Bernhard,
I have tried this using several versions of coot. I tried it first in
the coot that came packaged with ccp4 (Coot 0.5.2). I then tried
WinCoot-0.6-pre-1-revision-2411, which is one of the later revisions
of 0.6-pre, just to see if a more recent version would work. As far
as I can tell, I am using the correct versions of probe and reduce.
I am attaching a file with the relevant portion of the output
(starting with when I run "probe clashes," up until it fails).
Thanks for your help!
-Tom
On Mon, Oct 12, 2009 at 3:21 AM, Bernhard C. Lohkamp
<[log in to unmask]> wrote:
>
> Thomas,
>
>> I am trying to use molprobity to check a structure in coot (platform is
>> 64-bit vista). I followed the instructions found here to set up
>> molprobity:
>> http://www.ysbl.york.ac.uk/~lohkamp/coot/wincoot-faq.html . From the
>> logs,
>> it seems like reduce runs OK (it says that it "Added 6076 hydrogens").
>> However, at the very end, I get the message "BL WARNING:: reduce didnt run
>> ok, so stop here!" It seems like probe never runs.
>>
>> Does anyone know how to solve this?
>>
>
> Maybe you can give me some more information. Which version of WinCoot are
> you running and which versions of probe and reduce are you using? Make sure
> you use the right version of probe (2.12.something) and reduce
> (3.13.something). Note to self: update the website with respect to versions.
> If have the 'right' versions please sent me the console output. Hopefully
> that will give more information.
>
> B
>
>
write_pdb_file (0, "coot-molprobity/for-reduce.pdb")
BL INFO:: run reduce as C:\WinCoot\bin\reduce.exe coot-molprobity/for-reduce.pd
b > coot-molprobity/reduced.pdb
reduce: version 3.13 04/28/2008, Copyright 1997-2008, J. Michael Word
Processing file: "coot-molprobity/for-reduce.pdb"
Database of HETATM connections: "reduce_het_dict.txt"
Processing only 'A' conformations.
VDW dot density = 16/A^2
Orientation penalty scale = 1 (100%)
Eliminate contacts within 3 bonds.
Ignore atoms with |occupancy| <= 0.01 during adjustments.
Waters ignored if B-Factor >= 40 or |occupancy| < 0.66
Aromatic rings in amino acids accept hydrogen bonds.
Building His ring NH Hydrogens.
Flipping Asn, Gln and His groups.
For each flip state, bumps where gap is more than 0.4A are indicated with '!'.
Building or keeping OH & SH Hydrogens.
Rotating existing OH & SH Hydrogens
Rotating NH3 Hydrogens.
Processing Met methyls.
ERROR CTab(reduce_het_dict.txt): could not open
Singles(size 270): A 25 THR OG1 : A 33 SER OG : A 35 HIS : A 46 SER OG
: A 53 GLN : A 60 TYR OH : A 64 TYR OH : A 68 SER OG : A 70 HIS
: A 72 GLN : A 73 THR OG1 : A 75 LYS NZ : A 78 TYR OH : A 79 LYS NZ
: A 80 GLN : A 83 TYR OH : A 84 THR OG1 : A 91 SER OG : A 92 SER OG
: A 93 HIS : A 94 TYR OH : A 97 THR OG1 : A 99 LYS NZ : A 102 ASN
: A 103 ASN : A 111 TYR OH : A 113 SER OG : A 116 THR OG1 : A 119 HIS
: A 120 THR OG1 : B 25 THR OG1 : B 33 SER OG : B 35 HIS : B 46 SER OG
: B 53 GLN : B 60 TYR OH : B 64 TYR OH : B 68 SER OG : B 70 HIS
: B 72 GLN : B 73 THR OG1 : B 75 LYS NZ : B 78 TYR OH : B 79 LYS NZ
: B 83 TYR OH : B 84 THR OG1 : B 91 SER OG : B 92 SER OG : B 93 HIS
: B 94 TYR OH : B 97 THR OG1 : B 99 LYS NZ : B 102 ASN : B 103 ASN
: B 111 TYR OH : B 113 SER OG : B 116 THR OG1 : B 119 HIS : B 120 THR OG
1
: C 19 SER OG : C 23 GLN : C 24 ASN : C 31 ASN : C 32 SER OG
: C 33 LYS NZ : C 34 SER OG : C 36 MET CE : C 38 HIS : C 40 GLN
: C 46 THR OG1 : C 47 GLN : C 48 ASN : C 50 GLN : C 52 THR OG
1
: C 54 TYR OH : C 55 LYS NZ : C 58 TYR OH : C 60 LYS NZ : C 62 SER OG
: C 64 LYS NZ : C 65 SER OG : C 68 THR OG1 : C 70 THR OG1 : C 73 SER OG
: C 75 THR OG1 : C 76 GLN : C 78 SER OG : C 79 GLN : C 88 THR OG
1
: C 90 TYR OH : C 91 ASN : C 102 THR OG1 : C 106 THR OG1 : C 110 SER OG
: C 113 THR OG1 : C 116 SER OG : D 19 SER OG : D 23 GLN : D 24 ASN
: D 26 SER OG : D 31 ASN : D 32 SER OG : D 33 LYS NZ : D 34 SER OG
: D 36 MET CE : D 38 HIS : D 40 GLN : D 46 THR OG1 : D 47 GLN
: D 48 ASN : D 50 GLN : D 52 THR OG1 : D 54 TYR OH : D 55 LYS NZ
: D 58 TYR OH : D 60 LYS NZ : D 62 SER OG : D 64 LYS NZ : D 65 SER OG
: D 68 THR OG1 : D 70 THR OG1 : D 73 SER OG : D 75 THR OG1 : D 76 GLN
