diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/README.md b/benchmarks/ProteinDesign/FixedBackboneDesign/README.md new file mode 100644 index 00000000..ed24d99e --- /dev/null +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/README.md @@ -0,0 +1,25 @@ +# FixedBackboneDesign + +## Quick Start + +```bash +cd benchmarks/ProteinDesign/FixedBackboneDesign +mkdir -p outputs +python verification/evaluator.py prepare --raw-task data/raw_task.json --prepared-output outputs/prepared.pdb +python scripts/init.py --prepared-input outputs/prepared.pdb --solution-output outputs/solution.pdb +python verification/evaluator.py evaluate --native outputs/prepared.pdb --candidate outputs/solution.pdb --result-output outputs/result.json +``` + +## Background + +This task is inspired by Agent Rosetta (Teneggi et al., arXiv:2603.15952, ICML 2026), which demonstrates LLM-driven protein design using Rosetta. This benchmark adapts the fixed-backbone sequence design problem as a standalone engineering optimization task. + +## Unified Benchmark ID + +`ProteinDesign/FixedBackboneDesign` + +## Environment + +```bash +docker pull rosettacommons/rosetta:serial +``` diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/README_zh-CN.md b/benchmarks/ProteinDesign/FixedBackboneDesign/README_zh-CN.md new file mode 100644 index 00000000..1c47cac0 --- /dev/null +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/README_zh-CN.md @@ -0,0 +1,81 @@ +# FixedBackboneDesign - 固定骨架蛋白质序列设计 + +## 一句话解释 + +给定一个蛋白质的骨架结构（backbone），设计出最适合这个骨架的氨基酸序列，使 Rosetta 能量得分最低。 + +## 任务描述 + +本任务基于 Agent Rosetta 论文 (arXiv:2603.15952) 的 Case A：固定骨架规范氨基酸序列设计。Agent 需要从初始 baseline 出发，通过迭代优化找到总能量更低的氨基酸序列。 + +## 文件结构 + +``` +FixedBackboneDesign/ +├── Task.md # 任务详情（英文） +├── Task_zh-CN.md # 任务详情（中文） +├── README.md # 本文件（导航） +├── scripts/ +│ └── init.py # [可编辑] baseline 解法（含 EVOLVE-BLOCK） +├── data/ +│ └── raw_task.json # 任务配置 +├── references/ +│ ├── constants.json # Rosetta 能量函数参数 +│ └── petrobind/ # PDB 结构文件 +├── frontier_eval/ # unified task 元数据 +├── verification/ +│ ├── evaluator.py # [核心] PyRosetta 评分入口 +│ ├── requirements.txt +│ └── docker/ +│ └── Dockerfile +└── baseline/ # [可选] 参考实现存档 +``` + +## 运行方式 + +### 本地三步运行 + +```bash +cd benchmarks/ProteinDesign/FixedBackboneDesign +mkdir -p outputs + +# 1. prepare（由 evaluator 完成数据准备） +python verification/evaluator.py prepare \ + --raw-task data/raw_task.json \ + --prepared-output outputs/prepared.pdb + +# 2. 运行 baseline 生成设计结果 +python scripts/init.py \ + --prepared-input outputs/prepared.pdb \ + --solution-output outputs/solution.pdb + +# 3. 评估设计结果 +python verification/evaluator.py evaluate \ + --native outputs/prepared.pdb \ + --candidate outputs/solution.pdb \ + --result-output outputs/result.json +``` + +### Unified task 方式 + +```bash +python -m frontier_eval \ + task=unified \ + task.benchmark=ProteinDesign/FixedBackboneDesign \ + task.runtime.isolation_mode=docker \ + task.runtime.docker_image=rosettacommons/rosetta:serial \ + algorithm=openevolve \ + algorithm.iterations=0 +``` + +## 统一 benchmark ID + +- `ProteinDesign/FixedBackboneDesign` + +## 环境准备 + +本任务需要 Rosetta 环境，推荐使用官方 Docker 镜像： + +```bash +docker pull rosettacommons/rosetta:serial +``` diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/Task.md b/benchmarks/ProteinDesign/FixedBackboneDesign/Task.md new file mode 100644 index 00000000..a28a5e2a --- /dev/null +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/Task.md @@ -0,0 +1,37 @@ +# FixedBackboneDesign + +## Overview + +Design the optimal amino acid sequence for a given fixed protein backbone. This task corresponds to Case A (Fixed-Backbone Canonical Amino Acid Sequence Design) of the Agent Rosetta paper (arXiv:2603.15952, ICML 2026). + +## Input + +The candidate script (`scripts/init.py`) receives: + +- `--prepared-input`: Path to a PDB file with the target backbone and design position annotations +- `--solution-output`: Path where the designed structure should be written + +## Output + +The candidate must output a PDB file at `--solution-output` containing: +1. The original backbone coordinates (unchanged) +2. Designed amino acid substitutions at specified positions +3. Only standard 20 amino acids (no non-canonical residues) + +## Scoring + +The evaluator uses PyRosetta's `ref2015` score function to compute: + +- **total_energy**: Sum of all energy terms +- **baseline_energy**: Energy of the native (starting) sequence +- **improvement**: baseline_energy - total_energy (positive = better) +- **combined_score**: Normalized improvement = improvement / |baseline_energy| + +Energy terms reported: `fa_atr`, `fa_rep`, `fa_sol`, `fa_elec`, `hbond_bb_sc`, `hbond_sc`, `p_aa_pp`, `ref` + +## Constraints + +- Only modify `scripts/init.py` +- Do NOT modify backbone coordinates +- Only use the 20 standard amino acids +- Output must be a valid PDB file diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/Task_zh-CN.md b/benchmarks/ProteinDesign/FixedBackboneDesign/Task_zh-CN.md new file mode 100644 index 00000000..561b3759 --- /dev/null +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/Task_zh-CN.md @@ -0,0 +1,37 @@ +# FixedBackboneDesign - 固定骨架蛋白质序列设计 + +## 概述 + +给定一个固定的蛋白质骨架（backbone），设计出最稳定的氨基酸序列。本任务对应 Agent Rosetta 论文（arXiv:2603.15952, ICML 2026）的 Case A：固定骨架规范氨基酸序列设计。 + +## 输入 + +candidate 脚本（`scripts/init.py`）接收以下参数： + +- `--prepared-input`：包含目标骨架和设计位置标注的 PDB 文件路径 +- `--solution-output`：设计结果 PDB 的输出路径 + +## 输出 + +candidate 必须在 `--solution-output` 输出一个 PDB 文件，包含： +1. 原始的骨架坐标（保持不变） +2. 在指定位置替换为设计后的氨基酸 +3. 只能使用 20 种标准氨基酸（不允许非规范氨基酸） + +## 评分方式 + +评估器使用 PyRosetta 的 `ref2015` 能量函数计算： + +- **total_energy**：所有能量项的加和 +- **baseline_energy**：初始序列的能量 +- **improvement**：baseline_energy - total_energy（正数表示改进） +- **combined_score**：归一化改进值 = improvement / |baseline_energy| + +报告的能量项：`fa_atr`、`fa_rep`、`fa_sol`、`fa_elec`、`hbond_bb_sc`、`hbond_sc`、`p_aa_pp`、`ref` + +## 约束 + +- 只能修改 `scripts/init.py` +- 不得修改骨架坐标 +- 只能使用 20 种标准氨基酸 +- 输出必须是有效的 PDB 文件 diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/baseline/result_log.txt b/benchmarks/ProteinDesign/FixedBackboneDesign/baseline/result_log.txt new file mode 100644 index 00000000..590881e7 --- /dev/null +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/baseline/result_log.txt @@ -0,0 +1,31 @@ +FixedBackboneDesign baseline (no additional indexes beyond initial) +============================================================== +Date: 2026-07-14 +Evaluator: verification/evaluator.py (evaluate() function) +Candidate: scripts/init.py (baseline: single-round PackRotamers with default settings) +Environment: Docker (rosettacommons/rosetta:serial), PyRosetta ref2015 + +Results: +-------- +valid: 1.0 +combined_score: 0.025 +native_energy: -169.18 +total_energy: -173.48 +improvement: +4.30 + +Energy terms: + fa_atr: -377.73 + fa_rep: 110.97 + fa_sol: 245.04 + fa_elec: -133.95 + hbond_bb_sc: -4.62 + hbond_sc: -6.87 + p_aa_pp: -23.02 + ref: 12.74 + +Note: +- The baseline uses a single-round PackRotamersMover with packer.task(). +- Non-design positions are prevented from repacking via prevent_repacking(). +- Constraint verification (_verify_constraints) passed: no backbone movement, + no unexpected mutations at non-design positions. +- Random seed fixed to 42 for reproducibility. diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/data/raw_task.json b/benchmarks/ProteinDesign/FixedBackboneDesign/data/raw_task.json new file mode 100644 index 00000000..26fe88a5 --- /dev/null +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/data/raw_task.json @@ -0,0 +1,14 @@ +{ + "task_name": "fixed_backbone_design_demo", + "description": "Fixed-backbone protein sequence design using PyRosetta ref2015 scoring", + "pdb_id": "1ubq", + "pdb_path": "references/petrobind/1ubq.pdb", + "design_positions": [2, 4, 6, 8, 10, 12, 14, 16], + "native_sequence": "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG", + "energy_function": "ref2015", + "task_config": { + "n_design_positions": 8, + "allow_design_of_native": true, + "description": "Design 8 core positions of ubiquitin (PDB 1UBQ)" + } +} diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/agent_files.txt b/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/agent_files.txt new file mode 100644 index 00000000..62896765 --- /dev/null +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/agent_files.txt @@ -0,0 +1,8 @@ +Task.md +Task_zh-CN.md +scripts/init.py +verification/evaluator.py +verification/requirements.txt +data/raw_task.json +references/constants.json +references/petrobind/1ubq.pdb diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/artifact_files.txt b/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/artifact_files.txt new file mode 100644 index 00000000..0756dacf --- /dev/null +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/artifact_files.txt @@ -0,0 +1,3 @@ +metrics.json +outputs/*.pdb +outputs/*.meta.json diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/candidate_destination.txt b/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/candidate_destination.txt new file mode 100644 index 00000000..b9411b3d --- /dev/null +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/candidate_destination.txt @@ -0,0 +1 @@ +scripts/init.py diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/constraints.txt b/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/constraints.txt new file mode 100644 index 00000000..cae3dc16 --- /dev/null +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/constraints.txt @@ -0,0 +1,6 @@ +1) Only modify `scripts/init.py` — it is the ONLY editable file. +2) Keep CLI contract unchanged: the candidate must accept `--prepared-input` and `--solution-output`. +3) Output must be a PDB file with designed amino acid substitutions. +4) Only use the 20 standard amino acids (no non-canonical residues). +5) Do NOT modify the backbone coordinates (fixed-backbone design). +6) Optimize the Rosetta total_score (lower is better). Use the ref2015 score function. diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/copy_files.txt b/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/copy_files.txt new file mode 100644 index 00000000..3136147f --- /dev/null +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/copy_files.txt @@ -0,0 +1,4 @@ +scripts +data +verification +references diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/eval_command.txt b/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/eval_command.txt new file mode 100644 index 00000000..613443e7 --- /dev/null +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/eval_command.txt @@ -0,0 +1 @@ +{python} {benchmark}/verification/evaluator.py {candidate} diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/eval_cwd.txt b/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/eval_cwd.txt new file mode 100644 index 00000000..9c558e35 --- /dev/null +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/eval_cwd.txt @@ -0,0 +1 @@ +. diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/initial_program.txt b/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/initial_program.txt new file mode 100644 index 00000000..b9411b3d --- /dev/null +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/initial_program.txt @@ -0,0 +1 @@ +scripts/init.py diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/readonly_files.txt b/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/readonly_files.txt new file mode 100644 index 00000000..bf3fde93 --- /dev/null +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/readonly_files.txt @@ -0,0 +1,3 @@ +data +verification +references diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/references/constants.json b/benchmarks/ProteinDesign/FixedBackboneDesign/references/constants.json new file mode 100644 index 00000000..e36a29bc --- /dev/null +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/references/constants.json @@ -0,0 +1,13 @@ +{ + "energy_function": "ref2015", + "score_terms": { + "fa_atr": {"weight": 1.0, "description": "Lennard-Jones attractive (van der Waals)"}, + "fa_rep": {"weight": 0.55, "description": "Lennard-Jones repulsive (steric clash)"}, + "fa_sol": {"weight": 1.0, "description": "Lazaridis-Karplus solvation energy"}, + "fa_elec": {"weight": 1.0, "description": "Coulomb electrostatic potential"}, + "hbond_bb_sc": {"weight": 1.0, "description": "Backbone-sidechain hydrogen bonds"}, + "hbond_sc": {"weight": 1.0, "description": "Sidechain-sidechain hydrogen bonds"}, + "p_aa_pp": {"weight": 0.6, "description": "Ramachandran torsion preference"}, + "ref": {"weight": 1.0, "description": "Per-residue reference energy"} + } +} diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/references/petrobind/1ubq.pdb b/benchmarks/ProteinDesign/FixedBackboneDesign/references/petrobind/1ubq.pdb new file mode 100644 index 00000000..ac5211c1 --- /dev/null +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/references/petrobind/1ubq.pdb @@ -0,0 +1,970 @@ +HEADER CHROMOSOMAL PROTEIN 02-JAN-87 1UBQ +TITLE STRUCTURE OF UBIQUITIN REFINED AT 1.8 ANGSTROMS RESOLUTION +COMPND MOL_ID: 1; +COMPND 2 MOLECULE: UBIQUITIN; +COMPND 3 CHAIN: A; +COMPND 4 ENGINEERED: YES +SOURCE MOL_ID: 1; +SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; +SOURCE 3 ORGANISM_COMMON: HUMAN; +SOURCE 4 ORGANISM_TAXID: 9606 +KEYWDS CHROMOSOMAL PROTEIN +EXPDTA X-RAY DIFFRACTION +AUTHOR S.VIJAY-KUMAR,C.E.BUGG,W.J.COOK +REVDAT 6 14-FEB-24 1UBQ 1 REMARK +REVDAT 5 09-MAR-11 1UBQ 1 REMARK +REVDAT 4 24-FEB-09 1UBQ 1 VERSN +REVDAT 3 01-APR-03 1UBQ 1 JRNL +REVDAT 2 16-JUL-87 1UBQ 1 JRNL REMARK +REVDAT 1 16-APR-87 1UBQ 0 +JRNL AUTH S.VIJAY-KUMAR,C.E.BUGG,W.J.COOK +JRNL TITL STRUCTURE OF UBIQUITIN REFINED AT 1.8 A RESOLUTION. +JRNL REF J.MOL.BIOL. V. 194 531 1987 +JRNL REFN ISSN 0022-2836 +JRNL PMID 3041007 +JRNL DOI 10.1016/0022-2836(87)90679-6 +REMARK 1 +REMARK 1 REFERENCE 1 +REMARK 1 AUTH S.VIJAY-KUMAR,C.E.BUGG,K.D.WILKINSON,R.D.VIERSTRA, +REMARK 1 AUTH 2 P.M.HATFIELD,W.J.COOK +REMARK 1 TITL COMPARISON OF THE THREE-DIMENSIONAL STRUCTURES OF HUMAN, +REMARK 1 TITL 2 YEAST, AND OAT UBIQUITIN +REMARK 1 REF J.BIOL.CHEM. V. 262 6396 1987 +REMARK 1 REFN ISSN 0021-9258 +REMARK 1 REFERENCE 2 +REMARK 1 AUTH S.VIJAY-KUMAR,C.E.BUGG,K.D.WILKINSON,W.J.COOK +REMARK 1 TITL THREE-DIMENSIONAL STRUCTURE OF UBIQUITIN AT 2.8 ANGSTROMS +REMARK 1 TITL 2 RESOLUTION +REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 82 3582 1985 +REMARK 1 REFN ISSN 0027-8424 +REMARK 1 REFERENCE 3 +REMARK 1 AUTH W.J.COOK,F.L.SUDDATH,C.E.BUGG,G.GOLDSTEIN +REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY INVESTIGATION OF +REMARK 1 TITL 2 UBIQUITIN, A NON-HISTONE CHROMOSOMAL PROTEIN +REMARK 1 REF J.MOL.BIOL. V. 130 353 1979 +REMARK 1 REFN ISSN 0022-2836 +REMARK 1 REFERENCE 4 +REMARK 1 AUTH D.H.SCHLESINGER,G.GOLDSTEIN +REMARK 1 TITL MOLECULAR CONSERVATION OF 74 AMINO ACID SEQUENCE OF +REMARK 1 TITL 2 UBIQUITIN BETWEEN CATTLE AND MAN +REMARK 1 REF NATURE V. 255 423 1975 +REMARK 1 REFN ISSN 0028-0836 +REMARK 2 +REMARK 2 RESOLUTION. 1.80 ANGSTROMS. +REMARK 3 +REMARK 3 REFINEMENT. +REMARK 3 PROGRAM : PROLSQ +REMARK 3 AUTHORS : KONNERT,HENDRICKSON +REMARK 3 +REMARK 3 DATA USED IN REFINEMENT. +REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 +REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL +REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL +REMARK 3 COMPLETENESS FOR RANGE (%) : NULL +REMARK 3 NUMBER OF REFLECTIONS : NULL +REMARK 3 +REMARK 3 FIT TO DATA USED IN REFINEMENT. +REMARK 3 CROSS-VALIDATION METHOD : NULL +REMARK 3 FREE R VALUE TEST SET SELECTION : NULL +REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 +REMARK 3 R VALUE (WORKING SET) : NULL +REMARK 3 FREE R VALUE : NULL +REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL +REMARK 3 FREE R VALUE TEST SET COUNT : NULL +REMARK 3 +REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. +REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL +REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL +REMARK 3 FREE R VALUE (NO CUTOFF) : NULL +REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL +REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL +REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL +REMARK 3 +REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. +REMARK 3 PROTEIN ATOMS : 602 +REMARK 3 NUCLEIC ACID ATOMS : 0 +REMARK 3 HETEROGEN ATOMS : 0 +REMARK 3 SOLVENT ATOMS : 58 +REMARK 3 +REMARK 3 B VALUES. +REMARK 3 FROM WILSON PLOT (A**2) : NULL +REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL +REMARK 3 OVERALL ANISOTROPIC B VALUE. +REMARK 3 B11 (A**2) : NULL +REMARK 3 B22 (A**2) : NULL +REMARK 3 B33 (A**2) : NULL +REMARK 3 B12 (A**2) : NULL +REMARK 3 B13 (A**2) : NULL +REMARK 3 B23 (A**2) : NULL +REMARK 3 +REMARK 3 ESTIMATED COORDINATE ERROR. +REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL +REMARK 3 ESD FROM SIGMAA (A) : NULL +REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL +REMARK 3 +REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. +REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA +REMARK 3 BOND LENGTH (A) : 0.016 ; NULL +REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL +REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL +REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL +REMARK 3 +REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL +REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL +REMARK 3 +REMARK 3 NON-BONDED CONTACT RESTRAINTS. +REMARK 3 SINGLE TORSION (A) : NULL ; NULL +REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL +REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL +REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL +REMARK 3 +REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. +REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL +REMARK 3 PLANAR (DEGREES) : NULL ; NULL +REMARK 3 STAGGERED (DEGREES) : NULL ; NULL +REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL +REMARK 3 +REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA +REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL +REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL +REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL +REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL +REMARK 3 +REMARK 3 OTHER REFINEMENT REMARKS: NULL +REMARK 4 +REMARK 4 1UBQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 +REMARK 100 +REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. +REMARK 100 THE DEPOSITION ID IS D_1000176905. +REMARK 200 +REMARK 200 EXPERIMENTAL DETAILS +REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION +REMARK 200 DATE OF DATA COLLECTION : NULL +REMARK 200 TEMPERATURE (KELVIN) : NULL +REMARK 200 PH : NULL +REMARK 200 NUMBER OF CRYSTALS USED : NULL +REMARK 200 +REMARK 200 SYNCHROTRON (Y/N) : NULL +REMARK 200 RADIATION SOURCE : NULL +REMARK 200 BEAMLINE : NULL +REMARK 200 X-RAY GENERATOR MODEL : NULL +REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL +REMARK 200 WAVELENGTH OR RANGE (A) : NULL +REMARK 200 MONOCHROMATOR : NULL +REMARK 200 OPTICS : NULL +REMARK 200 +REMARK 200 DETECTOR TYPE : NULL +REMARK 200 DETECTOR MANUFACTURER : NULL +REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL +REMARK 200 DATA SCALING SOFTWARE : NULL +REMARK 200 +REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL +REMARK 200 RESOLUTION RANGE HIGH (A) : NULL +REMARK 200 RESOLUTION RANGE LOW (A) : NULL +REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL +REMARK 200 +REMARK 200 OVERALL. +REMARK 200 COMPLETENESS FOR RANGE (%) : NULL +REMARK 200 DATA REDUNDANCY : NULL +REMARK 200 R MERGE (I) : NULL +REMARK 200 R SYM (I) : NULL +REMARK 200 FOR THE DATA SET : NULL +REMARK 200 +REMARK 200 IN THE HIGHEST RESOLUTION SHELL. +REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL +REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL +REMARK 200 COMPLETENESS FOR SHELL (%) : NULL +REMARK 200 DATA REDUNDANCY IN SHELL : NULL +REMARK 200 R MERGE FOR SHELL (I) : NULL +REMARK 200 R SYM FOR SHELL (I) : NULL +REMARK 200 FOR SHELL : NULL +REMARK 200 +REMARK 200 DIFFRACTION PROTOCOL: NULL +REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL +REMARK 200 SOFTWARE USED: NULL +REMARK 200 STARTING MODEL: NULL +REMARK 200 +REMARK 200 REMARK: NULL +REMARK 280 +REMARK 280 CRYSTAL +REMARK 280 SOLVENT CONTENT, VS (%): 32.94 +REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 +REMARK 280 +REMARK 280 CRYSTALLIZATION CONDITIONS: NULL +REMARK 290 +REMARK 290 CRYSTALLOGRAPHIC SYMMETRY +REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 +REMARK 290 +REMARK 290 SYMOP SYMMETRY +REMARK 290 NNNMMM OPERATOR +REMARK 290 1555 X,Y,Z +REMARK 290 2555 -X+1/2,-Y,Z+1/2 +REMARK 290 3555 -X,Y+1/2,-Z+1/2 +REMARK 290 4555 X+1/2,-Y+1/2,-Z +REMARK 290 +REMARK 290 WHERE NNN -> OPERATOR NUMBER +REMARK 290 MMM -> TRANSLATION VECTOR +REMARK 290 +REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS +REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM +REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY +REMARK 290 RELATED MOLECULES. +REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 +REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 +REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 25.42000 +REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 +REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 14.47500 +REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.38500 +REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 14.47500 +REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.42000 +REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.38500 +REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 +REMARK 290 +REMARK 290 REMARK: NULL +REMARK 300 +REMARK 300 BIOMOLECULE: 1 +REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM +REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN +REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON +REMARK 300 BURIED SURFACE AREA. +REMARK 350 +REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN +REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE +REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS +REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND +REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. +REMARK 350 +REMARK 350 BIOMOLECULE: 1 +REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC +REMARK 350 APPLY THE FOLLOWING TO CHAINS: A +REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 +REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 +REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 +REMARK 500 +REMARK 500 GEOMETRY AND STEREOCHEMISTRY +REMARK 500 SUBTOPIC: CLOSE CONTACTS +REMARK 500 +REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC +REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 +REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A +REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 +REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE +REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. +REMARK 500 +REMARK 500 DISTANCE CUTOFF: +REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS +REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS +REMARK 500 +REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE +REMARK 500 OE2 GLU A 16 NH1 ARG A 72 1554 2.02 +REMARK 500 NZ LYS A 48 OXT GLY A 76 4467 2.16 +REMARK 500 +REMARK 500 REMARK: NULL +REMARK 500 +REMARK 500 GEOMETRY AND STEREOCHEMISTRY +REMARK 500 SUBTOPIC: COVALENT BOND ANGLES +REMARK 500 +REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES +REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE +REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN +REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). +REMARK 500 +REMARK 500 STANDARD TABLE: +REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) +REMARK 500 +REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 +REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 +REMARK 500 +REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 +REMARK 500 LEU A 15 CA - CB - CG ANGL. DEV. = 14.0 DEGREES +REMARK 500 ARG A 54 CD - NE - CZ ANGL. DEV. = 12.4 DEGREES +REMARK 500 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES +REMARK 500 +REMARK 500 REMARK: NULL +DBREF 1UBQ A 1 76 UNP P62988 UBIQ_HUMAN 1 76 +SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE +SEQRES 2 A 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL +SEQRES 3 A 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP +SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP +SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER +SEQRES 6 A 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY +FORMUL 2 HOH *58(H2 O) +HELIX 1 H1 ILE A 23 GLU A 34 1 12 +HELIX 2 H2 LEU A 56 TYR A 59 5 4 +SHEET 1 BET 5 GLY A 10 VAL A 17 0 +SHEET 2 BET 5 MET A 1 THR A 7 -1 +SHEET 3 BET 5 GLU A 64 ARG A 72 1 +SHEET 4 BET 5 GLN A 40 PHE A 45 -1 +SHEET 5 BET 5 LYS A 48 LEU A 50 -1 +CRYST1 50.840 42.770 28.950 90.00 90.00 90.00 P 21 21 21 4 +ORIGX1 1.000000 0.000000 0.000000 0.00000 +ORIGX2 0.000000 1.000000 0.000000 0.00000 +ORIGX3 0.000000 0.000000 1.000000 0.00000 +SCALE1 0.019670 0.000000 0.000000 0.00000 +SCALE2 0.000000 0.023381 0.000000 0.00000 +SCALE3 0.000000 0.000000 0.034542 0.00000 +ATOM 1 N MET A 1 27.340 24.430 2.614 1.00 9.67 N +ATOM 2 CA MET A 1 26.266 25.413 2.842 1.00 10.38 C +ATOM 3 C MET A 1 26.913 26.639 3.531 1.00 9.62 C +ATOM 4 O MET A 1 27.886 26.463 4.263 1.00 9.62 O +ATOM 5 CB MET A 1 25.112 24.880 3.649 1.00 13.77 C +ATOM 6 CG MET A 1 25.353 24.860 5.134 1.00 16.29 C +ATOM 7 SD MET A 1 23.930 23.959 5.904 1.00 17.17 S +ATOM 8 CE MET A 1 24.447 23.984 7.620 1.00 16.11 C +ATOM 9 N GLN A 2 26.335 27.770 3.258 1.00 9.27 N +ATOM 10 CA GLN A 2 26.850 29.021 3.898 1.00 9.07 C +ATOM 11 C GLN A 2 26.100 29.253 5.202 1.00 8.72 C +ATOM 12 O GLN A 2 24.865 29.024 5.330 1.00 8.22 O +ATOM 13 CB GLN A 2 26.733 30.148 2.905 1.00 14.46 C +ATOM 14 CG GLN A 2 26.882 31.546 3.409 1.00 17.01 C +ATOM 15 CD GLN A 2 26.786 32.562 2.270 1.00 20.10 C +ATOM 16 OE1 GLN A 2 27.783 33.160 1.870 1.00 21.89 O +ATOM 17 NE2 GLN A 2 25.562 32.733 1.806 1.00 19.49 N +ATOM 18 N ILE A 3 26.849 29.656 6.217 1.00 5.87 N +ATOM 19 CA ILE A 3 26.235 30.058 7.497 1.00 5.07 C +ATOM 20 C ILE A 3 26.882 31.428 7.862 1.00 4.01 C +ATOM 21 O ILE A 3 27.906 31.711 7.264 1.00 4.61 O +ATOM 22 CB ILE A 3 26.344 29.050 8.645 1.00 6.55 C +ATOM 23 CG1 ILE A 3 27.810 28.748 8.999 1.00 4.72 C +ATOM 24 CG2 ILE A 3 25.491 27.771 8.287 1.00 5.58 C +ATOM 25 CD1 ILE A 3 27.967 28.087 10.417 1.00 10.83 C +ATOM 26 N PHE A 4 26.214 32.097 8.771 1.00 4.55 N +ATOM 27 CA PHE A 4 26.772 33.436 9.197 1.00 4.68 C +ATOM 28 C PHE A 4 27.151 33.362 10.650 1.00 5.30 C +ATOM 29 O PHE A 4 26.350 32.778 11.395 1.00 5.58 O +ATOM 30 CB PHE A 4 25.695 34.498 8.946 1.00 4.83 C +ATOM 31 CG PHE A 4 25.288 34.609 7.499 1.00 7.97 C +ATOM 32 CD1 PHE A 4 24.147 33.966 7.038 1.00 6.69 C +ATOM 33 CD2 PHE A 4 26.136 35.346 6.640 1.00 8.34 C +ATOM 34 CE1 PHE A 4 23.812 34.031 5.677 1.00 9.10 C +ATOM 35 CE2 PHE A 4 25.810 35.392 5.267 1.00 10.61 C +ATOM 36 CZ PHE A 4 24.620 34.778 4.853 1.00 8.90 C +ATOM 37 N VAL A 5 28.260 33.943 11.096 1.00 4.44 N +ATOM 38 CA VAL A 5 28.605 33.965 12.503 1.00 3.87 C +ATOM 39 C VAL A 5 28.638 35.461 12.900 1.00 4.93 C +ATOM 40 O VAL A 5 29.522 36.103 12.320 1.00 6.84 O +ATOM 41 CB VAL A 5 29.963 33.317 12.814 1.00 2.99 C +ATOM 42 CG1 VAL A 5 30.211 33.394 14.304 1.00 5.28 C +ATOM 43 CG2 VAL A 5 29.957 31.838 12.352 1.00 9.13 C +ATOM 44 N LYS A 6 27.751 35.867 13.740 1.00 6.04 N +ATOM 45 CA LYS A 6 27.691 37.315 14.143 1.00 6.12 C +ATOM 46 C LYS A 6 28.469 37.475 15.420 1.00 6.57 C +ATOM 47 O LYS A 6 28.213 36.753 16.411 1.00 5.76 O +ATOM 48 CB LYS A 6 26.219 37.684 14.307 1.00 7.45 C +ATOM 49 CG LYS A 6 25.884 39.139 14.615 1.00 11.12 C +ATOM 50 CD LYS A 6 24.348 39.296 14.642 1.00 14.54 C +ATOM 51 CE LYS A 6 23.865 40.723 14.749 1.00 18.84 C +ATOM 52 NZ LYS A 6 22.375 40.720 14.907 1.00 20.55 N +ATOM 53 N THR A 7 29.426 38.430 15.446 1.00 7.41 N +ATOM 54 CA THR A 7 30.225 38.643 16.662 1.00 7.48 C +ATOM 55 C THR A 7 29.664 39.839 17.434 1.00 8.75 C +ATOM 56 O THR A 7 28.850 40.565 16.859 1.00 8.58 O +ATOM 57 CB THR A 7 31.744 38.879 16.299 1.00 9.61 C +ATOM 58 OG1 THR A 7 31.737 40.257 15.824 1.00 11.78 O +ATOM 59 CG2 THR A 7 32.260 37.969 15.171 1.00 9.17 C +ATOM 60 N LEU A 8 30.132 40.069 18.642 1.00 9.84 N +ATOM 61 CA LEU A 8 29.607 41.180 19.467 1.00 14.15 C +ATOM 62 C LEU A 8 30.075 42.538 18.984 1.00 17.37 C +ATOM 63 O LEU A 8 29.586 43.570 19.483 1.00 17.01 O +ATOM 64 CB LEU A 8 29.919 40.890 20.938 1.00 16.63 C +ATOM 65 CG LEU A 8 29.183 39.722 21.581 1.00 18.88 C +ATOM 66 CD1 LEU A 8 29.308 39.750 23.095 1.00 19.31 C +ATOM 67 CD2 LEU A 8 27.700 39.721 21.228 1.00 18.59 C +ATOM 68 N THR A 9 30.991 42.571 17.998 1.00 18.33 N +ATOM 69 CA THR A 9 31.422 43.940 17.553 1.00 19.24 C +ATOM 70 C THR A 9 30.755 44.351 16.277 1.00 19.48 C +ATOM 71 O THR A 9 31.207 45.268 15.566 1.00 23.14 O +ATOM 72 CB THR A 9 32.979 43.918 17.445 1.00 18.97 C +ATOM 73 OG1 THR A 9 33.174 43.067 16.265 1.00 20.24 O +ATOM 74 CG2 THR A 9 33.657 43.319 18.672 1.00 19.70 C +ATOM 75 N GLY A 10 29.721 43.673 15.885 1.00 19.43 N +ATOM 76 CA GLY A 10 28.978 43.960 14.678 1.00 18.74 C +ATOM 77 C GLY A 10 29.604 43.507 13.393 1.00 17.62 C +ATOM 78 O GLY A 10 29.219 43.981 12.301 1.00 19.74 O +ATOM 79 N LYS A 11 30.563 42.623 13.495 1.00 13.56 N +ATOM 80 CA LYS A 11 31.191 42.012 12.331 1.00 11.91 C +ATOM 81 C LYS A 11 30.459 40.666 12.130 1.00 10.18 C +ATOM 82 O LYS A 11 30.253 39.991 13.133 1.00 9.10 O +ATOM 83 CB LYS A 11 32.672 41.717 12.505 1.00 13.43 C +ATOM 84 CG LYS A 11 33.280 41.086 11.227 1.00 16.69 C +ATOM 85 CD LYS A 11 34.762 40.799 11.470 1.00 17.92 C +ATOM 86 CE LYS A 11 35.614 40.847 10.240 1.00 20.81 C +ATOM 87 NZ LYS A 11 35.100 40.073 9.101 1.00 21.93 N +ATOM 88 N THR A 12 30.163 40.338 10.886 1.00 9.63 N +ATOM 89 CA THR A 12 29.542 39.020 10.653 1.00 9.85 C +ATOM 90 C THR A 12 30.494 38.261 9.729 1.00 11.66 C +ATOM 91 O THR A 12 30.849 38.850 8.706 1.00 12.33 O +ATOM 92 CB THR A 12 28.113 39.049 10.015 1.00 10.85 C +ATOM 93 OG1 THR A 12 27.280 39.722 10.996 1.00 10.91 O +ATOM 94 CG2 THR A 12 27.588 37.635 9.715 1.00 9.63 C +ATOM 95 N ILE A 13 30.795 37.015 10.095 1.00 10.42 N +ATOM 96 CA ILE A 13 31.720 36.289 9.176 1.00 11.84 C +ATOM 97 C ILE A 13 30.955 35.211 8.459 1.00 10.55 C +ATOM 98 O ILE A 13 30.025 34.618 9.040 1.00 11.92 O +ATOM 99 CB ILE A 13 32.995 35.883 9.934 1.00 14.86 C +ATOM 100 CG1 ILE A 13 33.306 34.381 9.840 1.00 14.87 C +ATOM 101 CG2 ILE A 13 33.109 36.381 11.435 1.00 17.08 C +ATOM 102 CD1 ILE A 13 34.535 34.028 10.720 1.00 16.46 C +ATOM 103 N THR A 14 31.244 34.986 7.197 1.00 9.39 N +ATOM 104 CA THR A 14 30.505 33.884 6.512 1.00 9.63 C +ATOM 105 C THR A 14 31.409 32.680 6.446 1.00 11.20 C +ATOM 106 O THR A 14 32.619 32.812 6.125 1.00 11.63 O +ATOM 107 CB THR A 14 30.091 34.393 5.078 1.00 10.38 C +ATOM 108 OG1 THR A 14 31.440 34.513 4.487 1.00 16.30 O +ATOM 109 CG2 THR A 14 29.420 35.756 5.119 1.00 11.66 C +ATOM 110 N LEU A 15 30.884 31.485 6.666 1.00 8.29 N +ATOM 111 CA LEU A 15 31.677 30.275 6.639 1.00 9.03 C +ATOM 112 C LEU A 15 31.022 29.288 5.665 1.00 8.59 C +ATOM 113 O LEU A 15 29.809 29.395 5.545 1.00 7.79 O +ATOM 114 CB LEU A 15 31.562 29.686 8.045 1.00 11.08 C +ATOM 115 CG LEU A 15 32.631 29.444 9.060 1.00 15.79 C +ATOM 116 CD1 LEU A 15 33.814 30.390 9.030 1.00 15.88 C +ATOM 117 CD2 LEU A 15 31.945 29.449 10.436 1.00 15.27 C +ATOM 118 N GLU A 16 31.834 28.412 5.125 1.00 11.04 N +ATOM 119 CA GLU A 16 31.220 27.341 4.275 1.00 11.50 C +ATOM 120 C GLU A 16 31.440 26.079 5.080 1.00 10.13 C +ATOM 121 O GLU A 16 32.576 25.802 5.461 1.00 9.83 O +ATOM 122 CB GLU A 16 31.827 27.262 2.894 1.00 17.22 C +ATOM 123 CG GLU A 16 31.363 28.410 1.962 1.00 23.33 C +ATOM 124 CD GLU A 16 31.671 28.291 0.498 1.00 26.99 C +ATOM 125 OE1 GLU A 