41] [V2] STAGE7:   PyMOL>print("ROTAMER_PICK resi=175 aa=GLU best_idx=" + str(best_idx) + " strain=" + str(best_strain))
[2026-05-12 12:33:41] [V2] STAGE7:   ROTAMER_PICK resi=175 aa=GLU best_idx=0 strain=1e+30
[2026-05-12 12:33:44] [V2] STAGE6:   meeko receptor R175E_apo rc=2
[2026-05-12 12:33:44] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:33:45] [V2] STAGE6:   obabel receptor R175E_apo rc=0
[2026-05-12 12:33:47] [V2] STAGE6:   meeko receptor R175E_holo rc=2
[2026-05-12 12:33:47] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:33:47] [V2] STAGE6:   obabel receptor R175E_holo rc=0
[2026-05-12 12:34:05] [V2] STAGE7:   R175E apo: top=-7.10, ddG=-0.30, rmsd=5.58
[2026-05-12 12:34:19] [V2] STAGE7:   R175E holo: top=-6.36, ddG=-3.15, rmsd=2.21
[2026-05-12 12:34:19] [V2] STAGE7: [11/21] R176E (opposite)
[2026-05-12 12:34:19] [V2] STAGE7:   PyMOL>print("ROTAMER_PICK resi=176 aa=GLU best_idx=" + str(best_idx) + " strain=" + str(best_strain))
[2026-05-12 12:34:19] [V2] STAGE7:   ROTAMER_PICK resi=176 aa=GLU best_idx=0 strain=1e+30
[2026-05-12 12:34:22] [V2] STAGE6:   meeko receptor R176E_apo rc=2
[2026-05-12 12:34:22] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:34:24] [V2] STAGE6:   obabel receptor R176E_apo rc=0
[2026-05-12 12:34:25] [V2] STAGE6:   meeko receptor R176E_holo rc=2
[2026-05-12 12:34:25] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:34:25] [V2] STAGE6:   obabel receptor R176E_holo rc=0
[2026-05-12 12:34:42] [V2] STAGE7:   R176E apo: top=-7.15, ddG=-0.36, rmsd=5.64
[2026-05-12 12:34:56] [V2] STAGE7:   R176E holo: top=-6.41, ddG=-3.20, rmsd=2.23
[2026-05-12 12:34:56] [V2] STAGE7: [12/21] C195S (opposite)
[2026-05-12 12:34:56] [V2] STAGE7:   PyMOL>print("ROTAMER_PICK resi=195 aa=SER best_idx=" + str(best_idx) + " strain=" + str(best_strain))
[2026-05-12 12:34:56] [V2] STAGE7:   ROTAMER_PICK resi=195 aa=SER best_idx=0 strain=1e+30
[2026-05-12 12:35:00] [V2] STAGE6:   meeko receptor C195S_apo rc=2
[2026-05-12 12:35:00] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:35:01] [V2] STAGE6:   obabel receptor C195S_apo rc=0
[2026-05-12 12:35:02] [V2] STAGE6:   meeko receptor C195S_holo rc=2
[2026-05-12 12:35:02] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:35:03] [V2] STAGE6:   obabel receptor C195S_holo rc=0
[2026-05-12 12:35:20] [V2] STAGE7:   C195S apo: top=-7.85, ddG=-1.05, rmsd=3.09
[2026-05-12 12:35:36] [V2] STAGE7:   C195S holo: top=-8.00, ddG=-4.79, rmsd=2.17
[2026-05-12 12:35:36] [V2] STAGE7: [13/21] R215E (opposite)
[2026-05-12 12:35:36] [V2] STAGE7:   PyMOL>print("ROTAMER_PICK resi=215 aa=GLU best_idx=" + str(best_idx) + " strain=" + str(best_strain))
[2026-05-12 12:35:36] [V2] STAGE7:   ROTAMER_PICK resi=215 aa=GLU best_idx=0 strain=1e+30
[2026-05-12 12:35:39] [V2] STAGE6:   meeko receptor R215E_apo rc=2
[2026-05-12 12:35:39] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:35:41] [V2] STAGE6:   obabel receptor R215E_apo rc=0
[2026-05-12 12:35:42] [V2] STAGE6:   meeko receptor R215E_holo rc=2
[2026-05-12 12:35:42] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:35:43] [V2] STAGE6:   obabel receptor R215E_holo rc=0
[2026-05-12 12:36:01] [V2] STAGE7:   R215E apo: top=-7.31, ddG=-0.51, rmsd=5.88
[2026-05-12 12:36:18] [V2] STAGE7:   R215E holo: top=-7.24, ddG=-4.02, rmsd=2.19
[2026-05-12 12:36:18] [V2] STAGE7: [14/21] N226D (opposite)
[2026-05-12 12:36:18] [V2] STAGE7:   PyMOL>print("ROTAMER_PICK resi=226 aa=ASP best_idx=" + str(best_idx) + " strain=" + str(best_strain))
[2026-05-12 12:36:18] [V2] STAGE7:   ROTAMER_PICK resi=226 aa=ASP best_idx=0 strain=1e+30
[2026-05-12 12:36:21] [V2] STAGE6:   meeko receptor N226D_apo rc=2
[2026-05-12 12:36:21] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:36:23] [V2] STAGE6:   obabel receptor N226D_apo rc=0
[2026-05-12 12:36:24] [V2] STAGE6:   meeko receptor N226D_holo rc=2
[2026-05-12 12:36:24] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:36:25] [V2] STAGE6:   obabel receptor N226D_holo rc=0
[2026-05-12 12:36:42] [V2] STAGE7:   N226D apo: top=-7.36, ddG=-0.57, rmsd=5.59
[2026-05-12 12:36:57] [V2] STAGE7:   N226D holo: top=-5.90, ddG=-2.69, rmsd=2.19
[2026-05-12 12:36:57] [V2] STAGE7: [15/21] C195A_H196A (double_dyad)
[2026-05-12 12:36:58] [V2] STAGE7:   PyMOL>print("ROTAMER_PICK resi=195 aa=ALA best_idx=" + str(best_idx) + " strain=" + str(best_strain))
[2026-05-12 12:36:58] [V2] STAGE7:   ROTAMER_PICK resi=195 aa=ALA best_idx=0 strain=1e+30
[2026-05-12 12:36:58] [V2] STAGE7:   PyMOL>print("ROTAMER_PICK resi=196 aa=ALA best_idx=" + str(best_idx) + " strain=" + str(best_strain))
[2026-05-12 12:36:58] [V2] STAGE7:   ROTAMER_PICK resi=196 aa=ALA best_idx=0 strain=1e+30
[2026-05-12 12:37:01] [V2] STAGE6:   meeko receptor C195A_H196A_apo rc=2
[2026-05-12 12:37:01] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:37:03] [V2] STAGE6:   obabel receptor C195A_H196A_apo rc=0
[2026-05-12 12:37:04] [V2] STAGE6:   meeko receptor C195A_H196A_holo rc=2
[2026-05-12 12:37:04] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:37:05] [V2] STAGE6:   obabel receptor C195A_H196A_holo rc=0
[2026-05-12 12:37:20] [V2] STAGE7:   C195A_H196A apo: top=-7.79, ddG=-1.00, rmsd=3.04
[2026-05-12 12:37:35] [V2] STAGE7:   C195A_H196A holo: top=-7.59, ddG=-4.37, rmsd=3.92
[2026-05-12 12:37:35] [V2] STAGE7: [16/21] R175E_R176E (double_phosclamp)
[2026-05-12 12:37:36] [V2] STAGE7:   PyMOL>print("ROTAMER_PICK resi=175 aa=GLU best_idx=" + str(best_idx) + " strain=" + str(best_strain))
[2026-05-12 12:37:36] [V2] STAGE7:   ROTAMER_PICK resi=175 aa=GLU best_idx=0 strain=1e+30
[2026-05-12 12:37:36] [V2] STAGE7:   PyMOL>print("ROTAMER_PICK resi=176 aa=GLU best_idx=" + str(best_idx) + " strain=" + str(best_strain))
[2026-05-12 12:37:36] [V2] STAGE7:   ROTAMER_PICK resi=176 aa=GLU best_idx=0 strain=1e+30
[2026-05-12 12:37:39] [V2] STAGE6:   meeko receptor R175E_R176E_apo rc=2
[2026-05-12 12:37:39] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:37:40] [V2] STAGE6:   obabel receptor R175E_R176E_apo rc=0
[2026-05-12 12:37:42] [V2] STAGE6:   meeko receptor R175E_R176E_holo rc=2
[2026-05-12 12:37:42] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:37:42] [V2] STAGE6:   obabel receptor R175E_R176E_holo rc=0
[2026-05-12 12:37:58] [V2] STAGE7:   R175E_R176E apo: top=-7.15, ddG=-0.36, rmsd=5.64
[2026-05-12 12:38:13] [V2] STAGE7:   R175E_R176E holo: top=-6.41, ddG=-3.20, rmsd=2.23
[2026-05-12 12:38:13] [V2] STAGE7: [17/21] C195S_H196N (double_polar_neutral)
[2026-05-12 12:38:13] [V2] STAGE7:   PyMOL>print("ROTAMER_PICK resi=195 aa=SER best_idx=" + str(best_idx) + " strain=" + str(best_strain))
[2026-05-12 12:38:13] [V2] STAGE7:   ROTAMER_PICK resi=195 aa=SER best_idx=0 strain=1e+30
[2026-05-12 12:38:13] [V2] STAGE7:   PyMOL>print("ROTAMER_PICK resi=196 aa=ASN best_idx=" + str(best_idx) + " strain=" + str(best_strain))
[2026-05-12 12:38:13] [V2] STAGE7:   ROTAMER_PICK resi=196 aa=ASN best_idx=0 strain=1e+30
[2026-05-12 12:38:16] [V2] STAGE6:   meeko receptor C195S_H196N_apo rc=2
[2026-05-12 12:38:16] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:38:17] [V2] STAGE6:   obabel receptor C195S_H196N_apo rc=0
[2026-05-12 12:38:19] [V2] STAGE6:   meeko receptor C195S_H196N_holo rc=2
[2026-05-12 12:38:19] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:38:19] [V2] STAGE6:   obabel receptor C195S_H196N_holo rc=0
[2026-05-12 12:38:35] [V2] STAGE7:   C195S_H196N apo: top=-7.84, ddG=-1.04, rmsd=3.01
[2026-05-12 12:38:50] [V2] STAGE7:   C195S_H196N holo: top=-7.47, ddG=-4.25, rmsd=2.20
[2026-05-12 12:38:50] [V2] STAGE7: [18/21] R215A_N226A (double_substrate_orient)
[2026-05-12 12:38:50] [V2] STAGE7:   PyMOL>print("ROTAMER_PICK resi=215 aa=ALA best_idx=" + str(best_idx) + " strain=" + str(best_strain))
[2026-05-12 12:38:50] [V2] STAGE7:   ROTAMER_PICK resi=215 aa=ALA best_idx=0 strain=1e+30
[2026-05-12 12:38:50] [V2] STAGE7:   PyMOL>print("ROTAMER_PICK resi=226 aa=ALA best_idx=" + str(best_idx) + " strain=" + str(best_strain))
[2026-05-12 12:38:50] [V2] STAGE7:   ROTAMER_PICK resi=226 aa=ALA best_idx=0 strain=1e+30
[2026-05-12 12:38:53] [V2] STAGE6:   meeko receptor R215A_N226A_apo rc=2
[2026-05-12 12:38:53] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:38:54] [V2] STAGE6:   obabel receptor R215A_N226A_apo rc=0
[2026-05-12 12:38:56] [V2] STAGE6:   meeko receptor R215A_N226A_holo rc=2
[2026-05-12 12:38:56] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:38:56] [V2] STAGE6:   obabel receptor R215A_N226A_holo rc=0
[2026-05-12 12:39:12] [V2] STAGE7:   R215A_N226A apo: top=-7.13, ddG=-0.33, rmsd=5.64
[2026-05-12 12:39:27] [V2] STAGE7:   R215A_N226A holo: top=-6.86, ddG=-3.65, rmsd=2.29
[2026-05-12 12:39:27] [V2] STAGE7: [19/21] Y258F_F225Y (double_aromatic_swap)
[2026-05-12 12:39:28] [V2] STAGE7:   PyMOL>print("ROTAMER_PICK resi=258 aa=PHE best_idx=" + str(best_idx) + " strain=" + str(best_strain))
[2026-05-12 12:39:28] [V2] STAGE7:   ROTAMER_PICK resi=258 aa=PHE best_idx=0 strain=1e+30
[2026-05-12 12:39:28] [V2] STAGE7:   PyMOL>print("ROTAMER_PICK resi=225 aa=TYR best_idx=" + str(best_idx) + " strain=" + str(best_strain))
[2026-05-12 12:39:28] [V2] STAGE7:   ROTAMER_PICK resi=225 aa=TYR best_idx=0 strain=1e+30
[2026-05-12 12:39:31] [V2] STAGE6:   meeko receptor Y258F_F225Y_apo rc=2
[2026-05-12 12:39:31] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:39:32] [V2] STAGE6:   obabel receptor Y258F_F225Y_apo rc=0
[2026-05-12 12:39:34] [V2] STAGE6:   meeko receptor Y258F_F225Y_holo rc=2
[2026-05-12 12:39:34] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:39:34] [V2] STAGE6:   obabel receptor Y258F_F225Y_holo rc=0
[2026-05-12 12:39:50] [V2] STAGE7:   Y258F_F225Y apo: top=-7.08, ddG=-0.28, rmsd=5.25
[2026-05-12 12:40:04] [V2] STAGE7:   Y258F_F225Y holo: top=-6.08, ddG=-2.87, rmsd=2.18
[2026-05-12 12:40:04] [V2] STAGE7: [20/21] T170A (control_surface)
[2026-05-12 12:40:05] [V2] STAGE7:   PyMOL>print("ROTAMER_PICK resi=170 aa=ALA best_idx=" + str(best_idx) + " strain=" + str(best_strain))
[2026-05-12 12:40:05] [V2] STAGE7:   ROTAMER_PICK resi=170 aa=ALA best_idx=0 strain=1e+30
[2026-05-12 12:40:08] [V2] STAGE6:   meeko receptor T170A_apo rc=2
[2026-05-12 12:40:08] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:40:09] [V2] STAGE6:   obabel receptor T170A_apo rc=0
[2026-05-12 12:40:10] [V2] STAGE6:   meeko receptor T170A_holo rc=2
[2026-05-12 12:40:10] [V2] STAGE6:   meeko stderr: 
mk_prepare_receptor.py: error: unrecognized arguments: --no-flexible

[2026-05-12 12:40:11] [V2] STAGE6:   obabel receptor T170A_holo rc=0
[2026-05-12 12:40:27] [V2] STAGE7:   T170A apo: top=-7.10, ddG=-0.30, rmsd=5.58
[2026-05-12 12:40:41] [V2] STAGE7:   T170A holo: top=-4.49, ddG=-1.27, rmsd=2.53
[2026-05-12 12:40:41] [V2] STAGE7: [21/21] G217W (explore_g217w)
[2026-05-12 12:40:41] [V2] STAGE7:   PyMOL>print("ROTAMER_PICK resi=217 aa=TRP best_idx=" + str(best_idx) + " strain=" + str(best_strain))
[2026-05-12 12:40:41] [V2] STAGE7:   ROTAMER_PICK resi=217 aa=TRP best_idx=0 strain=1e+30
[2026-05-12 12:40:41] [V2] STAGE7:   clashes detected: [(217, 'CG', 252, 'CD2', np.float32(1.4953969)), (217, 'CD1', 252, 'CD2', np.float32(1.3784181)), (217, 'CD2', 214, 'OE1', np.float32(1.6130123))]...
