Starting phenix.real_space_refine on Thu Feb 5 07:45:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s9h_54678/02_2026/9s9h_54678.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s9h_54678/02_2026/9s9h_54678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9s9h_54678/02_2026/9s9h_54678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s9h_54678/02_2026/9s9h_54678.map" model { file = "/net/cci-nas-00/data/ceres_data/9s9h_54678/02_2026/9s9h_54678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s9h_54678/02_2026/9s9h_54678.cif" } resolution = 4.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 9860 2.51 5 N 2670 2.21 5 O 3060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15650 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1565 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 1.74, per 1000 atoms: 0.11 Number of scatterers: 15650 At special positions: 0 Unit cell: (73.692, 82.236, 257.388, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 3060 8.00 N 2670 7.00 C 9860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " TYR C 5 " - " SER G 4 " " GLU C 6 " - " TYR G 5 " " VAL C 7 " - " GLU G 6 " " LEU C 8 " - " VAL G 7 " " THR C 9 " - " LEU G 8 " " LYS C 10 " - " THR G 9 " " PHE C 11 " - " LYS G 10 " " ILE C 12 " - " PHE G 11 " " GLY C 13 " - " ILE G 12 " " GLN C 14 " - " GLY G 13 " " LYS C 15 " - " GLN G 14 " " VAL C 16 " - " LYS G 15 " " LYS C 17 " - " VAL G 16 " " ASP C 18 " - " LYS G 17 " " ILE C 19 " - " ASP G 18 " " TYR C 20 " - " ILE G 19 " " GLY C 21 " - " TYR G 20 " " ARG C 22 " - " GLY G 21 " " GLU C 23 " - " ARG G 22 " " PHE C 24 " - " GLU G 23 " " GLY C 25 " - " PHE G 24 " " TYR C 26 " - " GLY G 25 " " LEU C 27 " - " TYR G 26 " " ILE C 28 " - " LEU G 27 " " HIS C 29 " - " ILE G 28 " " VAL C 30 " - " HIS G 29 " " TYR C 31 " - " VAL G 30 " " SER C 32 " - " TYR G 31 " " GLU C 33 " - " SER G 32 " " ILE C 34 " - " GLU G 33 " " ASP C 35 " - " ILE G 34 " " GLY C 36 " - " ASP G 35 " " SER C 37 " - " GLY G 36 " " ILE C 38 " - " SER G 37 " " THR C 39 " - " ILE G 38 " " GLY C 40 " - " THR G 39 " " ILE C 41 " - " GLY G 40 " " GLU C 42 " - " ILE G 41 " " VAL C 43 " - " GLU G 42 " " ALA C 44 " - " VAL G 43 " " GLN C 45 " - " ALA G 44 " " GLY C 46 " - " GLN G 45 " " SER C 47 " - " GLY G 46 " " SER C 48 " - " SER G 47 " " ILE C 49 " - " SER G 48 " " LEU C 50 " - " ILE G 49 " " THR C 51 " - " LEU G 50 " " MET C 52 " - " THR G 51 " " GLY C 53 " - " MET G 52 " " PRO C 54 " - " GLY G 53 " " GLU C 55 " - " PRO G 54 " " ARG C 56 " - " GLU G 55 " " ILE C 57 " - " ARG G 56 " " LYS C 58 " - " ILE G 57 " " LEU C 59 " - " LYS G 58 " " ASP C 60 " - " LEU G 59 " " GLY C 61 " - " ASP G 60 " " ASP C 62 " - " GLY G 61 " " SER C 63 " - " ASP G 62 " " ILE C 64 " - " SER G 63 " " LEU C 65 " - " ILE G 64 " " ILE C 66 " - " LEU G 65 " " LEU C 67 " - " ILE G 66 " " PRO C 68 " - " LEU G 67 " " ASP C 69 " - " PRO G 68 " " TRP C 70 " - " ASP G 69 " " LYS C 71 " - " TRP G 70 " " ALA C 72 " - " LYS G 71 " " GLU C 73 " - " ALA G 72 " " ALA C 74 " - " GLU G 73 " " ILE C 75 " - " ALA G 74 " " ARG C 76 " - " ILE G 75 " " ILE C 77 " - " ARG G 76 " " LEU C 78 " - " ILE G 77 " " SER C 79 " - " LEU G 78 " " LEU C 80 " - " SER G 79 " " MET C 81 " - " LEU G 80 " " GLU C 82 " - " MET G 81 " " LYS C 83 " - " GLU G 82 " " ILE C 84 " - " LYS G 83 " " ARG C 85 " - " ILE G 84 " " LYS C 86 " - " ARG G 85 " " ARG C 87 " - " LYS G 86 " " GLN C 88 " - " ARG G 87 " " ARG C 89 " - " GLN G 88 " " ALA C 90 " - " ARG G 89 " " LEU C 91 " - " ALA G 90 " " GLU C 92 " - " LEU G 91 " " GLU C 93 " - " GLU G 92 " " LEU C 94 " - " GLU G 93 " " TYR C 95 " - " LEU G 94 " " ASN C 96 " - " TYR G 95 " " LYS C 97 " - " ASN G 96 " " GLN C 98 " - " LYS G 97 " " GLU C 99 " - " GLN G 98 " " ILE C 100 " - " GLU G 99 " " PRO C 101 " - " ILE G 100 " " LYS C 102 " - " PRO G 101 " " SER C 103 " - " LYS G 102 " " ASP C 104 " - " SER G 103 " " TYR C 105 " - " ASP G 104 " " ASP C 106 " - " TYR G 105 " " ASP C 107 " - " ASP G 106 " " MET C 108 " - " ASP G 107 " " LYS C 109 " - " MET G 108 " " ARG C 110 " - " LYS G 109 " " LYS C 111 " - " ARG G 110 " " LEU C 112 " - " LYS G 111 " " ASP C 113 " - " LEU G 112 " " THR C 114 " - " ASP G 113 " " GLU C 115 " - " THR G 114 " " MET C 116 " - " GLU G 115 " " LEU C 117 " - " MET G 116 " " LYS C 118 " - " LEU G 117 " " VAL C 119 " - " LYS G 118 " " LYS C 120 " - " VAL G 119 " " ASP C 121 " - " LYS G 120 " " ASP C 122 " - " ASP G 121 " " GLN C 123 " - " ASP G 122 " " ASN C 124 " - " GLN G 123 " " LYS C 125 " - " ASN G 124 " " LEU C 126 " - " LYS G 125 " " LYS C 127 " - " LEU G 126 " " GLY C 128 " - " LYS G 127 " " LYS C 129 " - " GLY G 128 " " LEU C 130 " - " LYS G 129 " " LYS C 131 " - " LEU G 130 " " SER C 132 " - " LYS G 131 " " ARG C 133 " - " SER G 132 " " LEU C 134 " - " ARG G 133 " " ASN C 135 " - " LEU G 134 " " ASP C 136 " - " ASN G 135 " " ILE C 137 " - " ASP G 136 " " GLU C 138 " - " ILE G 137 " " ASP C 139 " - " GLU G 138 " " GLN C 140 " - " ASP G 139 " " LEU C 141 " - " GLN G 140 " " ALA C 142 " - " LEU G 141 " " HIS C 143 " - " ALA G 142 " " ILE C 144 " - " HIS G 143 " " ASP C 145 " - " ILE G 144 " " LYS C 146 " - " ASP G 145 " " ALA C 147 " - " LYS G 146 " " VAL C 148 " - " ALA G 147 " " ILE C 149 " - " VAL G 148 " " SER C 150 " - " ILE G 149 " " LEU C 151 " - " SER G 150 " " LYS C 152 " - " LEU G 151 " " MET C 153 " - " LYS G 152 " " SER C 154 " - " MET G 153 " " TYR C 155 " - " SER G 154 " " ILE C 156 " - " TYR G 155 " " SER C 157 " - " ILE G 156 " " SER C 158 " - " SER G 157 " " GLU C 159 " - " SER G 158 " " ILE C 160 " - " GLU G 159 " " PRO C 161 " - " ILE G 160 " " GLU C 162 " - " PRO G 161 " " ASN C 163 " - " GLU G 162 " " ALA C 164 " - " ASN G 163 " " TYR C 165 " - " ALA G 164 " " LYS C 166 " - " TYR G 165 " " GLY C 167 " - " LYS G 166 " " SER C 168 " - " GLY G 167 " " MET C 169 " - " SER G 168 " " GLU C 170 " - " MET G 169 " " VAL C 171 " - " GLU G 170 " " LEU C 172 " - " VAL G 171 " " ARG C 173 " - " LEU G 172 " " GLN C 174 " - " ARG G 173 " " SER C 175 " - " GLN G 174 " " LYS C 176 " - " SER G 175 " " ASP C 177 " - " LYS G 176 " " SER C 178 " - " ASP G 177 " " TYR C 179 " - " SER G 178 " " THR C 180 " - " TYR G 179 " " LEU C 181 " - " THR G 180 " " GLU C 182 " - " LEU G 181 " " ARG C 183 " - " GLU G 182 " " ASP C 184 " - " ARG G 183 " " ASP C 185 " - " ASP G 184 " " ILE C 186 " - " ASP G 185 " " ARG C 187 " - " ILE G 186 " " LYS C 188 " - " ARG G 187 " " THR C 189 " - " LYS G 188 " " LEU C 190 " - " THR G 189 " " ASP C 191 " - " LEU G 190 " " ARG C 192 " - " ASP G 191 " " LEU C 193 " - " ARG G 192 " " ASP C 194 " - " LEU G 193 " " SER C 195 " - " ASP G 194 " " LEU C 196 " - " SER G 195 " " TYR D 5 " - " SER H 4 " " GLU D 6 " - " TYR H 5 " " VAL D 7 " - " GLU H 6 " " LEU D 8 " - " VAL H 7 " " THR D 9 " - " LEU H 8 " " LYS D 10 " - " THR H 9 " " PHE D 11 " - " LYS H 10 " " ILE D 12 " - " PHE H 11 " " GLY D 13 " - " ILE H 12 " " GLN D 14 " - " GLY H 13 " " LYS D 15 " - " GLN H 14 " " VAL D 16 " - " LYS H 15 " " LYS D 17 " - " VAL H 16 " " ASP D 18 " - " LYS H 17 " " ILE D 19 " - " ASP H 18 " " TYR D 20 " - " ILE H 19 " " GLY D 21 " - " TYR H 20 " " ARG D 22 " - " GLY H 21 " " GLU D 23 " - " ARG H 22 " " PHE D 24 " - " GLU H 23 " " GLY D 25 " - " PHE H 24 " " TYR D 26 " - " GLY H 25 " " LEU D 27 " - " TYR H 26 " " ILE D 28 " - " LEU H 27 " " HIS D 29 " - " ILE H 28 " " VAL D 30 " - " HIS H 29 " " TYR D 31 " - " VAL H 30 " " SER D 32 " - " TYR H 31 " " GLU D 33 " - " SER H 32 " " ILE D 34 " - " GLU H 33 " " ASP D 35 " - " ILE H 34 " " GLY D 36 " - " ASP H 35 " " SER D 37 " - " GLY H 36 " " ILE D 38 " - " SER H 37 " " THR D 39 " - " ILE H 38 " " GLY D 40 " - " THR H 39 " " ILE D 41 " - " GLY H 40 " " GLU D 42 " - " ILE H 41 " " VAL D 43 " - " GLU H 42 " " ALA D 44 " - " VAL H 43 " " GLN D 45 " - " ALA H 44 " " GLY D 46 " - " GLN H 45 " " SER D 47 " - " GLY H 46 " " SER D 48 " - " SER H 47 " " ILE D 49 " - " SER H 48 " " LEU D 50 " - " ILE H 49 " " THR D 51 " - " LEU H 50 " " MET D 52 " - " THR H 51 " " GLY D 53 " - " MET H 52 " " PRO D 54 " - " GLY H 53 " " GLU D 55 " - " PRO H 54 " " ARG D 56 " - " GLU H 55 " " ILE D 57 " - " ARG H 56 " " LYS D 58 " - " ILE H 57 " " LEU D 59 " - " LYS H 58 " " ASP D 60 " - " LEU H 59 " " GLY D 61 " - " ASP H 60 " " ASP D 62 " - " GLY H 61 " " SER D 63 " - " ASP H 62 " " ILE D 64 " - " SER H 63 " " LEU D 65 " - " ILE H 64 " " ILE D 66 " - " LEU H 65 " " LEU D 67 " - " ILE H 66 " " PRO D 68 " - " LEU H 67 " " ASP D 69 " - " PRO H 68 " " TRP D 70 " - " ASP H 69 " " LYS D 71 " - " TRP H 70 " " ALA D 72 " - " LYS H 71 " " GLU D 73 " - " ALA H 72 " " ALA D 74 " - " GLU H 73 " " ILE D 75 " - " ALA H 74 " " ARG D 76 " - " ILE H 75 " " ILE D 77 " - " ARG H 76 " " LEU D 78 " - " ILE H 77 " " SER D 79 " - " LEU H 78 " " LEU D 80 " - " SER H 79 " " MET D 81 " - " LEU H 80 " " GLU D 82 " - " MET H 81 " " LYS D 83 " - " GLU H 82 " " ILE D 84 " - " LYS H 83 " " ARG D 85 " - " ILE H 84 " " LYS D 86 " - " ARG H 85 " " ARG D 87 " - " LYS H 86 " " GLN D 88 " - " ARG H 87 " " ARG D 89 " - " GLN H 88 " " ALA D 90 " - " ARG H 89 " " LEU D 91 " - " ALA H 90 " " GLU D 92 " - " LEU H 91 " " GLU D 93 " - " GLU H 92 " " LEU D 94 " - " GLU H 93 " " TYR D 95 " - " LEU H 94 " " ASN D 96 " - " TYR H 95 " " LYS D 97 " - " ASN H 96 " " GLN D 98 " - " LYS H 97 " " GLU D 99 " - " GLN H 98 " " ILE D 100 " - " GLU H 99 " " PRO D 101 " - " ILE H 100 " " LYS D 102 " - " PRO H 101 " " SER D 103 " - " LYS H 102 " " ASP D 104 " - " SER H 103 " " TYR D 105 " - " ASP H 104 " " ASP D 106 " - " TYR H 105 " " ASP D 107 " - " ASP H 106 " " MET D 108 " - " ASP H 107 " " LYS D 109 " - " MET H 108 " " ARG D 110 " - " LYS H 109 " " LYS D 111 " - " ARG H 110 " " LEU D 112 " - " LYS H 111 " " ASP D 113 " - " LEU H 112 " " THR D 114 " - " ASP H 113 " " GLU D 115 " - " THR H 114 " " MET D 116 " - " GLU H 115 " " LEU D 117 " - " MET H 116 " " LYS D 118 " - " LEU H 117 " " VAL D 119 " - " LYS H 118 " " LYS D 120 " - " VAL H 119 " " ASP D 121 " - " LYS H 120 " " ASP D 122 " - " ASP H 121 " " GLN D 123 " - " ASP H 122 " " ASN D 124 " - " GLN H 123 " " LYS D 125 " - " ASN H 124 " " LEU D 126 " - " LYS H 125 " " LYS D 127 " - " LEU H 126 " " GLY D 128 " - " LYS H 127 " " LYS D 129 " - " GLY H 128 " " LEU D 130 " - " LYS H 129 " " LYS D 131 " - " LEU H 130 " " SER D 132 " - " LYS H 131 " " ARG D 133 " - " SER H 132 " " LEU D 134 " - " ARG H 133 " " ASN D 135 " - " LEU H 134 " " ASP D 136 " - " ASN H 135 " " ILE D 137 " - " ASP H 136 " " GLU D 138 " - " ILE H 137 " " ASP D 139 " - " GLU H 138 " " GLN D 140 " - " ASP H 139 " " LEU D 141 " - " GLN H 140 " " ALA D 142 " - " LEU H 141 " " HIS D 143 " - " ALA H 142 " " ILE D 144 " - " HIS H 143 " " ASP D 145 " - " ILE H 144 " " LYS D 146 " - " ASP H 145 " " ALA D 147 " - " LYS H 146 " " VAL D 148 " - " ALA H 147 " " ILE D 149 " - " VAL H 148 " " SER D 150 " - " ILE H 149 " " LEU D 151 " - " SER H 150 " " LYS D 152 " - " LEU H 151 " " MET D 153 " - " LYS H 152 " " SER D 154 " - " MET H 153 " " TYR D 155 " - " SER H 154 " " ILE D 156 " - " TYR H 155 " " SER D 157 " - " ILE H 156 " " SER D 158 " - " SER H 157 " " GLU D 159 " - " SER H 158 " " ILE D 160 " - " GLU H 159 " " PRO D 161 " - " ILE H 160 " " GLU D 162 " - " PRO H 161 " " ASN D 163 " - " GLU H 162 " " ALA D 164 " - " ASN H 163 " " TYR D 165 " - " ALA H 164 " " LYS D 166 " - " TYR H 165 " " GLY D 167 " - " LYS H 166 " " SER D 168 " - " GLY H 167 " " MET D 169 " - " SER H 168 " " GLU D 170 " - " MET H 169 " " VAL D 171 " - " GLU H 170 " " LEU D 172 " - " VAL H 171 " " ARG D 173 " - " LEU H 172 " " GLN D 174 " - " ARG H 173 " " SER D 175 " - " GLN H 174 " " LYS D 176 " - " SER H 175 " " ASP D 177 " - " LYS H 176 " " SER D 178 " - " ASP H 177 " " TYR D 179 " - " SER H 178 " " THR D 180 " - " TYR H 179 " " LEU D 181 " - " THR H 180 " " GLU D 182 " - " LEU H 181 " " ARG D 183 " - " GLU H 182 " " ASP D 184 " - " ARG H 183 " " ASP D 185 " - " ASP H 184 " " ILE D 186 " - " ASP H 185 " " ARG D 187 " - " ILE H 186 " " LYS D 188 " - " ARG H 187 " " THR D 189 " - " LYS H 188 " " LEU D 190 " - " THR H 189 " " ASP D 191 " - " LEU H 190 " " ARG D 192 " - " ASP H 191 " " LEU D 193 " - " ARG H 192 " " ASP D 194 " - " LEU H 193 " " SER D 195 " - " ASP H 194 " " LEU D 196 " - " SER H 195 " " TYR E 5 " - " SER I 4 " " GLU E 6 " - " TYR I 5 " " VAL E 7 " - " GLU I 6 " " LEU E 8 " - " VAL I 7 " " THR E 9 " - " LEU I 8 " " LYS E 10 " - " THR I 9 " " PHE E 11 " - " LYS I 10 " " ILE E 12 " - " PHE I 11 " " GLY E 13 " - " ILE I 12 " " GLN E 14 " - " GLY I 13 " " LYS E 15 " - " GLN I 14 " " VAL E 16 " - " LYS I 15 " " LYS E 17 " - " VAL I 16 " " ASP E 18 " - " LYS I 17 " " ILE E 19 " - " ASP I 18 " " TYR E 20 " - " ILE I 19 " " GLY E 21 " - " TYR I 20 " " ARG E 22 " - " GLY I 21 " " GLU E 23 " - " ARG I 22 " " PHE E 24 " - " GLU I 23 " " GLY E 25 " - " PHE I 24 " " TYR E 26 " - " GLY I 25 " " LEU E 27 " - " TYR I 26 " " ILE E 28 " - " LEU I 27 " " HIS E 29 " - " ILE I 28 " " VAL E 30 " - " HIS I 29 " " TYR E 31 " - " VAL I 30 " " SER E 32 " - " TYR I 31 " " GLU E 33 " - " SER I 32 " " ILE E 34 " - " GLU I 33 " " ASP E 35 " - " ILE I 34 " " GLY E 36 " - " ASP I 35 " " SER E 37 " - " GLY I 36 " " ILE E 38 " - " SER I 37 " " THR E 39 " - " ILE I 38 " " GLY E 40 " - " THR I 39 " " ILE E 41 " - " GLY I 40 " " GLU E 42 " - " ILE I 41 " " VAL E 43 " - " GLU I 42 " " ALA E 44 " - " VAL I 43 " " GLN E 45 " - " ALA I 44 " " GLY E 46 " - " GLN I 45 " " SER E 47 " - " GLY I 46 " " SER E 48 " - " SER I 47 " " ILE E 49 " - " SER I 48 " " LEU E 50 " - " ILE I 49 " " THR E 51 " - " LEU I 50 " " MET E 52 " - " THR I 51 " " GLY E 53 " - " MET I 52 " " PRO E 54 " - " GLY I 53 " " GLU E 55 " - " PRO I 54 " " ARG E 56 " - " GLU I 55 " " ILE E 57 " - " ARG I 56 " " LYS E 58 " - " ILE I 57 " " LEU E 59 " - " LYS I 58 " " ASP E 60 " - " LEU I 59 " " GLY E 61 " - " ASP I 60 " " ASP E 62 " - " GLY I 61 " " SER E 63 " - " ASP I 62 " " ILE E 64 " - " SER I 63 " " LEU E 65 " - " ILE I 64 " " ILE E 66 " - " LEU I 65 " " LEU E 67 " - " ILE I 66 " " PRO E 68 " - " LEU I 67 " " ASP E 69 " - " PRO I 68 " " TRP E 70 " - " ASP I 69 " " LYS E 71 " - " TRP I 70 " " ALA E 72 " - " LYS I 71 " " GLU E 73 " - " ALA I 72 " " ALA E 74 " - " GLU I 73 " " ILE E 75 " - " ALA I 74 " " ARG E 76 " - " ILE I 75 " " ILE E 77 " - " ARG I 76 " " LEU E 78 " - " ILE I 77 " " SER E 79 " - " LEU I 78 " " LEU E 80 " - " SER I 79 " " MET E 81 " - " LEU I 80 " " GLU E 82 " - " MET I 81 " " LYS E 83 " - " GLU I 82 " " ILE E 84 " - " LYS I 83 " " ARG E 85 " - " ILE I 84 " " LYS E 86 " - " ARG I 85 " " ARG E 87 " - " LYS I 86 " " GLN E 88 " - " ARG I 87 " " ARG E 89 " - " GLN I 88 " " ALA E 90 " - " ARG I 89 " " LEU E 91 " - " ALA I 90 " " GLU E 92 " - " LEU I 91 " " GLU E 93 " - " GLU I 92 " " LEU E 94 " - " GLU I 93 " " TYR E 95 " - " LEU I 94 " " ASN E 96 " - " TYR I 95 " " LYS E 97 " - " ASN I 96 " " GLN E 98 " - " LYS I 97 " " GLU E 99 " - " GLN I 98 " " ILE E 100 " - " GLU I 99 " " PRO E 101 " - " ILE I 100 " " LYS E 102 " - " PRO I 101 " " SER E 103 " - " LYS I 102 " " ASP E 104 " - " SER I 103 " " TYR E 105 " - " ASP I 104 " " ASP E 106 " - " TYR I 105 " " ASP E 107 " - " ASP I 106 " " MET E 108 " - " ASP I 107 " " LYS E 109 " - " MET I 108 " " ARG E 110 " - " LYS I 109 " " LYS E 111 " - " ARG I 110 " " LEU E 112 " - " LYS I 111 " " ASP E 113 " - " LEU I 112 " " THR E 114 " - " ASP I 113 " " GLU E 115 " - " THR I 114 " " MET E 116 " - " GLU I 115 " " LEU E 117 " - " MET I 116 " " LYS E 118 " - " LEU I 117 " " VAL E 119 " - " LYS I 118 " " LYS E 120 " - " VAL I 119 " " ASP E 121 " - " LYS I 120 " " ASP E 122 " - " ASP I 121 " " GLN E 123 " - " ASP I 122 " " ASN E 124 " - " GLN I 123 " " LYS E 125 " - " ASN I 124 " " LEU E 126 " - " LYS I 125 " " LYS E 127 " - " LEU I 126 " " GLY E 128 " - " LYS I 127 " " LYS E 129 " - " GLY I 128 " " LEU E 130 " - " LYS I 129 " " LYS E 131 " - " LEU I 130 " " SER E 132 " - " LYS I 131 " " ARG E 133 " - " SER I 132 " " LEU E 134 " - " ARG I 133 " " ASN E 135 " - " LEU I 134 " " ASP E 136 " - " ASN I 135 " " ILE E 137 " - " ASP I 136 " " GLU E 138 " - " ILE I 137 " " ASP E 139 " - " GLU I 138 " " GLN E 140 " - " ASP I 139 " " LEU E 141 " - " GLN I 140 " " ALA E 142 " - " LEU I 141 " " HIS E 143 " - " ALA I 142 " " ILE E 144 " - " HIS I 143 " " ASP E 145 " - " ILE I 144 " " LYS E 146 " - " ASP I 145 " " ALA E 147 " - " LYS I 146 " " VAL E 148 " - " ALA I 147 " " ILE E 149 " - " VAL I 148 " " SER E 150 " - " ILE I 149 " " LEU E 151 " - " SER I 150 " " LYS E 152 " - " LEU I 151 " " MET E 153 " - " LYS I 152 " " SER E 154 " - " MET I 153 " " TYR E 155 " - " SER I 154 " " ILE E 156 " - " TYR I 155 " " SER E 157 " - " ILE I 156 " " SER E 158 " - " SER I 157 " " GLU E 159 " - " SER I 158 " " ILE E 160 " - " GLU I 159 " " PRO E 161 " - " ILE I 160 " " GLU E 162 " - " PRO I 161 " " ASN E 163 " - " GLU I 162 " " ALA E 164 " - " ASN I 163 " " TYR E 165 " - " ALA I 164 " " LYS E 166 " - " TYR I 165 " " GLY E 167 " - " LYS I 166 " " SER E 168 " - " GLY I 167 " " MET E 169 " - " SER I 168 " " GLU E 170 " - " MET I 169 " " VAL E 171 " - " GLU I 170 " " LEU E 172 " - " VAL I 171 " " ARG E 173 " - " LEU I 172 " " GLN E 174 " - " ARG I 173 " " SER E 175 " - " GLN I 174 " " LYS E 