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1419: Medium Monomer Design

Closed since about 5 years ago

Intermediate Overall Design

Summary


Created
August 18, 2017
Expires
Max points
100
Description

This puzzle challenges players to design a single-chain protein with 75-90 residues. We've adjusted the scoring function here so that alanine residues are more tolerable in loops (they are still restricted in helices and sheets!). The starting structure has 75 residues, but more can be added at a cost of 23 points per residue. See the puzzle comments for filter details. The Baker Lab will run folding predictions on your solutions for this puzzle, and those that perform well will be synthesized in the lab. Remember, you can use the Upload for Scientists button for up to 5 designs that you want us to look at, even if they are not the best-scoring solutions!

Top groups


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Comments


bkoep Staff Lv 1

Residue IE Score: Monitors that all PHE, TYR, and TRP residues are scoring well.

Core Existence: Ensures that at least 30% of the residues are buried in the core of your design.

Secondary Structure: Checks that no more than 50% of residues are in helices; penalties are incurred if more than 50% of residues form helices.

Secondary Structure Design: Penalizes all CYS residues. Penalizes GLY, ALA residues in sheets; penalizes GLY, ALA, SER, THR in helices.

Residue Count: Penalizes extra residues inserted beyond the starting 75. Players may use up to 90 residues in total.

Ideal Loops: Penalizes loops that do not conform to preferred ABEGO patterns. Use Auto Structures to see which residues count as "loops."

Mike Cassidy Lv 1

Crashed twice; taking my computer down:

com.apple.message.domain: com.apple.crashreporter.writereport.cpu_resource.diag
com.apple.message.signature: Foldit
com.apple.message.signature2: UNBUNDLED ||| ??? (1.0) ((null))
com.apple.message.signature3: cpu usage
com.apple.message.result: noop
com.apple.message.summarize: YES
SenderMachUUID: CE4C7F36-9981-3467-92E7-EA2CD33C84BC

Process: WindowServer [204]
Path: /System/Library/PrivateFrameworks/SkyLight.framework/Versions/A/Resources/WindowServer
Identifier: WindowServer
Version: 600.00 (15)
Code Type: X86-64 (Native)
Parent Process: launchd [1]
Responsible: WindowServer [204]
User ID: 88

Date/Time: 2017-08-23 10:53:31.945 -0400
OS Version: Mac OS X 10.12.6 (16G29)
Report Version: 12
Anonymous UUID: 33EE3CDF-5594-343C-1DA0-97104E3F3B3E

Sleep/Wake UUID: 263A460C-9566-4254-9CDF-9FDF2C0DFCE6

Time Awake Since Boot: 46000 seconds
Time Since Wake: 4300 seconds

System Integrity Protection: enabled

Crashed Thread: 0 Dispatch queue: com.apple.main-thread

Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Exception Note: EXC_CORPSE_NOTIFY

Application Specific Information:
Assertion failed: (false && "10 seconds of continuous GPU Driver unreadiness, relaunching WindowServer"), function void IMGGraphicsStackReadinessFailure(), file Server/Windows/Updater.cc, line 2864.

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fffdd9d2d42 __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fffddac0457 pthread_kill + 90
2 libsystem_c.dylib 0x00007fffdd938420 abort + 129
3 libsystem_c.dylib 0x00007fffdd8ff893 __assert_rtn + 320
4 com.apple.SkyLight 0x00007fffd9d5e5be update_display_callback(void*, double) + 796
5 com.apple.SkyLight 0x00007fffd9c97c9a run_timer_pass + 700
6 com.apple.SkyLight 0x00007fffd9bdf125 CGXRunOneServicesPass + 149
7 com.apple.SkyLight 0x00007fffd9be08cf SLXServer + 3843
8 WindowServer 0x00000001055d4dde 0x1055d4000 + 3550
9 libdyld.dylib 0x00007fffdd8a4235 start + 1

Thread 1:
0 libsystem_kernel.dylib 0x00007fffdd9cb34a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fffdd9ca797 mach_msg + 55
2 com.apple.CoreDisplay 0x00007fffc80752bc CoreDisplay::Mach::Server::Start() + 132
3 com.apple.CoreDisplay 0x00007fffc8075f41 void* std::__1::__thread_proxy<std::__1::tuple<void (CoreDisplay::Mach::Server::)(), CoreDisplay::Mach::Server> >(void*) + 113
4 libsystem_pthread.dylib 0x00007fffddabd93b _pthread_body + 180
5 libsystem_pthread.dylib 0x00007fffddabd887 _pthread_start + 286
6 libsystem_pthread.dylib 0x00007fffddabd08d thread_start + 13

