From 7d5c041a04cbf310ee7856a732bd4190e885fee4 Mon Sep 17 00:00:00 2001 From: c7w Date: Tue, 30 Jun 2026 20:37:28 +0800 Subject: [PATCH 1/5] Add Medal Score metric, v1-lite split, and released score artifacts - Medal Score: peer-relative gold/silver/bronze podium (normalized to [0,1]), reported on v1 (47 tasks) and the v1-lite subset (10 tasks). READMEs now lead with Medal Score; average rank stays on the website leaderboard. - leaderboard/: ship the frozen podium baselines (medal_podium.csv), published leaderboard (medal_leaderboard.csv), raw score table (exp1_models_raw.csv), a submission scorer (score_submission.py), and an example submission. Un-ignore leaderboard/*.csv. - v1-lite: add frontier_eval/conf/batch/v1_lite.yaml (10-task subset across all five categories, distinct families, gradual-improvement tasks). Co-Authored-By: Claude Opus 4.8 (1M context) --- .gitignore | 2 + README.md | 38 +++++--- README_zh-CN.md | 31 ++++--- frontier_eval/conf/batch/v1_lite.yaml | 83 +++++++++++++++++ leaderboard/README.md | 62 +++++++++++++ leaderboard/exp1_models_raw.csv | 48 ++++++++++ leaderboard/medal_leaderboard.csv | 9 ++ leaderboard/medal_podium.csv | 48 ++++++++++ leaderboard/score_submission.py | 124 ++++++++++++++++++++++++++ leaderboard/submission_example.csv | 48 ++++++++++ 10 files changed, 469 insertions(+), 24 deletions(-) create mode 100644 frontier_eval/conf/batch/v1_lite.yaml create mode 100644 leaderboard/README.md create mode 100644 leaderboard/exp1_models_raw.csv create mode 100644 leaderboard/medal_leaderboard.csv create mode 100644 leaderboard/medal_podium.csv create mode 100644 leaderboard/score_submission.py create mode 100644 leaderboard/submission_example.csv diff --git a/.gitignore b/.gitignore index 8a45ae5c..bf3b45cf 100644 --- a/.gitignore +++ b/.gitignore @@ -16,6 +16,7 @@ benchmarks/Astrodynamics/MannedLunarLanding/results.txt benchmarks/Astrodynamics/MannedLunarLanding/outputlog.txt .vscode *.csv +!leaderboard/*.csv *.h5ad *.h5ad.tmp *.h5ad.tmp.* @@ -46,6 +47,7 @@ outputlog.txt frontier_eval/conf/batch/* !frontier_eval/conf/batch/example_matrix.yaml !frontier_eval/conf/batch/v1.yaml +!frontier_eval/conf/batch/v1_lite.yaml metrics.json artifacts.json debug-*.log diff --git a/README.md b/README.md index 0fdf60bf..98acef96 100644 --- a/README.md +++ b/README.md @@ -14,6 +14,10 @@ Frontier-Eng is a benchmark for **generative optimization**: agents iteratively The benchmark currently covers **47 tasks** across computing, quantum information, operations research, robotics and control, optics and communications, and physical sciences. The project homepage and paper frame it as a missing evaluation axis between pass/fail coding benchmarks and real engineering work: most engineering problems start from a feasible baseline and reward iterative improvement, not one-shot correctness. +## News + +- **2026-06-30** — **New scoring metric: the Medal Score (gold/silver/bronze).** Alongside average rank, we now release a peer-relative *Medal Score* (normalized to `[0,1]`). On each task the top-3 best-feasible scores in the v1 snapshot are frozen as gold/silver/bronze baselines; a model earns 1.00 / 0.67 / 0.33 for reaching each, averaged over the task set, and is reported on both v1 (47 tasks) and v1-lite (10 tasks). It rewards only reaching each task's frontier and ignores negligible long-tail margins, making cross-task aggregation fairer. Per-task podium values and the leaderboard live in [`leaderboard/`](leaderboard/README.md). +- **2026-06-30** — **`v1-lite` released.** A 10-task representative subset of `v1` covering all five categories with distinct benchmark families, selected for tasks whose scores climb gradually under budget (not one-shot-saturated or all-or-nothing). Run it with `frontier_eval/conf/batch/v1_lite.yaml`. ## 0. Host Requirements @@ -97,6 +101,14 @@ bash scripts/batch/validate_v1_task_envs.sh That command runs the batch config for the `v1` problem set with `algorithm.iterations=0`, which evaluates each task's shipped baseline instead of asking an LLM to improve it. +### `v1-lite` quick subset + +For fast iteration and ablations, use the 10-task `v1-lite` matrix +([`frontier_eval/conf/batch/v1_lite.yaml`](frontier_eval/conf/batch/v1_lite.yaml)) +instead of the full `v1` config. It spans all five categories with distinct +benchmark families and favors tasks whose scores improve gradually under budget, +so a short run still exercises the full optimization loop. + If you want the full `v1` problem set with normal optimization runs later, see [`run.md`](run.md). ## Where To Go Next @@ -108,18 +120,20 @@ If you want the full `v1` problem set with normal optimization runs later, see [ ## Leaderboard -Detailed leaderboard: [lab.einsia.ai/frontier-eng/leaderboard.html](https://lab.einsia.ai/frontier-eng/leaderboard.html) - -| Rank | Model | Average Rank | -| :--: | :--- | --: | -| 1 | GPT-5.4 | 3.54 | -| 2 | Claude Opus 4.6 | 3.63 | -| 3 | GLM-5 | 4.34 | -| 4 | DeepSeek V3.2 | 4.76 | -| 5 | Gemini 3.1 Pro Preview | 5.53 | -| 6 | Grok 4.20 | 5.82 | -| 7 | SEED 2.0 Pro | 5.86 | -| 8 | Qwen3 Coder Next | 6.71 | +Detailed leaderboard (incl. average rank): [lab.einsia.ai/frontier-eng/leaderboard](https://lab.einsia.ai/frontier-eng/leaderboard). Released score tables and the per-task medal podium: [`leaderboard/`](leaderboard/README.md). + +**Medal Score** (gold/silver/bronze podium, higher is better, normalized to `[0,1]` = mean per-task podium credit). On each task the top-3 best scores in the **v1 snapshot (2026-04-14)** are frozen as gold/silver/bronze baselines; a model earns 1.00 / 0.67 / 0.33 for reaching each. Reported on both the full **v1** set (47 tasks) and the **v1-lite** subset (10 tasks); gold/silver/bronze counts are for v1 (see [`leaderboard/`](leaderboard/README.md)): + +| Rank | Model | Medal (v1) | Medal (v1-lite) | 🥇 | 🥈 | 🥉 | +| :--: | :--- | --: | --: | --: | --: | --: | +| 1 | GPT-5.4 | 0.596 | 0.667 | 24 | 5 | 2 | +| 2 | Claude Opus 4.6 | 0.490 | 0.501 | 9 | 18 | 6 | +| 3 | GLM-5 | 0.312 | 0.233 | 4 | 10 | 12 | +| 4 | DeepSeek V3.2 | 0.248 | 0.166 | 3 | 9 | 8 | +| 5 | Gemini 3.1 Pro Preview | 0.213 | 0.200 | 3 | 6 | 9 | +| 6 | Seed 2.0 Pro | 0.185 | 0.100 | 3 | 7 | 3 | +| 7 | Grok 4.20 | 0.184 | 0.133 | 3 | 6 | 5 | +| 8 | Qwen3 Coder Next | 0.121 | 0.000 | 3 | 3 | 2 | ## Contributing diff --git a/README_zh-CN.md b/README_zh-CN.md index 75ddd213..26e66e5b 100644 --- a/README_zh-CN.md +++ b/README_zh-CN.md @@ -8,6 +8,11 @@ Frontier-Eng 是一个面向 **generative optimization** 的 benchmark：Agent 当前版本包含 **47 个任务**，覆盖计算系统、量子信息、运筹优化、机器人控制、光学通信、物理与工程设计。主页和论文的核心观点是：真实工程问题通常从一个可行 baseline 出发，价值来自持续优化，而不是 pass/fail。 +## News + +- **2026-06-30** — **新增评测指标：金银铜 Medal Score。** 在 average rank 之外，我们发布同侪相对的 *Medal Score*（归一化到 `[0,1]`）：每道题取 v1 snapshot 中最好的前三名分数冻结为金/银/铜 baseline，模型达到金/银/铜分别得 1.00 / 0.67 / 0.33，对题集求均值；同时汇报 v1（47 题）与 v1-lite（10 题）。它只奖励"达到该题最前沿（领奖台）"，忽略长尾里可忽略的微小差距，使跨题汇总更公平。每题 podium 分数与榜单见 [`leaderboard/`](leaderboard/README.md)。 +- **2026-06-30** — **发布 `v1-lite`。** `v1` 的 10 题代表性子集，覆盖全部五大类、family 各不相同，专选"分数随预算逐步提升（而非一步做满或非高即低）"的题，配置见 `frontier_eval/conf/batch/v1_lite.yaml`。 + ## 这个 benchmark 在测什么 和传统 agent benchmark 相比，Frontier-Eng 更关注三件事： @@ -110,18 +115,20 @@ bash scripts/batch/validate_v1_task_envs.sh ## Leaderboard -详细榜单见 [lab.einsia.ai/frontier-eng/leaderboard.html](https://lab.einsia.ai/frontier-eng/leaderboard.html)。 - -| 排名 | Model | Average Rank | -| :--: | :--- | --: | -| 1 | Claude Opus 4.6 | 3.18 | -| 2 | GLM-5 | 4.02 | -| 3 | DeepSeek V3.2 | 4.41 | -| 4 | Gemini 3.1 Pro Preview | 5.34 | -| 5 | Grok 4.20 | 5.60 | -| 6 | SEED 2.0 Pro | 5.63 | -| 7 | GPT-5.4 | 5.68 | -| 8 | Qwen3 Coder Next | 6.68 | +详细榜单（含 average rank）见 [lab.einsia.ai/frontier-eng/leaderboard](https://lab.einsia.ai/frontier-eng/leaderboard)。发布的分数表与每题金银铜 podium 见 [`leaderboard/`](leaderboard/README.md)。 + +**Medal Score**（金银铜 podium，越高越好，归一化到 `[0,1]`，即每题领奖台得分的均值）。每题取 **v1 snapshot (2026-04-14)** 的前三名分数冻结为金/银/铜 baseline，模型达到金/银/铜分别得 1.00 / 0.67 / 0.33。同时汇报 **v1**（47 题）与 **v1-lite**（10 题）两个集合；金银铜次数为 v1（`gpt-5.4` 采用其 47 题全量重测结果）： + +| 排名 | Model | Medal (v1) | Medal (v1-lite) | 🥇 | 🥈 | 🥉 | +| :--: | :--- | --: | --: | --: | --: | --: | +| 1 | GPT-5.4 | 0.596 | 0.667 | 24 | 5 | 2 | +| 2 | Claude Opus 4.6 | 0.490 | 0.501 | 9 | 18 | 6 | +| 3 | GLM-5 | 0.312 | 0.233 | 4 | 10 | 12 | +| 4 | DeepSeek V3.2 | 0.248 | 0.166 | 3 | 9 | 8 | +| 5 | Gemini 3.1 Pro Preview | 0.213 | 0.200 | 3 | 6 | 9 | +| 6 | Seed 2.0 Pro | 0.185 | 0.100 | 3 | 7 | 3 | +| 7 | Grok 4.20 | 0.184 | 0.133 | 3 | 6 | 5 | +| 8 | Qwen3 Coder Next | 0.121 | 0.000 | 3 | 3 | 2 | ## 贡献 diff --git a/frontier_eval/conf/batch/v1_lite.yaml b/frontier_eval/conf/batch/v1_lite.yaml new file mode 100644 index 00000000..284cc45a --- /dev/null +++ b/frontier_eval/conf/batch/v1_lite.yaml @@ -0,0 +1,83 @@ +# Frontier-Eng v1-lite batch matrix. +# +# v1-lite is a 10-task representative subset of the full 47-task v1 set, chosen +# for fast iteration and ablation. Tasks are selected to (a) cover all five +# engineering categories with distinct benchmark families and (b) reward +# incremental optimization -- their best-feasible scores climb gradually with +# budget instead of saturating in one shot or splitting all-or-nothing. The +# selection rule (top-graduality task per family, 2 per category) is documented +# and reproduced by Einsia-lab/scripts/build_frontier_metrics.py. +# +# Overrides for each task mirror frontier_eval/conf/batch/v1.yaml exactly. +# +version: 1 +tasks: +- name: unified + label: ComputerSystems/MallocLab + overrides: + - task.benchmark=ComputerSystems/MallocLab +- name: unified + label: QuantumComputing/task_01_routing_qftentangled + overrides: + - task.benchmark=QuantumComputing/task_01_routing_qftentangled + - task.runtime.env_name=frontier-v1-main +- name: unified + label: JobShop/abz + overrides: + - task.benchmark=JobShop/abz + - task.runtime.python_path=uv-env:frontier-v1-main +- name: unified + label: InventoryOptimization/disruption_eoqd + overrides: + - task.benchmark=InventoryOptimization/disruption_eoqd + - task.runtime.env_name=frontier-v1-main +- name: unified + label: EnergyStorage/BatteryFastChargingSPMe + overrides: + - task.benchmark=EnergyStorage/BatteryFastChargingSPMe +- name: unified + label: Robotics/RobotArmCycleTimeOptimization + overrides: + - task.benchmark=Robotics/RobotArmCycleTimeOptimization + - task.runtime.env_name=frontier-v1-main + - algorithm.oe.evaluator.timeout=600 +- name: unified + label: Optics/holographic_multiplane_focusing + overrides: + - task.benchmark=Optics/holographic_multiplane_focusing + - task.runtime.env_name=frontier-v1-main + - algorithm.oe.evaluator.timeout=600 +- name: unified + label: WirelessChannelSimulation/HighReliableSimulation + overrides: + - task.benchmark=WirelessChannelSimulation/HighReliableSimulation +- name: unified + label: ReactionOptimisation/snar_multiobjective + overrides: + - task.benchmark=ReactionOptimisation/snar_multiobjective + - task.runtime.python_path=uv-env:frontier-v1-summit + - algorithm.oe.evaluator.timeout=600 +- name: unified + label: StructuralOptimization/TopologyOptimization + overrides: + - task.benchmark=StructuralOptimization/TopologyOptimization + - task.runtime.env_name=frontier-v1-main +algorithms: +- name: openevolve + overrides: + - algorithm.iterations=100 + - algorithm.oe.evaluator.timeout=300 +llms: +- name: v1 + api_base: ${oc.env:OPENAI_API_BASE,https://api.openai.com/v1} + model: ${oc.env:OPENAI_MODEL,gpt-4o-mini} + api_key_env: OPENAI_API_KEY +llm_config: openai_compatible +common_overrides: +- llm.temperature=0.7 +- llm.timeout=60 +run: + name: v1_lite + base_dir: runs/batch + max_parallel: 4 + fail_fast: false diff --git a/leaderboard/README.md b/leaderboard/README.md new file mode 100644 index 00000000..25e039b9 --- /dev/null +++ b/leaderboard/README.md @@ -0,0 +1,62 @@ +# Leaderboard & Medal Score + +Released score artifacts for the Frontier-Eng `v1` set (Experiment 1: foundation +models under `openevolve`, 100 iterations, same initial programs and frozen +verifiers; `gpt-5.4` uses its full 47-task retest). + +| File | Contents | +|---|---| +| `medal_podium.csv` | Frozen per-task **gold / silver / bronze** threshold scores and the model that set each. | +| `medal_leaderboard.csv` | Per-model normalized **Medal Score** on v1 and v1-lite, with gold/silver/bronze counts. | +| `exp1_models_raw.csv` | Best-feasible score of each model on each of the 47 tasks (higher is better); source of the podium. | +| `score_submission.py` | Scores a new submission against the frozen podium. | +| `submission_example.csv` | Example submission (claude-opus-4.6) — scoring it reproduces its leaderboard line. | + +## Medal Score + +On each task the top-3 best scores in the **v1 snapshot (2026-04-14)** are frozen +as peer baselines — gold (1st), silver (2nd), bronze (3rd). A model earns +**1.00** for reaching the gold score, **0.67** for silver, **0.33** for bronze, +otherwise 0; its Medal Score is the **mean** of this credit over a task set +(normalized to `[0,1]`). It credits only reaching each task's frontier (the +podium) and ignores negligible margins in the long tail — a fairer aggregate +than crediting every ordinal rank when the question is "how often does a model +reach the best-known solutions?" We report it on both the full **v1** set +(47 tasks) and the **v1-lite** subset (10 tasks). (Average rank and other +diagnostics are on the [website leaderboard](https://lab.einsia.ai/frontier-eng/leaderboard).) + +> `gpt-oss-120b` is part of the paper's 9-model rank tables, but its per-task raw +> scores were not retained; the released podium is therefore computed over the 8 +> models with available raw scores. + +## Medal leaderboard (normalized; gold/silver/bronze counts are for v1) + +| Rank | Model | Medal (v1) | Medal (v1-lite) | 🥇 | 🥈 | 🥉 | +| :--: | :--- | --: | --: | --: | --: | --: | +| 1 | gpt-5.4 | 0.596 | 0.667 | 24 | 5 | 2 | +| 2 | claude-opus-4.6 | 0.490 | 0.501 | 9 | 18 | 6 | +| 3 | glm-5 | 0.312 | 0.233 | 4 | 10 | 12 | +| 4 | deepseek-v3.2 | 0.248 | 0.166 | 3 | 9 | 8 | +| 5 | gemini-3.1-pro-preview | 0.213 | 0.200 | 3 | 6 | 9 | +| 6 | seed-2.0-pro | 0.185 | 0.100 | 3 | 7 | 3 | +| 7 | grok-4.20 | 0.184 | 0.133 | 3 | 6 | 5 | +| 8 | qwen3-coder-next | 0.121 | 0.000 | 3 | 3 | 2 | + +## Score your own model + +Put your model's best score per task in a CSV (`Task,Score`, one row per task, +task names as in `medal_podium.csv`), then: + +```bash +python leaderboard/score_submission.py your_scores.csv +# -> Medal Score (v1, 47 tasks) : 0.xxx (gold .., silver .., bronze ..) +# Medal Score (v1-lite, 10 tasks) : 0.xxx +``` + +Sanity check (reproduces claude-opus-4.6's line, 0.490 / 0.501): + +```bash +python leaderboard/score_submission.py leaderboard/submission_example.csv +``` + +Interactive view: [lab.einsia.ai/frontier-eng/leaderboard](https://lab.einsia.ai/frontier-eng/leaderboard) diff --git a/leaderboard/exp1_models_raw.csv b/leaderboard/exp1_models_raw.csv new file mode 100644 index 00000000..1b720953 --- /dev/null +++ b/leaderboard/exp1_models_raw.csv @@ -0,0 +1,48 @@ +Task,Baseline,claude-opus-4.6_best,deepseek-v3.2_best,gemini-3.1-pro-preview_best,glm-5_best,gpt-5.4_best,grok-4.20_best,qwen3-coder-next_best,seed-2.0-pro_best,,,,,,,,,, +Aerodynamics_CarAerodynamicsSensing,0.9617,0.9624,0.9632,0.9632,0.9628,0.9630695838481188,0.9624,0.9632,0.9624,,,,,,,,,, +Astrodynamics_MannedLunarLanding,4577.437,6027.3126,6079.2455,4674.9462,6839.0331,6660.942428,4577.437,4577.437,4733.0435,,,,,,,,,, +ComputerSystems_MallocLab,28,96,53,48,86,28,57,32,38,,,,,,,,,, +Cryptographic_AES-128,7.5209,11.8617,12.4591,10.2396,7.9669,39.824967043300866,10.8615,5.5501,7.9481,,,,,,,,,, +Cryptographic_SHA-256,9.8274,16.7955,9.718,9.942,15.1655,26.34045367870492,17.2504,9.8475,15.2838,,,,,,,,,, +Cryptographic_SHA3-256,16.0932,17.4003,17.0749,16.2255,17.5778,37.44512785396786,16.0594,16.5292,18.3478,,,,,,,,,, +EnergyStorage_BatteryFastChargingProfile,71.2806,120.8025,111.4518,116.6532,118.7678,121.99136502281442,99.6875,89.8416,115.6882,,,,,,,,,, +EnergyStorage_BatteryFastChargingSPMe,66.1636,71.8225,91.0079,92.3198,78.0896,122.94304361063023,76.4657,79.0273,76.4122,,,,,,,,,, +EngDesign,1.3571,1.3571,21.7143,27,25.5714,1.3571428571428572,27,25.5714,27,,,,,,,,,, +InventoryOptimization_disruption_eoqd,0.3642,0.6473,0.6381,0.639,0.6303,1,0.6359,0.6225,0.6321,,,,,,,,,, +InventoryOptimization_finite_horizon_dp,0.3673,0.9596,0.8025,0.7559,0.7965,0.9606835281410351,0.8547,0.4413,0.7323,,,,,,,,,, +InventoryOptimization_general_meio,0.1825,0.9929,0.9893,0.9839,0.9165,0.9999999999999999,0.9236,0.7819,0.6973,,,,,,,,,, +InventoryOptimization_joint_replenishment,0.3034,0.8822,0.8822,0.8822,0.8822,1,0.8822,0.8821,0.8822,,,,,,,,,, +InventoryOptimization_tree_gsm_safety_stock,0.3813,0.75,0.6606,0.6606,0.6606,1,0.6606,0.6606,0.6606,,,,,,,,,, +JobShop_abz,80.5042,96.1035,88.3614,86.751,88.4924,91.23143065488635,87.6717,85.603,86.672,,,,,,,,,, +JobShop_swv,81.6325,89.4966,82.3575,82.3141,87.1611,87.33430826602005,85.5068,82.6129,82.4153,,,,,,,,,, +JobShop_ta,78.8,90.8322,84.9043,85.7065,86.8095,86.16070055174835,84.9136,85.5489,83.9694,,,,,,,,,, +KernelEngineering_FlashAttention,55.2957,983.5001,987.2034,991.8896,381.6257,182687.44188255747,324.919,525.5567,1218.5163,,,,,,,,,, +KernelEngineering_MLA,0.7828,1000.3859,0.8936,1253.2017,20.1972,1132.0659025372765,19.8651,0.9271,19.987,,,,,,,,,, +KernelEngineering_TriMul,47.1274,357.1636,85.5923,54.5774,110.8785,47.88292233116043,165.0294,49.1232,84.9069,,,,,,,,,, +Optics_adaptive_fault_tolerant_fusion,0.3959,0.6398,0.64,0.6398,0.6398,0.455046169,0.6398,0.6398,0.6398,,,,,,,,,, +Optics_adaptive_temporal_smooth_control,0.3152,0.8419,0.8419,0.8419,0.8417,0.841880414,0.842,0.8421,0.8421,,,,,,,,,, +Optics_fiber_guardband_spectrum_packing,0.3861,0.6692,0.657,0.6629,0.6692,0.6754289215686274,0.6629,0.657,0.657,,,,,,,,,, +Optics_fiber_mcs_power_scheduling,0.3297,0.6542,0.5182,0.4796,0.6491,0.6608370