Starting phenix.real_space_refine on Thu Aug 6 16:07:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s9h_54678/08_2026/9s9h_54678.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s9h_54678/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9s9h_54678/08_2026/9s9h_54678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s9h_54678/08_2026/9s9h_54678.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9s9h_54678/08_2026/9s9h_54678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s9h_54678/08_2026/9s9h_54678.map" } 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-2.2rc3-6140/lib/python3.11/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: 1.83, per 1000 atoms: 0.12 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: 4.99 Conformation dependent library (CDL) restraints added in 699.3 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: 0.27 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: 3.07 Time building geometry restraints manager: 5.54 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: 0.06 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: 2.140 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.060 Find NCS groups from input model: 0.160 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 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/Z covalent geometry : bond 0.00548 / 0.26 (15830) covalent geometry : angle 0.61850 / 0.38 (21180) hydrogen bonds : bond 0.12285 / 8.27 ( 1170) hydrogen bonds : angle 5.73031 / 3.94 ( 3510) link_TRANS : bond 0.01272 / 0.87 ( 1536) link_TRANS : angle 1.33067 / 0.93 ( 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 : 0.587 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: 0.1369 time to fit residues: 50.9101 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 : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 50.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 50.0000 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 50.0000 chunk 103 optimal weight: 5.9990 chunk 77 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 51.7833 > 50:) chunk 122 optimal weight: 40.0000 chunk 91 optimal weight: 30.0000 chunk 149 optimal weight: 30.0000 overall best weight: 21.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.080944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.065143 restraints weight = 173588.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.066519 restraints weight = 102985.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.067452 restraints weight = 69939.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.068163 restraints weight = 53089.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.068456 restraints weight = 44046.558| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 1.5672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.098 2.782 17366 Z= 6.218 Angle : 9.428 66.438 25788 Z= 5.900 Chirality : 0.482 4.223 2380 Planarity : 0.050 0.413 2680 Dihedral : 31.860 117.000 2130 Min Nonbonded Distance : 1.132 Molprobity Statistics. All-atom Clashscore : 524.62 Ramachandran Plot: Outliers : 37.59 % Allowed : 19.11 % Favored : 43.30 % Rotamer: Outliers : 30.51 % Allowed : 21.59 % Favored : 47.90 % Cbeta Deviations : 57.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 37.50 % Twisted General : 40.05 % 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: -8.24 (0.10), residues: 1910 helix: -4.91 (0.07), residues: 874 sheet: -4.34 (0.49), residues: 70 loop : -6.35 (0.12), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.052 0.005 ARG D 22 TYR 0.127 0.016 TYR D 20 PHE 0.096 0.019 PHE E 11 TRP 0.151 0.027 TRP F 70 HIS 0.062 0.015 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.08562 / 5.09 (15830) covalent geometry : angle 8.17756 / 5.44 (21180) hydrogen bonds : bond 0.70932 / 47.79 ( 1170) hydrogen bonds : angle 23.16795 / 16.29 ( 3510) link_TRANS : bond 0.18237 / 12.12 ( 1536) link_TRANS : angle 13.78675 / 9.57 ( 4608) *********************** REFINEMENT MACRO_CYCLE 2 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 955 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 537 poor density : 418 time to evaluate : 0.647 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: A 140 GLN cc_start: 0.9354 (OUTLIER) cc_final: 0.8866 (tp40) REVERT: B 88 GLN cc_start: 0.8638 (mt0) cc_final: 0.8297 (mt0) REVERT: B 153 MET cc_start: 0.8869 (tpp) cc_final: 0.8657 (tpt) REVERT: C 15 LYS cc_start: 0.9534 (ttpp) cc_final: 0.9303 (tptp) REVERT: C 22 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.5952 (mtm110) REVERT: C 85 ARG cc_start: 0.9490 (OUTLIER) cc_final: 0.9280 (mmt180) REVERT: D 31 TYR cc_start: 0.6961 (m-10) cc_final: 0.5752 (m-80) REVERT: D 119 VAL cc_start: 0.9056 (OUTLIER) cc_final: 0.8789 (t) REVERT: D 196 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7575 (tp) REVERT: E 31 TYR cc_start: 0.7372 (m-80) cc_final: 0.6977 (m-80) REVERT: F 29 HIS cc_start: 0.1470 (OUTLIER) cc_final: 0.1217 (t-90) REVERT: F 31 TYR cc_start: 0.7031 (m-80) cc_final: 0.6829 (m-10) REVERT: F 92 GLU cc_start: 0.9700 (mm-30) cc_final: 0.9337 (tp30) REVERT: F 190 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9292 (tp) REVERT: G 22 ARG cc_start: 0.8842 (ttm-80) cc_final: 0.8618 (ttm-80) REVERT: G 24 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.8271 (p90) REVERT: G 58 LYS cc_start: 0.9391 (tttt) cc_final: 0.9090 (tptt) REVERT: I 88 GLN cc_start: 0.9440 (tt0) cc_final: 0.9153 (tm-30) REVERT: J 55 GLU cc_start: 0.9610 (OUTLIER) cc_final: 0.9339 (pm20) REVERT: J 58 LYS cc_start: 0.9270 (tttt) cc_final: 0.9022 (tptt) REVERT: J 73 GLU cc_start: 0.9577 (mm-30) cc_final: 0.9318 (mm-30) outliers start: 537 outliers final: 264 residues processed: 789 average time/residue: 0.1564 time to fit residues: 176.8248 Evaluate side-chains 614 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 273 poor density : 341 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 103 optimal weight: 50.0000 chunk 122 optimal weight: 50.0000 chunk 142 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 100 optimal weight: 50.0000 chunk 115 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 170 optimal weight: 50.0000 chunk 42 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 GLN A 140 GLN ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 GLN ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 HIS ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN ** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 ASN ** I 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.099601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.084166 restraints weight = 171612.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.084092 restraints weight = 150267.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.085336 restraints weight = 106094.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.086333 restraints weight = 70562.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.086523 restraints weight = 53365.214| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 1.9625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.092 2.805 17366 Z= 6.066 Angle : 9.008 89.119 25788 Z= 5.718 Chirality : 0.394 4.347 2380 Planarity : 0.045 0.270 2680 Dihedral : 33.266 112.172 2130 Min Nonbonded Distance : 1.160 Molprobity Statistics. All-atom Clashscore : 403.60 Ramachandran Plot: Outliers : 34.55 % Allowed : 21.62 % Favored : 43.82 % Rotamer: Outliers : 14.55 % Allowed : 17.44 % Favored : 68.01 % Cbeta Deviations : 51.86 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 32.50 % Twisted General : 41.54 % 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: -7.86 (0.12), residues: 1910 helix: -4.42 (0.11), residues: 857 sheet: -2.57 (0.55), residues: 78 loop : -6.49 (0.11), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG G 22 TYR 0.094 0.010 TYR F 5 PHE 0.110 0.014 PHE G 24 TRP 0.071 0.015 TRP E 70 HIS 0.053 0.010 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.07816 / 4.96 (15830) covalent geometry : angle 7.54232 / 5.18 (21180) hydrogen bonds : bond 0.77970 / 52.39 ( 1170) hydrogen bonds : angle 23.67492 / 16.69 ( 3510) link_TRANS : bond 0.17849 / 11.86 ( 1536) link_TRANS : angle 13.87913 / 9.61 ( 4608) *********************** REFINEMENT MACRO_CYCLE 3 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 754 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 256 poor density : 498 time to evaluate : 0.660 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: A 163 ASN cc_start: 0.7881 (OUTLIER) cc_final: 0.7566 (p0) REVERT: C 42 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8040 (tp30) REVERT: C 143 HIS cc_start: 0.2295 (t-90) cc_final: 0.1816 (t-90) REVERT: D 163 ASN cc_start: 0.8903 (p0) cc_final: 0.8619 (p0) REVERT: E 8 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7278 (mp) REVERT: E 135 ASN cc_start: 0.9613 (t0) cc_final: 0.9387 (t0) REVERT: F 39 THR cc_start: 0.6997 (OUTLIER) cc_final: 0.6758 (t) REVERT: F 92 GLU cc_start: 0.9425 (mm-30) cc_final: 0.8842 (tp30) REVERT: F 93 GLU cc_start: 0.9625 (pt0) cc_final: 0.9307 (pm20) REVERT: G 35 ASP cc_start: 0.9467 (t0) cc_final: 0.8786 (t0) REVERT: H 51 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.8846 (m) REVERT: H 141 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8626 (tt) REVERT: H 163 ASN cc_start: 0.9348 (m110) cc_final: 0.8971 (m110) REVERT: I 52 MET cc_start: 0.8860 (mtm) cc_final: 0.8585 (mmp) REVERT: I 122 ASP cc_start: 0.8922 (OUTLIER) cc_final: 0.8714 (m-30) REVERT: J 95 TYR cc_start: 0.9085 (OUTLIER) cc_final: 0.8346 (t80) REVERT: J 107 ASP cc_start: 0.9298 (m-30) cc_final: 0.9030 (t0) outliers start: 256 outliers final: 83 residues processed: 673 average time/residue: 0.1623 time to fit residues: 154.3300 Evaluate side-chains 457 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 366 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 182 optimal weight: 40.0000 chunk 145 optimal weight: 50.0000 chunk 22 optimal weight: 0.9990 chunk 109 optimal weight: 50.0000 chunk 164 optimal weight: 30.0000 chunk 56 optimal weight: 50.0000 chunk 44 optimal weight: 8.9990 chunk 121 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 GLN ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 ASN G 124 ASN ** G 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.092595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.078079 restraints weight = 176631.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.079793 restraints weight = 101545.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.080906 restraints weight = 65816.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.081755 restraints weight = 47913.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.082314 restraints weight = 37621.442| |-----------------------------------------------------------------------------| r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 2.0327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.090 2.787 17366 Z= 5.975 Angle : 8.919 77.617 25788 Z= 5.672 Chirality : 0.375 4.295 2380 Planarity : 0.045 0.273 2680 Dihedral : 33.846 111.533 2130 Min Nonbonded Distance : 1.157 Molprobity Statistics. All-atom Clashscore : 400.09 Ramachandran Plot: Outliers : 33.77 % Allowed : 23.93 % Favored : 42.30 % Rotamer: Outliers : 7.95 % Allowed : 18.07 % Favored : 73.98 % Cbeta Deviations : 51.69 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 37.50 % Twisted General : 40.64 % 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: -7.78 (0.12), residues: 1910 helix: -4.26 (0.12), residues: 812 sheet: -2.62 (0.57), residues: 76 loop : -6.49 (0.11), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.003 ARG H 56 TYR 0.100 0.010 TYR G 179 PHE 0.097 0.014 PHE G 24 TRP 0.068 0.012 TRP E 70 HIS 0.063 0.012 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.07634 / 4.90 (15830) covalent geometry : angle 7.38491 / 5.11 (21180) hydrogen bonds : bond 0.78887 / 52.97 ( 1170) hydrogen bonds : angle 24.03705 / 16.93 ( 3510) link_TRANS : bond 0.17489 / 11.64 ( 1536) link_TRANS : angle 13.94788 / 9.67 ( 4608) *********************** REFINEMENT MACRO_CYCLE 4 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 591 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 451 time to evaluate : 0.599 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: B 151 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9020 (tp) REVERT: C 24 PHE cc_start: 0.8597 (t80) cc_final: 0.8331 (t80) REVERT: C 143 HIS cc_start: 0.2091 (t-90) cc_final: 0.1773 (t-90) REVERT: C 187 ARG cc_start: 0.9694 (mtt-85) cc_final: 0.9207 (tpm170) REVERT: D 95 TYR cc_start: 0.9608 (t80) cc_final: 0.9380 (t80) REVERT: E 24 PHE cc_start: 0.7770 (t80) cc_final: 0.7534 (t80) REVERT: E 135 ASN cc_start: 0.9629 (t0) cc_final: 0.9397 (t0) REVERT: G 187 ARG cc_start: 0.9703 (mpp-170) cc_final: 0.9295 (mpp-170) REVERT: G 188 LYS cc_start: 0.9625 (pttm) cc_final: 0.9309 (pttm) REVERT: I 136 ASP cc_start: 0.9061 (m-30) cc_final: 0.8815 (m-30) outliers start: 140 outliers final: 45 residues processed: 546 average time/residue: 0.1578 time to fit residues: 123.0488 Evaluate