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Income Taxes (Tables) | 12 Months Ended
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Dec. 31, 2016
Provision for Income Taxes | The provision for income taxes consists of the following (in thousands):
|  | Year Ended December 31, |
|  | 2016 |  |  | 2015 |  |  | 2014 |
Current |  |  |  |  |  |  |  |  |  |  |  |
U.S. federal |  | $ | — |  |  | $ | — |  |  | $ | — |
U.S. state |  |  | — |  |  |  | — |  |  |  | — |
Non-U.S. |  |  | — |  |  |  | — |  |  |  | — |
Total current |  |  | — |  |  |  | — |  |  |  | — |
Deferred |  |  |  |  |  |  |  |  |  |  |  |
U.S. federal |  |  | (43,814 | ) |  |  | 109,512 |  |  |  | 57,873 |
U.S. state |  |  | (4,311 | ) |  |  | (29,394 | ) |  |  | 7,631 |
Non-U.S. |  |  | — |  |  |  | — |  |  |  | — |
Total deferred |  |  | (48,125 | ) |  |  | 80,118 |  |  |  | 65,504 |
Valuation allowance |  |  | 48,125 |  |  |  | (80,118 | ) |  |  | (65,504 | )
Total |  | $ | — |  |  | $ | — |  |  | $ | — |
Components of Net Deferred Tax Assets | Components of the net deferred tax assets as of December 31, 2016 and 2015, are as follows (in thousands):
|  | December 31, |
|  | 2016 |  |  | 2015 |
Deferred tax assets: |  |  |  |  |  |  |  |
Net operating loss carryforwards |  | $ | 712,124 |  |  | $ | 721,588 |
Research and development credits |  |  | 77,998 |  |  |  | 73,646 |
Capitalized research |  |  | 5,117 |  |  |  | 5,872 |
Payments from collaboration |  |  | — |  |  |  | 52,484 |
Milestone Rights |  |  | 3,242 |  |  |  | 3,242 |
Accrued expenses |  |  | 440 |  |  |  | 251 |
Loss on purchase commitment |  |  | 36,775 |  |  |  | 24,084 |
Non-qualified stock option expense |  |  | 17,331 |  |  |  | 16,941 |
Capitalized patent costs |  |  | 8,781 |  |  |  | 8,574 |
Other |  |  | 7,380 |  |  |  | 7,186 |
Depreciation |  |  | 45,310 |  |  |  | 48,755 |
Total net deferred tax assets |  |  | 914,498 |  |  |  | 962,623 |
Valuation allowance |  |  | (914,498 | ) |  |  | (962,623 | )
Net deferred tax assets |  | $ | — |  |  | $ | — |
Effective Income Tax Rate | The Company’s effective income tax rate differs from the statutory federal income tax rate as follows for the years ended December 31, 2016, 2015 and 2014:
|  | December 31, |
|  | 2016 |  |  | 2015 |  |  | 2014 |
Federal tax benefit rate |  |  | 35.0 | % |  |  | 35.0 | % |  |  | 35.0 | %
Permanent items |  |  | (1.9 | ) |  |  | — |  |  |  | 0.9 |
Intercompany transfer of intellectual property |  |  | 0.9 |  |  |  | (1.0 | ) |  |  | (4.1 | )
Valuation allowance |  |  | (34.0 | ) |  |  | (34.0 | ) |  |  | (31.8 | )
Effective income tax rate |  |  | — | % |  |  | — | % |  |  | — | %

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- Definition Tabular disclosure of the components of income tax expense attributable to continuing operations for each year presented including, but not limited to: current tax expense (benefit), deferred tax expense (benefit), investment tax credits, government grants, the benefits of operating loss carryforwards, tax expense that results from allocating certain tax benefits either directly to contributed capital or to reduce goodwill or other noncurrent intangible assets of an acquired entity, adjustments of a deferred tax liability or asset for enacted changes in tax laws or rates or a change in the tax status of the entity, and adjustments of the beginning-of-the-year balances of a valuation allowance because of a change in circumstances that causes a change in judgment about the realizability of the related deferred tax asset in future years. + References Reference 1: http://www.xbrl.org/2003/role/presentationRef -Publisher FASB -Name Accounting Standards Codification -Topic 740 -SubTopic 10 -Section 50 -Paragraph 9 -URI http://asc.fasb.org/extlink&oid=65882285&loc=d3e32639-109319 + Details
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- Definition Tabular disclosure of the components of net deferred tax asset or liability recognized in an entity's statement of financial position, including the following: the total of all deferred tax liabilities, the total of all deferred tax assets, the total valuation allowance recognized for deferred tax assets. + References Reference 1: http://www.xbrl.org/2003/role/presentationRef -Publisher FASB -Name Accounting Standards Codification -Topic 740 -SubTopic 10 -Section 50 -Paragraph 2 -URI http://asc.fasb.org/extlink&oid=65882285&loc=d3e32537-109319 + Details
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- Definition Tabular disclosure of the reconciliation using percentage or dollar amounts of the reported amount of income tax expense attributable to continuing operations for the year to the amount of income tax expense that would result from applying domestic federal statutory tax rates to pretax income from continuing operations. + References Reference 1: http://www.xbrl.org/2003/role/presentationRef -Publisher FASB -Name Accounting Standards Codification -Topic 740 -SubTopic 10 -Section 50 -Paragraph 12 -URI http://asc.fasb.org/extlink&oid=65882285&loc=d3e32687-109319 + Details
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