[2026-05-12 12:40:41] [V2] STAGE7:   G217W has heavy-atom clashes <1.8A — DROPPING per spec
[2026-05-12 12:40:41] [V2] STAGE7: Wrote /Users/ario/conserved_site_project/07b_mut_docking_v2/mutant_results_v2.csv (40 rows)
[2026-05-12 12:40:41] [V2] STAGE7: viewer file PyMOL load test: OK (sample=R50A_apo_complex.pdb)
[2026-05-12 12:40:41] [V2] STAGE7: Stage 7 v2 DONE: 40 successful runs, 1 skipped
[2026-05-12 12:41:14] [V2] STAGE8: Stage 8 v2 starting
[2026-05-12 12:41:14] [V2] STAGE8: loaded 40 rows
[2026-05-12 12:41:14] [V2] STAGE8: wrote pivot: ['mutant', 'category', 'ddG_vs_wt_apo', 'ddG_vs_wt_holo', 'rmsd_to_native_apo', 'rmsd_to_native_holo', 'top_affinity_apo', 'top_affinity_holo']
[2026-05-12 12:41:14] [V2] STAGE8: top apo destabilizers: [['Q214A', 0.1299999999999999], ['R50E', -0.2039999999999997], ['R50A', -0.2690000000000001], ['Y258F_F225Y', -0.2830000000000003], ['R175E', -0.3029999999999999]]
[2026-05-12 12:41:14] [V2] STAGE8: top holo destabilizers: [['H196A', -1.1690000000000005], ['T170A', -1.2700000000000005], ['R50E', -2.173], ['N226D', -2.6879999999999997], ['R50A', -2.7910000000000004]]
[2026-05-12 12:41:14] [V2] STAGE8: wrote ddg_apo_holo.png
[2026-05-12 12:41:14] [V2] STAGE8: wrote ddg_apo_vs_holo.png
[2026-05-12 12:41:14] [V2] STAGE8: wrote ddg_by_category.png
[2026-05-12 12:41:14] [V2] STAGE8: summary: {'n_mutants_total': 20, 'n_apo': 20, 'n_holo': 20, 'wt_apo_aff': -6.798, 'wt_holo_aff': -3.215, 'top5_destabilising_apo': [{'mutant': 'Q214A', 'ddG_vs_wt': 0.1299999999999999}, {'mutant': 'R50E', 'ddG_vs_wt': -0.2039999999999997}, {'mutant': 'R50A', 'ddG_vs_wt': -0.2690000000000001}, {'mutant': 'Y258F_F225Y', 'ddG_vs_wt': -0.2830000000000003}, {'mutant': 'R175E', 'ddG_vs_wt': -0.3029999999999999}], 'top5_destabilising_holo': [{'mutant': 'H196A', 'ddG_vs_wt': -1.1690000000000005}, {'mutant': 'T170A', 'ddG_vs_wt': -1.2700000000000005}, {'mutant': 'R50E', 'ddG_vs_wt': -2.173}, {'mutant': 'N226D', 'ddG_vs_wt': -2.6879999999999997}, {'mutant': 'R50A', 'ddG_vs_wt': -2.7910000000000004}], 'apo_holo_correlation': 0.6337560620851608}
[2026-05-12 12:41:14] [V2] STAGE8: Stage 8 v2 DONE
[2026-05-12 12:41:19] [V2] STAGE9: Stage 9 v2 starting
[2026-05-12 12:41:52] [V2] STAGE9: Stage 9 v2 starting
[2026-05-12 12:41:53] [V2] STAGE9: wrote /Users/ario/conserved_site_project/09b_report_v2/report.html
[2026-05-12 12:41:54] [V2] STAGE9: wrote /Users/ario/conserved_site_project/09b_report_v2/report.pdf (3849031 bytes)
[2026-05-12 12:41:54] [V2] STAGE9: wrote /Users/ario/conserved_site_project/09b_report_v2/report.docx (4007762 bytes)
[2026-05-12 12:41:54] [V2] STAGE9: Stage 9 v2 DONE
[V2] 2026-05-12 12:42:03 Pipeline v2 COMPLETE - all 9 stages done
[2026-05-12 12:56:42] [V3] STAGE6: Stage 6 v3 starting
[2026-05-12 12:56:42] [V3] STAGE6:   [cofA] reprotonate rc=0
[2026-05-12 12:56:43] [V3] STAGE6:   [cofB] reprotonate rc=0
[2026-05-12 12:56:43] [V3] STAGE6: crystal dUMP centroid: [-0.1365499496459961, 4.231900215148926, 15.159449577331543]
[2026-05-12 12:56:44] [V3] STAGE6:   [APO_dimer] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 12:56:44] [V3] STAGE6:   apo receptor OK via obabel_gasteiger, max|q|=0.507
[2026-05-12 12:56:44] [V3] STAGE6:   [HOLO_dimer] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 12:56:44] [V3] STAGE6:   holo receptor OK via obabel_gasteiger, max|q|=0.507
[2026-05-12 12:56:44] [V3] STAGE6:   vina[WT_apo_seed42] seed=42 exh=96 center=(-0.14,4.23,15.16)
[2026-05-12 12:57:15] [V3] STAGE6:   WT apo seed42: top=-9.20 n=27 rmsd=2.34
[2026-05-12 12:57:15] [V3] STAGE6:   vina[WT_apo_seed7] seed=7 exh=96 center=(-0.14,4.23,15.16)
[2026-05-12 12:57:48] [V3] STAGE6:   WT apo seed7: top=-9.13 n=29 rmsd=2.33
[2026-05-12 12:57:48] [V3] STAGE6:   WT apo BEST seed = 7 (rmsd=2.33, top=-9.13)
[2026-05-12 12:57:49] [V3] STAGE6:   vina[WT_holo_seed42] seed=42 exh=96 center=(-0.14,4.23,15.16)
[2026-05-12 12:58:37] [V3] STAGE6:   WT holo seed42: top=-8.31 n=3 rmsd=2.08
[2026-05-12 12:58:37] [V3] STAGE6:   vina[WT_holo_seed7] seed=7 exh=96 center=(-0.14,4.23,15.16)
[2026-05-12 12:59:23] [V3] STAGE6:   WT holo seed7: top=-8.31 n=2 rmsd=2.14
[2026-05-12 12:59:23] [V3] STAGE6:   WT holo BEST seed = 42 (rmsd=2.08, top=-8.31)
[2026-05-12 12:59:24] [V3] STAGE6: Stage 6 v3 DONE
[2026-05-12 13:01:17] [V3] STAGE7: Stage 7 v3 starting
[2026-05-12 13:01:18] [V3] STAGE7: ref seq len=313
[2026-05-12 13:01:18] [V3] STAGE7: Built panel of 20 mutants (no G217W)
[2026-05-12 13:01:18] [V3] STAGE7: centroid (crystal dUMP): [-0.1365499496459961, 4.231900215148926, 15.159449577331543]
[2026-05-12 13:01:18] [V3] STAGE7: WT apo aff = -9.13, WT holo aff = -8.31
[2026-05-12 13:01:18] [V3] STAGE7: [1/20] R50A (ala_scan)
[2026-05-12 13:01:19] [V3] STAGE7:   sculpt: OK
[2026-05-12 13:01:22] [V3] STAGE6:   [R50A_apo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:01:22] [V3] STAGE6:   [R50A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:01:33] [V3] STAGE7:   R50A apo: top=-8.62 delta=+0.51 n=20 rmsd=2.42 mis_docked=False
[2026-05-12 13:01:44] [V3] STAGE7:   R50A holo: top=-7.61 delta=+0.70 n=20 rmsd=2.09 mis_docked=False
[2026-05-12 13:01:44] [V3] STAGE7: [2/20] W109A (ala_scan)
[2026-05-12 13:01:45] [V3] STAGE7:   sculpt: OK
[2026-05-12 13:01:48] [V3] STAGE6:   [W109A_apo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:01:48] [V3] STAGE6:   [W109A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:01:59] [V3] STAGE7:   W109A apo: top=-8.88 delta=+0.25 n=19 rmsd=2.46 mis_docked=False
[2026-05-12 13:02:13] [V3] STAGE7:   W109A holo: top=-8.08 delta=+0.23 n=3 rmsd=2.17 mis_docked=False
[2026-05-12 13:02:13] [V3] STAGE7: [3/20] R175A (ala_scan)
[2026-05-12 13:02:13] [V3] STAGE7:   sculpt: OK
[2026-05-12 13:02:17] [V3] STAGE6:   [R175A_apo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:02:17] [V3] STAGE6:   [R175A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:02:28] [V3] STAGE7:   R175A apo: top=-9.02 delta=+0.11 n=20 rmsd=2.30 mis_docked=False
[2026-05-12 13:02:43] [V3] STAGE7:   R175A holo: top=-8.24 delta=+0.07 n=2 rmsd=2.13 mis_docked=False
[2026-05-12 13:02:43] [V3] STAGE7: [4/20] R176A (ala_scan)
[2026-05-12 13:02:44] [V3] STAGE7:   sculpt: OK
[2026-05-12 13:02:47] [V3] STAGE6:   [R176A_apo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:02:47] [V3] STAGE6:   [R176A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:02:59] [V3] STAGE7:   R176A apo: top=-9.02 delta=+0.11 n=20 rmsd=2.31 mis_docked=False
[2026-05-12 13:03:13] [V3] STAGE7:   R176A holo: top=-8.24 delta=+0.07 n=2 rmsd=2.13 mis_docked=False
[2026-05-12 13:03:13] [V3] STAGE7: [5/20] C195A (ala_scan)
[2026-05-12 13:03:14] [V3] STAGE7:   sculpt: OK
[2026-05-12 13:03:17] [V3] STAGE6:   [C195A_apo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:03:17] [V3] STAGE6:   [C195A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:03:29] [V3] STAGE7:   C195A apo: top=-9.46 delta=-0.33 n=20 rmsd=2.09 mis_docked=False
[2026-05-12 13:03:41] [V3] STAGE7:   C195A holo: top=-10.61 delta=-2.29 n=3 rmsd=2.15 mis_docked=False
[2026-05-12 13:03:41] [V3] STAGE7: [6/20] H196A (ala_scan)
[2026-05-12 13:03:42] [V3] STAGE7:   sculpt: OK
[2026-05-12 13:03:45] [V3] STAGE6:   [H196A_apo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:03:45] [V3] STAGE6:   [H196A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:03:56] [V3] STAGE7:   H196A apo: top=-8.86 delta=+0.27 n=19 rmsd=2.31 mis_docked=False
[2026-05-12 13:04:12] [V3] STAGE7:   H196A holo: top=-7.81 delta=+0.50 n=4 rmsd=2.18 mis_docked=False
[2026-05-12 13:04:12] [V3] STAGE7: [7/20] Q214A (ala_scan)
[2026-05-12 13:04:12] [V3] STAGE7:   sculpt: OK
[2026-05-12 13:04:16] [V3] STAGE6:   [Q214A_apo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:04:16] [V3] STAGE6:   [Q214A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:04:27] [V3] STAGE7:   Q214A apo: top=-8.65 delta=+0.48 n=19 rmsd=2.36 mis_docked=False
[2026-05-12 13:04:43] [V3] STAGE7:   Q214A holo: top=-8.26 delta=+0.06 n=2 rmsd=2.13 mis_docked=False
[2026-05-12 13:04:43] [V3] STAGE7: [8/20] R215A (ala_scan)
[2026-05-12 13:04:44] [V3] STAGE7:   sculpt: OK
[2026-05-12 13:04:47] [V3] STAGE6:   [R215A_apo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:04:48] [V3] STAGE6:   [R215A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:04:59] [V3] STAGE7:   R215A apo: top=-8.63 delta=+0.50 n=20 rmsd=2.25 mis_docked=False
[2026-05-12 13:05:14] [V3] STAGE7:   R215A holo: top=-7.89 delta=+0.42 n=4 rmsd=2.18 mis_docked=False
[2026-05-12 13:05:14] [V3] STAGE7: [9/20] R50E (opposite)
[2026-05-12 13:05:15] [V3] STAGE7:   sculpt: OK
[2026-05-12 13:05:18] [V3] STAGE6:   [R50E_apo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:05:19] [V3] STAGE6:   [R50E_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:05:30] [V3] STAGE7:   R50E apo: top=-8.78 delta=+0.35 n=20 rmsd=2.35 mis_docked=False
[2026-05-12 13:05:42] [V3] STAGE7:   R50E holo: top=-7.40 delta=+0.91 n=20 rmsd=6.93 mis_docked=True
[2026-05-12 13:05:42] [V3] STAGE7: [10/20] R175E (opposite)
[2026-05-12 13:05:42] [V3] STAGE7:   sculpt: OK
[2026-05-12 13:05:45] [V3] STAGE6:   [R175E_apo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:05:46] [V3] STAGE6:   [R175E_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:05:57] [V3] STAGE7:   R175E apo: top=-9.04 delta=+0.09 n=20 rmsd=2.39 mis_docked=False
[2026-05-12 13:06:12] [V3] STAGE7:   R175E holo: top=-8.29 delta=+0.03 n=2 rmsd=2.05 mis_docked=False
[2026-05-12 13:06:12] [V3] STAGE7: [11/20] R176E (opposite)
[2026-05-12 13:06:13] [V3] STAGE7:   sculpt: OK
[2026-05-12 13:06:16] [V3] STAGE6:   [R176E_apo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:06:17] [V3] STAGE6:   [R176E_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:06:28] [V3] STAGE7:   R176E apo: top=-9.02 delta=+0.11 n=20 rmsd=2.31 mis_docked=False
[2026-05-12 13:06:43] [V3] STAGE7:   R176E holo: top=-8.29 delta=+0.03 n=2 rmsd=2.15 mis_docked=False
[2026-05-12 13:06:43] [V3] STAGE7: [12/20] C195S (opposite)
[2026-05-12 13:06:43] [V3] STAGE7:   sculpt: OK
[2026-05-12 13:06:46] [V3] STAGE6:   [C195S_apo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:06:47] [V3] STAGE6:   [C195S_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:06:58] [V3] STAGE7:   C195S apo: top=-9.55 delta=-0.42 n=20 rmsd=2.14 mis_docked=False
[2026-05-12 13:07:11] [V3] STAGE7:   C195S holo: top=-10.29 delta=-1.98 n=2 rmsd=2.17 mis_docked=False
[2026-05-12 13:07:11] [V3] STAGE7: [13/20] R215E (opposite)
[2026-05-12 13:07:11] [V3] STAGE7:   sculpt: OK
[2026-05-12 13:07:11] [V3] STAGE7:   1 clashes <1.8A: [(215, 'OE2', 197, 'CB', 0.5643286108970642)]
[2026-05-12 13:07:14] [V3] STAGE6:   [R215E_apo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:07:15] [V3] STAGE6:   [R215E_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:07:26] [V3] STAGE7:   R215E apo: top=-8.59 delta=+0.54 n=19 rmsd=2.43 mis_docked=False
[2026-05-12 13:07:41] [V3] STAGE7:   R215E holo: top=-7.86 delta=+0.45 n=4 rmsd=2.10 mis_docked=False
[2026-05-12 13:07:41] [V3] STAGE7: [14/20] N226D (opposite)
[2026-05-12 13:07:42] [V3] STAGE7:   sculpt: OK
[2026-05-12 13:07:45] [V3] STAGE6:   [N226D_apo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:07:45] [V3] STAGE6:   [N226D_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:07:56] [V3] STAGE7:   N226D apo: top=-8.78 delta=+0.35 n=20 rmsd=2.40 mis_docked=False
[2026-05-12 13:08:11] [V3] STAGE7:   N226D holo: top=-7.87 delta=+0.44 n=2 rmsd=2.13 mis_docked=False
[2026-05-12 13:08:11] [V3] STAGE7: [15/20] C195A_H196A (double_dyad)
[2026-05-12 13:08:11] [V3] STAGE7:   sculpt: OK
[2026-05-12 13:08:14] [V3] STAGE6:   [C195A_H196A_apo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:08:15] [V3] STAGE6:   [C195A_H196A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:08:26] [V3] STAGE7:   C195A_H196A apo: top=-9.12 delta=+0.01 n=20 rmsd=2.11 mis_docked=False
[2026-05-12 13:08:39] [V3] STAGE7:   C195A_H196A holo: top=-10.16 delta=-1.84 n=3 rmsd=2.13 mis_docked=False
[2026-05-12 13:08:39] [V3] STAGE7: [16/20] R175E_R176E (double_phosclamp)
[2026-05-12 13:08:40] [V3] STAGE7:   sculpt: OK
[2026-05-12 13:08:43] [V3] STAGE6:   [R175E_R176E_apo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:08:43] [V3] STAGE6:   [R175E_R176E_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:08:55] [V3] STAGE7:   R175E_R176E apo: top=-9.02 delta=+0.11 n=20 rmsd=2.31 mis_docked=False
[2026-05-12 13:09:11] [V3] STAGE7:   R175E_R176E holo: top=-8.30 delta=+0.02 n=2 rmsd=2.14 mis_docked=False
[2026-05-12 13:09:11] [V3] STAGE7: [17/20] C195S_H196N (double_polar_neutral)
[2026-05-12 13:09:11] [V3] STAGE7:   sculpt: OK
[2026-05-12 13:09:14] [V3] STAGE6:   [C195S_H196N_apo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:09:15] [V3] STAGE6:   [C195S_H196N_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:09:26] [V3] STAGE7:   C195S_H196N apo: top=-9.34 delta=-0.21 n=20 rmsd=2.08 mis_docked=False
[2026-05-12 13:09:38] [V3] STAGE7:   C195S_H196N holo: top=-9.84 delta=-1.53 n=4 rmsd=2.07 mis_docked=False
[2026-05-12 13:09:38] [V3] STAGE7: [18/20] R215A_N226A (double_substrate_orient)
[2026-05-12 13:09:39] [V3] STAGE7:   sculpt: OK
[2026-05-12 13:09:42] [V3] STAGE6:   [R215A_N226A_apo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:09:43] [V3] STAGE6:   [R215A_N226A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:09:54] [V3] STAGE7:   R215A_N226A apo: top=-8.05 delta=+1.08 n=20 rmsd=5.34 mis_docked=True
[2026-05-12 13:10:08] [V3] STAGE7:   R215A_N226A holo: top=-7.59 delta=+0.73 n=4 rmsd=2.31 mis_docked=False
[2026-05-12 13:10:08] [V3] STAGE7: [19/20] Y258F_F225Y (double_aromatic_swap)
[2026-05-12 13:10:08] [V3] STAGE7:   sculpt: OK
[2026-05-12 13:10:11] [V3] STAGE6:   [Y258F_F225Y_apo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:10:12] [V3] STAGE6:   [Y258F_F225Y_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:10:23] [V3] STAGE7:   Y258F_F225Y apo: top=-8.88 delta=+0.25 n=20 rmsd=2.45 mis_docked=False
[2026-05-12 13:10:39] [V3] STAGE7:   Y258F_F225Y holo: top=-8.12 delta=+0.20 n=2 rmsd=2.14 mis_docked=False
[2026-05-12 13:10:39] [V3] STAGE7: [20/20] T170A (control_surface)
[2026-05-12 13:10:39] [V3] STAGE7:   sculpt: OK
[2026-05-12 13:10:42] [V3] STAGE6:   [T170A_apo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:10:43] [V3] STAGE6:   [T170A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:10:54] [V3] STAGE7:   T170A apo: top=-9.02 delta=+0.11 n=20 rmsd=2.30 mis_docked=False
[2026-05-12 13:11:09] [V3] STAGE7:   T170A holo: top=-8.29 delta=+0.03 n=3 rmsd=2.18 mis_docked=False
[2026-05-12 13:11:09] [V3] STAGE7: wrote /Users/ario/conserved_site_project/07c_mut_docking_v3/mutant_results_v3.csv (40 rows)
[2026-05-12 13:11:09] [V3] STAGE7: Stage 7 v3 DONE: 40 runs, 0 skipped
[2026-05-12 13:11:40] [V3] STAGE8: Stage 8 v3 starting
[2026-05-12 13:11:40] [V3] STAGE8: loaded 40 rows
[2026-05-12 13:11:40] [V3] STAGE8: wrote pivot: ['mutant', 'category', 'delta_vina_vs_wt_apo', 'delta_vina_vs_wt_holo', 'mis_docked_apo', 'mis_docked_holo', 'n_modes_apo', 'n_modes_holo']...
[2026-05-12 13:11:40] [V3] STAGE8: top apo destab (well-docked): [['R215E', 0.5410000000000004, 2.42580130725254], ['R50A', 0.5090000000000003, 2.4166652516683764], ['R215A', 0.5, 2.2464490849617618], ['Q214A', 0.4750000000000014, 2.356671062897535], ['N226D', 0.3500000000000014, 2.397877221341776]]
[2026-05-12 13:11:40] [V3] STAGE8: top holo destab (well-docked): [['R215A_N226A', 0.726, 2.3084502395744604], ['R50A', 0.7039999999999997, 2.0921804444876977], ['H196A', 0.5030000000000001, 2.1763053728118313], ['R215E', 0.4519999999999999, 2.1046988789004506], ['N226D', 0.4409999999999998, 2.132076958676749]]
[2026-05-12 13:11:41] [V3] STAGE8: summary: top3 apo (well-docked) = [('R215E', 0.5410000000000004), ('R50A', 0.5090000000000003), ('R215A', 0.5)]
[2026-05-12 13:11:41] [V3] STAGE8: Stage 8 v3 DONE
[2026-05-12 13:11:47] [V3] STAGE9: Stage 9 v3 starting
[2026-05-12 13:11:47] [V3] STAGE9: wrote /Users/ario/conserved_site_project/09c_report_v3/report.html
[2026-05-12 13:11:48] [V3] STAGE9: wrote /Users/ario/conserved_site_project/09c_report_v3/report.pdf (377319 bytes)
[2026-05-12 13:11:48] [V3] STAGE9: wrote /Users/ario/conserved_site_project/09c_report_v3/report.docx (314084 bytes)
[2026-05-12 13:11:48] [V3] STAGE9: Stage 9 v3 DONE
[2026-05-12 13:26:16] [V4] STAGE3: Stage 3 v4 starting (REAL cofactor reprotonation)
[2026-05-12 13:26:18] [V4] STAGE3:   found 2 -COOH groups
[2026-05-12 13:26:18] [V4] STAGE3:   SMILES (no H): Cc1nc(=O)c2cc(CN(C)c3ccc(C(=O)N[C@@H](CCC(=O)[O-])C(=O)[O-])s3)ccc2[nH]1
[2026-05-12 13:26:18] [V4] STAGE3:   protonated SDF written
[2026-05-12 13:26:18] [V4] STAGE3:   obabel canonical SMILES: [O-]C(=O)CC[C@@H](C(=O)[O-])NC(=O)c1ccc(s1)N(Cc1ccc2c(c1)c(=O)nc([nH]2)C)C
[2026-05-12 13:26:18] [V4] STAGE3:   protonated heavy count: 32, crystal heavy count: 32
[2026-05-12 13:26:18] [V4] STAGE3:   crystal elements: ['N', 'C', 'C', 'N', 'C', 'O', 'C', 'C', 'C', 'C']...
[2026-05-12 13:26:18] [V4] STAGE3:   mol elements:     ['N', 'C', 'C', 'N', 'C', 'O', 'C', 'C', 'C', 'C']...