side-chains 392 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 346 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 111 optimal weight: 40.0000 chunk 158 optimal weight: 3.9990 chunk 87 optimal weight: 30.0000 chunk 95 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 72 optimal weight: 20.0000 chunk 132 optimal weight: 40.0000 chunk 65 optimal weight: 40.0000 chunk 186 optimal weight: 30.0000 chunk 166 optimal weight: 40.0000 chunk 133 optimal weight: 2.9990 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 GLN ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.093342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.078590 restraints weight = 175274.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.080322 restraints weight = 101164.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.081564 restraints weight = 65346.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.082227 restraints weight = 46499.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.082867 restraints weight = 37880.779| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 2.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.088 2.717 17366 Z= 5.913 Angle : 8.871 76.169 25788 Z= 5.652 Chirality : 0.370 4.266 2380 Planarity : 0.046 0.273 2680 Dihedral : 34.079 129.202 2130 Min Nonbonded Distance : 1.153 Molprobity Statistics. All-atom Clashscore : 397.81 Ramachandran Plot: Outliers : 34.08 % Allowed : 23.30 % Favored : 42.62 % Rotamer: Outliers : 6.08 % Allowed : 15.85 % Favored : 78.07 % Cbeta Deviations : 51.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 37.50 % Twisted General : 41.01 % 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: -7.75 (0.12), residues: 1910 helix: -4.22 (0.12), residues: 808 sheet: -2.80 (0.66), residues: 56 loop : -6.42 (0.11), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.002 ARG I 56 TYR 0.113 0.010 TYR D 31 PHE 0.096 0.012 PHE G 24 TRP 0.086 0.014 TRP C 70 HIS 0.062 0.012 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.07535 / 4.85 (15830) covalent geometry : angle 7.29802 / 5.07 (21180) hydrogen bonds : bond 0.79295 / 53.21 ( 1170) hydrogen bonds : angle 24.15975 / 16.98 ( 3510) link_TRANS : bond 0.17283 / 11.50 ( 1536) link_TRANS : angle 13.98559 / 9.70 ( 4608) *********************** REFINEMENT MACRO_CYCLE 5 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 530 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 423 time to evaluate : 0.858 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: B 151 LEU cc_start: 0.9535 (tp) cc_final: 0.9246 (mt) REVERT: C 143 HIS cc_start: 0.2812 (t-90) cc_final: 0.2388 (t70) REVERT: C 187 ARG cc_start: 0.9598 (tpp-160) cc_final: 0.9225 (tpm170) REVERT: D 95 TYR cc_start: 0.9608 (t80) cc_final: 0.9403 (t80) REVERT: E 135 ASN cc_start: 0.9647 (t0) cc_final: 0.9437 (t0) REVERT: F 66 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7787 (mm) REVERT: G 187 ARG cc_start: 0.9682 (mpp-170) cc_final: 0.9426 (mpp-170) REVERT: G 188 LYS cc_start: 0.9664 (pttm) cc_final: 0.9458 (pttm) REVERT: H 14 GLN cc_start: 0.8662 (pt0) cc_final: 0.8053 (pt0) REVERT: H 187 ARG cc_start: 0.9427 (mtt-85) cc_final: 0.9214 (mtt-85) REVERT: I 29 HIS cc_start: 0.7369 (OUTLIER) cc_final: 0.6991 (t-90) REVERT: I 136 ASP cc_start: 0.9110 (m-30) cc_final: 0.8891 (m-30) outliers start: 107 outliers final: 41 residues processed: 497 average time/residue: 0.1562 time to fit residues: 110.6131 Evaluate side-chains 376 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 333 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 159 optimal weight: 30.0000 chunk 39 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 112 optimal weight: 40.0000 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 64 optimal weight: 50.0000 chunk 178 optimal weight: 40.0000 chunk 100 optimal weight: 50.0000 chunk 127 optimal weight: 50.0000 chunk 134 optimal weight: 5.9990 overall best weight: 9.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 GLN ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 GLN ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.090417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.075982 restraints weight = 197959.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.077472 restraints weight = 142606.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.077348 restraints weight = 105807.