Thread 2:
0 libsystem_kernel.dylib 0x00007fffdd9cb34a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fffdd9ca797 mach_msg + 55
2 com.apple.CoreFoundation 0x00007fffc8125434 __CFRunLoopServiceMachPort + 212
3 com.apple.CoreFoundation 0x00007fffc81248c1 __CFRunLoopRun + 1361
4 com.apple.CoreFoundation 0x00007fffc8124114 CFRunLoopRunSpecific + 420
5 com.apple.CoreFoundation 0x00007fffc8163b91 CFRunLoopRun + 97
6 com.apple.DFRDisplay 0x00000001057744b1 DFRDisplayRunloopThread + 119
7 libsystem_pthread.dylib 0x00007fffddabd93b _pthread_body + 180
8 libsystem_pthread.dylib 0x00007fffddabd887 _pthread_start + 286
9 libsystem_pthread.dylib 0x00007fffddabd08d thread_start + 13

Thread 3:: com.apple.coreanimation.render-server
0 libsystem_kernel.dylib 0x00007fffdd9cb34a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fffdd9ca797 mach_msg + 55
2 com.apple.QuartzCore 0x00007fffcdd08bd4 CA::Render::Server::server_thread(void*) + 272
3 com.apple.QuartzCore 0x00007fffcddb93ab thread_fun + 25
4 libsystem_pthread.dylib 0x00007fffddabd93b _pthread_body + 180
5 libsystem_pthread.dylib 0x00007fffddabd887 _pthread_start + 286
6 libsystem_pthread.dylib 0x00007fffddabd08d thread_start + 13

Thread 4:
0 libsystem_kernel.dylib 0x00007fffdd9d344e __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fffddabd48e _pthread_wqthread + 1023
2 libsystem_pthread.dylib 0x00007fffddabd07d start_wqthread + 13

Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x0000000000000006 rcx: 0x00007fff5a62b598 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x0000000000000006 rbp: 0x00007fff5a62b5c0 rsp: 0x00007fff5a62b598
r8: 0x0000000000000000 r9: 0x0000000000000b30 r10: 0x0000000008000000 r11: 0x0000000000000206
r12: 0x000000013d888028 r13: 0x000000013d888000 r14: 0x00007fffe67b83c0 r15: 0x00007fffd9dfcec0
rip: 0x00007fffdd9d2d42 rfl: 0x0000000000000206 cr2: 0x00007fffe679a128

Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133

Binary Images:
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0x7fffdcc21fff liblangid.dylib (126) <2085E7A7-9A34-3735-87F4-F174EF8EABF0> /usr/lib/liblangid.dylib 0x7fffdcc22000 - 0x7fffdcc3bffb liblzma.5.dylib (10) <44BD0279-99DD-36B5-8A6E-C11432E2098D> /usr/lib/liblzma.5.dylib 0x7fffdcc3c000 - 0x7fffdcc52ff7 libmarisa.dylib (5) <9030D214-5D0F-30CB-AC03-902C63909362> /usr/lib/libmarisa.dylib 0x7fffdcc53000 - 0x7fffdcefbff7 libmecabra.dylib (744.8) /usr/lib/libmecabra.dylib 0x7fffdcf2e000 - 0x7fffdcfa8ff3 libnetwork.dylib (856.60.1) <191E99F5-4723-3180-8013-02AF2F9AE4B8> /usr/lib/libnetwork.dylib 0x7fffdcfa9000 - 0x7fffdd37b047 libobjc.A.dylib (709.1) <70614861-0340-32E2-85ED-FE65759CDFFA> /usr/lib/libobjc.A.dylib 0x7fffdd37e000 - 0x7fffdd382fff libpam.2.dylib (21.30.1) <71EB0D88-DE84-3C8D-A2C5-58AA282BC5BC> /usr/lib/libpam.2.dylib 0x7fffdd383000 - 0x7fffdd3b4fff libpcap.A.dylib (67.60.1) /usr/lib/libpcap.A.dylib 0x7fffdd3d1000 - 0x7fffdd3edffb libresolv.9.dylib (64) /usr/lib/libresolv.9.dylib 0x7fffdd43d000 - 0x7fffdd58bff7 libsqlite3.dylib (254.8) <1ECF7DF7-7A07-3B4B-A63B-F4EFF6BC7ACF> /usr/lib/libsqlite3.dylib 0x7fffdd680000 - 0x7fffdd68dfff libxar.1.dylib (357) <69547C64-E811-326F-BBED-490C6361BDCB> /usr/lib/libxar.1.dylib 0x7fffdd68e000 - 0x7fffdd77dfff libxml2.2.dylib (30.17) /usr/lib/libxml2.2.dylib 0x7fffdd77e000 - 0x7fffdd7a7fff libxslt.1.dylib (15.9) <00735AD5-B62D-3E83-86AC-5533E4E2B102> /usr/lib/libxslt.1.dylib 0x7fffdd7a8000 - 0x7fffdd7b9ff3 libz.1.dylib (67) <46E3FFA2-4328-327A-8D34-A03E20BFFB8E> /usr/lib/libz.1.dylib 0x7fffdd7c8000 - 0x7fffdd7ccff7 libcache.dylib (79) <093A4DAB-8385-3D47-A350-E20CB7CCF7BF> /usr/lib/system/libcache.dylib 0x7fffdd7cd000 - 0x7fffdd7d7fff libcommonCrypto.dylib (60092.50.5) <8A64D1B0-C70E-385C-92F0-E669079FDA90> /usr/lib/system/libcommonCrypto.dylib 0x7fffdd7d8000 - 0x7fffdd7dffff libcompiler_rt.dylib (62) <55D47421-772A-32AB-B529-1A46C2F43B4D> /usr/lib/system/libcompiler_rt.dylib 0x7fffdd7e0000 - 0x7fffdd7e8fff libcopyfile.dylib (138) <819BEA3C-DF11-3E3D-A1A1-5A51C5BF1961> /usr/lib/system/libcopyfile.dylib 0x7fffdd7e9000 - 0x7fffdd86cfdf libcorecrypto.dylib (442.50.19) <65D7165E-2E71-335D-A2D6-33F78E2DF0C1> /usr/lib/system/libcorecrypto.dylib 0x7fffdd86d000 - 0x7fffdd89efff libdispatch.dylib (703.50.37) <6582BAD6-ED27-3B30-B620-90B1C5A4AE3C> /usr/lib/system/libdispatch.dylib 0x7fffdd89f000 - 0x7fffdd8a4ffb libdyld.dylib (433.5) <9B2AC56D-107C-3541-A127-9094A751F2C9> /usr/lib/system/libdyld.dylib 0x7fffdd8a5000 - 0x7fffdd8a5ffb libkeymgr.dylib (28) <7AA011A9-DC21-3488-BF73-3B5B14D1FDD6> /usr/lib/system/libkeymgr.dylib 0x7fffdd8a6000 - 0x7fffdd8b2fff libkxld.dylib (3789.70.16) /usr/lib/system/libkxld.dylib 0x7fffdd8b3000 - 0x7fffdd8b3fff liblaunch.dylib (972.70.1) /usr/lib/system/liblaunch.dylib 0x7fffdd8b4000 - 0x7fffdd8b9ff3 libmacho.dylib (898) <17D5D855-F6C3-3B04-B680-E9BF02EF8AED> /usr/lib/system/libmacho.dylib 0x7fffdd8ba000 - 0x7fffdd8bcff3 libquarantine.dylib (85.50.1) <12448CC2-378E-35F3-BE33-9DC395A5B970> /usr/lib/system/libquarantine.dylib 0x7fffdd8bd000 - 0x7fffdd8beffb libremovefile.dylib (45) <38D4CB9C-10CD-30D3-8B7B-A515EC75FE85> /usr/lib/system/libremovefile.dylib 0x7fffdd8bf000 - 0x7fffdd8d7ff7 libsystem_asl.dylib (349.50.5) <096E4228-3B7C-30A6-8B13-EC909A64499A> /usr/lib/system/libsystem_asl.dylib 0x7fffdd8d8000 - 0x7fffdd8d8ff7 libsystem_blocks.dylib (67) <10DC5404-73AB-35B3-A277-A8AFECB476EB> /usr/lib/system/libsystem_blocks.dylib 0x7fffdd8d9000 - 0x7fffdd966fef libsystem_c.dylib (1158.50.2) /usr/lib/system/libsystem_c.dylib 0x7fffdd967000 - 0x7fffdd96affb libsystem_configuration.dylib (888.60.2) /usr/lib/system/libsystem_configuration.dylib 0x7fffdd96b000 - 0x7fffdd96efff libsystem_coreservices.dylib (41.4) <7D26DE79-B424-3450-85E1-F7FAB32714AB> /usr/lib/system/libsystem_coreservices.dylib 0x7fffdd96f000 - 0x7fffdd987fff libsystem_coretls.dylib (121.50.4) /usr/lib/system/libsystem_coretls.dylib 0x7fffdd988000 - 0x7fffdd98efff libsystem_dnssd.dylib (765.50.9) /usr/lib/system/libsystem_dnssd.dylib 0x7fffdd98f000 - 0x7fffdd9b8ff7 libsystem_info.dylib (503.50.4) <611DB84C-BF70-3F92-8702-B9F28A900920> /usr/lib/system/libsystem_info.dylib 0x7fffdd9b9000 - 0x7fffdd9dbff7 libsystem_kernel.dylib (3789.70.16) <34B1F16C-BC9C-3C5F-9045-0CAE91CB5914> /usr/lib/system/libsystem_kernel.dylib 0x7fffdd9dc000 - 0x7fffdda23fe7 libsystem_m.dylib (3121.6) <86D499B5-BBDC-3D3B-8A4E-97AE8E6672A4> /usr/lib/system/libsystem_m.dylib 0x7fffdda24000 - 0x7fffdda42ff7 libsystem_malloc.dylib (116.50.8) /usr/lib/system/libsystem_malloc.dylib 0x7fffdda43000 - 0x7fffdda9cffb libsystem_network.dylib (856.60.1) <369D0221-56CA-3C3E-9EDE-94B41CAE77B7> /usr/lib/system/libsystem_network.dylib 0x7fffdda9d000 - 0x7fffddaa6ff3 libsystem_networkextension.dylib (563.60.2) /usr/lib/system/libsystem_networkextension.dylib 0x7fffddaa7000 - 0x7fffddab0ff3 libsystem_notify.dylib (165.20.1) /usr/lib/system/libsystem_notify.dylib 0x7fffddab1000 - 0x7fffddab9fe7 libsystem_platform.dylib (126.50.8) <897462FD-B318-321B-A554-E61982630F7E> /usr/lib/system/libsystem_platform.dylib 0x7fffddaba000 - 0x7fffddac4ff7 libsystem_pthread.dylib (218.60.3) /usr/lib/system/libsystem_pthread.dylib 0x7fffddac5000 - 0x7fffddac8ff7 libsystem_sandbox.dylib (592.70.1) <4B92EC49-ACD0-36AE-B07A-A2B8152EAF9D> /usr/lib/system/libsystem_sandbox.dylib 0x7fffddac9000 - 0x7fffddacaff3 libsystem_secinit.dylib (24.50.4) /usr/lib/system/libsystem_secinit.dylib 0x7fffddacb000 - 0x7fffddad2ffb libsystem_symptoms.dylib (532.50.47) <3390E07C-C1CE-348F-ADBD-2C5440B45EAA> /usr/lib/system/libsystem_symptoms.dylib 0x7fffddad3000 - 0x7fffddae6ff7 libsystem_trace.dylib (518.70.1) /usr/lib/system/libsystem_trace.dylib 0x7fffddae7000 - 0x7fffddaecffb libunwind.dylib (35.3) <3D50D8A8-C460-334D-A519-2DA841102C6B> /usr/lib/system/libunwind.dylib 0x7fffddaed000 - 0x7fffddb16ff7 libxpc.dylib (972.70.1) /usr/lib/system/libxpc.dylib