[2026-05-12 13:26:18] [V4] STAGE3:   element order matches; using direct Kabsch alignment
[2026-05-12 13:26:18] [V4] STAGE3:   alignment RMSD heavy = 2.709 A
[2026-05-12 13:26:18] [V4] STAGE3:   wrote /Users/ario/conserved_site_project/03d_structure_v4/cofactor_chainA_v4.pdb
[2026-05-12 13:26:18] [V4] STAGE3:   protonated heavy count: 32, crystal heavy count: 32
[2026-05-12 13:26:18] [V4] STAGE3:   crystal elements: ['N', 'C', 'C', 'N', 'C', 'O', 'C', 'C', 'C', 'C']...
[2026-05-12 13:26:18] [V4] STAGE3:   mol elements:     ['N', 'C', 'C', 'N', 'C', 'O', 'C', 'C', 'C', 'C']...
[2026-05-12 13:26:18] [V4] STAGE3:   element order matches; using direct Kabsch alignment
[2026-05-12 13:26:18] [V4] STAGE3:   alignment RMSD heavy = 2.666 A
[2026-05-12 13:26:18] [V4] STAGE3:   wrote /Users/ario/conserved_site_project/03d_structure_v4/cofactor_chainB_v4.pdb
[2026-05-12 13:26:18] [V4] STAGE3:   chain A: v2_md5=c3a555f6f0444de7cac58d2797c90eb5 v4_md5=e6f06a08f8910fff680286de98c2e1d2
[2026-05-12 13:26:18] [V4] STAGE3:   chain A: MD5 differs (good)
[2026-05-12 13:26:18] [V4] STAGE3:   chain B: v2_md5=6dcb536725c93aa7cdd52c36a46ca3f7 v4_md5=9900570337d49678d67b31e076657cec
[2026-05-12 13:26:18] [V4] STAGE3:   chain B: MD5 differs (good)
[2026-05-12 13:26:18] [V4] STAGE3: Stage 3 v4 DONE
[2026-05-12 13:29:16] [V4] STAGE6: Stage 6 v4 starting (multi-seed sweep, affinity-based selection)
[2026-05-12 13:29:16] [V4] STAGE6: crystal dUMP centroid: [-0.13655, 4.2319, 15.159450000000001]
[2026-05-12 13:29:18] [V4] STAGE6:   [APO_dimer] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:29:18] [V4] STAGE6:   apo receptor OK via obabel_gasteiger, max|q|=0.507
[2026-05-12 13:29:18] [V4] STAGE6:   [HOLO_dimer] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:29:18] [V4] STAGE6:   holo receptor OK via obabel_gasteiger, max|q|=0.507
[2026-05-12 13:29:18] [V4] STAGE6:   vina[wt_apo] seed=42 exh=96 center=(-0.14,4.23,15.16)
[2026-05-12 13:29:54] [V4] STAGE6:   wt_apo seed42: top=-9.20 n=27 rmsd=0.91
[2026-05-12 13:29:54] [V4] STAGE6:   vina[wt_apo] seed=7 exh=96 center=(-0.14,4.23,15.16)
[2026-05-12 13:30:32] [V4] STAGE6:   wt_apo seed7: top=-9.13 n=29 rmsd=0.89
[2026-05-12 13:30:32] [V4] STAGE6:   vina[wt_apo] seed=13 exh=96 center=(-0.14,4.23,15.16)
[2026-05-12 13:31:09] [V4] STAGE6:   wt_apo seed13: top=-9.12 n=28 rmsd=0.86
[2026-05-12 13:31:09] [V4] STAGE6:   vina[wt_apo] seed=99 exh=96 center=(-0.14,4.23,15.16)
[2026-05-12 13:31:49] [V4] STAGE6:   wt_apo seed99: top=-9.08 n=28 rmsd=0.97
[2026-05-12 13:31:49] [V4] STAGE6:   vina[wt_apo] seed=256 exh=96 center=(-0.14,4.23,15.16)
[2026-05-12 13:32:25] [V4] STAGE6:   wt_apo seed256: top=-9.19 n=29 rmsd=0.92
[2026-05-12 13:32:25] [V4] STAGE6:   WT apo BEST seed = 42 (top=-9.20, n_modes=27, rmsd=0.91)
[2026-05-12 13:32:25] [V4] STAGE6:   WT apo named-pose RMSD vs crystal = 3.802
[2026-05-12 13:32:25] [V4] STAGE6:   vina[wt_holo] seed=42 exh=96 center=(-0.14,4.23,15.16)
[2026-05-12 13:33:20] [V4] STAGE6:   wt_holo seed42: top=-5.09 n=31 rmsd=12.24
[2026-05-12 13:33:20] [V4] STAGE6:   vina[wt_holo] seed=7 exh=96 center=(-0.14,4.23,15.16)
[2026-05-12 13:34:14] [V4] STAGE6:   wt_holo seed7: top=-5.22 n=30 rmsd=12.95
[2026-05-12 13:34:14] [V4] STAGE6:   vina[wt_holo] seed=13 exh=96 center=(-0.14,4.23,15.16)
[2026-05-12 13:35:09] [V4] STAGE6:   wt_holo seed13: top=-5.11 n=30 rmsd=12.23
[2026-05-12 13:35:09] [V4] STAGE6:   vina[wt_holo] seed=99 exh=96 center=(-0.14,4.23,15.16)
[2026-05-12 13:36:04] [V4] STAGE6:   wt_holo seed99: top=-5.22 n=31 rmsd=12.93
[2026-05-12 13:36:04] [V4] STAGE6:   vina[wt_holo] seed=256 exh=96 center=(-0.14,4.23,15.16)
[2026-05-12 13:36:58] [V4] STAGE6:   wt_holo seed256: top=-5.24 n=30 rmsd=12.95
[2026-05-12 13:36:58] [V4] STAGE6:   WT holo BEST seed = 256 (top=-5.24, n_modes=30, rmsd=12.95)
[2026-05-12 13:36:58] [V4] STAGE6:   WT holo named-pose RMSD vs crystal = 12.917
[2026-05-12 13:36:58] [V4] STAGE6: Stage 6 v4 DONE
[2026-05-12 13:37:54] [V4] STAGE7: Stage 7 v4 starting
[2026-05-12 13:37:54] [V4] STAGE7: Found 20 mutants from v3
[2026-05-12 13:37:54] [V4] STAGE7: centroid (crystal dUMP): [-0.13655, 4.2319, 15.159450000000001]
[2026-05-12 13:37:54] [V4] STAGE7: WT v4 apo aff = -9.20, WT v4 holo aff = -5.24
[2026-05-12 13:37:54] [V4] STAGE7: [1/20] C195A (ala_scan)
[2026-05-12 13:37:55] [V4] STAGE7:   [C195A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:38:10] [V4] STAGE7:   C195A holo: top=-6.99 delta=-1.75 n=12 rmsd=3.77 mis_docked=True low_conf=False
[2026-05-12 13:38:10] [V4] STAGE7:   C195A apo (reused v3): top=-9.46 delta=-0.26 n=20 rmsd=2.09
[2026-05-12 13:38:10] [V4] STAGE7: [2/20] C195A_H196A (double_dyad)
[2026-05-12 13:38:11] [V4] STAGE7:   [C195A_H196A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:38:25] [V4] STAGE7:   C195A_H196A holo: top=-7.88 delta=-2.64 n=2 rmsd=4.25 mis_docked=True low_conf=True
[2026-05-12 13:38:25] [V4] STAGE7:   C195A_H196A apo (reused v3): top=-9.12 delta=+0.08 n=20 rmsd=2.11
[2026-05-12 13:38:25] [V4] STAGE7: [3/20] C195S (opposite)
[2026-05-12 13:38:26] [V4] STAGE7:   [C195S_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:38:42] [V4] STAGE7:   C195S holo: top=-6.05 delta=-0.81 n=18 rmsd=3.49 mis_docked=True low_conf=False
[2026-05-12 13:38:42] [V4] STAGE7:   C195S apo (reused v3): top=-9.55 delta=-0.36 n=20 rmsd=2.14
[2026-05-12 13:38:42] [V4] STAGE7: [4/20] C195S_H196N (double_polar_neutral)
[2026-05-12 13:38:42] [V4] STAGE7:   [C195S_H196N_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:38:58] [V4] STAGE7:   C195S_H196N holo: top=-6.28 delta=-1.04 n=19 rmsd=4.12 mis_docked=True low_conf=False
[2026-05-12 13:38:58] [V4] STAGE7:   C195S_H196N apo (reused v3): top=-9.34 delta=-0.14 n=20 rmsd=2.08
[2026-05-12 13:38:58] [V4] STAGE7: [5/20] H196A (ala_scan)
[2026-05-12 13:38:59] [V4] STAGE7:   [H196A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:39:16] [V4] STAGE7:   H196A holo: top=-5.16 delta=+0.09 n=19 rmsd=11.76 mis_docked=True low_conf=False
[2026-05-12 13:39:16] [V4] STAGE7:   H196A apo (reused v3): top=-8.86 delta=+0.34 n=19 rmsd=2.31
[2026-05-12 13:39:16] [V4] STAGE7: [6/20] N226D (opposite)
[2026-05-12 13:39:16] [V4] STAGE7:   [N226D_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:39:33] [V4] STAGE7:   N226D holo: top=-5.08 delta=+0.16 n=17 rmsd=13.00 mis_docked=True low_conf=False
[2026-05-12 13:39:33] [V4] STAGE7:   N226D apo (reused v3): top=-8.78 delta=+0.42 n=20 rmsd=2.40
[2026-05-12 13:39:33] [V4] STAGE7: [7/20] Q214A (ala_scan)
[2026-05-12 13:39:34] [V4] STAGE7:   [Q214A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:39:49] [V4] STAGE7:   Q214A holo: top=-5.08 delta=+0.16 n=20 rmsd=12.91 mis_docked=True low_conf=False
[2026-05-12 13:39:49] [V4] STAGE7:   Q214A apo (reused v3): top=-8.65 delta=+0.54 n=19 rmsd=2.36
[2026-05-12 13:39:49] [V4] STAGE7: [8/20] R175A (ala_scan)
[2026-05-12 13:39:50] [V4] STAGE7:   [R175A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:40:07] [V4] STAGE7:   R175A holo: top=-5.12 delta=+0.13 n=19 rmsd=11.82 mis_docked=True low_conf=False
[2026-05-12 13:40:07] [V4] STAGE7:   R175A apo (reused v3): top=-9.02 delta=+0.18 n=20 rmsd=2.30
[2026-05-12 13:40:07] [V4] STAGE7: [9/20] R175E (opposite)
[2026-05-12 13:40:07] [V4] STAGE7:   [R175E_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:40:24] [V4] STAGE7:   R175E holo: top=-5.10 delta=+0.14 n=18 rmsd=12.19 mis_docked=True low_conf=False
[2026-05-12 13:40:24] [V4] STAGE7:   R175E apo (reused v3): top=-9.04 delta=+0.16 n=20 rmsd=2.39
[2026-05-12 13:40:24] [V4] STAGE7: [10/20] R175E_R176E (double_phosclamp)
[2026-05-12 13:40:24] [V4] STAGE7:   [R175E_R176E_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:40:41] [V4] STAGE7:   R175E_R176E holo: top=-5.04 delta=+0.20 n=19 rmsd=12.19 mis_docked=True low_conf=False
[2026-05-12 13:40:41] [V4] STAGE7:   R175E_R176E apo (reused v3): top=-9.02 delta=+0.18 n=20 rmsd=2.31
[2026-05-12 13:40:41] [V4] STAGE7: [11/20] R176A (ala_scan)
[2026-05-12 13:40:42] [V4] STAGE7:   [R176A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:40:58] [V4] STAGE7:   R176A holo: top=-5.06 delta=+0.18 n=19 rmsd=11.79 mis_docked=True low_conf=False
[2026-05-12 13:40:58] [V4] STAGE7:   R176A apo (reused v3): top=-9.02 delta=+0.18 n=20 rmsd=2.31
[2026-05-12 13:40:58] [V4] STAGE7: [12/20] R176E (opposite)
[2026-05-12 13:40:58] [V4] STAGE7:   [R176E_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:41:15] [V4] STAGE7:   R176E holo: top=-5.04 delta=+0.20 n=19 rmsd=12.19 mis_docked=True low_conf=False
[2026-05-12 13:41:15] [V4] STAGE7:   R176E apo (reused v3): top=-9.02 delta=+0.18 n=20 rmsd=2.31
[2026-05-12 13:41:15] [V4] STAGE7: [13/20] R215A (ala_scan)
[2026-05-12 13:41:16] [V4] STAGE7:   [R215A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:41:31] [V4] STAGE7:   R215A holo: top=-6.53 delta=-1.29 n=15 rmsd=3.78 mis_docked=True low_conf=False
[2026-05-12 13:41:31] [V4] STAGE7:   R215A apo (reused v3): top=-8.63 delta=+0.57 n=20 rmsd=2.25
[2026-05-12 13:41:31] [V4] STAGE7: [14/20] R215A_N226A (double_substrate_orient)
[2026-05-12 13:41:32] [V4] STAGE7:   [R215A_N226A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:41:47] [V4] STAGE7:   R215A_N226A holo: top=-6.46 delta=-1.22 n=14 rmsd=3.79 mis_docked=True low_conf=False
[2026-05-12 13:41:47] [V4] STAGE7:   R215A_N226A apo (reused v3): top=-8.05 delta=+1.15 n=20 rmsd=5.34
[2026-05-12 13:41:47] [V4] STAGE7: [15/20] R215E (opposite)
[2026-05-12 13:41:48] [V4] STAGE7:   [R215E_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:42:03] [V4] STAGE7:   R215E holo: top=-6.76 delta=-1.51 n=8 rmsd=3.77 mis_docked=True low_conf=False
[2026-05-12 13:42:03] [V4] STAGE7:   R215E apo (reused v3): top=-8.59 delta=+0.61 n=19 rmsd=2.43
[2026-05-12 13:42:03] [V4] STAGE7: [16/20] R50A (ala_scan)
[2026-05-12 13:42:03] [V4] STAGE7:   [R50A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:42:16] [V4] STAGE7:   R50A holo: top=-6.86 delta=-1.62 n=20 rmsd=8.66 mis_docked=True low_conf=False
[2026-05-12 13:42:16] [V4] STAGE7:   R50A apo (reused v3): top=-8.62 delta=+0.58 n=20 rmsd=2.42
[2026-05-12 13:42:16] [V4] STAGE7: [17/20] R50E (opposite)
[2026-05-12 13:42:16] [V4] STAGE7:   [R50E_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:42:30] [V4] STAGE7:   R50E holo: top=-6.84 delta=-1.59 n=19 rmsd=5.78 mis_docked=True low_conf=False
[2026-05-12 13:42:30] [V4] STAGE7:   R50E apo (reused v3): top=-8.78 delta=+0.41 n=20 rmsd=2.35
[2026-05-12 13:42:30] [V4] STAGE7: [18/20] T170A (control_surface)
[2026-05-12 13:42:31] [V4] STAGE7:   [T170A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:42:47] [V4] STAGE7:   T170A holo: top=-5.07 delta=+0.17 n=20 rmsd=12.94 mis_docked=True low_conf=False
[2026-05-12 13:42:47] [V4] STAGE7:   T170A apo (reused v3): top=-9.02 delta=+0.18 n=20 rmsd=2.30
[2026-05-12 13:42:47] [V4] STAGE7: [19/20] W109A (ala_scan)
[2026-05-12 13:42:48] [V4] STAGE7:   [W109A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:43:02] [V4] STAGE7:   W109A holo: top=-7.04 delta=-1.80 n=19 rmsd=8.40 mis_docked=True low_conf=False
[2026-05-12 13:43:02] [V4] STAGE7:   W109A apo (reused v3): top=-8.88 delta=+0.32 n=19 rmsd=2.46
[2026-05-12 13:43:02] [V4] STAGE7: [20/20] Y258F_F225Y (double_aromatic_swap)
[2026-05-12 13:43:03] [V4] STAGE7:   [Y258F_F225Y_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 13:43:20] [V4] STAGE7:   Y258F_F225Y holo: top=-5.14 delta=+0.11 n=18 rmsd=11.77 mis_docked=True low_conf=False
[2026-05-12 13:43:20] [V4] STAGE7:   Y258F_F225Y apo (reused v3): top=-8.88 delta=+0.32 n=20 rmsd=2.45
[2026-05-12 13:43:20] [V4] STAGE7: wrote /Users/ario/conserved_site_project/07d_mut_docking_v4/mutant_results_v4.csv (42 rows including WT reference)
[2026-05-12 13:43:20] [V4] STAGE7: Stage 7 v4 DONE: 40 rows, 0 skipped
[2026-05-12 13:43:55] [V4] STAGE8: Stage 8 v4 starting
[2026-05-12 13:43:55] [V4] STAGE8: loaded 42 rows (including WT reference)
[2026-05-12 13:43:55] [V4] STAGE8: top apo destab (well-docked, n>=5): [['R215E', 0.6109999999999989, 2.42580130725254, 19], ['R50A', 0.5789999999999988, 2.4166652516683764, 20], ['R215A', 0.5699999999999985, 2.2464490849617618, 20], ['Q214A', 0.5449999999999999, 2.356671062897535, 19], ['N226D', 0.4199999999999999, 2.397877221341776, 20]]
[2026-05-12 13:43:55] [V4] STAGE8: top holo destab (well-docked, n>=5): []
[2026-05-12 13:43:55] [V4] STAGE8: summary written
[2026-05-12 13:43:55] [V4] STAGE8: Pearson r = None, Spearman ρ = None, filtered Spearman ρ = None (n=0)
[2026-05-12 13:43:55] [V4] STAGE8: Stage 8 v4 DONE
[2026-05-12 13:45:36] [V4] STAGE8: Stage 8 v4 starting
[2026-05-12 13:45:36] [V4] STAGE8: loaded 42 rows (including WT reference)
[2026-05-12 13:45:36] [V4] STAGE8: WT holo itself is RMSD=12.95 A vs crystal (ionised cofactor displaces dUMP). Holo mis_docked redefined as |RMSD - WT_holo_RMSD| > 3 A.