: D 78 SER OG : D 79 GLN : D 88 THR OG1 : D 90 TYR OH : D 91 ASN
: D 102 THR OG1 : D 106 THR OG1 : D 110 SER OG : D 113 THR OG1 : D 116 SER OG
: E 19 SER OG : E 23 GLN : E 24 ASN : E 31 ASN : E 32 SER OG
: E 33 LYS NZ : E 34 SER OG : E 36 MET CE : E 38 HIS : E 40 GLN
: E 46 THR OG1 : E 47 GLN : E 48 ASN : E 50 GLN : E 52 THR OG
1
: E 54 TYR OH : E 55 LYS NZ : E 58 TYR OH : E 60 LYS NZ : E 62 SER OG
: E 64 LYS NZ : E 65 SER OG : E 68 THR OG1 : E 70 THR OG1 : E 73 SER OG
: E 75 THR OG1 : E 76 GLN : E 78 SER OG : E 79 GLN : E 88 THR OG
1
: E 90 TYR OH : E 91 ASN : E 102 THR OG1 : E 106 THR OG1 : E 110 SER OG
: E 113 THR OG1 : E 116 SER OG : F 25 THR OG1 : F 33 SER OG : F 35 HIS
: F 46 SER OG : F 53 GLN : F 60 TYR OH : F 64 TYR OH : F 68 SER OG
: F 70 HIS : F 72 GLN : F 73 THR OG1 : F 75 LYS NZ : F 78 TYR OH
: F 80 GLN : F 82 TYR OH : F 83 TYR OH : F 84 THR OG1 : F 87 ASN
: F 91 SER OG : F 92 SER OG : F 93 HIS : F 94 TYR OH : F 97 THR OG
1
: F 99 LYS NZ : F 102 ASN : F 111 TYR OH : F 113 SER OG : F 116 THR OG
1
: F 119 HIS : F 120 THR OG1 : G 19 SER OG : G 23 GLN : G 24 ASN
: G 26 SER OG : G 31 ASN : G 32 SER OG : G 33 LYS NZ : G 34 SER OG
: G 36 MET CE : G 38 HIS : G 40 GLN : G 46 THR OG1 : G 47 GLN
: G 48 ASN : G 50 GLN : G 52 THR OG1 : G 54 TYR OH : G 55 LYS NZ
: G 58 TYR OH : G 60 LYS NZ : G 62 SER OG : G 64 LYS NZ : G 65 SER OG
: G 68 THR OG1 : G 70 THR OG1 : G 73 SER OG : G 75 THR OG1 : G 76 GLN
: G 78 SER OG : G 79 GLN : G 88 THR OG1 : G 90 TYR OH : G 91 ASN
: G 102 THR OG1 : G 106 THR OG1 : G 110 SER OG : G 113 THR OG1 : G 116 SER OG
: H 25 THR OG1 : H 33 SER OG : H 35 HIS : H 46 SER OG : H 53 GLN
: H 60 TYR OH : H 64 TYR OH : H 68 SER OG : H 70 HIS : H 72 GLN
: H 73 THR OG1 : H 75 LYS NZ : H 78 TYR OH : H 79 LYS NZ : H 80 GLN
: H 82 TYR OH : H 83 TYR OH : H 84 THR OG1 : H 87 ASN : H 91 SER OG
: H 92 SER OG : H 93 HIS : H 94 TYR OH : H 97 THR OG1 : H 99 LYS NZ
: H 102 ASN : H 111 TYR OH : H 113 SER OG : H 116 THR OG1 : H 119 HIS
: H 120 THR OG1
Set 1 (size 2): H 103 ASN : A 87 ASN
Set 2 (size 2): H 54 ASN : H 52 ASN
Set 3 (size 2): H 42 SER OG : H 41 THR OG1
Set 4 (size 2): H 48 THR OG1 : H 32 SER OG
Set 5 (size 2): G 100 ASN : G 98 THR OG1
Set 6 (size 2): B 80 GLN : F 79 LYS NZ
Set 7 (size 2): F 54 ASN : F 52 ASN
Set 8 (size 2): F 42 SER OG : F 41 THR OG1
Set 9 (size 2): F 48 THR OG1 : F 32 SER OG
Set 10 (size 2): E 100 ASN : E 98 THR OG1
Set 11 (size 2): E 26 SER OG : B 82 TYR OH
Set 12 (size 2): D 100 ASN : D 98 THR OG1
Set 13 (size 2): C 100 ASN : C 98 THR OG1
Set 14 (size 2): B 87 ASN : F 103 ASN
Set 15 (size 2): B 54 ASN : B 52 ASN
Set 16 (size 2): B 48 THR OG1 : B 32 SER OG
Set 17 (size 2): B 41 THR OG1 : B 42 SER OG
Set 18 (size 2): A 82 TYR OH : C 26 SER OG
Set 19 (size 2): A 54 ASN : A 52 ASN
Set 20 (size 2): A 48 THR OG1 : A 32 SER OG
Set 21 (size 2): A 41 THR OG1 : A 42 SER OG
orientation 1: A 25 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: A 33 SER OG : rot 180: bump=0.000, HB=0.005, total=0.005
orientation 1: A 35 HIS : no HD1: bump=-0.026, HB=0.000, total=-0.026
orientation 1: A 46 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 2: A 53 GLN :FLIP amide: bump=-0.124, HB=0.000, total=-0.124
orientation 1: A 60 TYR OH : rot 180: bump=-0.494, HB=0.000, total=-0.494
orientation 1: A 64 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: A 68 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: A 70 HIS : no HD1: bump=0.000, HB=0.000, total=0.000
orientation 1: A 72 GLN : amide: bump=-0.130, HB=0.000, total=-0.130
orientation 1: A 73 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 3: A 75 LYS NZ :NH3+ 164: bump=-0.003, HB=0.000, total=-0.003
orientation 4: A 78 TYR OH : rot 77: bump=-0.000, HB=0.097, total=0.096
orientation 1: A 79 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000
orientation 1: A 80 GLN : amide: bump=-0.036, HB=0.000, total=-0.036
orientation 1: A 83 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: A 84 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: A 91 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 3: A 92 SER OG : rot 28: bump=0.000, HB=0.154, total=0.154
orientation 2: A 93 HIS : no HE2: bump=0.000, HB=0.000, total=0.000
