Server and PHP Errors! HELP!

My google webmaster tools for my website: http://www.equestrianempire.com is having a server error that says:

Server Error 500: wp-content/themes/Newspaper/

I am hosting with WP-ENGINE and they have told me that the error is a 500 error and upon looking at my apache error log, they have found the following:

[Tue Jan 27 12:14:22 2015] [error] [client 72.173.87.182] Directory index forbidden by Options directive: /nas/wp/www/sites/aarontaylor/wp-content/themes/Newspaper/js/, referer: http://www.equestrianempire.com/rider-killed-by-horse-she-raised-since-birth/
[Tue Jan 27 13:58:32 2015] [error] [client 184.20.57.174] Directory index forbidden by Options directive: /nas/wp/www/sites/aarontaylor/wp-content/themes/Newspaper/js/, referer: http://www.equestrianempire.com/10-things-you-give-up-when-you-start-to-ride-horses/
[Tue Jan 27 15:43:16 2015] [error] [client 192.64.61.159] [WPE Monitoring] Stopwatch php.pod-3132.function.mysql_query.duration exceeded 1000ms. Was: 1544ms.\n#0 wpe\\measure\\LoggingStopwatch->logStackTrace(1544) called at [/nas/wp/www/common/production/measure.php:198]\n#1 wpe\\measure\\LoggingStopwatch->lap_ended(1544) called at [/nas/wp/www/common/production/measure.php:134]\n#2 wpe\\measure\\Stopwatch->lapstart() called at [/nas/wp/www/common/production/measure.php:152]\n#3 wpe\\measure\\Stopwatch->stop() called at [/nas/wp/www/common/production/statsd_monitoring.php(256) : runkit created function:19]\n#4 mysql_query(UPDATE wp_postmeta SET meta_value = ‘549’ WHERE post_id = 1163 AND meta_key = ‘post_views_count’ /* From [www.equestrianempire.com/wp-admin/admin-ajax.php] in [/nas/wp/www/cluster-3132/aarontaylor/wp-content/themes/Newspaper/includes/wp_booster/td_ajax.php:452] */, Resource id #28) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/wp-db.php:1663]\n#5 wpdb->_do_query(UPDATE wp_postmeta SET meta_value = ‘549’ WHERE post_id = 1163 AND meta_key = ‘post_views_count’ /* From [www.equestrianempire.com/wp-admin/admin-ajax.php] in [/nas/wp/www/cluster-3132/aarontaylor/wp-content/themes/Newspaper/includes/wp_booster/td_ajax.php:452] */) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/wp-db.php:1567]\n#6 wpdb->query(UPDATE wp_postmeta SET meta_value = ‘549’ WHERE post_id = 1163 AND meta_key = ‘post_views_count’) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/wp-db.php:1799]\n#7 wpdb->update(wp_postmeta, Array ([meta_value] => 549), Array ([post_id] => 1163,[meta_key] => post_views_count)) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/meta.php:248]\n#8 update_metadata(post, 1163, post_views_count, 549, ) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/post.php:1959]\n#9 update_post_meta(1163, post_views_count, 549) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/themes/Newspaper/includes/wp_booster/td_ajax.php:452]\n#10 td_ajax_update_views()\n#11 call_user_func_array(td_ajax_update_views, Array ([0] => )) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/plugin.php:496]\n#12 do_action(wp_ajax_nopriv_td_ajax_update_views) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-admin/admin-ajax.php:95]\n, referer: http://www.equestrianempire.com/rider-killed-by-horse-she-raised-since-birth/
[Tue Jan 27 15:43:16 2015] [error] [client 192.64.61.159] [WPE Monitoring] Slow mysql_query() call was running query:\nUPDATE wp_postmeta SET meta_value = ‘549’ WHERE post_id = 1163 AND meta_key = ‘post_views_count’ /* From [www.equestrianempire.com/wp-admin/admin-ajax.php] in [/nas/wp/www/cluster-3132/aarontaylor/wp-content/themes/Newspaper/includes/wp_booster/td_ajax.php:452] */, referer: http://www.equestrianempire.com/rider-killed-by-horse-she-raised-since-birth/
[Tue Jan 27 15:54:06 2015] [error] [client 204.101.161.159] Directory index forbidden by Options directive: /nas/wp/www/sites/aarontaylor/wp-content/uploads/, referer: bing.com
[Tue Jan 27 17:29:19 2015] [error] [client 71.57.155.98] [WPE Monitoring] Stopwatch php.pod-3132.function.mysql_query.duration exceeded 1000ms. Was: 2685ms.\n#0 wpe\\measure\\LoggingStopwatch->logStackTrace(2685) called at [/nas/wp/www/common/production/measure.php:198]\n#1 wpe\\measure\\LoggingStopwatch->lap_ended(2685) called at [/nas/wp/www/common/production/measure.php:134]\n#2 wpe\\measure\\Stopwatch->lapstart() called at [/nas/wp/www/common/production/measure.php:152]\n#3 wpe\\measure\\Stopwatch->stop() called at [/nas/wp/www/common/production/statsd_monitoring.php(256) : runkit created function:19]\n#4 mysql_query(OPTIMIZE TABLE wp_bp_groups_groupmeta /* From [www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize] in [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128] */, Resource id #28) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/wp-db.php:1663]\n#5 wpdb->_do_query(OPTIMIZE TABLE wp_bp_groups_groupmeta /* From [www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize] in [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128] */) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/wp-db.php:1567]\n#6 wpdb->query(OPTIMIZE TABLE wp_bp_groups_groupmeta) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128]\n#7 optimizeTablesQuick(yes) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:528]\n#8 include_once(/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-admin.php:76]\n#9 include_once(/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-admin.php) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize.php:76]\n#10 wp_optimize_menu()\n#11 call_user_func_array(wp_optimize_menu, Array ([0] => )) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/plugin.php:496]\n#12 do_action(toplevel_page_WP-Optimize) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-admin/admin.php:212]\n, referer: http://www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize
