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Openers Jeet Raval (17) and Tom Latham (five) were at the crease at the close as New Zealand still trailed by 394 runs with all ten wickets in hand on a grass-less Dubai stadium pitch.
Earlier, Haris Sohial knocked a career best 147 and Babar Azam scored 127 not out as they added 186 for the fifth wicket after Pakistan resumed at 207-4.
New Zealand lead the three-match series 1-0 after winning the first Test by just four runs in Abu Dhabi last week.