176 " - " SER I 175 " " ASP E 177 " - " LYS I 176 " " SER E 178 " - " ASP I 177 " " TYR E 179 " - " SER I 178 " " THR E 180 " - " TYR I 179 " " LEU E 181 " - " THR I 180 " " GLU E 182 " - " LEU I 181 " " ARG E 183 " - " GLU I 182 " " ASP E 184 " - " ARG I 183 " " ASP E 185 " - " ASP I 184 " " ILE E 186 " - " ASP I 185 " " ARG E 187 " - " ILE I 186 " " LYS E 188 " - " ARG I 187 " " THR E 189 " - " LYS I 188 " " LEU E 190 " - " THR I 189 " " ASP E 191 " - " LEU I 190 " " ARG E 192 " - " ASP I 191 " " LEU E 193 " - " ARG I 192 " " ASP E 194 " - " LEU I 193 " " SER E 195 " - " ASP I 194 " " LEU E 196 " - " SER I 195 " " TYR F 5 " - " SER J 4 " " GLU F 6 " - " TYR J 5 " " VAL F 7 " - " GLU J 6 " " LEU F 8 " - " VAL J 7 " " THR F 9 " - " LEU J 8 " " LYS F 10 " - " THR J 9 " " PHE F 11 " - " LYS J 10 " " ILE F 12 " - " PHE J 11 " " GLY F 13 " - " ILE J 12 " " GLN F 14 " - " GLY J 13 " " LYS F 15 " - " GLN J 14 " " VAL F 16 " - " LYS J 15 " " LYS F 17 " - " VAL J 16 " " ASP F 18 " - " LYS J 17 " " ILE F 19 " - " ASP J 18 " " TYR F 20 " - " ILE J 19 " " GLY F 21 " - " TYR J 20 " " ARG F 22 " - " GLY J 21 " " GLU F 23 " - " ARG J 22 " " PHE F 24 " - " GLU J 23 " " GLY F 25 " - " PHE J 24 " " TYR F 26 " - " GLY J 25 " " LEU F 27 " - " TYR J 26 " " ILE F 28 " - " LEU J 27 " " HIS F 29 " - " ILE J 28 " " VAL F 30 " - " HIS J 29 " " TYR F 31 " - " VAL J 30 " " SER F 32 " - " TYR J 31 " " GLU F 33 " - " SER J 32 " " ILE F 34 " - " GLU J 33 " " ASP F 35 " - " ILE J 34 " " GLY F 36 " - " ASP J 35 " " SER F 37 " - " GLY J 36 " " ILE F 38 " - " SER J 37 " " THR F 39 " - " ILE J 38 " " GLY F 40 " - " THR J 39 " " ILE F 41 " - " GLY J 40 " " GLU F 42 " - " ILE J 41 " " VAL F 43 " - " GLU J 42 " " ALA F 44 " - " VAL J 43 " " GLN F 45 " - " ALA J 44 " " GLY F 46 " - " GLN J 45 " " SER F 47 " - " GLY J 46 " " SER F 48 " - " SER J 47 " " ILE F 49 " - " SER J 48 " " LEU F 50 " - " ILE J 49 " " THR F 51 " - " LEU J 50 " " MET F 52 " - " THR J 51 " " GLY F 53 " - " MET J 52 " " PRO F 54 " - " GLY J 53 " " GLU F 55 " - " PRO J 54 " " ARG F 56 " - " GLU J 55 " " ILE F 57 " - " ARG J 56 " " LYS F 58 " - " ILE J 57 " " LEU F 59 " - " LYS J 58 " " ASP F 60 " - " LEU J 59 " " GLY F 61 " - " ASP J 60 " " ASP F 62 " - " GLY J 61 " " SER F 63 " - " ASP J 62 " " ILE F 64 " - " SER J 63 " " LEU F 65 " - " ILE J 64 " " ILE F 66 " - " LEU J 65 " " LEU F 67 " - " ILE J 66 " " PRO F 68 " - " LEU J 67 " " ASP F 69 " - " PRO J 68 " " TRP F 70 " - " ASP J 69 " " LYS F 71 " - " TRP J 70 " " ALA F 72 " - " LYS J 71 " " GLU F 73 " - " ALA J 72 " " ALA F 74 " - " GLU J 73 " " ILE F 75 " - " ALA J 74 " " ARG F 76 " - " ILE J 75 " " ILE F 77 " - " ARG J 76 " " LEU F 78 " - " ILE J 77 " " SER F 79 " - " LEU J 78 " " LEU F 80 " - " SER J 79 " " MET F 81 " - " LEU J 80 " " GLU F 82 " - " MET J 81 " " LYS F 83 " - " GLU J 82 " " ILE F 84 " - " LYS J 83 " " ARG F 85 " - " ILE J 84 " " LYS F 86 " - " ARG J 85 " " ARG F 87 " - " LYS J 86 " " GLN F 88 " - " ARG J 87 " " ARG F 89 " - " GLN J 88 " " ALA F 90 " - " ARG J 89 " " LEU F 91 " - " ALA J 90 " " GLU F 92 " - " LEU J 91 " " GLU F 93 " - " GLU J 92 " " LEU F 94 " - " GLU J 93 " " TYR F 95 " - " LEU J 94 " " ASN F 96 " - " TYR J 95 " " LYS F 97 " - " ASN J 96 " " GLN F 98 " - " LYS J 97 " " GLU F 99 " - " GLN J 98 " " ILE F 100 " - " GLU J 99 " " PRO F 101 " - " ILE J 100 " " LYS F 102 " - " PRO J 101 " " SER F 103 " - " LYS J 102 " " ASP F 104 " - " SER J 103 " " TYR F 105 " - " ASP J 104 " " ASP F 106 " - " TYR J 105 " " ASP F 107 " - " ASP J 106 " " MET F 108 " - " ASP J 107 " " LYS F 109 " - " MET J 108 " " ARG F 110 " - " LYS J 109 " " LYS F 111 " - " ARG J 110 " " LEU F 112 " - " LYS J 111 " " ASP F 113 " - " LEU J 112 " " THR F 114 " - " ASP J 113 " " GLU F 115 " - " THR J 114 " " MET F 116 " - " GLU J 115 " " LEU F 117 " - " MET J 116 " " LYS F 118 " - " LEU J 117 " " VAL F 119 " - " LYS J 118 " " LYS F 120 " - " VAL J 119 " " ASP F 121 " - " LYS J 120 " " ASP F 122 " - " ASP J 121 " " GLN F 123 " - " ASP J 122 " " ASN F 124 " - " GLN J 123 " " LYS F 125 " - " ASN J 124 " " LEU F 126 " - " LYS J 125 " " LYS F 127 " - " LEU J 126 " " GLY F 128 " - " LYS J 127 " " LYS F 129 " - " GLY J 128 " " LEU F 130 " - " LYS J 129 " " LYS F 131 " - " LEU J 130 " " SER F 132 " - " LYS J 131 " " ARG F 133 " - " SER J 132 " " LEU F 134 " - " ARG J 133 " " ASN F 135 " - " LEU J 134 " " ASP F 136 " - " ASN J 135 " " ILE F 137 " - " ASP J 136 " " GLU F 138 " - " ILE J 137 " " ASP F 139 " - " GLU J 138 " " GLN F 140 " - " ASP J 139 " " LEU F 141 " - " GLN J 140 " " ALA F 142 " - " LEU J 141 " " HIS F 143 " - " ALA J 142 " " ILE F 144 " - " HIS J 143 " " ASP F 145 " - " ILE J 144 " " LYS F 146 " - " ASP J 145 " " ALA F 147 " - " LYS J 146 " " VAL F 148 " - " ALA J 147 " " ILE F 149 " - " VAL J 148 " " SER F 150 " - " ILE J 149 " " LEU F 151 " - " SER J 150 " " LYS F 152 " - " LEU J 151 " " MET F 153 " - " LYS J 152 " " SER F 154 " - " MET J 153 " " TYR F 155 " - " SER J 154 " " ILE F 156 " - " TYR J 155 " " SER F 157 " - " ILE J 156 " " SER F 158 " - " SER J 157 " " GLU F 159 " - " SER J 158 " " ILE F 160 " - " GLU J 159 " " PRO F 161 " - " ILE J 160 " " GLU F 162 " - " PRO J 161 " " ASN F 163 " - " GLU J 162 " " ALA F 164 " - " ASN J 163 " " TYR F 165 " - " ALA J 164 " " LYS F 166 " - " TYR J 165 " " GLY F 167 " - " LYS J 166 " " SER F 168 " - " GLY J 167 " " MET F 169 " - " SER J 168 " " GLU F 170 " - " MET J 169 " " VAL F 171 " - " GLU J 170 " " LEU F 172 " - " VAL J 171 " " ARG F 173 " - " LEU J 172 " " GLN F 174 " - " ARG J 173 " " SER F 175 " - " GLN J 174 " " LYS F 176 " - " SER J 175 " " ASP F 177 " - " LYS J 176 " " SER F 178 " - " ASP J 177 " " TYR F 179 " - " SER J 178 " " THR F 180 " - " TYR J 179 " " LEU F 181 " - " THR J 180 " " GLU F 182 " - " LEU J 181 " " ARG F 183 " - " GLU J 182 " " ASP F 184 " - " ARG J 183 " " ASP F 185 " - " ASP J 184 " " ILE F 186 " - " ASP J 185 " " ARG F 187 " - " ILE J 186 " " LYS F 188 " - " ARG J 187 " " THR F 189 " - " LYS J 188 " " LEU F 190 " - " THR J 189 " " ASP F 191 " - " LEU J 190 " " ARG F 192 " - " ASP J 191 " " LEU F 193 " - " ARG J 192 " " ASP F 194 " - " LEU J 193 " " SER F 195 " - " ASP J 194 " " LEU F 196 " - " SER J 195 " " TYR G 5 " - " SER C 4 " " GLU G 6 " - " TYR C 5 " " VAL G 7 " - " GLU C 6 " " LEU G 8 " - " VAL C 7 " " THR G 9 " - " LEU C 8 " " LYS G 10 " - " THR C 9 " " PHE G 11 " - " LYS C 10 " " ILE G 12 " - " PHE C 11 " " GLY G 13 " - " ILE C 12 " " GLN G 14 " - " GLY C 13 " " LYS G 15 " - " GLN C 14 " " VAL G 16 " - " LYS C 15 " " LYS G 17 " - " VAL C 16 " " ASP G 18 " - " LYS C 17 " " ILE G 19 " - " ASP C 18 " " TYR G 20 " - " ILE C 19 " " GLY G 21 " - " TYR C 20 " " ARG G 22 " - " GLY C 21 " " GLU G 23 " - " ARG C 22 " " PHE G 24 " - " GLU C 23 " " GLY G 25 " - " PHE C 24 " " TYR G 26 " - " GLY C 25 " " LEU G 27 " - " TYR C 26 " " ILE G 28 " - " LEU C 27 " " HIS G 29 " - " ILE C 28 " " VAL G 30 " - " HIS C 29 " " TYR G 31 " - " VAL C 30 " " SER G 32 " - " TYR C 31 " " GLU G 33 " - " SER C 32 " " ILE G 34 " - " GLU C 33 " " ASP G 35 " - " ILE C 34 " " GLY G 36 " - " ASP C 35 " " SER G 37 " - " GLY C 36 " " ILE G 38 " - " SER C 37 " " THR G 39 " - " ILE C 38 " " GLY G 40 " - " THR C 39 " " ILE G 41 " - " GLY C 40 " " GLU G 42 " - " ILE C 41 " " VAL G 43 " - " GLU C 42 " " ALA G 44 " - " VAL C 43 " " GLN G 45 " - " ALA C 44 " " GLY G 46 " - " GLN C 45 " " SER G 47 " - " GLY C 46 " " SER G 48 " - " SER C 47 " " ILE G 49 " - " SER C 48 " " LEU G 50 " - " ILE C 49 " " THR G 51 " - " LEU C 50 " " MET G 52 " - " THR C 51 " " GLY G 53 " - " MET C 52 " " PRO G 54 " - " GLY C 53 " " GLU G 55 " - " PRO C 54 " " ARG G 56 " - " GLU C 55 " " ILE G 57 " - " ARG C 56 " " LYS G 58 " - " ILE C 57 " " LEU G 59 " - " LYS C 58 " " ASP G 60 " - " LEU C 59 " " GLY G 61 " - " ASP C 60 " " ASP G 62 " - " GLY C 61 " " SER G 63 " - " ASP C 62 " " ILE G 64 " - " SER C 63 " " LEU G 65 " - " ILE C 64 " " ILE G 66 " - " LEU C 65 " " LEU G 67 " - " ILE C 66 " " PRO G 68 " - " LEU C 67 " " ASP G 69 " - " PRO C 68 " " TRP G 70 " - " ASP C 69 " " LYS G 71 " - " TRP C 70 " " ALA G 72 " - " LYS C 71 " " GLU G 73 " - " ALA C 72 " " ALA G 74 " - " GLU C 73 " " ILE G 75 " - " ALA C 74 " " ARG G 76 " - " ILE C 75 " " ILE G 77 " - " ARG C 76 " " LEU G 78 " - " ILE C 77 " " SER G 79 " - " LEU C 78 " " LEU G 80 " - " SER C 79 " " MET G 81 " - " LEU C 80 " " GLU G 82 " - " MET C 81 " " LYS G 83 " - " GLU C 82 " " ILE G 84 " - " LYS C 83 " " ARG G 85 " - " ILE C 84 " " LYS G 86 " - " ARG C 85 " " ARG G 87 " - " LYS C 86 " " GLN G 88 " - " ARG C 87 " " ARG G 89 " - " GLN C 88 " " ALA G 90 " - " ARG C 89 " " LEU G 91 " - " ALA C 90 " " GLU G 92 " - " LEU C 91 " " GLU G 93 " - " GLU C 92 " " LEU G 94 " - " GLU C 93 " " TYR G 95 " - " LEU C 94 " " ASN G 96 " - " TYR C 95 " " LYS G 97 " - " ASN C 96 " " GLN G 98 " - " LYS C 97 " " GLU G 99 " - " GLN C 98 " " ILE G 100 " - " GLU C 99 " " PRO G 101 " - " ILE C 100 " " LYS G 102 " - " PRO C 101 " " SER G 103 " - " LYS C 102 " " ASP G 104 " - " SER C 103 " " TYR G 105 " - " ASP C 104 " " ASP G 106 " - " TYR C 105 " " ASP G 107 " - " ASP C 106 " " MET G 108 " - " ASP C 107 " " LYS G 109 " - " MET C 108 " " ARG G 110 " - " LYS C 109 " " LYS G 111 " - " ARG C 110 " " LEU G 112 " - " LYS C 111 " " ASP G 113 " - " LEU C 112 " " THR G 114 " - " ASP C 113 " " GLU G 115 " - " THR C 114 " " MET G 116 " - " GLU C 115 " " LEU G 117 " - " MET C 116 " " LYS G 118 " - " LEU C 117 " " VAL G 119 " - " LYS C 118 " " LYS G 120 " - " VAL C 119 " " ASP G 121 " - " LYS C 120 " " ASP G 122 " - " ASP C 121 " " GLN G 123 " - " ASP C 122 " " ASN G 124 " - " GLN C 123 " " LYS G 125 " - " ASN C 124 " " LEU G 126 " - " LYS C 125 " " LYS G 127 " - " LEU C 126 " " GLY G 128 " - " LYS C 127 " " LYS G 129 " - " GLY C 128 " " LEU G 130 " - " LYS C 129 " " LYS G 131 " - " LEU C 130 " " SER G 132 " - " LYS C 131 " " ARG G 133 " - " SER C 132 " " LEU G 134 " - " ARG C 133 " " ASN G 135 " - " LEU C 134 " " ASP G 136 " - " ASN C 135 " " ILE G 137 " - " ASP C 136 " " GLU G 138 " - " ILE C 137 " " ASP G 139 " - " GLU C 138 " " GLN G 140 " - " ASP C 139 " " LEU G 141 " - " GLN C 140 " " ALA G 142 " - " LEU C 141 " " HIS G 143 " - " ALA C 142 " " ILE G 144 " - " HIS C 143 " " ASP G 145 " - " ILE C 144 " " LYS G 146 " - " ASP C 145 " " ALA G 147 " - " LYS C 146 " " VAL G 148 " - " ALA C 147 " " ILE G 149 " - " VAL C 148 " " SER G 150 " - " ILE C 149 " " LEU G 151 " - " SER C 150 " " LYS G 152 " - " LEU C 151 " " MET G 153 " - " LYS C 152 " " SER G 154 " - " MET C 153 " " TYR G 155 " - " SER C 154 " " ILE G 156 " - " TYR C 155 " " SER G 157 " - " ILE C 156 " " SER G 158 " - " SER C 157 " " GLU G 159 " - " SER C 158 " " ILE G 160 " - " GLU C 159 " " PRO G 161 " - " ILE C 160 " " GLU G 162 " - " PRO C 161 " " ASN G 163 " - " GLU C 162 " " ALA G 164 " - " ASN C 163 " " TYR G 165 " - " ALA C 164 " " LYS G 166 " - " TYR C 165 " " GLY G 167 " - " LYS C 166 " " SER G 168 " - " GLY C 167 " " MET G 169 " - " SER C 168 " " GLU G 170 " - " MET C 169 " " VAL G 171 " - " GLU C 170 " " LEU G 172 " - " VAL C 171 " " ARG G 173 " - " LEU C 172 " " GLN G 174 " - " ARG C 173 " " SER G 175 " - " GLN C 174 " " LYS G 176 " - " SER C 175 " " ASP G 177 " - " LYS C 176 " " SER G 178 " - " ASP C 177 " " TYR G 179 " - " SER C 178 " " THR G 180 " - " TYR C 179 " " LEU G 181 " - " THR C 180 " " GLU G 182 " - " LEU C 181 " " ARG G 183 " - " GLU C 182 " " ASP G 184 " - " ARG C 183 " " ASP G 185 " - " ASP C 184 " " ILE G 186 " - " ASP C 185 " " ARG G 187 " - " ILE C 186 " " LYS G 188 " - " ARG C 187 " " THR G 189 " - " LYS C 188 " " LEU G 190 " - " THR C 189 " " ASP G 191 " - " LEU C 190 " " ARG G 192 " - " ASP C 191 " " LEU G 193 " - " ARG C 192 " " ASP G 194 " - " LEU C 193 " " SER G 195 " - " ASP C 194 " " LEU G 196 " - " SER C 195 " " TYR H 5 " - " SER D 4 " " GLU H 6 " - " TYR D 5 " " VAL H 7 " - " GLU D 6 " " LEU H 8 " - " VAL D 7 " " THR H 9 " - " LEU D 8 " " LYS H 10 " - " THR D 9 " " PHE H 11 " - " LYS D 10 " " ILE H 12 " - " PHE D 11 " " GLY H 13 " - " ILE D 12 " " GLN H 14 " - " GLY D 13 " " LYS H 15 " - " GLN D 14 " " VAL H 16 " - " LYS D 15 " " LYS H 17 " - " VAL D 16 " " ASP H 18 " - " LYS D 17 " " ILE H 19 " - " ASP D 18 " " TYR H 20 " - " ILE D 19 " " GLY H 21 " - " TYR D 20 " " ARG H 22 " - " GLY D 21 " " GLU H 23 " - " ARG D 22 " " PHE H 24 " - " GLU D 23 " " GLY H 25 " - " PHE D 24 " " TYR H 26 " - " GLY D 25 " " LEU H 27 " - " TYR D 26 " " ILE H 28 " - " LEU D 27 " " HIS H 29 " - " ILE D 28 " " VAL H 30 " - " HIS D 29 " " TYR H 31 " - " VAL D 30 " " SER H 32 " - " TYR D 31 " " GLU H 33 " - " SER D 32 " " ILE H 34 " - " GLU D 33 " " ASP H 35 " - " ILE D 34 " " GLY H 36 " - " ASP D 35 " " SER H 37 " - " GLY D 36 " " ILE H 38 " - " SER D 37 " " THR H 39 " - " ILE D 38 " " GLY H 40 " - " THR D 39 " " ILE H 41 " - " GLY D 40 " " GLU H 42 " - " ILE D 41 " " VAL H 43 " - " GLU D 42 " " ALA H 44 " - " VAL D 43 " " GLN H 45 " - " ALA D 44 " " GLY H 46 " - " GLN D 45 " " SER H 47 " - " GLY D 46 " " SER H 48 " - " SER D 47 " " ILE H 49 " - " SER D 48 " " LEU H 50 " - " ILE D 49 " " THR H 51 " - " LEU D 50 " " MET H 52 " - " THR D 51 " " GLY H 53 " - " MET D 52 " " PRO H 54 " - " GLY D 53 " " GLU H 55 " - " PRO D 54 " " ARG H 56 " - " GLU D 55 " " ILE H 57 " - " ARG D 56 " " LYS H 58 " - " ILE D 57 " " LEU H 59 " - " LYS D 58 " " ASP H 60 " - " LEU D 59 " " GLY H 61 " - " ASP D 60 " " ASP H 62 " - " GLY D 61 " " SER H 63 " - " ASP D 62 " " ILE H 64 " - " SER D 63 " " LEU H 65 " - " ILE D 64 " " ILE H 66 " - " LEU D 65 " " LEU H 67 " - " ILE D 66 " " PRO H 68 " - " LEU D 67 " " ASP H 69 " - " PRO D 68 " " TRP H 70 " - " ASP D 69 " " LYS H 71 " - " TRP D 70 " " ALA H 72 " - " LYS D 71 " " GLU H 73 " - " ALA D 72 " " ALA H 74 " - " GLU D 73 " " ILE H 75 " - " ALA D 74 " " ARG H 76 " - " ILE D 75 " " ILE H 77 " - " ARG D 76 " " LEU H 78 " - " ILE D 77 " " SER H 79 " - " LEU D 78 " " LEU H 80 " - " SER D 79 " " MET H 81 " - " LEU D 80 " " GLU H 82 " - " MET D 81 " " LYS H 83 " - " GLU D 82 " " ILE H 84 " - " LYS D 83 " " ARG H 85 " - " ILE D 84 " " LYS H 86 " - " ARG D 85 " " ARG H 87 " - " LYS D 86 " " GLN H 88 " - " ARG D 87 " " ARG H 89 " - " GLN D 88 " " ALA H 90 " - " ARG D 89 " " LEU H 91 " - " ALA D 90 " " GLU H 92 " - " LEU D 91 " " GLU H 93 " - " GLU D 92 " " LEU H 94 " - " GLU D 93 " " TYR H 95 " - " LEU D 94 " " ASN H 96 " - " TYR D 95 " " LYS H 97 " - " ASN D 96 " " GLN H 98 " - " LYS D 97 " " GLU H 99 " - " GLN D 98 " " ILE H 100 " - " GLU D 99 " " PRO H 101 " - " ILE D 100 " " LYS H 102 " - " PRO D 101 " " SER H 103 " - " LYS D 102 " " ASP H 104 " - " SER D 103 " " TYR H 105 " - " ASP D 104 " " ASP H 106 " - " TYR D 105 " " ASP H 107 " - " ASP D 106 " " MET H 108 " - " ASP D 107 " " LYS H 109 " - " MET D 108 " " ARG H 110 " - " LYS D 109 " " LYS H 111 " - " ARG D 110 " " LEU H 112 " - " LYS D 111 " " ASP H 113 " - " LEU D 112 " " THR H 114 " - " ASP D 113 " " GLU H 115 " - " THR D 114 " " MET H 116 " - " GLU D 115 " " LEU H 117 " - " MET D 116 " " LYS H 118 " - " LEU D 117 " " VAL H 119 " - " LYS D 118 " " LYS H 120 " - " VAL D 119 " " ASP H 121 " - " LYS D 120 " " ASP H 122 " - " ASP D 121 " " GLN H 123 " - " ASP D 122 " " ASN H 124 " - " GLN D 123 " " LYS H 125 " - " ASN D 124 " " LEU H 126 " - " LYS D 125 " " LYS H 127 " - " LEU D 126 " " GLY H 128 " - " LYS D 127 " " LYS H 129 " - " GLY D 128 " " LEU H 130 " - " LYS D 129 " " LYS H 131 " - " LEU D 130 " " SER H 132 " - " LYS D 131 " " ARG H 133 " - " SER D 132 " " LEU H 134 " - " ARG D 133 " " ASN H 135 " - " LEU D 134 " " ASP H 136 " - " ASN D 135 " " ILE H 137 " - " ASP D 136 " " GLU H 138 " - " ILE D 137 " " ASP H 139 " - " GLU D 138 " " GLN H 140 " - " ASP D 139 " " LEU H 141 " - " GLN D 140 " " ALA H 142 " - " LEU D 141 " " HIS H 143 " - " ALA D 142 " " ILE H 144 " - " HIS D 143 " " ASP H 145 " - " ILE D 144 " " LYS H 146 " - " ASP D 145 " " ALA H 147 " - " LYS D 146 " " VAL H 148 " - " ALA D 147 " " ILE H 149 " - " VAL D 148 " " SER H 150 " - " ILE D 149 " " LEU H 151 " - " SER D 150 " " LYS H 152 " - " LEU D 151 " " MET H 153 " - " LYS D 152 " " SER H 154 " - " MET D 153 " " TYR H 155 " - " SER D 154 " " ILE H 156 " - " TYR D 155 " " SER H 157 " - " ILE D 156 " " SER H 158 " - " SER D 157 " " GLU H 159 " - " SER D 158 " " ILE H 160 " - " GLU D 159 " " PRO H 161 " - " ILE D 160 " " GLU H 162 " - " PRO D 161 " " ASN H 163 " - " GLU D 162 " " ALA H 164 " - " ASN D 163 " " TYR H 165 " - " ALA D 164 " " LYS H 166 " - " TYR D 165 " " GLY H 167 " - " LYS D 166 " " SER H 168 " - " GLY D 167 " " MET H 169 " - " SER D 168 " " GLU H 170 " - " MET D 169 " " VAL H 171 " - " GLU D 170 " " LEU H 172 " - " VAL D 171 " " ARG H 173 " - " LEU D 172 " " GLN H 174 " - " ARG D 173 " " SER H 175 " - " GLN D 174 " " LYS H 176 " - " SER D 175 " " ASP H 177 " - " LYS D 176 " " SER H 178 " - " ASP D 177 " " TYR H 179 " - " SER D 178 " " THR H 180 " - " TYR D 179 " " LEU H 181 " - " THR D 180 " " GLU H 182 " - " LEU D 181 " " ARG H 183 " - " GLU D 182 " " ASP H 184 " - " ARG D 183 " " ASP H 185 " - " ASP D 184 " " ILE H 186 " - " ASP D 185 " " ARG H 187 " - " ILE D 186 " " LYS H 188 " - " ARG D 187 " " THR H 189 " - " LYS D 188 " " LEU H 190 " - " THR D 189 " " ASP H 191 " - " LEU D 190 " " ARG H 192 " - " ASP D 191 " " LEU H 193 " - " ARG D 192 " " ASP H 194 " - " LEU D 193 " " SER H 195 " - " ASP D 194 " " LEU H 196 " - " SER D 195 " " TYR I 5 " - " SER E 4 " " GLU I 6 " - " TYR E 5 " " VAL I 7 " - " GLU E 6 " " LEU I 8 " - " VAL E 7 " " THR I 9 " - " LEU E 8 " " LYS I 10 " - " THR E 9 " " PHE I 11 " - " LYS E 10 " " ILE I 12 " - " PHE E 11 " " GLY I 13 " - " ILE E 12 " " GLN I 14 " - " GLY E 13 " " LYS I 15 " - " GLN E 14 " " VAL I 16 " - " LYS E 15 " " LYS I 17 " - " VAL E 16 " " ASP I 18 " - " LYS E 17 " " ILE I 19 " - " ASP E 18 " " TYR I 20 " - " ILE E 19 " " GLY I 21 " - " TYR E 20 " " ARG I 22 " - " GLY E 21 " " GLU I 23 " - " ARG E 22 " " PHE I 24 " - " GLU E 23 " " GLY I 25 " - " PHE E 24 " " TYR I 26 " - " GLY E 25 " " LEU I 27 " - " TYR E 26 " " ILE I 28 " - " LEU E 27 " " HIS I 29 " - " ILE E 28 " " VAL I 30 " - " HIS E 29 " " TYR I 31 " - " VAL E 30 " " SER I 32 " - " TYR E 31 " " GLU I 33 " - " SER E 32 " " ILE I 34 " - " GLU E 33 " " ASP I 35 " - " ILE E 34 " " GLY I 36 " - " ASP E 35 " " SER I 37 " - " GLY E 36 " " ILE I 38 " - " SER E 37 " " THR I 39 " - " ILE E 38 " " GLY I 40 " - " THR E 39 " " ILE I 41 " - " GLY E 40 " " GLU I 42 " - " ILE E 41 " " VAL I 43 " - " GLU E 42 " " ALA I 44 " - " VAL E 43 " " GLN I 45 " - " ALA E 44 " " GLY I 46 " - " GLN E 45 " " SER I 47 " - " GLY E 46 " " SER I 48 " - " SER E 47 " " ILE I 49 " - " SER E 48 " " LEU I 50 " - " ILE E 49 " " THR I 51 " - " LEU E 50 " " MET I 52 " - " THR E 51 " " GLY I 53 " - " MET E 52 " " PRO I 54 " - " GLY E 53 " " GLU I 55 " - " PRO E 54 " " ARG I 56 " - " GLU E 55 " " ILE I 57 " - " ARG E 56 " " LYS I 58 " - " ILE E 57 " " LEU I 59 " - " LYS E 58 " " ASP I 60 " - " LEU E 59 " " GLY I 61 " - " ASP E 60 " " ASP I 62 " - " GLY E 61 " " SER I 63 " - " ASP E 62 " " ILE I 64 " - " SER E 63 " " LEU I 65 " - " ILE E 64 " " ILE I 66 " - " LEU E 65 " " LEU I 67 " - " ILE E 66 " " PRO I 68 " - " LEU E 67 " " ASP I 69 " - " PRO E 68 " " TRP I 70 " - " ASP E 69 " " LYS I 71 " - " TRP E 70 " " ALA I 72 " - " LYS E 71 " " GLU I 73 " - " ALA E 72 " " ALA I 74 " - " GLU E 73 " " ILE I 75 " - " ALA E 74 " " ARG I 76 " - " ILE E 75 " " ILE I 77 " - " ARG E 76 " " LEU I 78 " - " ILE E 77 " " SER I 79 " - " LEU E 78 " " LEU I 80 " - " SER E 79 " " MET I 81 " - " LEU E 80 " " GLU I 82 " - " MET E 81 " " LYS I 83 " - " GLU E 82 " " ILE I 84 " - " LYS E 83 " " ARG I 85 " - " ILE E 84 " " LYS I 86 " - " ARG E 85 " " ARG I 87 " - " LYS E 86 " " GLN I 88 " - " ARG E 87 " " ARG I 89 " - " GLN E 88 " " ALA I 90 " - " ARG E 89 " " LEU I 91 " - " ALA E 90 " " GLU I 92 " - " LEU E 91 " " GLU I 93 " - " GLU E 92 " " LEU I 94 " - " GLU E 93 " " TYR I 95 " - " LEU E 94 " " ASN I 96 " - " TYR E 95 " " LYS I 97 " - " ASN E 96 " " GLN I 98 " - " LYS E 97 " " GLU I 99 " - " GLN E 98 " " ILE I 100 " - " GLU E 99 " " PRO I 101 " - " ILE E 100 " " LYS I 102 " - " PRO E 101 " " SER I 103 " - " LYS E 102 " " ASP I 104 " - " SER E 103 " " TYR I 105 " - " ASP E 104 " " ASP I 106 " - " TYR E 105 " " ASP I 107 " - " ASP E 106 " " MET I 108 " - " ASP E 107 " " LYS I 109 " - " MET E 108 " " ARG I 110 " - " LYS E 109 " " LYS I 111 " - " ARG E 110 " " LEU I 112 " - " LYS E 111 " " ASP I 113 " - " LEU E 112 " " THR I 114 " - " ASP E 113 " " GLU I 115 " - " THR E 114 " " MET I 116 " - " GLU E 115 " " LEU I 117 " - " MET E 116 " " LYS I 118 " - " LEU E 117 " " VAL I 119 " - " LYS E 118 " " LYS I 120 " - " VAL E 119 " " ASP I 121 " - " LYS E 120 " " ASP I 122 " - " ASP E 121 " " GLN I 123 " - " ASP E 122 " " ASN I 124 " - " GLN E 123 " " LYS I 125 " - " ASN E 124 " " LEU I 126 " - " LYS E 125 " " LYS I 127 " - " LEU E 126 " " GLY I 128 " - " LYS E 127 " " LYS I 129 " - " GLY E 128 " " LEU I 130 " - " LYS E 129 " " LYS I 131 " - " LEU E 130 " " SER I 132 " - " LYS E 131 " " ARG I 133 " - " SER E 132 " " LEU I 134 " - " ARG E 133 " " ASN I 135 " - " LEU E 134 " " ASP I 136 " - " ASN E 135 " " ILE I 137 " - " ASP E 136 " " GLU I 138 " - " ILE E 137 " " ASP I 139 " - " GLU E 138 " " GLN I 140 " - " ASP E 139 " " LEU I 141 " - " GLN E 140 " " ALA I 142 " - " LEU E 141 " " HIS I 143 " - " ALA E 142 " " ILE I 144 " - " HIS E 143 " " ASP I 145 " - " ILE E 144 " " LYS I 146 " - " ASP E 145 " " ALA I 147 " - " LYS E 146 " " VAL I 148 " - " ALA E 147 " " ILE I 149 " - " VAL E 148 " " SER I 150 " - " ILE E 149 " " LEU I 151 " - " SER E 150 " " LYS I 152 " - " LEU E 151 " " MET I 153 " - " LYS E 152 " " SER I 154 " - " MET E 153 " " TYR I 155 " - " SER E 154 " " ILE I 156 " - " TYR E 155 " " SER I 157 " - " ILE E 156 " " SER I 158 " - " SER E 157 " " GLU I 159 " - " SER E 158 " " ILE I 160 " - " GLU E 159 " " PRO I 161 " - " ILE E 160 " " GLU I 162 " - " PRO E 161 " " ASN I 163 " - " GLU E 162 " " ALA I 164 " - " ASN E 163 " " TYR I 165 " - " ALA E 164 " " LYS I 166 " - " TYR E 165 " " GLY I 167 " - " LYS E 166 " " SER I 168 " - " GLY E 167 " " MET I 169 " - " SER E 168 " " GLU I 170 " - " MET E 169 " " VAL I 171 " - " GLU E 170 " " LEU I 172 " - " VAL E 171 " " ARG I 173 " - " LEU E 172 " " GLN I 174 " - " ARG E 173 " " SER I 175 " - " GLN E 174 " " LYS I 176 " - " SER E 175 " " ASP I 177 " - " LYS E 176 " " SER I 178 " - " ASP E 177 " " TYR I 179 " - " SER E 178 " " THR I 180 " - " TYR E 179 " " LEU I 181 " - " THR E 180 " " GLU I 182 " - " LEU E 181 " " ARG I 183 " - " GLU E 182 " " ASP I 184 " - " ARG E 183 " " ASP I 185 " - " ASP E 184 " " ILE I 186 " - " ASP E 185 " " ARG I 187 " - " ILE E 186 " " LYS I 188 " - " ARG E 187 " " THR I 189 " - " LYS E 188 " " LEU I 190 " - " THR E 189 " " ASP I 191 " - " LEU E 190 " " ARG I 192 " - " ASP E 191 " " LEU I 193 " - " ARG E 192 " " ASP I 194 " - " LEU E 193 " " SER I 195 " - " ASP E 194 " " LEU I 196 " - " SER E 195 " " TYR J 5 " - " SER F 4 " " GLU J 6 " - " TYR F 5 " " VAL J 7 " - " GLU F 6 " " LEU J 8 " - " VAL F 7 " " THR J 9 " - " LEU F 8 " " LYS J 10 " - " THR F 9 " " PHE J 11 " - " LYS F 10 " " ILE J 12 " - " PHE F 11 " " GLY J 13 " - " ILE F 12 " " GLN J 14 " - " GLY F 13 " " LYS J 15 " - " GLN F 14 " " VAL J 16 " - " LYS F 15 " " LYS J 17 " - " VAL F 16 " " ASP J 18 " - " LYS F 17 " " ILE J 19 " - " ASP F 18 " " TYR J 20 " - " ILE F 19 " " GLY J 21 " - " TYR F 20 " " ARG J 22 " - " GLY F 21 " " GLU J 23 " - " ARG F 22 " " PHE J 24 " - " GLU F 23 " " GLY J 25 " - " PHE F 24 " " TYR J 26 " - " GLY F 25 " " LEU J 27 " - " TYR F 26 " " ILE J 28 " - " LEU F 27 " " HIS J 29 " - " ILE F 28 " " VAL J 30 " - " HIS F 29 " " TYR J 31 " - " VAL F 30 " " SER J 32 " - " TYR F 31 " " GLU J 33 " - " SER F 32 " " ILE J 34 " - " GLU F 33 " " ASP J 35 " - " ILE F 34 " " GLY J 36 " - " ASP F 35 " " SER J 37 " - " GLY F 36 " " ILE J 38 " - " SER F 37 " " THR J 39 " - " ILE F 38 " " GLY J 40 " - " THR F 39 " " ILE J 41 " - " GLY F 40 " " GLU J 42 " - " ILE F 41 " " VAL J 43 " - " GLU F 42 " " ALA J 44 " - " VAL F 43 " " GLN J 45 " - " ALA F 44 " " GLY J 46 " - " GLN F 45 " " SER J 47 " - " GLY F 46 " " SER J 48 " - " SER F 47 " " ILE J 49 " - " SER F 48 " " LEU J 50 " - " ILE F 49 " " THR J 51 " - " LEU F 50 " " MET J 52 " - " THR F 51 " " GLY J 53 " - " MET F 52 " " PRO J 54 " - " GLY F 53 " " GLU J 55 " - " PRO F 54 " " ARG J 56 " - " GLU F 55 " " ILE J 57 " - " ARG F 56 " " LYS J 58 " - " ILE F 57 " " LEU J 59 " - " LYS F 58 " " ASP J 60 " - " LEU F 59 " " GLY J 61 " - " ASP F 60 " " ASP J 62 " - " GLY F 61 " " SER J 63 " - " ASP F 62 " " ILE J 64 " - " SER F 63 " " LEU J 65 " - " ILE F 64 " " ILE J 66 " - " LEU F 65 " " LEU J 67 " - " ILE F 66 " " PRO J 68 " - " LEU F 67 " " ASP J 69 " - " PRO F 68 " " TRP J 70 " - " ASP F 69 " " LYS J 71 " - " TRP F 70 " " ALA J 72 " - " LYS F 71 " " GLU J 73 " - " ALA F 72 " " ALA J 74 " - " GLU F 73 " " ILE J 75 " - " ALA F 74 " " ARG J 76 " - " ILE F 75 " " ILE J 77 " - " ARG F 76 " " LEU J 78 " - " ILE F 77 " " SER J 79 " - " LEU F 78 " " LEU J 80 " - " SER F 79 " " MET J 81 " - " LEU F 80 " " GLU J 82 " - " MET F 81 " " LYS J 83 " - " GLU F 82 " " ILE J 84 " - " LYS F 83 " " ARG J 85 " - " ILE F 84 " " LYS J 86 " - " ARG F 85 " " ARG J 87 " - " LYS F 86 " " GLN J 88 " - " ARG F 87 " " ARG J 89 " - " GLN F 88 " " ALA J 90 " - " ARG F 89 " " LEU J 91 " - " ALA F 90 " " GLU J 92 " - " LEU F 91 " " GLU J 93 " - " GLU F 92 " " LEU J 94 " - " GLU F 93 " " TYR J 95 " - " LEU F 94 " " ASN J 96 " - " TYR F 95 " " LYS J 97 " - " ASN F 96 " " GLN J 98 " - " LYS F 97 " " GLU J 99 " - " GLN F 98 " " ILE J 100 " - " GLU F 99 " " PRO J 101 " - " ILE F 100 " " LYS J 102 " - " PRO F 101 " " SER J 103 " - " LYS F 102 " " ASP J 104 " - " SER F 103 " " TYR J 105 " - " ASP F 104 " " ASP J 