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.077571 restraints weight = 104043.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.077698 restraints weight = 96281.497| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 2.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.087 2.690 17366 Z= 5.864 Angle : 8.882 72.786 25788 Z= 5.656 Chirality : 0.367 4.005 2380 Planarity : 0.046 0.278 2680 Dihedral : 34.269 129.137 2130 Min Nonbonded Distance : 1.140 Molprobity Statistics. All-atom Clashscore : 407.30 Ramachandran Plot: Outliers : 33.66 % Allowed : 24.40 % Favored : 41.94 % Rotamer: Outliers : 4.49 % Allowed : 14.38 % Favored : 81.14 % Cbeta Deviations : 51.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 42.50 % Twisted General : 41.01 % 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: -7.91 (0.12), residues: 1910 helix: -4.34 (0.11), residues: 790 sheet: -3.93 (0.63), residues: 56 loop : -6.43 (0.11), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.002 ARG I 56 TYR 0.110 0.011 TYR G 179 PHE 0.078 0.014 PHE J 11 TRP 0.076 0.013 TRP F 70 HIS 0.050 0.013 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.07441 / 4.81 (15830) covalent geometry : angle 7.31022 / 5.08 (21180) hydrogen bonds : bond 0.79363 / 53.24 ( 1170) hydrogen bonds : angle 24.24048 / 17.03 ( 3510) link_TRANS : bond 0.17141 / 11.41 ( 1536) link_TRANS : angle 13.99403 / 9.71 ( 4608) *********************** REFINEMENT MACRO_CYCLE 6 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 485 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 406 time to evaluate : 0.657 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: C 143 HIS cc_start: 0.2787 (t-90) cc_final: 0.2442 (t-170) REVERT: C 187 ARG cc_start: 0.9623 (tpp-160) cc_final: 0.9301 (tpm170) REVERT: D 55 GLU cc_start: 0.7831 (pp20) cc_final: 0.7631 (tp30) REVERT: G 187 ARG cc_start: 0.9701 (mpp-170) cc_final: 0.9397 (mpp-170) REVERT: H 14 GLN cc_start: 0.8982 (pt0) cc_final: 0.8637 (pt0) REVERT: H 143 HIS cc_start: 0.8425 (t-90) cc_final: 0.8086 (t-90) REVERT: H 176 LYS cc_start: 0.8931 (tmmt) cc_final: 0.8683 (tmmt) REVERT: I 136 ASP cc_start: 0.9226 (m-30) cc_final: 0.8990 (m-30) outliers start: 79 outliers final: 32 residues processed: 461 average time/residue: 0.1522 time to fit residues: 101.2432 Evaluate side-chains 370 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 338 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 49 optimal weight: 50.0000 chunk 165 optimal weight: 50.0000 chunk 131 optimal weight: 50.0000 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 81 optimal weight: 20.0000 chunk 185 optimal weight: 30.0000 chunk 123 optimal weight: 30.0000 chunk 132 optimal weight: 40.0000 chunk 161 optimal weight: 20.0000 chunk 179 optimal weight: 40.0000 overall best weight: 14.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 45 GLN ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 ASN ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.087342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.073084 restraints weight = 192145.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.073296 restraints weight = 143279.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.074304 restraints weight = 112911.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.075148 restraints weight = 74959.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.075169 restraints weight = 61232.624| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 2.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.088 2.630 17366 Z= 5.817 Angle : 8.923 74.189 25788 Z= 5.673 Chirality : 0.375 4.124 2380 Planarity : 0.047 0.283 2680 Dihedral : 34.505 126.599 2130 Min Nonbonded Distance : 1.139 Molprobity Statistics. All-atom Clashscore : 434.52 Ramachandran Plot: Outliers : 33.40 % Allowed : 25.86 % Favored : 40.73 % Rotamer: Outliers : 2.27 % Allowed : 12.95 % Favored : 84.77 % Cbeta Deviations : 50.98 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 42.50 % Twisted General : 41.06 % 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: -8.23 (0.10), residues: 1910 helix: -4.73 (0.09), residues: 785 sheet: -3.69 (0.63), residues: 46 loop : -6.51 (0.11), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.003 ARG F 56 TYR 0.125 0.013 TYR G 155 PHE 0.108 0.014 PHE J 11 TRP 0.075 0.017 TRP F 70 HIS 0.077 0.016 