。
She called me very late last night.
Literal
She [topic-は] last-night extremely late me [to-に] phone [object-を] called-toward-me.
大変 functions adverbially as 'extremely,' modifying the adverbial 遅く (the く-form of the i-adjective 遅い 'late'). The verb phrase 電話をかけてくる pairs the standard collocation 電話をかける ('to place a call') with the directional auxiliary ~てくる, which encodes that the action came toward the speaker — without it, the sentence could equally describe an outgoing call. Japanese deixis is built right into the verb morphology: who acts on whom is part of the form, not just inferred from context.