106 " - " TYR F 105 " " ASP J 107 " - " ASP F 106 " " MET J 108 " - " ASP F 107 " " LYS J 109 " - " MET F 108 " " ARG J 110 " - " LYS F 109 " " LYS J 111 " - " ARG F 110 " " LEU J 112 " - " LYS F 111 " " ASP J 113 " - " LEU F 112 " " THR J 114 " - " ASP F 113 " " GLU J 115 " - " THR F 114 " " MET J 116 " - " GLU F 115 " " LEU J 117 " - " MET F 116 " " LYS J 118 " - " LEU F 117 " " VAL J 119 " - " LYS F 118 " " LYS J 120 " - " VAL F 119 " " ASP J 121 " - " LYS F 120 " " ASP J 122 " - " ASP F 121 " " GLN J 123 " - " ASP F 122 " " ASN J 124 " - " GLN F 123 " " LYS J 125 " - " ASN F 124 " " LEU J 126 " - " LYS F 125 " " LYS J 127 " - " LEU F 126 " " GLY J 128 " - " LYS F 127 " " LYS J 129 " - " GLY F 128 " " LEU J 130 " - " LYS F 129 " " LYS J 131 " - " LEU F 130 " " SER J 132 " - " LYS F 131 " " ARG J 133 " - " SER F 132 " " LEU J 134 " - " ARG F 133 " " ASN J 135 " - " LEU F 134 " " ASP J 136 " - " ASN F 135 " " ILE J 137 " - " ASP F 136 " " GLU J 138 " - " ILE F 137 " " ASP J 139 " - " GLU F 138 " " GLN J 140 " - " ASP F 139 " " LEU J 141 " - " GLN F 140 " " ALA J 142 " - " LEU F 141 " " HIS J 143 " - " ALA F 142 " " ILE J 144 " - " HIS F 143 " " ASP J 145 " - " ILE F 144 " " LYS J 146 " - " ASP F 145 " " ALA J 147 " - " LYS F 146 " " VAL J 148 " - " ALA F 147 " " ILE J 149 " - " VAL F 148 " " SER J 150 " - " ILE F 149 " " LEU J 151 " - " SER F 150 " " LYS J 152 " - " LEU F 151 " " MET J 153 " - " LYS F 152 " " SER J 154 " - " MET F 153 " " TYR J 155 " - " SER F 154 " " ILE J 156 " - " TYR F 155 " " SER J 157 " - " ILE F 156 " " SER J 158 " - " SER F 157 " " GLU J 159 " - " SER F 158 " " ILE J 160 " - " GLU F 159 " " PRO J 161 " - " ILE F 160 " " GLU J 162 " - " PRO F 161 " " ASN J 163 " - " GLU F 162 " " ALA J 164 " - " ASN F 163 " " TYR J 165 " - " ALA F 164 " " LYS J 166 " - " TYR F 165 " " GLY J 167 " - " LYS F 166 " " SER J 168 " - " GLY F 167 " " MET J 169 " - " SER F 168 " " GLU J 170 " - " MET F 169 " " VAL J 171 " - " GLU F 170 " " LEU J 172 " - " VAL F 171 " " ARG J 173 " - " LEU F 172 " " GLN J 174 " - " ARG F 173 " " SER J 175 " - " GLN F 174 " " LYS J 176 " - " SER F 175 " " ASP J 177 " - " LYS F 176 " " SER J 178 " - " ASP F 177 " " TYR J 179 " - " SER F 178 " " THR J 180 " - " TYR F 179 " " LEU J 181 " - " THR F 180 " " GLU J 182 " - " LEU F 181 " " ARG J 183 " - " GLU F 182 " " ASP J 184 " - " ARG F 183 " " ASP J 185 " - " ASP F 184 " " ILE J 186 " - " ASP F 185 " " ARG J 187 " - " ILE F 186 " " LYS J 188 " - " ARG F 187 " " THR J 189 " - " LYS F 188 " " LEU J 190 " - " THR F 189 " " ASP J 191 " - " LEU F 190 " " ARG J 192 " - " ASP F 191 " " LEU J 193 " - " ARG F 192 " " ASP J 194 " - " LEU F 193 " " SER J 195 " - " ASP F 194 " " LEU J 196 " - " SER F 195 " Time building additional restraints: 5.11 Conformation dependent library (CDL) restraints added in 679.2 milliseconds 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 20 sheets defined 68.4% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 5 through 11 removed outlier: 3.876A pdb=" N THR A 9 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A 10 " --> pdb=" O GLU A 6 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE A 11 " --> pdb=" O VAL A 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 5 through 11' Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 68 through 96 Processing helix chain 'A' and resid 101 through 157 removed outlier: 3.516A pdb=" N LYS A 118 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 157 " --> pdb=" O MET A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 196 removed outlier: 3.763A pdb=" N LEU A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 removed outlier: 3.877A pdb=" N THR B 9 " --> pdb=" O TYR B 5 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 10 " --> pdb=" O GLU B 6 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE B 11 " --> pdb=" O VAL B 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 5 through 11' Processing helix chain 'B' and resid 53 through 55 No H-bonds generated for 'chain 'B' and resid 53 through 55' Processing helix chain 'B' and resid 68 through 96 Processing helix chain 'B' and resid 101 through 157 removed outlier: 3.516A pdb=" N LYS B 118 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B 157 " --> pdb=" O MET B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 196 removed outlier: 3.763A pdb=" N LEU B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 11 removed outlier: 3.876A pdb=" N THR C 9 " --> pdb=" O TYR C 5 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS C 10 " --> pdb=" O GLU C 6 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE C 11 " --> pdb=" O VAL C 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 5 through 11' Processing helix chain 'C' and resid 53 through 55 No H-bonds generated for 'chain 'C' and resid 53 through 55' Processing helix chain 'C' and resid 68 through 96 Processing helix chain 'C' and resid 101 through 157 removed outlier: 3.516A pdb=" N LYS C 118 " --> pdb=" O THR C 114 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C 157 " --> pdb=" O MET C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 196 removed outlier: 3.763A pdb=" N LEU C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 11 removed outlier: 3.876A pdb=" N THR D 9 " --> pdb=" O TYR D 5 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS D 10 " --> pdb=" O GLU D 6 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE D 11 " --> pdb=" O VAL D 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 5 through 11' Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 68 through 96 Processing helix chain 'D' and resid 101 through 157 removed outlier: 3.516A pdb=" N LYS D 118 " --> pdb=" O THR D 114 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER D 157 " --> pdb=" O MET D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 196 removed outlier: 3.763A pdb=" N LEU D 196 " --> pdb=" O ARG D 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 11 removed outlier: 3.876A pdb=" N THR E 9 " --> pdb=" O TYR E 5 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS E 10 " --> pdb=" O GLU E 6 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE E 11 " --> pdb=" O VAL E 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 5 through 11' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 68 through 96 Processing helix chain 'E' and resid 101 through 157 removed outlier: 3.516A pdb=" N LYS E 118 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER E 157 " --> pdb=" O MET E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 196 removed outlier: 3.763A pdb=" N LEU E 196 " --> pdb=" O ARG E 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 11 removed outlier: 3.876A pdb=" N THR F 9 " --> pdb=" O TYR F 5 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS F 10 " --> pdb=" O GLU F 6 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE F 11 " --> pdb=" O VAL F 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 5 through 11' Processing helix chain 'F' and resid 53 through 55 No H-bonds generated for 'chain 'F' and resid 53 through 55' Processing helix chain 'F' and resid 68 through 96 Processing helix chain 'F' and resid 101 through 157 removed outlier: 3.516A pdb=" N LYS F 118 " --> pdb=" O THR F 114 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER F 157 " --> pdb=" O MET F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 196 removed outlier: 3.763A pdb=" N LEU F 196 " --> pdb=" O ARG F 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 11 removed outlier: 3.876A pdb=" N THR G 9 " --> pdb=" O TYR G 5 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS G 10 " --> pdb=" O GLU G 6 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE G 11 " --> pdb=" O VAL G 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 5 through 11' Processing helix chain 'G' and resid 53 through 55 No H-bonds generated for 'chain 'G' and resid 53 through 55' Processing helix chain 'G' and resid 68 through 96 Processing helix chain 'G' and resid 101 through 157 removed outlier: 3.516A pdb=" N LYS G 118 " --> pdb=" O THR G 114 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER G 157 " --> pdb=" O MET G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 196 removed outlier: 3.763A pdb=" N LEU G 196 " --> pdb=" O ARG G 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 11 removed outlier: 3.878A pdb=" N THR H 9 " --> pdb=" O TYR H 5 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS H 10 " --> pdb=" O GLU H 6 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE H 11 " --> pdb=" O VAL H 