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 <bernh...@chem.gl.ac.uk> 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)