External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 91
thread_create: 0
thread_set_state: 0
Calls made by this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by all processes on this machine:
task_for_pid: 23997
thread_create: 0
thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=273.9M resident=0K(0%) swapped_out_or_unallocated=273.9M(100%)
Writable regions: Total=1.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.1G(100%)

                            VIRTUAL   REGION  REGION TYPE                        SIZE    COUNT (non-coalesced)  ===========                     =======  =======  Activity Tracing                   256K        2  CG backing stores                 51.7M      131  CG framebuffers                  775.0M        7  CG framebuffers (reserved)        35.0M        6         reserved VM address space (unallocated) CG image                          1188K       19  CoreAnimation                     75.1M      247  CoreUI image data                  244K        8  Dispatch continuations            16.0M        2  Image IO                          1508K       22  Kernel Alloc Once                    8K        2  MALLOC                           240.3M       57  MALLOC guard page                   48K       10  Memory Tag 252                    20.0M        3  OpenGL GLSL                        256K        4  STACK GUARD                       56.0M        6  Stack                             10.0M        6  VM_ALLOCATE                        968K       55  __CGSERVER                           4K        2  __DATA                            30.9M      210  __GLSLBUILTINS                    2588K        2  __IMAGE                            528K        2  __LINKEDIT                       116.3M       13  __TEXT                           157.6M      212  __UNICODE                          556K        2  mapped file                       24.7M        2  shared memory                      172K       16  ===========                     =======  =======  TOTAL                              1.6G     1022  TOTAL, minus reserved VM space     1.5G     1022 

Susume Lv 1

I think this may be the pertinent error message in that Mac output: "10 seconds of continuous GPU Driver unreadiness, relaunching WindowServer".

There are numerous reports around the web from 2016 of this mac error message relating to various apps under Sierra, although I don't find any reports from 2017. Are you up to date on OS updates? Have you recently changed anything about your graphics or monitor(s)?