[2026-05-12 13:45:36] [V4] STAGE8: top apo destab (well-docked, n>=5): [['R215E', 0.6109999999999989, 2.42580130725254, 19], ['R50A', 0.5789999999999988, 2.4166652516683764, 20], ['R215A', 0.5699999999999985, 2.2464490849617618, 20], ['Q214A', 0.5449999999999999, 2.356671062897535, 19], ['N226D', 0.4199999999999999, 2.397877221341776, 20]]
[2026-05-12 13:45:36] [V4] STAGE8: top holo destab (well-docked, n>=5): [['R176E', 0.2039999999999997, 12.186796240193727, 19], ['R175E_R176E', 0.2039999999999997, 12.186796240193727, 19], ['R176A', 0.1820000000000003, 11.786282206446613, 19], ['T170A', 0.1710000000000002, 12.94482042169763, 20], ['N226D', 0.1639999999999997, 13.001087527587837, 17]]
[2026-05-12 13:45:37] [V4] STAGE8: summary written
[2026-05-12 13:45:37] [V4] STAGE8: Pearson r = -0.30136180770091225, Spearman ρ = -0.45065162847137524, filtered Spearman ρ = 0.6000000000000001 (n=4)
[2026-05-12 13:45:37] [V4] STAGE8: Stage 8 v4 DONE
[2026-05-12 13:45:54] [V4] STAGE9: Stage 9 v4 starting
[2026-05-12 13:45:54] [V4] STAGE9: wrote /Users/ario/conserved_site_project/09d_report_v4/report.html
[2026-05-12 13:45:55] [V4] STAGE9: wrote /Users/ario/conserved_site_project/09d_report_v4/report.pdf (252362 bytes)
[2026-05-12 13:45:55] [V4] STAGE9: wrote /Users/ario/conserved_site_project/09d_report_v4/report.docx (197556 bytes)
[2026-05-12 13:45:55] [V4] STAGE9: Stage 9 v4 DONE
[2026-05-12 13:59:25] [V5] STAGE3: Stage 3 v5 starting (IN-PLACE cofactor reprotonation; no Kabsch)
[2026-05-12 13:59:25] [V5] STAGE3:   chain A heavy atoms: 32
[2026-05-12 13:59:25] [V5] STAGE3:   chain B heavy atoms: 32
[2026-05-12 13:59:25] [V5] STAGE3: Chain A:
[2026-05-12 13:59:26] [V5] STAGE3:   template heavy atoms: 34, crystal heavy atoms: 32
[2026-05-12 13:59:26] [V5] STAGE3:   WARNING heavy-atom count mismatch (34 vs 32)
[2026-05-12 13:59:26] [V5] STAGE3:   rdDetermineBonds path failed (No matching found); using direct heavy-mol bond transfer
[2026-05-12 14:00:54] [V5] STAGE3: Stage 3 v5 starting (IN-PLACE cofactor reprotonation; no Kabsch)
[2026-05-12 14:00:54] [V5] STAGE3:   chain A heavy atoms: 32
[2026-05-12 14:00:54] [V5] STAGE3:   chain B heavy atoms: 32
[2026-05-12 14:00:54] [V5] STAGE3: Chain A:
[2026-05-12 14:00:54] [V5] STAGE3:   template heavy atoms: 32, crystal heavy atoms: 32
[2026-05-12 14:00:54] [V5] STAGE3:   element order matches index-by-index
[2026-05-12 14:00:54] [V5] STAGE3:   found 2 -COOH groups in template (will deprotonate)
[2026-05-12 14:00:54] [V5] STAGE3:   SMILES (no H): Cc1nc(=O)c2cc(CN(C)c3ccc(C(=O)N[C@@H](CCC(=O)[O-])C(=O)[O-])s3)ccc2[nH]1
[2026-05-12 14:00:54] [V5] STAGE3:   carboxylate [O-] count: 2
[2026-05-12 14:00:54] [V5] STAGE3:   wrote /Users/ario/conserved_site_project/03e_structure_v5/cofactor_chainA_v5.pdb (md5=0e0b87ba50dcda7d9239b5dba806b290)
[2026-05-12 14:00:54] [V5] STAGE3: Chain B:
[2026-05-12 14:00:54] [V5] STAGE3:   template heavy atoms: 32, crystal heavy atoms: 32
[2026-05-12 14:00:54] [V5] STAGE3:   element order matches index-by-index
[2026-05-12 14:00:54] [V5] STAGE3:   found 2 -COOH groups in template (will deprotonate)
[2026-05-12 14:00:54] [V5] STAGE3:   SMILES (no H): Cc1nc(=O)c2cc(CN(C)c3ccc(C(=O)N[C@@H](CCC(=O)[O-])C(=O)[O-])s3)ccc2[nH]1
[2026-05-12 14:00:54] [V5] STAGE3:   carboxylate [O-] count: 2
[2026-05-12 14:00:54] [V5] STAGE3:   wrote /Users/ario/conserved_site_project/03e_structure_v5/cofactor_chainB_v5.pdb (md5=1aea7b012749ab7ade8b1f724ec45982)
[2026-05-12 14:00:54] [V5] STAGE3:   verify A: heavy-atom RMSD vs 1HVY chain-A D16 = 0.000000 A (matched 32 of 32 atoms)
[2026-05-12 14:00:54] [V5] STAGE3:   verify B: heavy-atom RMSD vs 1HVY chain-B D16 = 0.000000 A (matched 32 of 32 atoms)
[2026-05-12 14:00:54] [V5] STAGE3:   v5 chain-A md5 = 0e0b87ba50dcda7d9239b5dba806b290
[2026-05-12 14:00:54] [V5] STAGE3:   v4 chain-A md5 = e6f06a08f8910fff680286de98c2e1d2
[2026-05-12 14:00:54] [V5] STAGE3:   protein dimer heavy atoms: 4650
[2026-05-12 14:00:54] [V5] STAGE3:   chain A clashes < 1.8 A: 0
[2026-05-12 14:00:54] [V5] STAGE3:   chain B clashes < 1.8 A: 0
[2026-05-12 14:00:54] [V5] STAGE3:   chain A near-clashes < 2.0 A: 0
[2026-05-12 14:01:07] [V5] STAGE3: Stage 3 v5 starting (IN-PLACE cofactor reprotonation; no Kabsch)
[2026-05-12 14:01:07] [V5] STAGE3:   chain A heavy atoms: 32
[2026-05-12 14:01:07] [V5] STAGE3:   chain B heavy atoms: 32
[2026-05-12 14:01:07] [V5] STAGE3: Chain A:
[2026-05-12 14:01:07] [V5] STAGE3:   template heavy atoms: 32, crystal heavy atoms: 32
[2026-05-12 14:01:07] [V5] STAGE3:   element order matches index-by-index
[2026-05-12 14:01:07] [V5] STAGE3:   found 2 -COOH groups in template (will deprotonate)
[2026-05-12 14:01:07] [V5] STAGE3:   SMILES (no H): Cc1nc(=O)c2cc(CN(C)c3ccc(C(=O)N[C@@H](CCC(=O)[O-])C(=O)[O-])s3)ccc2[nH]1
[2026-05-12 14:01:07] [V5] STAGE3:   carboxylate [O-] count: 2
[2026-05-12 14:01:07] [V5] STAGE3:   wrote /Users/ario/conserved_site_project/03e_structure_v5/cofactor_chainA_v5.pdb (md5=0e0b87ba50dcda7d9239b5dba806b290)
[2026-05-12 14:01:07] [V5] STAGE3: Chain B:
[2026-05-12 14:01:07] [V5] STAGE3:   template heavy atoms: 32, crystal heavy atoms: 32
[2026-05-12 14:01:07] [V5] STAGE3:   element order matches index-by-index
[2026-05-12 14:01:07] [V5] STAGE3:   found 2 -COOH groups in template (will deprotonate)
[2026-05-12 14:01:07] [V5] STAGE3:   SMILES (no H): Cc1nc(=O)c2cc(CN(C)c3ccc(C(=O)N[C@@H](CCC(=O)[O-])C(=O)[O-])s3)ccc2[nH]1
[2026-05-12 14:01:07] [V5] STAGE3:   carboxylate [O-] count: 2
[2026-05-12 14:01:07] [V5] STAGE3:   wrote /Users/ario/conserved_site_project/03e_structure_v5/cofactor_chainB_v5.pdb (md5=1aea7b012749ab7ade8b1f724ec45982)
[2026-05-12 14:01:07] [V5] STAGE3:   verify A: heavy-atom RMSD vs 1HVY chain-A D16 = 0.000000 A (matched 32 of 32 atoms)
[2026-05-12 14:01:07] [V5] STAGE3:   verify B: heavy-atom RMSD vs 1HVY chain-B D16 = 0.000000 A (matched 32 of 32 atoms)
[2026-05-12 14:01:07] [V5] STAGE3:   v5 chain-A md5 = 0e0b87ba50dcda7d9239b5dba806b290
[2026-05-12 14:01:07] [V5] STAGE3:   v4 chain-A md5 = e6f06a08f8910fff680286de98c2e1d2
[2026-05-12 14:01:07] [V5] STAGE3:   protein dimer heavy atoms: 4650
[2026-05-12 14:01:07] [V5] STAGE3:   chain A clashes < 1.8 A: 0
[2026-05-12 14:01:07] [V5] STAGE3:   chain B clashes < 1.8 A: 0
[2026-05-12 14:01:07] [V5] STAGE3:   chain A near-clashes < 2.0 A: 0
[2026-05-12 14:01:07] [V5] STAGE3: Stage 3 v5 DONE
[2026-05-12 14:02:21] [V5] STAGE6: Stage 6 v5 starting
[2026-05-12 14:02:21] [V5] STAGE6:   centroid (crystal dUMP): [-0.13655, 4.2319, 15.159450000000001]
[2026-05-12 14:02:21] [V5] STAGE6:   apo PDBQT copied from v4 (max|q|=0.507)
[2026-05-12 14:02:22] [V5] STAGE6:   [HOLO_dimer_v5] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 14:02:22] [V5] STAGE6:   holo PDBQT OK via obabel_gasteiger, max|q|=0.507
[2026-05-12 14:02:22] [V5] STAGE6:   WT apo (reused from v4): top=-9.20 rmsd=0.91
[2026-05-12 14:02:22] [V5] STAGE6:   vina[wt_holo] seed=42 exh=96
[2026-05-12 14:03:08] [V5] STAGE6:   wt_holo seed42: top=-8.21 n=2 rmsd=0.32
[2026-05-12 14:03:08] [V5] STAGE6:   vina[wt_holo] seed=7 exh=96
[2026-05-12 14:03:54] [V5] STAGE6:   wt_holo seed7: top=-8.23 n=2 rmsd=0.33
[2026-05-12 14:03:54] [V5] STAGE6:   vina[wt_holo] seed=13 exh=96
[2026-05-12 14:04:41] [V5] STAGE6:   wt_holo seed13: top=-8.25 n=2 rmsd=0.33
[2026-05-12 14:04:41] [V5] STAGE6:   vina[wt_holo] seed=99 exh=96
[2026-05-12 14:05:25] [V5] STAGE6:   wt_holo seed99: top=-8.22 n=2 rmsd=0.33
[2026-05-12 14:05:25] [V5] STAGE6:   vina[wt_holo] seed=256 exh=96
[2026-05-12 14:06:10] [V5] STAGE6:   wt_holo seed256: top=-8.21 n=3 rmsd=0.34
[2026-05-12 14:06:10] [V5] STAGE6:   WT holo: max n_modes=3 <10, escalating to exh=128
[2026-05-12 14:06:10] [V5] STAGE6:   vina[wt_holo] seed=1 exh=128
[2026-05-12 14:07:09] [V5] STAGE6:   wt_holo seed1: top=-8.22 n=2 rmsd=0.33
[2026-05-12 14:07:09] [V5] STAGE6:   vina[wt_holo] seed=2025 exh=128
[2026-05-12 14:08:10] [V5] STAGE6:   wt_holo seed2025: top=-8.22 n=2 rmsd=0.33
[2026-05-12 14:08:10] [V5] STAGE6:   vina[wt_holo] seed=31337 exh=128
[2026-05-12 14:09:11] [V5] STAGE6:   wt_holo seed31337: top=-8.25 n=2 rmsd=0.33
[2026-05-12 14:09:11] [V5] STAGE6:   WT holo: after fallback, max n_modes=3
[2026-05-12 14:09:11] [V5] STAGE6:   WT holo BEST seed = 13 top=-8.25 n_modes=2 rmsd=0.33
[2026-05-12 14:09:11] [V5] STAGE6:   WT holo named-pose RMSD vs crystal = 0.999
[2026-05-12 14:09:11] [V5] STAGE6: Stage 6 v5 DONE
[2026-05-12 14:10:30] [V5] STAGE7: Stage 7 v5 starting
[2026-05-12 14:10:30] [V5] STAGE7: Found 20 mutants from v3
[2026-05-12 14:10:30] [V5] STAGE7:   centroid: [-0.13655, 4.2319, 15.159450000000001]
[2026-05-12 14:10:30] [V5] STAGE7:   WT v5 apo aff = -9.20, WT v5 holo aff = -8.25
[2026-05-12 14:10:30] [V5] STAGE7: [1/20] C195A (ala_scan)
[2026-05-12 14:10:30] [V5] STAGE7:   [C195A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 14:10:42] [V5] STAGE7:   C195A holo: top=-10.49 delta=-2.25 n=2 rmsd=0.34 mis_docked=False low_conf=True
[2026-05-12 14:10:42] [V5] STAGE7:   C195A apo (reused v3): top=-9.46 delta=-0.26 n=20 rmsd=2.09
[2026-05-12 14:10:42] [V5] STAGE7: [2/20] C195A_H196A (double_dyad)
[2026-05-12 14:10:43] [V5] STAGE7:   [C195A_H196A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 14:10:55] [V5] STAGE7:   C195A_H196A holo: top=-10.03 delta=-1.78 n=4 rmsd=0.36 mis_docked=False low_conf=True
[2026-05-12 14:10:55] [V5] STAGE7:   C195A_H196A apo (reused v3): top=-9.12 delta=+0.08 n=20 rmsd=2.11
[2026-05-12 14:10:55] [V5] STAGE7: [3/20] C195S (opposite)
[2026-05-12 14:10:55] [V5] STAGE7:   [C195S_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 14:11:08] [V5] STAGE7:   C195S holo: top=-10.21 delta=-1.97 n=3 rmsd=0.30 mis_docked=False low_conf=True
[2026-05-12 14:11:08] [V5] STAGE7:   C195S apo (reused v3): top=-9.55 delta=-0.36 n=20 rmsd=2.14
[2026-05-12 14:11:08] [V5] STAGE7: [4/20] C195S_H196N (double_polar_neutral)
[2026-05-12 14:11:09] [V5] STAGE7:   [C195S_H196N_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 14:11:21] [V5] STAGE7:   C195S_H196N holo: top=-9.78 delta=-1.53 n=4 rmsd=0.30 mis_docked=False low_conf=True
[2026-05-12 14:11:21] [V5] STAGE7:   C195S_H196N apo (reused v3): top=-9.34 delta=-0.14 n=20 rmsd=2.08
[2026-05-12 14:11:21] [V5] STAGE7: [5/20] H196A (ala_scan)
[2026-05-12 14:11:21] [V5] STAGE7:   [H196A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 14:11:35] [V5] STAGE7:   H196A holo: top=-7.76 delta=+0.49 n=5 rmsd=0.34 mis_docked=False low_conf=False
[2026-05-12 14:11:35] [V5] STAGE7:   H196A apo (reused v3): top=-8.86 delta=+0.34 n=19 rmsd=2.31
[2026-05-12 14:11:35] [V5] STAGE7: [6/20] N226D (opposite)
[2026-05-12 14:11:36] [V5] STAGE7:   [N226D_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 14:11:50] [V5] STAGE7:   N226D holo: top=-7.80 delta=+0.45 n=4 rmsd=0.34 mis_docked=False low_conf=True
[2026-05-12 14:11:50] [V5] STAGE7:   N226D apo (reused v3): top=-8.78 delta=+0.42 n=20 rmsd=2.40
[2026-05-12 14:11:50] [V5] STAGE7: [7/20] Q214A (ala_scan)
[2026-05-12 14:11:51] [V5] STAGE7:   [Q214A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 14:12:06] [V5] STAGE7:   Q214A holo: top=-8.17 delta=+0.08 n=2 rmsd=0.34 mis_docked=False low_conf=True
[2026-05-12 14:12:06] [V5] STAGE7:   Q214A apo (reused v3): top=-8.65 delta=+0.54 n=19 rmsd=2.36
[2026-05-12 14:12:06] [V5] STAGE7: [8/20] R175A (ala_scan)
[2026-05-12 14:12:07] [V5] STAGE7:   [R175A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 14:12:21] [V5] STAGE7:   R175A holo: top=-8.19 delta=+0.06 n=2 rmsd=0.34 mis_docked=False low_conf=True
[2026-05-12 14:12:21] [V5] STAGE7:   R175A apo (reused v3): top=-9.02 delta=+0.18 n=20 rmsd=2.30
[2026-05-12 14:12:21] [V5] STAGE7: [9/20] R175E (opposite)
[2026-05-12 14:12:22] [V5] STAGE7:   [R175E_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 14:12:36] [V5] STAGE7:   R175E holo: top=-8.19 delta=+0.06 n=2 rmsd=0.34 mis_docked=False low_conf=True
[2026-05-12 14:12:36] [V5] STAGE7:   R175E apo (reused v3): top=-9.04 delta=+0.16 n=20 rmsd=2.39
[2026-05-12 14:12:36] [V5] STAGE7: [10/20] R175E_R176E (double_phosclamp)
[2026-05-12 14:12:36] [V5] STAGE7:   [R175E_R176E_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 14:12:50] [V5] STAGE7:   R175E_R176E holo: top=-8.20 delta=+0.05 n=2 rmsd=0.35 mis_docked=False low_conf=True
[2026-05-12 14:12:50] [V5] STAGE7:   R175E_R176E apo (reused v3): top=-9.02 delta=+0.18 n=20 rmsd=2.31
[2026-05-12 14:12:50] [V5] STAGE7: [11/20] R176A (ala_scan)
[2026-05-12 14:12:51] [V5] STAGE7:   [R176A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 14:13:05] [V5] STAGE7:   R176A holo: top=-8.19 delta=+0.06 n=2 rmsd=0.34 mis_docked=False low_conf=True
[2026-05-12 14:13:05] [V5] STAGE7:   R176A apo (reused v3): top=-9.02 delta=+0.18 n=20 rmsd=2.31
[2026-05-12 14:13:05] [V5] STAGE7: [12/20] R176E (opposite)
[2026-05-12 14:13:06] [V5] STAGE7:   [R176E_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 14:13:20] [V5] STAGE7:   R176E holo: top=-8.20 delta=+0.05 n=2 rmsd=0.35 mis_docked=False low_conf=True
[2026-05-12 14:13:20] [V5] STAGE7:   R176E apo (reused v3): top=-9.02 delta=+0.18 n=20 rmsd=2.31
[2026-05-12 14:13:20] [V5] STAGE7: [13/20] R215A (ala_scan)
[2026-05-12 14:13:20] [V5] STAGE7:   [R215A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 14:13:34] [V5] STAGE7:   R215A holo: top=-7.81 delta=+0.44 n=5 rmsd=0.40 mis_docked=False low_conf=False
[2026-05-12 14:13:34] [V5] STAGE7:   R215A apo (reused v3): top=-8.63 delta=+0.57 n=20 rmsd=2.25
[2026-05-12 14:13:34] [V5] STAGE7: [14/20] R215A_N226A (double_substrate_orient)
[2026-05-12 14:13:35] [V5] STAGE7:   [R215A_N226A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 14:13:49] [V5] STAGE7:   R215A_N226A holo: top=-7.48 delta=+0.77 n=9 rmsd=0.60 mis_docked=False low_conf=False
[2026-05-12 14:13:49] [V5] STAGE7:   R215A_N226A apo (reused v3): top=-8.05 delta=+1.15 n=20 rmsd=5.34
[2026-05-12 14:13:49] [V5] STAGE7: [15/20] R215E (opposite)
[2026-05-12 14:13:50] [V5] STAGE7:   [R215E_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 14:14:08] [V5] STAGE7:   R215E holo: top=-7.78 delta=+0.47 n=5 rmsd=0.39 mis_docked=False low_conf=False
[2026-05-12 14:14:08] [V5] STAGE7:   R215E apo (reused v3): top=-8.59 delta=+0.61 n=19 rmsd=2.43
[2026-05-12 14:14:08] [V5] STAGE7: [16/20] R50A (ala_scan)
[2026-05-12 14:14:09] [V5] STAGE7:   [R50A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 14:14:22] [V5] STAGE7:   R50A holo: top=-7.42 delta=+0.83 n=20 rmsd=5.53 mis_docked=True low_conf=False
[2026-05-12 14:14:22] [V5] STAGE7:   R50A apo (reused v3): top=-8.62 delta=+0.58 n=20 rmsd=2.42
[2026-05-12 14:14:22] [V5] STAGE7: [17/20] R50E (opposite)
[2026-05-12 14:14:22] [V5] STAGE7:   [R50E_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 14:14:36] [V5] STAGE7:   R50E holo: top=-7.77 delta=+0.48 n=20 rmsd=5.65 mis_docked=True low_conf=False
[2026-05-12 14:14:36] [V5] STAGE7:   R50E apo (reused v3): top=-8.78 delta=+0.41 n=20 rmsd=2.35
[2026-05-12 14:14:36] [V5] STAGE7: [18/20] T170A (control_surface)
[2026-05-12 14:14:37] [V5] STAGE7:   [T170A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 14:14:53] [V5] STAGE7:   T170A holo: top=-8.20 delta=+0.05 n=2 rmsd=0.35 mis_docked=False low_conf=True
[2026-05-12 14:14:53] [V5] STAGE7:   T170A apo (reused v3): top=-9.02 delta=+0.18 n=20 rmsd=2.30
[2026-05-12 14:14:53] [V5] STAGE7: [19/20] W109A (ala_scan)
[2026-05-12 14:14:54] [V5] STAGE7:   [W109A_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 14:15:09] [V5] STAGE7:   W109A holo: top=-7.98 delta=+0.27 n=2 rmsd=0.34 mis_docked=False low_conf=True
[2026-05-12 14:15:09] [V5] STAGE7:   W109A apo (reused v3): top=-8.88 delta=+0.32 n=19 rmsd=2.46
[2026-05-12 14:15:09] [V5] STAGE7: [20/20] Y258F_F225Y (double_aromatic_swap)
[2026-05-12 14:15:10] [V5] STAGE7:   [Y258F_F225Y_holo] obabel-gasteiger rc=0 max|q|=0.507
[2026-05-12 14:15:26] [V5] STAGE7:   Y258F_F225Y holo: top=-8.05 delta=+0.20 n=2 rmsd=0.35 mis_docked=False low_conf=True
[2026-05-12 14:15:26] [V5] STAGE7:   Y258F_F225Y apo (reused v3): top=-8.88 delta=+0.32 n=20 rmsd=2.45
[2026-05-12 14:15:26] [V5] STAGE7: wrote /Users/ario/conserved_site_project/07e_mut_docking_v5/mutant_results_v5.csv (42 rows including WT reference)
[2026-05-12 14:15:26] [V5] STAGE7: Stage 7 v5 DONE: 40 rows, 0 skipped
[2026-05-12 14:16:48] [V5] STAGE8: Stage 8 v5 starting
[2026-05-12 14:16:48] [V5] STAGE8: loaded 42 rows (including WT reference)
[2026-05-12 14:16:48] [V5] STAGE8: WT holo RMSD vs crystal = 0.334 A; standard mis_docked (RMSD > 3 A vs crystal) applies. v4-style dual-RMSD-reference is not needed in v5.