16 30.869 28.621 -0.366 1.00 28.86 O +ATOM 126 OE2 GLU A 16 32.835 27.861 0.278 1.00 28.90 O +ATOM 127 N VAL A 17 30.310 25.458 5.384 1.00 8.99 N +ATOM 128 CA VAL A 17 30.288 24.245 6.193 1.00 8.85 C +ATOM 129 C VAL A 17 29.279 23.227 5.641 1.00 8.04 C +ATOM 130 O VAL A 17 28.478 23.522 4.725 1.00 8.99 O +ATOM 131 CB VAL A 17 29.903 24.590 7.665 1.00 9.78 C +ATOM 132 CG1 VAL A 17 30.862 25.496 8.389 1.00 12.05 C +ATOM 133 CG2 VAL A 17 28.476 25.135 7.705 1.00 10.54 C +ATOM 134 N GLU A 18 29.380 22.057 6.232 1.00 7.29 N +ATOM 135 CA GLU A 18 28.468 20.940 5.980 1.00 7.08 C +ATOM 136 C GLU A 18 27.819 20.609 7.316 1.00 6.45 C +ATOM 137 O GLU A 18 28.449 20.674 8.360 1.00 5.28 O +ATOM 138 CB GLU A 18 29.213 19.697 5.506 1.00 10.28 C +ATOM 139 CG GLU A 18 29.728 19.755 4.060 1.00 12.65 C +ATOM 140 CD GLU A 18 28.754 20.061 2.978 1.00 14.15 C +ATOM 141 OE1 GLU A 18 27.546 19.992 2.985 1.00 14.33 O +ATOM 142 OE2 GLU A 18 29.336 20.423 1.904 1.00 18.17 O +ATOM 143 N PRO A 19 26.559 20.220 7.288 1.00 7.24 N +ATOM 144 CA PRO A 19 25.829 19.825 8.494 1.00 7.07 C +ATOM 145 C PRO A 19 26.541 18.732 9.251 1.00 6.65 C +ATOM 146 O PRO A 19 26.333 18.536 10.457 1.00 6.37 O +ATOM 147 CB PRO A 19 24.469 19.332 7.952 1.00 7.61 C +ATOM 148 CG PRO A 19 24.299 20.134 6.704 1.00 8.16 C +ATOM 149 CD PRO A 19 25.714 20.108 6.073 1.00 7.49 C +ATOM 150 N SER A 20 27.361 17.959 8.559 1.00 6.80 N +ATOM 151 CA SER A 20 28.054 16.835 9.210 1.00 6.28 C +ATOM 152 C SER A 20 29.258 17.318 9.984 1.00 8.45 C +ATOM 153 O SER A 20 29.930 16.477 10.606 1.00 7.26 O +ATOM 154 CB SER A 20 28.523 15.820 8.182 1.00 8.57 C +ATOM 155 OG SER A 20 28.946 16.445 6.967 1.00 11.13 O +ATOM 156 N ASP A 21 29.599 18.599 9.828 1.00 7.50 N +ATOM 157 CA ASP A 21 30.796 19.083 10.566 1.00 7.70 C +ATOM 158 C ASP A 21 30.491 19.162 12.040 1.00 7.08 C +ATOM 159 O ASP A 21 29.367 19.523 12.441 1.00 8.11 O +ATOM 160 CB ASP A 21 31.155 20.515 10.048 1.00 11.00 C +ATOM 161 CG ASP A 21 31.923 20.436 8.755 1.00 15.32 C +ATOM 162 OD1 ASP A 21 32.493 19.374 8.456 1.00 18.03 O +ATOM 163 OD2 ASP A 21 31.838 21.402 7.968 1.00 14.36 O +ATOM 164 N THR A 22 31.510 18.936 12.852 1.00 5.37 N +ATOM 165 CA THR A 22 31.398 19.064 14.286 1.00 6.01 C +ATOM 166 C THR A 22 31.593 20.553 14.655 1.00 8.01 C +ATOM 167 O THR A 22 32.159 21.311 13.861 1.00 8.11 O +ATOM 168 CB THR A 22 32.492 18.193 14.995 1.00 8.92 C +ATOM 169 OG1 THR A 22 33.778 18.739 14.516 1.00 10.22 O +ATOM 170 CG2 THR A 22 32.352 16.700 14.630 1.00 9.65 C +ATOM 171 N ILE A 23 31.113 20.863 15.860 1.00 8.32 N +ATOM 172 CA ILE A 23 31.288 22.201 16.417 1.00 9.92 C +ATOM 173 C ILE A 23 32.776 22.519 16.577 1.00 10.01 C +ATOM 174 O ILE A 23 33.233 23.659 16.384 1.00 8.71 O +ATOM 175 CB ILE A 23 30.520 22.300 17.764 1.00 10.78 C +ATOM 176 CG1 ILE A 23 29.006 22.043 17.442 1.00 11.38 C +ATOM 177 CG2 ILE A 23 30.832 23.699 18.358 1.00 10.90 C +ATOM 178 CD1 ILE A 23 28.407 22.948 16.366 1.00 12.30 C +ATOM 179 N GLU A 24 33.548 21.526 16.950 1.00 9.54 N +ATOM 180 CA GLU A 24 35.031 21.722 17.069 1.00 11.81 C +ATOM 181 C GLU A 24 35.615 22.190 15.759 1.00 11.14 C +ATOM 182 O GLU A 24 36.532 23.046 15.724 1.00 10.62 O +ATOM 183 CB GLU A 24 35.667 20.383 17.447 1.00 19.24 C +ATOM 184 CG GLU A 24 37.128 20.293 17.872 1.00 27.76 C +ATOM 185 CD GLU A 24 37.561 18.851 18.082 1.00 32.92 C +ATOM 186 OE1 GLU A 24 37.758 18.024 17.195 1.00 34.80 O +ATOM 187 OE2 GLU A 24 37.628 18.599 19.313 1.00 36.51 O +ATOM 188 N ASN A 25 35.139 21.624 14.662 1.00 9.43 N +ATOM 189 CA ASN A 25 35.590 21.945 13.302 1.00 10.96 C +ATOM 190 C ASN A 25 35.238 23.382 12.920 1.00 9.68 C +ATOM 191 O ASN A 25 36.066 24.109 12.333 1.00 9.33 O +ATOM 192 CB ASN A 25 35.064 20.957 12.255 1.00 16.78 C +ATOM 193 CG ASN A 25 35.541 21.418 10.871 1.00 22.31 C +ATOM 194 OD1 ASN A 25 36.772 21.623 10.676 1.00 25.66 O +ATOM 195 ND2 ASN A 25 34.628 21.595 9.920 1.00 24.70 N +ATOM 196 N VAL A 26 34.007 23.745 13.250 1.00 6.52 N +ATOM 197 CA VAL A 26 33.533 25.097 12.978 1.00 5.53 C +ATOM 198 C VAL A 26 34.441 26.099 13.684 1.00 4.42 C +ATOM 199 O VAL A 26 34.883 27.090 13.093 1.00 3.40 O +ATOM 200 CB VAL A 26 32.060 25.257 13.364 1.00 3.86 C +ATOM 201 CG1 VAL A 26 31.684 26.749 13.342 1.00 7.25 C +ATOM 202 CG2 VAL A 26 31.152 24.421 12.477 1.00 8.12 C +ATOM 203 N LYS A 27 34.734 25.822 14.949 1.00 2.64 N +ATOM 204 CA LYS A 27 35.596 26.715 15.736 1.00 4.14 C +ATOM 205 C LYS A 27 36.975 26.826 15.107 1.00 5.58 C +ATOM 206 O LYS A 27 37.579 27.926 15.159 1.00 4.11 O +ATOM 207 CB LYS A 27 35.715 26.203 17.172 1.00 3.97 C +ATOM 208 CG LYS A 27 34.343 26.445 17.898 1.00 7.45 C +ATOM 209 CD LYS A 27 34.509 26.077 19.360 1.00 9.02 C +ATOM 210 CE LYS A 27 33.206 26.311 20.122 1.00 12.90 C +ATOM 211 NZ LYS A 27 33.455 25.910 21.546 1.00 15.47 N +ATOM 212 N ALA A 28 37.499 25.743 14.571 1.00 6.61 N +ATOM 213 CA ALA A 28 38.794 25.761 13.880 1.00 7.74 C +ATOM 214 C ALA A 28 38.728 26.591 12.611 1.00 9.17 C +ATOM 215 O ALA A 28 39.704 27.346 12.277 1.00 11.45 O +ATOM 216 CB ALA A 28 39.285 24.336 13.566 1.00 7.68 C +ATOM 217 N LYS A 29 37.633 26.543 11.867 1.00 8.96 N +ATOM 218 CA LYS A 29 37.471 27.391 10.668 1.00 7.90 C +ATOM 219 C LYS A 29 37.441 28.882 11.052 1.00 6.92 C +ATOM 220 O LYS A 29 38.020 29.772 10.382 1.00 6.87 O +ATOM 221 CB LYS A 29 36.193 27.058 9.911 1.00 10.28 C +ATOM 222 CG LYS A 29 36.153 25.620 9.409 1.00 14.94 C +ATOM 223 CD LYS A 29 34.758 25.280 8.900 1.00 19.69 C +ATOM 224 CE LYS A 29 34.793 24.264 7.767 1.00 22.63 C +ATOM 225 NZ LYS A 29 34.914 24.944 6.441 1.00 24.98 N +ATOM 226 N ILE A 30 36.811 29.170 12.192 1.00 4.57 N +ATOM 227 CA ILE A 30 36.731 30.570 12.645 1.00 5.58 C +ATOM 228 C ILE A 30 38.148 30.981 13.069 1.00 7.26 C +ATOM 229 O ILE A 30 38.544 32.150 12.856 1.00 9.46 O +ATOM 230 CB ILE A 30 35.708 30.776 13.806 1.00 5.36 C +ATOM 231 CG1 ILE A 30 34.228 30.630 13.319 1.00 2.94 C +ATOM 232 CG2 ILE A 30 35.874 32.138 14.512 1.00 2.78 C +ATOM 233 CD1 ILE A 30 33.284 30.504 14.552 1.00 2.00 C +ATOM 234 N GLN A 31 38.883 30.110 13.713 1.00 7.06 N +ATOM 235 CA GLN A 31 40.269 30.508 14.115 1.00 8.67 C +ATOM 236 C GLN A 31 41.092 30.808 12.851 1.00 10.90 C +ATOM 237 O GLN A 31 41.828 31.808 12.681 1.00 9.63 O +ATOM 238 CB GLN A 31 40.996 29.399 14.865 1.00 9.12 C +ATOM 239 CG GLN A 31 42.445 29.848 15.182 1.00 10.76 C +ATOM 240 CD GLN A 31 43.090 28.828 16.095 1.00 13.78 C +ATOM 241 OE1 GLN A 31 42.770 27.655 15.906 1.00 14.48 O +ATOM 242 NE2 GLN A 31 43.898 29.252 17.050 1.00 14.76 N +ATOM 243 N ASP A 32 41.001 29.878 11.931 1.00 10.93 N +ATOM 244 CA ASP A 32 41.718 30.022 10.643 1.00 14.01 C +ATOM 245 C ASP A 32 41.399 31.338 9.967 1.00 14.04 C +ATOM 246 O ASP A 32 42.260 32.036 9.381 1.00 13.39 O +ATOM 247 CB ASP A 32 41.398 28.780 9.810 1.00 18.01 C +ATOM 248 CG ASP A 32 42.626 28.557 8.928 1.00 24.33 C +ATOM 249 OD1 ASP A 32 43.666 28.262 9.539 1.00 26.29 O +ATOM 250 OD2 ASP A 32 42.430 28.812 7.728 1.00 25.17 O +ATOM 251 N LYS A 33 40.117 31.750 9.988 1.00 14.22 N +ATOM 252 CA LYS A 33 39.808 32.994 9.233 1.00 14.00 C +ATOM 253 C LYS A 33 39.837 34.271 9.995 1.00 12.37 C +ATOM 254 O LYS A 33 40.164 35.323 9.345 1.00 12.17 O +ATOM 255 CB LYS A 33 38.615 32.801 8.320 1.00 18.62 C +ATOM 256 CG LYS A 33 37.220 32.822 8.827 1.00 24.00 C +ATOM 257 CD LYS A 33 36.351 33.613 7.838 1.00 27.61 C +ATOM 258 CE LYS A 33 36.322 32.944 6.477 1.00 27.64 C +ATOM 259 NZ LYS A 33 35.768 33.945 5.489 1.00 30.06 N +ATOM 260 N GLU A 34 39.655 34.335 11.285 1.00 10.11 N +ATOM 261 CA GLU A 34 39.676 35.547 12.072 1.00 10.07 C +ATOM 262 C GLU A 34 40.675 35.527 13.200 1.00 9.32 C +ATOM 263 O GLU A 34 40.814 36.528 13.911 1.00 11.61 O +ATOM 264 CB GLU A 34 38.290 35.814 12.698 1.00 14.77 C +ATOM 265 CG GLU A 34 37.156 35.985 11.688 1.00 18.75 C +ATOM 266 CD GLU A 34 37.192 37.361 11.033 1.00 22.28 C +ATOM 267 OE1 GLU A 34 37.519 38.360 11.645 1.00 21.95 O +ATOM 268 OE2 GLU A 34 36.861 37.320 9.822 1.00 25.19 O +ATOM 269 N GLY A 35 41.317 34.393 13.432 1.00 7.22 N +ATOM 270 CA GLY A 35 42.345 34.269 14.431 1.00 6.29 C +ATOM 271 C GLY A 35 41.949 34.076 15.842 1.00 6.93 C +ATOM 272 O GLY A 35 42.829 34.000 16.739 1.00 7.41 O +ATOM 273 N ILE A 36 40.642 33.916 16.112 1.00 5.86 N +ATOM 274 CA ILE A 36 40.226 33.716 17.509 1.00 6.07 C +ATOM 275 C ILE A 36 40.449 32.278 17.945 1.00 6.36 C +ATOM 276 O ILE A 36 39.936 31.336 17.315 1.00 6.18 O +ATOM 277 CB ILE A 36 38.693 34.106 17.595 1.00 7.47 C +ATOM 278 CG1 ILE A 36 38.471 35.546 17.045 1.00 8.52 C +ATOM 279 CG2 ILE A 36 38.146 33.932 19.027 1.00 7.36 C +ATOM 280 CD1 ILE A 36 36.958 35.746 16.680 1.00 9.49 C +ATOM 281 N PRO A 37 41.189 32.085 19.031 1.00 8.65 N +ATOM 282 CA PRO A 37 41.461 30.751 19.594 1.00 9.18 C +ATOM 283 C PRO A 37 40.168 30.026 19.918 1.00 9.85 C +ATOM 284 O PRO A 37 39.264 30.662 20.521 1.00 8.51 O +ATOM 285 CB PRO A 37 42.195 31.142 20.913 1.00 11.42 C +ATOM 286 CG PRO A 37 42.904 32.414 20.553 1.00 9.27 C +ATOM 287 CD PRO A 37 41.822 33.188 19.813 1.00 8.33 C +ATOM 288 N PRO A 38 40.059 28.758 19.607 1.00 8.71 N +ATOM 289 CA PRO A 38 38.817 28.020 19.889 1.00 9.08 C +ATOM 290 C PRO A 38 38.421 28.048 21.341 1.00 9.28 C +ATOM 291 O PRO A 38 37.213 28.036 21.704 1.00 6.50 O +ATOM 292 CB PRO A 38 39.090 26.629 19.325 1.00 10.31 C +ATOM 293 CG PRO A 38 40.082 26.904 18.198 1.00 10.81 C +ATOM 294 CD PRO A 38 41.035 27.909 18.879 1.00 12.00 C +ATOM 295 N ASP A 39 39.374 28.090 22.240 1.00 11.20 N +ATOM 296 CA ASP A 39 39.063 28.063 23.695 1.00 14.96 C +ATOM 297 C ASP A 39 38.365 29.335 24.159 1.00 13.99 C +ATOM 298 O ASP A 39 37.684 29.390 25.221 1.00 13.75 O +ATOM 299 CB ASP A 39 40.340 27.692 24.468 1.00 24.16 C +ATOM 300 CG ASP A 39 40.559 28.585 25.675 1.00 31.06 C +ATOM 301 OD1 ASP A 39 40.716 29.809 25.456 1.00 35.55 O +ATOM 302 OD2 ASP A 39 40.549 28.090 26.840 1.00 34.22 O +ATOM 303 N GLN A 40 38.419 30.373 23.341 1.00 11.60 N +ATOM 304 CA GLN A 40 37.738 31.637 23.712 1.00 10.76 C +ATOM 305 C GLN A 40 36.334 31.742 23.087 1.00 8.01 C +ATOM 306 O GLN A 40 35.574 32.618 23.483 1.00 8.96 O +ATOM 307 CB GLN A 40 38.528 32.854 23.182 1.00 11.14 C +ATOM 308 CG GLN A 40 39.919 32.854 23.840 1.00 14.85 C +ATOM 309 CD GLN A 40 40.760 34.036 23.394 1.00 16.11 C +ATOM 310 OE1 GLN A 40 41.975 34.008 23.624 1.00 20.52 O +ATOM 311 NE2 GLN A 40 40.140 35.007 22.775 1.00 18.16 N +ATOM 312 N GLN A 41 36.000 30.860 22.172 1.00 6.52 N +ATOM 313 CA GLN A 41 34.738 30.875 21.473 1.00 3.87 C +ATOM 314 C GLN A 41 33.589 30.189 22.181 1.00 4.79 C +ATOM 315 O GLN A 41 33.580 29.009 22.499 1.00 6.34 O +ATOM 316 CB GLN A 41 34.876 30.237 20.066 1.00 4.20 C +ATOM 317 CG GLN A 41 36.012 30.860 19.221 1.00 3.20 C +ATOM 318 CD GLN A 41 36.083 