The skull seems out of proportion with its thick, heavy body because it is so narrow and the jaws are delicate and fine.
What's the meaning of "seems out of" ?
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proportion means the sense of scale between two shapes or objects. If something is in proportion with another object, it is the correct size in relation to it. If it is out of proportion, it is too big or small.
seems means looks like it would be and implies a level of uncertainty - the author does not say that it is definitely out of proportion, but that due to the size of the thick, heavy body, the skull looks like it should be bigger.