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.07500 / 4.78 (15830) covalent geometry : angle 7.36991 / 5.10 (21180) hydrogen bonds : bond 0.78592 / 52.73 ( 1170) hydrogen bonds : angle 24.43832 / 17.16 ( 3510) link_TRANS : bond 0.16990 / 11.32 ( 1536) link_TRANS : angle 13.99725 / 9.71 ( 4608) *********************** REFINEMENT MACRO_CYCLE 7 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 412 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 372 time to evaluate : 0.664 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: C 143 HIS cc_start: 0.2956 (t-90) cc_final: 0.2714 (t-170) REVERT: C 187 ARG cc_start: 0.9654 (tpp-160) cc_final: 0.9422 (tpm170) REVERT: G 45 GLN cc_start: 0.9298 (mm110) cc_final: 0.9078 (tp40) REVERT: G 188 LYS cc_start: 0.9738 (pttm) cc_final: 0.9524 (pttm) REVERT: H 14 GLN cc_start: 0.9200 (pt0) cc_final: 0.8801 (pt0) REVERT: H 26 TYR cc_start: 0.6063 (OUTLIER) cc_final: 0.5780 (m-10) outliers start: 40 outliers final: 12 residues processed: 397 average time/residue: 0.1491 time to fit residues: 86.8692 Evaluate side-chains 312 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 299 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 107 optimal weight: 50.0000 chunk 138 optimal weight: 50.0000 chunk 116 optimal weight: 5.9990 chunk 135 optimal weight: 20.0000 chunk 71 optimal weight: 30.0000 chunk 38 optimal weight: 9.9990 chunk 127 optimal weight: 50.0000 chunk 20 optimal weight: 0.0470 chunk 9 optimal weight: 1.9990 chunk 157 optimal weight: 50.0000 chunk 84 optimal weight: 9.9990 overall best weight: 5.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** F 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 HIS ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.093466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.079267 restraints weight = 182481.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.080844 restraints weight = 118886.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.081375 restraints weight = 87005.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.081984 restraints weight = 67005.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.082362 restraints weight = 52410.043| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 2.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.087 2.590 17366 Z= 5.886 Angle : 8.887 73.626 25788 Z= 5.653 Chirality : 0.365 4.012 2380 Planarity : 0.046 0.284 2680 Dihedral : 34.491 128.248 2130 Min Nonbonded Distance : 1.140 Molprobity Statistics. All-atom Clashscore : 394.74 Ramachandran Plot: Outliers : 33.87 % Allowed : 24.50 % Favored : 41.62 % Rotamer: Outliers : 1.25 % Allowed : 7.56 % Favored : 91.19 % Cbeta Deviations : 50.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 40.00 % Twisted General : 41.86 % 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: -7.92 (0.12), residues: 1910 helix: -4.29 (0.12), residues: 783 sheet: -4.26 (0.56), residues: 60 loop : -6.47 (0.11), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.002 ARG I 56 TYR 0.123 0.010 TYR D 31 PHE 0.088 0.012 PHE H 24 TRP 0.066 0.012 TRP E 70 HIS 0.061 0.015 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.07406 / 4.84 (15830) covalent geometry : angle 7.33682 / 5.08 (21180) hydrogen bonds : bond 0.80401 / 53.92 ( 1170) hydrogen bonds : angle 24.36600 / 17.13 ( 3510) link_TRANS : bond 0.17155 / 11.43 ( 1536) link_TRANS : angle 13.94996 / 9.68 ( 4608) *********************** REFINEMENT MACRO_CYCLE 8 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 416 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 394 time to evaluate : 0.665 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: B 151 LEU cc_start: 0.9405 (tp) cc_final: 0.9174 (mt) REVERT: C 177 ASP cc_start: 0.9278 (t70) cc_final: 0.9062 (t70) REVERT: C 187 ARG cc_start: 0.9609 (tpp-160) cc_final: 0.9176 (tpm170) REVERT: D 97 LYS cc_start: 0.9190 (mmpt) cc_final: 0.8935 (mmtt) REVERT: D 137 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8316 (mt) REVERT: F 55 GLU cc_start: 0.9451 (mp0) cc_final: 0.9237 (mp0) REVERT: G 45 GLN cc_start: 0.9323 (mm110) cc_final: 0.9117 (tp40) REVERT: H 14 GLN cc_start: 0.8766 (pt0) cc_final: 0.8336 (pt0) REVERT: J 114 THR cc_start: 0.9452 (p) cc_final: 0.9221 (p) outliers start: 22 outliers final: 9 residues processed: 410 average time/residue: 0.1615 time to fit residues: 94.1949 Evaluate side-chains 313 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 303 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 43 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 172 optimal weight: 30.0000 chunk 35 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 179 optimal weight: 30.0000 chunk 37 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 45 GLN ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 HIS ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.095083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.080765 restraints weight = 167772.