The Duke of York and all the King's Council remained shut up in Oxford. Fairfax found the city well prepared for a siege. "The rising ground to the north was protected by many strong bulwarks flanking one another. Round about the line, both upon the bulwarks and the curtain, was strongly set with storm poles. Outside the ditch was a strong palisade beyond which were many pits dug so that a single footman could not without difficulty approach to the trench. Within the city were 5000 foot, and the place was well supplied with stores. All this strength being apprehended and considered by Sir Thomas Fairfax, he concluded that this was no place to be taken at a running pull, but likely rather to prove a business of time, hazard and industry." Accordingly he proceeded to make a fortified camp on Headington Hill, to make a bridge over the Cherwell near Marston, and establish a post between the Cherwell and Isis on the north for the main body of his troops. Lines were drawn from Headington to S. Bartholomew's common road, and from thence to Campus pits. A memento of the siege, a cannon shot which is said to have struck the gateway tower of S. John's College, is preserved in the library of that college. Little progress, however, had been made with the siege, though the defence was for a lost cause, when Charles, who had been handed over by the Scots to a Committee of the House, sent orders to the governor to make conditions and surrender the place to Fairfax. Honourable terms were granted. Fairfax had expressed his earnest desire to preserve a place "so famous for learning from ruin." His first act, for he was a scholar as well as a soldier, was to protect the Bodleian. A clause to the effect that all churches, colleges and schools should be preserved from harm was inserted in the Articles of Surrender. The liberties and privileges of the city and the University were guaranteed, and on 24th June the garrison, some three thousand strong, marched out in drenching rain over Magdalen Bridge, colours flying and drums beating, between files of Roundhead infantry.