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 5 through 11' Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 68 through 96 Processing helix chain 'H' and resid 101 through 157 removed outlier: 3.516A pdb=" N LYS H 118 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER H 157 " --> pdb=" O MET H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 196 removed outlier: 3.764A pdb=" N LEU H 196 " --> pdb=" O ARG H 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 11 removed outlier: 3.876A pdb=" N THR I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS I 10 " --> pdb=" O GLU I 6 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE I 11 " --> pdb=" O VAL I 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 5 through 11' Processing helix chain 'I' and resid 53 through 55 No H-bonds generated for 'chain 'I' and resid 53 through 55' Processing helix chain 'I' and resid 68 through 96 Processing helix chain 'I' and resid 101 through 157 removed outlier: 3.515A pdb=" N LYS I 118 " --> pdb=" O THR I 114 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER I 157 " --> pdb=" O MET I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 196 removed outlier: 3.763A pdb=" N LEU I 196 " --> pdb=" O ARG I 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 11 removed outlier: 3.877A pdb=" N THR J 9 " --> pdb=" O TYR J 5 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS J 10 " --> pdb=" O GLU J 6 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE J 11 " --> pdb=" O VAL J 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 5 through 11' Processing helix chain 'J' and resid 53 through 55 No H-bonds generated for 'chain 'J' and resid 53 through 55' Processing helix chain 'J' and resid 68 through 96 Processing helix chain 'J' and resid 101 through 157 removed outlier: 3.516A pdb=" N LYS J 118 " --> pdb=" O THR J 114 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER J 157 " --> pdb=" O MET J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 196 removed outlier: 3.763A pdb=" N LEU J 196 " --> pdb=" O ARG J 192 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 15 through 17 removed outlier: 6.870A pdb=" N VAL A 16 " --> pdb=" O PHE A 24 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU A 42 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL A 30 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLY A 40 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER A 32 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE A 38 " --> pdb=" O SER A 32 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 57 through 59 Processing sheet with id=3, first strand: chain 'B' and resid 15 through 17 removed outlier: 6.870A pdb=" N VAL B 16 " --> pdb=" O PHE B 24 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU B 42 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL B 30 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLY B 40 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER B 32 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE B 38 " --> pdb=" O SER B 32 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'B' and resid 57 through 59 Processing sheet with id=5, first strand: chain 'C' and resid 15 through 17 removed outlier: 6.869A pdb=" N VAL C 16 " --> pdb=" O PHE C 24 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU C 42 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL C 30 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLY C 40 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER C 32 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE C 38 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'C' and resid 57 through 59 Processing sheet with id=7, first strand: chain 'D' and resid 15 through 17 removed outlier: 6.870A pdb=" N VAL D 16 " --> pdb=" O PHE D 24 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU D 42 " --> pdb=" O ILE D 28 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL D 30 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLY D 40 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER D 32 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE D 38 " --> pdb=" O SER D 32 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'D' and resid 57 through 59 Processing sheet with id=9, first strand: chain 'E' and resid 15 through 17 removed outlier: 6.869A pdb=" N VAL E 16 " --> pdb=" O PHE E 24 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLU E 42 " --> pdb=" O ILE E 28 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL E 30 " --> pdb=" O GLY E 40 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLY E 40 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER E 32 " --> pdb=" O ILE E 38 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE E 38 " --> pdb=" O SER E 32 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'E' and resid 57 through 59 Processing sheet with id=11, first strand: chain 'F' and resid 15 through 17 removed outlier: 6.870A pdb=" N VAL F 16 " --> pdb=" O PHE F 24 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU F 42 " --> pdb=" O ILE F 28 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VAL F 30 " --> pdb=" O GLY F 40 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLY F 40 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER F 32 " --> pdb=" O ILE F 38 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE F 38 " --> pdb=" O SER F 32 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'F' and resid 57 through 59 Processing sheet with id=13, first strand: chain 'G' and resid 15 through 17 removed outlier: 6.870A pdb=" N VAL G 16 " --> pdb=" O PHE G 24 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU G 42 " --> pdb=" O ILE G 28 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VAL G 30 " --> pdb=" O GLY G 40 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLY G 40 " --> pdb=" O VAL G 30 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER G 32 " --> pdb=" O ILE G 38 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE G 38 " --> pdb=" O SER G 32 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'G' and resid 57 through 59 Processing sheet with id=15, first strand: chain 'H' and resid 15 through 17 removed outlier: 6.870A pdb=" N VAL H 16 " --> pdb=" O PHE H 24 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU H 42 " --> pdb=" O ILE H 28 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL H 30 " --> pdb=" O GLY H 40 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLY H 40 " --> pdb=" O VAL H 30 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER H 32 " --> pdb=" O ILE H 38 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE H 38 " --> pdb=" O SER H 32 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'H' and resid 57 through 59 Processing sheet with id=17, first strand: chain 'I' and resid 15 through 17 removed outlier: 6.870A pdb=" N VAL I 16 " --> pdb=" O PHE I 24 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU I 42 " --> pdb=" O ILE I 28 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL I 30 " --> pdb=" O GLY I 40 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLY I 40 " --> pdb=" O VAL I 30 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER I 32 " --> pdb=" O ILE I 38 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE I 38 " --> pdb=" O SER I 32 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'I' and resid 57 through 59 Processing sheet with id=19, first strand: chain 'J' and resid 15 through 17 removed outlier: 6.869A pdb=" N VAL J 16 " --> pdb=" O PHE J 24 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLU J 42 " --> pdb=" O ILE J 28 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL J 30 " --> pdb=" O GLY J 40 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLY J 40 " --> pdb=" O VAL J 30 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER J 32 " --> pdb=" O ILE J 38 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE J 38 " --> pdb=" O SER J 32 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'J' and resid 57 through 59 1170 hydrogen bonds defined for protein. 3510 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.97 Time building geometry restraints manager: 5.