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.082419 restraints weight = 98728.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.083500 restraints weight = 65111.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 78)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.084409 restraints weight = 47940.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.084900 restraints weight = 37822.479| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 2.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.087 2.597 17366 Z= 5.895 Angle : 8.910 73.903 25788 Z= 5.657 Chirality : 0.372 3.978 2380 Planarity : 0.046 0.284 2680 Dihedral : 34.505 126.029 2130 Min Nonbonded Distance : 1.145 Molprobity Statistics. All-atom Clashscore : 389.18 Ramachandran Plot: Outliers : 33.66 % Allowed : 24.24 % Favored : 42.09 % Rotamer: Outliers : 0.45 % Allowed : 6.14 % Favored : 93.41 % Cbeta Deviations : 50.87 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 40.00 % Twisted General : 41.97 % 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: -7.73 (0.12), residues: 1910 helix: -4.10 (0.13), residues: 771 sheet: -4.05 (0.61), residues: 58 loop : -6.38 (0.11), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG I 192 TYR 0.115 0.010 TYR G 155 PHE 0.093 0.011 PHE H 24 TRP 0.069 0.011 TRP E 70 HIS 0.061 0.016 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.07436 / 4.85 (15830) covalent geometry : angle 7.38115 / 5.09 (21180) hydrogen bonds : bond 0.80900 / 54.25 ( 1170) hydrogen bonds : angle 24.32436 / 17.10 ( 3510) link_TRANS : bond 0.17168 / 11.44 ( 1536) link_TRANS : angle 13.92371 / 9.65 ( 4608) *********************** REFINEMENT MACRO_CYCLE 9 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 391 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 383 time to evaluate : 0.686 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: C 153 MET cc_start: -0.1950 (ttm) cc_final: -0.2202 (ttm) REVERT: C 177 ASP cc_start: 0.9311 (t70) cc_final: 0.9103 (t70) REVERT: C 187 ARG cc_start: 0.9659 (tpp-160) cc_final: 0.9212 (tpm170) REVERT: D 97 LYS cc_start: 0.8942 (mmpt) cc_final: 0.8713 (mmpt) REVERT: F 81 MET cc_start: 0.8875 (tpt) cc_final: 0.8388 (tpt) REVERT: F 183 ARG cc_start: 0.9663 (tpm170) cc_final: 0.9395 (tpm170) REVERT: H 140 GLN cc_start: 0.8964 (tp40) cc_final: 0.8483 (tt0) REVERT: I 98 GLN cc_start: 0.8184 (mp10) cc_final: 0.7932 (mp10) outliers start: 8 outliers final: 7 residues processed: 390 average time/residue: 0.1674 time to fit residues: 91.6679 Evaluate side-chains 313 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 306 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 130 optimal weight: 10.0000 chunk 49 optimal weight: 50.0000 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 146 optimal weight: 40.0000 chunk 166 optimal weight: 40.0000 chunk 74 optimal weight: 30.0000 chunk 84 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 47 optimal weight: 20.0000 chunk 177 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.095897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.081634 restraints weight = 188719.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.083336 restraints weight = 122569.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.084024 restraints weight = 83634.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.084610 restraints weight = 60859.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.085156 restraints weight = 46898.602| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 2.