Dear Johannes and co-authors,

Thank you for your responses to the reviewers’ comments and for submitting a revised manuscript. Having read the reviewers’ comments and your responses, I would like to recommend that your paper be published in GMD, subject to the following minor revisions:

1. Reviewer #1 (Nicholas H. Savage) asked the following question about Section 2.2: How large an impact does the correction of negative MMRs have on the budget of transported species? Although this was adequately addressed in your response, a corresponding change to your manuscript was not carried out. I suggest that you address this question within the manuscript itself because other readers may have a similar question and may not necessarily read the details in your online response.

2. In Section 2.3 you clarify that MEGAN emissions calculated offline are used. Can you confirm in the manuscript whether these are added to the model with a diurnal cycle or not?

3. In Section 2.4.3, lines 362-363, I suggest that you replace “The C-IFS lightning emissions were 4.9 TgN/yr at T159 resolution and 5.7 Tg N/yr at T255 resolution” is replaced with “The C-IFS lightning emissions, using the parameterisation of Meijer et al. 2001 based on convective precipitation, were 363 4.9 TgN/yr at T159 resolution and 5.7 Tg N/yr at T255 resolution. “ Although it is mentioned earlier, given your discussion of both possible parameterisations, this addition will help emphasise to the reader which parameterisation is being used in the evaluation runs.

4. In section 2.5.1, line 494: I suggest that you replace “factor” with either “ratio” or “fraction”

5. In section 2.6, line 483: Make “inter-comparison” plural

6. In section 2.6, line 486: Replace “multi model ensemble” with “two multi model ensembles”

7. In section 2.6, line 510: Replace “modeling” with “modelling”

8. In section 2.6, add Banda et al. (2014) as mentioned in your response to the query regarding prescribed surface ch4 concentrations

9. In section 3.2.1, line 613, please add that no consideration is given to the horizontal movement of the aircraft when sampling the model.

10. I refer to Reviewer #1’s query on Section 3.3: Does the lower bias in C-IFS imply that the Cariolle scheme is performing better in the lower stratosphere than the MOZAIC chemistry? If so, please comment on this and implications for future choices of upper boundary conditions for ozone - if the Cariolle scheme is cheaper and better, why are you planning to add a detailed stratospheric chemistry scheme to CB05? In response, you mention that “Please note that the stratospheric ozone was nudged to the MACC re-analysis above the tropopause”. However, this isn’t entirely clear from the revised manuscript. In particular, in Section 2.5.4, it says “Additionally, stratospheric O3 in C-IFS can be nudged to O3 analyses of either the MACC re-analysis (Inness et al., 2013) or ERA interim (Dee et al., 2011).” I suggest that you make it more explicit that stratospheric ozone is nudged towards MACC reanalysis.

11. I refer to Reviewer #2’s comment “p. 7761: It would be much easier to follow the arguments about the size of biases if the actual bias were plotted for each model. For example, the argument that "the bias of MOZ seems stronger over land" is hard to verify from these plots.” May I suggest that you include both absolute columns as well as biases in Figures 6 and 7?

12. Finally, the Executive Editors request that model description and evaluation papers such as yours should include a section on “Code availability”. See http://www.geosci-model-dev.net/6/1233/2013/gmd-6-1233-2013.html for further details. Could I please ask that you include such a section in your revised manuscript?

Thank you once again for submitting your manuscript to GMD,
Fiona O’Connor