[Tue Jan 27 17:29:19 2015] [error] [client 71.57.155.98] [WPE Monitoring] Slow mysql_query() call was running query:\nOPTIMIZE TABLE wp_bp_groups_groupmeta /* From [www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize] in [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128] */, referer: http://www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize
[Tue Jan 27 17:29:30 2015] [error] [client 71.57.155.98] [WPE Monitoring] Stopwatch php.pod-3132.function.mysql_query.duration exceeded 1000ms. Was: 1483ms.\n#0 wpe\\measure\\LoggingStopwatch->logStackTrace(1483) called at [/nas/wp/www/common/production/measure.php:198]\n#1 wpe\\measure\\LoggingStopwatch->lap_ended(1483) called at [/nas/wp/www/common/production/measure.php:134]\n#2 wpe\\measure\\Stopwatch->lapstart() called at [/nas/wp/www/common/production/measure.php:152]\n#3 wpe\\measure\\Stopwatch->stop() called at [/nas/wp/www/common/production/statsd_monitoring.php(256) : runkit created function:19]\n#4 mysql_query(OPTIMIZE TABLE wp_options /* From [www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize] in [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128] */, Resource id #28) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/wp-db.php:1663]\n#5 wpdb->_do_query(OPTIMIZE TABLE wp_options /* From [www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize] in [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128] */) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/wp-db.php:1567]\n#6 wpdb->query(OPTIMIZE TABLE wp_options) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128]\n#7 optimizeTablesQuick(yes) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:528]\n#8 include_once(/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-admin.php:76]\n#9 include_once(/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-admin.php) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize.php:76]\n#10 wp_optimize_menu()\n#11 call_user_func_array(wp_optimize_menu, Array ([0] => )) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/plugin.php:496]\n#12 do_action(toplevel_page_WP-Optimize) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-admin/admin.php:212]\n, referer: http://www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize
[Tue Jan 27 17:29:30 2015] [error] [client 71.57.155.98] [WPE Monitoring] Slow mysql_query() call was running query:\nOPTIMIZE TABLE wp_options /* From [www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize] in [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128] */, referer: http://www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize
[Tue Jan 27 17:29:33 2015] [error] [client 71.57.155.98] [WPE Monitoring] Stopwatch php.pod-3132.function.mysql_query.duration exceeded 1000ms. Was: 1586ms.\n#0 wpe\\measure\\LoggingStopwatch->logStackTrace(1586) called at [/nas/wp/www/common/production/measure.php:198]\n#1 wpe\\measure\\LoggingStopwatch->lap_ended(1586) called at [/nas/wp/www/common/production/measure.php:134]\n#2 wpe\\measure\\Stopwatch->lapstart() called at [/nas/wp/www/common/production/measure.php:152]\n#3 wpe\\measure\\Stopwatch->stop() called at [/nas/wp/www/common/production/statsd_monitoring.php(256) : runkit created function:19]\n#4 mysql_query(OPTIMIZE TABLE wp_bp_groups_groupmeta /* From [www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize] in [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128] */, Resource id #28) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/wp-db.php:1663]\n#5 wpdb->_do_query(OPTIMIZE TABLE wp_bp_groups_groupmeta /* From [www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize] in [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128] */) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/wp-db.php:1567]\n#6 wpdb->query(OPTIMIZE TABLE wp_bp_groups_groupmeta) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128]\n#7 optimizeTablesQuick(yes) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:528]\n#8 include_once(/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-admin.php:76]\n#9 include_once(/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-admin.php) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize.php:76]\n#10 wp_optimize_menu()\n#11 call_user_func_array(wp_optimize_menu, Array ([0] => )) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/plugin.php:496]\n#12 do_action(toplevel_page_WP-Optimize) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-admin/admin.php:212]\n, referer: http://www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize
[Tue Jan 27 17:29:33 2015] [error] [client 71.57.155.98] [WPE Monitoring] Slow mysql_query() call was running query:\nOPTIMIZE TABLE wp_bp_groups_groupmeta /* From [www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize] in [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128] */, referer: http://www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize
[Tue Jan 27 17:29:37 2015] [error] [client 71.57.155.98] [WPE Monitoring] Stopwatch php.pod-3132.function.mysql_query.duration exceeded 1000ms. Was: 4033ms.\n#0 wpe\\measure\\LoggingStopwatch->logStackTrace(4033) called at [/nas/wp/www/common/production/measure.php:198]\n#1 wpe\\measure\\LoggingStopwatch->lap_ended(4033) called at [/nas/wp/www/common/production/measure.php:134]\n#2 wpe\\measure\\Stopwatch->lapstart() called at [/nas/wp/www/common/production/measure.php:152]\n#3 wpe\\measure\\Stopwatch->stop() called at [/nas/wp/www/common/production/statsd_monitoring.php(256) : runkit created function:19]\n#4 mysql_query(OPTIMIZE TABLE wp_bp_groups_members /* From [www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize] in [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128] */, Resource id #28) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/wp-db.php:1663]\n#5 wpdb->_do_query(OPTIMIZE TABLE wp_bp_groups_members /* From [www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize] in [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128] */) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/wp-db.php:1567]\n#6 wpdb->query(OPTIMIZE TABLE wp_bp_groups_members) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128]\n#7 optimizeTablesQuick(yes) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:528]\n#8 include_once(/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-admin.php:76]\n#9 include_once(/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-admin.php) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize.php:76]\n#10 wp_optimize_menu()\n#11 call_user_func_array(wp_optimize_menu, Array ([0] => )) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/plugin.php:496]\n#12 do_action(toplevel_page_WP-Optimize) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-admin/admin.php:212]\n, referer: http://www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize
[Tue Jan 27 17:29:37 2015] [error] [client 71.57.155.98] [WPE Monitoring] Slow mysql_query() call was running query:\nOPTIMIZE TABLE wp_bp_groups_members /* From [www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize] in [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128] */, referer: http://www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize
[Tue Jan 27 17:29:37 2015] [error] [client 71.57.155.98] [WPE Monitoring] Stopwatch php.pod-3132.function.mysql_query.duration exceeded 1000ms. Was: 7353ms.\n#0 wpe\\measure\\LoggingStopwatch->logStackTrace(7353) called at [/nas/wp/www/common/production/measure.php:198]\n#1 wpe\\measure\\LoggingStopwatch->lap_ended(7353) called at [/nas/wp/www/common/production/measure.php:134]\n#2 wpe\\measure\\Stopwatch->lapstart() called at [/nas/wp/www/common/production/measure.php:152]\n#3 wpe\\measure\\Stopwatch->stop() called at [/nas/wp/www/common/production/statsd_monitoring.php(256) : runkit created function:19]\n#4 mysql_query(OPTIMIZE TABLE wp_postmeta /* From [www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize] in [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128] */, Resource id #28) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/wp-db.php:1663]\n#5 wpdb->_do_query(OPTIMIZE TABLE wp_postmeta /* From [www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize] in [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128] */) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/wp-db.php:1567]\n#6 wpdb->query(OPTIMIZE TABLE wp_postmeta) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128]\n#7 optimizeTablesQuick(yes) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:528]\n#8 include_once(/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-admin.php:76]\n#9 include_once(/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-admin.php) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize.php:76]\n#10 wp_optimize_menu()\n#11 call_user_func_array(wp_optimize_menu, Array ([0] => )) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/plugin.php:496]\n#12 do_action(toplevel_page_WP-Optimize) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-admin/admin.php:212]\n, referer: http://www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize
[Tue Jan 27 17:29:37 2015] [error] [client 71.57.155.98] [WPE Monitoring] Slow mysql_query() call was running query:\nOPTIMIZE TABLE wp_postmeta /* From [www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize] in [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128] */, referer: http://www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize
[Tue Jan 27 17:29:39 2015] [error] [client 71.57.155.98] [WPE Monitoring] Stopwatch php.pod-3132.function.mysql_query.duration exceeded 1000ms. Was: 1629ms.\n#0 wpe\\measure\\LoggingStopwatch->logStackTrace(1629) called at [/nas/wp/www/common/production/measure.php:198]\n#1 wpe\\measure\\LoggingStopwatch->lap_ended(1629) called at [/nas/wp/www/common/production/measure.php:134]\n#2 wpe\\measure\\Stopwatch->lapstart() called at [/nas/wp/www/common/production/measure.php:152]\n#3 wpe\\measure\\Stopwatch->stop() called at [/nas/wp/www/common/production/statsd_monitoring.php(256) : runkit created function:19]\n#4 mysql_query(OPTIMIZE TABLE wp_ewwwio_images /* From [www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize] in [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128] */, Resource id #28) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/wp-db.php:1663]\n#5 wpdb->_do_query(OPTIMIZE TABLE wp_ewwwio_images /* From [www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize] in [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128] */) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/wp-db.php:1567]\n#6 wpdb->query(OPTIMIZE TABLE wp_ewwwio_images) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128]\n#7 optimizeTablesQuick(yes) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:528]\n#8 include_once(/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-admin.php:76]\n#9 include_once(/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-admin.php) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize.php:76]\n#10 wp_optimize_menu()\n#11 call_user_func_array(wp_optimize_menu, Array ([0] => )) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/plugin.php:496]\n#12 do_action(toplevel_page_WP-Optimize) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-admin/admin.php:212]\n, referer: http://www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize
[Tue Jan 27 17:29:39 2015] [error] [client 71.57.155.98] [WPE Monitoring] Slow mysql_query() call was running query:\nOPTIMIZE TABLE wp_ewwwio_images /* From [www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize] in [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128] */, referer: http://www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize
[Tue Jan 27 17:29:39 2015] [error] [client 71.57.155.98] [WPE Monitoring] Stopwatch php.pod-3132.function.mysql_query.duration exceeded 1000ms. Was: 1636ms.\n#0 wpe\\measure\\LoggingStopwatch->logStackTrace(1636) called at [/nas/wp/www/common/production/measure.php:198]\n#1 wpe\\measure\\LoggingStopwatch->lap_ended(1636) called at [/nas/wp/www/common/production/measure.php:134]\n#2 wpe\\measure\\Stopwatch->lapstart() called at [/nas/wp/www/common/production/measure.php:152]\n#3 wpe\\measure\\Stopwatch->stop() called at [/nas/wp/www/common/production/statsd_monitoring.php(256) : runkit created function:19]\n#4 mysql_query(OPTIMIZE TABLE wp_term_taxonomy /* From [www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize] in [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128] */, Resource id #28) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/wp-db.php:1663]\n#5 wpdb->_do_query(OPTIMIZE TABLE wp_term_taxonomy /* From [www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize] in [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128] */) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/wp-db.php:1567]\n#6 wpdb->query(OPTIMIZE TABLE wp_term_taxonomy) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128]\n#7 optimizeTablesQuick(yes) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:528]\n#8 include_once(/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-admin.php:76]\n#9 include_once(/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-admin.php) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize.php:76]\n#10 wp_optimize_menu()\n#11 call_user_func_array(wp_optimize_menu, Array ([0] => )) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-includes/plugin.php:496]\n#12 do_action(toplevel_page_WP-Optimize) called at [/nas/wp/www/cluster-3132/aarontaylor/wp-admin/admin.php:212]\n, referer: http://www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize
[Tue Jan 27 17:29:39 2015] [error] [client 71.57.155.98] [WPE Monitoring] Slow mysql_query() call was running query:\nOPTIMIZE TABLE wp_term_taxonomy /* From [www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize] in [/nas/wp/www/cluster-3132/aarontaylor/wp-content/plugins/wp-optimize/wp-optimize-main.php:128] */, referer: http://www.equestrianempire.com/wp-admin/admin.php?page=WP-Optimize
[Tue Jan 27 17:33:18 2015] [error] [client 192.171.117.234] PHP Fatal error: Call to undefined function get_header() in /nas/wp/www/cluster-3132/aarontaylor/wp-content/themes/Newspaper/index.php on line 6
[Tue Jan 27 17:34:36 2015] [error] [client 71.57.155.98] PHP Fatal error: Call to undefined function get_header() in /nas/wp/www/cluster-3132/aarontaylor/wp-content/themes/Newspaper/index.php on line 6
[Tue Jan 27 17:35:09 2015] [error] [client 71.57.155.98] PHP Fatal error: Call to undefined function get_header() in /nas/wp/www/cluster-3132/aarontaylor/wp-content/themes/Newspaper/index.php on line 6
[Tue Jan 27 17:36:34 2015] [error] [client 150.70.173.48] PHP Fatal error: Call to undefined function get_header() in /nas/wp/www/cluster-3132/aarontaylor/wp-content/themes/Newspaper/index.php on line 6

I have no made any changes or modifications to the code and I’m very unsure of what to do, as I do not understand PHP. Thank you!

most of those errors look related to wp-optimize plugin … so that is separate problem.

Also looks like some kind of permissions issue on the /js/ folder.