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5170 1.34 - 1.46: 2057 1.46 - 1.57: 8483 1.57 - 1.69: 0 1.69 - 1.80: 120 Bond restraints: 15830 Sorted by residual: bond pdb=" C ILE F 66 " pdb=" N LEU F 67 " ideal model delta sigma weight residual 1.340 1.262 0.078 5.87e-02 2.90e+02 1.78e+00 bond pdb=" C ILE H 66 " pdb=" N LEU H 67 " ideal model delta sigma weight residual 1.340 1.262 0.078 5.87e-02 2.90e+02 1.77e+00 bond pdb=" C ILE D 66 " pdb=" N LEU D 67 " ideal model delta sigma weight residual 1.340 1.262 0.078 5.87e-02 2.90e+02 1.77e+00 bond pdb=" C ILE G 66 " pdb=" N LEU G 67 " ideal model delta sigma weight residual 1.340 1.262 0.078 5.87e-02 2.90e+02 1.77e+00 bond pdb=" C ILE C 66 " pdb=" N LEU C 67 " ideal model delta sigma weight residual 1.340 1.262 0.078 5.87e-02 2.90e+02 1.77e+00 ... (remaining 15825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.96: 19260 0.96 - 1.93: 1595 1.93 - 2.89: 226 2.89 - 3.86: 69 3.86 - 4.82: 30 Bond angle restraints: 21180 Sorted by residual: angle pdb=" C GLU E 23 " pdb=" N PHE E 24 " pdb=" CA PHE E 24 " ideal model delta sigma weight residual 122.36 117.84 4.52 1.72e+00 3.38e-01 6.91e+00 angle pdb=" C GLU D 23 " pdb=" N PHE D 24 " pdb=" CA PHE D 24 " ideal model delta sigma weight residual 122.36 117.84 4.52 1.72e+00 3.38e-01 6.90e+00 angle pdb=" C GLU G 23 " pdb=" N PHE G 24 " pdb=" CA PHE G 24 " ideal model delta sigma weight residual 122.36 117.85 4.51 1.72e+00 3.38e-01 6.89e+00 angle pdb=" C GLU I 23 " pdb=" N PHE I 24 " pdb=" CA PHE I 24 " ideal model delta sigma weight residual 122.36 117.86 4.50 1.72e+00 3.38e-01 6.85e+00 angle pdb=" C GLU A 23 " pdb=" N PHE A 24 " pdb=" CA PHE A 24 " ideal model delta sigma weight residual 122.36 117.86 4.50 1.72e+00 3.38e-01 6.83e+00 ... (remaining 21175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.37: 11770 15.37 - 30.74: 1915 30.74 - 46.11: 682 46.11 - 61.47: 223 61.47 - 76.84: 38 Dihedral angle restraints: 14628 sinusoidal: 7422 harmonic: 7206 Sorted by residual: dihedral pdb=" CA PRO F 68 " pdb=" N PRO F 68 " pdb=" C LEU J 67 " pdb=" CA LEU J 67 " ideal model delta harmonic sigma weight residual 180.00 163.08 16.92 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA LEU C 67 " pdb=" C LEU C 67 " pdb=" N PRO G 68 " pdb=" CA PRO G 68 " ideal model delta harmonic sigma weight residual 180.00 163.10 16.90 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA LEU C 67 " pdb=" C LEU C 67 " pdb=" N PRO C 68 " pdb=" CA PRO C 68 " ideal model delta harmonic sigma weight residual 180.00 163.11 16.89 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 14625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1526 0.031 - 0.061: 604 0.061 - 0.092: 174 0.092 - 0.123: 60 0.123 - 0.153: 16 Chirality restraints: 2380 Sorted by residual: chirality pdb=" CA ILE G 49 " pdb=" N ILE G 49 " pdb=" C ILE G 49 " pdb=" CB ILE G 49 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA ILE I 49 " pdb=" N ILE I 49 " pdb=" C ILE I 49 " pdb=" CB ILE I 49 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CA ILE A 49 " pdb=" N ILE A 49 " pdb=" C ILE A 49 " pdb=" CB ILE A 49 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 ... (remaining 2377 not shown) Planarity restraints: 4216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N SER E 158 " -0.007 2.00e-02 2.50e+03 1.21e-02 1.46e+00 pdb=" CA SER I 157 " -0.006 2.00e-02 2.50e+03 pdb=" C SER I 157 " 0.021 2.00e-02 2.50e+03 pdb=" O SER I 157 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY E 53 " -0.016 5.00e-02 4.00e+02 2.50e-02 1.00e+00 pdb=" N PRO E 54 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO E 54 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 54 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY I 53 " -0.016 5.00e-02 4.00e+02 2.49e-02 9.93e-01 pdb=" N PRO I 54 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO I 54 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO I 54 " -0.014 5.00e-02 4.00e+02 ... (remaining 4213 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 4724 0.98 - 1.96: 11132 1.96 - 2.94: 27809 2.94 - 3.92: 82005 3.92 - 4.90: 135014 Warning: very small nonbonded interaction distances. Nonbonded interactions: 260684 Sorted by model distance: nonbonded pdb=" ND2 ASN D 135 " pdb=" ND2 ASN H 135 " model vdw 0.000 3.200 nonbonded pdb=" OE2 GLU D 138 " pdb=" OE2 GLU H 138 " model vdw 0.000 3.040 nonbonded pdb=" CD LYS D 131 " pdb=" CD LYS H 131 " model vdw 0.000 3.840 nonbonded pdb=" O SER D 132 " pdb=" O SER H 132 " model vdw 0.000 3.040 nonbonded pdb=" CB ASN D 135 " pdb=" CB ASN H 135 " model vdw 0.000 3.840 ... (remaining 260679 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.280 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 17366 Z= 0.367 Angle : 0.794 4.819 25788 Z= 0.464 Chirality : 0.038 0.153 2380 Planarity : 0.003 0.025 2680 Dihedral : 13.837 69.521 6360 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 24.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.57 % Allowed : 8.24 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.16), residues: 1910 helix: 0.04 (0.12), residues: 1160 sheet: -1.75 (0.25), residues: 330 loop : -1.70 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 110 TYR 0.009 0.001 TYR G 31 PHE 0.005 0.002 PHE I 11 TRP 0.004 0.002 TRP F 70 HIS 0.003 0.001 HIS I 29 Details of bonding type rmsd covalent geometry : bond 0.00548 (15830) covalent geometry : angle 0.61850 (21180) hydrogen bonds : bond 0.12285 ( 1170) hydrogen bonds : angle 5.73031 ( 3510) link_TRANS : bond 0.01272 ( 1536) link_TRANS : angle 1.33067 ( 4608) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 239 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 TYR cc_start: 0.7804 (m-80) cc_final: 0.7483 (m-80) REVERT: A 52 MET cc_start: 0.7979 (ttp) cc_final: 0.7573 (ptm) REVERT: B 31 TYR cc_start: 0.7415 (m-80) cc_final: 0.6994 (m-80) REVERT: B 52 MET cc_start: 0.7991 (ttp) cc_final: 0.7558 (ptm) outliers start: 10 outliers final: 8 residues processed: 249 average time/residue: 0.1349 time to fit residues: 49.6379 Evaluate side-chains 232 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 224 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.7833 > 50: distance: 22 - 28: 3.530 distance: 28 - 29: 10.452 distance: 28 - 225: 3.538 distance: 29 - 30: 9.280 distance: 30 - 31: 8.289 distance: 30 - 32: 17.437 distance: 30 - 235: 14.768 distance: 32 - 33: 18.706 distance: 32 - 233: 6.700 distance: 33 - 34: 11.884 distance: 33 - 36: 35.252 distance: 34 - 35: 11.780 distance: 34 - 41: 11.016 distance: 34 - 244: 11.360 distance: 36 - 37: 21.551 distance: 37 - 38: 13.024 distance: 38 - 39: 7.251 distance: 38 - 40: 11.748 distance: 41 - 42: 17.355 distance: 41 - 237: 17.735 distance: 42 - 43: 7.047 distance: 42 - 45: 21.945 distance: 43 - 44: 9.712 distance: 43 - 50: 9.157 distance: 43 - 253: 5.866 distance: 45 - 46: 35.418 distance: 46 - 47: 32.375 distance: 47 - 48: 7.883 distance: 48 - 49: 18.962 distance: 50 - 51: 7.204 distance: 50 - 246: 10.397 distance: 51 - 52: 13.269 distance: 51 - 54: 20.154 distance: 52 - 53: 7.322 distance: 52 - 57: 14.492 distance: 52 - 260: 13.706 distance: 53 - 118: 13.940 distance: 54 - 55: 8.952 distance: 54 - 56: 16.174 distance: 57 - 58: 12.695 distance: 57 - 255: 10.915 distance: 58 - 59: 11.151 distance: 58 - 61: 18.304 distance: 59 - 60: 15.862 distance: 59 - 66: 18.535 distance: 59 - 269: 15.042 distance: 61 - 62: 19.131 distance: 62 - 63: 15.316 distance: 63 - 64: 31.105 distance: 64 - 65: 21.701 distance: 66 - 67: 10.488 distance: 66 - 262: 9.183 distance: 67 - 68: 3.793 distance: 67 - 70: 7.937 distance: 68 - 69: 11.942 distance: 68 - 74: 8.589 distance: 68 - 277: 9.592 distance: 70 - 71: 12.769 distance: 71 - 72: 14.148 distance: 71 - 73: 10.837 distance: 74 - 75: 7.694 distance: 74 - 271: 10.139 distance: 75 - 76: 7.389 distance: 75 - 78: 15.502 distance: 76 - 77: 9.884 distance: 76 - 82: 9.791 distance: 76 - 285: 14.111 distance: 78 - 79: 22.008 distance: 78 - 80: 24.652 distance: 79 - 81: 20.144 distance: 82 - 83: 22.929 distance: 82 - 279: 20.737 distance: 83 - 84: 25.579 distance: 83 - 86: 19.988 distance: 84 - 85: 22.173 distance: 84 - 94: 19.594 distance: 84 - 297: 17.064 distance: 86 - 87: 15.732 distance: 87 - 88: 7.890 distance: 87 - 89: 6.729 distance: 88 - 90: 9.566 distance: 89 - 91: 8.380 distance: 90 - 92: 9.563 distance: 91 - 92: 15.644 distance: 92 - 93: 10.049 distance: 94 - 95: 13.105 distance: 94 - 287: 4.067 distance: 95 - 96: 5.165 distance: 96 - 97: 11.721 distance: 96 - 98: 25.193 distance: 96 - 301: 10.549 distance: 98 - 99: 32.164 distance: 98 - 299: 17.272 distance: 99 - 100: 39.954 distance: 99 - 102: 23.480 distance: 100 - 101: 12.123 distance: 100 - 109: 16.994 distance: 100 - 312: 16.977 distance: 102 - 103: 34.911 distance: 103 - 104: 23.389 distance: 104 - 105: 14.310 distance: 105 - 106: 15.294 distance: 106 - 107: 13.170 distance: 106 - 108: 12.064 distance: 178 - 186: 3.017 distance: 382 - 390: 3.017