[2026-05-12 14:16:48] [V5] STAGE8: top apo destab (clean): [['R215E', 0.6109999999999989], ['R50A', 0.5789999999999988], ['R215A', 0.5699999999999985], ['Q214A', 0.5449999999999999], ['N226D', 0.4199999999999999]]
[2026-05-12 14:16:48] [V5] STAGE8: top holo destab (clean): [['R215A_N226A', 0.7720000000000002], ['H196A', 0.4910000000000005], ['R215E', 0.4700000000000006], ['R215A', 0.4430000000000005]]
[2026-05-12 14:16:48] [V5] STAGE8:   n mutants holo |Δ| > 0.85: 0
[2026-05-12 14:16:48] [V5] STAGE8: Pearson r = -0.7401065909147103, Spearman ρ = -0.5, null_correlation=True
[2026-05-12 14:16:48] [V5] STAGE8: n above noise (holo): 0
[2026-05-12 14:16:48] [V5] STAGE8: Stage 8 v5 DONE
[2026-05-12 14:21:12] [V5] STAGE9: Stage 9 v5 starting
[2026-05-12 14:21:13] [V5] STAGE9: wrote /Users/ario/conserved_site_project/09e_report_v5/report.html
[2026-05-12 14:21:14] [V5] STAGE9: wrote /Users/ario/conserved_site_project/09e_report_v5/report.pdf (256701 bytes)
[2026-05-12 14:21:14] [V5] STAGE9: wrote /Users/ario/conserved_site_project/09e_report_v5/report.docx (202051 bytes)
[2026-05-12 14:21:14] [V5] STAGE9: Stage 9 v5 DONE
2026-05-12 14:47:31 [MODELLER:step1_clean_pdb] INFO Reading /Users/ario/conserved_site_project/03_structure/1hvy.pdb
2026-05-12 14:47:31 [MODELLER:step1_clean_pdb] INFO Wrote chain-A-only PDB: /Users/ario/conserved_site_project/10_modeller/01_clean_pdb/1hvy_chainA.pdb (187928 bytes)
2026-05-12 14:47:31 [MODELLER:step1_clean_pdb] INFO Assertion passed: only chain A present in output PDB
2026-05-12 14:47:31 [MODELLER:step1_clean_pdb] INFO Extracted chain-A sequence length: 287
2026-05-12 14:47:31 [MODELLER:step1_clean_pdb] INFO Wrote FASTA: /Users/ario/conserved_site_project/10_modeller/01_clean_pdb/1hvy_chainA.fasta
2026-05-12 14:47:31 [MODELLER:step1_clean_pdb] INFO Identity vs P04818: 91.69% (matches=287 / canonical=313)
2026-05-12 14:47:31 [MODELLER:step1_clean_pdb] INFO STEP 1 OK
2026-05-12 14:48:32 [MODELLER:step2_blast] INFO Query length: 287
2026-05-12 14:48:32 [MODELLER:step2_blast] INFO Running NCBIWWW.qblast on pdb DB (this may take 1-3 minutes)...
2026-05-12 14:48:36 [MODELLER:step2_blast] INFO BLAST result XML written: /Users/ario/conserved_site_project/10_modeller/02_blast/blast.xml (61927 bytes)
2026-05-12 14:48:36 [MODELLER:step2_blast] INFO Parsed 29 BLAST hits
2026-05-12 14:48:36 [MODELLER:step2_blast] INFO Wrote /Users/ario/conserved_site_project/10_modeller/02_blast/blast.tsv
2026-05-12 14:48:36 [MODELLER:step2_blast] INFO After identity/coverage filter: 0 candidates
2026-05-12 14:48:36 [MODELLER:step2_blast] WARNING Only 0 templates selected (wanted 3)
2026-05-12 14:48:36 [MODELLER:step2_blast] ERROR No usable templates — abort
2026-05-12 14:49:07 [MODELLER:step2_blast] INFO Query length: 287
2026-05-12 14:49:07 [MODELLER:step2_blast] INFO Running NCBIWWW.qblast on pdb DB (this may take 1-3 minutes)...
2026-05-12 14:50:10 [MODELLER:step2_blast] INFO BLAST result XML written: /Users/ario/conserved_site_project/10_modeller/02_blast/blast.xml (342768 bytes)
2026-05-12 14:50:10 [MODELLER:step2_blast] INFO Parsed 167 BLAST hits
2026-05-12 14:50:10 [MODELLER:step2_blast] INFO Wrote /Users/ario/conserved_site_project/10_modeller/02_blast/blast.tsv
2026-05-12 14:50:10 [MODELLER:step2_blast] INFO After identity/coverage filter: 100 candidates
2026-05-12 14:50:10 [MODELLER:step2_blast] INFO Downloading https://files.rcsb.org/download/3IHI.pdb
2026-05-12 14:50:11 [MODELLER:step2_blast] INFO Selected 3IHI_A identity=92.71% cov=1.00 res=1.94
2026-05-12 14:50:12 [MODELLER:step2_blast] INFO Downloading https://files.rcsb.org/download/1RTS.pdb
2026-05-12 14:50:13 [MODELLER:step2_blast] INFO Skip 1RTS: resolution 3.30 > 2.50
2026-05-12 14:50:13 [MODELLER:step2_blast] INFO Downloading https://files.rcsb.org/download/6K7Q.pdb
2026-05-12 14:50:16 [MODELLER:step2_blast] INFO Selected 6K7Q_A identity=75.96% cov=1.00 res=2.27
2026-05-12 14:50:17 [MODELLER:step2_blast] INFO Downloading https://files.rcsb.org/download/5H39.pdb
2026-05-12 14:50:18 [MODELLER:step2_blast] INFO Selected 5H39_A identity=72.28% cov=0.99 res=2.0
2026-05-12 14:50:18 [MODELLER:step2_blast] INFO Wrote /Users/ario/conserved_site_project/10_modeller/02_blast/selected_templates.json
2026-05-12 14:50:18 [MODELLER:step2_blast] INFO STEP 2 OK: 3 templates selected
2026-05-12 14:51:09 [MODELLER:step3_clustalw_pir] INFO Templates: [('3IHI', 'A'), ('6K7Q', 'A'), ('5H39', 'A')]
2026-05-12 14:51:09 [MODELLER:step3_clustalw_pir] INFO Target residue range 26-313 (len=287)
2026-05-12 14:51:09 [MODELLER:step3_clustalw_pir] INFO Template 3IHI_A: range 21-300, len=280
2026-05-12 14:51:09 [MODELLER:step3_clustalw_pir] INFO Template 6K7Q_A: range 1-285, len=272
2026-05-12 14:51:09 [MODELLER:step3_clustalw_pir] INFO Template 5H39_A: range 51-335, len=285
2026-05-12 14:51:09 [MODELLER:step3_clustalw_pir] INFO Wrote /Users/ario/conserved_site_project/10_modeller/03_alignment/input.fasta (4 records)
2026-05-12 14:51:09 [MODELLER:step3_clustalw_pir] INFO Running ClustalW: /opt/homebrew/bin/clustalw -INFILE=/Users/ario/conserved_site_project/10_modeller/03_alignment/input.fasta -ALIGN -OUTFILE=/Users/ario/conserved_site_project/10_modeller/03_alignment/aligned.aln -OUTPUT=CLUSTAL
2026-05-12 14:51:09 [MODELLER:step3_clustalw_pir] INFO ClustalW done; written /Users/ario/conserved_site_project/10_modeller/03_alignment/aligned.aln (1916 bytes)
2026-05-12 14:51:09 [MODELLER:step3_clustalw_pir] INFO Aligned columns: 289
2026-05-12 14:51:09 [MODELLER:step3_clustalw_pir] INFO Wrote /Users/ario/conserved_site_project/10_modeller/03_alignment/alignment.ali and /Users/ario/conserved_site_project/10_modeller/03_alignment/alignment.pir
2026-05-12 14:51:09 [MODELLER:step3_clustalw_pir] INFO knowns: ['3IHI_A', '6K7Q_A', '5H39_A']
2026-05-12 14:51:09 [MODELLER:step3_clustalw_pir] INFO STEP 3 OK
2026-05-12 14:52:00 [MODELLER:step4_run_modeller] INFO Starting AutoModel.make()  knowns=['3IHI_A', '6K7Q_A', '5H39_A']  models=1..10
2026-05-12 14:52:18 [MODELLER:step3_clustalw_pir] INFO Templates: [('3IHI', 'A'), ('6K7Q', 'A'), ('5H39', 'A')]
2026-05-12 14:52:18 [MODELLER:step3_clustalw_pir] INFO Target residue range 26-313 (len=287)
2026-05-12 14:52:18 [MODELLER:step3_clustalw_pir] INFO Template 3IHI_A: range 21-300, len=280
2026-05-12 14:52:18 [MODELLER:step3_clustalw_pir] INFO Template 6K7Q_A: range 1-285, len=272
2026-05-12 14:52:18 [MODELLER:step3_clustalw_pir] INFO Template 5H39_A: range 51-335, len=285
2026-05-12 14:52:18 [MODELLER:step3_clustalw_pir] INFO Wrote /Users/ario/conserved_site_project/10_modeller/03_alignment/input.fasta (4 records)
2026-05-12 14:52:18 [MODELLER:step3_clustalw_pir] INFO Running ClustalW: /opt/homebrew/bin/clustalw -INFILE=/Users/ario/conserved_site_project/10_modeller/03_alignment/input.fasta -ALIGN -OUTFILE=/Users/ario/conserved_site_project/10_modeller/03_alignment/aligned.aln -OUTPUT=CLUSTAL
2026-05-12 14:52:18 [MODELLER:step3_clustalw_pir] INFO ClustalW done; written /Users/ario/conserved_site_project/10_modeller/03_alignment/aligned.aln (1916 bytes)
2026-05-12 14:52:18 [MODELLER:step3_clustalw_pir] INFO Aligned columns: 289
2026-05-12 14:52:18 [MODELLER:step3_clustalw_pir] INFO Wrote /Users/ario/conserved_site_project/10_modeller/03_alignment/alignment.ali and /Users/ario/conserved_site_project/10_modeller/03_alignment/alignment.pir
2026-05-12 14:52:18 [MODELLER:step3_clustalw_pir] INFO knowns: ['3IHI_A', '6K7Q_A', '5H39_A']
2026-05-12 14:52:18 [MODELLER:step3_clustalw_pir] INFO STEP 3 OK
2026-05-12 14:52:22 [MODELLER:step4_run_modeller] INFO Starting AutoModel.make()  knowns=['3IHI_A', '6K7Q_A', '5H39_A']  models=1..10
2026-05-12 14:54:05 [MODELLER:step4_run_modeller] INFO AutoModel.make() done
2026-05-12 14:54:05 [MODELLER:step4_run_modeller] INFO Model target.B99990001.pdb  molpdf=10027.02734375  DOPE=-35404.66796875  GA341=[1.0, 0.3831549882888794, -253.2482147216797, -20.819490432739258, -10.076574325561523, -8.025050163269043, -8.030832290649414, -11.766022682189941]
2026-05-12 14:54:05 [MODELLER:step4_run_modeller] INFO Model target.B99990002.pdb  molpdf=10202.59375  DOPE=-35644.9140625  GA341=[1.0, 0.3764180839061737, -236.084228515625, -19.803714752197266, -9.411252975463867, -7.582737922668457, -7.718956470489502, -10.278803825378418]
2026-05-12 14:54:05 [MODELLER:step4_run_modeller] INFO Model target.B99990003.pdb  molpdf=9911.490234375  DOPE=-35775.74609375  GA341=[1.0, 0.38793906569480896, -247.85536193847656, -19.281057357788086, -9.591482162475586, -7.928945541381836, -7.642152309417725, -10.287302017211914]
2026-05-12 14:54:05 [MODELLER:step4_run_modeller] INFO Model target.B99990004.pdb  molpdf=10178.56640625  DOPE=-35409.90234375  GA341=[1.0, 0.3819543719291687, -240.0302276611328, -19.31285285949707, -9.378911018371582, -7.761666774749756, -7.824333667755127, -10.470483779907227]
2026-05-12 14:54:05 [MODELLER:step4_run_modeller] INFO Model target.B99990005.pdb  molpdf=9964.7216796875  DOPE=-35499.63671875  GA341=[1.0, 0.36837038397789, -252.65988159179688, -20.34021759033203, -9.868331909179688, -7.9442291259765625, -7.724201679229736, -10.566646575927734]
2026-05-12 14:54:05 [MODELLER:step4_run_modeller] INFO Model target.B99990006.pdb  molpdf=9941.2529296875  DOPE=-35314.4375  GA341=[1.0, 0.3788973391056061, -231.68470764160156, -15.742748260498047, -8.289785385131836, -7.572717189788818, -6.6785478591918945, -9.584381103515625]
2026-05-12 14:54:05 [MODELLER:step4_run_modeller] INFO Model target.B99990007.pdb  molpdf=9961.4970703125  DOPE=-35548.33203125  GA341=[1.0, 0.3840775787830353, -229.08041381835938, -15.5330228805542, -8.262154579162598, -7.672802448272705, -6.559135437011719, -9.576098442077637]
2026-05-12 14:54:05 [MODELLER:step4_run_modeller] INFO Model target.B99990008.pdb  molpdf=10003.2421875  DOPE=-35458.8515625  GA341=[1.0, 0.3811359703540802, -229.28225708007812, -15.445743560791016, -8.281309127807617, -7.538204669952393, -6.676283836364746, -9.534928321838379]
2026-05-12 14:54:05 [MODELLER:step4_run_modeller] INFO Model target.B99990009.pdb  molpdf=9962.1474609375  DOPE=-35383.765625  GA341=[1.0, 0.3745937645435333, -243.01092529296875, -18.727495193481445, -9.350387573242188, -7.8331170082092285, -7.385254859924316, -10.114384651184082]
2026-05-12 14:54:05 [MODELLER:step4_run_modeller] INFO Model target.B99990010.pdb  molpdf=9890.28125  DOPE=-35390.81640625  GA341=[1.0, 0.3856862187385559, -249.62246704101562, -16.947376251220703, -8.938376426696777, -7.7811055183410645, -6.982367992401123, -9.884419441223145]
2026-05-12 14:54:05 [MODELLER:step4_run_modeller] INFO Moved 10 models to /Users/ario/conserved_site_project/10_modeller/04_modeller_run/models
2026-05-12 14:54:05 [MODELLER:step4_run_modeller] INFO Wrote /Users/ario/conserved_site_project/10_modeller/04_modeller_run/scores.csv
2026-05-12 14:54:05 [MODELLER:step4_run_modeller] INFO Best (by DOPE) -> target.B99990003.pdb (copied to best_model.pdb)
2026-05-12 14:54:05 [MODELLER:step4_run_modeller] INFO STEP 4 OK: 10 models
2026-05-12 14:55:12 [MODELLER:step5_pymol_compare] INFO Comparing 10 models against 1hvy_chainA.pdb
2026-05-12 14:55:12 [MODELLER:step5_pymol_compare] INFO PyMOL [pair01]
2026-05-12 14:55:13 [MODELLER:step5_pymol_compare] WARNING RMSD parse failed for 1: [Errno 2] No such file or directory: '/Users/ario/conserved_site_project/10_modeller/05_comparison/_pairwise_model01.json'
2026-05-12 14:55:13 [MODELLER:step5_pymol_compare] INFO Model 01  RMSD=nan Å  n_atoms=0
2026-05-12 14:55:13 [MODELLER:step5_pymol_compare] INFO PyMOL [heat01]
2026-05-12 14:55:13 [MODELLER:step5_pymol_compare] INFO PyMOL [pair02]
2026-05-12 14:55:14 [MODELLER:step5_pymol_compare] WARNING RMSD parse failed for 2: [Errno 2] No such file or directory: '/Users/ario/conserved_site_project/10_modeller/05_comparison/_pairwise_model02.json'
2026-05-12 14:55:14 [MODELLER:step5_pymol_compare] INFO Model 02  RMSD=nan Å  n_atoms=0
2026-05-12 14:55:14 [MODELLER:step5_pymol_compare] INFO PyMOL [heat02]
2026-05-12 14:55:14 [MODELLER:step5_pymol_compare] INFO PyMOL [pair03]
2026-05-12 14:55:14 [MODELLER:step5_pymol_compare] WARNING RMSD parse failed for 3: [Errno 2] No such file or directory: '/Users/ario/conserved_site_project/10_modeller/05_comparison/_pairwise_model03.json'
2026-05-12 14:55:14 [MODELLER:step5_pymol_compare] INFO Model 03  RMSD=nan Å  n_atoms=0
2026-05-12 14:55:14 [MODELLER:step5_pymol_compare] INFO PyMOL [heat03]
2026-05-12 14:55:14 [MODELLER:step5_pymol_compare] INFO PyMOL [pair04]
2026-05-12 14:55:15 [MODELLER:step5_pymol_compare] WARNING RMSD parse failed for 4: [Errno 2] No such file or directory: '/Users/ario/conserved_site_project/10_modeller/05_comparison/_pairwise_model04.json'
2026-05-12 14:55:15 [MODELLER:step5_pymol_compare] INFO Model 04  RMSD=nan Å  n_atoms=0
2026-05-12 14:55:15 [MODELLER:step5_pymol_compare] INFO PyMOL [heat04]
2026-05-12 14:55:15 [MODELLER:step5_pymol_compare] INFO PyMOL [pair05]
2026-05-12 14:55:15 [MODELLER:step5_pymol_compare] WARNING RMSD parse failed for 5: [Errno 2] No such file or directory: '/Users/ario/conserved_site_project/10_modeller/05_comparison/_pairwise_model05.json'
2026-05-12 14:55:15 [MODELLER:step5_pymol_compare] INFO Model 05  RMSD=nan Å  n_atoms=0