951757289,0.4557,0.4458,0.6491,,,,,,,,,, +Optics_fiber_wdm_channel_power_allocation,0.3255,0.6675,0.6679,0.6619,0.6686,0.6964207451370852,0.6664,0.6666,0.6654,,,,,,,,,, +Optics_holographic_multifocus_power_ratio,0.3927,0.8072,0.8265,0.5368,0.711,0.9999999999663148,0.4058,0.5875,0.5626,,,,,,,,,, +Optics_holographic_multiplane_focusing,0.3302,0.6002,0.7196,0.4398,0.4516,0.9999999999886867,0.474,0.5631,0.5303,,,,,,,,,, +Optics_phase_dammann_uniform_orders,26.8969,99.7995,97.3436,97.9498,97.8709,99.99999999999999,94.4055,95.9998,69.0576,,,,,,,,,, +Optics_phase_fourier_pattern_holography,32.6457,82.1276,74.5838,76.6371,76.0127,99.99998936790779,74.217,67.3393,72.4578,,,,,,,,,, +PyPortfolioOpt_robust_mvo_rebalance,32.9804,99.9946,84.941,77.165,82.8015,99.99460428985267,99.983,85.5194,83.0681,,,,,,,,,, +QuantumComputing_task_01_routing_qftentangled,0.209,5.0479,3.6155,0.209,3.7681,6.507945106686525,3.7655,3.2471,3.6783,,,,,,,,,, +QuantumComputing_task_02_clifford_t_synthesis,1.7134,1.6633,1.7134,1.7134,7.4236,1.7133669376223557,1.6633,1.7134,1.7134,,,,,,,,,, +QuantumComputing_task_03_cross_target_qaoa,2.4149,2.5781,5.103,2.9782,5.0301,2.4149139615375192,2.6363,2.4517,2.9782,,,,,,,,,, +ReactionOptimisation_mit_case1_mixed,87.3082,98.6621,98.6041,96.5437,95.9314,98.66214557690091,87.3082,95.3732,95.4297,,,,,,,,,, +ReactionOptimisation_reizman_suzuki_pareto,63.5202,82.3427,82.0329,79.473,82.9901,82.24612252072882,63.5202,81.4666,79.7011,,,,,,,,,, +ReactionOptimisation_snar_multiobjective,57.5234,87.3657,82.7881,80.1521,81.7614,100,72.3909,72.8477,79.427,,,,,,,,,, +Robotics_DynamicObstacleAvoidanceNavigation,0.0722,0.086,0.0856,0.0834,0.0857,0.08571428571428559,0.0817,0.0765,0.0855,,,,,,,,,, +Robotics_PIDTuning,0.0366,0.1632,0.151,0.1521,0.1515,0.1511172761100511,0.1585,0.1422,0.1514,,,,,,,,,, +Robotics_QuadrupedGaitOptimization,0.0218,0.0219,0.0749,0.0218,0.1085,0.022154337029969478,0.0227,0.0232,0.0218,,,,,,,,,, +Robotics_RobotArmCycleTimeOptimization,0.2922,0.4158,0.3923,0.4305,0.4219,0.4356212836221511,0.3923,0.3155,0.3256,,,,,,,,,, +Robotics_UAVInspectionCoverageWithWind,28.8519,28.8519,38.8024,28.8519,35.1121,30.121714802877325,55.9109,32.8468,32.1552,,,,,,,,,, +SingleCellAnalysis_predict_modality,0.5467,0.5467,0.5467,0.5467,0.5467,1,0.5467,0.5467,0.5467,,,,,,,,,, +StructuralOptimization_ISCSO2015,-5401.589,-968.4567,-1120.212,-5401.589,-1139.3354,-5401.589002,-1318.7566,-1308.2575,-1302.2288,,,,,,,,,, +StructuralOptimization_ISCSO2023,-77813242.9,-16477799.48,-55182772.3,-20092179.33,-17840974.17,-77813242.9,-30028112.28,-66126744.97,-42625693.78,,,,,,,,,, +StructuralOptimization_TopologyOptimization,-195.9153,-190.1498,-190.3706,-189.3039,-188.4673,-195.9152621,-185.7983,-192.8488,-190.0603,,,,,,,,,, +SustainableDataCenterControl_hand_written_control,8.3294,21.5657,15.292,12.9088,19.5978,8.5903,14.2432,30.1873,29.2868,,,,,,,,,, +WirelessChannelSimulation_HighReliableSimulation,192.5193,292.3228,291.9451,232.9071,248.0119,231.22403446412542,245.7082,259.9776,304.0437,,,,,,,,,, \ No newline at end of file diff --git a/leaderboard/medal_leaderboard.csv b/leaderboard/medal_leaderboard.csv new file mode 100644 index 00000000..20b35004 --- /dev/null +++ b/leaderboard/medal_leaderboard.csv @@ -0,0 +1,9 @@ +Rank,Model,Medal_v1,Medal_v1lite,Gold,Silver,Bronze +1,gpt-5.4,0.596,0.667,24,5,2 +2,claude-opus-4.6,0.49,0.501,9,18,6 +3,glm-5,0.312,0.233,4,10,12 +4,deepseek-v3.2,0.248,0.166,3,9,8 +5,gemini-3.1-pro-preview,0.213,0.2,3,6,9 +6,seed-2.0-pro,0.185,0.1,3,7,3 +7,grok-4.20,0.184,0.133,3,6,5 +8,qwen3-coder-next,0.121,0.0,3,3,2 diff --git a/leaderboard/medal_podium.csv b/leaderboard/medal_podium.csv new file mode 100644 index 00000000..8059fced --- /dev/null +++ b/leaderboard/medal_podium.csv @@ -0,0 +1,48 @@ +Task,Baseline,Gold,Gold_model,Silver,Silver_model,Bronze,Bronze_model +Aerodynamics_CarAerodynamicsSensing,0.9617,0.9632,deepseek-v3.2/gemini-3.1-pro-preview/qwen3-coder-next,0.9632,deepseek-v3.2/gemini-3.1-pro-preview/qwen3-coder-next,0.9632,deepseek-v3.2/gemini-3.1-pro-preview/qwen3-coder-next +Astrodynamics_MannedLunarLanding,4577.437,6839.0331,glm-5,6660.942428,gpt-5.4,6079.2455,deepseek-v3.2 +ComputerSystems_MallocLab,28,96.0,claude-opus-4.6,86.0,glm-5,57.0,grok-4.20 +Cryptographic_AES-128,7.5209,39.824967043300866,gpt-5.4,12.4591,deepseek-v3.2,11.8617,claude-opus-4.6 +Cryptographic_SHA-256,9.8274,26.34045367870492,gpt-5.4,17.2504,grok-4.20,16.7955,claude-opus-4.6 +Cryptographic_SHA3-256,16.0932,37.44512785396786,gpt-5.4,18.3478,seed-2.0-pro,17.5778,glm-5 +EnergyStorage_BatteryFastChargingProfile,71.2806,121.99136502281442,gpt-5.4,120.8025,claude-opus-4.6,118.7678,glm-5 +EnergyStorage_BatteryFastChargingSPMe,66.1636,122.94304361063023,gpt-5.4,92.3198,gemini-3.1-pro-preview,91.0079,deepseek-v3.2 +EngDesign,1.3571,27.0,gemini-3.1-pro-preview/grok-4.20/seed-2.0-pro,27.0,gemini-3.1-pro-preview/grok-4.20/seed-2.0-pro,27.0,gemini-3.1-pro-preview/grok-4.20/seed-2.0-pro +InventoryOptimization_disruption_eoqd,0.3642,1.0,gpt-5.4,0.6473,claude-opus-4.6,0.639,gemini-3.1-pro-preview +InventoryOptimization_finite_horizon_dp,0.3673,0.9606835281410351,gpt-5.4,0.9596,claude-opus-4.6,0.8547,grok-4.20 +InventoryOptimization_general_meio,0.1825,0.9999999999999999,gpt-5.4,0.9929,claude-opus-4.6,0.9893,deepseek-v3.2 +InventoryOptimization_joint_replenishment,0.3034,1.0,gpt-5.4,0.8822,claude-opus-4.6/deepseek-v3.2/gemini-3.1-pro-preview/glm-5/grok-4.20/seed-2.0-pro,0.8822,claude-opus-4.6/deepseek-v3.2/gemini-3.1-pro-preview/glm-5/grok-4.20/seed-2.0-pro +InventoryOptimization_tree_gsm_safety_stock,0.3813,1.0,gpt-5.4,0.75,claude-opus-4.6,0.6606,deepseek-v3.2/gemini-3.1-pro-preview/glm-5/grok-4.20/qwen3-coder-next/seed-2.0-pro +JobShop_abz,80.5042,96.1035,claude-opus-4.6,91.23143065488635,gpt-5.4,88.4924,glm-5 +JobShop_swv,81.6325,89.4966,claude-opus-4.6,87.33430826602005,gpt-5.4,87.1611,glm-5 +JobShop_ta,78.8,90.8322,claude-opus-4.6,86.8095,glm-5,86.16070055174835,gpt-5.4 +KernelEngineering_FlashAttention,55.2957,182687.44188255747,gpt-5.4,1218.5163,seed-2.0-pro,991.8896,gemini-3.1-pro-preview +KernelEngineering_MLA,0.7828,1253.2017,gemini-3.1-pro-preview,1132.0659025372765,gpt-5.4,1000.3859,claude-opus-4.6 +KernelEngineering_TriMul,47.1274,357.1636,claude-opus-4.6,165.0294,grok-4.20,110.8785,glm-5 +Optics_adaptive_fault_tolerant_fusion,0.3959,0.64,deepseek-v3.2,0.6398,claude-opus-4.6/gemini-3.1-pro-preview/glm-5/grok-4.20/qwen3-coder-next/seed-2.0-pro,0.6398,claude-opus-4.6/gemini-3.1-pro-preview/glm-5/grok-4.20/qwen3-coder-next/seed-2.0-pro +Optics_adaptive_temporal_smooth_control,0.3152,0.8421,qwen3-coder-next/seed-2.0-pro,0.8421,qwen3-coder-next/seed-2.0-pro,0.842,grok-4.20 +Optics_fiber_guardband_spectrum_packing,0.3861,0.6754289215686274,gpt-5.4,0.6692,claude-opus-4.6/glm-5,0.6692,claude-opus-4.6/glm-5 +Optics_fiber_mcs_power_scheduling,0.3297,0.6608370951757289,gpt-5.4,0.6542,claude-opus-4.6,0.6491,glm-5/seed-2.0-pro +Optics_fiber_wdm_channel_power_allocation,0.3255,0.6964207451370852,gpt-5.4,0.6686,glm-5,0.6679,deepseek-v3.2 +Optics_holographic_multifocus_power_ratio,0.3927,0.9999999999663148,gpt-5.4,0.8265,deepseek-v3.2,0.8072,claude-opus-4.6 +Optics_holographic_multiplane_focusing,0.3302,0.9999999999886867,gpt-5.4,0.7196,deepseek-v3.2,0.6002,claude-opus-4.6 +Optics_phase_dammann_uniform_orders,26.8969,99.99999999999999,gpt-5.4,99.7995,claude-opus-4.6,97.9498,gemini-3.1-pro-preview +Optics_phase_fourier_pattern_holography,32.6457,99.99998936790779,gpt-5.4,82.1276,claude-opus-4.6,76.6371,gemini-3.1-pro-preview +PyPortfolioOpt_robust_mvo_rebalance,32.9804,99.99460428985267,gpt-5.4,99.9946,claude-opus-4.6,99.983,grok-4.20 +QuantumComputing_task_01_routing_qftentangled,0.209,6.507945106686525,gpt-5.4,5.0479,claude-opus-4.6,3.7681,glm-5 +QuantumComputing_task_02_clifford_t_synthesis,1.7134,7.4236,glm-5,1.7134,deepseek-v3.2/gemini-3.1-pro-preview/qwen3-coder-next/seed-2.0-pro,1.7134,deepseek-v3.2/gemini-3.1-pro-preview/qwen3-coder-next/seed-2.0-pro +QuantumComputing_task_03_cross_target_qaoa,2.4149,5.103,deepseek-v3.2,5.0301,glm-5,2.9782,gemini-3.1-pro-preview/seed-2.0-pro +ReactionOptimisation_mit_case1_mixed,87.3082,98.66214557690091,gpt-5.4,98.6621,claude-opus-4.6,98.6041,deepseek-v3.2 +ReactionOptimisation_reizman_suzuki_pareto,63.5202,82.9901,glm-5,82.3427,claude-opus-4.6,82.24612252072882,gpt-5.4 +ReactionOptimisation_snar_multiobjective,57.5234,100.0,gpt-5.4,87.3657,claude-opus-4.6,82.7881,deepseek-v3.2 +Robotics_DynamicObstacleAvoidanceNavigation,0.0722,0.086,claude-opus-4.6,0.08571428571428559,gpt-5.4,0.0857,glm-5 +Robotics_PIDTuning,0.0366,0.1632,claude-opus-4.6,0.1585,grok-4.20,0.1521,gemini-3.1-pro-preview +Robotics_QuadrupedGaitOptimization,0.0218,0.1085,glm-5,0.0749,deepseek-v3.2,0.0232,qwen3-coder-next +Robotics_RobotArmCycleTimeOptimization,0.2922,0.4356212836221511,gpt-5.4,0.4305,gemini-3.1-pro-preview,0.4219,glm-5 +Robotics_UAVInspectionCoverageWithWind,28.8519,55.9109,grok-4.20,38.8024,deepseek-v3.2,35.1121,glm-5 +SingleCellAnalysis_predict_modality,0.5467,1.0,gpt-5.4,0.5467,claude-opus-4.6/deepseek-v3.2/gemini-3.1-pro-preview/glm-5/grok-4.20/qwen3-coder-next/seed-2.0-pro,0.5467,claude-opus-4.6/deepseek-v3.2/gemini-3.1-pro-preview/glm-5/grok-4.20/qwen3-coder-next/seed-2.0-pro +StructuralOptimization_ISCSO2015,-5401.589,-968.4567,claude-opus-4.6,-1120.212,deepseek-v3.2,-1139.3354,glm-5 +StructuralOptimization_ISCSO2023,-77813242.9,-16477799.48,claude-opus-4.6,-17840974.17,glm-5,-20092179.33,gemini-3.1-pro-preview +StructuralOptimization_TopologyOptimization,-195.9153,-185.7983,grok-4.20,-188.4673,glm-5,-189.3039,gemini-3.1-pro-preview +SustainableDataCenterControl_hand_written_control,8.3294,30.1873,qwen3-coder-next,29.2868,seed-2.0-pro,21.5657,claude-opus-4.6 +WirelessChannelSimulation_HighReliableSimulation,192.5193,304.0437,seed-2.0-pro,292.3228,claude-opus-4.6,291.9451,deepseek-v3.2 diff --git a/leaderboard/score_submission.py b/leaderboard/score_submission.py new file mode 100644 index 00000000..1c25561e --- /dev/null +++ b/leaderboard/score_submission.py @@ -0,0 +1,124 @@ +#!/usr/bin/env python3 +"""Score a submission against the frozen Frontier-Eng Medal podium. + +The gold/silver/bronze baselines are frozen at the v1 snapshot (2026-04-14) and +shipped in ``medal_podium.csv``. This script takes a new model's best-feasible +score on each task and reports its Medal Score, so anyone can be scored against +the released benchmark without rerunning the reference models. + +Usage +----- + python leaderboard/score_submission.py [--verbose] + +Submission CSV format (header required): two columns, ``Task,Score``, one row +per task, using the task names from ``medal_podium.csv`` (e.g. ``JobShop_abz``). +Higher score is better on every task. Missing tasks score 0. See +``submission_example.csv`` (the claude-opus-4.6 column) for a working example; +scoring it reproduces its leaderboard line (Medal v1 = 0.490, v1-lite = 0.501). + +Metric +------ +On each task a submission earns 1.00 / 0.67 / 0.33 for reaching the gold / +silver / bronze score, else 0. The Medal Score is the mean of this credit, +normalized to [0, 1], reported on the full v1 set (47 tasks) and the v1-lite +subset (10 tasks). +""" + +import argparse +import csv +from pathlib import Path + +HERE = Path(__file__).resolve().parent +GOLD, SILVER, BRONZE = 1.00, 0.67, 0.33 + +# v1-lite: 10-task representative subset (frontier_eval/conf/batch/v1_lite.yaml). +V1_LITE = { + "QuantumComputing_task_01_routing_qftentangled", "ComputerSystems_MallocLab", + "JobShop_abz", "InventoryOptimization_disruption_eoqd", + "EnergyStorage_BatteryFastChargingSPMe", "Robotics_RobotArmCycleTimeOptimization", + "Optics_holographic_multiplane_focusing", "WirelessChannelSimulation_HighReliableSimulation", + "ReactionOptimisation_snar_multiobjective", "StructuralOptimization_TopologyOptimization", +} + + +def load_podium(path): + """task -> (gold, silver, bronze) thresholds (higher is better).""" + podium = {} + with open(path, encoding="utf-8-sig") as f: + for row in csv.DictReader(f): + podium[row["Task"]] = ( + float(row["Gold"]), float(row["Silver"]), float(row["Bronze"])) + return podium + + +def load_submission(path): + """task -> score. Accepts a 'Task,Score' header or any two-column CSV.""" + scores = {} + with open(path, encoding="utf-8-sig") as f: + reader = csv.reader(f) + first = next(reader) + if not (first[1].strip().lower() in ("score", "best", "value")): + f.seek(0) # no recognizable header -> treat all rows as data + reader = csv.reader(f) + for row in reader: + if len(row) < 2 or not row[0].strip(): + continue + try: + scores[row[0].strip()] = float(row[1]) + except ValueError: + continue # skip header/garbage rows + return scores + + +def tier(score, gold, silver, bronze): + if score >= gold: + return GOLD, "gold" + if score >= silver: + return SILVER, "silver" + if score >= bronze: + return BRONZE, "bronze" + return 0.0, None + + +def score(podium, submission, verbose=False): + per_task = {} + counts = {"gold": 0, "silver": 0, "bronze": 0} + missing = [] + for task, (g, s, b) in podium.items(): + if task not in submission: + per_task[task] = 0.0 + missing.append(task) + continue + pts, name = tier(submission[task], g, s, b) + per_task[task] = pts + if name: + counts[name] += 1 + medal_v1 = sum(per_task.values()) / len(podium) + lite = [t for t in podium if t in V1_LITE] + medal_lite = sum(per_task[t] for t in lite) / len(lite) + + print(f"Medal Score (v1, 47 tasks) : {medal_v1:.3f}" + f" (gold {counts['gold']}, silver {counts['silver']}, bronze {counts['bronze']})") + print(f"Medal Score (v1-lite, 10 tasks) : {medal_lite:.3f}") + if missing: + print(f"\n[warn] {len(missing)} task(s) absent from submission (scored 0): " + f"{', '.join(missing[:5])}{' ...' if len(missing) > 5 else ''}") + if verbose: + print("\nper-task credit:") + for task in podium: + print(f" {per_task[task]:.2f} {task}") + return medal_v1, medal_lite + + +def main(): + ap = argparse.ArgumentParser(description="Score a submission against the frozen Medal podium.") + ap.add_argument("submission", help="CSV with columns Task,Score (one row per task)") + ap.add_argument("--podium", default=str(HERE / "medal_podium.csv"), + help="frozen gold/silver/bronze baselines (default: leaderboard/medal_podium.csv)") + ap.add_argument("--verbose", action="store_true", help="print per-task medal credit") + args = ap.parse_args() + score(load_podium(args.podium), load_submission(args.submission), args.verbose) + + +if __name__ == "__main__": + main() diff --git a/leaderboard/submission_example.csv b/leaderboard/submission_example.csv new file mode 100644 index 00000000..82f4c1a8 --- /dev/null +++ b/leaderboard/submission_example.csv @@ -0,0 +1,48 @@ +Task,Score +Aerodynamics_CarAerodynamicsSensing,0.9624 +Astrodynamics_MannedLunarLanding,6027.3126 +ComputerSystems_MallocLab,96 +Cryptographic_AES-128,11.8617 +Cryptographic_SHA-256,16.7955 +Cryptographic_SHA3-256,17.4003 +EnergyStorage_BatteryFastChargingProfile,120.8025 +EnergyStorage_BatteryFastChargingSPMe,71.8225 +EngDesign,1.3571 +InventoryOptimization_disruption_eoqd,0.6473 +InventoryOptimization_finite_horizon_dp,0.9596 +InventoryOptimization_general_meio,0.9929 +InventoryOptimization_joint_replenishment,0.8822 +InventoryOptimization_tree_gsm_safety_stock,0.75 +JobShop_abz,96.1035 +JobShop_swv,89.4966 +JobShop_ta,90.8322 +KernelEngineering_FlashAttention,983.5001 +KernelEngineering_MLA,1000.3859 +KernelEngineering_TriMul,357.1636 +Optics_adaptive_fault_tolerant_fusion,0.6398 +Optics_adaptive_temporal_smooth_control,0.8419 +Optics_fiber_guardband_spectrum_packing,0.6692 +Optics_fiber_mcs_power_scheduling,0.6542 +Optics_fiber_wdm_channel_power_allocation,0.6675 +Optics_holographic_multifocus_power_ratio,0.8072 +Optics_holographic_multiplane_focusing,0.6002 +Optics_phase_dammann_uniform_orders,99.7995 +Optics_phase_fourier_pattern_holography,82.1276 +PyPortfolioOpt_robust_mvo_rebalance,99.9946 +QuantumComputing_task_01_routing_qftentangled,5.0479 +QuantumComputing_task_02_clifford_t_synthesis,1.6633 +QuantumComputing_task_03_cross_target_qaoa,2.5781 +ReactionOptimisation_mit_case1_mixed,98.6621 +ReactionOptimisation_reizman_suzuki_pareto,82.3427 +ReactionOptimisation_snar_multiobjective,87.3657 +Robotics_DynamicObstacleAvoidanceNavigation,0.086 +Robotics_PIDTuning,0.1632 +Robotics_QuadrupedGaitOptimization,0.0219 +Robotics_RobotArmCycleTimeOptimization,0.4158 +Robotics_UAVInspectionCoverageWithWind,28.8519 +SingleCellAnalysis_predict_modality,0.5467 +StructuralOptimization_ISCSO2015,-968.4567 +StructuralOptimization_ISCSO2023,-16477799.48 +StructuralOptimization_TopologyOptimization,-190.1498 +SustainableDataCenterControl_hand_written_control,21.5657 +WirelessChannelSimulation_HighReliableSimulation,292.3228 From 88d79ae69011a43b67694da1e0929821c19b57fe Mon Sep 17 00:00:00 2001 From: han Date: Wed, 8 Jul 2026 17:19:36 +0800 Subject: [PATCH 2/5] feat(ProteinDesign): add FixedBackboneDesign task --- .../FixedBackboneDesign/README.md | 21 + .../FixedBackboneDesign/README_zh-CN.md | 81 ++ .../ProteinDesign/FixedBackboneDesign/Task.md | 37 + .../FixedBackboneDesign/Task_zh-CN.md | 37 + .../FixedBackboneDesign/data/raw_task.json | 14 + .../frontier_eval/agent_files.txt | 8 + .../frontier_eval/artifact_files.txt | 3 + .../frontier_eval/candidate_destination.txt | 1 + .../frontier_eval/constraints.txt | 6 + .../frontier_eval/copy_files.txt | 4 + .../frontier_eval/eval_command.txt | 1 + .../frontier_eval/eval_cwd.txt | 1 + .../frontier_eval/initial_program.txt | 1 + .../frontier_eval/readonly_files.txt | 3 + .../references/constants.json | 13 + .../references/petrobind/1ubq.pdb | 970 +++++++++++++++++ .../references/petrobind/2ci2.pdb | 978 ++++++++++++++++++ .../FixedBackboneDesign/scripts/init.py | 161 +++ .../verification/docker/Dockerfile | 10 + .../verification/evaluator.py | 306 ++++++ .../verification/requirements.txt | 6 + benchmarks/ProteinDesign/README.md | 33 + benchmarks/ProteinDesign/README_zh-CN.md | 33 + .../task/protein_design_fixed_backbone.yaml | 7 + 24 files changed, 2735 insertions(+) create mode 100644 benchmarks/ProteinDesign/FixedBackboneDesign/README.md create mode 100644 benchmarks/ProteinDesign/FixedBackboneDesign/README_zh-CN.md create mode 100644 benchmarks/ProteinDesign/FixedBackboneDesign/Task.md create mode 100644 benchmarks/ProteinDesign/FixedBackboneDesign/Task_zh-CN.md create mode 100644 benchmarks/ProteinDesign/FixedBackboneDesign/data/raw_task.json create mode 100644 benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/agent_files.txt create mode 100644 benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/artifact_files.txt create mode 100644 benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/candidate_destination.txt create mode 100644 benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/constraints.txt create mode 100644 benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/copy_files.txt create mode 100644 benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/eval_command.txt create mode 100644 benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/eval_cwd.txt create mode 100644 benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/initial_program.txt create mode 100644 benchmarks/ProteinDesign/FixedBackboneDesign/frontier_eval/readonly_files.txt create mode 100644 benchmarks/ProteinDesign/FixedBackboneDesign/references/constants.json create mode 100644 benchmarks/ProteinDesign/FixedBackboneDesign/references/petrobind/1ubq.pdb create mode 100644 benchmarks/ProteinDesign/FixedBackboneDesign/references/petrobind/2ci2.pdb create mode 100644 benchmarks/ProteinDesign/FixedBackboneDesign/scripts/init.py create mode 100644 benchmarks/ProteinDesign/FixedBackboneDesign/verification/docker/Dockerfile create mode 100644 benchmarks/ProteinDesign/FixedBackboneDesign/verification/evaluator.py create mode 100644 benchmarks/ProteinDesign/FixedBackboneDesign/verification/requirements.txt create mode 100644 benchmarks/ProteinDesign/README.md create mode 100644 benchmarks/ProteinDesign/README_zh-CN.md create mode 100644 frontier_eval/conf/task/protein_design_fixed_backbone.yaml diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/README.md b/benchmarks/ProteinDesign/FixedBackboneDesign/README.md new file mode 100644 index 00000000..4c340c5c --- /dev/null +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/README.md @@ -0,0 +1,21 @@ +# 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 +``` + +## 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/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..57c27f02 --- /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": 1.0, "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/references/petrobind/2ci2.pdb b/benchmarks/ProteinDesign/FixedBackboneDesign/references/petrobind/2ci2.pdb new file mode 100644 index 00000000..e24e5aae --- /dev/null +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/references/petrobind/2ci2.pdb @@ -0,0 +1,978 @@ +HEADER PROTEINASE INHIBITOR (CHYMOTRYPSIN) 05-SEP-88 2CI2 +TITLE CRYSTAL AND MOLECULAR STRUCTURE OF THE SERINE PROTEINASE INHIBITOR CI- +TITLE 2 2 FROM BARLEY SEEDS +COMPND MOL_ID: 1; +COMPND 2 MOLECULE: CHYMOTRYPSIN INHIBITOR 2; +COMPND 3 CHAIN: I; +COMPND 4 ENGINEERED: YES +SOURCE MOL_ID: 1; +SOURCE 2 ORGANISM_SCIENTIFIC: HORDEUM VULGARE; +SOURCE 3 ORGANISM_TAXID: 4513 +KEYWDS PROTEINASE INHIBITOR (CHYMOTRYPSIN) +EXPDTA X-RAY DIFFRACTION +AUTHOR C.A.MCPHALEN,M.N.G.JAMES +REVDAT 5 14-FEB-24 2CI2 1 SEQADV +REVDAT 4 29-NOV-17 2CI2 1 HELIX +REVDAT 3 24-FEB-09 2CI2 1 VERSN +REVDAT 2 01-APR-03 2CI2 1 JRNL +REVDAT 1 07-SEP-88 2CI2 0 +SPRSDE 07-SEP-88 2CI2 1CI2 +JRNL AUTH C.A.MCPHALEN,M.N.JAMES +JRNL TITL CRYSTAL AND MOLECULAR STRUCTURE OF THE SERINE PROTEINASE +JRNL TITL 2 INHIBITOR CI-2 FROM BARLEY SEEDS. +JRNL REF BIOCHEMISTRY V. 26 261 1987 +JRNL REFN ISSN 0006-2960 +JRNL PMID 3828302 +JRNL DOI 10.1021/BI00375A036 +REMARK 1 +REMARK 1 REFERENCE 1 +REMARK 1 AUTH G.M.CLORE,A.M.GRONENBORN,M.N.G.JAMES,M.KJAER,C.A.MCPHALEN, +REMARK 1 AUTH 2 F.M.POULSEN +REMARK 1 TITL COMPARISON OF THE SOLUTION AND X-RAY STRUCTURES OF BARLEY +REMARK 1 TITL 2 SERINE PROTEINASE INHIBITOR 2 +REMARK 1 REF PROTEIN ENG. V. 1 313 1987 +REMARK 1 REFN ISSN 0269-2139 +REMARK 1 REFERENCE 2 +REMARK 1 AUTH C.A.MCPHALEN,I.SVENDSEN,I.JONASSEN,M.N.G.JAMES +REMARK 1 TITL CRYSTAL AND MOLECULAR STRUCTURE OF CHYMOTRYPSIN INHIBITOR 2 +REMARK 1 TITL 2 FROM BARLEY SEEDS IN COMPLEX WITH SUBTILISIN NOVO +REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 82 7242 1985 +REMARK 1 REFN ISSN 0027-8424 +REMARK 1 REFERENCE 3 +REMARK 1 AUTH C.A.MCPHALEN,C.EVANS,K.HAYAKAWA,I.JONASSEN,I.SVENDSEN, +REMARK 1 AUTH 2 M.N.G.JAMES +REMARK 1 TITL PRELIMINARY CRYSTALLOGRAPHIC DATA FOR THE SERINE PROTEASE +REMARK 1 TITL 2 INHIBITOR CI-2 FROM BARLEY SEEDS +REMARK 1 REF J.MOL.BIOL. V. 168 445 1983 +REMARK 1 REFN ISSN 0022-2836 +REMARK 2 +REMARK 2 RESOLUTION. 2.00 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) : 2.00 +REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 +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) : 0.198 +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 : 521 +REMARK 3 NUCLEIC ACID ATOMS : 0 +REMARK 3 HETEROGEN ATOMS : 0 +REMARK 3 SOLVENT ATOMS : 64 +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) : 0.007 ; 0.008 +REMARK 3 ANGLE DISTANCE (A) : 0.029 ; 0.016 +REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.021 ; 0.016 +REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL +REMARK 3 +REMARK 3 PLANE RESTRAINT (A) : 0.014 ; 0.012 +REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.123 ; 0.080 +REMARK 3 +REMARK 3 NON-BONDED CONTACT RESTRAINTS. +REMARK 3 SINGLE TORSION (A) : 0.297 ; 0.400 +REMARK 3 MULTIPLE TORSION (A) : 0.276 ; 0.400 +REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL +REMARK 3 H-BOND (X-H...Y) (A) : 0.240 ; 0.400 +REMARK 3 +REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. +REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL +REMARK 3 PLANAR (DEGREES) : 3.000 ; 2.800 +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) : 1.956 ; 2.000 +REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.909 ; 2.000 +REMARK 3 SIDE-CHAIN BOND (A**2) : 3.611 ; 3.000 +REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.285 ; 3.000 +REMARK 3 +REMARK 3 OTHER REFINEMENT REMARKS: NULL +REMARK 4 +REMARK 4 2CI2 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_1000177923. +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 (%): 37.29 +REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 +REMARK 280 +REMARK 280 CRYSTALLIZATION CONDITIONS: NULL +REMARK 290 +REMARK 290 CRYSTALLOGRAPHIC SYMMETRY +REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 6 2 2 +REMARK 290 +REMARK 290 SYMOP SYMMETRY +REMARK 290 NNNMMM OPERATOR +REMARK 290 1555 X,Y,Z +REMARK 290 2555 -Y,X-Y,Z +REMARK 290 3555 -X+Y,-X,Z +REMARK 290 4555 -X,-Y,Z +REMARK 290 5555 Y,-X+Y,Z +REMARK 290 6555 X-Y,X,Z +REMARK 290 7555 Y,X,-Z +REMARK 290 8555 X-Y,-Y,-Z +REMARK 290 9555 -X,-X+Y,-Z +REMARK 290 10555 -Y,-X,-Z +REMARK 290 11555 -X+Y,Y,-Z +REMARK 290 12555 X,X-Y,-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 -0.500000 -0.866025 0.000000 0.00000 +REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 +REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 +REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 +REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 +REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 +REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 +REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 +REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 +REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 +REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 +REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 +REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 +REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 +REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 +REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 +REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 +REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 +REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 +REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 +REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 +REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 +REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 +REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 +REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 0.00000 +REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 +REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 +REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 +REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 +REMARK 290 SMTRY3 12 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: HEXAMERIC +REMARK 350 APPLY THE FOLLOWING TO CHAINS: I +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 350 BIOMT1 2 0.500000 0.866025 0.000000 0.00000 +REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 +REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 +REMARK 350 BIOMT1 3 0.500000 -0.866025 0.000000 0.00000 +REMARK 350 BIOMT2 3 0.866025 0.500000 0.000000 0.00000 +REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 +REMARK 350 BIOMT1 4 -0.500000 0.866025 0.000000 0.00000 +REMARK 350 BIOMT2 4 -0.866025 -0.500000 0.000000 0.00000 +REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 +REMARK 350 BIOMT1 5 -0.500000 -0.866025 0.000000 0.00000 +REMARK 350 BIOMT2 5 0.866025 -0.500000 0.000000 0.00000 +REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 +REMARK 350 BIOMT1 6 -1.000000 0.000000 0.000000 0.00000 +REMARK 350 BIOMT2 6 0.000000 -1.000000 0.000000 0.00000 +REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000 +REMARK 465 +REMARK 465 MISSING RESIDUES +REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE +REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN +REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) +REMARK 465 +REMARK 465 M RES C SSSEQI +REMARK 465 SER I 1 +REMARK 465 SER I 2 +REMARK 465 VAL I 3 +REMARK 465 GLU I 4 +REMARK 465 LYS I 5 +REMARK 465 LYS I 6 +REMARK 465 PRO I 7 +REMARK 465 GLU I 8 +REMARK 465 GLY I 9 +REMARK 465 VAL I 10 +REMARK 465 ASN I 11 +REMARK 465 THR I 12 +REMARK 465 GLY I 13 +REMARK 465 ALA I 14 +REMARK 465 GLY I 15 +REMARK 465 ASP I 16 +REMARK 465 ARG I 17 +REMARK 465 HIS I 18 +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 ARG I 65 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES +REMARK 500 ARG I 81 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES +REMARK 500 +REMARK 500 REMARK: NULL +REMARK 500 +REMARK 500 GEOMETRY AND STEREOCHEMISTRY +REMARK 500 SUBTOPIC: TORSION ANGLES +REMARK 500 +REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: +REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; +REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). +REMARK 500 +REMARK 500 STANDARD TABLE: +REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) +REMARK 500 +REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- +REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 +REMARK 500 +REMARK 500 M RES CSSEQI PSI PHI +REMARK 500 LEU I 20 130.24 157.17 +REMARK 500 MET I 59 26.94 -63.17 +REMARK 500 ASP I 74 35.11 74.28 +REMARK 500 +REMARK 500 REMARK: NULL +REMARK 700 +REMARK 700 SHEET +REMARK 700 THE SHEET SPECIFIED BELOW IS AN IRREGULAR SHEET. ALL BUT +REMARK 700 ONE HYDROGEN BOND BETWEEN STRANDS 2 AND 3 ARE PROVIDED BY +REMARK 700 BRIDGING WATER MOLECULES. SEE THE REFERENCE CITED ON THE +REMARK 700 *JRNL* RECORDS ABOVE FOR DETAILS. +REMARK 800 +REMARK 800 SITE +REMARK 800 SITE_IDENTIFIER: RSB +REMARK 800 EVIDENCE_CODE: UNKNOWN +REMARK 800 SITE_DESCRIPTION: NULL +REMARK 999 +REMARK 999 SEQUENCE +REMARK 999 THE ORDER OF THE FIRST FOUR RESIDUES PRESENTED ON THE +REMARK 999 *SEQRES* RECORDS BELOW IS UNKNOWN. +DBREF 2CI2 I 1 83 UNP P01053 ICI2_HORVU 5 83 +SEQADV 2CI2 GLU I 78 UNP P01053 GLN 78 CONFLICT +SEQRES 1 I 83 SER SER VAL GLU LYS LYS PRO GLU GLY VAL ASN THR GLY +SEQRES 2 I 83 ALA GLY ASP ARG HIS ASN LEU LYS THR GLU TRP PRO GLU +SEQRES 3 I 83 LEU VAL GLY LYS SER VAL GLU GLU ALA LYS LYS VAL ILE +SEQRES 4 I 83 LEU GLN ASP LYS PRO GLU ALA GLN ILE ILE VAL LEU PRO +SEQRES 5 I 83 VAL GLY THR ILE VAL THR MET GLU TYR ARG ILE ASP ARG +SEQRES 6 I 83 VAL ARG LEU PHE VAL ASP LYS LEU ASP ASN ILE ALA GLU +SEQRES 7 I 83 VAL PRO ARG VAL GLY +FORMUL 2 HOH *64(H2 O) +HELIX 1 A SER I 31 LYS I 43 1 13 +SHEET 1 S1 4 THR I 22 TRP I 24 0 +SHEET 2 S1 4 PRO I 80 GLY I 83 -1 N VAL I 82 O THR I 22 +SHEET 3 S1 4 ASP I 64 ASP I 71 -1 O ARG I 65 N GLY I 83 +SHEET 4 S1 4 GLN I 47 VAL I 53 1 N GLN I 47 O ASP I 64 +SITE 1 RSB 2 MET I 59 GLU I 60 +CRYST1 69.015 69.015 52.890 90.00 90.00 120.00 P 6 2 2 12 +ORIGX1 0.014490 0.008366 0.000000 0.00000 +ORIGX2 0.000000 0.016731 0.000000 0.00000 +ORIGX3 0.000000 0.000000 0.018907 0.00000 +SCALE1 0.014490 0.008366 0.000000 0.00000 +SCALE2 0.000000 0.016731 0.000000 0.00000 +SCALE3 0.000000 0.000000 0.018907 0.00000 +ATOM 1 N ASN I 19 13.270 -37.510 4.242 1.00 57.52 N +ATOM 2 CA ASN I 19 11.912 -37.066 4.598 1.00 57.72 C +ATOM 3 C ASN I 19 11.944 -35.563 4.896 1.00 57.15 C +ATOM 4 O ASN I 19 12.868 -34.849 4.470 1.00 57.88 O +ATOM 5 CB ASN I 19 11.343 -37.905 5.734 1.00 60.98 C +ATOM 6 CG ASN I 19 12.005 -39.260 5.880 1.00 63.99 C +ATOM 7 OD1 ASN I 19 11.372 -40.233 6.316 1.00 66.43 O +ATOM 8 ND2 ASN I 19 13.283 -39.348 5.517 1.00 65.02 N +ATOM 9 N LEU I 20 10.919 -35.133 5.612 1.00 55.25 N +ATOM 10 CA LEU I 20 10.764 -33.739 6.038 1.00 50.58 C +ATOM 11 C LEU I 20 9.309 -33.373 6.344 1.00 47.16 C +ATOM 12 O LEU I 20 8.391 -33.655 5.556 1.00 45.57 O +ATOM 13 CB LEU I 20 11.424 -32.834 4.989 1.00 50.13 C +ATOM 14 CG LEU I 20 12.284 -31.692 5.507 1.00 50.99 C +ATOM 15 CD1 LEU I 20 13.117 -32.121 6.709 1.00 49.77 C +ATOM 16 CD2 LEU I 20 13.188 -31.215 4.370 1.00 52.95 C +ATOM 17 N LYS I 21 9.142 -32.770 7.517 1.00 42.72 N +ATOM 18 CA LYS I 21 7.845 -32.224 7.934 1.00 37.90 C +ATOM 19 C LYS I 21 8.045 -30.702 7.777 1.00 34.37 C +ATOM 20 O LYS I 21 8.932 -30.143 8.433 1.00 34.11 O +ATOM 21 CB LYS I 21 7.274 -32.526 9.297 1.00 35.30 C +ATOM 22 CG LYS I 21 5.763 -32.219 9.350 1.00 27.47 C +ATOM 23 CD LYS I 21 5.184 -32.467 10.728 1.00 28.32 C +ATOM 24 CE LYS I 21 3.676 -32.404 10.770 1.00 24.21 C +ATOM 25 NZ LYS I 21 3.194 -32.365 12.180 1.00 25.08 N +ATOM 26 N THR I 22 7.264 -30.158 6.866 1.00 31.34 N +ATOM 27 CA THR I 22 7.394 -28.744 6.505 1.00 27.32 C +ATOM 28 C THR I 22 6.144 -27.915 6.711 1.00 25.34 C +ATOM 29 O THR I 22 6.231 -26.683 6.537 1.00 24.28 O +ATOM 30 CB THR I 22 7.880 -28.674 4.996 1.00 25.48 C +ATOM 31 OG1 THR I 22 6.848 -29.388 4.246 1.00 25.70 O +ATOM 32 CG2 THR I 22 9.269 -29.293 4.817 1.00 27.40 C +ATOM 33 N GLU I 23 5.058 -28.574 7.079 1.00 23.62 N +ATOM 34 CA GLU I 23 3.798 -27.838 7.306 1.00 19.26 C +ATOM 35 C GLU I 23 2.991 -28.448 8.428 1.00 17.05 C +ATOM 36 O GLU I 23 2.997 -29.675 8.600 1.00 15.10 O +ATOM 37 CB GLU I 23 3.010 -27.695 6.045 1.00 23.29 C +ATOM 38 CG GLU I 23 2.195 -28.851 5.463 1.00 29.02 C +ATOM 39 CD GLU I 23 1.517 -28.258 4.241 1.00 33.08 C +ATOM 40 OE1 GLU I 23 2.221 -27.701 3.413 1.00 37.10 O +ATOM 41 OE2 GLU I 23 0.282 -28.290 4.322 1.00 39.26 O +ATOM 42 N TRP I 24 2.377 -27.565 9.190 1.00 14.26 N +ATOM 43 CA TRP I 24 1.619 -27.918 10.393 1.00 16.19 C +ATOM 44 C TRP I 24 0.164 -27.440 10.332 1.00 16.38 C +ATOM 45 O TRP I 24 -0.271 -26.673 11.204 1.00 16.67 O +ATOM 46 CB TRP I 24 2.335 -27.417 11.654 1.00 13.74 C +ATOM 47 CG TRP I 24 3.612 -28.094 12.010 1.00 17.24 C +ATOM 48 CD1 TRP I 24 3.795 -29.111 12.912 1.00 16.31 C +ATOM 49 CD2 TRP I 24 4.910 -27.835 11.449 1.00 14.54 C +ATOM 50 NE1 TRP I 24 5.111 -29.494 12.944 1.00 14.15 N +ATOM 51 CE2 TRP I 24 5.815 -28.737 12.055 1.00 15.43 C +ATOM 52 CE3 TRP I 24 5.370 -26.963 10.472 1.00 14.87 C +ATOM 53 CZ2 TRP I 24 7.168 -28.754 11.745 1.00 16.89 C +ATOM 54 CZ3 TRP I 24 6.711 -26.976 10.148 1.00 14.60 C +ATOM 55 CH2 TRP I 24 7.592 -27.859 10.769 1.00 17.78 C +ATOM 56 N PRO I 25 -0.557 -27.946 9.346 1.00 19.10 N +ATOM 57 CA PRO I 25 -1.975 -27.643 9.147 1.00 18.76 C +ATOM 58 C PRO I 25 -2.813 -27.859 10.394 1.00 19.70 C +ATOM 59 O PRO I 25 -3.818 -27.153 10.578 1.00 21.19 O +ATOM 60 CB PRO I 25 -2.427 -28.583 8.029 1.00 20.05 C +ATOM 61 CG PRO I 25 -1.359 -29.647 7.975 1.00 19.41 C +ATOM 62 CD PRO I 25 -0.074 -28.903 8.326 1.00 18.83 C +ATOM 63 N GLU I 26 -2.423 -28.821 11.209 1.00 20.43 N +ATOM 64 CA GLU I 26 -3.144 -29.188 12.429 1.00 19.22 C +ATOM 65 C GLU I 26 -3.049 -28.085 13.478 1.00 19.21 C +ATOM 66 O GLU I 26 -3.689 -28.202 14.531 1.00 21.13 O +ATOM 67 CB GLU I 26 -2.567 -30.438 13.098 1.00 22.19 C +ATOM 68 CG GLU I 26 -1.177 -30.335 13.745 1.00 21.65 C +ATOM 69 CD GLU I 26 -0.044 -30.775 12.862 1.00 20.90 C +ATOM 70 OE1 GLU I 26 -0.080 -30.647 11.658 1.00 14.10 O +ATOM 71 OE2 GLU I 26 0.922 -31.309 13.445 1.00 24.93 O +ATOM 72 N LEU I 27 -2.238 -27.086 13.191 1.00 17.70 N +ATOM 73 CA LEU I 27 -1.984 -26.008 14.143 1.00 16.78 C +ATOM 74 C LEU I 27 -2.874 -24.787 14.000 1.00 14.89 C +ATOM 75 O LEU I 27 -2.836 -24.019 14.989 1.00 15.43 O +ATOM 76 CB LEU I 27 -0.479 -25.685 14.144 1.00 18.14 C +ATOM 77 CG LEU I 27 0.431 -26.695 14.831 1.00 20.69 C +ATOM 78 CD1 LEU I 27 1.887 -26.248 14.756 1.00 23.78 C +ATOM 79 CD2 LEU I 27 -0.001 -26.836 16.287 1.00 18.89 C +ATOM 80 N VAL I 28 -3.593 -24.621 12.902 1.00 14.14 N +ATOM 81 CA VAL I 28 -4.454 -23.429 12.783 1.00 12.54 C +ATOM 82 C VAL I 28 -5.403 -23.380 13.979 1.00 13.06 C +ATOM 83 O VAL I 28 -6.045 -24.383 14.320 1.00 14.30 O +ATOM 84 CB VAL I 28 -5.161 -23.338 11.436 1.00 14.01 C +ATOM 85 CG1 VAL I 28 -6.027 -22.075 11.346 1.00 14.05 C +ATOM 86 CG2 VAL I 28 -4.190 -23.415 10.264 1.00 13.54 C +ATOM 87 N GLY I 29 -5.433 -22.237 14.631 1.00 12.49 N +ATOM 88 CA GLY I 29 -6.293 -21.956 15.772 1.00 12.66 C +ATOM 89 C GLY I 29 -5.701 -22.103 17.154 1.00 13.68 C +ATOM 90 O GLY I 29 -6.272 -21.579 18.129 1.00 12.22 O +ATOM 91 N LYS I 30 -4.604 -22.822 17.248 1.00 12.70 N +ATOM 92 CA LYS I 30 -3.896 -23.079 18.506 1.00 14.92 C +ATOM 93 C LYS I 30 -3.027 -21.887 18.909 1.00 13.30 C +ATOM 94 O LYS I 30 -2.670 -21.045 18.078 1.00 14.33 O +ATOM 95 CB LYS I 30 -3.026 -24.330 18.393 1.00 17.67 C +ATOM 96 CG LYS I 30 -3.741 -25.495 17.710 1.00 22.39 C +ATOM 97 CD LYS I 30 -3.498 -26.806 18.425 1.00 23.93 C +ATOM 98 CE LYS I 30 -4.686 -27.741 18.363 1.00 31.09 C +ATOM 99 NZ LYS I 30 -5.641 -27.360 17.290 1.00 34.91 N +ATOM 100 N SER I 31 -2.722 -21.833 20.192 1.00 14.78 N +ATOM 101 CA SER I 31 -1.879 -20.773 20.760 1.00 15.00 C +ATOM 102 C SER I 31 -0.441 -20.978 20.273 1.00 15.62 C +ATOM 103 O SER I 31 -0.049 -22.057 19.812 1.00 15.37 O +ATOM 104 CB SER I 31 -1.962 -20.751 22.276 1.00 14.91 C +ATOM 105 OG SER I 31 -1.076 -21.705 22.833 1.00 15.27 O +ATOM 106 N VAL I 32 0.300 -19.886 20.370 1.00 18.52 N +ATOM 107 CA VAL I 32 1.717 -19.835 20.003 1.00 16.46 C +ATOM 108 C VAL I 32 2.491 -20.764 20.945 1.00 16.12 C +ATOM 109 O VAL I 32 3.425 -21.427 20.495 1.00 16.39 O +ATOM 110 CB VAL I 32 2.268 -18.404 19.983 1.00 20.13 C +ATOM 111 CG1 VAL I 32 3.770 -18.408 20.295 1.00 22.99 C +ATOM 112 CG2 VAL I 32 2.032 -17.676 18.666 1.00 17.66 C +ATOM 113 N GLU I 33 2.078 -20.829 22.191 1.00 17.43 N +ATOM 114 CA GLU I 33 2.701 -21.664 23.222 1.00 19.39 C +ATOM 115 C GLU I 33 2.559 -23.138 22.851 1.00 20.42 C +ATOM 116 O GLU I 33 3.544 -23.906 22.774 1.00 20.10 O +ATOM 117 CB GLU I 33 2.121 -21.375 24.591 1.00 28.51 C +ATOM 118 CG GLU I 33 1.282 -20.147 24.847 1.00 41.74 C +ATOM 119 CD GLU I 33 1.059 -19.037 23.883 1.00 45.30 C +ATOM 120 OE1 GLU I 33 0.148 -18.217 23.941 1.00 46.73 O +ATOM 121 OE2 GLU I 33 1.912 -18.948 22.970 1.00 53.43 O +ATOM 122 N GLU I 34 1.326 -23.515 22.545 1.00 18.24 N +ATOM 123 CA GLU I 34 0.995 -24.867 22.108 1.00 17.75 C +ATOM 124 C GLU I 34 1.750 -25.158 20.810 1.00 18.11 C +ATOM 125 O GLU I 34 2.423 -26.201 20.740 1.00 20.56 O +ATOM 126 CB GLU I 34 -0.482 -25.120 21.881 1.00 20.05 C +ATOM 127 CG GLU I 34 -1.533 -24.790 22.925 1.00 26.42 C +ATOM 128 CD GLU I 34 -2.967 -25.103 22.598 1.00 29.37 C +ATOM 129 OE1 GLU I 34 -3.455 -26.226 22.649 1.00 31.64 O +ATOM 130 OE2 GLU I 34 -3.643 -24.098 22.267 1.00 27.80 O +ATOM 131 N ALA I 35 1.657 -24.281 19.832 1.00 14.83 N +ATOM 132 CA ALA I 35 2.301 -24.450 18.528 1.00 15.06 C +ATOM 133 C ALA I 35 3.813 -24.601 18.547 1.00 15.32 C +ATOM 134 O ALA I 35 4.350 -25.396 17.757 1.00 14.08 O +ATOM 135 CB ALA I 35 1.830 -23.345 17.595 1.00 15.31 C +ATOM 136 N LYS I 36 4.507 -23.894 19.410 1.00 17.27 N +ATOM 137 CA LYS I 36 5.962 -23.951 19.582 1.00 21.30 C +ATOM 138 C LYS I 36 6.380 -25.393 19.932 1.00 22.84 C +ATOM 139 O LYS I 36 7.258 -26.038 19.349 1.00 24.08 O +ATOM 140 CB LYS I 36 6.434 -23.122 20.776 1.00 24.87 C +ATOM 141 CG LYS I 36 7.002 -21.736 20.526 1.00 28.26 C +ATOM 142 CD LYS I 36 7.306 -21.034 21.850 1.00 30.78 C +ATOM 143 CE LYS I 36 7.796 -19.617 21.627 1.00 35.81 C +ATOM 144 NZ LYS I 36 7.133 -18.641 22.527 1.00 35.81 N +ATOM 145 N LYS I 37 5.723 -25.853 20.976 1.00 22.87 N +ATOM 146 CA LYS I 37 5.845 -27.168 21.584 1.00 22.10 C +ATOM 147 C LYS I 37 5.736 -28.313 20.594 1.00 21.22 C +ATOM 148 O LYS I 37 6.480 -29.300 20.733 1.00 23.27 O +ATOM 149 CB LYS I 37 4.737 -27.336 22.629 1.00 27.93 C +ATOM 150 CG LYS I 37 4.920 -28.562 23.515 1.00 32.57 C +ATOM 151 CD LYS I 37 4.224 -28.337 24.851 1.00 40.46 C +ATOM 152 CE LYS I 37 5.116 -27.599 25.832 1.00 44.72 C +ATOM 153 NZ LYS I 37 5.032 -26.134 25.566 1.00 49.32 N +ATOM 154 N VAL I 38 4.840 -28.194 19.634 1.00 19.75 N +ATOM 155 CA VAL I 38 4.604 -29.219 18.615 1.00 15.32 C +ATOM 156 C VAL I 38 5.710 -29.152 17.567 1.00 15.61 C +ATOM 157 O VAL I 38 6.352 -30.174 17.282 1.00 15.26 O +ATOM 158 CB VAL I 38 3.190 -29.150 18.018 1.00 14.16 C +ATOM 159 CG1 VAL I 38 3.086 -29.925 16.709 1.00 14.89 C +ATOM 160 CG2 VAL I 38 2.129 -29.627 18.988 1.00 12.55 C +ATOM 161 N ILE I 39 5.911 -27.960 17.040 1.00 16.80 N +ATOM 162 CA ILE I 39 6.950 -27.739 16.032 1.00 15.41 C +ATOM 163 C ILE I 39 8.308 -28.212 16.538 1.00 16.48 C +ATOM 164 O ILE I 39 9.023 -28.878 15.765 1.00 18.13 O +ATOM 165 CB ILE I 39 7.012 -26.274 15.505 1.00 16.94 C +ATOM 166 CG1 ILE I 39 5.719 -25.949 14.709 1.00 21.24 C +ATOM 167 CG2 ILE I 39 8.263 -26.029 14.605 1.00 16.53 C +ATOM 168 CD1 ILE I 39 5.392 -24.431 14.610 1.00 23.27 C +ATOM 169 N LEU I 40 8.657 -27.855 17.757 1.00 16.17 N +ATOM 170 CA LEU I 40 9.982 -28.217 18.293 1.00 18.63 C +ATOM 171 C LEU I 40 10.132 -29.728 18.443 1.00 21.07 C +ATOM 172 O LEU I 40 11.247 -30.268 18.393 1.00 20.70 O +ATOM 173 CB LEU I 40 10.263 -27.405 19.554 1.00 18.61 C +ATOM 174 CG LEU I 40 10.842 -26.016 19.388 1.00 17.07 C +ATOM 175 CD1 LEU I 40 11.090 -25.396 20.764 1.00 23.85 C +ATOM 176 CD2 LEU I 40 12.141 -26.077 18.591 1.00 19.94 C +ATOM 177 N GLN I 41 9.000 -30.365 18.645 1.00 23.16 N +ATOM 178 CA GLN I 41 8.891 -31.825 18.774 1.00 25.25 C +ATOM 179 C GLN I 41 9.318 -32.433 17.438 1.00 24.46 C +ATOM 180 O GLN I 41 10.207 -33.288 17.402 1.00 26.23 O +ATOM 181 CB GLN I 41 7.474 -32.234 19.153 1.00 32.52 C +ATOM 182 CG GLN I 41 7.314 -33.577 19.818 1.00 42.96 C +ATOM 183 CD GLN I 41 6.509 -33.578 21.095 1.00 46.29 C +ATOM 184 OE1 GLN I 41 6.503 -32.634 21.887 1.00 49.82 O +ATOM 185 NE2 GLN I 41 5.821 -34.705 21.308 1.00 48.08 N +ATOM 186 N ASP I 42 8.727 -31.943 16.370 1.00 23.73 N +ATOM 187 CA ASP I 42 8.929 -32.383 14.999 1.00 22.62 C +ATOM 188 C ASP I 42 10.168 -31.830 14.286 1.00 21.24 C +ATOM 189 O ASP I 42 10.572 -32.414 13.266 1.00 20.70 O +ATOM 190 CB ASP I 42 7.739 -32.008 14.101 1.00 21.43 C +ATOM 191 CG ASP I 42 6.391 -32.554 14.478 1.00 24.49 C +ATOM 192 OD1 ASP I 42 6.224 -33.424 15.341 1.00 30.00 O +ATOM 193 OD2 ASP I 42 5.429 -32.063 13.853 1.00 23.55 O +ATOM 194 N LYS I 43 10.612 -30.682 14.732 1.00 20.73 N +ATOM 195 CA LYS I 43 11.762 -29.988 14.115 1.00 18.42 C +ATOM 196 C LYS I 43 12.565 -29.299 15.217 1.00 18.96 C +ATOM 197 O LYS I 43 12.452 -28.083 15.438 1.00 19.44 O +ATOM 198 CB LYS I 43 11.264 -29.036 13.050 1.00 15.53 C +ATOM 199 CG LYS I 43 12.282 -28.156 12.359 1.00 16.07 C +ATOM 200 CD LYS I 43 11.660 -27.262 11.302 1.00 13.64 C +ATOM 201 CE LYS I 43 12.715 -26.577 10.456 1.00 14.15 C +ATOM 202 NZ LYS I 43 13.226 -27.491 9.406 1.00 10.85 N +ATOM 203 N PRO I 44 13.352 -30.106 15.923 1.00 16.81 N +ATOM 204 CA PRO I 44 14.183 -29.654 17.033 1.00 17.34 C +ATOM 205 C PRO I 44 15.097 -28.476 16.764 1.00 12.69 C +ATOM 206 O PRO I 44 15.460 -27.793 17.739 1.00 18.82 O +ATOM 207 CB PRO I 44 14.982 -30.902 17.434 1.00 19.36 C +ATOM 208 CG PRO I 44 14.134 -32.063 16.974 1.00 17.24 C +ATOM 209 CD PRO I 44 13.482 -31.566 15.700 1.00 18.51 C +ATOM 210 N GLU I 45 15.470 -28.229 15.542 1.00 13.52 N +ATOM 211 CA GLU I 45 16.354 -27.129 15.131 1.00 14.95 C +ATOM 212 C GLU I 45 15.625 -25.881 14.626 1.00 17.15 C +ATOM 213 O GLU I 45 16.271 -24.911 14.173 1.00 16.32 O +ATOM 214 CB GLU I 45 17.248 -27.546 13.952 1.00 9.98 C +ATOM 215 CG GLU I 45 16.644 -27.572 12.557 1.00 10.75 C +ATOM 216 CD GLU I 45 15.732 -28.688 12.165 1.00 8.14 C +ATOM 217 OE1 GLU I 45 15.371 -28.890 11.021 1.00 10.38 O +ATOM 218 OE2 GLU I 45 15.335 -29.407 13.092 1.00 7.28 O +ATOM 219 N ALA I 46 14.296 -25.926 14.640 1.00 16.99 N +ATOM 220 CA ALA I 46 13.480 -24.810 14.160 1.00 16.57 C +ATOM 221 C ALA I 46 13.766 -23.529 14.960 1.00 16.97 C +ATOM 222 O ALA I 46 13.978 -23.500 16.191 1.00 14.42 O +ATOM 223 CB ALA I 46 12.006 -25.178 14.177 1.00 18.81 C +ATOM 224 N GLN I 47 13.808 -22.469 14.161 1.00 15.12 N +ATOM 225 CA GLN I 47 13.934 -21.079 14.630 1.00 15.59 C +ATOM 226 C GLN I 47 12.529 -20.488 14.404 1.00 14.48 C +ATOM 227 O GLN I 47 12.125 -20.297 13.255 1.00 15.43 O +ATOM 228 CB GLN I 47 15.042 -20.280 13.971 1.00 14.57 C +ATOM 229 CG GLN I 47 16.441 -20.754 14.352 1.00 20.31 C +ATOM 230 CD GLN I 47 16.787 -20.674 15.818 1.00 20.92 C +ATOM 231 OE1 GLN I 47 16.587 -19.708 16.552 1.00 22.99 O +ATOM 232 NE2 GLN I 47 17.380 -21.750 16.340 1.00 26.19 N +ATOM 233 N ILE I 48 11.802 -20.339 15.498 1.00 16.27 N +ATOM 234 CA ILE I 48 10.406 -19.875 15.481 1.00 15.80 C +ATOM 235 C ILE I 48 10.296 -18.353 15.480 1.00 15.66 C +ATOM 236 O ILE I 48 10.807 -17.686 16.389 1.00 15.96 O +ATOM 237 CB ILE I 48 9.587 -20.549 16.640 1.00 17.30 C +ATOM 238 CG1 ILE I 48 9.667 -22.092 16.476 1.00 16.79 C +ATOM 239 CG2 ILE I 48 8.112 -20.079 16.733 1.00 15.04 C +ATOM 240 CD1 ILE I 48 9.075 -22.874 17.679 1.00 21.73 C +ATOM 241 N ILE I 49 9.612 -17.862 14.459 1.00 14.44 N +ATOM 242 CA ILE I 49 9.350 -16.429 14.248 1.00 12.51 C +ATOM 243 C ILE I 49 7.835 -16.209 14.313 1.00 10.43 C +ATOM 244 O ILE I 49 7.073 -16.959 13.687 1.00 12.52 O +ATOM 245 CB ILE I 49 9.962 -15.963 12.882 1.00 13.39 C +ATOM 246 CG1 ILE I 49 11.499 -16.164 12.865 1.00 15.31 C +ATOM 247 CG2 ILE I 49 9.580 -14.515 12.488 1.00 8.33 C +ATOM 248 CD1 ILE I 49 12.287 -15.564 14.052 1.00 12.08 C +ATOM 249 N VAL I 50 7.424 -15.222 15.077 1.00 9.95 N +ATOM 250 CA VAL I 50 6.021 -14.883 15.315 1.00 9.48 C +ATOM 251 C VAL I 50 5.676 -13.527 14.695 1.00 11.08 C +ATOM 252 O VAL I 50 6.168 -12.524 15.236 1.00 11.22 O +ATOM 253 CB VAL I 50 5.781 -14.853 16.844 1.00 11.04 C +ATOM 254 CG1 VAL I 50 4.377 -14.381 17.212 1.00 12.78 C +ATOM 255 CG2 VAL I 50 6.099 -16.175 17.517 1.00 13.08 C +ATOM 256 N LEU I 51 4.861 -13.525 13.658 1.00 10.84 N +ATOM 257 CA LEU I 51 4.434 -12.286 13.006 1.00 7.63 C +ATOM 258 C LEU I 51 2.903 -12.192 12.917 1.00 8.35 C +ATOM 259 O LEU I 51 2.209 -13.209 12.829 1.00 7.78 O +ATOM 260 CB LEU I 51 5.085 -12.267 11.629 1.00 6.43 C +ATOM 261 CG LEU I 51 6.571 -12.463 11.463 1.00 12.23 C +ATOM 262 CD1 LEU I 51 6.895 -12.729 9.987 1.00 11.51 C +ATOM 263 CD2 LEU I 51 7.308 -11.208 11.927 1.00 10.52 C +ATOM 264 N PRO I 52 2.416 -10.962 12.894 1.00 8.91 N +ATOM 265 CA PRO I 52 0.988 -10.679 12.717 1.00 8.08 C +ATOM 266 C PRO I 52 0.574 -11.041 11.295 1.00 11.02 C +ATOM 267 O PRO I 52 1.382 -10.841 10.366 1.00 11.03 O +ATOM 268 CB PRO I 52 0.884 -9.161 12.910 1.00 8.44 C +ATOM 269 CG PRO I 52 2.188 -8.710 13.474 1.00 8.74 C +ATOM 270 CD PRO I 52 3.218 -9.722 12.987 1.00 8.21 C +ATOM 271 N VAL I 53 -0.653 -11.520 11.104 1.00 13.73 N +ATOM 272 CA VAL I 53 -1.162 -11.852 9.752 1.00 13.43 C +ATOM 273 C VAL I 53 -1.148 -10.553 8.928 1.00 13.53 C +ATOM 274 O VAL I 53 -1.522 -9.509 9.485 1.00 12.58 O +ATOM 275 CB VAL I 53 -2.613 -12.380 9.772 1.00 14.76 C +ATOM 276 CG1 VAL I 53 -3.233 -12.469 8.383 1.00 12.98 C +ATOM 277 CG2 VAL I 53 -2.790 -13.681 10.534 1.00 17.50 C +ATOM 278 N GLY I 54 -0.799 -10.663 7.667 1.00 14.73 N +ATOM 279 CA GLY I 54 -0.750 -9.522 6.759 1.00 17.16 C +ATOM 280 C GLY I 54 0.641 -8.916 6.616 1.00 19.26 C +ATOM 281 O GLY I 54 0.775 -7.922 5.879 1.00 21.70 O +ATOM 282 N THR I 55 1.631 -9.482 7.278 1.00 19.90 N +ATOM 283 CA THR I 55 3.026 -9.024 7.221 1.00 19.01 C +ATOM 284 C THR I 55 3.733 -9.525 5.959 1.00 20.10 C +ATOM 285 O THR I 55 3.723 -10.705 5.577 1.00 20.03 O +ATOM 286 CB THR I 55 3.835 -9.379 8.534 1.00 13.94 C +ATOM 287 OG1 THR I 55 3.039 -8.848 9.638 1.00 14.28 O +ATOM 288 CG2 THR I 55 5.273 -8.870 8.656 1.00 11.44 C +ATOM 289 N ILE I 56 4.366 -8.581 5.287 1.00 21.85 N +ATOM 290 CA ILE I 56 5.139 -8.819 4.064 1.00 26.80 C +ATOM 291 C ILE I 56 6.579 -9.135 4.460 1.00 27.03 C +ATOM 292 O ILE I 56 7.249 -8.267 5.043 1.00 26.20 O +ATOM 293 CB ILE I 56 5.029 -7.574 3.114 1.00 34.95 C +ATOM 294 CG1 ILE I 56 3.532 -7.255 2.850 1.00 37.26 C +ATOM 295 CG2 ILE I 56 5.835 -7.765 1.797 1.00 38.25 C +ATOM 296 CD1 ILE I 56 3.165 -6.922 1.374 1.00 35.14 C +ATOM 297 N VAL I 57 7.016 -10.334 4.135 1.00 28.91 N +ATOM 298 CA VAL I 57 8.379 -10.774 4.491 1.00 31.56 C +ATOM 299 C VAL I 57 9.319 -10.718 3.294 1.00 35.26 C +ATOM 300 O VAL I 57 8.878 -10.587 2.133 1.00 35.25 O +ATOM 301 CB VAL I 57 8.280 -12.143 5.194 1.00 30.70 C +ATOM 302 CG1 VAL I 57 7.631 -12.051 6.575 1.00 31.82 C +ATOM 303 CG2 VAL I 57 7.560 -13.177 4.349 1.00 25.22 C +ATOM 304 N THR I 58 10.607 -10.825 3.594 1.00 38.04 N +ATOM 305 CA THR I 58 11.673 -10.826 2.570 1.00 41.77 C +ATOM 306 C THR I 58 11.719 -12.200 1.893 1.00 42.78 C +ATOM 307 O THR I 58 11.710 -13.236 2.588 1.00 44.39 O +ATOM 308 CB THR I 58 13.075 -10.436 3.177 1.00 43.20 C +ATOM 309 OG1 THR I 58 12.819 -9.628 4.374 1.00 47.09 O +ATOM 310 CG2 THR I 58 14.010 -9.719 2.198 1.00 45.92 C +ATOM 311 N MET I 59 11.805 -12.198 0.578 1.00 42.43 N +ATOM 312 CA MET I 59 11.790 -13.423 -0.231 1.00 42.89 C +ATOM 313 C MET I 59 12.923 -14.402 -0.034 1.00 41.48 C +ATOM 314 O MET I 59 13.182 -15.246 -0.920 1.00 43.82 O +ATOM 315 CB MET I 59 11.487 -13.044 -1.667 1.00 48.81 C +ATOM 316 CG MET I 59 12.377 -13.589 -2.744 1.00 50.54 C +ATOM 317 SD MET I 59 11.939 -12.708 -4.297 1.00 51.98 S +ATOM 318 CE MET I 59 13.386 -11.632 -4.439 1.00 52.05 C +ATOM 319 N GLU I 60 13.534 -14.434 1.126 1.00 41.22 N +ATOM 320 CA GLU I 60 14.630 -15.348 1.473 1.00 39.34 C +ATOM 321 C GLU I 60 14.165 -16.660 2.096 1.00 38.65 C +ATOM 322 O GLU I 60 13.464 -16.641 3.129 1.00 40.31 O +ATOM 323 CB GLU I 60 15.553 -14.670 2.495 1.00 41.16 C +ATOM 324 CG GLU I 60 15.004 -14.303 3.874 1.00 34.03 C +ATOM 325 CD GLU I 60 15.948 -13.599 4.798 1.00 28.96 C +ATOM 326 OE1 GLU I 60 16.303 -12.443 4.660 1.00 30.34 O +ATOM 327 OE2 GLU I 60 16.353 -14.327 5.723 1.00 28.34 O +ATOM 328 N TYR I 61 14.611 -17.778 1.555 1.00 36.27 N +ATOM 329 CA TYR I 61 14.251 -19.116 2.030 1.00 33.51 C +ATOM 330 C TYR I 61 15.194 -19.748 3.044 1.00 33.19 C +ATOM 331 O TYR I 61 16.326 -20.096 2.653 1.00 37.23 O +ATOM 332 CB TYR I 61 14.150 -20.079 0.814 1.00 29.28 C +ATOM 333 CG TYR I 61 13.798 -21.485 1.251 1.00 28.41 C +ATOM 334 CD1 TYR I 61 14.755 -22.500 1.318 1.00 31.55 C +ATOM 335 CD2 TYR I 61 12.497 -21.791 1.634 1.00 27.17 C +ATOM 336 CE1 TYR I 61 14.412 -23.787 1.735 1.00 28.91 C +ATOM 337 CE2 TYR I 61 12.136 -23.065 2.053 1.00 26.04 C +ATOM 338 CZ TYR I 61 13.097 -24.064 2.099 1.00 28.55 C +ATOM 339 OH TYR I 61 12.703 -25.305 2.513 1.00 26.67 O +ATOM 340 N ARG I 62 14.727 -20.014 4.255 1.00 29.39 N +ATOM 341 CA ARG I 62 15.539 -20.644 5.299 1.00 23.99 C +ATOM 342 C ARG I 62 14.903 -21.907 5.873 1.00 22.75 C +ATOM 343 O ARG I 62 13.892 -21.886 6.586 1.00 20.32 O +ATOM 344 CB ARG I 62 15.854 -19.676 6.440 1.00 27.80 C +ATOM 345 CG ARG I 62 16.717 -18.484 6.052 1.00 28.78 C +ATOM 346 CD ARG I 62 18.009 -18.462 6.782 1.00 32.63 C +ATOM 347 NE ARG I 62 17.969 -19.139 8.072 1.00 33.31 N +ATOM 348 CZ ARG I 62 19.023 -19.200 8.893 1.00 31.69 C +ATOM 349 NH1 ARG I 62 20.179 -18.614 8.592 1.00 28.13 N +ATOM 350 NH2 ARG I 62 18.915 -19.879 10.037 1.00 31.67 N +ATOM 351 N ILE I 63 15.581 -23.002 5.623 1.00 17.45 N +ATOM 352 CA ILE I 63 15.194 -24.357 6.003 1.00 18.72 C +ATOM 353 C ILE I 63 14.963 -24.580 7.480 1.00 18.40 C +ATOM 354 O ILE I 63 14.082 -25.410 7.839 1.00 23.17 O +ATOM 355 CB ILE I 63 16.213 -25.314 5.264 1.00 22.99 C +ATOM 356 CG1 ILE I 63 15.612 -26.713 4.984 1.00 26.52 C +ATOM 357 CG2 ILE I 63 17.599 -25.398 5.950 1.00 19.42 C +ATOM 358 CD1 ILE I 63 16.672 -27.837 4.742 1.00 24.70 C +ATOM 359 N ASP I 64 15.632 -23.860 8.364 1.00 14.60 N +ATOM 360 CA ASP I 64 15.500 -24.051 9.809 1.00 14.66 C +ATOM 361 C ASP I 64 14.469 -23.145 10.478 1.00 10.73 C +ATOM 362 O ASP I 64 14.340 -23.221 11.714 1.00 12.65 O +ATOM 363 CB ASP I 64 16.845 -23.914 10.535 1.00 19.91 C +ATOM 364 CG ASP I 64 17.527 -22.577 10.305 1.00 20.76 C +ATOM 365 OD1 ASP I 64 17.446 -21.999 9.205 1.00 21.61 O +ATOM 366 OD2 ASP I 64 18.137 -22.110 11.298 1.00 25.03 O +ATOM 367 N ARG I 65 13.870 -22.315 9.663 1.00 11.64 N +ATOM 368 CA ARG I 65 12.918 -21.309 10.141 1.00 12.51 C +ATOM 369 C ARG I 65 11.453 -21.716 10.025 1.00 12.85 C +ATOM 370 O ARG I 65 11.074 -22.245 8.974 1.00 12.01 O +ATOM 371 CB ARG I 65 13.130 -20.016 9.321 1.00 10.70 C +ATOM 372 CG ARG I 65 12.169 -18.890 9.687 1.00 14.03 C +ATOM 373 CD ARG I 65 12.644 -17.542 9.266 1.00 11.51 C +ATOM 374 NE ARG I 65 12.674 -17.387 7.831 1.00 15.20 N +ATOM 375 CZ ARG I 65 13.460 -16.613 7.090 1.00 15.39 C +ATOM 376 NH1 ARG I 65 14.340 -15.768 7.596 1.00 17.74 N +ATOM 377 NH2 ARG I 65 13.389 -16.713 5.764 1.00 16.07 N +ATOM 378 N VAL I 66 10.685 -21.359 11.050 1.00 10.71 N +ATOM 379 CA VAL I 66 9.240 -21.555 11.079 1.00 13.23 C +ATOM 380 C VAL I 66 8.541 -20.253 11.517 1.00 12.86 C +ATOM 381 O VAL I 66 8.570 -19.906 12.710 1.00 16.02 O +ATOM 382 CB VAL I 66 8.740 -22.721 11.951 1.00 11.53 C +ATOM 383 CG1 VAL I 66 7.216 -22.881 11.850 1.00 11.98 C +ATOM 384 CG2 VAL I 66 9.420 -24.045 11.659 1.00 13.94 C +ATOM 385 N ARG I 67 7.886 -19.619 10.566 1.00 9.65 N +ATOM 386 CA ARG I 67 7.130 -18.389 10.853 1.00 10.83 C +ATOM 387 C ARG I 67 5.717 -18.746 11.304 1.00 7.13 C +ATOM 388 O ARG I 67 5.057 -19.492 10.560 1.00 9.94 O +ATOM 389 CB ARG I 67 7.001 -17.538 9.570 1.00 11.98 C +ATOM 390 CG ARG I 67 8.290 -16.786 9.175 1.00 11.30 C +ATOM 391 CD ARG I 67 8.099 -16.286 7.796 1.00 15.42 C +ATOM 392 NE ARG I 67 9.218 -15.651 7.158 1.00 26.19 N +ATOM 393 CZ ARG I 67 9.598 -15.877 5.897 1.00 23.69 C +ATOM 394 NH1 ARG I 67 8.987 -16.777 5.135 1.00 25.11 N +ATOM 395 NH2 ARG I 67 10.603 -15.150 5.399 1.00 32.20 N +ATOM 396 N LEU I 68 5.264 -18.178 12.388 1.00 5.51 N +ATOM 397 CA LEU I 68 3.881 -18.326 12.864 1.00 7.63 C +ATOM 398 C LEU I 68 3.149 -17.004 12.584 1.00 6.35 C +ATOM 399 O LEU I 68 3.629 -15.965 13.056 1.00 8.97 O +ATOM 400 CB LEU I 68 3.893 -18.673 14.353 1.00 6.88 C +ATOM 401 CG LEU I 68 4.586 -19.961 14.774 1.00 11.18 C +ATOM 402 CD1 LEU I 68 4.451 -20.213 16.270 1.00 2.78 C +ATOM 403 CD2 LEU I 68 3.981 -21.071 13.922 1.00 10.53 C +ATOM 404 N PHE I 69 2.068 -17.071 11.845 1.00 5.58 N +ATOM 405 CA PHE I 69 1.254 -15.871 11.532 1.00 5.54 C +ATOM 406 C PHE I 69 0.064 -15.898 12.493 1.00 6.41 C +ATOM 407 O PHE I 69 -0.788 -16.799 12.467 1.00 7.94 O +ATOM 408 CB PHE I 69 0.923 -15.768 10.047 1.00 5.59 C +ATOM 409 CG PHE I 69 2.063 -15.303 9.185 1.00 12.09 C +ATOM 410 CD1 PHE I 69 2.924 -16.230 8.593 1.00 13.33 C +ATOM 411 CD2 PHE I 69 2.299 -13.936 8.992 1.00 10.83 C +ATOM 412 CE1 PHE I 69 4.008 -15.811 7.835 1.00 13.21 C +ATOM 413 CE2 PHE I 69 3.384 -13.491 8.239 1.00 11.69 C +ATOM 414 CZ PHE I 69 4.229 -14.445 7.653 1.00 11.95 C +ATOM 415 N VAL I 70 0.072 -14.937 13.400 1.00 7.81 N +ATOM 416 CA VAL I 70 -0.893 -14.807 14.480 1.00 6.70 C +ATOM 417 C VAL I 70 -1.933 -13.701 14.306 1.00 10.75 C +ATOM 418 O VAL I 70 -1.791 -12.706 13.598 1.00 8.45 O +ATOM 419 CB VAL I 70 -0.182 -14.794 15.849 1.00 3.28 C +ATOM 420 CG1 VAL I 70 0.815 -15.948 15.986 1.00 4.29 C +ATOM 421 CG2 VAL I 70 0.495 -13.475 16.183 1.00 3.98 C +ATOM 422 N ASP I 71 -3.046 -13.959 14.981 1.00 11.12 N +ATOM 423 CA ASP I 71 -4.238 -13.107 15.079 1.00 12.63 C +ATOM 424 C ASP I 71 -4.081 -12.235 16.333 1.00 14.44 C +ATOM 425 O ASP I 71 -3.074 -12.351 17.058 1.00 17.27 O +ATOM 426 CB ASP I 71 -5.514 -13.958 15.062 1.00 7.46 C +ATOM 427 CG ASP I 71 -5.869 -14.578 16.391 1.00 8.37 C +ATOM 428 OD1 ASP I 71 -5.102 -14.498 17.367 1.00 12.91 O +ATOM 429 OD2 ASP I 71 -6.946 -15.205 16.517 1.00 9.72 O +ATOM 430 N LYS I 72 -5.051 -11.380 16.574 1.00 13.75 N +ATOM 431 CA LYS I 72 -5.097 -10.438 17.680 1.00 13.74 C +ATOM 432 C LYS I 72 -4.946 -11.083 19.051 1.00 15.88 C +ATOM 433 O LYS I 72 -4.589 -10.376 20.015 1.00 16.72 O +ATOM 434 CB LYS I 72 -6.456 -9.729 17.730 1.00 13.34 C +ATOM 435 CG LYS I 72 -6.507 -8.381 17.036 1.00 20.82 C +ATOM 436 CD LYS I 72 -7.817 -7.657 17.322 1.00 21.70 C +ATOM 437 CE LYS I 72 -7.679 -6.538 18.330 1.00 21.57 C +ATOM 438 NZ LYS I 72 -8.402 -5.330 17.839 1.00 30.14 N +ATOM 439 N LEU I 73 -5.275 -12.356 19.142 1.00 16.38 N +ATOM 440 CA LEU I 73 -5.201 -13.055 20.437 1.00 18.38 C +ATOM 441 C LEU I 73 -3.989 -13.979 20.495 1.00 19.84 C +ATOM 442 O LEU I 73 -3.851 -14.718 21.490 1.00 22.48 O +ATOM 443 CB LEU I 73 -6.544 -13.733 20.702 1.00 22.11 C +ATOM 444 CG LEU I 73 -7.766 -12.854 20.907 1.00 22.63 C +ATOM 445 CD1 LEU I 73 -8.985 -13.712 21.224 1.00 24.13 C +ATOM 446 CD2 LEU I 73 -7.484 -11.876 22.047 1.00 24.80 C +ATOM 447 N ASP I 74 -3.163 -13.927 19.472 1.00 19.04 N +ATOM 448 CA ASP I 74 -1.954 -14.754 19.386 1.00 20.64 C +ATOM 449 C ASP I 74 -2.256 -16.222 19.066 1.00 17.76 C +ATOM 450 O ASP I 74 -1.538 -17.062 19.642 1.00 18.05 O +ATOM 451 CB ASP I 74 -1.118 -14.670 20.675 1.00 25.90 C +ATOM 452 CG ASP I 74 -0.466 -13.319 20.898 1.00 29.31 C +ATOM 453 OD1 ASP I 74 0.082 -12.750 19.940 1.00 30.95 O +ATOM 454 OD2 ASP I 74 -0.524 -12.847 22.054 1.00 30.81 O +ATOM 455 N ASN I 75 -3.259 -16.487 18.263 1.00 14.97 N +ATOM 456 CA ASN I 75 -3.598 -17.863 17.854 1.00 13.91 C +ATOM 457 C ASN I 75 -3.042 -18.012 16.436 1.00 12.18 C +ATOM 458 O ASN I 75 -2.896 -16.949 15.809 1.00 13.00 O +ATOM 459 CB ASN I 75 -5.101 -18.132 17.948 1.00 13.31 C +ATOM 460 CG ASN I 75 -5.494 -18.262 19.407 1.00 15.19 C +ATOM 461 OD1 ASN I 75 -4.723 -18.834 20.193 1.00 19.14 O +ATOM 462 ND2 ASN I 75 -6.631 -17.697 19.772 1.00 17.73 N +ATOM 463 N ILE I 76 -2.730 -19.221 16.019 1.00 11.90 N +ATOM 464 CA ILE I 76 -2.185 -19.433 14.667 1.00 12.65 C +ATOM 465 C ILE I 76 -3.342 -19.252 13.677 1.00 11.59 C +ATOM 466 O ILE I 76 -4.322 -20.009 13.762 1.00 14.18 O +ATOM 467 CB ILE I 76 -1.478 -20.810 14.457 1.00 9.22 C +ATOM 468 CG1 ILE I 76 -0.257 -21.048 15.354 1.00 13.74 C +ATOM 469 CG2 ILE I 76 -1.097 -21.028 12.960 1.00 6.37 C +ATOM 470 CD1 ILE I 76 0.140 -20.018 16.424 1.00 13.42 C +ATOM 471 N ALA I 77 -3.162 -18.316 12.767 1.00 9.88 N +ATOM 472 CA ALA I 77 -4.214 -17.967 11.809 1.00 8.17 C +ATOM 473 C ALA I 77 -4.079 -18.616 10.449 1.00 11.23 C +ATOM 474 O ALA I 77 -5.055 -18.635 9.669 1.00 11.49 O +ATOM 475 CB ALA I 77 -4.229 -16.428 11.726 1.00 4.65 C +ATOM 476 N GLU I 78 -2.891 -19.085 10.120 1.00 9.22 N +ATOM 477 CA GLU I 78 -2.597 -19.763 8.857 1.00 13.06 C +ATOM 478 C GLU I 78 -1.699 -20.960 9.151 1.00 10.24 C +ATOM 479 O GLU I 78 -1.083 -21.009 10.226 1.00 13.48 O +ATOM 480 CB GLU I 78 -1.928 -18.872 7.823 1.00 16.66 C +ATOM 481 CG GLU I 78 -1.442 -17.490 8.233 1.00 24.46 C +ATOM 482 CD GLU I 78 -1.217 -16.534 7.100 1.00 22.99 C +ATOM 483 OE1 GLU I 78 -0.765 -16.862 6.021 1.00 29.51 O +ATOM 484 OE2 GLU I 78 -1.530 -15.365 7.390 1.00 27.97 O +ATOM 485 N VAL I 79 -1.647 -21.889 8.224 1.00 12.11 N +ATOM 486 CA VAL I 79 -0.849 -23.111 8.362 1.00 11.23 C +ATOM 487 C VAL I 79 0.637 -22.743 8.418 1.00 10.70 C +ATOM 488 O VAL I 79 1.125 -22.175 7.430 1.00 12.86 O +ATOM 489 CB VAL I 79 -1.054 -24.095 7.183 1.00 13.33 C +ATOM 490 CG1 VAL I 79 -0.023 -25.223 7.255 1.00 10.05 C +ATOM 491 CG2 VAL I 79 -2.463 -24.645 7.074 1.00 10.55 C +ATOM 492 N PRO I 80 1.266 -23.104 9.509 1.00 9.97 N +ATOM 493 CA PRO I 80 2.714 -22.871 9.687 1.00 10.84 C +ATOM 494 C PRO I 80 3.493 -23.711 8.672 1.00 11.17 C +ATOM 495 O PRO I 80 3.107 -24.865 8.398 1.00 11.21 O +ATOM 496 CB PRO I 80 2.966 -23.306 11.130 1.00 12.38 C +ATOM 497 CG PRO I 80 1.620 -23.328 11.814 1.00 10.40 C +ATOM 498 CD PRO I 80 0.663 -23.737 10.696 1.00 11.53 C +ATOM 499 N ARG I 81 4.557 -23.162 8.131 1.00 10.29 N +ATOM 500 CA ARG I 81 5.395 -23.823 7.129 1.00 13.19 C +ATOM 501 C ARG I 81 6.855 -23.394 7.251 1.00 14.50 C +ATOM 502 O ARG I 81 7.114 -22.263 7.689 1.00 16.59 O +ATOM 503 CB ARG I 81 4.933 -23.501 5.698 1.00 14.36 C +ATOM 504 CG ARG I 81 3.956 -24.494 5.110 1.00 22.23 C +ATOM 505 CD ARG I 81 3.417 -24.045 3.794 1.00 33.13 C +ATOM 506 NE ARG I 81 2.449 -22.972 3.956 1.00 40.24 N +ATOM 507 CZ ARG I 81 1.124 -23.113 3.908 1.00 41.54 C +ATOM 508 NH1 ARG I 81 0.526 -24.221 3.488 1.00 40.91 N +ATOM 509 NH2 ARG I 81 0.385 -22.109 4.392 1.00 45.11 N +ATOM 510 N VAL I 82 7.747 -24.270 6.813 1.00 14.70 N +ATOM 511 CA VAL I 82 9.190 -23.996 6.828 1.00 13.66 C +ATOM 512 C VAL I 82 9.560 -22.976 5.747 1.00 13.30 C +ATOM 513 O VAL I 82 8.985 -23.009 4.640 1.00 12.70 O +ATOM 514 CB VAL I 82 10.004 -25.297 6.632 1.00 14.43 C +ATOM 515 CG1 VAL I 82 11.478 -24.982 6.349 1.00 17.60 C +ATOM 516 CG2 VAL I 82 9.882 -26.249 7.805 1.00 15.45 C +ATOM 517 N GLY I 83 10.551 -22.146 6.059 1.00 12.36 N +ATOM 518 CA GLY I 83 11.026 -21.174 5.057 1.00 13.03 C +ATOM 519 C GLY I 83 11.395 -19.829 5.657 1.00 11.77 C +ATOM 520 O GLY I 83 10.798 -19.541 6.714 1.00 15.36 O +ATOM 521 OXT GLY I 83 12.222 -19.137 5.054 1.00 16.40 O +TER 522 GLY I 83 +HETATM 523 O HOH I 84 -0.329 -13.254 6.640 1.00 24.81 O +HETATM 524 O HOH I 85 20.537 -17.890 5.103 0.98 51.62 O +HETATM 525 O HOH I 86 3.985 -5.480 6.143 0.93 22.19 O +HETATM 526 O HOH I 87 13.612 -14.849 -5.298 1.00 37.67 O +HETATM 527 O HOH I 88 2.323 -19.638 7.496 0.75 19.24 O +HETATM 528 O HOH I 89 8.493 -20.055 7.668 1.00 10.51 O +HETATM 529 O HOH I 90 1.392 -19.519 10.757 0.69 8.41 O +HETATM 530 O HOH I 91 14.304 -32.137 12.328 0.88 20.39 O +HETATM 531 O HOH I 92 8.165 -34.925 12.441 1.00 27.86 O +HETATM 532 O HOH I 93 -3.208 -8.404 12.277 0.80 18.92 O +HETATM 533 O HOH I 94 2.873 -36.659 17.649 0.48 20.25 O +HETATM 534 O HOH I 95 -8.502 -16.494 17.981 1.00 6.91 O +HETATM 535 O HOH I 96 13.110 -21.154 18.099 1.00 21.03 O +HETATM 536 O HOH I 97 15.611 -24.679 18.097 1.00 16.43 O +HETATM 537 O HOH I 98 -8.313 -18.290 22.531 1.00 34.75 O +HETATM 538 O HOH I 99 6.311 -23.358 23.845 1.00 42.27 O +HETATM 539 O HOH I 100 9.592 -7.442 4.540 1.00 21.71 O +HETATM 540 O HOH I 101 17.915 -14.447 0.209 1.00 46.91 O +HETATM 541 O HOH I 102 4.643 -20.183 7.815 0.79 11.79 O +HETATM 542 O HOH I 103 8.776 -39.486 8.344 0.33 20.46 O +HETATM 543 O HOH I 104 20.049 -19.093 13.191 0.88 25.50 O +HETATM 544 O HOH I 105 -1.050 -35.346 12.637 0.98 32.03 O +HETATM 545 O HOH I 106 -0.528 -37.282 13.452 0.74 34.20 O +HETATM 546 O HOH I 107 -2.814 -10.035 13.791 0.52 7.98 O +HETATM 547 O HOH I 108 7.629 -22.058 1.674 1.00 51.13 O +HETATM 548 O HOH I 109 2.064 -5.457 11.942 1.00 65.35 O +HETATM 549 O HOH I 110 23.048 -21.016 12.391 1.00 32.12 O +HETATM 550 O HOH I 111 2.660 -35.407 12.320 1.00 37.99 O +HETATM 551 O HOH I 112 19.516 -21.255 13.031 0.79 32.01 O +HETATM 552 O HOH I 113 21.191 -22.240 18.079 0.59 21.14 O +HETATM 553 O HOH I 114 6.941 -36.073 17.397 0.64 48.88 O +HETATM 554 O HOH I 115 -10.533 -17.031 20.300 0.55 21.45 O +HETATM 555 O HOH I 116 5.641 -38.800 22.958 1.00 52.61 O +HETATM 556 O HOH I 117 19.782 -25.123 22.901 0.75 34.24 O +HETATM 557 O HOH I 118 13.266 -20.427 23.057 0.64 34.89 O +HETATM 558 O HOH I 119 -5.628 -30.359 22.925 0.73 48.31 O +HETATM 559 O HOH I 120 8.529 -29.351 22.983 1.00 32.02 O +HETATM 560 O HOH I 121 13.517 -29.044 26.642 0.86 34.70 O +HETATM 561 O HOH I 122 0.323 -6.119 8.978 0.96 39.54 O +HETATM 562 O HOH I 123 -4.037 -15.671 6.351 1.00 35.45 O +HETATM 563 O HOH I 124 15.631 -11.826 -0.761 0.93 46.62 O +HETATM 564 O HOH I 125 4.800 -4.562 12.199 1.00 39.72 O +HETATM 565 O HOH I 126 13.468 -18.103 17.589 0.73 26.09 O +HETATM 566 O HOH I 127 -3.023 -2.235 18.293 1.00 41.70 O +HETATM 567 O HOH I 128 18.407 -24.479 17.873 0.52 9.70 O +HETATM 568 O HOH I 129 -7.836 -2.378 19.154 0.73 60.68 O +HETATM 569 O HOH I 130 21.030 -19.090 21.742 1.00 47.98 O +HETATM 570 O HOH I 131 1.881 -32.214 22.846 0.83 46.85 O +HETATM 571 O HOH I 132 -7.515 -4.664 22.763 0.83 35.53 O +HETATM 572 O HOH I 133 -2.229 -10.591 22.682 1.00 50.61 O +HETATM 573 O HOH I 134 22.150 -25.947 24.001 0.83 44.94 O +HETATM 574 O HOH I 135 11.224 -29.647 8.973 0.70 19.43 O +HETATM 575 O HOH I 136 5.258 -34.075 4.412 0.40 18.69 O +HETATM 576 O HOH I 137 1.459 -39.256 4.127 0.60 23.87 O +HETATM 577 O HOH I 138 4.530 -28.781 -0.047 1.00 43.13 O +HETATM 578 O HOH I 139 11.913 -34.478 18.581 0.64 33.68 O +HETATM 579 O HOH I 140 -5.065 -32.731 22.028 0.78 44.05 O +HETATM 580 O HOH I 141 -2.568 -32.082 23.071 1.00 50.49 O +HETATM 581 O HOH I 142 5.202 -19.362 24.595 1.00 47.01 O +HETATM 582 O HOH I 143 8.744 -16.337 23.550 0.95 39.33 O +HETATM 583 O HOH I 144 16.078 -37.479 4.200 1.00 32.94 O +HETATM 584 O HOH I 145 -3.995 -3.539 23.173 0.45 29.34 O +HETATM 585 O HOH I 146 -8.826 -33.316 22.007 0.73 42.83 O +HETATM 586 O HOH I 147 -1.791 -21.764 25.717 0.74 27.23 O +MASTER 341 0 0 1 4 0 1 6 585 1 0 7 +END diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/scripts/init.py b/benchmarks/ProteinDesign/FixedBackboneDesign/scripts/init.py new file mode 100644 index 00000000..315eb9eb --- /dev/null +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/scripts/init.py @@ -0,0 +1,161 @@ +#!/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", [])) + # Fallback: design all positions (safety net — real data should have meta) + print("[init] WARNING: no meta file found, designing all positions", file=sys.stderr) + import pyrosetta + pyrosetta.init(silent=True) + pose = pyrosetta.pose_from_file(str(prepared_pdb)) + return list(range(1, pose.total_residue() + 1)) + + +# 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) + + # 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 + packer = PackRotamersMover() + packer.score_function(scorefxn) + packer.task_factory(tf) + 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..a6ffb9db --- /dev/null +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/verification/evaluator.py @@ -0,0 +1,306 @@ +#!/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 json +import subprocess +import sys +from pathlib import Path +from typing import Any + + +# --------------------------------------------------------------------------- +# Prepare: load raw_task.json, load PDB, create a prepared reference PDB +# --------------------------------------------------------------------------- + +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 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) + + task = load_json(raw_task_path) + # raw_task.json is at /data/raw_task.json + # PDB paths in raw_task.json are relative to / + 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)) + + # Set up a PackerTask to repack the native side chains + scorefxn = pyrosetta.get_fa_scorefxn() + + # Repack the native side chains to get a baseline energy + # Use a simple TaskFactory that repacks all positions + 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) + + # Score the repacked native pose (this is the baseline energy) + 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)) + + # Also save metadata alongside the prepared PDB + 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, +) -> dict[str, Any]: + """ + Score a designed PDB using PyRosetta ref2015 and return metrics. + + Returns: + dict with keys: valid, combined_score, total_energy, baseline_energy, + improvement, and individual energy terms (fa_atr, fa_rep, ...) + """ + import pyrosetta + pyrosetta.init(silent=True) + + 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)) + candidate_energy = scorefxn(candidate_pose) + + # Extract individual energy terms + native_energies = native_pose.energies() + candidate_energies = candidate_pose.energies() + + # Get the score types used by ref2015 + score_types = [ + pyrosetta.rosetta.core.scoring.ScoreType.fa_atr, + pyrosetta.rosetta.core.scoring.ScoreType.fa_rep, + pyrosetta.rosetta.core.scoring.ScoreType.fa_sol, + pyrosetta.rosetta.core.scoring.ScoreType.fa_elec, + pyrosetta.rosetta.core.scoring.ScoreType.hbond_bb_sc, + pyrosetta.rosetta.core.scoring.ScoreType.hbond_sc, + pyrosetta.rosetta.core.scoring.ScoreType.p_aa_pp, + pyrosetta.rosetta.core.scoring.ScoreType.ref, + ] + term_names = { + 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", + } + + metrics: dict[str, Any] = {"valid": True} + + # Total energies + metrics["native_energy"] = round(native_energy, 6) + metrics["total_energy"] = round(candidate_energy, 6) + metrics["improvement"] = round(native_energy - candidate_energy, 6) + + # Combined score: normalized improvement + if abs(native_energy) > 1e-6: + metrics["combined_score"] = round((native_energy - candidate_energy) / abs(native_energy), 6) + else: + metrics["combined_score"] = 0.0 + + # Individual energy terms + for st in score_types: + name = term_names.get(st, str(st)) + native_term = native_energies.total_energies()[st] if hasattr(native_energies, "total_energies") else 0.0 + candidate_term = candidate_energies.total_energies()[st] if hasattr(candidate_energies, "total_energies") else 0.0 + metrics[f"native_{name}"] = round(float(native_term), 6) + metrics[name] = round(float(candidate_term), 6) + + # Detect invalid: NaN or Inf energies + import math + 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"] = -1e18 + + return metrics + + +def evaluate( + native_pdb: str | Path, + candidate_pdb: str | Path, + result_output: str | Path, +) -> None: + """Evaluate designed sequence and write result JSON.""" + metrics = evaluate_candidate(native_pdb, candidate_pdb) + dump_json(result_output, metrics) + print(f"[evaluator] total_energy={metrics['total_energy']:.4f} " + f"improvement={metrics['improvement']:.4f} " + f"valid={metrics['valid']}") + + +# --------------------------------------------------------------------------- +# Full pipeline: run_candidate_and_evaluate +# Matches the CONTRIBUTING.md test command pattern: +# python verification/evaluator.py scripts/init.py +# --------------------------------------------------------------------------- + +def run_candidate_and_evaluate(script_path: str | Path) -> int: + """ + Full automatic pipeline: + 1. Read raw_task.json and prepare the PDB + 2. Run the candidate script (design) + 3. Evaluate the designed structure + 4. Write metrics.json to the task root + """ + evaluator_dir = Path(__file__).resolve().parent + task_dir = evaluator_dir.parent # Task root directory + 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) + + # 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": -1e18, + "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 + + # Step 3: Evaluate + print(f"[evaluator] Evaluating designed structure") + metrics = evaluate_candidate(prepared_pdb, solution_pdb) + metrics["returncode"] = result.returncode + if result.returncode != 0: + metrics["valid"] = False + metrics["combined_score"] = -1e18 + metrics["error_message"] = f"candidate returned non-zero exit code: {result.returncode}" + + # Step 4: Write metrics.json + dump_json(metrics_path, metrics) + # Also print JSON to stdout for the unified framework + 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("--"): + # CONTRIBUTING.md test command format: python evaluator.py scripts/init.py + return run_candidate_and_evaluate(sys.argv[1]) + + parser = argparse.ArgumentParser( + description="PyRosetta evaluator for FixedBackboneDesign" + ) + subparsers = parser.add_subparsers(dest="command", required=True) + + # prepare + 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) + + # evaluate + 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) + + 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) + + 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 From 50480f3c8564421344da2f027953d85d7064fbad Mon Sep 17 00:00:00 2001 From: han Date: Tue, 14 Jul 2026 10:17:00 +0800 Subject: [PATCH 3/5] fix: address PR review - add constraint verification, reference hash protection, fix PackerTask config, set random seed, fix constants weights --- .../FixedBackboneDesign/README.md | 4 + .../references/constants.json | 2 +- .../references/petrobind/2ci2.pdb | 978 ------------------ .../FixedBackboneDesign/scripts/init.py | 5 +- .../verification/evaluator.py | 241 +++-- 5 files changed, 170 insertions(+), 1060 deletions(-) delete mode 100644 benchmarks/ProteinDesign/FixedBackboneDesign/references/petrobind/2ci2.pdb diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/README.md b/benchmarks/ProteinDesign/FixedBackboneDesign/README.md index 4c340c5c..ed24d99e 100644 --- a/benchmarks/ProteinDesign/FixedBackboneDesign/README.md +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/README.md @@ -10,6 +10,10 @@ python scripts/init.py --prepared-input outputs/prepared.pdb --solution-output o 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` diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/references/constants.json b/benchmarks/ProteinDesign/FixedBackboneDesign/references/constants.json index 57c27f02..e36a29bc 100644 --- a/benchmarks/ProteinDesign/FixedBackboneDesign/references/constants.json +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/references/constants.json @@ -7,7 +7,7 @@ "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": 1.0, "description": "Ramachandran torsion preference"}, + "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/2ci2.pdb b/benchmarks/ProteinDesign/FixedBackboneDesign/references/petrobind/2ci2.pdb deleted file mode 100644 index e24e5aae..00000000 --- a/benchmarks/ProteinDesign/FixedBackboneDesign/references/petrobind/2ci2.pdb +++ /dev/null @@ -1,978 +0,0 @@ -HEADER PROTEINASE INHIBITOR (CHYMOTRYPSIN) 05-SEP-88 2CI2 -TITLE CRYSTAL AND MOLECULAR STRUCTURE OF THE SERINE PROTEINASE INHIBITOR CI- -TITLE 2 2 FROM BARLEY SEEDS -COMPND MOL_ID: 1; -COMPND 2 MOLECULE: CHYMOTRYPSIN INHIBITOR 2; -COMPND 3 CHAIN: I; -COMPND 4 ENGINEERED: YES -SOURCE MOL_ID: 1; -SOURCE 2 ORGANISM_SCIENTIFIC: HORDEUM VULGARE; -SOURCE 3 ORGANISM_TAXID: 4513 -KEYWDS PROTEINASE INHIBITOR (CHYMOTRYPSIN) -EXPDTA X-RAY DIFFRACTION -AUTHOR C.A.MCPHALEN,M.N.G.JAMES -REVDAT 5 14-FEB-24 2CI2 1 SEQADV -REVDAT 4 29-NOV-17 2CI2 1 HELIX -REVDAT 3 24-FEB-09 2CI2 1 VERSN -REVDAT 2 01-APR-03 2CI2 1 JRNL -REVDAT 1 07-SEP-88 2CI2 0 -SPRSDE 07-SEP-88 2CI2 1CI2 -JRNL AUTH C.A.MCPHALEN,M.N.JAMES -JRNL TITL CRYSTAL AND MOLECULAR STRUCTURE OF THE SERINE PROTEINASE -JRNL TITL 2 INHIBITOR CI-2 FROM BARLEY SEEDS. -JRNL REF BIOCHEMISTRY V. 26 261 1987 -JRNL REFN ISSN 0006-2960 -JRNL PMID 3828302 -JRNL DOI 10.1021/BI00375A036 -REMARK 1 -REMARK 1 REFERENCE 1 -REMARK 1 AUTH G.M.CLORE,A.M.GRONENBORN,M.N.G.JAMES,M.KJAER,C.A.MCPHALEN, -REMARK 1 AUTH 2 F.M.POULSEN -REMARK 1 TITL COMPARISON OF THE SOLUTION AND X-RAY STRUCTURES OF BARLEY -REMARK 1 TITL 2 SERINE PROTEINASE INHIBITOR 2 -REMARK 1 REF PROTEIN ENG. V. 1 313 1987 -REMARK 1 REFN ISSN 0269-2139 -REMARK 1 REFERENCE 2 -REMARK 1 AUTH C.A.MCPHALEN,I.SVENDSEN,I.JONASSEN,M.N.G.JAMES -REMARK 1 TITL CRYSTAL AND MOLECULAR STRUCTURE OF CHYMOTRYPSIN INHIBITOR 2 -REMARK 1 TITL 2 FROM BARLEY SEEDS IN COMPLEX WITH SUBTILISIN NOVO -REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 82 7242 1985 -REMARK 1 REFN ISSN 0027-8424 -REMARK 1 REFERENCE 3 -REMARK 1 AUTH C.A.MCPHALEN,C.EVANS,K.HAYAKAWA,I.JONASSEN,I.SVENDSEN, -REMARK 1 AUTH 2 M.N.G.JAMES -REMARK 1 TITL PRELIMINARY CRYSTALLOGRAPHIC DATA FOR THE SERINE PROTEASE -REMARK 1 TITL 2 INHIBITOR CI-2 FROM BARLEY SEEDS -REMARK 1 REF J.MOL.BIOL. V. 168 445 1983 -REMARK 1 REFN ISSN 0022-2836 -REMARK 2 -REMARK 2 RESOLUTION. 