orientation 9: A 94 TYR OH : rot -140: bump=-6.977, HB=0.097, total=-6.880,
BADBUMP
orientation 1: A 97 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: A 99 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000
orientation 1: A 102 ASN : amide: bump=-0.489, HB=0.238, total=-0.251
orientation 2: A 103 ASN :FLIP amide: bump=-2.599, HB=0.391, total=-2.208,
BADBUMP
orientation 1: A 111 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: A 113 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 3: A 116 THR OG1 : rot -158: bump=-0.560, HB=1.318, total=0.758
orientation 1: A 119 HIS : no HD1: bump=0.000, HB=0.000, total=0.000
orientation 1: A 120 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 2: B 25 THR OG1 : rot -20: bump=-0.175, HB=0.369, total=0.194
orientation 1: B 33 SER OG : rot 180: bump=0.000, HB=0.004, total=0.004
orientation 1: B 35 HIS : no HD1: bump=-0.018, HB=0.000, total=-0.018
orientation 3: B 46 SER OG : rot 27: bump=-0.034, HB=0.149, total=0.116
orientation 2: B 53 GLN :FLIP amide: bump=-0.205, HB=0.000, total=-0.205
orientation 1: B 60 TYR OH : rot 180: bump=-0.542, HB=0.000, total=-0.542
orientation 1: B 64 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: B 68 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: B 70 HIS : no HD1: bump=0.000, HB=0.000, total=0.000
orientation 1: B 72 GLN : amide: bump=-0.104, HB=0.000, total=-0.104
orientation 1: B 73 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 3: B 75 LYS NZ :NH3+ 163: bump=-0.040, HB=0.000, total=-0.040
orientation 1: B 78 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: B 79 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000
orientation 1: B 83 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: B 84 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: B 91 SER OG : rot 180: bump=-0.011, HB=0.000, total=-0.011
orientation 3: B 92 SER OG : rot 27: bump=0.000, HB=0.231, total=0.231
orientation 2: B 93 HIS : no HE2: bump=0.000, HB=0.000, total=0.000
orientation 9: B 94 TYR OH : rot -140: bump=-7.283, HB=0.146, total=-7.137,
BADBUMP
orientation 1: B 97 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: B 99 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000
orientation 1: B 102 ASN : amide: bump=-0.436, HB=0.197, total=-0.238
orientation 2: B 103 ASN :FLIP amide: bump=-11.447, HB=1.059, total=-10.38
8, BADBUMP
orientation 1: B 111 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: B 113 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 3: B 116 THR OG1 : rot -155: bump=-0.602, HB=1.306, total=0.704
orientation 1: B 119 HIS : no HD1: bump=-0.242, HB=0.000, total=-0.242
orientation 1: B 120 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: C 19 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: C 23 GLN : amide: bump=-1.760, HB=0.796, total=-0.964,
BADBUMP
orientation 1: C 24 ASN : amide: bump=-0.293, HB=0.000, total=-0.293
orientation 2: C 31 ASN :FLIP amide: bump=-0.439, HB=0.000, total=-0.439
orientation 1: C 32 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: C 33 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000
orientation 1: C 34 SER OG : rot 154: bump=-0.340, HB=0.000, total=-0.340
orientation 3: C 36 MET CE :methyl 157: bump=-4.365, HB=0.000, total=-4.365,
BADBUMP
orientation 2: C 38 HIS : no HE2: bump=-6.508, HB=0.000, total=-6.508,
BADBUMP
orientation 1: C 40 GLN : amide: bump=-0.990, HB=0.000, total=-0.990
orientation 6: C 46 THR OG1 : rot -72: bump=-0.139, HB=1.271, total=1.131
orientation 1: C 47 GLN : amide: bump=-0.064, HB=0.488, total=0.424
orientation 1: C 48 ASN : amide: bump=-0.298, HB=0.000, total=-0.298
orientation 1: C 50 GLN : amide: bump=0.000, HB=0.000, total=0.000
orientation 1: C 52 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 4: C 54 TYR OH : rot 30: bump=0.000, HB=0.000, total=0.000
orientation 1: C 55 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000
orientation 1: C 58 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: C 60 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000
orientation 1: C 62 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 2: C 64 LYS NZ :NH3+ -155: bump=-0.079, HB=0.000, total=-0.079