2026-05-12 14:55:15 [MODELLER:step5_pymol_compare] INFO PyMOL [heat05]
2026-05-12 14:55:16 [MODELLER:step5_pymol_compare] INFO PyMOL [pair06]
2026-05-12 14:55:16 [MODELLER:step5_pymol_compare] WARNING RMSD parse failed for 6: [Errno 2] No such file or directory: '/Users/ario/conserved_site_project/10_modeller/05_comparison/_pairwise_model06.json'
2026-05-12 14:55:16 [MODELLER:step5_pymol_compare] INFO Model 06  RMSD=nan Å  n_atoms=0
2026-05-12 14:55:16 [MODELLER:step5_pymol_compare] INFO PyMOL [heat06]
2026-05-12 14:55:16 [MODELLER:step5_pymol_compare] INFO PyMOL [pair07]
2026-05-12 14:55:17 [MODELLER:step5_pymol_compare] WARNING RMSD parse failed for 7: [Errno 2] No such file or directory: '/Users/ario/conserved_site_project/10_modeller/05_comparison/_pairwise_model07.json'
2026-05-12 14:55:17 [MODELLER:step5_pymol_compare] INFO Model 07  RMSD=nan Å  n_atoms=0
2026-05-12 14:55:17 [MODELLER:step5_pymol_compare] INFO PyMOL [heat07]
2026-05-12 14:55:17 [MODELLER:step5_pymol_compare] INFO PyMOL [pair08]
2026-05-12 14:55:17 [MODELLER:step5_pymol_compare] WARNING RMSD parse failed for 8: [Errno 2] No such file or directory: '/Users/ario/conserved_site_project/10_modeller/05_comparison/_pairwise_model08.json'
2026-05-12 14:55:17 [MODELLER:step5_pymol_compare] INFO Model 08  RMSD=nan Å  n_atoms=0
2026-05-12 14:55:17 [MODELLER:step5_pymol_compare] INFO PyMOL [heat08]
2026-05-12 14:55:17 [MODELLER:step5_pymol_compare] INFO PyMOL [pair09]
2026-05-12 14:55:18 [MODELLER:step5_pymol_compare] WARNING RMSD parse failed for 9: [Errno 2] No such file or directory: '/Users/ario/conserved_site_project/10_modeller/05_comparison/_pairwise_model09.json'
2026-05-12 14:55:18 [MODELLER:step5_pymol_compare] INFO Model 09  RMSD=nan Å  n_atoms=0
2026-05-12 14:55:18 [MODELLER:step5_pymol_compare] INFO PyMOL [heat09]
2026-05-12 14:55:18 [MODELLER:step5_pymol_compare] INFO PyMOL [pair10]
2026-05-12 14:55:19 [MODELLER:step5_pymol_compare] WARNING RMSD parse failed for 10: [Errno 2] No such file or directory: '/Users/ario/conserved_site_project/10_modeller/05_comparison/_pairwise_model10.json'
2026-05-12 14:55:19 [MODELLER:step5_pymol_compare] INFO Model 10  RMSD=nan Å  n_atoms=0
2026-05-12 14:55:19 [MODELLER:step5_pymol_compare] INFO PyMOL [heat10]
2026-05-12 14:55:19 [MODELLER:step5_pymol_compare] INFO Wrote /Users/ario/conserved_site_project/10_modeller/05_comparison/rmsd_per_model.csv
2026-05-12 14:55:19 [MODELLER:step5_pymol_compare] INFO PyMOL [all_overlay]
2026-05-12 14:56:31 [MODELLER:step5_pymol_compare] INFO Best by RMSD: None   Best by DOPE: {'model_id': 3, 'model_pdb': 'target.B99990003.pdb', 'DOPE': -35775.74609375}
2026-05-12 14:56:31 [MODELLER:step5_pymol_compare] INFO STEP 5 OK
2026-05-12 14:57:49 [MODELLER:step5_pymol_compare] INFO Comparing 10 models against 1hvy_chainA.pdb
2026-05-12 14:57:49 [MODELLER:step5_pymol_compare] INFO PyMOL [pair01]
2026-05-12 14:57:50 [MODELLER:step5_pymol_compare] INFO Model 01  RMSD=0.388 Å  n_atoms=254
2026-05-12 14:57:50 [MODELLER:step5_pymol_compare] INFO PyMOL [heat01]
2026-05-12 14:57:51 [MODELLER:step5_pymol_compare] INFO PyMOL [pair02]
2026-05-12 14:57:51 [MODELLER:step5_pymol_compare] INFO Model 02  RMSD=0.372 Å  n_atoms=263
2026-05-12 14:57:51 [MODELLER:step5_pymol_compare] INFO PyMOL [heat02]
2026-05-12 14:57:52 [MODELLER:step5_pymol_compare] INFO PyMOL [pair03]
2026-05-12 14:57:52 [MODELLER:step5_pymol_compare] INFO Model 03  RMSD=0.371 Å  n_atoms=258
2026-05-12 14:57:52 [MODELLER:step5_pymol_compare] INFO PyMOL [heat03]
2026-05-12 14:57:52 [MODELLER:step5_pymol_compare] INFO PyMOL [pair04]
2026-05-12 14:57:53 [MODELLER:step5_pymol_compare] INFO Model 04  RMSD=0.389 Å  n_atoms=265
2026-05-12 14:57:53 [MODELLER:step5_pymol_compare] INFO PyMOL [heat04]
2026-05-12 14:57:53 [MODELLER:step5_pymol_compare] INFO PyMOL [pair05]
2026-05-12 14:57:54 [MODELLER:step5_pymol_compare] INFO Model 05  RMSD=0.386 Å  n_atoms=258
2026-05-12 14:57:54 [MODELLER:step5_pymol_compare] INFO PyMOL [heat05]
2026-05-12 14:57:54 [MODELLER:step5_pymol_compare] INFO PyMOL [pair06]
2026-05-12 14:57:55 [MODELLER:step5_pymol_compare] INFO Model 06  RMSD=0.390 Å  n_atoms=260
2026-05-12 14:57:55 [MODELLER:step5_pymol_compare] INFO PyMOL [heat06]
2026-05-12 14:57:55 [MODELLER:step5_pymol_compare] INFO PyMOL [pair07]
2026-05-12 14:57:56 [MODELLER:step5_pymol_compare] INFO Model 07  RMSD=0.385 Å  n_atoms=267
2026-05-12 14:57:56 [MODELLER:step5_pymol_compare] INFO PyMOL [heat07]
2026-05-12 14:57:56 [MODELLER:step5_pymol_compare] INFO PyMOL [pair08]
2026-05-12 14:57:57 [MODELLER:step5_pymol_compare] INFO Model 08  RMSD=0.370 Å  n_atoms=246
2026-05-12 14:57:57 [MODELLER:step5_pymol_compare] INFO PyMOL [heat08]
2026-05-12 14:57:57 [MODELLER:step5_pymol_compare] INFO PyMOL [pair09]
2026-05-12 14:57:58 [MODELLER:step5_pymol_compare] INFO Model 09  RMSD=0.387 Å  n_atoms=250
2026-05-12 14:57:58 [MODELLER:step5_pymol_compare] INFO PyMOL [heat09]
2026-05-12 14:57:58 [MODELLER:step5_pymol_compare] INFO PyMOL [pair10]
2026-05-12 14:57:59 [MODELLER:step5_pymol_compare] INFO Model 10  RMSD=0.367 Å  n_atoms=259
2026-05-12 14:57:59 [MODELLER:step5_pymol_compare] INFO PyMOL [heat10]
2026-05-12 14:57:59 [MODELLER:step5_pymol_compare] INFO Wrote /Users/ario/conserved_site_project/10_modeller/05_comparison/rmsd_per_model.csv
2026-05-12 14:57:59 [MODELLER:step5_pymol_compare] INFO PyMOL [all_overlay]
2026-05-12 14:59:08 [MODELLER:step5_pymol_compare] INFO Best by RMSD: {'model_id': 10, 'model_pdb': 'target.B99990010.pdb', 'rmsd_to_crystal': 0.3666912317276001, 'n_atoms_aligned': 259}   Best by DOPE: {'model_id': 3, 'model_pdb': 'target.B99990003.pdb', 'DOPE': -35775.74609375}
2026-05-12 14:59:08 [MODELLER:step5_pymol_compare] INFO STEP 5 OK
2026-05-12 15:01:02 [MODELLER:step6_validate] INFO Validating 10 models
2026-05-12 15:01:02 [MODELLER:step6_validate] INFO Rama model 01: favoured=84.6% allowed=13.0% outlier=2.5%
2026-05-12 15:01:02 [MODELLER:step6_validate] WARNING per_residue_dope failed for target.B99990001.pdb: 'Model' object has no attribute 'select_atoms'
2026-05-12 15:01:02 [MODELLER:step6_validate] WARNING No per-residue DOPE for target.B99990001.pdb
2026-05-12 15:01:02 [MODELLER:step6_validate] INFO Rama model 02: favoured=84.6% allowed=12.6% outlier=2.8%
2026-05-12 15:01:02 [MODELLER:step6_validate] WARNING per_residue_dope failed for target.B99990002.pdb: 'Model' object has no attribute 'select_atoms'
2026-05-12 15:01:02 [MODELLER:step6_validate] WARNING No per-residue DOPE for target.B99990002.pdb
2026-05-12 15:01:02 [MODELLER:step6_validate] INFO Rama model 03: favoured=84.6% allowed=13.0% outlier=2.5%
2026-05-12 15:01:03 [MODELLER:step6_validate] WARNING per_residue_dope failed for target.B99990003.pdb: 'Model' object has no attribute 'select_atoms'
2026-05-12 15:01:03 [MODELLER:step6_validate] WARNING No per-residue DOPE for target.B99990003.pdb
2026-05-12 15:01:03 [MODELLER:step6_validate] INFO Rama model 04: favoured=85.3% allowed=13.3% outlier=1.4%
2026-05-12 15:01:03 [MODELLER:step6_validate] WARNING per_residue_dope failed for target.B99990004.pdb: 'Model' object has no attribute 'select_atoms'
2026-05-12 15:01:03 [MODELLER:step6_validate] WARNING No per-residue DOPE for target.B99990004.pdb
2026-05-12 15:01:03 [MODELLER:step6_validate] INFO Rama model 05: favoured=84.6% allowed=12.6% outlier=2.8%
2026-05-12 15:01:03 [MODELLER:step6_validate] WARNING per_residue_dope failed for target.B99990005.pdb: 'Model' object has no attribute 'select_atoms'
2026-05-12 15:01:03 [MODELLER:step6_validate] WARNING No per-residue DOPE for target.B99990005.pdb
2026-05-12 15:01:03 [MODELLER:step6_validate] INFO Rama model 06: favoured=84.2% allowed=13.3% outlier=2.5%
2026-05-12 15:01:03 [MODELLER:step6_validate] WARNING per_residue_dope failed for target.B99990006.pdb: 'Model' object has no attribute 'select_atoms'
2026-05-12 15:01:03 [MODELLER:step6_validate] WARNING No per-residue DOPE for target.B99990006.pdb
2026-05-12 15:01:03 [MODELLER:step6_validate] INFO Rama model 07: favoured=83.5% allowed=14.4% outlier=2.1%
2026-05-12 15:01:03 [MODELLER:step6_validate] WARNING per_residue_dope failed for target.B99990007.pdb: 'Model' object has no attribute 'select_atoms'
2026-05-12 15:01:03 [MODELLER:step6_validate] WARNING No per-residue DOPE for target.B99990007.pdb
2026-05-12 15:01:03 [MODELLER:step6_validate] INFO Rama model 08: favoured=83.9% allowed=13.3% outlier=2.8%
2026-05-12 15:01:03 [MODELLER:step6_validate] WARNING per_residue_dope failed for target.B99990008.pdb: 'Model' object has no attribute 'select_atoms'
2026-05-12 15:01:03 [MODELLER:step6_validate] WARNING No per-residue DOPE for target.B99990008.pdb
2026-05-12 15:01:04 [MODELLER:step6_validate] INFO Rama model 09: favoured=84.9% allowed=12.6% outlier=2.5%
2026-05-12 15:01:04 [MODELLER:step6_validate] WARNING per_residue_dope failed for target.B99990009.pdb: 'Model' object has no attribute 'select_atoms'
2026-05-12 15:01:04 [MODELLER:step6_validate] WARNING No per-residue DOPE for target.B99990009.pdb
2026-05-12 15:01:04 [MODELLER:step6_validate] INFO Rama model 10: favoured=84.6% allowed=13.0% outlier=2.5%
2026-05-12 15:01:04 [MODELLER:step6_validate] WARNING per_residue_dope failed for target.B99990010.pdb: 'Model' object has no attribute 'select_atoms'
2026-05-12 15:01:04 [MODELLER:step6_validate] WARNING No per-residue DOPE for target.B99990010.pdb
2026-05-12 15:01:04 [MODELLER:step6_validate] INFO Wrote /Users/ario/conserved_site_project/10_modeller/06_validation/ramachandran_stats.csv
2026-05-12 15:01:04 [MODELLER:step6_validate] INFO Wrote /Users/ario/conserved_site_project/10_modeller/06_validation/SAVES_MANUAL.md
2026-05-12 15:01:04 [MODELLER:step6_validate] INFO STEP 6 OK
2026-05-12 15:01:55 [MODELLER:step6_validate] INFO Validating 10 models
2026-05-12 15:01:56 [MODELLER:step6_validate] INFO Rama model 01: favoured=84.6% allowed=13.0% outlier=2.5%
2026-05-12 15:01:57 [MODELLER:step6_validate] INFO Rama model 02: favoured=84.6% allowed=12.6% outlier=2.8%
2026-05-12 15:01:58 [MODELLER:step6_validate] INFO Rama model 03: favoured=84.6% allowed=13.0% outlier=2.5%
2026-05-12 15:01:59 [MODELLER:step6_validate] INFO Rama model 04: favoured=85.3% allowed=13.3% outlier=1.4%
2026-05-12 15:02:00 [MODELLER:step6_validate] INFO Rama model 05: favoured=84.6% allowed=12.6% outlier=2.8%
2026-05-12 15:02:01 [MODELLER:step6_validate] INFO Rama model 06: favoured=84.2% allowed=13.3% outlier=2.5%
2026-05-12 15:02:02 [MODELLER:step6_validate] INFO Rama model 07: favoured=83.5% allowed=14.4% outlier=2.1%
2026-05-12 15:02:03 [MODELLER:step6_validate] INFO Rama model 08: favoured=83.9% allowed=13.3% outlier=2.8%
2026-05-12 15:02:04 [MODELLER:step6_validate] INFO Rama model 09: favoured=84.9% allowed=12.6% outlier=2.5%
2026-05-12 15:02:05 [MODELLER:step6_validate] INFO Rama model 10: favoured=84.6% allowed=13.0% outlier=2.5%
2026-05-12 15:02:06 [MODELLER:step6_validate] INFO Wrote /Users/ario/conserved_site_project/10_modeller/06_validation/ramachandran_stats.csv
2026-05-12 15:02:06 [MODELLER:step6_validate] INFO Wrote /Users/ario/conserved_site_project/10_modeller/06_validation/SAVES_MANUAL.md
2026-05-12 15:02:06 [MODELLER:step6_validate] INFO STEP 6 OK
2026-05-12 15:04:11 [MODELLER:step7_viewers_report] INFO Wrote viewer model01.html and mirror modeller_model01.html
2026-05-12 15:04:11 [MODELLER:step7_viewers_report] INFO Wrote viewer model02.html and mirror modeller_model02.html
2026-05-12 15:04:11 [MODELLER:step7_viewers_report] INFO Wrote viewer model03.html and mirror modeller_model03.html
2026-05-12 15:04:11 [MODELLER:step7_viewers_report] INFO Wrote viewer model04.html and mirror modeller_model04.html
2026-05-12 15:04:11 [MODELLER:step7_viewers_report] INFO Wrote viewer model05.html and mirror modeller_model05.html
2026-05-12 15:04:11 [MODELLER:step7_viewers_report] INFO Wrote viewer model06.html and mirror modeller_model06.html
2026-05-12 15:04:11 [MODELLER:step7_viewers_report] INFO Wrote viewer model07.html and mirror modeller_model07.html
2026-05-12 15:04:11 [MODELLER:step7_viewers_report] INFO Wrote viewer model08.html and mirror modeller_model08.html
2026-05-12 15:04:11 [MODELLER:step7_viewers_report] INFO Wrote viewer model09.html and mirror modeller_model09.html
2026-05-12 15:04:11 [MODELLER:step7_viewers_report] INFO Wrote viewer model10.html and mirror modeller_model10.html
2026-05-12 15:04:11 [MODELLER:step7_viewers_report] INFO Updated /Users/ario/conserved_site_project/viewers/index.html with 10 homology-model links
2026-05-12 15:04:11 [MODELLER:step7_viewers_report] INFO Wrote /Users/ario/conserved_site_project/10_modeller/summary.json
2026-05-12 15:04:11 [MODELLER:step7_viewers_report] INFO Wrote /Users/ario/conserved_site_project/10_modeller/README_PHASE6.md
2026-05-12 15:04:12 [MODELLER:step7_viewers_report] INFO Wrote DOCX report: /Users/ario/conserved_site_project/09e_report_v5/report_PHASE6.docx (6707600 bytes)
2026-05-12 15:04:12 [MODELLER:step7_viewers_report] INFO STEP 7 OK
[V7] 2026-05-13T02:53:42Z Phase 7 start
[V7][taskA] 2026-05-13T02:54:55Z Task A start
[V7][taskA] 2026-05-13T02:54:55Z docking WT_apo seed=42
[V7][taskA] 2026-05-13T02:55:04Z docking WT_apo seed=7
[V7][taskA] 2026-05-13T02:55:13Z docking WT_apo seed=13
[V7][taskA] 2026-05-13T02:55:21Z docking WT_apo seed=99