2.00 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) : 2.00 -REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 -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) : 0.198 -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 : 521 -REMARK 3 NUCLEIC ACID ATOMS : 0 -REMARK 3 HETEROGEN ATOMS : 0 -REMARK 3 SOLVENT ATOMS : 64 -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) : 0.007 ; 0.008 -REMARK 3 ANGLE DISTANCE (A) : 0.029 ; 0.016 -REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.021 ; 0.016 -REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL -REMARK 3 -REMARK 3 PLANE RESTRAINT (A) : 0.014 ; 0.012 -REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.123 ; 0.080 -REMARK 3 -REMARK 3 NON-BONDED CONTACT RESTRAINTS. -REMARK 3 SINGLE TORSION (A) : 0.297 ; 0.400 -REMARK 3 MULTIPLE TORSION (A) : 0.276 ; 0.400 -REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL -REMARK 3 H-BOND (X-H...Y) (A) : 0.240 ; 0.400 -REMARK 3 -REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. -REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL -REMARK 3 PLANAR (DEGREES) : 3.000 ; 2.800 -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) : 1.956 ; 2.000 -REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.909 ; 2.000 -REMARK 3 SIDE-CHAIN BOND (A**2) : 3.611 ; 3.000 -REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.285 ; 3.000 -REMARK 3 -REMARK 3 OTHER REFINEMENT REMARKS: NULL -REMARK 4 -REMARK 4 2CI2 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_1000177923. -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 (%): 37.29 -REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 -REMARK 280 -REMARK 280 CRYSTALLIZATION CONDITIONS: NULL -REMARK 290 -REMARK 290 CRYSTALLOGRAPHIC SYMMETRY -REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 6 2 2 -REMARK 290 -REMARK 290 SYMOP SYMMETRY -REMARK 290 NNNMMM OPERATOR -REMARK 290 1555 X,Y,Z -REMARK 290 2555 -Y,X-Y,Z -REMARK 290 3555 -X+Y,-X,Z -REMARK 290 4555 -X,-Y,Z -REMARK 290 5555 Y,-X+Y,Z -REMARK 290 6555 X-Y,X,Z -REMARK 290 7555 Y,X,-Z -REMARK 290 8555 X-Y,-Y,-Z -REMARK 290 9555 -X,-X+Y,-Z -REMARK 290 10555 -Y,-X,-Z -REMARK 290 11555 -X+Y,Y,-Z -REMARK 290 12555 X,X-Y,-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 -0.500000 -0.866025 0.000000 0.00000 -REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 -REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 -REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 -REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 -REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 -REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 -REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 -REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 -REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 -REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 -REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 -REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 -REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 -REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 -REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 -REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 -REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 -REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 -REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 -REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 -REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 -REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 -REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 -REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 -REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 -REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 0.00000 -REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 -REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 -REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 -REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 -REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 -REMARK 290 SMTRY3 12 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: HEXAMERIC -REMARK 350 APPLY THE FOLLOWING TO CHAINS: I -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 350 BIOMT1 2 0.500000 0.866025 0.000000 0.00000 -REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 -REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 -REMARK 350 BIOMT1 3 0.500000 -0.866025 0.000000 0.00000 -REMARK 350 BIOMT2 3 0.866025 0.500000 0.000000 0.00000 -REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 -REMARK 350 BIOMT1 4 -0.500000 0.866025 0.000000 0.00000 -REMARK 350 BIOMT2 4 -0.866025 -0.500000 0.000000 0.00000 -REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 -REMARK 350 BIOMT1 5 -0.500000 -0.866025 0.000000 0.00000 -REMARK 350 BIOMT2 5 0.866025 -0.500000 0.000000 0.00000 -REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 -REMARK 350 BIOMT1 6 -1.000000 0.000000 0.000000 0.00000 -REMARK 350 BIOMT2 6 0.000000 -1.000000 0.000000 0.00000 -REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000 -REMARK 465 -REMARK 465 MISSING RESIDUES -REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE -REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN -REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) -REMARK 465 -REMARK 465 M RES C SSSEQI -REMARK 465 SER I 1 -REMARK 465 SER I 2 -REMARK 465 VAL I 3 -REMARK 465 GLU I 4 -REMARK 465 LYS I 5 -REMARK 465 LYS I 6 -REMARK 465 PRO I 7 -REMARK 465 GLU I 8 -REMARK 465 GLY I 9 -REMARK 465 VAL I 10 -REMARK 465 ASN I 11 -REMARK 465 THR I 12 -REMARK 465 GLY I 13 -REMARK 465 ALA I 14 -REMARK 465 GLY I 15 -REMARK 465 ASP I 16 -REMARK 465 ARG I 17 -REMARK 465 HIS I 18 -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 ARG I 65 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES -REMARK 500 ARG I 81 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES -REMARK 500 -REMARK 500 REMARK: NULL -REMARK 500 -REMARK 500 GEOMETRY AND STEREOCHEMISTRY -REMARK 500 SUBTOPIC: TORSION ANGLES -REMARK 500 -REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: -REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; -REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). -REMARK 500 -REMARK 500 STANDARD TABLE: -REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) -REMARK 500 -REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- -REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 -REMARK 500 -REMARK 500 M RES CSSEQI PSI PHI -REMARK 500 LEU I 20 130.24 157.17 -REMARK 500 MET I 59 26.94 -63.17 -REMARK 500 ASP I 74 35.11 74.28 -REMARK 500 -REMARK 500 REMARK: NULL -REMARK 700 -REMARK 700 SHEET -REMARK 700 THE SHEET SPECIFIED BELOW IS AN IRREGULAR SHEET. ALL BUT -REMARK 700 ONE HYDROGEN BOND BETWEEN STRANDS 2 AND 3 ARE PROVIDED BY -REMARK 700 BRIDGING WATER MOLECULES. SEE THE REFERENCE CITED ON THE -REMARK 700 *JRNL* RECORDS ABOVE FOR DETAILS. -REMARK 800 -REMARK 800 SITE -REMARK 800 SITE_IDENTIFIER: RSB -REMARK 800 EVIDENCE_CODE: UNKNOWN -REMARK 800 SITE_DESCRIPTION: NULL -REMARK 999 -REMARK 999 SEQUENCE -REMARK 999 THE ORDER OF THE FIRST FOUR RESIDUES PRESENTED ON THE -REMARK 999 *SEQRES* RECORDS BELOW IS UNKNOWN. -DBREF 2CI2 I 1 83 UNP P01053 ICI2_HORVU 5 83 -SEQADV 2CI2 GLU I 78 UNP P01053 GLN 78 CONFLICT -SEQRES 1 I 83 SER SER VAL GLU LYS LYS PRO GLU GLY VAL ASN THR GLY -SEQRES 2 I 83 ALA GLY ASP ARG HIS ASN LEU LYS THR GLU TRP PRO GLU -SEQRES 3 I 83 LEU VAL GLY LYS SER VAL GLU GLU ALA LYS LYS VAL ILE -SEQRES 4 I 83 LEU GLN ASP LYS PRO GLU ALA GLN ILE ILE VAL LEU PRO -SEQRES 5 I 83 VAL GLY THR ILE VAL THR MET GLU TYR ARG ILE ASP ARG -SEQRES 6 I 83 VAL ARG LEU PHE VAL ASP LYS LEU ASP ASN ILE ALA GLU -SEQRES 7 I 83 VAL PRO ARG VAL GLY -FORMUL 2 HOH *64(H2 O) -HELIX 1 A SER I 31 LYS I 43 1 13 -SHEET 1 S1 4 THR I 22 TRP I 24 0 -SHEET 2 S1 4 PRO I 80 GLY I 83 -1 N VAL I 82 O THR I 22 -SHEET 3 S1 4 ASP I 64 ASP I 71 -1 O ARG I 65 N GLY I 83 -SHEET 4 S1 4 GLN I 47 VAL I 53 1 N GLN I 47 O ASP I 64 -SITE 1 RSB 2 MET I 59 GLU I 60 -CRYST1 69.015 69.015 52.890 90.00 90.00 120.00 P 6 2 2 12 -ORIGX1 0.014490 0.008366 0.000000 0.00000 -ORIGX2 0.000000 0.016731 0.000000 0.00000 -ORIGX3 0.000000 0.000000 0.018907 0.00000 -SCALE1 0.014490 0.008366 0.000000 0.00000 -SCALE2 0.000000 0.016731 0.000000 0.00000 -SCALE3 0.000000 0.000000 0.018907 0.00000 -ATOM 1 N ASN I 19 13.270 -37.510 4.242 1.00 57.52 N -ATOM 2 CA ASN I 19 11.912 -37.066 4.598 1.00 57.72 C -ATOM 3 C ASN I 19 11.944 -35.563 4.896 1.00 57.15 C -ATOM 4 O ASN I 19 12.868 -34.849 4.470 1.00 57.88 O -ATOM 5 CB ASN I 19 11.343 -37.905 5.734 1.00 60.98 C -ATOM 6 CG ASN I 19 12.005 -39.260 5.880 1.00 63.99 C -ATOM 7 OD1 ASN I 19 11.372 -40.233 6.316 1.00 66.43 O -ATOM 8 ND2 ASN I 19 13.283 -39.348 5.517 1.00 65.02 N -ATOM 9 N LEU I 20 10.919 -35.133 5.612 1.00 55.25 N -ATOM 10 CA LEU I 20 10.764 -33.739 6.038 1.00 50.58 C -ATOM 11 C LEU I 20 9.309 -33.373 6.344 1.00 47.16 C -ATOM 12 O LEU I 20 8.391 -33.655 5.556 1.00 45.57 O -ATOM 13 CB LEU I 20 11.424 -32.834 4.989 1.00 50.13 C -ATOM 14 CG LEU I 20 12.284 -31.692 5.507 1.00 50.99 C -ATOM 15 CD1 LEU I 20 13.117 -32.121 6.709 1.00 49.77 C -ATOM 16 CD2 LEU I 20 13.188 -31.215 4.370 1.00 52.95 C -ATOM 17 N LYS I 21 9.142 -32.770 7.517 1.00 42.72 N -ATOM 18 CA LYS I 21 7.845 -32.224 7.934 1.00 37.90 C -ATOM 19 C LYS I 21 8.045 -30.702 7.777 1.00 34.37 C -ATOM 20 O LYS I 21 8.932 -30.143 8.433 1.00 34.11 O -ATOM 21 CB LYS I 21 7.274 -32.526 9.297 1.00 35.30 C -ATOM 22 CG LYS I 21 5.763 -32.219 9.350 1.00 27.47 C -ATOM 23 CD LYS I 21 5.184 -32.467 10.728 1.00 28.32 C -ATOM 24 CE LYS I 21 3.676 -32.404 10.770 1.00 24.21 C -ATOM 25 NZ LYS I 21 3.194 -32.365 12.180 1.00 25.08 N -ATOM 26 N THR I 22 7.264 -30.158 6.866 1.00 31.34 N -ATOM 27 CA THR I 22 7.394 -28.744 6.505 1.00 27.32 C -ATOM 28 C THR I 22 6.144 -27.915 6.711 1.00 25.34 C -ATOM 29 O THR I 22 6.231 -26.683 6.537 1.00 24.28 O -ATOM 30 CB THR I 22 7.880 -28.674 4.996 1.00 25.48 C -ATOM 31 OG1 THR I 22 6.848 -29.388 4.246 1.00 25.70 O -ATOM 32 CG2 THR I 22 9.269 -29.293 4.817 1.00 27.40 C -ATOM 33 N GLU I 23 5.058 -28.574 7.079 1.00 23.62 N -ATOM 34 CA GLU I 23 3.798 -27.838 7.306 1.00 19.26 C -ATOM 35 C GLU I 23 2.991 -28.448 8.428 1.00 17.05 C -ATOM 36 O GLU I 23 2.997 -29.675 8.600 1.00 15.10 O -ATOM 37 CB GLU I 23 3.010 -27.695 6.045 1.00 23.29 C -ATOM 38 CG GLU I 23 2.195 -28.851 5.463 1.00 29.02 C -ATOM 39 CD GLU I 23 1.517 -28.258 4.241 1.00 33.08 C -ATOM 40 OE1 GLU I 23 2.221 -27.701 3.413 1.00 37.10 O -ATOM 41 OE2 GLU I 23 0.282 -28.290 4.322 1.00 39.26 O -ATOM 42 N TRP I 24 2.377 -27.565 9.190 1.00 14.26 N -ATOM 43 CA TRP I 24 1.619 -27.918 10.393 1.00 16.19 C -ATOM 44 C TRP I 24 0.164 -27.440 10.332 1.00 16.38 C -ATOM 45 O TRP I 24 -0.271 -26.673 11.204 1.00 16.67 O -ATOM 46 CB TRP I 24 2.335 -27.417 11.654 1.00 13.74 C -ATOM 47 CG TRP I 24 3.612 -28.094 12.010 1.00 17.24 C -ATOM 48 CD1 TRP I 24 3.795 -29.111 12.912 1.00 16.31 C -ATOM 49 CD2 TRP I 24 4.910 -27.835 11.449 1.00 14.54 C -ATOM 50 NE1 TRP I 24 5.111 -29.494 12.944 1.00 14.15 N -ATOM 51 CE2 TRP I 24 5.815 -28.737 12.055 1.00 15.43 C -ATOM 52 CE3 TRP I 24 5.370 -26.963 10.472 1.00 14.87 C -ATOM 53 CZ2 TRP I 24 7.168 -28.754 11.745 1.00 16.89 C -ATOM 54 CZ3 TRP I 24 6.711 -26.976 10.148 1.00 14.60 C -ATOM 55 CH2 TRP I 24 7.592 -27.859 10.769 1.00 17.78 C -ATOM 56 N PRO I 25 -0.557 -27.946 9.346 1.00 19.10 N -ATOM 57 CA PRO I 25 -1.975 -27.643 9.147 1.00 18.76 C -ATOM 58 C PRO I 25 -2.813 -27.859 10.394 1.00 19.70 C -ATOM 59 O PRO I 25 -3.818 -27.153 10.578 1.00 21.19 O -ATOM 60 CB PRO I 25 -2.427 -28.583 8.029 1.00 20.05 C -ATOM 61 CG PRO I 25 -1.359 -29.647 7.975 1.00 19.41 C -ATOM 62 CD PRO I 25 -0.074 -28.903 8.326 1.00 18.83 C -ATOM 63 N GLU I 26 -2.423 -28.821 11.209 1.00 20.43 N -ATOM 64 CA GLU I 26 -3.144 -29.188 12.429 1.00 19.22 C -ATOM 65 C GLU I 26 -3.049 -28.085 13.478 1.00 19.21 C -ATOM 66 O GLU I 26 -3.689 -28.202 14.531 1.00 21.13 O -ATOM 67 CB GLU I 26 -2.567 -30.438 13.098 1.00 22.19 C -ATOM 68 CG GLU I 26 -1.177 -30.335 13.745 1.00 21.65 C -ATOM 69 CD GLU I 26 -0.044 -30.775 12.862 1.00 20.90 C -ATOM 70 OE1 GLU I 26 -0.080 -30.647 11.658 1.00 14.10 O -ATOM 71 OE2 GLU I 26 0.922 -31.309 13.445 1.00 24.93 O -ATOM 72 N LEU I 27 -2.238 -27.086 13.191 1.00 17.70 N -ATOM 73 CA LEU I 27 -1.984 -26.008 14.143 1.00 16.78 C -ATOM 74 C LEU I 27 -2.874 -24.787 14.000 1.00 14.89 C -ATOM 75 O LEU I 27 -2.836 -24.019 14.989 1.00 15.43 O -ATOM 76 CB LEU I 27 -0.479 -25.685 14.144 1.00 18.14 C -ATOM 77 CG LEU I 27 0.431 -26.695 14.831 1.00 20.69 C -ATOM 78 CD1 LEU I 27 1.887 -26.248 14.756 1.00 23.78 C -ATOM 79 CD2 LEU I 27 -0.001 -26.836 16.287 1.00 18.89 C -ATOM 80 N VAL I 28 -3.593 -24.621 12.902 1.00 14.14 N -ATOM 81 CA VAL I 28 -4.454 -23.429 12.783 1.00 12.54 C -ATOM 82 C VAL I 28 -5.403 -23.380 13.979 1.00 13.06 C -ATOM 83 O VAL I 28 -6.045 -24.383 14.320 1.00 14.30 O -ATOM 84 CB VAL I 28 -5.161 -23.338 11.436 1.00 14.01 C -ATOM 85 CG1 VAL I 28 -6.027 -22.075 11.346 1.00 14.05 C -ATOM 86 CG2 VAL I 28 -4.190 -23.415 10.264 1.00 13.54 C -ATOM 87 N GLY I 29 -5.433 -22.237 14.631 1.00 12.49 N -ATOM 88 CA GLY I 29 -6.293 -21.956 15.772 1.00 12.66 C -ATOM 89 C GLY I 29 -5.701 -22.103 17.154 1.00 13.68 C -ATOM 90 O GLY I 29 -6.272 -21.579 18.129 1.00 12.22 O -ATOM 91 N LYS I 30 -4.604 -22.822 17.248 1.00 12.70 N -ATOM 92 CA LYS I 30 -3.896 -23.079 18.506 1.00 14.92 C -ATOM 93 C LYS I 30 -3.027 -21.887 18.909 1.00 13.30 C -ATOM 94 O LYS I 30 -2.670 -21.045 18.078 1.00 14.33 O -ATOM 95 CB LYS I 30 -3.026 -24.330 18.393 1.00 17.67 C -ATOM 96 CG LYS I 30 -3.741 -25.495 17.710 1.00 22.39 C -ATOM 97 CD LYS I 30 -3.498 -26.806 18.425 1.00 23.93 C -ATOM 98 CE LYS I 30 -4.686 -27.741 18.363 1.00 31.09 C -ATOM 99 NZ LYS I 30 -5.641 -27.360 17.290 1.00 34.91 N -ATOM 100 N SER I 31 -2.722 -21.833 20.192 1.00 14.78 N -ATOM 101 CA SER I 31 -1.879 -20.773 20.760 1.00 15.00 C -ATOM 102 C SER I 31 -0.441 -20.978 20.273 1.00 15.62 C -ATOM 103 O SER I 31 -0.049 -22.057 19.812 1.00 15.37 O -ATOM 104 CB SER I 31 -1.962 -20.751 22.276 1.00 14.91 C -ATOM 105 OG SER I 31 -1.076 -21.705 22.833 1.00 15.27 O -ATOM 106 N VAL I 32 0.300 -19.886 20.370 1.00 18.52 N -ATOM 107 CA VAL I 32 1.717 -19.835 20.003 1.00 16.46 C -ATOM 108 C VAL I 32 2.491 -20.764 20.945 1.00 16.12 C -ATOM 109 O VAL I 32 3.425 -21.427 20.495 1.00 16.39 O -ATOM 110 CB VAL I 32 2.268 -18.404 19.983 1.00 20.13 C -ATOM 111 CG1 VAL I 32 3.770 -18.408 20.295 1.00 22.99 C -ATOM 112 CG2 VAL I 32 2.032 -17.676 18.666 1.00 17.66 C -ATOM 113 N GLU I 33 2.078 -20.829 22.191 1.00 17.43 N -ATOM 114 CA GLU I 33 2.701 -21.664 23.222 1.00 19.39 C -ATOM 115 C GLU I 33 2.559 -23.138 22.851 1.00 20.42 C -ATOM 116 O GLU I 33 3.544 -23.906 22.774 1.00 20.10 O -ATOM 117 CB GLU I 33 2.121 -21.375 24.591 1.00 28.51 C -ATOM 118 CG GLU I 33 1.282 -20.147 24.847 1.00 41.74 C -ATOM 119 CD GLU I 33 1.059 -19.037 23.883 1.00 45.30 C -ATOM 120 OE1 GLU I 33 0.148 -18.217 23.941 1.00 46.73 O -ATOM 121 OE2 GLU I 33 1.912 -18.948 22.970 1.00 53.43 O -ATOM 122 N GLU I 34 1.326 -23.515 22.545 1.00 18.24 N -ATOM 123 CA GLU I 34 0.995 -24.867 22.108 1.00 17.75 C -ATOM 124 C GLU I 34 1.750 -25.158 20.810 1.00 18.11 C -ATOM 125 O GLU I 34 2.423 -26.201 20.740 1.00 20.56 O -ATOM 126 CB GLU I 34 -0.482 -25.120 21.881 1.00 20.05 C -ATOM 127 CG GLU I 34 -1.533 -24.790 22.925 1.00 26.42 C -ATOM 128 CD GLU I 34 -2.967 -25.103 22.598 1.00 29.37 C -ATOM 129 OE1 GLU I 34 -3.455 -26.226 22.649 1.00 31.64 O -ATOM 130 OE2 GLU I 34 -3.643 -24.098 22.267 1.00 27.80 O -ATOM 131 N ALA I 35 1.657 -24.281 19.832 1.00 14.83 N -ATOM 132 CA