orientation 2: C 65 SER OG : rot -170: bump=-0.020, HB=0.000, total=-0.020
orientation 1: C 68 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: C 70 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: C 73 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 3: C 75 THR OG1 : rot -42: bump=0.000, HB=1.069, total=1.069
orientation 1: C 76 GLN : amide: bump=-0.983, HB=0.000, total=-0.983
orientation 2: C 78 SER OG : rot -140: bump=-0.006, HB=0.000, total=-0.006
orientation 1: C 79 GLN : amide: bump=0.000, HB=0.000, total=0.000
orientation 1: C 88 THR OG1 : rot 94: bump=-0.185, HB=0.737, total=0.552
orientation 4: C 90 TYR OH : rot 130: bump=0.000, HB=0.098, total=0.098
orientation 2: C 91 ASN :FLIP amide: bump=-0.190, HB=0.000, total=-0.190
orientation 1: C 102 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: C 106 THR OG1 : rot 59: bump=-0.074, HB=1.099, total=1.026
orientation 1: C 110 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 6: C 113 THR OG1 : rot -170: bump=-0.009, HB=1.221, total=1.212
orientation 1: C 116 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: D 19 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: D 23 GLN : amide: bump=-1.887, HB=1.060, total=-0.827
orientation 1: D 24 ASN : amide: bump=-0.394, HB=0.000, total=-0.394
orientation 1: D 26 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 2: D 31 ASN :FLIP amide: bump=-0.316, HB=0.000, total=-0.316
orientation 1: D 32 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: D 33 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000
orientation 1: D 34 SER OG : rot 152: bump=-0.371, HB=0.000, total=-0.371
orientation 3: D 36 MET CE :methyl 152: bump=-2.078, HB=0.000, total=-2.078,
BADBUMP
orientation 2: D 38 HIS : no HE2: bump=-5.403, HB=0.000, total=-5.403,
BADBUMP
orientation 1: D 40 GLN : amide: bump=-0.592, HB=0.000, total=-0.592
orientation 1: D 46 THR OG1 : rot -15: bump=-0.075, HB=1.289, total=1.214
orientation 1: D 47 GLN : amide: bump=-0.095, HB=0.541, total=0.446
orientation 1: D 48 ASN : amide: bump=-0.070, HB=0.000, total=-0.070
orientation 1: D 50 GLN : amide: bump=0.000, HB=0.000, total=0.000
orientation 1: D 52 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 4: D 54 TYR OH : rot 110: bump=0.000, HB=0.000, total=0.000
orientation 1: D 55 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000
orientation 1: D 58 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: D 60 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000
orientation 1: D 62 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 2: D 64 LYS NZ :NH3+ -159: bump=-0.075, HB=0.000, total=-0.075
orientation 1: D 65 SER OG : rot 180: bump=-0.171, HB=0.000, total=-0.171
orientation 1: D 68 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: D 70 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: D 73 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 4: D 75 THR OG1 : rot -46: bump=0.000, HB=1.156, total=1.156
orientation 1: D 76 GLN : amide: bump=-0.067, HB=0.114, total=0.047
orientation 2: D 78 SER OG : rot -170: bump=0.000, HB=0.000, total=0.000
orientation 1: D 79 GLN : amide: bump=0.000, HB=0.000, total=0.000
orientation 1: D 88 THR OG1 : rot 99: bump=-0.176, HB=0.763, total=0.588
orientation 8: D 90 TYR OH : rot -30: bump=0.000, HB=0.155, total=0.155
orientation 2: D 91 ASN :FLIP amide: bump=-0.204, HB=0.000, total=-0.204
orientation 1: D 102 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: D 106 THR OG1 : rot 67: bump=-0.047, HB=1.084, total=1.037
orientation 1: D 110 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 4: D 113 THR OG1 : rot -161: bump=0.000, HB=1.219, total=1.219
orientation 3: D 116 SER OG : rot -132: bump=0.000, HB=0.023, total=0.023
orientation 1: E 19 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: E 23 GLN : amide: bump=-1.835, HB=0.868, total=-0.968,
BADBUMP
orientation 1: E 24 ASN : amide: bump=-0.220, HB=0.000, total=-0.220
orientation 2: E 31 ASN :FLIP amide: bump=-0.476, HB=0.000, total=-0.476
orientation 1: E 32 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: E 33 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000
