According to a press release sent Tuesday, the company has reached an agreement with the Cray Group that includes the termination of CEO Tim Newkirk.
Newkirk has also resigned from the Board of Directors.
The company also announced it will reconvene the annual stockholders meeting on Dec. 17.
The Cray Group, which consists of a group of the company's founder's family members, had opposed the direction the company was taking.
The Kansas Court of Appeals had overturned a previous stay on the meeting, which had been scheduled for September.
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Another element of the agreement will allow the Cray Group to continue to hold proxy votes for the election of directors, governance proposals and the say-on-pay advisory vote.
All pending litigation between the group and the company will be dismissed and the company will reimburse the Cray Group for all, "reasonable legal fees and out-of-pocket costs and expenses incurred in connection with the matters related to the Annual Meeting."
In October, claims by the company against the Cray Group were dismissed in Johnson County District Court.