The largest later named Pueblo Bonito(Pretty Town)by the Spanish, rose in five terraced stories，contained more than 800 rooms，and could have housed a population of 1，000 or more.
【译句】最大的一座后来被西班牙人称为Pueblo Bonito(美丽的城镇)，是一个五层梯式楼，有800多间房子，能够容纳1 000人以上。
分句1：The largest rose in five terraced stories，contained more than 800 rooms，and could have housed a population of 1，000 or more;
分句2：later named Pueblo Bonito(Pretty Town)by the Spanish。
分句1嵌套了分句2，分句1的主语是the largest, 这是“the + 形容词”表示一个名词的结构，相当于“the largest one" 的省略的说法。
分句2是省略了“which was" 的定语从句，用来修饰分句1的主语the largest, 分句1内部是由三个并列的谓语构成的句子。