The San Francisco 49ers' negotiations with Brandon Aiyuk appear to have taken a huge turn for the worse

Despite failing to reach an agreement over a long-term contract extension, both Kyle Shanahan and John Lynch were pretty clear that they expected Brandon Aiyuk to practice with the San Francisco 49ers on Wednesday as they continued their preparations for the season opener with the New York Jets .

That did not happen, with Aiyuk's absence continuing despite head coach Shanahan revealing the All-Pro wide receiver had been cleared by doctors to practice following an apparent back injury.

"I know that he's been cleared by our doctors, so I hope that he's out there practicing today," Shanahan told a press conference.

Asked if Aiyuk, who has performed a 'hold-in' amid his contract impasse with the Niners, reporting to the facility but refusing to practice, may now be subject to fines for continuing to choose not to take part, Shanahan was non-committal.

"I'll deal with that when that happens, if that happens," he added.

That has now happened, with Aiyuk going against the words of both his head coach and GM Lynch.

Lynch bluntly said of the Aiyuk situation in his press conference: "I've seen these things look dire before, and they can quickly turn.

"So that gives you hope, that we've been in these situations before, and those things can quickly be forgotten. We'll remain hopeful. ... At some point, you've got to play."

Those final seven words were a key indicator of what the 49ers' mindset is at this point in an extremely fractious negotiation with Aiyuk. They have gone back to the table with their leading receiver from each of the last two seasons after seemingly going very close to trading him and, according to reports, ironed out the major components of an extension.

Yet minor details have prevented a resolution from being reached, and it seems the 49ers, with a primetime season opener, have ran out of patience.

But with Aiyuk unwilling to bend his team's request for him to practice, relations between the two sides now look to be at an all-time low. Lynch may remain hopeful that this impasse can be resolved but, right now, that conclusion to this protracted saga has never looked less likely.

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