orientation 1: E 34 SER OG : rot 140: bump=-0.456, HB=0.000, total=-0.456
orientation 3: E 36 MET CE :methyl 145: bump=-4.752, HB=0.000, total=-4.752,
BADBUMP
orientation 2: E 38 HIS : no HE2: bump=-8.566, HB=0.000, total=-8.566,
BADBUMP
orientation 1: E 40 GLN : amide: bump=-0.779, HB=0.000, total=-0.779
orientation 1: E 46 THR OG1 : rot -18: bump=-0.183, HB=1.411, total=1.227
orientation 1: E 47 GLN : amide: bump=-0.117, HB=0.720, total=0.603
orientation 1: E 48 ASN : amide: bump=-0.203, HB=0.000, total=-0.203
orientation 1: E 50 GLN : amide: bump=0.000, HB=0.000, total=0.000
orientation 1: E 52 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 4: E 54 TYR OH : rot 30: bump=-0.015, HB=0.000, total=-0.015
orientation 1: E 55 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000
orientation 1: E 58 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: E 60 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000
orientation 1: E 62 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 2: E 64 LYS NZ :NH3+ -152: bump=-0.133, HB=0.000, total=-0.133
orientation 1: E 65 SER OG : rot 180: bump=-0.017, HB=0.000, total=-0.017
orientation 1: E 68 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: E 70 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: E 73 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 4: E 75 THR OG1 : rot -49: bump=0.000, HB=1.163, total=1.163
orientation 1: E 76 GLN : amide: bump=-1.150, HB=0.000, total=-1.150
orientation 2: E 78 SER OG : rot -160: bump=-0.107, HB=0.000, total=-0.107
orientation 1: E 79 GLN : amide: bump=0.000, HB=0.000, total=0.000
orientation 1: E 88 THR OG1 : rot 95: bump=-0.317, HB=1.144, total=0.827
orientation 4: E 90 TYR OH : rot 130: bump=0.000, HB=0.079, total=0.079
orientation 2: E 91 ASN :FLIP amide: bump=-0.184, HB=0.000, total=-0.184
orientation 1: E 102 THR OG1 : rot 180: bump=0.000, HB=0.002, total=0.002
orientation 1: E 106 THR OG1 : rot 64: bump=-0.035, HB=0.998, total=0.963
orientation 1: E 110 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 3: E 113 THR OG1 : rot -167: bump=-0.049, HB=1.137, total=1.088
orientation 1: E 116 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 2: F 25 THR OG1 : rot -12: bump=-0.216, HB=0.379, total=0.163
orientation 1: F 33 SER OG : rot 180: bump=0.000, HB=0.050, total=0.050
orientation 5: F 35 HIS :FLIP no HE2: bump=-1.241, HB=0.000, total=-1.241
orientation 1: F 46 SER OG : rot 180: bump=-0.004, HB=0.000, total=-0.004
orientation 2: F 53 GLN :FLIP amide: bump=-0.092, HB=0.000, total=-0.092
orientation 5: F 60 TYR OH : rot 15: bump=-0.448, HB=0.000, total=-0.448
orientation 1: F 64 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: F 68 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: F 70 HIS : no HD1: bump=0.000, HB=0.000, total=0.000
orientation 1: F 72 GLN : amide: bump=-0.094, HB=0.000, total=-0.094
orientation 1: F 73 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 3: F 75 LYS NZ :NH3+ 168: bump=-0.034, HB=0.000, total=-0.034
orientation 1: F 78 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: F 80 GLN : amide: bump=-0.922, HB=1.024, total=0.102
orientation 4: F 82 TYR OH : rot 130: bump=-0.516, HB=0.000, total=-0.516
orientation 1: F 83 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: F 84 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 2: F 87 ASN :FLIP amide: bump=-0.112, HB=0.476, total=0.363
orientation 1: F 91 SER OG : rot 180: bump=-0.005, HB=0.000, total=-0.005
orientation 3: F 92 SER OG : rot 25: bump=0.000, HB=0.252, total=0.252
orientation 2: F 93 HIS : no HE2: bump=-0.000, HB=0.000, total=-0.000
orientation 9: F 94 TYR OH : rot -140: bump=-6.575, HB=0.064, total=-6.510,
BADBUMP
orientation 1: F 97 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: F 99 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000
orientation 1: F 102 ASN : amide: bump=-0.466, HB=0.252, total=-0.213
orientation 1: F 111 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: F 113 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 3: F 116 THR OG1 : rot -160: bump=-0.486, HB=1.286, total=0.799
