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Diagonalization of the core Hamiltonian provides usually is not the best guess for the SCF procedure to say the least, and thus, by default Gaussian uses a more sophisticated guess obtained by diagonalizing the Harris functional (Guess=Harris). With this default guess one get the same energy as OP reported:

Diagonalization of the core Hamiltonian provides usually not the best guess for the SCF procedure to say the least, and thus, by default Gaussian uses a more sophisticated guess obtained by diagonalizing the Harris functional (Guess=Harris). With this default guess one get the same energy as OP reported:

So, there is something wrong with the core Hamiltonian guess for this system, thus, SCF spits out some "strange" numbers. Strictly, speaking there is nothing strange with the numbers. Remember that SCF usually converges to a local minimum, and which particular depends on which part of the wave function space the initial guess placed the system in. And besides, you're not even guaranteed to have a minimum, SCF might converge to a stationary point of any kind.

So, there is something wrong with the core Hamiltonian guess for this system (I suspect the basis is too small for the core Hamiltonian guess to yield sensible results), thus, SCF spits out some "strange" numbers. Strictly, speaking there is nothing strange with the numbers. Remember that SCF usually converges to a local minimum, and which particular depends on which part of the wave function space the initial guess placed the system in. And besides, you're not even guaranteed to have a minimum, SCF might converge to a stationary point of any kind.

Diagonalization of the core Hamiltonian provides usually a terrible guess for the SCF procedure, and thus, by default Gaussian uses a more sophisticated guess obtained by diagonalizing the Harris functional (Guess=Harris). With this default guess one get the same energy as OP reported:

The energy of the first virtual orbital is negative which is odd. It is difficult to say what went wrong with the core Hamiltonian guess, but some clue can be provided if turning the symmetry on (this is another very sensible default turning which off was a bad idea, I think). The default guess yields the electronic state with a particular symmetry ($\sigma_{\mathrm{g}}$)

but the core Hamiltonian guess yields the electronic state with no symmetry

which is again suspicious. So, there is something wrong with the core Hamiltonian guess for this system, thus, SCF spits out some strange numbers.

  Remember that SCF usually converges to a local minimum, and which particular depends on which part of the wave function space the initial guess placed the system in.

Diagonalization of the core Hamiltonian provides usually is not the best guess for the SCF procedure to say the least, and thus, by default Gaussian uses a more sophisticated guess obtained by diagonalizing the Harris functional (Guess=Harris). With this default guess one get the same energy as OP reported:

The energy of the first virtual orbital is negative which is odd. It is difficult to say what went wrong with the core Hamiltonian guess, but some clue can be provided if turning the symmetry back on (this is another very sensible default turning which off was a bad idea, I think). 

The default guess yields the electronic state with a particular symmetry ($\sigma_{\mathrm{g}}$)

and converges within this symmetry

 Orbital symmetries:
       Occupied  (SGG) (SGU) (SGG) (SGU) (PIU) (PIU) (SGG)
       Virtual   (PIG) (PIG) (SGU)
 The electronic state is 1-SGG.

But the core Hamiltonian guess yields the electronic state with no symmetry

and converges within this state with no symmetry

 Orbital symmetries:
       Occupied  (SGG) (SGU) (SGG) (SGU) (PIU) (PIU) (PIG)
       Virtual   (SGG) (PIG) (SGU)
 Unable to determine electronic state:  partially filled degenerate orbitals.

which is again suspicious. 

So, there is something wrong with the core Hamiltonian guess for this system, thus, SCF spits out some "strange" numbers. Strictly, speaking there is nothing strange with the numbers. Remember that SCF usually converges to a local minimum, and which particular depends on which part of the wave function space the initial guess placed the system in. And besides, you're not even guaranteed to have a minimum, SCF might converge to a stationary point of any kind.