if( $hsp->length('total') > 1000 ) {
      if ( $hsp->percent_identity >= 90 ) {
	   if(	$hsp->score ){
	    if(	 $hsp->gaps ){
		 if(  $hsp->expect ){
			print  "Hit= ",    $hit->name, 
					" Length=",     $hsp->length('total'), 
					" Score=",		$hsp->score,"\n";
			print "Gaps=",	$hsp->gaps,
					" Expect=",		$hsp->expect,
					" Percent_id=", $hsp->percent_identity, "\n";
			my $aln = $hsp->get_aln;
			my $alnIO = Bio::AlignIO->new(-format =>"clustalw", -file => $out);
		    $alnIO->write_aln($aln);
		}
	   }
	  }
	 }
    }

##  better is to reduce the levels of "if" by using "and" or &&
if (      ($hsp->length('total') > 1000 )   
      &&  ($hsp->percent_identity >= 90 )
      &&  ($hsp->score )
      &&  ($hsp->gaps)
      &&  ($hsp->expect)
    ) 
    {
      #do your print stuff
    }