[V7][taskA] 2026-05-13T02:55:30Z docking WT_apo seed=256
[V7][taskA] 2026-05-13T02:55:39Z WT_apo: mean=-8.5512 sd=0.0496960763038691 spread=0.11299999999999955
[V7][taskA] 2026-05-13T02:55:39Z docking WT_holo seed=42
[V7][taskA] 2026-05-13T02:55:49Z docking WT_holo seed=7
[V7][taskA] 2026-05-13T02:55:59Z docking WT_holo seed=13
[V7][taskA] 2026-05-13T02:56:09Z docking WT_holo seed=99
[V7][taskA] 2026-05-13T02:56:19Z docking WT_holo seed=256
[V7][taskA] 2026-05-13T02:56:29Z WT_holo: mean=-7.4864 sd=0.011631852818876432 spread=0.02800000000000047
[V7][taskA] 2026-05-13T02:56:29Z docking R215A_N226A_holo seed=42
[V7][taskA] 2026-05-13T02:56:39Z docking R215A_N226A_holo seed=7
[V7][taskA] 2026-05-13T02:56:48Z docking R215A_N226A_holo seed=13
[V7][taskA] 2026-05-13T02:56:57Z docking R215A_N226A_holo seed=99
[V7][taskA] 2026-05-13T02:57:06Z docking R215A_N226A_holo seed=256
[V7][taskA] 2026-05-13T02:57:16Z R215A_N226A_holo: mean=-7.4886 sd=0.04363828594250698 spread=0.10899999999999999
[V7][taskA] 2026-05-13T02:57:16Z docking H196A_holo seed=42
[V7][taskA] 2026-05-13T02:57:25Z docking H196A_holo seed=7
[V7][taskA] 2026-05-13T02:57:34Z docking H196A_holo seed=13
[V7][taskA] 2026-05-13T02:57:44Z docking H196A_holo seed=99
[V7][taskA] 2026-05-13T02:57:54Z docking H196A_holo seed=256
[V7][taskA] 2026-05-13T02:58:03Z H196A_holo: mean=-7.5768 sd=0.05121230320928733 spread=0.12799999999999923
[V7][taskA] 2026-05-13T02:58:03Z docking R215E_holo seed=42
[V7][taskA] 2026-05-13T02:58:13Z docking R215E_holo seed=7
[V7][taskA] 2026-05-13T02:58:23Z docking R215E_holo seed=13
[V7][taskA] 2026-05-13T02:58:34Z docking R215E_holo seed=99
[V7][taskA] 2026-05-13T02:58:44Z docking R215E_holo seed=256
[V7][taskA] 2026-05-13T02:58:54Z R215E_holo: mean=-7.6726 sd=0.016379865689315282 spread=0.036000000000000476
[V7][taskA] 2026-05-13T02:58:54Z docking R50A_holo seed=42
[V7][taskA] 2026-05-13T02:59:06Z docking R50A_holo seed=7
[V7][taskA] 2026-05-13T02:59:17Z docking R50A_holo seed=13
[V7][taskA] 2026-05-13T02:59:28Z docking R50A_holo seed=99
[V7][taskA] 2026-05-13T02:59:38Z docking R50A_holo seed=256
[V7][taskA] 2026-05-13T02:59:48Z R50A_holo: mean=-7.4478 sd=0.01901841213140552 spread=0.041999999999999815
[V7][taskA] 2026-05-13T02:59:48Z docking C195A_holo seed=42
[V7][taskA] 2026-05-13T02:59:56Z docking C195A_holo seed=7
[V7][taskA] 2026-05-13T03:00:04Z docking C195A_holo seed=13
[V7][taskA] 2026-05-13T03:00:12Z docking C195A_holo seed=99
[V7][taskA] 2026-05-13T03:00:20Z docking C195A_holo seed=256
[V7][taskA] 2026-05-13T03:00:28Z C195A_holo: mean=-10.37 sd=0.01414213562373159 spread=0.030000000000001137
[V7][taskA] 2026-05-13T03:00:28Z docking R175E_R176E_holo seed=42
[V7][taskA] 2026-05-13T03:00:39Z docking R175E_R176E_holo seed=7
[V7][taskA] 2026-05-13T03:00:49Z docking R175E_R176E_holo seed=13
[V7][taskA] 2026-05-13T03:01:00Z docking R175E_R176E_holo seed=99
[V7][taskA] 2026-05-13T03:01:11Z docking R175E_R176E_holo seed=256
[V7][taskA] 2026-05-13T03:01:20Z R175E_R176E_holo: mean=-8.012599999999999 sd=0.02247887897560711 spread=0.056999999999999496
[V7][taskA] 2026-05-13T03:01:20Z docking T170A_holo seed=42
[V7][taskA] 2026-05-13T03:01:30Z docking T170A_holo seed=7
[V7][taskA] 2026-05-13T03:01:41Z docking T170A_holo seed=13
[V7][taskA] 2026-05-13T03:01:52Z docking T170A_holo seed=99
[V7][taskA] 2026-05-13T03:02:03Z docking T170A_holo seed=256
[V7][taskA] 2026-05-13T03:02:12Z T170A_holo: mean=-8.012599999999999 sd=0.02247887897560711 spread=0.056999999999999496
[V7][taskA] 2026-05-13T03:02:12Z docking Y258F_F225Y_holo seed=42
[V7][taskA] 2026-05-13T03:02:22Z docking Y258F_F225Y_holo seed=7
[V7][taskA] 2026-05-13T03:02:31Z docking Y258F_F225Y_holo seed=13
[V7][taskA] 2026-05-13T03:02:40Z docking Y258F_F225Y_holo seed=99
[V7][taskA] 2026-05-13T03:02:50Z docking Y258F_F225Y_holo seed=256
[V7][taskA] 2026-05-13T03:03:00Z Y258F_F225Y_holo: mean=-7.8702 sd=0.009833615815151743 spread=0.020000000000000462
[V7][taskA] 2026-05-13T03:03:00Z Task A done: csv=/Users/ario/conserved_site_project/12_phase7/01_replicas/multi_replica_results.csv agg=/Users/ario/conserved_site_project/12_phase7/01_replicas/multi_replica_aggregate.csv
[V7][taskC] 2026-05-13T03:03:53Z Task C start
[V7][taskC] 2026-05-13T03:03:53Z super AF-P04818-F1-model_v6.pdb -> 1hvy_chainA.pdb: RMSD=0.378 N=258
[V7][taskC] 2026-05-13T03:03:53Z align AF-P04818-F1-model_v6.pdb -> 1hvy_chainA.pdb: RMSD=0.378 N=258
[V7][taskC] 2026-05-13T03:03:53Z super refined_B99990003.pdb -> 1hvy_chainA.pdb: RMSD=0.373 N=257
[V7][taskC] 2026-05-13T03:03:53Z align refined_B99990003.pdb -> 1hvy_chainA.pdb: RMSD=0.373 N=257
[V7][taskC] 2026-05-13T03:03:54Z super refined_B99990010.pdb -> 1hvy_chainA.pdb: RMSD=0.394 N=261
[V7][taskC] 2026-05-13T03:03:54Z align refined_B99990010.pdb -> 1hvy_chainA.pdb: RMSD=0.394 N=261
[V7][taskC] 2026-05-13T03:03:54Z super AF-P04818-F1-model_v6.pdb -> refined_B99990003.pdb: RMSD=0.432 N=264
[V7][taskC] 2026-05-13T03:03:54Z align AF-P04818-F1-model_v6.pdb -> refined_B99990003.pdb: RMSD=0.432 N=264
[V7][taskC] 2026-05-13T03:03:57Z triple overlay rc=0, png exists=True
[V7][taskC] 2026-05-13T03:03:57Z 3Dmol viewer -> /Users/ario/conserved_site_project/viewers/alphafold_overlay.html
[V7][taskC] 2026-05-13T03:03:57Z comparison CSV -> /Users/ario/conserved_site_project/12_phase7/03_alphafold/comparison.csv
[V7][taskC] 2026-05-13T03:03:57Z Task C done
[V7][taskC] 2026-05-13T03:05:25Z Task C start
[V7][taskC] 2026-05-13T03:05:25Z super AF-P04818-F1-model_v6.pdb -> 1hvy_chainA.pdb: RMSD_conv=0.378/258  RMSD_raw=0.47/285
[V7][taskC] 2026-05-13T03:05:25Z align AF-P04818-F1-model_v6.pdb -> 1hvy_chainA.pdb: RMSD_conv=0.378/258  RMSD_raw=0.554/287
[V7][taskC] 2026-05-13T03:05:26Z super refined_B99990003.pdb -> 1hvy_chainA.pdb: RMSD_conv=0.373/257  RMSD_raw=0.516/285
[V7][taskC] 2026-05-13T03:05:26Z align refined_B99990003.pdb -> 1hvy_chainA.pdb: RMSD_conv=0.373/257  RMSD_raw=0.702/287
[V7][taskC] 2026-05-13T03:05:26Z super refined_B99990010.pdb -> 1hvy_chainA.pdb: RMSD_conv=0.394/261  RMSD_raw=0.497/284
[V7][taskC] 2026-05-13T03:05:26Z align refined_B99990010.pdb -> 1hvy_chainA.pdb: RMSD_conv=0.394/261  RMSD_raw=0.64/287
[V7][taskC] 2026-05-13T03:05:26Z super AF-P04818-F1-model_v6.pdb -> refined_B99990003.pdb: RMSD_conv=0.432/264  RMSD_raw=0.598/286
[V7][taskC] 2026-05-13T03:05:26Z align AF-P04818-F1-model_v6.pdb -> refined_B99990003.pdb: RMSD_conv=0.432/264  RMSD_raw=0.677/287
[V7][taskC] 2026-05-13T03:05:29Z triple overlay rc=0, png exists=True
[V7][taskC] 2026-05-13T03:05:29Z 3Dmol viewer -> /Users/ario/conserved_site_project/viewers/alphafold_overlay.html
[V7][taskC] 2026-05-13T03:05:29Z comparison CSV -> /Users/ario/conserved_site_project/12_phase7/03_alphafold/comparison.csv
[V7][taskC] 2026-05-13T03:05:29Z Task C done
[V7][taskD] 2026-05-13T03:06:58Z Task D start
[V7][taskD] 2026-05-13T03:06:58Z WT SASA from /Users/ario/conserved_site_project/03b_structure_v2/protein_dimer_h.pdb
[V7][taskD] 2026-05-13T03:07:09Z Task D start
[V7][taskD] 2026-05-13T03:07:09Z WT SASA from /Users/ario/conserved_site_project/03b_structure_v2/protein_dimer_h.pdb
[V7][taskD] 2026-05-13T03:07:11Z processed 20 mutants
[V7][taskD] 2026-05-13T03:07:11Z merged CSV -> /Users/ario/conserved_site_project/12_phase7/04_sasa/sasa_vs_dvina.csv
[V7][taskD] 2026-05-13T03:07:11Z correlation r(focus vs dvina) = -0.192; r(at_mut) = -0.211
[V7][taskD] 2026-05-13T03:07:11Z matplotlib plot -> /Users/ario/conserved_site_project/12_phase7/04_sasa/sasa_vs_dvina.png
[V7][taskD] 2026-05-13T03:07:11Z plotly -> /Users/ario/conserved_site_project/12_phase7/04_sasa/sasa_vs_dvina.html
[V7][taskD] 2026-05-13T03:07:11Z Task D done
[V7][taskE] 2026-05-13T03:08:06Z Task E start
[V7][taskE] 2026-05-13T03:08:06Z alignment: 10 taxa, 399 columns
[V7][taskE] 2026-05-13T03:08:07Z NJ Newick -> /Users/ario/conserved_site_project/12_phase7/05_phylogeny/tymS_tree.nwk
[V7][taskE] 2026-05-13T03:08:07Z matplotlib tree -> /Users/ario/conserved_site_project/12_phase7/05_phylogeny/tymS_tree.png
[V7][taskE] 2026-05-13T03:08:07Z plotly tree -> /Users/ario/conserved_site_project/12_phase7/05_phylogeny/tymS_tree.html
[V7][taskE] 2026-05-13T03:08:07Z Task E done
[V7][taskF] 2026-05-13T03:08:42Z Task F start
[V7][taskF] 2026-05-13T03:08:42Z plotting 25 points
[V7][taskF] 2026-05-13T03:08:42Z plotly 3D -> /Users/ario/conserved_site_project/12_phase7/06_3d_plot/mutation_3d.html
[V7][taskF] 2026-05-13T03:08:42Z png skipped: No module named 'kaleido'
[V7][taskF] 2026-05-13T03:08:42Z Task F done
[V7][taskF] 2026-05-13T03:08:48Z Task F start
[V7][taskF] 2026-05-13T03:08:48Z plotting 25 points
[V7][taskF] 2026-05-13T03:08:49Z plotly 3D -> /Users/ario/conserved_site_project/12_phase7/06_3d_plot/mutation_3d.html
[V7][taskF] 2026-05-13T03:08:57Z png -> /Users/ario/conserved_site_project/12_phase7/06_3d_plot/mutation_3d.png
[V7][taskF] 2026-05-13T03:08:57Z Task F done
[V7][taskG] 2026-05-13T03:10:03Z Task G start
[V7][taskG] 2026-05-13T03:10:08Z WT_holo render rc=0, png exists=True
[V7][taskG] 2026-05-13T03:10:13Z R215A_N226A render rc=0, png exists=True
[V7][taskG] 2026-05-13T03:10:18Z H196A render rc=0, png exists=True
[V7][taskG] 2026-05-13T03:10:23Z R215E render rc=0, png exists=True
[V7][taskG] 2026-05-13T03:10:28Z R50A render rc=0, png exists=True
[V7][taskG] 2026-05-13T03:10:33Z C195A render rc=0, png exists=True
[V7][taskG] 2026-05-13T03:10:39Z R175E_R176E render rc=0, png exists=True
[V7][taskG] 2026-05-13T03:10:39Z Task G done: 7 images
[V7] 2026-05-13T03:11:13Z Phase 7 complete (Tasks A-G)
[V7][taskC] 2026-05-13T03:38:37Z Task C start
[V7][taskC] 2026-05-13T03:38:37Z super AF-P04818-F1-model_v6.pdb -> 1hvy_chainA.pdb: RMSD_conv=0.378/258  RMSD_raw=0.47/285
[V7][taskC] 2026-05-13T03:38:37Z align AF-P04818-F1-model_v6.pdb -> 1hvy_chainA.pdb: RMSD_conv=0.378/258  RMSD_raw=0.554/287
[V7][taskC] 2026-05-13T03:38:37Z super refined_B99990003.pdb -> 1hvy_chainA.pdb: RMSD_conv=0.373/257  RMSD_raw=0.516/285
[V7][taskC] 2026-05-13T03:38:38Z align refined_B99990003.pdb -> 1hvy_chainA.pdb: RMSD_conv=0.373/257  RMSD_raw=0.702/287
[V7][taskC] 2026-05-13T03:38:38Z super refined_B99990010.pdb -> 1hvy_chainA.pdb: RMSD_conv=0.394/261  RMSD_raw=0.497/284
[V7][taskC] 2026-05-13T03:38:38Z align refined_B99990010.pdb -> 1hvy_chainA.pdb: RMSD_conv=0.394/261  RMSD_raw=0.64/287
[V7][taskC] 2026-05-13T03:38:38Z super AF-P04818-F1-model_v6.pdb -> refined_B99990003.pdb: RMSD_conv=0.432/264  RMSD_raw=0.598/286
[V7][taskC] 2026-05-13T03:38:38Z align AF-P04818-F1-model_v6.pdb -> refined_B99990003.pdb: RMSD_conv=0.432/264  RMSD_raw=0.677/287
[V7][taskC] 2026-05-13T03:38:41Z triple overlay rc=0, png exists=True
[V7][taskC] 2026-05-13T03:38:41Z 3Dmol viewer -> /Users/ario/conserved_site_project/viewers/alphafold_overlay.html
[V7][taskC] 2026-05-13T03:38:41Z comparison CSV -> /Users/ario/conserved_site_project/12_phase7/03_alphafold/comparison.csv
[V7][taskC] 2026-05-13T03:38:41Z Task C done
[V7][taskC] 2026-05-13T03:39:50Z Task C start
[V7][taskC] 2026-05-13T03:39:51Z super AF-P04818-F1-model_v6.pdb -> 1hvy_chainA.pdb: RMSD_conv=0.378/258  RMSD_raw=0.47/285
[V7][taskC] 2026-05-13T03:39:51Z align AF-P04818-F1-model_v6.pdb -> 1hvy_chainA.pdb: RMSD_conv=0.378/258  RMSD_raw=0.554/287
[V7][taskC] 2026-05-13T03:39:51Z super refined_B99990003.pdb -> 1hvy_chainA.pdb: RMSD_conv=0.373/257  RMSD_raw=0.516/285
[V7][taskC] 2026-05-13T03:39:51Z align refined_B99990003.pdb -> 1hvy_chainA.pdb: RMSD_conv=0.373/257  RMSD_raw=0.702/287
[V7][taskC] 2026-05-13T03:39:51Z super refined_B99990010.pdb -> 1hvy_chainA.pdb: RMSD_conv=0.394/261  RMSD_raw=0.497/284
[V7][taskC] 2026-05-13T03:39:51Z align refined_B99990010.pdb -> 1hvy_chainA.pdb: RMSD_conv=0.394/261  RMSD_raw=0.64/287
[V7][taskC] 2026-05-13T03:39:51Z super AF-P04818-F1-model_v6.pdb -> refined_B99990003.pdb: RMSD_conv=0.432/264  RMSD_raw=0.598/286
[V7][taskC] 2026-05-13T03:39:52Z align AF-P04818-F1-model_v6.pdb -> refined_B99990003.pdb: RMSD_conv=0.432/264  RMSD_raw=0.677/287
[V7][taskC] 2026-05-13T03:39:54Z triple overlay rc=0, png exists=True
[V7][taskC] 2026-05-13T03:39:54Z 3Dmol viewer -> /Users/ario/conserved_site_project/viewers/alphafold_overlay.html
[V7][taskC] 2026-05-13T03:39:54Z comparison CSV -> /Users/ario/conserved_site_project/12_phase7/03_alphafold/comparison.csv
[V7][taskC] 2026-05-13T03:39:54Z summary CSV (aggregated 3 sub-runs) -> /Users/ario/conserved_site_project/12_phase7/03_alphafold/summary.csv
[V7][taskC] 2026-05-13T03:39:54Z Task C done
[V7][taskG] 2026-05-13T05:02:06Z Task G start
[V7][taskG] 2026-05-13T05:02:11Z WT_holo render rc=0, png exists=True
[V7][taskG] 2026-05-13T05:02:16Z R215A_N226A render rc=0, png exists=True
[V7][taskG] 2026-05-13T05:02:21Z H196A render rc=0, png exists=True
[V7][taskG] 2026-05-13T05:02:27Z R215E render rc=0, png exists=True
[V7][taskG] 2026-05-13T05:02:33Z R50A render rc=0, png exists=True
[V7][taskG] 2026-05-13T05:02:39Z C195A render rc=0, png exists=True
[V7][taskG] 2026-05-13T05:02:44Z R175E_R176E render rc=0, png exists=True
[V7][taskG] 2026-05-13T05:02:44Z Task G done: 7 images
[V8][8a] 2026-05-13T05:37:39Z Phase 8a start; AUTOGRID=None
[V8][8a] 2026-05-13T05:37:39Z autogrid4 NOT FOUND on host; AD4 column will be empty (documented limitation).