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.088 2.554 17366 Z= 5.900 Angle : 8.938 74.104 25788 Z= 5.669 Chirality : 0.378 4.259 2380 Planarity : 0.047 0.284 2680 Dihedral : 34.486 127.385 2130 Min Nonbonded Distance : 1.147 Molprobity Statistics. All-atom Clashscore : 391.72 Ramachandran Plot: Outliers : 33.04 % Allowed : 25.13 % Favored : 41.83 % Rotamer: Outliers : 0.17 % Allowed : 2.61 % Favored : 97.22 % Cbeta Deviations : 50.55 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 40.00 % Twisted General : 41.70 % 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: -7.64 (0.13), residues: 1910 helix: -4.04 (0.13), residues: 759 sheet: -3.73 (0.55), residues: 68 loop : -6.33 (0.11), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.002 ARG E 56 TYR 0.142 0.011 TYR D 31 PHE 0.095 0.008 PHE H 24 TRP 0.069 0.010 TRP E 70 HIS 0.058 0.015 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.07506 / 4.86 (15830) covalent geometry : angle 7.42756 / 5.11 (21180) hydrogen bonds : bond 0.81124 / 54.42 ( 1170) hydrogen bonds : angle 24.31128 / 17.10 ( 3510) link_TRANS : bond 0.17175 / 11.45 ( 1536) link_TRANS : angle 13.91174 / 9.65 ( 4608) ********************** REFINEMENT MACRO_CYCLE 10 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 387 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 384 time to evaluate : 0.650 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: C 153 MET cc_start: -0.2146 (ttm) cc_final: -0.2416 (tmm) REVERT: C 177 ASP cc_start: 0.9301 (t70) cc_final: 0.9075 (t70) REVERT: C 187 ARG cc_start: 0.9598 (tpp-160) cc_final: 0.9127 (tpm170) REVERT: D 97 LYS cc_start: 0.9007 (mmpt) cc_final: 0.8773 (mmpt) REVERT: F 81 MET cc_start: 0.8849 (tpt) cc_final: 0.8426 (tpt) REVERT: G 188 LYS cc_start: 0.9720 (pttm) cc_final: 0.9503 (pttm) REVERT: H 176 LYS cc_start: 0.8780 (tmmt) cc_final: 0.8445 (tmmt) REVERT: I 180 THR cc_start: 0.9655 (p) cc_final: 0.9431 (p) REVERT: I 181 LEU cc_start: 0.9525 (mt) cc_final: 0.9100 (mt) REVERT: J 82 GLU cc_start: 0.9764 (mm-30) cc_final: 0.9555 (mm-30) outliers start: 3 outliers final: 3 residues processed: 385 average time/residue: 0.1613 time to fit residues: 87.7631 Evaluate side-chains 314 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 311 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 64 optimal weight: 50.0000 chunk 165 optimal weight: 40.0000 chunk 82 optimal weight: 20.0000 chunk 184 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 107 optimal weight: 50.0000 chunk 98 optimal weight: 8.9990 chunk 177 optimal weight: 7.9990 chunk 141 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 HIS ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** G 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.095088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.079717 restraints weight = 180132.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.081394 restraints weight = 117237.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.081778 restraints weight = 80916.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.081982 restraints weight = 83791.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.082649 restraints weight = 64913.804| |-----------------------------------------------------------------------------| r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 2.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.088 2.549 17366 Z= 5.873 Angle : 8.929 74.305 25788 Z= 5.664 Chirality : 0.380 4.212 2380 Planarity : 0.047 0.284 2680 Dihedral : 34.560 126.158 2130 Min Nonbonded Distance : 1.147 Molprobity Statistics. All-atom Clashscore : 396.65 Ramachandran Plot: Outliers : 32.93 % Allowed : 25.24 % Favored : 41.83 % Rotamer: Outliers : 0.17 % Allowed : 2.90 % Favored : 96.93 % Cbeta Deviations : 49.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 40.00 % Twisted General : 41.76 % 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: -7.75 (0.12), residues: 1910 helix: -4.11 (0.13), residues: 759 sheet: -4.13 (0.58), residues: 58 loop : -6.38 (0.11), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.047 0.003 ARG I 56 TYR 0.135 0.011 TYR D 31 PHE 0.093 0.010 PHE D 24 TRP 0.072 0.011 TRP E 70 HIS 0.060 0.015 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.07480 / 4.83 (15830) covalent geometry : angle 7.40792 / 5.10 (21180) hydrogen bonds : bond 0.81035 / 54.36 ( 1170) hydrogen bonds : angle 24.32392 / 17.11 ( 3510) link_TRANS : bond 0.17118 / 11.42 ( 1536) link_TRANS : angle 13.92594 / 9.66 ( 4608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4208.40 seconds wall clock time: 75 minutes 29.24 seconds (4529.24 seconds total)