Maximum runs of pdflatex reached

[tstumm]

When trying to compile my project I get the following error:

Latexmk: This is Latexmk, John Collins, 22 April 2016, version: 4.45.
Latexmk: Changing directory to '/Users/tobias/Dropbox/Seminararbeit/'
Rule 'biber .latex/main': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'library.bib'
------------
Run number 1 of rule 'biber .latex/main'
------------
------------
Running 'biber  ".latex/main"'
------------
Latexmk: Found biber source file(s) [.latex/main.bcf library.bib]
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      '.latex/main.bbl'
      'main.tex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -interaction=nonstopmode -file-line-error -synctex=1 -shell-escape -recorder -output-directory="/Users/tobias/Dropbox/Seminararbeit/.latex"  "main.tex"'
------------
SyncTeX: Can't rename /Users/tobias/Dropbox/Seminararbeit/.latex/main.synctex.gz(busy) to /Users/tobias/Dropbox/Seminararbeit/.latex/main.synctex.gz
Latexmk: Log file says output to '.latex/main.pdf'
Latexmk: Log file says output to '.latex/main.pdf'
Latexmk: Log file says output to '.latex/main.pdf'
Latexmk: Log file says output to '.latex/main.pdf'
Latexmk: ===For rule 'pdflatex', actual output '.latex/main.pdf'
       ======appears not to match expected output '/Users/tobias/Dropbox/Seminararbeit/.latex/main.pdf'
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      '/Users/tobias/Dropbox/Seminararbeit/.latex/main.aux'
------------
Run number 2 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -interaction=nonstopmode -file-line-error -synctex=1 -shell-escape -recorder -output-directory="/Users/tobias/Dropbox/Seminararbeit/.latex"  "main.tex"'
------------
Latexmk: Found input bbl file '.latex/main.bbl'
Latexmk: Log file says output to '.latex/main.pdf'
Latexmk: Log file says output to '.latex/main.pdf'
Latexmk: Log file says output to '.latex/main.pdf'
Latexmk: Log file says output to '.latex/main.pdf'
Latexmk: List of undefined refs and citations:
  Reference `fig:grammar' on page 12 undefined on input line 105
  Reference `fig:lexical' on page 11 undefined on input line 44
  Reference `fig:nonterminal' on page 12 undefined on input line 81
Latexmk: ===For rule 'pdflatex', actual output '.latex/main.pdf'
       ======appears not to match expected output '/Users/tobias/Dropbox/Seminararbeit/.latex/main.pdf'
Latexmk: Found biber source file(s) [.latex/main.bcf library.bib]
Latexmk: Summary of warnings:
  Latex failed to resolve 3 reference(s)
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      '.latex/main.aux'
      '.latex/main.run.xml'
      '/Users/tobias/Dropbox/Seminararbeit/.latex/main.aux'
------------
Run number 3 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -interaction=nonstopmode -file-line-error -synctex=1 -shell-escape -recorder -output-directory="/Users/tobias/Dropbox/Seminararbeit/.latex"  "main.tex"'
------------
Latexmk: Found input bbl file '.latex/main.bbl'
Latexmk: Log file says output to '.latex/main.pdf'
Latexmk: Log file says output to '.latex/main.pdf'
Latexmk: ===For rule 'pdflatex', actual output '.latex/main.pdf'
       ======appears not to match expected output '/Users/tobias/Dropbox/Seminararbeit/.latex/main.pdf'
Latexmk: Found biber source file(s) [.latex/main.bcf library.bib]
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      '.latex/clarification.aux'
      '.latex/main.aux'
      '.latex/main.run.xml'
      '/Users/tobias/Dropbox/Seminararbeit/.latex/main.aux'
------------
Run number 4 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -interaction=nonstopmode -file-line-error -synctex=1 -shell-escape -recorder -output-directory="/Users/tobias/Dropbox/Seminararbeit/.latex"  "main.tex"'
------------
Latexmk: Found input bbl file '.latex/main.bbl'
Latexmk: Log file says output to '.latex/main.pdf'
Latexmk: Log file says output to '.latex/main.pdf'
Latexmk: Log file says output to '.latex/main.pdf'
Latexmk: Log file says output to '.latex/main.pdf'
Latexmk: List of undefined refs and citations:
  Reference `fig:grammar' on page 12 undefined on input line 105
  Reference `fig:lexical' on page 11 undefined on input line 44
  Reference `fig:nonterminal' on page 12 undefined on input line 81
Latexmk: ===For rule 'pdflatex', actual output '.latex/main.pdf'
       ======appears not to match expected output '/Users/tobias/Dropbox/Seminararbeit/.latex/main.pdf'
Latexmk: Found biber source file(s) [.latex/main.bcf library.bib]
Latexmk: Summary of warnings:
  Latex failed to resolve 3 reference(s)
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      '.latex/main.aux'
      '.latex/main.run.xml'
      '/Users/tobias/Dropbox/Seminararbeit/.latex/main.aux'
------------
Run number 5 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -interaction=nonstopmode -file-line-error -synctex=1 -shell-escape -recorder -output-directory="/Users/tobias/Dropbox/Seminararbeit/.latex"  "main.tex"'
------------
SyncTeX: Can't rename /Users/tobias/Dropbox/Seminararbeit/.latex/main.synctex.gz(busy) to /Users/tobias/Dropbox/Seminararbeit/.latex/main.synctex.gz
Latexmk: Found input bbl file '.latex/main.bbl'
Latexmk: References changed.
Latexmk: References changed.
Latexmk: Log file says output to '.latex/main.pdf'
Latexmk: Log file says output to '.latex/main.pdf'
Latexmk: Log file says output to '.latex/main.pdf'
Latexmk: Log file says output to '.latex/main.pdf'
Latexmk: List of undefined refs and citations:
  Reference `fig:grammar' on page 12 undefined on input line 105
  Reference `fig:lexical' on page 11 undefined on input line 44
  Reference `fig:nonterminal' on page 12 undefined on input line 81
Latexmk: ===For rule 'pdflatex', actual output '.latex/main.pdf'
       ======appears not to match expected output '/Users/tobias/Dropbox/Seminararbeit/.latex/main.pdf'
Latexmk: Found biber source file(s) [.latex/main.bcf library.bib]
Latexmk: Summary of warnings:
  Latex failed to resolve 3 reference(s)
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      '.latex/main.aux'
      '/Users/tobias/Dropbox/Seminararbeit/.latex/main.aux'
Latexmk: Maximum runs of pdflatex reached without getting stable files
Latexmk: Did not finish processing file 'main.tex':
   'pdflatex' needed too many passes
Latexmk: Undoing directory change

Running latexmk -outdir=.latex -pdf main.tex -f -silent finishes after 4 runs. After running the above command, the compilation runs fine in Atom for the first time. Afterwards I get Latexmk: ===For rule 'pdflatex', actual output '.latex/main.pdf' ======appears not to match expected output '/Users/tobias/Dropbox/Seminararbeit/.latex/main.pdf' Latexmk: Found biber source file(s) [.latex/main.bcf library.bib] Latexmk: Summary of warnings: Latex failed to resolve 3 reference(s) Latexmk: Undoing directory change

This is pretty annoying.