orientation 1: F 119 HIS : no HD1: bump=-0.043, HB=0.000, total=-0.043
orientation 1: F 120 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: G 19 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: G 23 GLN : amide: bump=-2.435, HB=0.952, total=-1.483
orientation 1: G 24 ASN : amide: bump=-0.347, HB=0.000, total=-0.347
orientation 1: G 26 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 2: G 31 ASN :FLIP amide: bump=-0.351, HB=0.000, total=-0.351
orientation 1: G 32 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 2: G 33 LYS NZ :NH3+ -179: bump=0.000, HB=0.000, total=0.000
orientation 1: G 34 SER OG : rot 150: bump=-0.344, HB=0.000, total=-0.344
orientation 3: G 36 MET CE :methyl 148: bump=-2.272, HB=0.000, total=-2.272
orientation 2: G 38 HIS : no HE2: bump=-3.348, HB=0.000, total=-3.348
orientation 1: G 40 GLN : amide: bump=-0.526, HB=0.000, total=-0.526
orientation 2: G 46 THR OG1 : rot -16: bump=-0.095, HB=1.308, total=1.213
orientation 1: G 47 GLN : amide: bump=-0.088, HB=0.707, total=0.620
orientation 1: G 48 ASN : amide: bump=-0.058, HB=0.000, total=-0.058
orientation 1: G 50 GLN : amide: bump=0.000, HB=0.000, total=0.000
orientation 1: G 52 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 4: G 54 TYR OH : rot 30: bump=0.000, HB=0.000, total=0.000
orientation 2: G 55 LYS NZ :NH3+ -154: bump=0.000, HB=0.000, total=0.000
orientation 1: G 58 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: G 60 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000
orientation 1: G 62 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 2: G 64 LYS NZ :NH3+ -155: bump=-0.156, HB=0.000, total=-0.156
orientation 1: G 65 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: G 68 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: G 70 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: G 73 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 3: G 75 THR OG1 : rot -44: bump=0.000, HB=1.123, total=1.123
orientation 1: G 76 GLN : amide: bump=-0.052, HB=0.078, total=0.025
orientation 2: G 78 SER OG : rot 38: bump=-0.049, HB=0.268, total=0.219
orientation 1: G 79 GLN : amide: bump=0.000, HB=0.000, total=0.000
orientation 1: G 88 THR OG1 : rot 100: bump=-0.092, HB=0.761, total=0.669
orientation 4: G 90 TYR OH : rot 130: bump=0.000, HB=0.110, total=0.110
orientation 1: G 91 ASN : amide: bump=-0.601, HB=0.000, total=-0.601
orientation 1: G 102 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: G 106 THR OG1 : rot 65: bump=-0.087, HB=1.075, total=0.988
orientation 1: G 110 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 4: G 113 THR OG1 : rot -163: bump=0.000, HB=1.204, total=1.204
orientation 3: G 116 SER OG : rot -117: bump=0.000, HB=0.334, total=0.334
orientation 2: H 25 THR OG1 : rot -22: bump=-0.141, HB=0.257, total=0.116
orientation 1: H 33 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: H 35 HIS : no HD1: bump=-0.271, HB=0.000, total=-0.271
orientation 2: H 46 SER OG : rot 26: bump=-0.034, HB=0.106, total=0.072
orientation 2: H 53 GLN :FLIP amide: bump=-0.094, HB=0.000, total=-0.094
orientation 5: H 60 TYR OH : rot 15: bump=-0.554, HB=0.000, total=-0.554
orientation 1: H 64 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: H 68 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: H 70 HIS : no HD1: bump=0.000, HB=0.000, total=0.000
orientation 1: H 72 GLN : amide: bump=-0.151, HB=0.000, total=-0.151
orientation 1: H 73 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 3: H 75 LYS NZ :NH3+ 163: bump=-0.077, HB=0.000, total=-0.077
orientation 1: H 78 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: H 79 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000
orientation 1: H 80 GLN : amide: bump=-0.042, HB=0.000, total=-0.042
orientation 4: H 82 TYR OH : rot 120: bump=-0.130, HB=0.000, total=-0.130
orientation 1: H 83 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: H 84 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 2: H 87 ASN :FLIP amide: bump=-0.155, HB=0.454, total=0.299
orientation 1: H 91 SER OG : rot 180: bump=-0.048, HB=0.000, total=-0.048
orientation 3: H 92 SER OG : rot 22: bump=-0.000, HB=0.294, total=0.294