[V8][8a] 2026-05-13T05:37:39Z Targets: 42 rows from mutant_results_v5.csv
[V8][8a] 2026-05-13T05:37:40Z WT                 apo  vina=-8.718 vinardo=-6.334 d_vinardo=2.3840000000000003
[V8][8a] 2026-05-13T05:37:41Z WT                 holo vina=-7.407 vinardo=-5.112 d_vinardo=2.295
[V8][8a] 2026-05-13T05:37:41Z C195A              holo vina=-10.502 vinardo=-8.519 d_vinardo=1.9830000000000005
[V8][8a] 2026-05-13T05:37:41Z vina rc=1 scoring=vina lig=C195A_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:41Z vina rc=1 scoring=vinardo lig=C195A_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:41Z C195A              apo  vina=None vinardo=None d_vinardo=None
[V8][8a] 2026-05-13T05:37:42Z C195A_H196A        holo vina=-10.025 vinardo=-8.02 d_vinardo=2.005000000000001
[V8][8a] 2026-05-13T05:37:42Z vina rc=1 scoring=vina lig=C195A_H196A_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:42Z vina rc=1 scoring=vinardo lig=C195A_H196A_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:42Z C195A_H196A        apo  vina=None vinardo=None d_vinardo=None
[V8][8a] 2026-05-13T05:37:43Z C195S              holo vina=-10.209 vinardo=-8.39 d_vinardo=1.818999999999999
[V8][8a] 2026-05-13T05:37:43Z vina rc=1 scoring=vina lig=C195S_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:43Z vina rc=1 scoring=vinardo lig=C195S_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:43Z C195S              apo  vina=None vinardo=None d_vinardo=None
[V8][8a] 2026-05-13T05:37:44Z C195S_H196N        holo vina=-9.776 vinardo=-8.119 d_vinardo=1.657
[V8][8a] 2026-05-13T05:37:44Z vina rc=1 scoring=vina lig=C195S_H196N_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:44Z vina rc=1 scoring=vinardo lig=C195S_H196N_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:44Z C195S_H196N        apo  vina=None vinardo=None d_vinardo=None
[V8][8a] 2026-05-13T05:37:45Z H196A              holo vina=-7.758 vinardo=-6.009 d_vinardo=1.7489999999999997
[V8][8a] 2026-05-13T05:37:45Z vina rc=1 scoring=vina lig=H196A_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:45Z vina rc=1 scoring=vinardo lig=H196A_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:45Z H196A              apo  vina=None vinardo=None d_vinardo=None
[V8][8a] 2026-05-13T05:37:45Z N226D              holo vina=-7.806 vinardo=-5.922 d_vinardo=1.8840000000000003
[V8][8a] 2026-05-13T05:37:45Z vina rc=1 scoring=vina lig=N226D_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:45Z vina rc=1 scoring=vinardo lig=N226D_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:45Z N226D              apo  vina=None vinardo=None d_vinardo=None
[V8][8a] 2026-05-13T05:37:46Z Q214A              holo vina=-8.175 vinardo=-6.225 d_vinardo=1.950000000000001
[V8][8a] 2026-05-13T05:37:46Z vina rc=1 scoring=vina lig=Q214A_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:46Z vina rc=1 scoring=vinardo lig=Q214A_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:46Z Q214A              apo  vina=None vinardo=None d_vinardo=None
[V8][8a] 2026-05-13T05:37:47Z R175A              holo vina=-8.193 vinardo=-6.378 d_vinardo=1.8149999999999995
[V8][8a] 2026-05-13T05:37:47Z vina rc=1 scoring=vina lig=R175A_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:47Z vina rc=1 scoring=vinardo lig=R175A_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:47Z R175A              apo  vina=None vinardo=None d_vinardo=None
[V8][8a] 2026-05-13T05:37:48Z R175E              holo vina=-8.196 vinardo=-6.436 d_vinardo=1.7599999999999998
[V8][8a] 2026-05-13T05:37:48Z vina rc=1 scoring=vina lig=R175E_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:48Z vina rc=1 scoring=vinardo lig=R175E_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:48Z R175E              apo  vina=None vinardo=None d_vinardo=None
[V8][8a] 2026-05-13T05:37:49Z R175E_R176E        holo vina=-8.203 vinardo=-6.38 d_vinardo=1.8229999999999995
[V8][8a] 2026-05-13T05:37:49Z vina rc=1 scoring=vina lig=R175E_R176E_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:49Z vina rc=1 scoring=vinardo lig=R175E_R176E_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:49Z R175E_R176E        apo  vina=None vinardo=None d_vinardo=None
[V8][8a] 2026-05-13T05:37:49Z R176A              holo vina=-8.187 vinardo=-6.423 d_vinardo=1.7639999999999993
[V8][8a] 2026-05-13T05:37:49Z vina rc=1 scoring=vina lig=R176A_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:49Z vina rc=1 scoring=vinardo lig=R176A_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:49Z R176A              apo  vina=None vinardo=None d_vinardo=None
[V8][8a] 2026-05-13T05:37:50Z R176E              holo vina=-8.203 vinardo=-6.38 d_vinardo=1.8229999999999995
[V8][8a] 2026-05-13T05:37:50Z vina rc=1 scoring=vina lig=R176E_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:50Z vina rc=1 scoring=vinardo lig=R176E_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:50Z R176E              apo  vina=None vinardo=None d_vinardo=None
[V8][8a] 2026-05-13T05:37:51Z R215A              holo vina=-7.802 vinardo=-5.508 d_vinardo=2.2939999999999996
[V8][8a] 2026-05-13T05:37:51Z vina rc=1 scoring=vina lig=R215A_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:51Z vina rc=1 scoring=vinardo lig=R215A_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:51Z R215A              apo  vina=None vinardo=None d_vinardo=None
[V8][8a] 2026-05-13T05:37:52Z R215A_N226A        holo vina=-7.475 vinardo=-5.014 d_vinardo=2.4609999999999994
[V8][8a] 2026-05-13T05:37:52Z vina rc=1 scoring=vina lig=R215A_N226A_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:52Z vina rc=1 scoring=vinardo lig=R215A_N226A_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:52Z R215A_N226A        apo  vina=None vinardo=None d_vinardo=None
[V8][8a] 2026-05-13T05:37:53Z R215E              holo vina=-7.774 vinardo=-5.527 d_vinardo=2.247
[V8][8a] 2026-05-13T05:37:53Z vina rc=1 scoring=vina lig=R215E_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:53Z vina rc=1 scoring=vinardo lig=R215E_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:53Z R215E              apo  vina=None vinardo=None d_vinardo=None
[V8][8a] 2026-05-13T05:37:53Z R50A               holo vina=-7.42 vinardo=-4.055 d_vinardo=3.365
[V8][8a] 2026-05-13T05:37:53Z vina rc=1 scoring=vina lig=R50A_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:53Z vina rc=1 scoring=vinardo lig=R50A_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:53Z R50A               apo  vina=None vinardo=None d_vinardo=None
[V8][8a] 2026-05-13T05:37:54Z R50E               holo vina=-7.764 vinardo=-4.41 d_vinardo=3.354
[V8][8a] 2026-05-13T05:37:54Z vina rc=1 scoring=vina lig=R50E_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:54Z vina rc=1 scoring=vinardo lig=R50E_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:54Z R50E               apo  vina=None vinardo=None d_vinardo=None
[V8][8a] 2026-05-13T05:37:55Z T170A              holo vina=-8.203 vinardo=-6.38 d_vinardo=1.8229999999999995
[V8][8a] 2026-05-13T05:37:55Z vina rc=1 scoring=vina lig=T170A_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:55Z vina rc=1 scoring=vinardo lig=T170A_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:55Z T170A              apo  vina=None vinardo=None d_vinardo=None
[V8][8a] 2026-05-13T05:37:56Z W109A              holo vina=-7.976 vinardo=-6.343 d_vinardo=1.633
[V8][8a] 2026-05-13T05:37:56Z vina rc=1 scoring=vina lig=W109A_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:56Z vina rc=1 scoring=vinardo lig=W109A_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:56Z W109A              apo  vina=None vinardo=None d_vinardo=None
[V8][8a] 2026-05-13T05:37:56Z Y258F_F225Y        holo vina=-8.047 vinardo=-6.01 d_vinardo=2.037000000000001
[V8][8a] 2026-05-13T05:37:56Z vina rc=1 scoring=vina lig=Y258F_F225Y_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:56Z vina rc=1 scoring=vinardo lig=Y258F_F225Y_apo_top.pdbqt: 

PDBQT parsing error: Unexpected multi-MODEL tag found in rigid receptor. Only one model can be used for the rigid rece
[V8][8a] 2026-05-13T05:37:56Z Y258F_F225Y        apo  vina=None vinardo=None d_vinardo=None
[V8][8a] 2026-05-13T05:37:56Z wrote /Users/ario/conserved_site_project/13_phase8/01_alt_scoring/alt_scoring_results.csv with 42 rows
[V8][8a] 2026-05-13T05:42:29Z Phase 8a start; AUTOGRID=None
[V8][8a] 2026-05-13T05:42:29Z autogrid4 NOT FOUND on host; AD4 column will be empty (documented limitation).
[V8][8a] 2026-05-13T05:42:29Z Targets: 42 rows from mutant_results_v5.csv
[V8][8a] 2026-05-13T05:42:29Z WT                 apo  vina=-8.718 vinardo=-6.334 d_vinardo=2.3840000000000003
[V8][8a] 2026-05-13T05:42:30Z WT                 holo vina=-7.407 vinardo=-5.112 d_vinardo=2.295
[V8][8a] 2026-05-13T05:42:31Z C195A              holo vina=-10.502 vinardo=-8.519 d_vinardo=1.9830000000000005
[V8][8a] 2026-05-13T05:42:34Z C195A              apo  vina=-9.46 vinardo=-7.59 d_vinardo=1.870000000000001
[V8][8a] 2026-05-13T05:42:34Z C195A_H196A        holo vina=-10.025 vinardo=-8.02 d_vinardo=2.005000000000001
[V8][8a] 2026-05-13T05:42:37Z C195A_H196A        apo  vina=-9.118 vinardo=-7.176 d_vinardo=1.9420000000000002
[V8][8a] 2026-05-13T05:42:38Z C195S              holo vina=-10.209 vinardo=-8.39 d_vinardo=1.818999999999999
[V8][8a] 2026-05-13T05:42:40Z C195S              apo  vina=-9.549 vinardo=-7.699 d_vinardo=1.8499999999999996
[V8][8a] 2026-05-13T05:42:41Z C195S_H196N        holo vina=-9.776 vinardo=-8.119 d_vinardo=1.657
[V8][8a] 2026-05-13T05:42:44Z C195S_H196N        apo  vina=-9.337 vinardo=-7.505 d_vinardo=1.8319999999999999
[V8][8a] 2026-05-13T05:42:45Z H196A              holo vina=-7.758 vinardo=-6.009 d_vinardo=1.7489999999999997
[V8][8a] 2026-05-13T05:42:47Z H196A              apo  vina=-8.858 vinardo=-7.025 d_vinardo=1.8330000000000002
[V8][8a] 2026-05-13T05:42:48Z N226D              holo vina=-7.806 vinardo=-5.922 d_vinardo=1.8840000000000003
[V8][8a] 2026-05-13T05:42:50Z N226D              apo  vina=-8.778 vinardo=-6.838 d_vinardo=1.9400000000000004
[V8][8a] 2026-05-13T05:42:51Z Q214A              holo vina=-8.175 vinardo=-6.225 d_vinardo=1.950000000000001
[V8][8a] 2026-05-13T05:42:54Z Q214A              apo  vina=-8.654 vinardo=-6.792 d_vinardo=1.862
[V8][8a] 2026-05-13T05:42:55Z R175A              holo vina=-8.193 vinardo=-6.378 d_vinardo=1.8149999999999995
[V8][8a] 2026-05-13T05:42:57Z R175A              apo  vina=-9.021 vinardo=-7.115 d_vinardo=1.9060000000000006
[V8][8a] 2026-05-13T05:42:58Z R175E              holo vina=-8.196 vinardo=-6.436 d_vinardo=1.7599999999999998
[V8][8a] 2026-05-13T05:43:00Z R175E              apo  vina=-9.04 vinardo=-7.074 d_vinardo=1.9659999999999993
[V8][8a] 2026-05-13T05:43:01Z R175E_R176E        holo vina=-8.203 vinardo=-6.38 d_vinardo=1.8229999999999995
[V8][8a] 2026-05-13T05:43:03Z R175E_R176E        apo  vina=-9.022 vinardo=-7.055 d_vinardo=1.9670000000000005
[V8][8a] 2026-05-13T05:43:04Z R176A              holo vina=-8.187 vinardo=-6.423 d_vinardo=1.7639999999999993
[V8][8a] 2026-05-13T05:43:06Z R176A              apo  vina=-9.022 vinardo=-7.055 d_vinardo=1.9670000000000005
[V8][8a] 2026-05-13T05:43:07Z R176E              holo vina=-8.203 vinardo=-6.38 d_vinardo=1.8229999999999995
[V8][8a] 2026-05-13T05:43:10Z R176E              apo  vina=-9.022 vinardo=-7.055 d_vinardo=1.9670000000000005
[V8][8a] 2026-05-13T05:43:11Z R215A              holo vina=-7.802 vinardo=-5.508 d_vinardo=2.2939999999999996
[V8][8a] 2026-05-13T05:43:13Z R215A              apo  vina=-8.63 vinardo=-6.232 d_vinardo=2.3980000000000006
[V8][8a] 2026-05-13T05:43:14Z R215A_N226A        holo vina=-7.475 vinardo=-5.014 d_vinardo=2.4609999999999994
[V8][8a] 2026-05-13T05:43:16Z R215A_N226A        apo  vina=-8.049 vinardo=-5.852 d_vinardo=2.196999999999999
[V8][8a] 2026-05-13T05:43:17Z R215E              holo vina=-7.774 vinardo=-5.527 d_vinardo=2.247
[V8][8a] 2026-05-13T05:43:19Z R215E              apo  vina=-8.586 vinardo=-6.092 d_vinardo=2.4940000000000007
[V8][8a] 2026-05-13T05:43:20Z R50A               holo vina=-7.42 vinardo=-4.055 d_vinardo=3.365
[V8][8a] 2026-05-13T05:43:22Z R50A               apo  vina=-8.618 vinardo=-6.094 d_vinardo=2.524
[V8][8a] 2026-05-13T05:43:23Z R50E               holo vina=-7.764 vinardo=-4.41 d_vinardo=3.354
[V8][8a] 2026-05-13T05:43:25Z R50E               apo  vina=-8.782 vinardo=-6.282 d_vinardo=2.5
[V8][8a] 2026-05-13T05:43:26Z T170A              holo vina=-8.203 vinardo=-6.38 d_vinardo=1.8229999999999995
[V8][8a] 2026-05-13T05:43:29Z T170A              apo  vina=-9.021 vinardo=-7.115 d_vinardo=1.9060000000000006
[V8][8a] 2026-05-13T05:43:29Z W109A              holo vina=-7.976 vinardo=-6.343 d_vinardo=1.633
[V8][8a] 2026-05-13T05:43:32Z W109A              apo  vina=-8.873 vinardo=-7.159 d_vinardo=1.7139999999999995
[V8][8a] 2026-05-13T05:43:33Z Y258F_F225Y        holo vina=-8.047 vinardo=-6.01 d_vinardo=2.037000000000001
[V8][8a] 2026-05-13T05:43:35Z Y258F_F225Y        apo  vina=-8.876 vinardo=-6.896 d_vinardo=1.9799999999999995
[V8][8a] 2026-05-13T05:43:35Z wrote /Users/ario/conserved_site_project/13_phase8/01_alt_scoring/alt_scoring_results.csv with 42 rows
[V8][8b] 2026-05-13T05:57:48Z Phase 8b start; flex panel = [('A', 50), ('A', 109), ('A', 175), ('A', 176), ('A', 195), ('A', 196), ('A', 214), ('A', 215), ('A', 225), ('A', 226), ('A', 218), ('A', 222), ('A', 87), ('A', 51)]
[V8][8b] 2026-05-13T05:57:48Z === R215A_N226A ===
[V8][8b] 2026-05-13T05:57:49Z   flex_split WARN: residue GLY A:222 has no rotatable side chain; keeping rigid
[V8][8b] 2026-05-13T05:57:49Z   docking with --flex (exhaustiveness=32, modes=20)
[V8][8b] 2026-05-13T06:10:07Z   flex top_aff=None n_modes=0 elapsed=737.1769189834595s
[V8][8b] 2026-05-13T06:10:07Z === H196A ===
[V8][8b] 2026-05-13T06:10:09Z   flex_split WARN: residue GLY A:222 has no rotatable side chain; keeping rigid
[V8][8b] 2026-05-13T06:10:09Z   docking with --flex (exhaustiveness=32, modes=20)
[V8][8b] 2026-05-13T06:10:48Z Phase 8b start; flex panel = [('A', 50), ('A', 109), ('A', 175), ('A', 176), ('A', 195), ('A', 196), ('A', 214), ('A', 215)]
[V8][8b] 2026-05-13T06:10:48Z === R215A_N226A ===
[V8][8b] 2026-05-13T06:10:50Z   docking with --flex (exhaustiveness=8, modes=10)
[V8][8b] 2026-05-13T06:12:47Z   flex top_aff=-3.944 n_modes=10 elapsed=116.84s
[V8][8b] 2026-05-13T06:12:47Z === H196A ===
[V8][8b] 2026-05-13T06:12:48Z   docking with --flex (exhaustiveness=8, modes=10)
[V8][8b] 2026-05-13T06:15:03Z   flex top_aff=-1.279 n_modes=10 elapsed=134.6s
[V8][8b] 2026-05-13T06:15:03Z === R215E ===
[V8][8b] 2026-05-13T06:15:04Z   docking with --flex (exhaustiveness=8, modes=10)
[V8][8b] 2026-05-13T06:17:56Z   flex top_aff=-2.488 n_modes=10 elapsed=172.04s
[V8][8b] 2026-05-13T06:17:56Z === R50A ===
[V8][8b] 2026-05-13T06:17:58Z   docking with --flex (exhaustiveness=8, modes=10)
[V8][8b] 2026-05-13T06:20:16Z   flex top_aff=-3.974 n_modes=10 elapsed=138.26s
[V8][8b] 2026-05-13T06:20:16Z === C195A ===
[V8][8b] 2026-05-13T06:20:18Z   docking with --flex (exhaustiveness=8, modes=10)
[V8][8b] 2026-05-13T06:23:06Z   flex top_aff=-6.392 n_modes=10 elapsed=168.21s
[V8][8b] 2026-05-13T06:23:06Z === R175E_R176E ===
[V8][8b] 2026-05-13T06:23:08Z   docking with --flex (exhaustiveness=8, modes=10)
[V8][8b] 2026-05-13T06:25:23Z   flex top_aff=-5.519 n_modes=10 elapsed=135.16s
[V8][8b] 2026-05-13T06:25:23Z === T170A ===
[V8][8b] 2026-05-13T06:25:25Z   docking with --flex (exhaustiveness=8, modes=10)
[V8][8b] 2026-05-13T06:29:08Z   flex top_aff=-4.093 n_modes=10 elapsed=222.97s
[V8][8b] 2026-05-13T06:29:08Z === Y258F_F225Y ===
[V8][8b] 2026-05-13T06:29:10Z   docking with --flex (exhaustiveness=8, modes=10)
[V8][8b] 2026-05-13T06:32:50Z   flex top_aff=-4.923 n_modes=10 elapsed=219.48s
[V8][8b] 2026-05-13T06:32:50Z wrote /Users/ario/conserved_site_project/13_phase8/02_flexres/flexres_compare.csv with 8 rows