30.194 17.875 1.00 4.89 C +ATOM 319 OE1 GLN A 41 35.048 29.702 17.393 1.00 5.21 O +ATOM 320 NE2 GLN A 41 37.228 30.126 17.233 1.00 7.13 N +ATOM 321 N ARG A 42 32.478 30.917 22.269 1.00 5.73 N +ATOM 322 CA ARG A 42 31.200 30.329 22.780 1.00 6.97 C +ATOM 323 C ARG A 42 30.210 30.509 21.650 1.00 7.15 C +ATOM 324 O ARG A 42 29.978 31.726 21.269 1.00 7.33 O +ATOM 325 CB ARG A 42 30.847 30.931 24.118 1.00 13.23 C +ATOM 326 CG ARG A 42 29.412 30.796 24.598 1.00 21.27 C +ATOM 327 CD ARG A 42 29.271 31.314 26.016 1.00 26.14 C +ATOM 328 NE ARG A 42 27.875 31.317 26.443 1.00 32.26 N +ATOM 329 CZ ARG A 42 27.132 32.423 26.574 1.00 34.32 C +ATOM 330 NH1 ARG A 42 27.630 33.656 26.461 1.00 35.30 N +ATOM 331 NH2 ARG A 42 25.810 32.299 26.732 1.00 36.39 N +ATOM 332 N LEU A 43 29.694 29.436 21.054 1.00 4.65 N +ATOM 333 CA LEU A 43 28.762 29.573 19.906 1.00 3.51 C +ATOM 334 C LEU A 43 27.331 29.317 20.364 1.00 5.56 C +ATOM 335 O LEU A 43 27.101 28.346 21.097 1.00 4.19 O +ATOM 336 CB LEU A 43 29.151 28.655 18.755 1.00 3.74 C +ATOM 337 CG LEU A 43 30.416 28.912 17.980 1.00 6.32 C +ATOM 338 CD1 LEU A 43 30.738 27.693 17.122 1.00 9.55 C +ATOM 339 CD2 LEU A 43 30.205 30.168 17.129 1.00 6.41 C +ATOM 340 N ILE A 44 26.436 30.232 20.004 1.00 4.58 N +ATOM 341 CA ILE A 44 25.034 30.170 20.401 1.00 5.55 C +ATOM 342 C ILE A 44 24.101 30.149 19.196 1.00 5.46 C +ATOM 343 O ILE A 44 24.196 30.948 18.287 1.00 6.04 O +ATOM 344 CB ILE A 44 24.639 31.426 21.286 1.00 6.80 C +ATOM 345 CG1 ILE A 44 25.646 31.670 22.421 1.00 10.31 C +ATOM 346 CG2 ILE A 44 23.181 31.309 21.824 1.00 7.39 C +ATOM 347 CD1 ILE A 44 25.778 30.436 23.356 1.00 13.90 C +ATOM 348 N PHE A 45 23.141 29.187 19.241 1.00 6.75 N +ATOM 349 CA PHE A 45 22.126 29.062 18.183 1.00 4.70 C +ATOM 350 C PHE A 45 20.835 28.629 18.904 1.00 6.34 C +ATOM 351 O PHE A 45 20.821 27.734 19.749 1.00 5.45 O +ATOM 352 CB PHE A 45 22.494 28.057 17.109 1.00 5.51 C +ATOM 353 CG PHE A 45 21.447 27.869 16.026 1.00 5.98 C +ATOM 354 CD1 PHE A 45 21.325 28.813 15.005 1.00 6.86 C +ATOM 355 CD2 PHE A 45 20.638 26.735 16.053 1.00 5.87 C +ATOM 356 CE1 PHE A 45 20.369 28.648 14.001 1.00 6.68 C +ATOM 357 CE2 PHE A 45 19.677 26.539 15.051 1.00 6.64 C +ATOM 358 CZ PHE A 45 19.593 27.465 14.021 1.00 6.84 C +ATOM 359 N ALA A 46 19.810 29.378 18.578 1.00 6.53 N +ATOM 360 CA ALA A 46 18.443 29.143 19.083 1.00 7.15 C +ATOM 361 C ALA A 46 18.453 28.941 20.591 1.00 9.00 C +ATOM 362 O ALA A 46 17.860 27.994 21.128 1.00 11.15 O +ATOM 363 CB ALA A 46 17.864 27.977 18.346 1.00 8.99 C +ATOM 364 N GLY A 47 19.172 29.808 21.243 1.00 9.35 N +ATOM 365 CA GLY A 47 19.399 29.894 22.655 1.00 11.68 C +ATOM 366 C GLY A 47 20.083 28.729 23.321 1.00 11.14 C +ATOM 367 O GLY A 47 19.991 28.584 24.561 1.00 13.93 O +ATOM 368 N LYS A 48 20.801 27.931 22.578 1.00 10.47 N +ATOM 369 CA LYS A 48 21.550 26.796 23.133 1.00 8.82 C +ATOM 370 C LYS A 48 23.046 27.087 22.913 1.00 7.68 C +ATOM 371 O LYS A 48 23.383 27.627 21.870 1.00 6.47 O +ATOM 372 CB LYS A 48 21.242 25.519 22.391 1.00 9.74 C +ATOM 373 CG LYS A 48 19.762 25.077 22.455 1.00 14.14 C +ATOM 374 CD LYS A 48 19.634 23.885 21.531 1.00 16.32 C +ATOM 375 CE LYS A 48 18.791 24.221 20.313 1.00 20.04 C +ATOM 376 NZ LYS A 48 17.440 24.655 20.827 1.00 23.92 N +ATOM 377 N GLN A 49 23.880 26.727 23.851 1.00 8.89 N +ATOM 378 CA GLN A 49 25.349 26.872 23.643 1.00 7.18 C +ATOM 379 C GLN A 49 25.743 25.586 22.922 1.00 8.23 C +ATOM 380 O GLN A 49 25.325 24.489 23.378 1.00 9.70 O +ATOM 381 CB GLN A 49 26.070 27.025 24.960 1.00 11.67 C +ATOM 382 CG GLN A 49 27.553 27.356 24.695 1.00 15.82 C +ATOM 383 CD GLN A 49 28.262 27.576 26.020 1.00 20.21 C +ATOM 384 OE1 GLN A 49 29.189 26.840 26.335 1.00 23.23 O +ATOM 385 NE2 GLN A 49 27.777 28.585 26.739 1.00 20.67 N +ATOM 386 N LEU A 50 26.465 25.689 21.833 1.00 6.51 N +ATOM 387 CA LEU A 50 26.826 24.521 21.012 1.00 7.41 C +ATOM 388 C LEU A 50 27.994 23.781 21.643 1.00 8.27 C +ATOM 389 O LEU A 50 28.904 24.444 22.098 1.00 8.34 O +ATOM 390 CB LEU A 50 27.043 24.992 19.571 1.00 7.13 C +ATOM 391 CG LEU A 50 25.931 25.844 18.959 1.00 7.53 C +ATOM 392 CD1 LEU A 50 26.203 26.083 17.471 1.00 8.14 C +ATOM 393 CD2 LEU A 50 24.577 25.190 19.079 1.00 9.11 C +ATOM 394 N GLU A 51 27.942 22.448 21.648 1.00 9.43 N +ATOM 395 CA GLU A 51 29.015 21.657 22.288 1.00 11.90 C +ATOM 396 C GLU A 51 29.942 21.106 21.240 1.00 11.49 C +ATOM 397 O GLU A 51 29.470 20.677 20.190 1.00 9.88 O +ATOM 398 CB GLU A 51 28.348 20.540 23.066 1.00 16.56 C +ATOM 399 CG GLU A 51 29.247 19.456 23.705 1.00 26.06 C +ATOM 400 CD GLU A 51 28.722 19.047 25.066 1.00 29.86 C +ATOM 401 OE1 GLU A 51 29.139 18.132 25.746 1.00 32.13 O +ATOM 402 OE2 GLU A 51 27.777 19.842 25.367 1.00 33.44 O +ATOM 403 N ASP A 52 31.233 21.090 21.459 1.00 12.71 N +ATOM 404 CA ASP A 52 32.262 20.670 20.514 1.00 16.56 C +ATOM 405 C ASP A 52 32.128 19.364 19.750 1.00 15.83 C +ATOM 406 O ASP A 52 32.546 19.317 18.558 1.00 17.21 O +ATOM 407 CB ASP A 52 33.638 20.716 21.242 1.00 21.05 C +ATOM 408 CG ASP A 52 34.174 22.129 21.354 1.00 25.12 C +ATOM 409 OD1 ASP A 52 35.252 22.322 21.958 1.00 28.37 O +ATOM 410 OD2 ASP A 52 33.544 23.086 20.883 1.00 25.82 O +ATOM 411 N GLY A 53 31.697 18.311 20.406 1.00 15.00 N +ATOM 412 CA GLY A 53 31.568 16.962 19.825 1.00 11.77 C +ATOM 413 C GLY A 53 30.320 16.698 19.051 1.00 11.10 C +ATOM 414 O GLY A 53 30.198 15.657 18.366 1.00 11.25 O +ATOM 415 N ARG A 54 29.340 17.594 19.076 1.00 8.53 N +ATOM 416 CA ARG A 54 28.108 17.439 18.276 1.00 9.05 C +ATOM 417 C ARG A 54 28.375 17.999 16.887 1.00 8.96 C +ATOM 418 O ARG A 54 29.326 18.786 16.690 1.00 11.60 O +ATOM 419 CB ARG A 54 26.926 18.191 18.892 1.00 7.97 C +ATOM 420 CG ARG A 54 26.621 17.799 20.352 1.00 9.62 C +ATOM 421 CD ARG A 54 26.010 16.370 20.280 1.00 12.20 C +ATOM 422 NE ARG A 54 26.975 15.521 20.942 1.00 18.23 N +ATOM 423 CZ ARG A 54 27.603 14.423 20.655 1.00 22.08 C +ATOM 424 NH1 ARG A 54 27.479 13.733 19.537 1.00 23.38 N +ATOM 425 NH2 ARG A 54 28.519 13.967 21.550 1.00 25.50 N +ATOM 426 N THR A 55 27.510 17.689 15.954 1.00 9.05 N +ATOM 427 CA THR A 55 27.574 18.192 14.563 1.00 9.03 C +ATOM 428 C THR A 55 26.482 19.280 14.432 1.00 8.15 C +ATOM 429 O THR A 55 25.609 19.388 15.287 1.00 5.91 O +ATOM 430 CB THR A 55 27.299 17.055 13.533 1.00 11.15 C +ATOM 431 OG1 THR A 55 25.925 16.611 13.913 1.00 11.95 O +ATOM 432 CG2 THR A 55 28.236 15.864 13.558 1.00 11.71 C +ATOM 433 N LEU A 56 26.585 20.063 13.378 1.00 6.91 N +ATOM 434 CA LEU A 56 25.594 21.109 13.072 1.00 8.29 C +ATOM 435 C LEU A 56 24.241 20.436 12.857 1.00 8.05 C +ATOM 436 O LEU A 56 23.264 20.951 13.329 1.00 10.17 O +ATOM 437 CB LEU A 56 26.084 21.888 11.833 1.00 6.60 C +ATOM 438 CG LEU A 56 27.426 22.616 11.902 1.00 7.73 C +ATOM 439 CD1 LEU A 56 27.718 23.341 10.578 1.00 9.85 C +ATOM 440 CD2 LEU A 56 27.380 23.721 12.955 1.00 8.64 C +ATOM 441 N SER A 57 24.240 19.233 12.246 1.00 8.92 N +ATOM 442 CA SER A 57 22.924 18.583 12.025 1.00 9.00 C +ATOM 443 C SER A 57 22.229 18.244 13.325 1.00 9.44 C +ATOM 444 O SER A 57 20.963 18.253 13.395 1.00 10.91 O +ATOM 445 CB SER A 57 23.059 17.326 11.154 1.00 10.32 C +ATOM 446 OG SER A 57 23.914 16.395 11.755 1.00 13.59 O +ATOM 447 N ASP A 58 22.997 17.978 14.366 1.00 9.11 N +ATOM 448 CA ASP A 58 22.418 17.638 15.693 1.00 7.91 C +ATOM 449 C ASP A 58 21.460 18.737 16.163 1.00 9.12 C +ATOM 450 O ASP A 58 20.497 18.506 16.900 1.00 8.61 O +ATOM 451 CB ASP A 58 23.461 17.331 16.741 1.00 8.41 C +ATOM 452 CG ASP A 58 24.184 16.016 16.619 1.00 11.50 C +ATOM 453 OD1 ASP A 58 25.303 15.894 17.152 1.00 10.05 O +ATOM 454 OD2 ASP A 58 23.572 15.107 15.975 1.00 11.70 O +ATOM 455 N TYR A 59 21.846 19.954 15.905 1.00 7.97 N +ATOM 456 CA TYR A 59 21.079 21.149 16.251 1.00 8.45 C +ATOM 457 C TYR A 59 20.142 21.590 15.149 1.00 10.98 C +ATOM 458 O TYR A 59 19.499 22.645 15.321 1.00 12.95 O +ATOM 459 CB TYR A 59 22.085 22.254 16.581 1.00 7.94 C +ATOM 460 CG TYR A 59 22.945 21.951 17.785 1.00 6.91 C +ATOM 461 CD1 TYR A 59 24.272 21.544 17.644 1.00 4.59 C +ATOM 462 CD2 TYR A 59 22.437 22.157 19.065 1.00 6.98 C +ATOM 463 CE1 TYR A 59 25.052 21.285 18.776 1.00 5.39 C +ATOM 464 CE2 TYR A 59 23.204 21.907 20.192 1.00 6.52 C +ATOM 465 CZ TYR A 59 24.517 21.470 20.030 1.00 6.76 C +ATOM 466 OH TYR A 59 25.248 21.302 21.191 1.00 7.63 O +ATOM 467 N ASN A 60 19.993 20.884 14.049 1.00 12.38 N +ATOM 468 CA ASN A 60 19.065 21.352 12.999 1.00 13.94 C +ATOM 469 C ASN A 60 19.442 22.745 12.510 1.00 14.16 C +ATOM 470 O ASN A 60 18.571 23.610 12.289 1.00 14.26 O +ATOM 471 CB ASN A 60 17.586 21.282 13.461 1.00 19.23 C +ATOM 472 CG ASN A 60 16.576 21.258 12.315 1.00 22.65 C +ATOM 473 OD1 ASN A 60 15.440 21.819 12.378 1.00 25.45 O +ATOM 474 ND2 ASN A 60 16.924 20.586 11.216 1.00 24.09 N +ATOM 475 N ILE A 61 20.717 22.964 12.260 1.00 11.08 N +ATOM 476 CA ILE A 61 21.184 24.263 11.690 1.00 11.78 C +ATOM 477 C ILE A 61 21.110 24.111 10.173 1.00 13.74 C +ATOM 478 O ILE A 61 21.841 23.198 9.686 1.00 14.60 O +ATOM 479 CB ILE A 61 22.650 24.516 12.172 1.00 11.80 C +ATOM 480 CG1 ILE A 61 22.662 24.819 13.699 1.00 11.56 C +ATOM 481 CG2 ILE A 61 23.376 25.645 11.409 1.00 13.29 C +ATOM 482 CD1 ILE A 61 24.123 24.981 14.195 1.00 11.42 C +ATOM 483 N GLN A 62 20.291 24.875 9.507 1.00 13.97 N +ATOM 484 CA GLN A 62 20.081 24.773 8.033 1.00 15.52 C +ATOM 485 C GLN A 62 20.822 25.914 7.332 1.00 13.94 C +ATOM 486 O GLN A 62 21.323 26.830 8.008 1.00 12.15 O +ATOM 487 CB GLN A 62 18.599 24.736 7.727 1.00 19.53 C +ATOM 488 CG GLN A 62 17.819 23.434 7.900 1.00 26.38 C +ATOM 489 CD GLN A 62 16.509 23.529 7.116 1.00 30.61 C +ATOM 490 OE1 GLN A 62 15.446 22.980 7.433 1.00 33.23 O +ATOM 491 NE2 GLN A 62 16.539 24.293 6.009 1.00 32.71 N +ATOM 492 N LYS A 63 20.924 25.862 6.006 1.00 11.73 N +ATOM 493 CA LYS A 63 21.656 26.847 5.240 1.00 11.97 C +ATOM 494 C LYS A 63 21.127 28.240 5.574 1.00 10.41 C +ATOM 495 O LYS A 63 19.958 28.465 5.842 1.00 9.59 O +ATOM 496 CB LYS A 63 21.631 26.642 3.731 1.00 13.73 C +ATOM 497 CG LYS A 63 20.210 26.423 3.175 1.00 16.98 C +ATOM 498 CD LYS A 63 20.268 26.589 1.656 1.00 20.19 C +ATOM 499 CE LYS A 63 19.202 25.857 0.891 1.00 23.42 C +ATOM 500 NZ LYS A 63 17.884 26.544 1.075 1.00 25.97 N +ATOM 501 N GLU A 64 22.099 29.163 5.605 1.00 10.04 N +ATOM 502 CA GLU A 64 21.907 30.563 5.881 1.00 10.94 C +ATOM 503 C GLU A 64 21.466 30.953 7.261 1.00 9.74 C +ATOM 504 O GLU A 64 21.066 32.112 7.533 1.00 9.42 O +ATOM 505 CB GLU A 64 21.023 31.223 4.784 1.00 18.31 C +ATOM 506 CG GLU A 64 21.861 31.342 3.474 1.00 24.16 C +ATOM 507 CD GLU A 64 21.156 30.726 2.311 1.00 29.00 C +ATOM 508 OE1 GLU A 64 19.942 30.793 2.170 1.00 31.72 O +ATOM 509 OE2 GLU A 64 21.954 30.152 1.535 1.00 32.61 O +ATOM 510 N SER A 65 21.674 30.034 8.191 