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[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