ALA I 35 2.301 -24.450 18.528 1.00 15.06 C -ATOM 133 C ALA I 35 3.813 -24.601 18.547 1.00 15.32 C -ATOM 134 O ALA I 35 4.350 -25.396 17.757 1.00 14.08 O -ATOM 135 CB ALA I 35 1.830 -23.345 17.595 1.00 15.31 C -ATOM 136 N LYS I 36 4.507 -23.894 19.410 1.00 17.27 N -ATOM 137 CA LYS I 36 5.962 -23.951 19.582 1.00 21.30 C -ATOM 138 C LYS I 36 6.380 -25.393 19.932 1.00 22.84 C -ATOM 139 O LYS I 36 7.258 -26.038 19.349 1.00 24.08 O -ATOM 140 CB LYS I 36 6.434 -23.122 20.776 1.00 24.87 C -ATOM 141 CG LYS I 36 7.002 -21.736 20.526 1.00 28.26 C -ATOM 142 CD LYS I 36 7.306 -21.034 21.850 1.00 30.78 C -ATOM 143 CE LYS I 36 7.796 -19.617 21.627 1.00 35.81 C -ATOM 144 NZ LYS I 36 7.133 -18.641 22.527 1.00 35.81 N -ATOM 145 N LYS I 37 5.723 -25.853 20.976 1.00 22.87 N -ATOM 146 CA LYS I 37 5.845 -27.168 21.584 1.00 22.10 C -ATOM 147 C LYS I 37 5.736 -28.313 20.594 1.00 21.22 C -ATOM 148 O LYS I 37 6.480 -29.300 20.733 1.00 23.27 O -ATOM 149 CB LYS I 37 4.737 -27.336 22.629 1.00 27.93 C -ATOM 150 CG LYS I 37 4.920 -28.562 23.515 1.00 32.57 C -ATOM 151 CD LYS I 37 4.224 -28.337 24.851 1.00 40.46 C -ATOM 152 CE LYS I 37 5.116 -27.599 25.832 1.00 44.72 C -ATOM 153 NZ LYS I 37 5.032 -26.134 25.566 1.00 49.32 N -ATOM 154 N VAL I 38 4.840 -28.194 19.634 1.00 19.75 N -ATOM 155 CA VAL I 38 4.604 -29.219 18.615 1.00 15.32 C -ATOM 156 C VAL I 38 5.710 -29.152 17.567 1.00 15.61 C -ATOM 157 O VAL I 38 6.352 -30.174 17.282 1.00 15.26 O -ATOM 158 CB VAL I 38 3.190 -29.150 18.018 1.00 14.16 C -ATOM 159 CG1 VAL I 38 3.086 -29.925 16.709 1.00 14.89 C -ATOM 160 CG2 VAL I 38 2.129 -29.627 18.988 1.00 12.55 C -ATOM 161 N ILE I 39 5.911 -27.960 17.040 1.00 16.80 N -ATOM 162 CA ILE I 39 6.950 -27.739 16.032 1.00 15.41 C -ATOM 163 C ILE I 39 8.308 -28.212 16.538 1.00 16.48 C -ATOM 164 O ILE I 39 9.023 -28.878 15.765 1.00 18.13 O -ATOM 165 CB ILE I 39 7.012 -26.274 15.505 1.00 16.94 C -ATOM 166 CG1 ILE I 39 5.719 -25.949 14.709 1.00 21.24 C -ATOM 167 CG2 ILE I 39 8.263 -26.029 14.605 1.00 16.53 C -ATOM 168 CD1 ILE I 39 5.392 -24.431 14.610 1.00 23.27 C -ATOM 169 N LEU I 40 8.657 -27.855 17.757 1.00 16.17 N -ATOM 170 CA LEU I 40 9.982 -28.217 18.293 1.00 18.63 C -ATOM 171 C LEU I 40 10.132 -29.728 18.443 1.00 21.07 C -ATOM 172 O LEU I 40 11.247 -30.268 18.393 1.00 20.70 O -ATOM 173 CB LEU I 40 10.263 -27.405 19.554 1.00 18.61 C -ATOM 174 CG LEU I 40 10.842 -26.016 19.388 1.00 17.07 C -ATOM 175 CD1 LEU I 40 11.090 -25.396 20.764 1.00 23.85 C -ATOM 176 CD2 LEU I 40 12.141 -26.077 18.591 1.00 19.94 C -ATOM 177 N GLN I 41 9.000 -30.365 18.645 1.00 23.16 N -ATOM 178 CA GLN I 41 8.891 -31.825 18.774 1.00 25.25 C -ATOM 179 C GLN I 41 9.318 -32.433 17.438 1.00 24.46 C -ATOM 180 O GLN I 41 10.207 -33.288 17.402 1.00 26.23 O -ATOM 181 CB GLN I 41 7.474 -32.234 19.153 1.00 32.52 C -ATOM 182 CG GLN I 41 7.314 -33.577 19.818 1.00 42.96 C -ATOM 183 CD GLN I 41 6.509 -33.578 21.095 1.00 46.29 C -ATOM 184 OE1 GLN I 41 6.503 -32.634 21.887 1.00 49.82 O -ATOM 185 NE2 GLN I 41 5.821 -34.705 21.308 1.00 48.08 N -ATOM 186 N ASP I 42 8.727 -31.943 16.370 1.00 23.73 N -ATOM 187 CA ASP I 42 8.929 -32.383 14.999 1.00 22.62 C -ATOM 188 C ASP I 42 10.168 -31.830 14.286 1.00 21.24 C -ATOM 189 O ASP I 42 10.572 -32.414 13.266 1.00 20.70 O -ATOM 190 CB ASP I 42 7.739 -32.008 14.101 1.00 21.43 C -ATOM 191 CG ASP I 42 6.391 -32.554 14.478 1.00 24.49 C -ATOM 192 OD1 ASP I 42 6.224 -33.424 15.341 1.00 30.00 O -ATOM 193 OD2 ASP I 42 5.429 -32.063 13.853 1.00 23.55 O -ATOM 194 N LYS I 43 10.612 -30.682 14.732 1.00 20.73 N -ATOM 195 CA LYS I 43 11.762 -29.988 14.115 1.00 18.42 C -ATOM 196 C LYS I 43 12.565 -29.299 15.217 1.00 18.96 C -ATOM 197 O LYS I 43 12.452 -28.083 15.438 1.00 19.44 O -ATOM 198 CB LYS I 43 11.264 -29.036 13.050 1.00 15.53 C -ATOM 199 CG LYS I 43 12.282 -28.156 12.359 1.00 16.07 C -ATOM 200 CD LYS I 43 11.660 -27.262 11.302 1.00 13.64 C -ATOM 201 CE LYS I 43 12.715 -26.577 10.456 1.00 14.15 C -ATOM 202 NZ LYS I 43 13.226 -27.491 9.406 1.00 10.85 N -ATOM 203 N PRO I 44 13.352 -30.106 15.923 1.00 16.81 N -ATOM 204 CA PRO I 44 14.183 -29.654 17.033 1.00 17.34 C -ATOM 205 C PRO I 44 15.097 -28.476 16.764 1.00 12.69 C -ATOM 206 O PRO I 44 15.460 -27.793 17.739 1.00 18.82 O -ATOM 207 CB PRO I 44 14.982 -30.902 17.434 1.00 19.36 C -ATOM 208 CG PRO I 44 14.134 -32.063 16.974 1.00 17.24 C -ATOM 209 CD PRO I 44 13.482 -31.566 15.700 1.00 18.51 C -ATOM 210 N GLU I 45 15.470 -28.229 15.542 1.00 13.52 N -ATOM 211 CA GLU I 45 16.354 -27.129 15.131 1.00 14.95 C -ATOM 212 C GLU I 45 15.625 -25.881 14.626 1.00 17.15 C -ATOM 213 O GLU I 45 16.271 -24.911 14.173 1.00 16.32 O -ATOM 214 CB GLU I 45 17.248 -27.546 13.952 1.00 9.98 C -ATOM 215 CG GLU I 45 16.644 -27.572 12.557 1.00 10.75 C -ATOM 216 CD GLU I 45 15.732 -28.688 12.165 1.00 8.14 C -ATOM 217 OE1 GLU I 45 15.371 -28.890 11.021 1.00 10.38 O -ATOM 218 OE2 GLU I 45 15.335 -29.407 13.092 1.00 7.28 O -ATOM 219 N ALA I 46 14.296 -25.926 14.640 1.00 16.99 N -ATOM 220 CA ALA I 46 13.480 -24.810 14.160 1.00 16.57 C -ATOM 221 C ALA I 46 13.766 -23.529 14.960 1.00 16.97 C -ATOM 222 O ALA I 46 13.978 -23.500 16.191 1.00 14.42 O -ATOM 223 CB ALA I 46 12.006 -25.178 14.177 1.00 18.81 C -ATOM 224 N GLN I 47 13.808 -22.469 14.161 1.00 15.12 N -ATOM 225 CA GLN I 47 13.934 -21.079 14.630 1.00 15.59 C -ATOM 226 C GLN I 47 12.529 -20.488 14.404 1.00 14.48 C -ATOM 227 O GLN I 47 12.125 -20.297 13.255 1.00 15.43 O -ATOM 228 CB GLN I 47 15.042 -20.280 13.971 1.00 14.57 C -ATOM 229 CG GLN I 47 16.441 -20.754 14.352 1.00 20.31 C -ATOM 230 CD GLN I 47 16.787 -20.674 15.818 1.00 20.92 C -ATOM 231 OE1 GLN I 47 16.587 -19.708 16.552 1.00 22.99 O -ATOM 232 NE2 GLN I 47 17.380 -21.750 16.340 1.00 26.19 N -ATOM 233 N ILE I 48 11.802 -20.339 15.498 1.00 16.27 N -ATOM 234 CA ILE I 48 10.406 -19.875 15.481 1.00 15.80 C -ATOM 235 C ILE I 48 10.296 -18.353 15.480 1.00 15.66 C -ATOM 236 O ILE I 48 10.807 -17.686 16.389 1.00 15.96 O -ATOM 237 CB ILE I 48 9.587 -20.549 16.640 1.00 17.30 C -ATOM 238 CG1 ILE I 48 9.667 -22.092 16.476 1.00 16.79 C -ATOM 239 CG2 ILE I 48 8.112 -20.079 16.733 1.00 15.04 C -ATOM 240 CD1 ILE I 48 9.075 -22.874 17.679 1.00 21.73 C -ATOM 241 N ILE I 49 9.612 -17.862 14.459 1.00 14.44 N -ATOM 242 CA ILE I 49 9.350 -16.429 14.248 1.00 12.51 C -ATOM 243 C ILE I 49 7.835 -16.209 14.313 1.00 10.43 C -ATOM 244 O ILE I 49 7.073 -16.959 13.687 1.00 12.52 O -ATOM 245 CB ILE I 49 9.962 -15.963 12.882 1.00 13.39 C -ATOM 246 CG1 ILE I 49 11.499 -16.164 12.865 1.00 15.31 C -ATOM 247 CG2 ILE I 49 9.580 -14.515 12.488 1.00 8.33 C -ATOM 248 CD1 ILE I 49 12.287 -15.564 14.052 1.00 12.08 C -ATOM 249 N VAL I 50 7.424 -15.222 15.077 1.00 9.95 N -ATOM 250 CA VAL I 50 6.021 -14.883 15.315 1.00 9.48 C -ATOM 251 C VAL I 50 5.676 -13.527 14.695 1.00 11.08 C -ATOM 252 O VAL I 50 6.168 -12.524 15.236 1.00 11.22 O -ATOM 253 CB VAL I 50 5.781 -14.853 16.844 1.00 11.04 C -ATOM 254 CG1 VAL I 50 4.377 -14.381 17.212 1.00 12.78 C -ATOM 255 CG2 VAL I 50 6.099 -16.175 17.517 1.00 13.08 C -ATOM 256 N LEU I 51 4.861 -13.525 13.658 1.00 10.84 N -ATOM 257 CA LEU I 51 4.434 -12.286 13.006 1.00 7.63 C -ATOM 258 C LEU I 51 2.903 -12.192 12.917 1.00 8.35 C -ATOM 259 O LEU I 51 2.209 -13.209 12.829 1.00 7.78 O -ATOM 260 CB LEU I 51 5.085 -12.267 11.629 1.00 6.43 C -ATOM 261 CG LEU I 51 6.571 -12.463 11.463 1.00 12.23 C -ATOM 262 CD1 LEU I 51 6.895 -12.729 9.987 1.00 11.51 C -ATOM 263 CD2 LEU I 51 7.308 -11.208 11.927 1.00 10.52 C -ATOM 264 N PRO I 52 2.416 -10.962 12.894 1.00 8.91 N -ATOM 265 CA PRO I 52 0.988 -10.679 12.717 1.00 8.08 C -ATOM 266 C PRO I 52 0.574 -11.041 11.295 1.00 11.02 C -ATOM 267 O PRO I 52 1.382 -10.841 10.366 1.00 11.03 O -ATOM 268 CB PRO I 52 0.884 -9.161 12.910 1.00 8.44 C -ATOM 269 CG PRO I 52 2.188 -8.710 13.474 1.00 8.74 C -ATOM 270 CD PRO I 52 3.218 -9.722 12.987 1.00 8.21 C -ATOM 271 N VAL I 53 -0.653 -11.520 11.104 1.00 13.73 N -ATOM 272 CA VAL I 53 -1.162 -11.852 9.752 1.00 13.43 C -ATOM 273 C VAL I 53 -1.148 -10.553 8.928 1.00 13.53 C -ATOM 274 O VAL I 53 -1.522 -9.509 9.485 1.00 12.58 O -ATOM 275 CB VAL I 53 -2.613 -12.380 9.772 1.00 14.76 C -ATOM 276 CG1 VAL I 53 -3.233 -12.469 8.383 1.00 12.98 C -ATOM 277 CG2 VAL I 53 -2.790 -13.681 10.534 1.00 17.50 C -ATOM 278 N GLY I 54 -0.799 -10.663 7.667 1.00 14.73 N -ATOM 279 CA GLY I 54 -0.750 -9.522 6.759 1.00 17.16 C -ATOM 280 C GLY I 54 0.641 -8.916 6.616 1.00 19.26 C -ATOM 281 O GLY I 54 0.775 -7.922 5.879 1.00 21.70 O -ATOM 282 N THR I 55 1.631 -9.482 7.278 1.00 19.90 N -ATOM 283 CA THR I 55 3.026 -9.024 7.221 1.00 19.01 C -ATOM 284 C THR I 55 3.733 -9.525 5.959 1.00 20.10 C -ATOM 285 O THR I 55 3.723 -10.705 5.577 1.00 20.03 O -ATOM 286 CB THR I 55 3.835 -9.379 8.534 1.00 13.94 C -ATOM 287 OG1 THR I 55 3.039 -8.848 9.638 1.00 14.28 O -ATOM 288 CG2 THR I 55 5.273 -8.870 8.656 1.00 11.44 C -ATOM 289 N ILE I 56 4.366 -8.581 5.287 1.00 21.85 N -ATOM 290 CA ILE I 56 5.139 -8.819 4.064 1.00 26.80 C -ATOM 291 C ILE I 56 6.579 -9.135 4.460 1.00 27.03 C -ATOM 292 O ILE I 56 7.249 -8.267 5.043 1.00 26.20 O -ATOM 293 CB ILE I 56 5.029 -7.574 3.114 1.00 34.95 C -ATOM 294 CG1 ILE I 56 3.532 -7.255 2.850 1.00 37.26 C -ATOM 295 CG2 ILE I 56 5.835 -7.765 1.797 1.00 38.25 C -ATOM 296 CD1 ILE I 56 3.165 -6.922 1.374 1.00 35.14 C -ATOM 297 N VAL I 57 7.016 -10.334 4.135 1.00 28.91 N -ATOM 298 CA VAL I 57 8.379 -10.774 4.491 1.00 31.56 C -ATOM 299 C VAL I 57 9.319 -10.718 3.294 1.00 35.26 C -ATOM 300 O VAL I 57 8.878 -10.587 2.133 1.00 35.25 O -ATOM 301 CB VAL I 57 8.280 -12.143 5.194 1.00 30.70 C -ATOM 302 CG1 VAL I 57 7.631 -12.051 6.575 1.00 31.82 C -ATOM 303 CG2 VAL I 57 7.560 -13.177 4.349 1.00 25.22 C -ATOM 304 N THR I 58 10.607 -10.825 3.594 1.00 38.04 N -ATOM 305 CA THR I 58 11.673 -10.826 2.570 1.00 41.77 C -ATOM 306 C THR I 58 11.719 -12.200 1.893 1.00 42.78 C -ATOM 307 O THR I 58 11.710 -13.236 2.588 1.00 44.39 O -ATOM 308 CB THR I 58 13.075 -10.436 3.177 1.00 43.20 C -ATOM 309 OG1 THR I 58 12.819 -9.628 4.374 1.00 47.09 O -ATOM 310 CG2 THR I 58 14.010 -9.719 2.198 1.00 45.92 C -ATOM 311 N MET I 59 11.805 -12.198 0.578 1.00 42.43 N -ATOM 312 CA MET I 59 11.790 -13.423 -0.231 1.00 42.89 C -ATOM 313 C MET I 59 12.923 -14.402 -0.034 1.00 41.48 C -ATOM 314 O MET I 59 13.182 -15.246 -0.920 1.00 43.82 O -ATOM 315 CB MET I 59 11.487 -13.044 -1.667 1.00 48.81 C -ATOM 316 CG MET I 59 12.377 -13.589 -2.744 1.00 50.54 C -ATOM 317 SD MET I 59 11.939 -12.708 -4.297 1.00 51.98 S -ATOM 318 CE MET I 59 13.386 -11.632 -4.439 1.00 52.05 C -ATOM 319 N GLU I 60 13.534 -14.434 1.126 1.00 41.22 N -ATOM 320 CA GLU I 60 14.630 -15.348 1.473 1.00 39.34 C -ATOM 321 C GLU I 60 14.165 -16.660 2.096 1.00 38.65 C -ATOM 322 O GLU I 60 13.464 -16.641 3.129 1.00 40.31 O -ATOM 323 CB GLU I 60 15.553 -14.670 2.495 1.00 41.16 C -ATOM 324 CG GLU I 60 15.004 -14.303 3.874 1.00 34.03 C -ATOM 325 CD GLU I 60 15.948 -13.599 4.798 1.00 28.96 C -ATOM 326 OE1 GLU I 60 16.303 -12.443 4.660 1.00 30.34 O -ATOM 327 OE2 GLU I 60 16.353 -14.327 5.723 1.00 28.34 O -ATOM 328 N TYR I 61 14.611 -17.778 1.555 1.00 36.27 N -ATOM 329 CA TYR I 61 14.251 -19.116 2.030 1.00 33.51 C -ATOM 330 C TYR I 61 15.194 -19.748 3.044 1.00 33.19 C -ATOM 331 O TYR I 61 16.326 -20.096 2.653 1.00 37.23 O -ATOM 332 CB TYR I 61 14.150 -20.079 0.814 1.00 29.28 C -ATOM 333 CG TYR I 61 13.798 -21.485 1.251 1.00 28.41 C -ATOM 334 CD1 TYR I 61 14.755 -22.500 1.318 1.00 31.55 C -ATOM 335 CD2 TYR I 61 12.497 -21.791 1.634 1.00 27.17 C -ATOM 336 CE1 TYR I 61 14.412 -23.787 1.735 1.00 28.91 C -ATOM 337 CE2 TYR I 61 12.136 -23.065 2.053 1.00 26.04 C -ATOM 338 CZ TYR I 61 13.097 -24.064 2.099 1.00 28.55 C -ATOM 339 OH TYR I 61 12.703 -25.305 2.513 1.00 26.67 O -ATOM 340 N ARG I 62 14.727 -20.014 4.255 1.00 29.39 N -ATOM 341 CA ARG I 62 15.539 -20.644 5.299 1.00 23.99 C -ATOM 342 C ARG I 62 14.903 -21.907 5.873 1.00 22.75 C -ATOM 343 O ARG I 62 13.892 -21.886 6.586 1.00 20.32 O -ATOM 344 CB ARG I 62 15.854 -19.676 6.440 1.00 27.80 C -ATOM 345 CG ARG I 62 16.717 -18.484 6.052 1.00 28.78 C -ATOM 346 CD ARG I 62 18.009 -18.462 6.782 1.00 32.63 C -ATOM 347 NE ARG I 62 17.969 -19.139 8.072 1.00 33.31 N -ATOM 348 CZ ARG I 62 19.023 -19.200 8.893 1.00 31.69 C -ATOM 349 NH1 ARG I 62 20.179 -18.614 8.592 1.00 28.13 N -ATOM 350 NH2 ARG I 62 18.915 -19.879 10.037 1.00 31.67 N -ATOM 351 N ILE I 63 15.581 -23.002 5.623 1.00 17.45 N -ATOM 352 CA ILE I 63 15.194 -24.357 6.003 1.00 18.72 C -ATOM 353 C ILE I 63 14.963 -24.580 7.480 1.00 18.40 C -ATOM 354 O ILE I 63 14.082 -25.410 7.839 1.00 23.17 O -ATOM 355 CB ILE I 63 16.213 -25.314 5.264 1.00 22.99 C -ATOM 356 CG1 ILE I 63 15.612 -26.713 4.984 1.00 26.52 C -ATOM 357 CG2 ILE I 63 17.599 -25.398 5.950 1.00 19.42 C -ATOM 358 CD1 ILE I 63 16.672 -27.837 4.742 1.00 24.70 C -ATOM 359 N ASP I 64 15.632 -23.860 8.364 1.00 14.60 N -ATOM 360 CA ASP I 64 15.500 -24.051 9.809 1.00 14.66 C -ATOM 361 C ASP I 64 14.469 -23.145 10.478 1.00 10.73 C -ATOM 362 O ASP I 64 14.340 -23.221 11.714 1.00 12.65 O -ATOM 363 CB ASP I 64 16.845 -23.914 10.535 1.00 19.91 C -ATOM 364 CG ASP I 64 17.527 -22.577 10.305 1.00 20.76 C -ATOM 365 OD1 ASP I 64 17.446 -21.999 9.205 1.00 21.61 O -ATOM 366 OD2 ASP I 64 18.137 -22.110 11.298 1.00 25.03 O -ATOM 367 N ARG I 65 13.870 -22.315 9.663 1.00 11.64 N -ATOM 368 CA ARG I 65 12.918 -21.309 10.141 1.00 12.51 C -ATOM 369 C ARG I 65 11.453 -21.716 10.025 1.00 12.85 C -ATOM 370 O ARG I 65 11.074 -22.245 8.974 1.00 12.01 O -ATOM 371 CB ARG I 65 13.130 -20.016 9.321 1.00 10.70 C -ATOM 372 CG ARG I 65 12.169 -18.890 9.687 1.00 14.03 C -ATOM 373 CD ARG I 65 12.644 -17.542 9.266 1.00 11.51 C -ATOM 374 NE ARG I 65 12.674 -17.387 7.831 1.00 15.20 N -ATOM 375 CZ ARG I 65 13.460 -16.613 7.090 1.00 15.39 C -ATOM 376 NH1 ARG I 65 14.340 -15.768 7.596 1.00 17.74 N -ATOM 377 NH2 ARG I 65 13.389 -16.713 5.764 1.00 16.07 N -ATOM 378 N VAL I 66 10.685 -21.359 11.050 1.00 10.71 N -ATOM 379 CA VAL I 66 9.240 -21.555 11.079 1.00 13.23 C -ATOM 380 C VAL I 66 8.541 -20.253 11.517 1.00 12.86 C -ATOM 381 O VAL I 66 8.570 -19.906 12.710 1.00 16.02 O -ATOM 382 CB VAL I 66 8.740 -22.721 11.951 1.00 11.53 C -ATOM 383 CG1 VAL I 66 7.216 -22.881 11.850 1.00 11.98 C -ATOM 384 CG2 VAL I 66 9.420 -24.045 11.659 1.00 13.94 C -ATOM 385 N ARG I 67 7.886 -19.619 10.566 1.00 9.65 N -ATOM 386 CA ARG I 67 7.130 -18.389 10.853 1.00 10.83 C -ATOM 387 C ARG I 67 5.717 -18.746 11.304 1.00 7.13 C -ATOM 388 O ARG I 67 5.057 -19.492 10.560 1.00 9.94 O -ATOM 389 CB ARG I 67 7.001 -17.538 9.570 1.00 11.98 C -ATOM 390 CG ARG I 67 8.290 -16.786 9.175 1.00 11.30 C -ATOM 391 CD ARG I 67 8.099 -16.286 7.796 1.00 15.42 C -ATOM 392 NE ARG I 67 9.218 -15.651 7.158 1.00 26.19 N -ATOM 393 CZ ARG I 67 9.598 -15.877 5.897 1.00 23.69 C -ATOM 394 NH1 ARG I 67 8.987 -16.777 5.135 1.00 25.11 N -ATOM 395 NH2 ARG I 67 10.603 -15.150 5.399 1.00 32.20 N -ATOM 396 N LEU I 68 5.264 -18.178 12.388 1.00 5.51 N -ATOM 397 CA LEU I 68 3.881 -18.326 12.864 1.00 7.63 C -ATOM 398 C LEU I 68 3.149 -17.004 12.584 1.00 6.35 C -ATOM 399 O LEU I 68 3.629 -15.965 13.056 1.00 8.97 O -ATOM 400 CB LEU I 68 3.893 -18.673 14.353 1.00 6.88 C -ATOM 401 CG LEU I 68 4.586 -19.961 14.774 1.00 11.18 C -ATOM 402 CD1 LEU I 68 4.451 -20.213 16.270 1.00 2.78 C -ATOM 403 CD2 LEU I 68 3.981 -21.071 13.922 1.00 10.53 C -ATOM 404 N PHE I 69 2.068 -17.071 11.845 1.00 5.58 N -ATOM 405 CA PHE I 69 1.254 -15.871 11.532 1.00 5.54 C -ATOM 406 C PHE I 69 0.064 -15.898 12.493 1.00 6.41 C -ATOM 407 O PHE I 69 -0.788 -16.799 12.467 1.00 7.94 O -ATOM 408 CB PHE I 69 0.923 -15.768 10.047 1.00 5.59 C -ATOM 409 CG PHE I 69 2.063 -15.303 9.185 1.00 12.09 C -ATOM 410 CD1 PHE I 69 2.924 -16.230 8.593 1.00 13.33 C -ATOM 411 CD2 PHE I 69 2.299 -13.936 8.992 1.00 10.83 C -ATOM 412 CE1 PHE I 69 4.008 -15.811 7.835 1.00 13.21 C -ATOM 413 CE2 PHE I 69 3.384 -13.491 8.239 1.00 11.69 C -ATOM 414 CZ PHE I 69 4.229 -14.445 7.653 1.00 11.95 C -ATOM 415 N VAL I 70 0.072 -14.937 13.400 1.00 7.81 N -ATOM 416 CA VAL I 70 -0.893 -14.807 14.480 1.00 6.70 C -ATOM 417 C VAL I 70 -1.933 -13.701 14.306 1.00 10.75 C -ATOM 418 O VAL I 70 -1.791 -12.706 13.598 1.00 8.45 O -ATOM 419 CB VAL I 70 -0.182 -14.794 15.849 1.00 3.28 C -ATOM 420 CG1 VAL I 70 0.815 -15.948 15.986 1.00 4.29 C -ATOM 421 CG2 VAL I 70 0.495 -13.475 16.183 1.00 3.98 C -ATOM 422 N ASP I 71 -3.046 -13.959 14.981 1.00 11.12 N -ATOM 423 CA ASP I 71 -4.238 -13.107 15.079 1.00 12.63 C -ATOM 424 C ASP I 71 -4.081 -12.235 16.333 1.00 14.44 C -ATOM 425 O ASP I 71 -3.074 -12.351 17.058 1.00 17.27 O -ATOM 426 CB ASP I 71 -5.514 -13.958 15.062 1.00 7.46 C -ATOM 427 CG ASP I 71 -5.869 -14.578 16.391 1.00 8.37 C -ATOM 428 OD1 ASP I 71 -5.102 -14.498 17.367 1.00 12.91 O -ATOM 429 OD2 ASP I 71 -6.946 -15.205 16.517 1.00 9.72 O -ATOM 430 N LYS I 72 -5.051 -11.380 16.574 1.00 13.75 N -ATOM 431 CA LYS I 72 -5.097 -10.438 17.680 1.00 13.74 C -ATOM 432 C LYS I 72 -4.946 -11.083 19.051 1.00 15.88 C -ATOM 433 O LYS I 72 -4.589 -10.376 20.015 1.00 16.72 O -ATOM 434 CB LYS I 72 -6.456 -9.729 17.730 1.00 13.34 C -ATOM 435 CG LYS I 72 -6.507 -8.381 17.036 1.00 20.82 C -ATOM 436 CD LYS I 72 -7.817 -7.657 17.322 1.00 21.70 C -ATOM 437 CE LYS I 72 -7.679 -6.538 18.330 1.00 21.57 C -ATOM 438 NZ LYS I 72 -8.402 -5.330 17.839 1.00 30.14 N -ATOM 439 N LEU I 73 -5.275 -12.356 19.142 1.00 16.38 N -ATOM 440 CA LEU I 73 -5.201 -13.055 20.437 1.00 18.38 C -ATOM 441 C LEU I 73 -3.989 -13.979 20.495 1.00 19.84 C -ATOM 442 O LEU I 73 -3.851 -14.718 21.490 1.00 22.48 O -ATOM 443 CB LEU I 73 -6.544 -13.733 20.702 1.00 22.11 C -ATOM 444 CG LEU I 73 -7.766 -12.854 20.907 1.00 22.63 C -ATOM 445 CD1 LEU I 73 -8.985 -13.712 21.224 1.00 24.13 C -ATOM 446 CD2 LEU I 73 -7.484 -11.876 22.047 1.00 24.80 C -ATOM 447 N ASP I 74 -3.163 -13.927 19.472 1.00 19.04 N -ATOM 448 CA ASP I 74 -1.954 -14.754 19.386 1.00 20.64 C -ATOM 449 C ASP I 74 -2.256 -16.222 19.066 1.00 17.76 C -ATOM 450 O ASP I 74 -1.538 -17.062 19.642 1.00 18.05 O -ATOM 451 CB ASP I 74 -1.118 -14.670 20.675 1.00 25.90 C -ATOM 452 CG ASP I 74 -0.466 -13.319 20.898 1.00 29.31 C -ATOM 453 OD1 ASP I 74 0.082 -12.750 19.940 1.00 30.95 O -ATOM 454 OD2 ASP I 74 -0.524 -12.847 22.054 1.00 30.81 O -ATOM 455 N ASN I 75 -3.259 -16.487 18.263 1.00 14.97 N -ATOM 456 CA ASN I 75 -3.598 -17.863 17.854 1.00 13.91 C -ATOM 457 C ASN I 75 -3.042 -18.012 16.436 1.00 12.18 C -ATOM 458 O ASN I 75 -2.896 -16.949 15.809 1.00 13.00 O -ATOM 459 CB ASN I 75 -5.101 -18.132 17.948 1.00 13.31 C -ATOM 460 CG ASN I 75 -5.494 -18.262 19.407 1.00 15.19 C -ATOM 461 OD1 ASN I 75 -4.723 -18.834 20.193 1.00 19.14 O -ATOM 462 ND2 ASN I 75 -6.631 -17.697 19.772 1.00 17.73 N -ATOM 463 N ILE I 76 -2.730 -19.221 16.019 1.00 11.90 N -ATOM 464 CA ILE I 76 -2.185 -19.433 14.667 1.00 12.65 C -ATOM 465 C ILE I 76 -3.342 -19.252 13.677 1.00 11.59 C -ATOM 466 O ILE I 76 -4.322 -20.009 13.762 1.00 14.18 O -ATOM 467 CB ILE I 76 -1.478 -20.810 14.457 1.00 9.22 C -ATOM 468 CG1 ILE I 76 -0.257 -21.048 15.354 1.00 13.74 C -ATOM 469 CG2 ILE I 76 -1.097 -21.028 12.960 1.00 6.37 C -ATOM 470 CD1 ILE I 76 0.140 -20.018 16.424 1.00 13.42 C -ATOM 471 N ALA I 77 -3.162 -18.316 12.767 1.00 9.88 N -ATOM 472 CA ALA I 77 -4.214 -17.967 11.809 1.00 8.17 C -ATOM 473 C ALA I 77 -4.079 -18.616 10.449 1.00 11.23 C -ATOM 474 O ALA I 77 -5.055 -18.635 9.669 1.00 11.49 O -ATOM 475 CB ALA I 77 -4.229 -16.428 11.726 1.00 4.65 C -ATOM 476 N GLU I 78 -2.891 -19.085 10.120 1.00 9.22 N -ATOM 477 CA GLU I 78 -2.597 -19.763 8.857 1.00 13.06 C -ATOM 478 C GLU I 78 -1.699 -20.960 9.151 1.00 10.24 C -ATOM 479 O GLU I 78 -1.083 -21.009 10.226 1.00 13.48 O -ATOM 480 CB GLU I 78 -1.928 -18.872 7.823 1.00 16.66 C -ATOM 481 CG GLU I 78 -1.442 -17.490 8.233 1.00 24.46 C -ATOM 482 CD GLU I 78 -1.217 -16.534 7.100 1.00 22.99 C -ATOM 483 OE1 GLU I 78 -0.765 -16.862 6.021 1.00 29.51 O -ATOM 484 OE2 GLU I 78 -1.530 -15.365 7.390 1.00 27.97 O -ATOM 485 N VAL I 79 -1.647 -21.889 8.224 1.00 12.11 N -ATOM 486 CA VAL I 79 -0.849 -23.111 8.362 1.00 11.23 C -ATOM 487 C VAL I 79 0.637 -22.743 8.418 1.00 10.70 C -ATOM 488 O VAL I 79 1.125 -22.175 7.430 1.00 12.86 O -ATOM 489 CB VAL I 79 -1.054 -24.095 7.183 1.00 13.33 C -ATOM 490 CG1 VAL I 79 -0.023 -25.223 7.255 1.00 10.05 C -ATOM 491 CG2 VAL I 79 -2.463 -24.645 7.074 1.00 10.55 C -ATOM 492 N PRO I 80 1.266 -23.104 9.509 1.00 9.97 N -ATOM 493 CA PRO I 80 2.714 -22.871 9.687 1.00 10.84 C -ATOM 494 C PRO I 80 3.493 -23.711 8.672 1.00 11.17 C -ATOM 495 O PRO I 80 3.107 -24.865 8.398 1.00 11.21 O -ATOM 496 CB PRO I 80 2.966 -23.306 11.130 1.00 12.38 C -ATOM 497 CG PRO I 80 1.620 -23.328 11.814 1.00 10.40 C -ATOM 498 CD PRO I 80 0.663 -23.737 10.696 1.00 11.53 C -ATOM 499 N ARG I 81 4.557 -23.162 8.131 1.00 10.29 N -ATOM 500 CA ARG I 81 5.395 -23.823 7.129 1.00 13.19 C -ATOM 501 C ARG I 81 6.855 -23.394 7.251 1.00 14.50 C -ATOM 502 O ARG I 81 7.114 -22.263 7.689 1.00 16.59 O -ATOM 503 CB ARG I 81 4.933 -23.501 5.698 1.00 14.36 C -ATOM 504 CG ARG I 81 3.956 -24.494 5.110 1.00 22.23 C -ATOM 505 CD ARG I 81 3.417 -24.045 3.794 1.00 33.13 C -ATOM 506 NE ARG I 81 2.449 -22.972 3.956 1.00 40.24 N -ATOM 507 CZ ARG I 81 1.124 -23.113 3.908 1.00 41.54 C -ATOM 508 NH1 ARG I 81 0.526 -24.221 3.488 1.00 40.91 N -ATOM 509 NH2 ARG I 81 0.385 -22.109 4.392 1.00 45.11 N -ATOM 510 N VAL I 82 7.747 -24.270 6.813 1.00 14.70 N -ATOM 511 CA VAL I 82 9.190 -23.996 6.828 1.00 13.66 C -ATOM 512 C VAL I 82 9.560 -22.976 5.747 1.00 13.30 C -ATOM 513 O VAL I 82 8.985 -23.009 4.640 1.00 12.70 O -ATOM 514 CB VAL I 82 10.004 -25.297 6.632 1.00 14.43 C -ATOM 515 CG1 VAL I 82 11.478 -24.982 6.349 1.00 17.60 C -ATOM 516 CG2 VAL I 82 9.882 -26.249 7.805 1.00 15.45 C -ATOM 517 N GLY I 83 10.551 -22.146 6.059 1.00 12.36 N -ATOM 518 CA GLY I 83 11.026 -21.174 5.057 1.00 13.03 C -ATOM 519 C GLY I 83 11.395 -19.829 5.657 1.00 11.77 C -ATOM 520 O GLY I 83 10.798 -19.541 6.714 1.00 15.36 O -ATOM 521 OXT GLY I 83 12.222 -19.137 5.054 1.00 16.40 O -TER 522 GLY I 83 -HETATM 523 O HOH I 84 -0.329 -13.254 6.640 1.00 24.81 O -HETATM 524 O HOH I 85 20.537 -17.890 5.103 0.98 51.62 O -HETATM 525 O HOH I 86 3.985 -5.480 6.143 0.93 22.19 O -HETATM 526 O HOH I 87 13.612 -14.849 -5.298 1.00 37.67 O -HETATM 527 O HOH I 88 2.323 -19.638 7.496 0.75 19.24 O -HETATM 528 O HOH I 89 8.493 -20.055 7.668 1.00 10.51 O -HETATM 529 O HOH I 90 1.392 -19.519 10.757 0.69 8.41 O -HETATM 530 O HOH I 91 14.304 -32.137 12.328 0.88 20.39 O -HETATM 531 O HOH I 92 8.165 -34.925 12.441 1.00 27.86 O -HETATM 532 O HOH I 93 -3.208 -8.404 12.277 0.80 18.92 O -HETATM 533 O HOH I 94 2.873 -36.659 17.649 0.48 20.25 O -HETATM 534 O HOH I 95 -8.502 -16.494 17.981 1.00 6.91 O -HETATM 535 O HOH I 96 13.110 -21.154 18.099 1.00 21.03 O -HETATM 536 O HOH I 97 15.611 -24.679 18.097 1.00 16.43 O -HETATM 537 O HOH I 98 -8.313 -18.290 22.531 1.00 34.75 O -HETATM 538 O HOH I 99 6.311 -23.358 23.845 1.00 42.27 O -HETATM 539 O HOH I 100 9.592 -7.442 4.540 1.00 21.71 O -HETATM 540 O HOH I 101 17.915 -14.447 0.209 1.00 46.91 O -HETATM 541 O HOH I 102 4.643 -20.183 7.815 0.79 11.79 O -HETATM 542 O HOH I 103 8.776 -39.486 8.344 0.33 20.46 O -HETATM 543 O HOH I 104 20.049 -19.093 13.191 0.88 25.50 O -HETATM 544 O HOH I 105 -1.050 -35.346 12.637 0.98 32.03 O -HETATM 545 O HOH I 106 -0.528 -37.282 13.452 0.74 34.20 O -HETATM 546 O HOH I 107 -2.814 -10.035 13.791 0.52 7.98 O -HETATM 547 O HOH I 108 7.629 -22.058 1.674 1.00 51.13 O -HETATM 548 O HOH I 109 2.064 -5.457 11.942 1.00 65.35 O -HETATM 549 O HOH I 110 23.048 -21.016 12.391 1.00 32.12 O -HETATM 550 O HOH I 111 2.660 -35.407 12.320 1.00 37.99 O -HETATM 551 O HOH I 112 19.516 -21.255 13.031 0.79 32.01 O -HETATM 552 O HOH I 113 21.191 -22.240 18.079 0.59 21.14 O -HETATM 553 O HOH I 114 6.941 -36.073 17.397 0.64 48.88 O -HETATM 554 O HOH I 115 -10.533 -17.031 20.300 0.55 21.45 O -HETATM 555 O HOH I 116 5.641 -38.800 22.958 1.00 52.61 O -HETATM 556 O HOH I 117 19.782 -25.123 22.901 0.75 34.24 O -HETATM 557 O HOH I 118 13.266 -20.427 23.057 0.64 34.89 O -HETATM 558 O HOH I 119 -5.628 -30.359 22.925 0.73 48.31 O -HETATM 559 O HOH I 120 8.529 -29.351 22.983 1.00 32.02 O -HETATM 560 O HOH I 121 13.517 -29.044 26.642 0.86 34.70 O -HETATM 561 O HOH I 122 0.323 -6.119 8.978 0.96 39.54 O -HETATM 562 O HOH I 123 -4.037 -15.671 6.351 1.00 35.45 O -HETATM 563 O HOH I 124 15.631 -11.826 -0.761 0.93 46.62 O -HETATM 564 O HOH I 125 4.800 -4.562 12.199 1.00 39.72 O -HETATM 565 O HOH I 126 13.468 -18.103 17.589 0.73 26.09 O -HETATM 566 O HOH I 127 -3.023 -2.235 18.293 1.00 41.70 O -HETATM 567 O HOH I 128 18.407 -24.479 17.873 0.52 9.70 O -HETATM 568 O HOH I 129 -7.836 -2.378 19.154 0.73 60.68 O -HETATM 569 O HOH I 130 21.030 -19.090 21.742 1.00 47.98 O -HETATM 570 O HOH I 131 1.881 -32.214 22.846 0.83 46.85 O -HETATM 571 O HOH I 132 -7.515 -4.664 22.763 0.83 35.53 O -HETATM 572 O HOH I 133 -2.229 -10.591 22.682 1.00 50.61 O -HETATM 573 O HOH I 134 22.150 -25.947 24.001 0.83 44.94 O -HETATM 574 O HOH I 135 11.224 -29.647 8.973 0.70 19.43 O -HETATM 575 O HOH I 136 5.258 -34.075 4.412 0.40 18.69 O -HETATM 576 O HOH I 137 1.459 -39.256 4.127 0.60 23.87 O -HETATM 577 O HOH I 138 4.530 -28.781 -0.047 1.00 43.13 O -HETATM 578 O HOH I 139 11.913 -34.478 18.581 0.64 33.68 O -HETATM 579 O HOH I 140 -5.065 -32.731 22.028 0.78 44.05 O -HETATM 580 O HOH I 141 -2.568 -32.082 23.071 1.00 50.49 O -HETATM 581 O HOH I 142 5.202 -19.362 24.595 1.00 47.01 O -HETATM 582 O HOH I 143 8.744 -16.337 23.550 0.95 39.33 O -HETATM 583 O HOH I 144 16.078 -37.479 4.200 1.00 32.94 O -HETATM 584 O HOH I 145 -3.995 -3.539 23.173 0.45 29.34 O -HETATM 585 O HOH I 146 -8.826 -33.316 22.007 0.73 42.83 O -HETATM 586 O HOH I 147 -1.791 -21.764 25.717 0.74 27.23 O -MASTER 341 0 0 1 4 0 1 6 585 1 0 7 -END diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/scripts/init.py b/benchmarks/ProteinDesign/FixedBackboneDesign/scripts/init.py index 315eb9eb..f2091fdb 100644 --- a/benchmarks/ProteinDesign/FixedBackboneDesign/scripts/init.py +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/scripts/init.py @@ -82,6 +82,7 @@ def design_sequence( - 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)) @@ -102,10 +103,10 @@ def design_sequence( # Do not change non-design positions task.nonconst_residue_task(i).prevent_repacking() - # Run Packer + # Run Packer with the configured task (not the factory) packer = PackRotamersMover() packer.score_function(scorefxn) - packer.task_factory(tf) + packer.task(task) packer.apply(pose) # Score the designed pose diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/verification/evaluator.py b/benchmarks/ProteinDesign/FixedBackboneDesign/verification/evaluator.py index a6ffb9db..baa0d941 100644 --- a/benchmarks/ProteinDesign/FixedBackboneDesign/verification/evaluator.py +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/verification/evaluator.py @@ -13,15 +13,24 @@ 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", +} + # --------------------------------------------------------------------------- -# Prepare: load raw_task.json, load PDB, create a prepared reference PDB +# Read-only utilities # --------------------------------------------------------------------------- def load_json(path: str | Path) -> dict[str, Any]: @@ -36,6 +45,75 @@ def dump_json(path: str | Path, payload: dict[str, Any]) -> None: 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. @@ -43,10 +121,9 @@ def prepare(raw_task_path: str | Path, prepared_output: str | Path) -> None: """ import pyrosetta pyrosetta.init(silent=True) + pyrosetta.rosetta.basic.random.init_random_generators(42, "mt19937") task = load_json(raw_task_path) - # raw_task.json is at /data/raw_task.json - # PDB paths in raw_task.json are relative to / task_root = Path(raw_task_path).resolve().parent.parent pdb_path = Path(task["pdb_path"]) if not pdb_path.is_absolute(): @@ -58,11 +135,8 @@ def prepare(raw_task_path: str | Path, prepared_output: str | Path) -> None: # Load the native structure pose = pyrosetta.pose_from_file(str(pdb_path)) - # Set up a PackerTask to repack the native side chains + # Repack native side chains to get a baseline energy scorefxn = pyrosetta.get_fa_scorefxn() - - # Repack the native side chains to get a baseline energy - # Use a simple TaskFactory that repacks all positions tf = pyrosetta.rosetta.core.pack.task.TaskFactory() tf.push_back(pyrosetta.rosetta.core.pack.task.operation.RestrictToRepacking()) packer = pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover() @@ -70,7 +144,6 @@ def prepare(raw_task_path: str | Path, prepared_output: str | Path) -> None: packer.task_factory(tf) packer.apply(pose) - # Score the repacked native pose (this is the baseline energy) baseline_energy = scorefxn(pose) # Dump the repacked native pose as the prepared reference PDB @@ -78,7 +151,6 @@ def prepare(raw_task_path: str | Path, prepared_output: str | Path) -> None: output_path.parent.mkdir(parents=True, exist_ok=True) pose.dump_pdb(str(output_path)) - # Also save metadata alongside the prepared PDB meta = { "baseline_energy": round(baseline_energy, 6), "design_positions": design_positions, @@ -101,16 +173,18 @@ def prepare(raw_task_path: str | Path, prepared_output: str | Path) -> None: 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 return metrics. + Score a designed PDB using PyRosetta ref2015 and verify task constraints. Returns: - dict with keys: valid, combined_score, total_energy, baseline_energy, - improvement, and individual energy terms (fa_atr, fa_rep, ...) + 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() @@ -120,62 +194,58 @@ def evaluate_candidate( # Score candidate candidate_pose = pyrosetta.pose_from_file(str(candidate_pdb)) - candidate_energy = scorefxn(candidate_pose) - # Extract individual energy terms - native_energies = native_pose.energies() - candidate_energies = candidate_pose.energies() + # 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, + } - # Get the score types used by ref2015 - score_types = [ - pyrosetta.rosetta.core.scoring.ScoreType.fa_atr, - pyrosetta.rosetta.core.scoring.ScoreType.fa_rep, - pyrosetta.rosetta.core.scoring.ScoreType.fa_sol, - pyrosetta.rosetta.core.scoring.ScoreType.fa_elec, - pyrosetta.rosetta.core.scoring.ScoreType.hbond_bb_sc, - pyrosetta.rosetta.core.scoring.ScoreType.hbond_sc, - pyrosetta.rosetta.core.scoring.ScoreType.p_aa_pp, - pyrosetta.rosetta.core.scoring.ScoreType.ref, - ] - term_names = { - 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", - } + candidate_energy = scorefxn(candidate_pose) + # Collect metrics metrics: dict[str, Any] = {"valid": True} - - # Total energies metrics["native_energy"] = round(native_energy, 6) metrics["total_energy"] = round(candidate_energy, 6) metrics["improvement"] = round(native_energy - candidate_energy, 6) - # Combined score: normalized improvement if abs(native_energy) > 1e-6: metrics["combined_score"] = round((native_energy - candidate_energy) / abs(native_energy), 6) else: metrics["combined_score"] = 0.0 - # Individual energy terms - for st in score_types: - name = term_names.get(st, str(st)) - native_term = native_energies.total_energies()[st] if hasattr(native_energies, "total_energies") else 0.0 - candidate_term = candidate_energies.total_energies()[st] if hasattr(candidate_energies, "total_energies") else 0.0 - metrics[f"native_{name}"] = round(float(native_term), 6) - metrics[name] = round(float(candidate_term), 6) - - # Detect invalid: NaN or Inf energies - import math + # 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"] = -1e18 + metrics["combined_score"] = INVALID_COMBINED_SCORE return metrics @@ -184,31 +254,24 @@ 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) + metrics = evaluate_candidate(native_pdb, candidate_pdb, design_positions) dump_json(result_output, metrics) - print(f"[evaluator] total_energy={metrics['total_energy']:.4f} " - f"improvement={metrics['improvement']:.4f} " - f"valid={metrics['valid']}") + 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: run_candidate_and_evaluate -# Matches the CONTRIBUTING.md test command pattern: -# python verification/evaluator.py scripts/init.py +# Full pipeline # --------------------------------------------------------------------------- def run_candidate_and_evaluate(script_path: str | Path) -> int: - """ - Full automatic pipeline: - 1. Read raw_task.json and prepare the PDB - 2. Run the candidate script (design) - 3. Evaluate the designed structure - 4. Write metrics.json to the task root - """ + """Full automatic pipeline matching CONTRIBUTING.md test command format.""" evaluator_dir = Path(__file__).resolve().parent - task_dir = evaluator_dir.parent # Task root directory + task_dir = evaluator_dir.parent raw_task = task_dir / "data" / "raw_task.json" outputs_dir = task_dir / "outputs" outputs_dir.mkdir(exist_ok=True) @@ -221,6 +284,18 @@ def run_candidate_and_evaluate(script_path: str | Path) -> int: 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: @@ -240,7 +315,7 @@ def run_candidate_and_evaluate(script_path: str | Path) -> int: print("[evaluator] ERROR: candidate timed out (300s)") metrics = { "valid": False, - "combined_score": -1e18, + "combined_score": INVALID_COMBINED_SCORE, "total_energy": 0.0, "error_message": "candidate timed out", } @@ -251,18 +326,30 @@ def run_candidate_and_evaluate(script_path: str | Path) -> int: print(f"[evaluator] ERROR: candidate script not found: {script_path}") return 1 - # Step 3: Evaluate + # 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) + metrics = evaluate_candidate(prepared_pdb, solution_pdb, design_positions) metrics["returncode"] = result.returncode if result.returncode != 0: metrics["valid"] = False - metrics["combined_score"] = -1e18 + 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) - # Also print JSON to stdout for the unified framework print(json.dumps(metrics)) return 0 if metrics.get("valid", False) else 1 @@ -273,32 +360,28 @@ def run_candidate_and_evaluate(script_path: str | Path) -> int: def main() -> int: if len(sys.argv) == 2 and not sys.argv[1].startswith("--"): - # CONTRIBUTING.md test command format: python evaluator.py scripts/init.py return run_candidate_and_evaluate(sys.argv[1]) - parser = argparse.ArgumentParser( - description="PyRosetta evaluator for FixedBackboneDesign" - ) + parser = argparse.ArgumentParser(description="PyRosetta evaluator for FixedBackboneDesign") subparsers = parser.add_subparsers(dest="command", required=True) - # prepare 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) - # evaluate 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) - + evaluate(args.native, args.candidate, args.result_output, args.design_positions) return 0 From 6930698d8984f0b399564d5e07a1cbba99a4683c Mon Sep 17 00:00:00 2001 From: han Date: Tue, 14 Jul 2026 15:43:21 +0800 Subject: [PATCH 4/5] chore: add baseline result_log.txt --- .../baseline/result_log.txt | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 benchmarks/ProteinDesign/FixedBackboneDesign/baseline/result_log.txt 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. From ebd319891bfdf61816b76e5c1633d5e3e9d82fe2 Mon Sep 17 00:00:00 2001 From: han Date: Wed, 15 Jul 2026 15:47:28 +0800 Subject: [PATCH 5/5] fix: raise FileNotFoundError instead of silent fallback in load_design_positions --- .../ProteinDesign/FixedBackboneDesign/scripts/init.py | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/benchmarks/ProteinDesign/FixedBackboneDesign/scripts/init.py b/benchmarks/ProteinDesign/FixedBackboneDesign/scripts/init.py index f2091fdb..81faffcf 100644 --- a/benchmarks/ProteinDesign/FixedBackboneDesign/scripts/init.py +++ b/benchmarks/ProteinDesign/FixedBackboneDesign/scripts/init.py @@ -47,12 +47,10 @@ def load_design_positions(prepared_pdb: str | Path) -> list[int]: if meta_path.exists(): meta = load_json(meta_path) return list(meta.get("design_positions", [])) - # Fallback: design all positions (safety net — real data should have meta) - print("[init] WARNING: no meta file found, designing all positions", file=sys.stderr) - import pyrosetta - pyrosetta.init(silent=True) - pose = pyrosetta.pose_from_file(str(prepared_pdb)) - return list(range(1, pose.total_residue() + 1)) + 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