orientation 1: H 93 HIS : no HD1: bump=0.000, HB=0.000, total=0.000
orientation 1: H 94 TYR OH : rot 180: bump=-6.088, HB=0.064, total=-6.024,
BADBUMP
orientation 1: H 97 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: H 99 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000
orientation 1: H 102 ASN : amide: bump=-0.532, HB=0.285, total=-0.248
orientation 1: H 111 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 1: H 113 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000
orientation 3: H 116 THR OG1 : rot -163: bump=-0.713, HB=1.257, total=0.544
orientation 1: H 119 HIS : no HD1: bump=-0.022, HB=0.000, total=-0.022
orientation 1: H 120 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000
Processing set: H 103 ASN [2]: A 87 ASN [2]
permutations: 4
Computing dot scores
Num optimizations problems to be solved for this clique: 4
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following low resolution optimization: -45.798
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following high resolution, local optimization: -45.798
Processing set: H 54 ASN [2]: H 52 ASN [2]
permutations: 4
Computing dot scores
Num optimizations problems to be solved for this clique: 4
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following low resolution optimization: -32.907
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following high resolution, local optimization: -32.907
Processing set: H 42 SER OG [2]: H 41 THR OG1 [2]
permutations: 4
Computing dot scores
Num optimizations problems to be solved for this clique: 1
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following low resolution optimization: -0.000
> : -0.000
Optimal score following high resolution, local optimization: -0.000
Processing set: H 48 THR OG1 [6]: H 32 SER OG [8]
permutations: 48
Computing dot scores
Num optimizations problems to be solved for this clique: 1
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following low resolution optimization: 3.512
> : 3.533
Optimal score following high resolution, local optimization: 3.533
Processing set: G 100 ASN [2]: G 98 THR OG1 [2]
permutations: 4
Computing dot scores
Num optimizations problems to be solved for this clique: 3
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following low resolution optimization: -0.054
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
> : -0.048
Optimal score following high resolution, local optimization: -0.048
Processing set: B 80 GLN [2]: F 79 LYS NZ [4]
permutations: 8
Computing dot scores
Num optimizations problems to be solved for this clique: 3
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following low resolution optimization: -0.076
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
> : -0.076
Optimal score following high resolution, local optimization: -0.076
Processing set: F 54 ASN [2]: F 52 ASN [2]
permutations: 4
Computing dot scores
Num optimizations problems to be solved for this clique: 4
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following low resolution optimization: -32.786
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following high resolution, local optimization: -32.786
Processing set: F 42 SER OG [2]: F 41 THR OG1 [2]
permutations: 4
Computing dot scores
Num optimizations problems to be solved for this clique: 1
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following low resolution optimization: 0.000
> : 0.000
Optimal score following high resolution, local optimization: 0.000
Processing set: F 48 THR OG1 [6]: F 32 SER OG [8]
permutations: 48
Computing dot scores
Num optimizations problems to be solved for this clique: 1
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following low resolution optimization: 3.438
> : 3.626
Optimal score following high resolution, local optimization: 3.626
Processing set: E 100 ASN [2]: E 98 THR OG1 [2]
permutations: 4
Computing dot scores
Num optimizations problems to be solved for this clique: 3
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following low resolution optimization: -0.197
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
> : -0.194
Optimal score following high resolution, local optimization: -0.194