1.00 6.85 N +ATOM 511 CA SER A 65 21.419 30.253 9.620 1.00 6.90 C +ATOM 512 C SER A 65 22.504 31.228 10.136 1.00 4.72 C +ATOM 513 O SER A 65 23.579 31.321 9.554 1.00 3.91 O +ATOM 514 CB SER A 65 21.637 28.923 10.353 1.00 7.28 C +ATOM 515 OG SER A 65 20.544 28.047 10.059 1.00 10.56 O +ATOM 516 N THR A 66 22.241 31.873 11.241 1.00 4.48 N +ATOM 517 CA THR A 66 23.212 32.762 11.891 1.00 3.80 C +ATOM 518 C THR A 66 23.509 32.224 13.290 1.00 4.60 C +ATOM 519 O THR A 66 22.544 31.942 14.034 1.00 5.33 O +ATOM 520 CB THR A 66 22.699 34.267 11.985 1.00 2.85 C +ATOM 521 OG1 THR A 66 22.495 34.690 10.589 1.00 2.15 O +ATOM 522 CG2 THR A 66 23.727 35.131 12.722 1.00 3.40 C +ATOM 523 N LEU A 67 24.790 32.021 13.618 1.00 4.17 N +ATOM 524 CA LEU A 67 25.149 31.609 14.980 1.00 3.85 C +ATOM 525 C LEU A 67 25.698 32.876 15.669 1.00 3.80 C +ATOM 526 O LEU A 67 26.158 33.730 14.894 1.00 5.54 O +ATOM 527 CB LEU A 67 26.310 30.594 14.967 1.00 7.18 C +ATOM 528 CG LEU A 67 26.290 29.480 13.960 1.00 9.67 C +ATOM 529 CD1 LEU A 67 27.393 28.442 14.229 1.00 8.12 C +ATOM 530 CD2 LEU A 67 24.942 28.807 13.952 1.00 11.66 C +ATOM 531 N HIS A 68 25.621 32.945 16.950 1.00 2.94 N +ATOM 532 CA HIS A 68 26.179 34.127 17.650 1.00 4.17 C +ATOM 533 C HIS A 68 27.475 33.651 18.304 1.00 5.32 C +ATOM 534 O HIS A 68 27.507 32.587 18.958 1.00 7.70 O +ATOM 535 CB HIS A 68 25.214 34.565 18.780 1.00 5.57 C +ATOM 536 CG HIS A 68 23.978 35.121 18.126 1.00 9.95 C +ATOM 537 ND1 HIS A 68 23.853 36.432 17.781 1.00 13.74 N +ATOM 538 CD2 HIS A 68 22.824 34.514 17.782 1.00 12.79 C +ATOM 539 CE1 HIS A 68 22.674 36.627 17.200 1.00 14.75 C +ATOM 540 NE2 HIS A 68 22.045 35.455 17.173 1.00 16.30 N +ATOM 541 N LEU A 69 28.525 34.447 18.189 1.00 5.29 N +ATOM 542 CA LEU A 69 29.801 34.145 18.829 1.00 3.97 C +ATOM 543 C LEU A 69 30.052 35.042 20.004 1.00 5.07 C +ATOM 544 O LEU A 69 30.105 36.305 19.788 1.00 4.34 O +ATOM 545 CB LEU A 69 30.925 34.304 17.753 1.00 6.08 C +ATOM 546 CG LEU A 69 32.345 34.183 18.358 1.00 7.37 C +ATOM 547 CD1 LEU A 69 32.555 32.783 18.870 1.00 6.87 C +ATOM 548 CD2 LEU A 69 33.361 34.491 17.245 1.00 9.96 C +ATOM 549 N VAL A 70 30.124 34.533 21.191 1.00 4.29 N +ATOM 550 CA VAL A 70 30.479 35.369 22.374 1.00 6.26 C +ATOM 551 C VAL A 70 31.901 34.910 22.728 1.00 9.22 C +ATOM 552 O VAL A 70 32.190 33.696 22.635 1.00 9.36 O +ATOM 553 CB VAL A 70 29.472 35.181 23.498 1.00 8.69 C +ATOM 554 CG1 VAL A 70 29.821 35.957 24.765 1.00 9.76 C +ATOM 555 CG2 VAL A 70 28.049 35.454 23.071 1.00 8.54 C +ATOM 556 N LEU A 71 32.763 35.831 23.090 1.00 12.71 N +ATOM 557 CA LEU A 71 34.145 35.472 23.481 1.00 16.06 C +ATOM 558 C LEU A 71 34.239 35.353 24.979 1.00 18.09 C +ATOM 559 O LEU A 71 33.707 36.197 25.728 1.00 19.26 O +ATOM 560 CB LEU A 71 35.114 36.564 22.907 1.00 17.10 C +ATOM 561 CG LEU A 71 35.926 35.979 21.737 1.00 19.37 C +ATOM 562 CD1 LEU A 71 35.003 35.084 20.920 1.00 17.51 C +ATOM 563 CD2 LEU A 71 36.533 37.087 20.917 1.00 19.57 C +ATOM 564 N ARG A 72 34.930 34.384 25.451 1.00 21.47 N +ATOM 565 CA ARG A 72 35.161 34.174 26.896 1.00 25.83 C +ATOM 566 C ARG A 72 36.671 34.296 27.089 1.00 27.74 C +ATOM 567 O ARG A 72 37.305 33.233 26.795 1.00 30.65 O +ATOM 568 CB ARG A 72 34.717 32.760 27.286 1.00 28.49 C +ATOM 569 CG ARG A 72 35.752 32.054 28.160 1.00 31.79 C +ATOM 570 CD ARG A 72 35.612 30.577 28.044 1.00 34.05 C +ATOM 571 NE ARG A 72 35.040 30.252 26.730 1.00 35.08 N +ATOM 572 CZ ARG A 72 34.338 29.103 26.650 1.00 34.67 C +ATOM 573 NH1 ARG A 72 34.110 28.437 27.768 1.00 35.02 N +ATOM 574 NH2 ARG A 72 34.014 28.657 25.457 1.00 34.97 N +ATOM 575 N LEU A 73 37.197 35.397 27.513 0.45 28.93 N +ATOM 576 CA LEU A 73 38.668 35.502 27.680 0.45 30.76 C +ATOM 577 C LEU A 73 39.076 34.931 29.031 0.45 32.18 C +ATOM 578 O LEU A 73 38.297 34.946 29.996 0.45 32.31 O +ATOM 579 CB LEU A 73 39.080 36.941 27.406 0.45 30.53 C +ATOM 580 CG LEU A 73 39.502 37.340 26.002 0.45 30.16 C +ATOM 581 CD1 LEU A 73 38.684 36.647 24.923 0.45 29.57 C +ATOM 582 CD2 LEU A 73 39.337 38.854 25.862 0.45 29.11 C +ATOM 583 N ARG A 74 40.294 34.412 29.045 0.45 33.82 N +ATOM 584 CA ARG A 74 40.873 33.802 30.253 0.45 35.33 C +ATOM 585 C ARG A 74 41.765 34.829 30.944 0.45 36.22 C +ATOM 586 O ARG A 74 42.945 34.994 30.583 0.45 36.70 O +ATOM 587 CB ARG A 74 41.651 32.529 29.923 0.45 36.91 C +ATOM 588 CG ARG A 74 41.608 31.444 30.989 0.45 38.62 C +ATOM 589 CD ARG A 74 41.896 30.080 30.456 0.45 39.75 C +ATOM 590 NE ARG A 74 43.311 29.735 30.563 0.45 41.13 N +ATOM 591 CZ ARG A 74 44.174 29.905 29.554 0.45 41.91 C +ATOM 592 NH1 ARG A 74 43.754 30.312 28.356 0.45 42.75 N +ATOM 593 NH2 ARG A 74 45.477 29.726 29.763 0.45 41.93 N +ATOM 594 N GLY A 75 41.165 35.531 31.898 0.25 36.31 N +ATOM 595 CA GLY A 75 41.845 36.550 32.686 0.25 36.07 C +ATOM 596 C GLY A 75 41.251 37.941 32.588 0.25 36.16 C +ATOM 597 O GLY A 75 41.102 38.523 31.500 0.25 36.26 O +ATOM 598 N GLY A 76 40.946 38.472 33.757 0.25 36.05 N +ATOM 599 CA GLY A 76 40.373 39.813 33.944 0.25 36.19 C +ATOM 600 C GLY A 76 40.031 39.992 35.432 0.25 36.20 C +ATOM 601 O GLY A 76 38.933 40.525 35.687 0.25 36.13 O +ATOM 602 OXT GLY A 76 40.862 39.575 36.251 0.25 36.27 O +TER 603 GLY A 76 +HETATM 604 O HOH A 77 45.747 30.081 19.708 1.00 12.43 O +HETATM 605 O HOH A 78 19.168 31.868 17.050 1.00 12.65 O +HETATM 606 O HOH A 79 32.010 38.387 19.636 1.00 12.83 O +HETATM 607 O HOH A 80 42.084 27.361 21.953 1.00 22.27 O +HETATM 608 O HOH A 81 21.314 20.644 8.719 1.00 18.33 O +HETATM 609 O HOH A 82 31.965 38.637 3.699 1.00 31.69 O +HETATM 610 O HOH A 83 27.707 15.908 4.653 1.00 20.30 O +HETATM 611 O HOH A 84 19.969 32.720 14.769 1.00 10.14 O +HETATM 612 O HOH A 85 29.847 13.577 10.864 1.00 29.65 O +HETATM 613 O HOH A 86 23.893 27.864 1.501 1.00 23.48 O +HETATM 614 O HOH A 87 19.638 23.312 4.775 1.00 18.40 O +HETATM 615 O HOH A 88 34.628 29.369 4.779 1.00 26.17 O +HETATM 616 O HOH A 89 42.240 24.744 25.707 1.00 31.34 O +HETATM 617 O HOH A 90 30.290 42.500 8.820 1.00 16.49 O +HETATM 618 O HOH A 91 24.512 39.162 10.841 1.00 13.14 O +HETATM 619 O HOH A 92 26.557 43.450 19.940 1.00 19.38 O +HETATM 620 O HOH A 93 42.535 22.385 13.872 1.00 29.35 O +HETATM 621 O HOH A 94 42.440 26.381 12.686 1.00 29.46 O +HETATM 622 O HOH A 95 22.651 14.457 13.085 1.00 22.07 O +HETATM 623 O HOH A 96 35.325 26.551 23.202 1.00 15.20 O +HETATM 624 O HOH A 97 23.629 20.940 3.146 1.00 15.45 O +HETATM 625 O HOH A 98 25.928 21.774 2.325 1.00 13.70 O +HETATM 626 O HOH A 99 33.388 21.973 5.659 1.00 24.89 O +HETATM 627 O HOH A 100 18.326 23.911 17.697 1.00 24.10 O +HETATM 628 O HOH A 101 18.160 27.072 10.662 1.00 20.76 O +HETATM 629 O HOH A 102 34.746 17.167 18.219 1.00 32.86 O +HETATM 630 O HOH A 103 19.801 32.364 20.210 1.00 21.09 O +HETATM 631 O HOH A 104 30.285 26.829 22.191 1.00 8.56 O +HETATM 632 O HOH A 105 44.612 32.306 16.961 1.00 7.69 O +HETATM 633 O HOH A 106 16.287 25.999 13.142 0.78 28.90 O +HETATM 634 O HOH A 107 27.101 42.135 15.494 0.51 23.36 O +HETATM 635 O HOH A 108 37.209 23.795 21.367 0.74 27.88 O +HETATM 636 O HOH A 109 19.582 32.034 -0.685 0.49 22.24 O +HETATM 637 O HOH A 110 28.824 25.094 0.886 0.77 36.99 O +HETATM 638 O HOH A 111 25.146 19.162 25.323 0.87 36.70 O +HETATM 639 O HOH A 112 20.747 37.769 14.674 0.85 29.64 O +HETATM 640 O HOH A 113 16.035 17.841 8.765 0.61 23.89 O +HETATM 641 O HOH A 114 35.712 46.814 12.926 0.48 27.11 O +HETATM 642 O HOH A 115 15.570 27.475 7.482 0.51 24.18 O +HETATM 643 O HOH A 116 33.447 21.075 2.918 0.59 26.03 O +HETATM 644 O HOH A 117 41.116 39.021 13.061 0.63 22.39 O +HETATM 645 O HOH A 118 32.346 13.689 18.912 0.48 24.09 O +HETATM 646 O HOH A 119 31.197 13.048 7.920 0.71 29.54 O +HETATM 647 O HOH A 120 42.853 39.375 29.308 0.64 46.90 O +HETATM 648 O HOH A 121 39.646 23.959 9.699 0.41 18.25 O +HETATM 649 O HOH A 122 34.405 45.181 13.420 0.87 26.13 O +HETATM 650 O HOH A 123 26.517 24.300 27.592 0.41 21.02 O +HETATM 651 O HOH A 124 40.740 38.734 9.602 0.45 16.60 O +HETATM 652 O HOH A 125 31.494 18.276 23.170 0.67 26.53 O +HETATM 653 O HOH A 126 37.752 30.947 1.059 0.87 32.52 O +HETATM 654 O HOH A 127 31.771 16.941 7.511 0.64 15.94 O +HETATM 655 O HOH A 128 41.628 24.537 10.145 0.57 22.53 O +HETATM 656 O HOH A 129 28.988 22.175 -1.744 0.56 29.32 O +HETATM 657 O HOH A 130 14.882 16.539 10.692 0.53 24.82 O +HETATM 658 O HOH A 131 32.589 40.385 7.523 0.36 26.01 O +HETATM 659 O HOH A 132 38.363 30.369 5.579 0.49 35.45 O +HETATM 660 O HOH A 133 27.841 46.062 17.589 0.81 32.15 O +HETATM 661 O HOH A 134 37.667 43.421 17.000 0.50 33.32 O +MASTER 260 0 0 2 5 0 0 6 660 1 0 6 +END diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/scripts/init.py b/benchmarks/ProteinDesign/FixedBackboneDesign/scripts/init.py new file mode 100644 index 00000000..81faffcf --- /dev/null +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/scripts/init.py @@ -0,0 +1,160 @@ +#!/usr/bin/env python3 +""" +FixedBackboneDesign baseline solution. + +This file is the target of agent evolution. Code inside EVOLVE-BLOCK +can be modified by the agent; everything outside is read-only. + +CLI contract: + --prepared-input Path to prepared PDB (with design position metadata) + --solution-output Path to write the designed PDB +""" + +from __future__ import annotations + +import argparse +import json +import sys +from pathlib import Path +from typing import Any + + +# --------------------------------------------------------------------------- +# Read-only utilities (CLI contract, I/O) +# --------------------------------------------------------------------------- + +def load_json(path: str | Path) -> dict[str, Any]: + with Path(path).open() as f: + return json.load(f) + + +def dump_json(path: str | Path, payload: dict[str, Any]) -> None: + target = Path(path) + target.parent.mkdir(parents=True, exist_ok=True) + with target.open("w") as f: + json.dump(payload, f, indent=2, sort_keys=True) + + +def load_design_positions(prepared_pdb: str | Path) -> list[int]: + """ + Read design positions from the meta JSON accompanying the prepared PDB. + The meta file is at the same path but with .meta.json extension. + """ + p = Path(prepared_pdb) + meta_path = p.with_suffix(".pdb.meta.json") + if not meta_path.exists(): + meta_path = p.with_suffix(".meta.json") + if meta_path.exists(): + meta = load_json(meta_path) + return list(meta.get("design_positions", [])) + raise FileNotFoundError( + f"Meta file not found at {p.with_suffix('.pdb.meta.json')} or {p.with_suffix('.meta.json')}. " + f"Ensure evaluator.prepare() was called first." + ) + + +# EVOLVE-BLOCK-START +# --------------------------------------------------------------------------- +# Editable region — agent may modify the design algorithm below +# --------------------------------------------------------------------------- + +import pyrosetta +from pyrosetta.rosetta.core.pack.task import TaskFactory +from pyrosetta.rosetta.core.pack.task.operation import PreventRepacking +from pyrosetta.rosetta.protocols.minimization_packing import PackRotamersMover + + +def design_sequence( + prepared_pdb: str | Path, + solution_output: str | Path, + design_positions: list[int], +) -> dict[str, Any]: + """ + Fixed-backbone sequence design using PyRosetta PackRotamersMover. + + This is a basic baseline: one round of design with default options. + Improvements could include: + - Multiple design rounds with iterations + - Monte Carlo simulated annealing + - Backbone flexibility (small shear moves) + - Custom rotamer sampling with extra rotamers + """ + pyrosetta.init(silent=True) + pyrosetta.rosetta.basic.random.init_random_generators(42, "mt19937") + + # Load the prepared PDB + pose = pyrosetta.pose_from_file(str(prepared_pdb)) + scorefxn = pyrosetta.get_fa_scorefxn() + + # Create a PackerTask for sequence design + # By default, all positions are designable with all 20 canonical AAs + tf = TaskFactory() + task = tf.create_task_and_apply_taskoperations(pose) + + # Configure per-residue behavior + for i in range(1, pose.total_residue() + 1): + if i in design_positions: + # Allow repacking (side chain optimization) at design positions + # Default behavior: all 20 AAs allowed + pass + else: + # Do not change non-design positions + task.nonconst_residue_task(i).prevent_repacking() + + # Run Packer with the configured task (not the factory) + packer = PackRotamersMover() + packer.score_function(scorefxn) + packer.task(task) + packer.apply(pose) + + # Score the designed pose + final_energy = scorefxn(pose) + + # Write output PDB + output_path = Path(solution_output) + output_path.parent.mkdir(parents=True, exist_ok=True) + pose.dump_pdb(str(output_path)) + + # Collect metadata + result = { + "final_energy": round(float(final_energy), 6), + "n_designed_positions": len(design_positions), + "solver": "packrotamers_single_round", + "design_positions": sorted(design_positions), + } + return result + + +# EVOLVE-BLOCK-END +# --------------------------------------------------------------------------- +# End of editable region +# --------------------------------------------------------------------------- + + +# --------------------------------------------------------------------------- +# Read-only main entry point +# --------------------------------------------------------------------------- + +def main() -> None: + parser = argparse.ArgumentParser( + description="FixedBackboneDesign baseline — design protein sequence" + ) + parser.add_argument("--prepared-input", required=True, help="Prepared PDB file") + parser.add_argument("--solution-output", required=True, help="Output PDB path") + args = parser.parse_args() + + design_positions = load_design_positions(args.prepared_input) + + result = design_sequence( + prepared_pdb=args.prepared_input, + solution_output=args.solution_output, + design_positions=design_positions, + ) + + # Print summary + print(f"[init] Designed {result['n_designed_positions']} positions, " + f"final energy: {result['final_energy']:.4f}") + + +if __name__ == "__main__": + main() diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/verification/docker/Dockerfile b/benchmarks/ProteinDesign/FixedBackboneDesign/verification/docker/Dockerfile new file mode 100644 index 00000000..2b31752d --- /dev/null +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/verification/docker/Dockerfile @@ -0,0 +1,10 @@ +FROM rosettacommons/rosetta:serial + +# Set working directory +WORKDIR /workspace + +# Verify PyRosetta is available +RUN python3 -c "import pyrosetta; pyrosetta.init(silent=True); print('PyRosetta ready: ' + pyrosetta.__version__)" + +# Default command +CMD ["python3"] diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/verification/evaluator.py b/benchmarks/ProteinDesign/FixedBackboneDesign/verification/evaluator.py new file mode 100644 index 00000000..baa0d941 --- /dev/null +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/verification/evaluator.py @@ -0,0 +1,389 @@ +#!/usr/bin/env python3 +""" +PyRosetta-based evaluator for FixedBackboneDesign task. + +Usage (CONTRIBUTING.md test command format): + python verification/evaluator.py scripts/init.py + +Usage (step-by-step for local development): + python verification/evaluator.py prepare --raw-task data/raw_task.json --prepared-output outputs/prepared.pdb + python verification/evaluator.py evaluate --native outputs/prepared.pdb --candidate outputs/solution.pdb --result-output outputs/result.json +""" + +from __future__ import annotations + +import argparse +import hashlib +import json +import math +import subprocess +import sys +from pathlib import Path +from typing import Any + +INVALID_COMBINED_SCORE = -1e18 +_REFERENCE_AMINO_ACIDS = { + "ALA", "ARG", "ASN", "ASP", "CYS", "GLN", "GLU", "GLY", + "HIS", "ILE", "LEU", "LYS", "MET", "PHE", "PRO", + "SER", "THR", "TRP", "TYR", "VAL", +} + + +# --------------------------------------------------------------------------- +# Read-only utilities +# --------------------------------------------------------------------------- + +def load_json(path: str | Path) -> dict[str, Any]: + with Path(path).open() as f: + return json.load(f) + + +def dump_json(path: str | Path, payload: dict[str, Any]) -> None: + target = Path(path) + target.parent.mkdir(parents=True, exist_ok=True) + with target.open("w") as f: + json.dump(payload, f, indent=2, sort_keys=True) + + +def _hash_file(path: str | Path) -> str: + """SHA-256 hash of a file. Used to detect unauthorized reference modifications.""" + h = hashlib.sha256() + with open(path, "rb") as f: + for chunk in iter(lambda: f.read(65536), b""): + h.update(chunk) + return h.hexdigest() + + +# --------------------------------------------------------------------------- +# Constraint verification +# --------------------------------------------------------------------------- + +def _verify_constraints(native_pose, candidate_pose, design_positions: list[int]) -> tuple[bool, str]: + """ + Verify that the candidate satisfies FixedBackboneDesign constraints. + + Checks: + 1. Same number of residues + 2. Non-design positions: same amino acid type + 3. Non-design positions: backbone atoms (N, CA, C, O) unchanged + 4. Design positions: only standard amino acids + """ + # 1. Residue count + if native_pose.total_residue() != candidate_pose.total_residue(): + return False, ( + f"residue count mismatch: native={native_pose.total_residue()}, " + f"candidate={candidate_pose.total_residue()}" + ) + + design_set = set(design_positions) + backbone_atoms = {"N", "CA", "C", "O"} + + for i in range(1, native_pose.total_residue() + 1): + native_res = native_pose.residue(i) + candidate_res = candidate_pose.residue(i) + + if i in design_set: + # Design positions: only standard amino acids allowed + res_name = candidate_res.name3() + if res_name not in _REFERENCE_AMINO_ACIDS: + return False, f"non-standard amino acid at design position {i}: {res_name}" + else: + # Non-design positions: amino acid type must be preserved + if native_res.name3() != candidate_res.name3(): + return False, ( + f"unexpected mutation at non-design position {i}: " + f"{native_res.name3()} -> {candidate_res.name3()}" + ) + + # Backbone atom coordinates must not move + for atom_name in backbone_atoms: + if native_res.has(atom_name) and candidate_res.has(atom_name): + native_xyz = native_res.xyz(atom_name) + candidate_xyz = candidate_res.xyz(atom_name) + dist = native_xyz.distance(candidate_xyz) + if dist > 0.01: + return False, ( + f"backbone atom {atom_name} moved at position {i}: " + f"{dist:.6f} Å (threshold: 0.01 Å)" + ) + + return True, "" + + +# --------------------------------------------------------------------------- +# Prepare: load raw_task.json, load PDB, create a prepared reference PDB +# --------------------------------------------------------------------------- + +def prepare(raw_task_path: str | Path, prepared_output: str | Path) -> None: + """ + Read raw_task.json, load the PDB, and output a prepared PDB file. + The prepared PDB serves as the reference (native) structure. + """ + import pyrosetta + pyrosetta.init(silent=True) + pyrosetta.rosetta.basic.random.init_random_generators(42, "mt19937") + + task = load_json(raw_task_path) + task_root = Path(raw_task_path).resolve().parent.parent + pdb_path = Path(task["pdb_path"]) + if not pdb_path.is_absolute(): + pdb_path = task_root / pdb_path + + design_positions = task["design_positions"] + task_config = task.get("task_config", {}) + + # Load the native structure + pose = pyrosetta.pose_from_file(str(pdb_path)) + + # Repack native side chains to get a baseline energy + scorefxn = pyrosetta.get_fa_scorefxn() + tf = pyrosetta.rosetta.core.pack.task.TaskFactory() + tf.push_back(pyrosetta.rosetta.core.pack.task.operation.RestrictToRepacking()) + packer = pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover() + packer.score_function(scorefxn) + packer.task_factory(tf) + packer.apply(pose) + + baseline_energy = scorefxn(pose) + + # Dump the repacked native pose as the prepared reference PDB + output_path = Path(prepared_output) + output_path.parent.mkdir(parents=True, exist_ok=True) + pose.dump_pdb(str(output_path)) + + meta = { + "baseline_energy": round(baseline_energy, 6), + "design_positions": design_positions, + "n_design_positions": len(design_positions), + "pdb_source": task.get("pdb_id", str(pdb_path.name)), + "native_sequence": task.get("native_sequence", ""), + "energy_function": task.get("energy_function", "ref2015"), + "task_config": task_config, + } + meta_path = Path(prepared_output).with_suffix(".meta.json") + dump_json(meta_path, meta) + print(f"[evaluator] Prepared reference: {output_path}") + print(f"[evaluator] Baseline energy: {baseline_energy:.4f}") + + +# --------------------------------------------------------------------------- +# Evaluate: score the candidate PDB against the native reference +# --------------------------------------------------------------------------- + +def evaluate_candidate( + native_pdb: str | Path, + candidate_pdb: str | Path, + design_positions: list[int] | None = None, +) -> dict[str, Any]: + """ + Score a designed PDB using PyRosetta ref2015 and verify task constraints. + + Returns: + dict with keys: valid, combined_score, total_energy, native_energy, + improvement, and individual energy terms + """ + import pyrosetta + pyrosetta.init(silent=True) + pyrosetta.rosetta.basic.random.init_random_generators(42, "mt19937") + + scorefxn = pyrosetta.get_fa_scorefxn() + + # Score native + native_pose = pyrosetta.pose_from_file(str(native_pdb)) + native_energy = scorefxn(native_pose) + + # Score candidate + candidate_pose = pyrosetta.pose_from_file(str(candidate_pdb)) + + # Verify task constraints before scoring + if design_positions is not None: + valid, msg = _verify_constraints(native_pose, candidate_pose, design_positions) + if not valid: + return { + "valid": False, + "combined_score": INVALID_COMBINED_SCORE, + "error_message": msg, + "native_energy": round(native_energy, 6), + "total_energy": 0.0, + } + + candidate_energy = scorefxn(candidate_pose) + + # Collect metrics + metrics: dict[str, Any] = {"valid": True} + metrics["native_energy"] = round(native_energy, 6) + metrics["total_energy"] = round(candidate_energy, 6) + metrics["improvement"] = round(native_energy - candidate_energy, 6) + + if abs(native_energy) > 1e-6: + metrics["combined_score"] = round((native_energy - candidate_energy) / abs(native_energy), 6) + else: + metrics["combined_score"] = 0.0 + + # Energy terms + native_energies = native_pose.energies() + candidate_energies = candidate_pose.energies() + score_types = [ + (pyrosetta.rosetta.core.scoring.ScoreType.fa_atr, "fa_atr"), + (pyrosetta.rosetta.core.scoring.ScoreType.fa_rep, "fa_rep"), + (pyrosetta.rosetta.core.scoring.ScoreType.fa_sol, "fa_sol"), + (pyrosetta.rosetta.core.scoring.ScoreType.fa_elec, "fa_elec"), + (pyrosetta.rosetta.core.scoring.ScoreType.hbond_bb_sc, "hbond_bb_sc"), + (pyrosetta.rosetta.core.scoring.ScoreType.hbond_sc, "hbond_sc"), + (pyrosetta.rosetta.core.scoring.ScoreType.p_aa_pp, "p_aa_pp"), + (pyrosetta.rosetta.core.scoring.ScoreType.ref, "ref"), + ] + for st, name in score_types: + try: + metrics[f"native_{name}"] = round(float(native_energies.total_energies()[st]), 6) + metrics[name] = round(float(candidate_energies.total_energies()[st]), 6) + except Exception: + pass + + # NaN/Inf check + for key in ("total_energy", "native_energy"): + val = metrics.get(key, 0.0) + if math.isnan(val) or math.isinf(val): + metrics["valid"] = False + metrics["combined_score"] = INVALID_COMBINED_SCORE + + return metrics + + +def evaluate( + native_pdb: str | Path, + candidate_pdb: str | Path, + result_output: str | Path, + design_positions: list[int] | None = None, +) -> None: + """Evaluate designed sequence and write result JSON.""" + metrics = evaluate_candidate(native_pdb, candidate_pdb, design_positions) + dump_json(result_output, metrics) + print(f"[evaluator] total_energy={metrics.get('total_energy', 0):.4f} " + f"improvement={metrics.get('improvement', 0):.4f} " + f"valid={metrics.get('valid', False)}") + + +# --------------------------------------------------------------------------- +# Full pipeline +# --------------------------------------------------------------------------- + +def run_candidate_and_evaluate(script_path: str | Path) -> int: + """Full automatic pipeline matching CONTRIBUTING.md test command format.""" + evaluator_dir = Path(__file__).resolve().parent + task_dir = evaluator_dir.parent + raw_task = task_dir / "data" / "raw_task.json" + outputs_dir = task_dir / "outputs" + outputs_dir.mkdir(exist_ok=True) + + prepared_pdb = outputs_dir / "prepared.pdb" + solution_pdb = outputs_dir / "solution.pdb" + metrics_path = task_dir / "metrics.json" + + # Step 1: Prepare + print(f"[evaluator] Preparing from {raw_task}") + prepare(raw_task, prepared_pdb) + + # Record reference file hash before candidate runs + ref_hash_before = _hash_file(prepared_pdb) + + # Read design positions for constraint verification + meta_path = prepared_pdb.with_suffix(".pdb.meta.json") + if not meta_path.exists(): + meta_path = prepared_pdb.with_suffix(".meta.json") + design_positions: list[int] = [] + if meta_path.exists(): + meta = load_json(meta_path) + design_positions = list(meta.get("design_positions", [])) + + # Step 2: Run candidate + print(f"[evaluator] Running candidate: {script_path}") + try: + result = subprocess.run( + [sys.executable, str(script_path), + "--prepared-input", str(prepared_pdb), + "--solution-output", str(solution_pdb)], + capture_output=True, + text=True, + timeout=300, + cwd=str(task_dir), + ) + print(result.stdout[-2000:] if len(result.stdout) > 2000 else result.stdout) + if result.stderr: + print(f"[evaluator] candidate stderr:\n{result.stderr[-2000:]}", file=sys.stderr) + except subprocess.TimeoutExpired: + print("[evaluator] ERROR: candidate timed out (300s)") + metrics = { + "valid": False, + "combined_score": INVALID_COMBINED_SCORE, + "total_energy": 0.0, + "error_message": "candidate timed out", + } + dump_json(metrics_path, metrics) + print(json.dumps(metrics)) + return 1 + except FileNotFoundError: + print(f"[evaluator] ERROR: candidate script not found: {script_path}") + return 1 + + # Verify reference file was not modified by candidate + ref_hash_after = _hash_file(prepared_pdb) + if ref_hash_before != ref_hash_after: + print("[evaluator] ERROR: reference file was modified by candidate") + metrics = { + "valid": False, + "combined_score": INVALID_COMBINED_SCORE, + "error_message": "reference file was modified by candidate", + } + dump_json(metrics_path, metrics) + print(json.dumps(metrics)) + return 1 + + # Step 3: Evaluate with constraint verification + print(f"[evaluator] Evaluating designed structure") + metrics = evaluate_candidate(prepared_pdb, solution_pdb, design_positions) + metrics["returncode"] = result.returncode + if result.returncode != 0: + metrics["valid"] = False + metrics["combined_score"] = INVALID_COMBINED_SCORE + metrics["error_message"] = f"candidate returned non-zero exit code: {result.returncode}" + + # Step 4: Write metrics.json + dump_json(metrics_path, metrics) + print(json.dumps(metrics)) + return 0 if metrics.get("valid", False) else 1 + + +# --------------------------------------------------------------------------- +# CLI entry point +# --------------------------------------------------------------------------- + +def main() -> int: + if len(sys.argv) == 2 and not sys.argv[1].startswith("--"): + return run_candidate_and_evaluate(sys.argv[1]) + + parser = argparse.ArgumentParser(description="PyRosetta evaluator for FixedBackboneDesign") + subparsers = parser.add_subparsers(dest="command", required=True) + + p_prep = subparsers.add_parser("prepare", help="Prepare reference PDB from raw task") + p_prep.add_argument("--raw-task", required=True) + p_prep.add_argument("--prepared-output", required=True) + + p_eval = subparsers.add_parser("evaluate", help="Evaluate designed PDB") + p_eval.add_argument("--native", required=True) + p_eval.add_argument("--candidate", required=True) + p_eval.add_argument("--result-output", required=True) + p_eval.add_argument("--design-positions", nargs="*", type=int, default=None, + help="Optional list of allowed design positions for constraint check") + + args = parser.parse_args() + + if args.command == "prepare": + prepare(args.raw_task, args.prepared_output) + elif args.command == "evaluate": + evaluate(args.native, args.candidate, args.result_output, args.design_positions) + return 0 + + +if __name__ == "__main__": + sys.exit(main()) diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/verification/requirements.txt b/benchmarks/ProteinDesign/FixedBackboneDesign/verification/requirements.txt new file mode 100644 index 00000000..53383abb --- /dev/null +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/verification/requirements.txt @@ -0,0 +1,6 @@ +# PyRosetta - install from RosettaCommons quarterly release channel: +# pip install pyrosetta --find-links https://west.rosettacommons.org/pyrosetta/quarterly/release +# +# Or use the official Docker image which has PyRosetta pre-installed: +# docker pull rosettacommons/rosetta:serial +pyrosetta>=2025.0 diff --git a/benchmarks/ProteinDesign/README.md b/benchmarks/ProteinDesign/README.md new file mode 100644 index 00000000..54292a47 --- /dev/null +++ b/benchmarks/ProteinDesign/README.md @@ -0,0 +1,33 @@ +# ProteinDesign - Protein Design + +## Background + +Protein design is a core problem in bioengineering: given a target structure (backbone), find the amino acid sequence that maximizes stability. This benchmark focuses on computation-driven protein sequence design optimization. + +This domain task is based on "Protein Design with Agent Rosetta: A Case Study for Specialized Scientific Agents" (arXiv:2603.15952, ICML 2026), using PyRosetta (Rosetta's Python bindings) as the scoring engine. + +## Tasks + +| Task | Description | +|------|-------------| +| [FixedBackboneDesign](FixedBackboneDesign/Task.md) | Fixed-backbone protein sequence design optimization | + +## Environment Setup + +Tasks in this domain use the official Rosetta Docker image for evaluation to ensure environment consistency. + +```bash +docker pull rosettacommons/rosetta:serial +``` + +Quick run command: + +```bash +python -m frontier_eval \ + task=unified \ + task.benchmark=ProteinDesign/FixedBackboneDesign \ + task.runtime.isolation_mode=docker \ + task.runtime.docker_image=rosettacommons/rosetta:serial \ + algorithm=openevolve \ + algorithm.iterations=0 +``` diff --git a/benchmarks/ProteinDesign/README_zh-CN.md b/benchmarks/ProteinDesign/README_zh-CN.md new file mode 100644 index 00000000..bc3fe194 --- /dev/null +++ b/benchmarks/ProteinDesign/README_zh-CN.md @@ -0,0 +1,33 @@ +# ProteinDesign - 蛋白质设计 + +## 背景 + +蛋白质设计是生物工程的核心问题：给定一个目标结构（骨架），找到最稳定的氨基酸序列。本 benchmark 关注计算驱动的蛋白质序列设计优化。 + +本领域任务基于 "Protein Design with Agent Rosetta: A Case Study for Specialized Scientific Agents" (arXiv:2603.15952, ICML 2026)，使用 PyRosetta（Rosetta 的 Python 绑定）作为评分引擎。 + +## 任务列表 + +| 任务 | 描述 | +|------|------| +| [FixedBackboneDesign](FixedBackboneDesign/Task_zh-CN.md) | 固定骨架蛋白质序列设计优化 | + +## 环境配置 + +本领域任务使用官方 Rosetta Docker 镜像运行评测，确保环境一致性。 + +```bash +docker pull rosettacommons/rosetta:serial +``` + +快捷运行命令： + +```bash +python -m frontier_eval \ + task=unified \ + task.benchmark=ProteinDesign/FixedBackboneDesign \ + task.runtime.isolation_mode=docker \ + task.runtime.docker_image=rosettacommons/rosetta:serial \ + algorithm=openevolve \ + algorithm.iterations=0 +``` diff --git a/frontier_eval/conf/task/protein_design_fixed_backbone.yaml b/frontier_eval/conf/task/protein_design_fixed_backbone.yaml new file mode 100644 index 00000000..12427911 --- /dev/null +++ b/frontier_eval/conf/task/protein_design_fixed_backbone.yaml @@ -0,0 +1,7 @@ +name: unified +benchmark: ProteinDesign/FixedBackboneDesign + +runtime: + isolation_mode: docker + docker_image: rosettacommons/rosetta:serial + python_path: python3