Several protesters and one army major killed in Khartoum as tear gas and live rounds fired against demonstrators.

At least five demonstrators and one army major have been killed in Sudan’s capital, Khartoum, hours after protest leaders and the ruling generals reached a deal on transitional authorities to run the country following the overthrow of President Omar al-Bashir last month.

The flare-up of violence on Monday came as the prosecutor general’s office said al-Bashir had been charged over the killings of protesters during the mass protests that led to the end of his 30-year rule on April 11.

The major and protesters were killed at a sit-in outside the army headquarters in Khartoum where thousands of protesters remain camped for weeks, demanding that the army generals who took power after toppling al-Bashir step down.

Three soldiers and several protesters and civilians were also wounded when “unidentified elements” fired shots at the Khartoum sit-in, the ruling military council said.

A doctors’ committee linked to the protest movement later said four more protesters had been shot dead, but did not specify if they were killed at the sit-in.

In an overnight press briefing, the transitional military council said it would never fire on peaceful protesters, but added that rogue elements had made their way into the groups of protesters to cause trouble.

“There are people who are infiltrating these groups; they are armed and they targeted some of our military personnel,” Huthaifah Abdul Malik, head of military intelligence, said.

“We are aware of these people, their elements and plans of provocation. We know the means that they use. They have targeted the military with armed ammunition, but these outlaws were using barricaded areas to target some of our soldiers,” he added.

“We reaffirm that we are monitoring all those outlaws and we know who are infiltrating and are provoking the military and all their components.”

Protesters’ denial

But protesters told Al Jazeera they were sure the crowds outside the army headquarters were not armed, saying everyone coming in out of the sit-in area was being searched at the several barricades set up by them on the roads leading to the site.

“We also spoke to some of the people who have been receiving treatment at the medical clinics set up in the square and they said they were sure they had seen men wearing the uniforms of the [paramilitary] Rapid Support Forces (RSF) attacking them,” Al Jazeera’s Hiba Morgan, reporting from Khartoum, said.

“So the military, as much as it is denying the fact that their forces and the RSF have anything to do with the attacks and the deaths on the protesters, as well as the death of one of their members, they are going to have a hard time to earn the confidence and the trust of the protesters after what happened today.”

Earlier, the umbrella protest movement, the Freedom and Change alliance, said the violence was to “disturb the breakthrough in the negotiations”, blaming the bloodshed on the former rulers.

On Monday morning, police and the RSF dismantled barricades and dispersed about 100 protesters who had blocked a road leading from Khartoum North to al-Mek Nimir Bridge and the centre of the capital.

For a second day, demonstrators blocked Nile Street, a major avenue running south of the Blue Nile, placing burning branches and stones across the road, as well as several other streets north and south of the river.

Later, RSF men used gunfire to disperse protesters next to Blue Nile bridge and thick clouds of tear gas were fired near Jumhuriya Street south of the river, where the RSF were seen beating a rickshaw driver as they patrolled in vehicles armed with sticks and guns, witnesses told Reuters News Agency.

Apparent breakthrough

Meanwhile, talks between the military and an opposition alliance over the handing to civilian rule resumed on Monday, with both sides saying they had produced agreement on the duties and authorities of sovereign, executive and legislative bodies.

“We discussed the structure of the transitional authority and agreed on it completely, and we also agreed on the system of governance in the transitional period,” said Lieutenant General Shams al-Din Kabashi, spokesman of the transitional military council.

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“We will continue tomorrow with talks on the ratio of participation on the sovereign level … and the length of the transitional period,” he said. “God willing, we will agree on these two points.”

Taha Osman, a spokesman for the protest movement, confirmed a deal had been reached following a deadlock in negotiations.

“At today’s meeting, we agreed on the structure of the authorities and their powers,” Osman told the AFP news agency.

“The authorities are as follows – the sovereign council, the cabinet and the legislative body,” he said.

Osman also said that another meeting would be held on Tuesday “to discuss the period of transition and the composition of the authorities”.

The generals insist the transitional period should be two years, while protesters want it to be four years.

“The question is how much pressure can the opposition put on the military council, because most of the power that they have comes from the protesters on the streets,” Al Jazeera’s Morgan said.

“Many of them have been calling for the opposition coalition to stop negotiating with the transitional government; they are saying that they are the people of the country and they are the ones who decide who has legitimacy and the right to govern them.”

Al-Bashir charged

The apparent breakthrough came as Sudan‘s acting prosecutor general Al-Waleed Sayyed Ahmed said al-Bashir “and others have been charged for inciting and participating in the killing of demonstrators”.

The charges form part of an investigation into the death of a medic killed during a protest in the capital’s eastern district of Burri, his office said in a statement.

Ninety people were killed in protest-related violence after demonstrations initially erupted in December over a government decision to triple the price of bread, the doctors’ committee said last month. The official death toll is 65.

Earlier this month, the public prosecutor ordered al-Bashir to be interrogated on charges of money laundering and financing terrorism.

There has been no comment from al-Bashir, who is in prison in Khartoum.