Processing set: E 26 SER OG [2]: B 82 TYR OH [11]
permutations: 22
Computing dot scores
Num optimizations problems to be solved for this clique: 1
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following low resolution optimization: 0.000
> : 0.000
Optimal score following high resolution, local optimization: 0.000
Processing set: D 100 ASN [2]: D 98 THR OG1 [2]
permutations: 4
Computing dot scores
Num optimizations problems to be solved for this clique: 3
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following low resolution optimization: 0.036
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
> : 0.037
Optimal score following high resolution, local optimization: 0.037
Processing set: C 100 ASN [2]: C 98 THR OG1 [2]
permutations: 4
Computing dot scores
Num optimizations problems to be solved for this clique: 3
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following low resolution optimization: -0.051
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
> : -0.031
Optimal score following high resolution, local optimization: -0.031
Processing set: B 87 ASN [2]: F 103 ASN [2]
permutations: 4
Computing dot scores
Num optimizations problems to be solved for this clique: 4
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following low resolution optimization: -32.852
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following high resolution, local optimization: -32.852
Processing set: B 54 ASN [2]: B 52 ASN [2]
permutations: 4
Computing dot scores
Num optimizations problems to be solved for this clique: 4
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following low resolution optimization: -32.885
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following high resolution, local optimization: -32.885
Processing set: B 48 THR OG1 [5]: B 32 SER OG [8]
permutations: 40
Computing dot scores
Num optimizations problems to be solved for this clique: 1
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following low resolution optimization: 3.303
> : 3.304
Optimal score following high resolution, local optimization: 3.304
Processing set: B 41 THR OG1 [2]: B 42 SER OG [2]
permutations: 4
Computing dot scores
Num optimizations problems to be solved for this clique: 1
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following low resolution optimization: 0.610
> : 0.610
Optimal score following high resolution, local optimization: 0.610
Processing set: A 82 TYR OH [11]: C 26 SER OG [3]
permutations: 33
Computing dot scores
Num optimizations problems to be solved for this clique: 1
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following low resolution optimization: 0.001
> : 0.001
Optimal score following high resolution, local optimization: 0.001
Processing set: A 54 ASN [2]: A 52 ASN [2]
permutations: 4
Computing dot scores
Num optimizations problems to be solved for this clique: 4
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following low resolution optimization: -32.501
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following high resolution, local optimization: -32.501
Processing set: A 48 THR OG1 [6]: A 32 SER OG [8]
permutations: 48
Computing dot scores
Num optimizations problems to be solved for this clique: 1
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following low resolution optimization: 3.420
> : 3.666
Optimal score following high resolution, local optimization: 3.666
Processing set: A 41 THR OG1 [2]: A 42 SER OG [2]
permutations: 4
Computing dot scores
Num optimizations problems to be solved for this clique: 1
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following low resolution optimization: 0.420
> : 0.541
Optimal score following high resolution, local optimization: 0.541
Found 0 hydrogens (0 hets)
Standardized 0 hydrogens (0 hets)
Added 6124 hydrogens (0 hets)
Removed 0 hydrogens (0 hets)
Adjusted 222 group(s)
If you publish work which uses reduce, please cite:
Word, et. al. (1999) J. Mol. Biol. 285, 1735-1747.
For more information see http://kinemage.biochem.duke.edu
BL WARNING:: reduce didnt run ok, so stop here!
run_generic_script (probe, 0)
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