$ reduce -METALBump0.865 -BUILD docking.pdb > docking_reduce.pdb reduce: version 3.24 07/24/2013, Copyright 1997-2013, J. Michael Word Processing file: "docking.pdb" Database of HETATM connections: "/usr/local/reduce_wwPDB_het_dict.txt" 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. SKIPPED H( A 46 HIS HD1 ): A 46 HIS ND1 bonds- A 154 CUCU+2 (H bumps) SKIPPED H( A 48 HIS HE2 ): A 48 HIS NE2 bonds- A 154 CUCU+2 (H bumps) SKIPPED H( A 63 HIS HD1 ): A 63 HIS ND1 bonds- A 155 ZN2ZN+2 (H bumps) SKIPPED H( A 71 HIS HD1 ): A 71 HIS ND1 bonds- A 155 ZN2ZN+2 (H bumps) SKIPPED H( A 80 HIS HD1 ): A 80 HIS ND1 bonds- A 155 ZN2ZN+2 (H bumps) SKIPPED H( A 120 HIS HE2 ): A 120 HIS NE2 bonds- A 154 CUCU+2 (H bumps) SKIPPED H( A 201 HIS HD1 ): A 201 HIS ND1 bonds- A 309 CUCU+2 (H bumps) SKIPPED H( A 203 HIS HE2 ): A 203 HIS NE2 bonds- A 309 CUCU+2 (H bumps) SKIPPED H( A 218 HIS HD1 ): A 218 HIS ND1 bonds- B 310 ZN2ZN+2 (H bumps) SKIPPED H( A 218 HIS HE2 ): A 218 HIS NE2 bonds- A 309 CUCU+2 (H bumps) SKIPPED H( A 226 HIS HD1 ): A 226 HIS ND1 bonds- B 310 ZN2ZN+2 (H bumps) SKIPPED H( A 235 HIS HD1 ): A 235 HIS ND1 bonds- B 310 ZN2ZN+2 (H bumps) SKIPPED H( A 275 HIS HE2 ): A 275 HIS NE2 bonds- A 309 CUCU+2 (H bumps) Singles(size 70): A 1 ALA N : A 2 THR OG1 : A 3 LYS NZ : A 6 CYS SG : A 15 GLN : A 19 ASN : A 23 LYS NZ : A 30 LYS NZ : A 34 SER OG : A 36 LYS NZ : A 53 ASN : A 54 THR OG1 : A 58 THR OG1 : A 59 SER OG : A 65 ASN : A 68 SER OG : A 70 LYS NZ : A 75 LYS NZ : A 86 ASN : A 88 THR OG1 : A 91 LYS NZ : A 98 SER OG : A 102 SER OG : A 107 SER OG : A 110 HIS : A 111 CYS SG : A 116 THR OG1 : A 122 LYS NZ : A 128 LYS NZ : A 134 SER OG : A 135 THR OG1 : A 136 LYS NZ : A 137 THR OG1 : A 142 SER OG : A 153 GLN : A 157 THR OG1 : A 158 LYS NZ : A 161 CYS SG : A 164 LYS NZ : A 170 GLN : A 174 ASN : A 178 LYS NZ : A 180 SER OG : A 181 ASN : A 185 LYS NZ : A 189 SER OG : A 191 LYS NZ : A 209 THR OG1 : A 213 THR OG1 : A 214 SER OG : A 220 ASN : A 223 SER OG : A 225 LYS NZ : A 230 LYS NZ : A 241 ASN : A 243 THR OG1 : A 246 LYS NZ : A 253 SER OG : A 257 SER OG : A 265 HIS : A 266 CYS SG : A 271 THR OG1 : A 277 LYS NZ : A 283 LYS NZ : A 289 SER OG : A 290 THR OG1 : A 291 LYS NZ : A 292 THR OG1 : A 297 SER OG : A 308 GLN Set 1 (size 2): A 294 ASN : A 286 ASN Set 2 (size 2): A 198 HIS : A 194 THR OG1 Set 3 (size 3): A 260 SER OG : A 262 SER OG : A 177 GLN Set 4 (size 2): A 139 ASN : A 131 ASN Set 5 (size 2): A 43 HIS : A 39 THR OG1 Set 6 (size 2): A 25 SER OG : A 26 ASN Set 7 (size 2): A 22 GLN : A 105 SER OG Set 8 (size 2): A 9 LYS NZ : A 208 ASN orientation 1: A 1 ALA N :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 2 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 3 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 6 CYS SG : rot 130: bump=-0.954, HB=0.000, total=-0.954 orientation 1: A 15 GLN : amide: bump=-0.038, HB=0.000, total=-0.038 orientation 1: A 19 ASN : amide: bump=0.000, HB=0.000, total=0.000 orientation 1: A 23 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 30 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 2: A 34 SER OG : rot -68: bump=0.000, HB=0.012, total=0.012 orientation 1: A 36 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 53 ASN : amide: bump=-0.784, HB=0.000, total=-0.784 orientation 2: A 54 THR OG1 : rot -65: bump=-0.006, HB=1.279, total=1.274 orientation 1: A 58 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 4: A 59 SER OG : rot 75: bump=-0.100, HB=1.798, total=1.698 orientation 1: A 65 ASN : amide: bump=-0.667, HB=0.703, total=0.037 orientation 1: A 68 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 2: A 70 LYS NZ :NH3+ -161: bump=-0.348, HB=0.000, total=-0.348 orientation 1: A 75 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 86 ASN : amide: bump=-0.008, HB=1.458, total=1.450 orientation 1: A 88 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 91 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 98 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 102 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 107 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 2: A 110 HIS : no HE2: bump=0.000, HB=0.157, total=0.157 orientation 1: A 111 CYS SG : rot 180: bump=-0.064, HB=0.176, total=0.112 orientation 2: A 116 THR OG1 : rot 127: bump=-0.749, HB=1.308, total=0.559 orientation 1: A 122 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 128 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 2: A 134 SER OG : rot 61: bump=-0.049, HB=1.313, total=1.265 orientation 3: A 135 THR OG1 : rot -38: bump=0.000, HB=0.578, total=0.578 orientation 1: A 136 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 7: A 137 THR OG1 : rot -144: bump=-0.028, HB=1.368, total=1.340 orientation 1: A 142 SER OG : rot 180: bump=-0.266, HB=0.000, total=-0.266 orientation 1: A 153 GLN : amide: bump=0.000, HB=0.000, total=0.000 orientation 1: A 157 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 2: A 158 LYS NZ :NH3+ -131: bump=0.000, HB=0.037, total=0.037 orientation 2: A 161 CYS SG : rot 105: bump=-0.477, HB=0.002, total=-0.475 orientation 1: A 164 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 170 GLN : amide: bump=-0.262, HB=0.000, total=-0.262 orientation 1: A 174 ASN : amide: bump=0.000, HB=0.000, total=0.000 orientation 3: A 178 LYS NZ :NH3+ 168: bump=0.000, HB=0.000, total=0.000 orientation 6: A 180 SER OG : rot -70: bump=-1.595, HB=1.096, total=-0.499, BADBUMP orientation 1: A 181 ASN : amide: bump=-6.130, HB=0.000, total=-6.130, BADBUMP orientation 1: A 185 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 189 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 191 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 3: A 209 THR OG1 : rot -75: bump=0.000, HB=1.295, total=1.295 orientation 1: A 213 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 2: A 214 SER OG : rot 83: bump=0.000, HB=1.474, total=1.474 orientation 1: A 220 ASN : amide: bump=-0.496, HB=0.388, total=-0.108 orientation 1: A 223 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 225 LYS NZ :NH3+ -164: bump=-8.411, HB=0.000, total=-8.411, BADBUMP orientation 1: A 230 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 241 ASN : amide: bump=-0.003, HB=1.442, total=1.438 orientation 1: A 243 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 246 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 253 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 257 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 2: A 265 HIS : no HE2: bump=-0.117, HB=0.301, total=0.184 orientation 1: A 266 CYS SG : rot 180: bump=0.000, HB=0.144, total=0.144 orientation 1: A 271 THR OG1 : rot 121: bump=-0.785, HB=1.168, total=0.383 orientation 1: A 277 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 283 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 3: A 289 SER OG : rot 62: bump=-0.183, HB=1.849, total=1.665 orientation 4: A 290 THR OG1 : rot -47: bump=0.000, HB=1.262, total=1.262 orientation 1: A 291 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 4: A 292 THR OG1 : rot -109: bump=-0.008, HB=1.293, total=1.285 orientation 1: A 297 SER OG : rot 180: bump=-0.496, HB=0.000, total=-0.496 orientation 1: A 308 GLN : amide: bump=0.000, HB=0.000, total=0.000 Processing set: A 294 ASN [2]: A 286 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: 0.739 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: 0.739 Processing set: A 198 HIS [6]: A 194 THR OG1 [4] permutations: 24 Computing dot scores Num optimizations problems to be solved for this clique: 5 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 1.828 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 1.828 Optimal score following high resolution, local optimization: 1.828 Processing set: A 260 SER OG [5]: A 262 SER OG [2]: A 177 GLN [2] permutations: 20 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: 2.083 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 2.257 Optimal score following high resolution, local optimization: 2.257 Processing set: A 139 ASN [2]: A 131 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: 0.975 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: 0.975 Processing set: A 43 HIS [6]: A 39 THR OG1 [4] permutations: 24 Computing dot scores Num optimizations problems to be solved for this clique: 5 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 1.691 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 1.691 Optimal score following high resolution, local optimization: 1.691 Processing set: A 25 SER OG [1]: A 26 ASN [2] permutations: 2 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: 0.189 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 0.189 Optimal score following high resolution, local optimization: 0.189 Processing set: A 22 GLN [2]: A 105 SER OG [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: 1.790 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 1.924 Optimal score following high resolution, local optimization: 1.924 Processing set: A 9 LYS NZ [4]: A 208 ASN [2] 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: -0.412 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : -0.375 Optimal score following high resolution, local optimization: -0.375 Found 0 hydrogens (0 hets) Standardized 0 hydrogens (0 hets) Added 2162 hydrogens (0 hets) Removed 0 hydrogens (0 hets) Adjusted 49 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